Science.gov

Sample records for 17s u2 snrnp

  1. 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

  2. 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.

  3. Cwc24p Is a General Saccharomyces cerevisiae Splicing Factor Required for the Stable U2 snRNP Binding to Primary Transcripts

    PubMed Central

    Coltri, Patricia P.; Oliveira, Carla C.

    2012-01-01

    Splicing of primary transcripts is an essential process for the control of gene expression. Specific conserved sequences in premature transcripts are important to recruit the spliceosome machinery. The Saccharomyces cerevisiae catalytic spliceosome is composed of about 60 proteins and 5 snRNAs (U1, U2, U4/U6 and U5). Among these proteins, there are core components and regulatory factors, which might stabilize or facilitate splicing of specific substrates. Assembly of a catalytic complex depends on the dynamics of interactions between these proteins and RNAs. Cwc24p is an essential S. cerevisiae protein, originally identified as a component of the NTC complex, and later shown to affect splicing in vivo. In this work, we show that Cwc24p also affects splicing in vitro. We show that Cwc24p is important for the U2 snRNP binding to primary transcripts, co-migrates with spliceosomes, and that it interacts with Brr2p. Additionally, we show that Cwc24p is important for the stable binding of Prp19p to the spliceosome. We propose a model in which Cwc24p is required for stabilizing the U2 association with primary transcripts, and therefore, especially important for splicing of RNAs containing non-consensus branchpoint sequences. PMID:23029180

  4. 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

  5. Mammalian splicing factor SF1 interacts with SURP domains of U2 snRNP-associated proteins.

    PubMed

    Crisci, Angela; Raleff, Flore; Bagdiul, Ivona; Raabe, Monika; Urlaub, Henning; Rain, Jean-Christophe; Krämer, Angela

    2015-12-01

    Splicing factor 1 (SF1) recognizes the branch point sequence (BPS) at the 3' splice site during the formation of early complex E, thereby pre-bulging the BPS adenosine, thought to facilitate subsequent base-pairing of the U2 snRNA with the BPS. The 65-kDa subunit of U2 snRNP auxiliary factor (U2AF65) interacts with SF1 and was shown to recruit the U2 snRNP to the spliceosome. Co-immunoprecipitation experiments of SF1-interacting proteins from HeLa cell extracts shown here are consistent with the presence of SF1 in early splicing complexes. Surprisingly almost all U2 snRNP proteins were found associated with SF1. Yeast two-hybrid screens identified two SURP domain-containing U2 snRNP proteins as partners of SF1. A short, evolutionarily conserved region of SF1 interacts with the SURP domains, stressing their role in protein-protein interactions. A reduction of A complex formation in SF1-depleted extracts could be rescued with recombinant SF1 containing the SURP-interaction domain, but only partial rescue was observed with SF1 lacking this sequence. Thus, SF1 can initially recruit the U2 snRNP to the spliceosome during E complex formation, whereas U2AF65 may stabilize the association of the U2 snRNP with the spliceosome at later times. In addition, these findings may have implications for alternative splicing decisions. PMID:26420826

  6. Mammalian splicing factor SF1 interacts with SURP domains of U2 snRNP-associated proteins

    PubMed Central

    Crisci, Angela; Raleff, Flore; Bagdiul, Ivona; Raabe, Monika; Urlaub, Henning; Rain, Jean-Christophe; Krämer, Angela

    2015-01-01

    Splicing factor 1 (SF1) recognizes the branch point sequence (BPS) at the 3′ splice site during the formation of early complex E, thereby pre-bulging the BPS adenosine, thought to facilitate subsequent base-pairing of the U2 snRNA with the BPS. The 65-kDa subunit of U2 snRNP auxiliary factor (U2AF65) interacts with SF1 and was shown to recruit the U2 snRNP to the spliceosome. Co-immunoprecipitation experiments of SF1-interacting proteins from HeLa cell extracts shown here are consistent with the presence of SF1 in early splicing complexes. Surprisingly almost all U2 snRNP proteins were found associated with SF1. Yeast two-hybrid screens identified two SURP domain-containing U2 snRNP proteins as partners of SF1. A short, evolutionarily conserved region of SF1 interacts with the SURP domains, stressing their role in protein–protein interactions. A reduction of A complex formation in SF1-depleted extracts could be rescued with recombinant SF1 containing the SURP-interaction domain, but only partial rescue was observed with SF1 lacking this sequence. Thus, SF1 can initially recruit the U2 snRNP to the spliceosome during E complex formation, whereas U2AF65 may stabilize the association of the U2 snRNP with the spliceosome at later times. In addition, these findings may have implications for alternative splicing decisions. PMID:26420826

  7. Antibodies specific for N6-methyladenosine react with intact snRNPs U2 and U4/U6.

    PubMed

    Bringmann, P; Lührmann, R

    1987-03-23

    Antibodies specific for N6-methyladenosine (m6A) were elicited in rabbits and used to study the accessibility in intact snRNPs of the m6A residues present in the snRNAs U2, U4 and U6. The antibody quantitatively precipitates snRNPs U2 and U4/U6 from total nucleoplasmic snRNPs U1-U6 isolated from HeLa cells, which demonstrates that the m6A residues of the respective snRNAs are not protected by snRNP proteins in the snRNP particles. While the anti-m6A IgG does not react at all with U5 RNPs lacking m6A, a significant amount of U1 RNPs was co-precipitated despite the fact that U1 RNA does not contain m6A either. Since anti-m6A IgG does not react with purified U1 RNPs and co-precipitation of U1 RNPs is dependent on the presence of U2 RNPs but not of U4/U6 RNPs, these data indicate an interaction between snRNPs U1 and U2 in vitro. The anti-m6A precipitation pattern described above was also observed with snRNPs isolation from mouse Ehrlich ascites tumor cells, indicating similar three-dimensional arrangements of snRNAs in homologous snRNP particles from different organisms. PMID:2951275

  8. 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

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

    PubMed

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

    2016-07-01

    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

  10. An unusual chemical reactivity of Sm site adenosines strongly correlates with proper assembly of core U snRNP particles.

    PubMed

    Hartmuth, K; Raker, V A; Huber, J; Branlant, C; Lührmann, R

    1999-01-01

    The small nuclear ribonucleoprotein particles (snRNP) U1, U2, U4, and U5 contain a common set of eight Sm proteins that bind to the conserved single-stranded 5'-PuAU3-6GPu-3' (Sm binding site) region of their constituent U snRNA (small nuclear RNA), forming the Sm core RNP. Using native and in vitro reconstituted U1 snRNPs, accessibility of the RNA within the Sm core RNP to chemical structure probes was analyzed. Hydroxyl radical footprinting of in vitro reconstituted U1 snRNP demonstrated that riboses within a large continuous RNA region, including the Sm binding site, were protected. This protection was dependent on the binding of the Sm proteins. In contrast with the riboses, the phosphate groups within the Sm core site were accessible to modifying reagents. The invariant adenosine residue at the 5' end, as well as an adenosine two nucleotides downstream of the Sm binding site, showed an unexpected reactivity with dimethyl sulfate. This novel reactivity could be attributed to N7-methylation of the adenosine and was not observed in naked RNA, indicating that it is an intrinsic property of the RNA- protein interactions within the Sm core RNP. Further, this reactivity was observed concomitantly with formation of the Sm subcore intermediate during Sm core RNP assembly. As the Sm subcore can be viewed as the commitment complex in this assembly pathway, these results suggest that the peculiar reactivity of the Sm site adenosine bases may be diagnostic for proper assembly of the Sm core RNP. Consistent with this idea, a strong correlation was found between the unusual N7-A methylation sensitivity of the Sm core RNP and its ability to be imported into the nucleus of Xenopus laevis oocytes. PMID:9878394

  11. Sm protein methylation is dispensable for snRNP assembly in Drosophila melanogaster

    PubMed Central

    Gonsalvez, Graydon B.; Praveen, Kavita; Hicks, Amanda J.; Tian, Liping; Matera, A. Gregory

    2008-01-01

    Sm proteins form stable ribonucleoprotein (RNP) complexes with small nuclear (sn)RNAs and are core components of the eukaryotic spliceosome. In vivo, the assembly of Sm proteins onto snRNAs requires the survival motor neurons (SMN) complex. Several reports have shown that SMN protein binds with high affinity to symmetric dimethylarginine (sDMA) residues present on the C-terminal tails of SmB, SmD1, and SmD3. This post-translational modification is thought to play a crucial role in snRNP assembly. In human cells, two distinct protein arginine methyltransferases (PRMT5 and PRMT7) are required for snRNP biogenesis. However, in Drosophila, loss of Dart5 (the fruit fly PRMT5 ortholog) has little effect on snRNP assembly, and homozygous mutants are completely viable. To resolve these apparent differences, we examined this topic in detail and found that Drosophila Sm proteins are also methylated by two methyltransferases, Dart5/PRMT5 and Dart7/PRMT7. Unlike dart5, we found that dart7 is an essential gene. However, the lethality associated with loss of Dart7 protein is apparently unrelated to defects in snRNP assembly. To conclusively test the requirement for sDMA modification of Sm proteins in Drosophila snRNP assembly, we constructed a fly strain that exclusively expresses an isoform of SmD1 that cannot be sDMA modified. Interestingly, these flies were viable, and snRNP assays revealed no defects in comparison to wild type. In contrast, dart5 mutants displayed a strong synthetic lethal phenotype in the presence of a hypomorphic Smn mutation. We therefore conclude that dart5 is required for viability when SMN is limiting. PMID:18369183

  12. U2AF1 Mutations Alter Sequence Specificity of pre-mRNA Binding and Splicing

    PubMed Central

    Okeyo-Owuor, Theresa; White, Brian S.; Chatrikhi, Rakesh; Mohan, Dipika R.; Kim, Sanghyun; Griffith, Malachi; Ding, Li; Ketkar-Kulkarni, Shamika; Hundal, Jasreet; Laird, Kholiswa M.; Kielkopf, Clara L.; Ley, Timothy J.; Walter, Matthew J.; Graubert, Timothy A.

    2014-01-01

    We previously identified missense mutations in the U2AF1 splicing factor affecting codons S34 (S34F and S34Y) or Q157 (Q157R and Q157P) in 11% of patients with de novo myelodysplastic syndromes (MDS). Although the role of U2AF1 as an accessory factor in the U2 snRNP is well established, it is not yet clear how mutations affect splicing or contribute to MDS pathophysiology. We analyzed splice junctions in RNA-seq data generated from transfected CD34+ hematopoietic cells and found significant differences in the abundance of known and novel junctions in samples expressing mutant U2AF1 (S34F). For selected transcripts, splicing alterations detected by RNA-seq were confirmed by analysis of primary de novo MDS patient samples. These effects were not due to impaired U2AF1 (S34F) localization as it co-localized normally with U2AF2 within nuclear speckles. We further found evidence in the RNA-seq data for decreased affinity of U2AF1 (S34F) for uridine (relative to cytidine) at the e-3 position immediately upstream of the splice acceptor site and corroborated this finding using affinity binding assays. These data suggest that the S34F mutation alters U2AF1 function in the context of specific RNA sequences, leading to aberrant alternative splicing of target genes, some of which may be relevant for MDS pathogenesis. PMID:25311244

  13. PUF60: a novel U2AF65-related splicing activity.

    PubMed Central

    Page-McCaw, P S; Amonlirdviman, K; Sharp, P A

    1999-01-01

    We have identified a new pyrimidine-tract binding factor, PUF, that is required, together with U2AF, for efficient reconstitution of RNA splicing in vitro. The activity has been purified and consists of two proteins, PUF60 and the previously described splicing factor p54. p54 and PUF60 form a stable complex in vitro when cotranslated in a reaction mixture. PUF activity, in conjunction with U2AF, facilitates the association of U2 snRNP with the pre-mRNA. This reaction is dependent upon the presence of the large subunit of U2AF, U2AF65, but not the small subunit U2AF35. PUF60 is homologous to both U2AF65 and the yeast splicing factor Mud2p. The C-terminal domain of PUF60, the PUMP domain, is distantly related to the RNA-recognition motif domain, and is probably important in protein-protein interactions. PMID:10606266

  14. The spliceosomal snRNP core complex of Trypanosoma brucei: Cloning and functional analysis reveals seven Sm protein constituents

    PubMed Central

    Palfi, Zsofia; Lücke, Stephan; Lahm, Hans-Werner; Lane, William S.; Kruft, Volker; Bragado-Nilsson, Elisabeth; Séraphin, Bertrand; Bindereif, Albrecht

    2000-01-01

    Each of the trypanosome small nuclear ribonucleoproteins (snRNPs) U2, U4/U6, and U5, as well as the spliced leader (SL) RNP, contains a core of common proteins, which we have previously identified. This core is unusual because it is not recognized by anti-Sm Abs and it associates with an Sm-related sequence in the trypanosome small nuclear RNAs (snRNAs). Using peptide sequences derived from affinity-purified U2 snRNP proteins, we have cloned cDNAs for five common proteins of 8.5, 10, 12.5, 14, and 15 kDa of Trypanosoma brucei and identified them as Sm proteins SmF (8.5 kDa), -E (10 kDa), -D1 (12.5 kDa), -G (14 kDa), and -D2 (15 kDa), respectively. Furthermore, we found the trypanosome SmB (T. brucei) and SmD3 (Trypanosoma cruzi) homologues through database searches, thus completing a set of seven canonical Sm proteins. Sequence comparisons of the trypanosome proteins revealed several deviations in highly conserved positions from the Sm consensus motif. We have identified a network of specific heterodimeric and -trimeric Sm protein interactions in vitro. These results are summarized in a model of the trypanosome Sm core, which argues for a strong conservation of the Sm particle structure. The conservation extends also to the functional level, because at least one trypanosome Sm protein, SmG, was able to specifically complement a corresponding mutation in yeast. PMID:10900267

  15. Spatial regulation of cytoplasmic snRNP assembly at the cellular level

    PubMed Central

    Hyjek, Malwina; Wojciechowska, Natalia; Rudzka, Magda; Kołowerzo-Lubnau, Agnieszka; Smoliński, Dariusz Jan

    2015-01-01

    Small nuclear ribonucleoproteins (snRNPs) play a crucial role in pre-mRNA splicing in all eukaryotic cells. In contrast to the relatively broad knowledge on snRNP assembly within the nucleus, the spatial organization of the cytoplasmic stages of their maturation remains poorly understood. Nevertheless, sparse research indicates that, similar to the nuclear steps, the crucial processes of cytoplasmic snRNP assembly may also be strictly spatially regulated. In European larch microsporocytes, it was determined that the cytoplasmic assembly of snRNPs within a cell might occur in two distinct spatial manners, which depend on the rate of de novo snRNP formation in relation to the steady state of these particles within the nucleus. During periods of moderate expression of splicing elements, the cytoplasmic assembly of snRNPs occurred diffusely throughout the cytoplasm. Increased expression of both Sm proteins and U snRNA triggered the accumulation of these particles within distinct, non-membranous RNP-rich granules, which are referred to as snRNP-rich cytoplasmic bodies. PMID:26320237

  16. Cloning of Caenorhabditis U2AF65: an alternatively spliced RNA containing a novel exon.

    PubMed Central

    Zorio, D A; Lea, K; Blumenthal, T

    1997-01-01

    The U2 small nuclear ribonucleoprotein particle (snRNP) auxiliary factor, U2AF, is an essential splicing factor required for recognition of the polypyrimidine tract and subsequent U2 snRNP assembly at the branch point. Because Caenorhabditis elegans introns lack both polypyrimidine tract and branch point consensus sequences but have a very highly conserved UUUUCAG/R consensus at their 3' splice sites, we hypothesized that U2AF might serve to recognize this sequence and thus promote intron recognition in C. elegans. Here we report the cloning of the gene for the large subunit of U2AF, uaf-1. Three classes of cDNA were identified. In the most abundant class the open reading frame is similar to that for the U2AF65 from mammals and flies. The remaining two classes result from an alternative splicing event in which an exon containing an in-frame stop codon is inserted near the beginning of the second RNA recognition motif. However, this alternative mRNA is apparently not translated. Interestingly, the inserted exon contains 10 matches to the 3' splice site consensus. To determine whether this feature is conserved, we sequenced uaf-1 from the related nematode Caenorhabditis briggsae. It is composed of six exons, including an alternatively spliced third exon interrupting the gene at the same location as in C. elegans. uaf-1 is contained in an operon with the rab-18 gene in both species. Although the alternative exons from the two species are not highly conserved and would not encode related polypeptides, the C. briggsae alternative exon has 18 matches to the 3' splice site consensus. We hypothesize that the array of 3' splice site-like sequences in the pre-mRNA and alternatively spliced exon may have a regulatory role. The alternatively spliced RNA accumulates at high levels following starvation, suggesting that this RNA may represent an adaption for reducing U2AF65 levels when pre-mRNA levels are low. PMID:9001248

  17. Both Loss-of-Function and Gain-of-Function Mutations in Snf Define a Role for Snrnp Proteins in Regulating Sex-Lethal Pre-mRNA Splicing in Drosophila Development

    PubMed Central

    Salz, H. K.; Flickinger, T. W.

    1996-01-01

    The Drosophila snf gene encodes a protein with functional homology to the mammalian U1A and U2B" snRNP proteins. Studies, based on the analysis of three viable alleles, have suggested a role for snf in establishing the female-specific splicing pattern of the sex determination switch gene, Sex-lethal. Here, we show that the non-sex-specific lethal null allele is required for female sex determination, arguing against the formal possibility that the viable alleles disrupt a function unrelated to snf's wild-type function. Moreover, we find snf is required for normal cell growth and/or survival, as expected for a protein involved in a cell-vital process such as RNA splicing. We also show that of the three viable alleles only one, snf(JA2), is a partial loss-of-function mutation. The other two viable alleles, snf(1621) and snf(e8H), encode antimorphic proteins. We find the antimorphic proteins are mislocalized and correlate their mislocalization with their molecular lesions and mutant phenotypes. Finally, we provide genetic evidence that the antimorphic alleles interfere with the autoregulatory splicing function of the Sex-lethal protein. Based on these studies we suggest a model in which the snRNP protein, Snf, functions with Sex-lethal to block recognition of the regulated male-specific exon. PMID:8878676

  18. 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.

  19. FUS functions in coupling transcription to splicing by mediating an interaction between RNAP II and U1 snRNP

    PubMed Central

    Yu, Yong; Reed, Robin

    2015-01-01

    Pre-mRNA splicing is coupled to transcription by RNA polymerase II (RNAP II). We previously showed that U1 small nuclear ribonucleoprotein (snRNP) associates with RNAP II, and both RNAP II and U1 snRNP are also the most abundant factors associated with the protein fused-in-sarcoma (FUS), which is mutated to cause the neurodegenerative disease amyotrophic lateral sclerosis. Here, we show that an antisense morpholino that base-pairs to the 5′ end of U1 snRNA blocks splicing in the coupled system and completely disrupts the association between U1 snRNP and both FUS and RNAP II, but has no effect on the association between FUS and RNAP II. Conversely, we found that U1 snRNP does not interact with RNAP II in FUS knockdown extracts. Moreover, using these extracts, we found that FUS must be present during the transcription reaction in order for splicing to occur. Together, our data lead to a model that FUS functions in coupling transcription to splicing via mediating an interaction between RNAP II and U1 snRNP. PMID:26124092

  20. KAP1 Recruitment of the 7SK snRNP Complex to Promoters Enables Transcription Elongation by RNA Polymerase II.

    PubMed

    McNamara, Ryan P; Reeder, Jonathan E; McMillan, Elizabeth A; Bacon, Curtis W; McCann, Jennifer L; D'Orso, Iván

    2016-01-01

    The transition from transcription initiation to elongation at promoters of primary response genes (PRGs) in metazoan cells is controlled by inducible transcription factors, which utilize P-TEFb to phosphorylate RNA polymerase II (Pol II) in response to stimuli. Prior to stimulation, a fraction of P-TEFb is recruited to promoter-proximal regions in a catalytically inactive state bound to the 7SK small nuclear ribonucleoprotein (snRNP) complex. However, it remains unclear how and why the 7SK snRNP is assembled at these sites. Here we report that the transcriptional regulator KAP1 continuously tethers the 7SK snRNP to PRG promoters to facilitate P-TEFb recruitment and productive elongation in response to stimulation. Remarkably, besides PRGs, genome-wide studies revealed that KAP1 and 7SK snRNP co-occupy most promoter-proximal regions containing paused Pol II. Collectively, we provide evidence of an unprecedented mechanism controlling 7SK snRNP delivery to promoter-proximal regions to facilitate "on-site" P-TEFb activation and Pol II elongation. PMID:26725010

  1. 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.

  2. The PSI-U1 snRNP interaction regulates male mating behavior in Drosophila.

    PubMed

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

    2016-05-10

    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

  3. 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.

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

    PubMed Central

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

    2015-01-01

    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. PMID:25795785

  5. Yeast ortholog of the Drosophila crooked neck protein promotes spliceosome assembly through stable U4/U6.U5 snRNP addition.

    PubMed Central

    Chung, S; McLean, M R; Rymond, B C

    1999-01-01

    Mutants in the Drosophila crooked neck (crn) gene show an embryonic lethal phenotype with severe developmental defects. The unusual crn protein consists of sixteen tandem repeats of the 34 amino acid tetratricopeptide (TPR) protein recognition domain. Crn-like TPR elements are found in several RNA processing proteins, although it is unknown how the TPR repeats or the crn protein contribute to Drosophila development. We have isolated a Saccharomyces cerevisiae gene, CLF1, that encodes a crooked neck-like factor. CLF1 is an essential gene but the lethal phenotype of a clf1::HIS3 chromosomal null mutant can be rescued by plasmid-based expression of CLF1 or the Drosophila crn open reading frame. Clf1p is required in vivo and in vitro for pre-mRNA 5' splice site cleavage. Extracts depleted of Clf1p arrest spliceosome assembly after U2 snRNP addition but prior to productive U4/U6.U5 association. Yeast two-hybrid analyses and in vitro binding studies show that Clf1p interacts specifically and differentially with the U1 snRNP-Prp40p protein and the yeast U2AF65 homolog, Mud2p. Intriguingly, Prp40p and Mud2p also bind the phylogenetically conserved branchpoint binding protein (BBP/SF1). Our results indicate that Clf1p acts as a scaffolding protein in spliceosome assembly and suggest that Clf1p may support the cross-intron bridge during the prespliceosome-to-spliceosome transition. PMID:10445879

  6. Genome-wide analysis of KAP1, the 7SK snRNP complex, and RNA polymerase II

    PubMed Central

    McNamara, Ryan P.; Guzman, Carlos; Reeder, Jonathan E.; D'Orso, Iván

    2016-01-01

    The transition of RNA polymerase II (Pol II) from transcription initiation into productive elongation in eukaryotic cells is regulated by the P-TEFb kinase, which phosphorylates the C-terminal domain of paused Pol II at promoter-proximal regions. Our recent study found that P-TEFb (in an inhibited state bound to the 7SK snRNP complex) interacts with the KAP1/TRIM28 transcriptional regulator, and that KAP1 and the 7SK snRNP co-occupy most gene promoters containing paused Pol II. Here we provide a detailed experimental description and analysis of the ChIP-seq datasets that have been deposited into Gene Expression Omnibus (GEO): GS72622, so that independent groups can replicate and expand upon these findings. We propose these datasets would provide valuable information for researchers studying mechanisms of transcriptional regulation including Pol II pausing and pause release. PMID:26981421

  7. Use of RNA tertiary interaction modules for the crystallisation of the spliceosomal snRNP core domain.

    PubMed

    Leung, Adelaine K W; Kambach, Christian; Kondo, Yasushi; Kampmann, Martin; Jinek, Martin; Nagai, Kiyoshi

    2010-09-10

    RNA is known to perform diverse roles in the cell, often as ribonucleoprotein (RNP) particles. While the crystal structure of these RNP particles could provide crucial insights into their functions, crystallographic work on RNP complexes is often hampered by difficulties in obtaining well-diffracting crystals. The small nuclear ribonucleoprotein (snRNP) core domain, acting as an assembly nucleus for the maturation of snRNPs, plays a crucial role in the biogenesis of four of the spliceosomal snRNPs. We have succeeded in crystallising the human U4 snRNP core domain containing seven Sm proteins and a truncated U4 snRNA variant. The most critical factor in our success in the crystallisation was the introduction of various tertiary interaction modules into the RNA that could promote crystal packing without altering the core structure. Here, we describe various strategies employed in our crystallisation effort that could be applied to crystallisation of other RNP particles. PMID:20643141

  8. Direct cross-linking of snRNP proteins F and 70K to snRNAs by ultra-violet radiation in situ.

    PubMed Central

    Woppmann, A; Rinke, J; Lührmann, R

    1988-01-01

    Protein-RNA interactions in small nuclear ribonucleoproteins (UsnRNPs) from HeLa cells were investigated by irradiation of purified nucleoplasmic snRNPs U1 to U6 with UV light at 254 nm. The cross-linked proteins were analyzed on one- and two-dimensional gel electrophoresis systems, and the existence of a stable cross-linkage was demonstrated by isolating protein-oligonucleotide complexes from snRNPs containing 32P-labelled snRNAs after exhaustive digestion with a mixture of RNases of different specificities. The primary target of the UV-light induced cross-linking reaction between protein and RNA was protein F. It was also found to be cross-linked to U1 snRNA in purified U1 snRNPs. Protein F is known to be one of the common snRNP proteins, which together with D, E and G protect a 15-25 nucleotide long stretch of snRNAs U1, U2, U4 and U5, the so-called domain A or Sm binding site against nuclease digestion (Liautard et al., 1982). It is therefore likely that the core-protein may bind directly and specifically to the common snRNA domain A, or else to a sub-region of this. The second protein which was demonstrated to be cross-linked to snRNA was the U1 specific protein 70K. Since it has been shown that binding of protein 70K to U1 RNP requires the presence of the 5' stem and loop of U1 RNA (Hamm et al., 1987) it is likely that the 70K protein directly interacts with a sub-region of the first stem loop structure. Images PMID:2974540

  9. Functional mammalian spliceosomal complex E contains SMN complex proteins in addition to U1 and U2 snRNPs

    PubMed Central

    Makarov, Evgeny M.; Owen, Nicholas; Bottrill, Andrew; Makarova, Olga V.

    2012-01-01

    Spliceosomes remove introns from primary gene transcripts. They assemble de novo on each intron through a series of steps that involve the incorporation of five snRNP particles and multiple non-snRNP proteins. In mammals, all the intermediate complexes have been characterized on one transcript (MINX), with the exception of the very first, complex E. We have purified this complex by two independent procedures using antibodies to either U1-A or PRPF40A proteins, which are known to associate at an early stage of assembly. We demonstrate that the purified complexes are functional in splicing using commitment assays. These complexes contain components expected to be in the E complex and a number of previously unrecognized factors, including survival of motor neurons (SMN) and proteins of the SMN-associated complex. Depletion of the SMN complex proteins from nuclear extracts inhibits formation of the E complex and causes non-productive complexes to accumulate. This suggests that the SMN complex stabilizes the association of U1 and U2 snRNPs with pre-mRNA. In addition, the antibody to PRPF40A precipitated U2 snRNPs from nuclear extracts, indicating that PRPF40A associates with U2 snRNPs. PMID:22110043

  10. Conserved zinc fingers mediate multiple functions of ZFP100, a U7snRNP associated protein

    PubMed Central

    Wagner, Eric J.; Ospina, Jason K.; Hu, Yue; Dundr, Miroslav; Matera, A. Gregory; Marzluff, William F.

    2006-01-01

    Formation of the 3′ end of replication-dependent histone mRNAs is most robust during S phase and is mediated by both the stem–loop binding protein (SLBP) and the U7 snRNP. We previously identified a 100-kDa zinc finger protein (ZFP100) as a component of U7 snRNP that interacts with the SLBP/pre-mRNA complex. Here, we show that myc- or GFP-tagged ZFP100 overexpressed after transfection is concentrated in Cajal bodies (CBs), and unlike components of the spliceosomal snRNPs, photobleaching experiments demonstrate that ZFP100 is stably associated with CBs. Of the 18 zinc fingers contained within ZFP100, the region encompassing fingers 2–6 is sufficient to maintain CB localization. Zn fingers 5–10 are required for maximal binding of ZFP100 to a 20-amino-acid region of Lsm11, a U7 snRNP core protein. Expression of ZFP100 stimulates histone mRNA processing in vivo, assayed by activation of a reporter gene that encodes a GFP mRNA ending in a histone 3′ end. Importantly, the domain that is required for CB localization and Lsm11 binding is also sufficient to stimulate histone pre-mRNA processing in vivo. Comparisons with other mammalian ZFP100 orthologs show that the central Zn fingers sufficient for in vivo activity are most highly conserved, whereas the number and sequence of the Zn fingers in the N- and C-terminal domains vary. PMID:16714279

  11. U1 snRNP is mislocalized in ALS patient fibroblasts bearing NLS mutations in FUS and is required for motor neuron outgrowth in zebrafish.

    PubMed

    Yu, Yong; Chi, Binkai; Xia, Wei; Gangopadhyay, Jaya; Yamazaki, Tomohiro; Winkelbauer-Hurt, Marlene E; Yin, Shanye; Eliasse, Yoan; Adams, Edward; Shaw, Christopher E; Reed, Robin

    2015-03-31

    Mutations in FUS cause amyotrophic lateral sclerosis (ALS), but the molecular pathways leading to neurodegeneration remain obscure. We previously found that U1 snRNP is the most abundant FUS interactor. Here, we report that components of the U1 snRNP core particle (Sm proteins and U1 snRNA), but not the mature U1 snRNP-specific proteins (U1-70K, U1A and U1C), co-mislocalize with FUS to the cytoplasm in ALS patient fibroblasts harboring mutations in the FUS nuclear localization signal (NLS). Similar results were obtained in HeLa cells expressing the ALS-causing FUS R495X NLS mutation, and mislocalization of Sm proteins is RRM-dependent. Moreover, as observed with FUS, knockdown of any of the U1 snRNP-specific proteins results in a dramatic loss of SMN-containing Gems. Significantly, knockdown of U1 snRNP in zebrafish results in motor axon truncations, a phenotype also observed with FUS, SMN and TDP-43 knockdowns. Our observations linking U1 snRNP to ALS patient cells with FUS mutations, SMN-containing Gems, and motor neurons indicate that U1 snRNP is a component of a molecular pathway associated with motor neuron disease. Linking an essential canonical splicing factor (U1 snRNP) to this pathway provides strong new evidence that splicing defects may be involved in pathogenesis and that this pathway is a potential therapeutic target. PMID:25735748

  12. U1 snRNP is mislocalized in ALS patient fibroblasts bearing NLS mutations in FUS and is required for motor neuron outgrowth in zebrafish

    PubMed Central

    Yu, Yong; Chi, Binkai; Xia, Wei; Gangopadhyay, Jaya; Yamazaki, Tomohiro; Winkelbauer-Hurt, Marlene E.; Yin, Shanye; Eliasse, Yoan; Adams, Edward; Shaw, Christopher E.; Reed, Robin

    2015-01-01

    Mutations in FUS cause amyotrophic lateral sclerosis (ALS), but the molecular pathways leading to neurodegeneration remain obscure. We previously found that U1 snRNP is the most abundant FUS interactor. Here, we report that components of the U1 snRNP core particle (Sm proteins and U1 snRNA), but not the mature U1 snRNP-specific proteins (U1-70K, U1A and U1C), co-mislocalize with FUS to the cytoplasm in ALS patient fibroblasts harboring mutations in the FUS nuclear localization signal (NLS). Similar results were obtained in HeLa cells expressing the ALS-causing FUS R495X NLS mutation, and mislocalization of Sm proteins is RRM-dependent. Moreover, as observed with FUS, knockdown of any of the U1 snRNP-specific proteins results in a dramatic loss of SMN-containing Gems. Significantly, knockdown of U1 snRNP in zebrafish results in motor axon truncations, a phenotype also observed with FUS, SMN and TDP-43 knockdowns. Our observations linking U1 snRNP to ALS patient cells with FUS mutations, SMN-containing Gems, and motor neurons indicate that U1 snRNP is a component of a molecular pathway associated with motor neuron disease. Linking an essential canonical splicing factor (U1 snRNP) to this pathway provides strong new evidence that splicing defects may be involved in pathogenesis and that this pathway is a potential therapeutic target. PMID:25735748

  13. 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

  14. Functional organization of the Sm core in the crystal structure of human U1 snRNP

    PubMed Central

    Weber, Gert; Trowitzsch, Simon; Kastner, Berthold; Lührmann, Reinhard; Wahl, Markus C

    2010-01-01

    U1 small nuclear ribonucleoprotein (snRNP) recognizes the 5′-splice site early during spliceosome assembly. It represents a prototype spliceosomal subunit containing a paradigmatic Sm core RNP. The crystal structure of human U1 snRNP obtained from natively purified material by in situ limited proteolysis at 4.4 Å resolution reveals how the seven Sm proteins, each recognize one nucleotide of the Sm site RNA using their Sm1 and Sm2 motifs. Proteins D1 and D2 guide the snRNA into and out of the Sm ring, and proteins F and E mediate a direct interaction between the Sm site termini. Terminal extensions of proteins D1, D2 and B/B′, and extended internal loops in D2 and B/B′ support a four-way RNA junction and a 3′-terminal stem-loop on opposite sides of the Sm core RNP, respectively. On a higher organizational level, the core RNP presents multiple attachment sites for the U1-specific 70K protein. The intricate, multi-layered interplay of proteins and RNA rationalizes the hierarchical assembly of U snRNPs in vitro and in vivo. PMID:21113136

  15. 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

  16. Vought SB2U-2 Vindicator

    NASA Technical Reports Server (NTRS)

    1939-01-01

    Vought SB2U-2 Vindicator: The Navy was in the transition from biplanes to monoplanes when it ordered the SB2U. Used for diving tests, this Vought SB2U-2 Vindicator was one of approximately 169 SB2Us built.

  17. 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

    2015-01-01

    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. PMID:25555158

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

    PubMed Central

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

    2015-01-01

    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. DOI: http://dx.doi.org/10.7554/eLife.04986.001 PMID:25555158

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

    PubMed

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

    2001-01-01

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

  20. Electronic structure of U2PtC2 and U2RhC2

    DOE PAGESBeta

    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.

  1. U1 adaptors result in reduction of multiple pre-mRNA species principally by sequestering U1snRNP.

    PubMed

    Vickers, Timothy A; Sabripour, Mahyar; Crooke, Stanley T

    2011-05-01

    U1 Adaptors are a recently reported novel approach for targeted reduction of mRNA transcripts. A U1 adaptor oligonucleotide comprising of a target-complimentary hybridization domain and a U1 recruitment domain, directs the U1 snRNP complex to the terminal exon of a targeted gene, subsequently inhibiting poly(A) tail addition and leading to degradation of that RNA species within the nucleus. Here, we present data demonstrating U1 adapter-mediated gene silencing can result in significant 'off-target' silencing effects as demonstrated by the reduction of multiple mRNA species that were not intended to be targeted. Our data suggest that a substantial portion of this U1 adaptor-mediated off-target mRNA reduction is the result of sequestration U1 snRNP at levels sufficient to affect splicing and processing of non-target transcripts. PMID:21415007

  2. The conserved central domain of yeast U6 snRNA: importance of U2-U6 helix Ia in spliceosome assembly.

    PubMed Central

    Ryan, Daniel E; Abelson, John

    2002-01-01

    In the pre-mRNA processing machinery of eukaryotic cells, U6 snRNA is located at or near the active site for pre-mRNA splicing catalysis, and U6 is involved in catalyzing the first chemical step of splicing. We have further defined the roles of key features of yeast U6 snRNA in the splicing process. By assaying spliceosome assembly and splicing in yeast extracts, we found that mutations of yeast U6 nt 56 and 57 are similar to previously reported deletions of U2 nt 27 or 28, all within yeast U2-U6 helix Ia. These mutations lead to the accumulation of yeast A1 spliceosomes, which form just prior to the Prp2 ATPase step and the first chemical step of splicing. These results strongly suggest that, at a late stage of spliceosome assembly, the presence of U2-U6 helix Ia is important for promoting the first chemical step of splicing, presumably by bringing together the 5' splice site region of pre-mRNA, which is base paired to U6 snRNA, and the branchsite region of the intron, which is base paired to U2 snRNA, for activation of the first chemical step of splicing, as previously proposed by Madhani and Guthrie [Cell, 1992, 71: 803-817]. In the 3' intramolecular stem-loop of U6, mutation G81C causes an allele-specific accumulation of U6 snRNP. Base pairing of the U6 3' stem-loop in yeast spliceosomes does not extend as far as to include the U6 sequence of U2-U6 helix Ib, in contrast to the human U6 3' stem-loop structure. PMID:12212854

  3. 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. PMID:27268418

  4. ALS-causative mutations in FUS/TLS confer gain and loss of function by altered association with SMN and U1-snRNP.

    PubMed

    Sun, Shuying; Ling, Shuo-Chien; Qiu, Jinsong; Albuquerque, Claudio P; Zhou, Yu; Tokunaga, Seiya; Li, Hairi; Qiu, Haiyan; Bui, Anh; Yeo, Gene W; Huang, Eric J; Eggan, Kevin; Zhou, Huilin; Fu, Xiang-Dong; Lagier-Tourenne, Clotilde; Cleveland, Don W

    2015-01-01

    The RNA-binding protein FUS/TLS, mutation in which is causative of the fatal motor neuron disease amyotrophic lateral sclerosis (ALS), is demonstrated to directly bind to the U1-snRNP and SMN complexes. ALS-causative mutations in FUS/TLS are shown to abnormally enhance their interaction with SMN and dysregulate its function, including loss of Gems and altered levels of small nuclear RNAs. The same mutants are found to have reduced association with U1-snRNP. Correspondingly, global RNA analysis reveals a mutant-dependent loss of splicing activity, with ALS-linked mutants failing to reverse changes caused by loss of wild-type FUS/TLS. Furthermore, a common FUS/TLS mutant-associated RNA splicing signature is identified in ALS patient fibroblasts. Taken together, these studies establish potentially converging disease mechanisms in ALS and spinal muscular atrophy, with ALS-causative mutants acquiring properties representing both gain (dysregulation of SMN) and loss (reduced RNA processing mediated by U1-snRNP) of function. PMID:25625564

  5. Structural Basis of Brr2-Prp8 Interactions and Implications for U5 snRNP Biogenesis and the Spliceosome Active Site

    PubMed Central

    Nguyen, Thi Hoang Duong; Li, Jade; Galej, Wojciech P.; Oshikane, Hiroyuki; Newman, Andrew J.; Nagai, Kiyoshi

    2013-01-01

    Summary The U5 small nuclear ribonucleoprotein particle (snRNP) helicase Brr2 disrupts the U4/U6 small nuclear RNA (snRNA) duplex and allows U6 snRNA to engage in an intricate RNA network at the active center of the spliceosome. Here, we present the structure of yeast Brr2 in complex with the Jab1/MPN domain of Prp8, which stimulates Brr2 activity. Contrary to previous reports, our crystal structure and mutagenesis data show that the Jab1/MPN domain binds exclusively to the N-terminal helicase cassette. The residues in the Jab1/MPN domain, whose mutations in human Prp8 cause the degenerative eye disease retinitis pigmentosa, are found at or near the interface with Brr2, clarifying its molecular pathology. In the cytoplasm, Prp8 forms a precursor complex with U5 snRNA, seven Sm proteins, Snu114, and Aar2, but after nuclear import, Brr2 replaces Aar2 to form mature U5 snRNP. Our structure explains why Aar2 and Brr2 are mutually exclusive and provides important insights into the assembly of U5 snRNP. PMID:23727230

  6. Time-resolved quantitative proteomics implicates the core snRNP protein SmB together with SMN in neural trafficking.

    PubMed

    Prescott, Alan R; Bales, Alexandra; James, John; Trinkle-Mulcahy, Laura; Sleeman, Judith E

    2014-02-15

    The biogenesis of splicing snRNPs (small nuclear ribonucleoproteins) is a complex process, beginning and ending in the nucleus of the cell but including key stages that take place in the cytoplasm. In particular, the SMN (survival motor neuron) protein complex is required for addition of the core Sm proteins to the snRNP. Insufficiency of SMN results in the inherited neurodegenerative condition, spinal muscular atrophy (SMA). Details of the physical organization of the cytoplasmic stages of snRNP biogenesis are unknown. Here, we use time-resolved quantitative proteomics to identify proteins that associate preferentially with either newly assembled or mature splicing snRNPs. We identified highly mobile SmB protein-trafficking vesicles in neural cells, which are dependent on the cellular levels of SMN and SmB for their morphology and mobility. We propose that these represent a family of related vesicles, some of which play a role in snRNP biogenesis and some that might play more diverse roles in cellular RNA metabolism. PMID:24357717

  7. The Mechanism of Release of P-TEFb and HEXIM1 from the 7SK snRNP by Viral and Cellular Activators Includes a Conformational Change in 7SK

    PubMed Central

    Krueger, Brian J.; Varzavand, Katayoun; Cooper, Jeffrey J.; Price, David H.

    2010-01-01

    Background The positive transcription elongation factor, P-TEFb, is required for the production of mRNAs, however the majority of the factor is present in the 7SK snRNP where it is inactivated by HEXIM1. Expression of HIV-1 Tat leads to release of P-TEFb and HEXIM1 from the 7SK snRNP in vivo, but the release mechanisms are unclear. Methodology/Principal Findings We developed an in vitro P-TEFb release assay in which the 7SK snRNP immunoprecipitated from HeLa cell lysates using antibodies to LARP7 was incubated with potential release factors. We found that P-TEFb was directly released from the 7SK snRNP by HIV-1 Tat or the P-TEFb binding region of the cellular activator Brd4. Glycerol gradient sedimentation analysis was used to demonstrate that the same Brd4 protein transfected into HeLa cells caused the release of P-TEFb and HEXIM1 from the 7SK snRNP in vivo. Although HEXIM1 binds tightly to 7SK RNA in vitro, release of P-TEFb from the 7SK snRNP is accompanied by the loss of HEXIM1. Using a chemical modification method, we determined that concomitant with the release of HEXIM1, 7SK underwent a major conformational change that blocks re-association of HEXIM1. Conclusions/Significance Given that promoter proximally paused polymerases are present on most human genes, understanding how activators recruit P-TEFb to those genes is critical. Our findings reveal that the two tested activators can extract P-TEFb from the 7SK snRNP. Importantly, we found that after P-TEFb is extracted a dramatic conformational change occurred in 7SK concomitant with the ejection of HEXIM1. Based on our findings, we hypothesize that reincorporation of HEXIM1 into the 7SK snRNP is likely the regulated step of reassembly of the 7SK snRNP containing P-TEFb. PMID:20808803

  8. A physical and expression map of the D17S1810-D17S1353 region spanning the central areolar choroidal dystrophy locus.

    PubMed

    Lichanska, A M; McGibbon, D; Silvestri, G; Hughes, A E

    2001-01-01

    Central areolar choroidal dystrophy (CACD) causes bilateral irreversible central visual loss in the 5th to 7th decades. The authors previously described a large pedigree with the disorder, which showed linkage to chromosome 17p13.2-->p13.1 between microsatellite markers D17S1353 and D17S1810. 17p13 is very rich in genes that cause retinal diseases. We have now constructed a detailed and ordered physical map of the critical CACD region which spans up to 2.4 Mb. The new transcript map contains thirteen genes and seven expressed sequence tags (ESTs) that are eye-expressed, and therefore are positional candidates. Several of these have been screened, but no disease-causing mutations were found in CACD patients. PMID:11474177

  9. SMN, the Spinal Muscular Atrophy Protein, Forms a Pre-Import Snrnp Complex with Snurportin1 and Importin β

    PubMed Central

    Narayanan, Usha; Ospina, Jason K.; Frey, Mark R.; Hebert, Michael D.; Matera, A. Gregory

    2006-01-01

    The survival of motor neuron (SMN) protein is mutated in patients with spinal muscular atrophy (SMA). SMN is part of a multiprotein complex required for biogenesis of the Sm class of small nuclear ribonucleoproteins (snRNPs). Following assembly of the Sm core domain, snRNPs are transported to the nucleus via importin β. Sm snRNPs contain a nuclear localization signal (NLS) consisting of a 2,2,7-trimethylguanosine (TMG) cap and the Sm core. Snurportin1 (SPN) is the adaptor protein that recognizes both the TMG cap and importin β. Here, we report that a mutant SPN construct lacking the importin β binding domain (IBB), but containing an intact TMG cap-binding domain, localizes primarily to the nucleus, whereas full-length SPN localizes to the cytoplasm. The nuclear localization of the mutant SPN was not a result of passive diffusion through the nuclear pores. Importantly, we found that SPN interacts with SMN, Gemin3, Sm snRNPs and importin β. In the presence of ribonucleases, the interactions with SMN and Sm proteins were abolished, indicating that snRNAs mediate this interplay. Cell fractionation studies showed that SPN binds preferentially to cytoplasmic SMN complexes. Notably, we found that SMN directly interacts with importin β in a GST-pulldown assay, suggesting that the SMN complex might represent the Sm core NLS receptor predicted by previous studies. Therefore, we conclude that, following Sm protein assembly, the SMN complex persists until the final stages of cytoplasmic snRNP maturation and may provide somatic cell RNPs with an alternative NLS. PMID:12095920

  10. Drift sight replacement in the U-2

    NASA Astrophysics Data System (ADS)

    Bialecki, Lawrence J.

    2005-05-01

    When first deployed in the mid 1950s, the U-2 had an inverted periscope (Drift Sight) to provide the pilot a view of the area below the aircraft. During a recent glass cockpit upgrade, this periscope was removed. This paper discusses: " The development activity leading up to flight test of an Electro Optical Viewsight System (EOVS) replacement for the Drift Sight. The impact and design consideration of using an inexpensive Commercial Off the Shelf (COTS) cameral module, originally designed for small hand held video cameras, " The process used to develop the basic requirements and how early input from the user community lead to an effective design (e.g.., Hand Grip), " The ruggedization techniques necessary to ensure the camera would meet the vibration, thermal, and Electro Magnetic Interface (EMI) environment, " Actual system performance data, " Growth "hooks" and how they were accommodated in a firm fixed price contract.

  11. 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...

  12. 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. PMID:16578795

  13. 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

  14. Strong allelic association between Sjoegren-Larsson syndrome and D17S805

    SciTech Connect

    Pigg, M.; Jagell, S.; Sillen, A.

    1994-09-01

    Sjoegren-Larsson Syndrom (SLS) is characterized by congenital ichthyosis, spastic di- or tetraplegia and mental retardation. It is an autosomal recessive trait that has been described in many populations, but is particularly frequent in the northern part of Sweden. A defect in the enzyme fatty alcohol: NAD+ oxidoreductase (FAD) has been suggested, but the molecular mechanism has not been elucidated. Based on linkage analysis and allelic association, the disorder has now been mapped to chromosome 17. Meiotic recombinations suggests that the gene is flanked by D17S805 on the centromeric and D17S783 and D17S925 on the telomeric side. These three markers map to the same location in reference pedigrees. Strong allelic association (chi-square 60.28, p<0.0003) to D17S805 suggests that the mutation is located at a limited distance on the telomeric side of this marker. It is possible that the gene can be identified by functional complementation of SLS cells using YACs from this region. Alternatively, positional cloning should be possible in this presumable small area. The markers identified are close and informative enough to allow accurate genetic diagnosis.

  15. 103Rh-NMR studies in the superconductor Rh17S15

    NASA Astrophysics Data System (ADS)

    Koyama, T.; Kanda, K.; Ueda, K.; Mito, T.; Kohara, T.; Nakamura, H.

    2010-01-01

    103Rh nuclear magnetic resonance (NMR) measurements have been performed in the superconductor Rh17S15 with the transition temperature TC=5.4 K. The observed 103Rh-NMR spectrum shows an asymmetric shape with several peaks, reflecting the local symmetry around each Rh site. We have identified the observed NMR lines corresponding to four different Rh sites and obtained the temperature (T) dependence of the Knight shift of 24m site. The isotropic part of the Knight shift Kiso decreases with decreasing T, indicating the existence of the electron correlation in Rh17S15. In the superconducting state, the resonance lines shift to higher frequencies owing to a decrease of the spin part of the Knight shift with negative hyperfine coupling.

  16. Release of Positive Transcription Elongation Factor b (P-TEFb) from 7SK Small Nuclear Ribonucleoprotein (snRNP) Activates Hexamethylene Bisacetamide-inducible Protein (HEXIM1) Transcription*

    PubMed Central

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

    2014-01-01

    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. PMID:24515107

  17. 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…

  18. 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

  19. 103Rh NMR investigation of the superconductor Rh17S15

    NASA Astrophysics Data System (ADS)

    Koyama, T.; Kanda, K.; Motoyama, G.; Ueda, K.; Mito, T.; Kohara, T.; Nakamura, H.

    2010-12-01

    We present 103Rh NMR studies for the superconductor Rh17S15 (Tc = 5.4 K). We have identified the observed NMR lines corresponding to four different Rh sites in the cubic unit cell and deduced the temperature (T) dependence of the Knight shift components in Rh 24m site whose point symmetry is not axial. The isotropic part of the Knight shift K decreases with T in the normal state, indicating the negative hyperfine coupling and the enhancement of the spin susceptibility at lower T. The sudden change of K below Tc is an indication of the spin-singlet Cooper paring.

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

    PubMed

    Cho, Y J; Chema, D; Moskow, J J; Cho, M; Schroeder, W T; Overbeek, P; Buchberg, A M; Duvic, 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, high-lighting 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' and 3' untranslated sequences are conserved. Similar RNA folding patterns of the 5' 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. PMID:7557989

  1. 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.

  2. Stem-loop 1 of the U1 snRNP plays a critical role in the suppression of HIV-1 polyadenylation.

    PubMed Central

    Ashe, M P; Furger, A; Proudfoot, N J

    2000-01-01

    The inactivity or occlusion of the HIV-1 poly(A) signal when in the 5' long terminal repeat (LTR) has been mechanistically investigated. First we show that neither the homologous HIV-1 promoter nor the close proximity of this RNA processing signal to the transcript initiation site is required for the occlusion effect. Instead we demonstrate that the major splice donor (MSD) site positioned about 200 bp downstream maintains the poly(A) site in an inactive state. Although mutation of MSD results in activation of the 5' LTR poly(A) signal, this effect can be suppressed by targeting U1 snRNAs near to the mutated MSD by base pairing. We show that hybrid U7-U1 snRNAs can also suppress the poly(A) signal and that this suppression is dependent on the U1 stem-loop 1. In particular the binding site for the U1 snRNP protein 70K that binds to the loop structure of stem-loop 1 is associated with poly(A) site occlusion. These experiments were carried out with an HIV-1 proviral construct and as such emphasize the physiological importance of this splice donor-poly(A) site interaction. PMID:10688356

  3. 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

    Wang, Cong; Yang, Shuiyuan; 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

  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. The budding yeast U5 snRNP Prp8 is a highly conserved protein which links RNA splicing with cell cycle progression.

    PubMed Central

    Shea, J E; Toyn, J H; Johnston, L H

    1994-01-01

    The dbf3 mutation was originally obtained in a screen for DNA synthesis mutants with a cell cycle phenotype in the budding yeast Saccharomyces cerevisiae. We have now isolated the DBF3 gene and found it to be an essential gene with an ORF of 7239 nucleotides, potentially encoding a large protein of 268 kDa. We also obtained an allele-specific high copy number suppressor of the dbf3-1 allele, encoded by the known SSB1 gene, a member of the Hsp70 family of heat shock proteins. The sequence of the Dbf3 protein is 58% identical over 2300 amino acid residues to a predicted protein from Caenorhabditis elegans. Furthermore, partial sequences with 61% amino acid sequence identity were deduced from two files of human cDNA in the EST nucleotide database so that Dbf3 is a highly conserved protein. The nucleotide sequence of DBF3 turned out to be identical to the yeast gene PRP8, which encodes a U5 snRNP required for pre-mRNA splicing. This surprising result led us to further characterise the phenotype of dbf3 which confirmed its role in the cell cycle and showed it to function early, around the time of S phase. This data suggests a hitherto unexpected link between pre-mRNA splicing and the cell cycle. Images PMID:7838707

  6. 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 ).

  7. Validation of probe EFD52 (D17S26) for forensic DNA analysis.

    PubMed

    Nelson, M S; Benzinger, E A; Budzynski, M J; Boodee, M T; Matthews, A; Buel, E; Schwartz, M B; von Beroldingen, C; Wampler, R L; Coons, T M

    1996-07-01

    Validation studies that meet TWGDAM (The Working Group on DNA Analysis Methods) and CAC (California Association of Criminalists) guidelines for RFLP (restriction fragment length polymorphism) analysis were performed with the DNA probe EFD52 (D17S26). These studies demonstrate that the probe EFD52 is suitable for forensic casework. No unexpected DNA banding patterns were obtained from controlled studies examining various tissues, sample consistency over many gels, mixtures of body fluids, various substrates, various contaminants and non-human DNA sources. Of all the animal DNAs tested, only one higher primate yielded a single band to EFD52 hybridization. The sensitivity of EFD52 was shown to be comparable to that of other forensic probes. Population frequency distribution tables were prepared from over 4000 alleles and two-locus studies were conducted on nine forensically useful probes. Black, White, Hispanic and Lumbee Indian populations were found to be in Hardy-Weinberg and linkage equilibrium. Comparisons between victim blood standards and epithelial fractions of mixed strains from sexual assault cases were used to demonstrate the robustness of the EFD52 probe in forensic casework. PMID:8754565

  8. Purification of the individual snRNPs U1, U2, U5 and U4/U6 from HeLa cells and characterization of their protein constituents.

    PubMed Central

    Bringmann, P; Lührmann, R

    1986-01-01

    A procedure is described for the purification of the individual major small nuclear ribonucleoproteins (snRNPs) U1, U2, U5 and U4/U6 from HeLa cells. The salient feature of the method is the combined usage of antibodies against 2,2,7-trimethylguanosine (m3G) and 6-methyladenosine (m6A) for differential immune affinity chromatography of the snRNPs. While anti-m3G affinity columns allow the separation of snRNPs U1, U2 and U5 from U4/U6 RNPs, anti-m6A antibodies selectively react with snRNPs U2 and U4/U6. Our technique further incorporates immune affinity chromatography of snRNPs with antibodies against snRNP proteins in addition to ion exchange chromatography. The procedure avoids the usage of denaturing agents, so as to maintain the native structure of the particles. This is mainly provided for by the possibility of eluting the anti-m3G and anti-m6A bound snRNPs with excess of the respective nucleosides. We have so far identified 12 polypeptides as constituents of the major snRNPs U1 to U6. Seven proteins of approximate mol. wts 29 kd (B'), 28 kd (B), 16 kd (D), 15.5 kd (D'), 12 kd (E), 11 kd (F) and 9 kd (G) were present in each of the individual snRNPs U1, U2, U5 and U4/U6. In addition to the common proteins, U1 RNPs contain three unique polypeptides of mol. wts 70 kd, 34 kd (A) and 22 kd (C). U2 RNPs are characterized by the presence of a 33-kd and a 28.5-kd protein, denoted A' and B". We could not detect any unique polypeptide confined to the purified snRNPs U5 or U4/U6.(ABSTRACT TRUNCATED AT 250 WORDS) Images Fig. 1. Fig. 3. Fig. 4. Fig. 5. Fig. 6. Fig. 7. Fig. 8. PMID:2951249

  9. Disruption of snRNP biogenesis factors Tgs1 and pICln induces phenotypes that mirror aspects of SMN-Gemins complex perturbation in Drosophila, providing new insights into spinal muscular atrophy.

    PubMed

    Borg, Rebecca M; Fenech Salerno, Benji; Vassallo, Neville; Bordonne, Rémy; Cauchi, Ruben J

    2016-10-01

    The neuromuscular disorder, spinal muscular atrophy (SMA), results from insufficient levels of the survival motor neuron (SMN) protein. Together with Gemins 2-8 and Unrip, SMN forms the large macromolecular SMN-Gemins complex, which is known to be indispensable for chaperoning the assembly of spliceosomal small nuclear ribonucleoproteins (snRNPs). It remains unclear whether disruption of this function is responsible for the selective neuromuscular degeneration in SMA. In the present study, we first show that loss of wmd, the Drosophila Unrip orthologue, has a negative impact on the motor system. However, due to lack of a functional relationship between wmd/Unrip and Gemin3, it is likely that Unrip joined the SMN-Gemins complex only recently in evolution. Second, we uncover that disruption of either Tgs1 or pICln, two cardinal players in snRNP biogenesis, results in viability and motor phenotypes that closely resemble those previously uncovered on loss of the constituent members of the SMN-Gemins complex. Interestingly, overexpression of both factors leads to motor dysfunction in Drosophila, a situation analogous to that of Gemin2. Toxicity is conserved in the yeast S. pombe where pICln overexpression induces a surplus of Sm proteins in the cytoplasm, indicating that a block in snRNP biogenesis is partly responsible for this phenotype. Importantly, we show a strong functional relationship and a physical interaction between Gemin3 and either Tgs1 or pICln. We propose that snRNP biogenesis is the pathway connecting the SMN-Gemins complex to a functional neuromuscular system, and its disturbance most likely leads to the motor dysfunction that is typical in SMA. PMID:27388936

  10. General Approach for Tetramer Based Identification of Autoantigen Reactive B Cells: Characterization of La and snRNP Reactive B Cells in Autoimmune BXD2 Mice

    PubMed Central

    Hamilton, Jennie A.; Li, Jun; Wu, Qi; Yang, PingAr; Luo, Bao; Li, Hao; Bradley, John E.; Taylor, Justin J.; Randall, Troy D.; Mountz, John D.; Hsu, Hui-Chen

    2015-01-01

    Autoreactive B cells are associated with the development of several autoimmune diseases, including systemic lupus erythematosus (SLE) and rheumatoid arthritis (RA). The low frequency of these cells represents a major barrier to their analysis. Antigen-tetramers prepared from linear epitopes represent a promising strategy for the identification of small subsets of antigen-reactive immune cells. This is challenging given the requirement for identification and validation of linear epitopes and the complexity of autoantibody responses, including the broad spectrum of autoantibody specificities and the contribution of isotype to pathogenicity. We therefore tested a two-tiered peptide microarray approach, coupled with epitope mapping of known autoantigens, to identify and characterize autoepitopes using the BXD2 autoimmune mouse model. Microarray results were verified through comparison with established age-associated profiles of autoantigen specificities and autoantibody class switching in BXD2 and control (B6) mice and high-throughput ELISA and ELISPOT analyses of synthetic peptides. Tetramers were prepared from two linear peptides derived from two ribonucleic acid binding proteins (RBP): lupus La and 70 kDa U1 small nuclear ribonucleoprotein (snRNP). Flow cyotmetric analysis of tetramer-reactive B-cell subsets revealed a significantly higher frequency and greater numbers of RBP-reactive marginal zone precursor (MZ-P), transitional T3 and PDL-2+CD80+ memory B cells, with significantly elevated CD69 and CD86 observed in RBP+ MZ-P B cells in the spleens of BXD2 compared to B6 mice, suggesting a regulatory defect. This study establishes a feasible strategy for the characterization of autoantigen-specific B-cell subsets in different models of autoimmunity and, potentially, humans. PMID:25888644

  11. Severe neurological decompression sickness in a U-2 pilot.

    PubMed

    Jersey, Sean L; Baril, Robert T; McCarty, Richmond D; Millhouse, Christina M

    2010-01-01

    Severe neurological decompression sickness (DCS) has been a rare entity in the U.S. Air Force, including the U-2 community. In over 50 yr of operation, few U-2 pilots reported severe neurological DCS in flight despite the extreme altitudes at which they operate. This article describes a near-fatal case of neurological DCS that occurred during a combat mission. The injury left the pilot with permanent cognitive deficits that correlated with focal lesions present on magnetic resonance imaging of his brain. To our knowledge, the images presented herein are the first to show radiological evidence of brain injury induced by altitude DCS. Though only a single case, the objective and clinical findings in the case pilot are similar to results documented in divers suffering DCS with central nervous system injury and victims of traumatic brain injury. DCS will remain a potentially serious threat to current and future air and space operations. PMID:20058739

  12. 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.

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

    PubMed Central

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

    2015-01-01

    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. PMID:17932117

  14. 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.

  15. Quick look data report for COMET Test U2

    SciTech Connect

    Farmer, M.T.; Spencer, B.W.; Kilsdonk, D.J.; Aeschlimann, R.W.

    1998-01-08

    Investigations are underway at Forschungszentrum Karlsruhe (FZK) addressing methods to terminate and stabilize a core melt accident situation ex-vessel. In this approach, the molten core-concrete interaction (MCCI) begins erosion of the concrete, and after erosion proceeds to some modest depth, it exposes and unseals an array of tubes. The tubes are connected to a water reservoir pressurized by static water head. Upon unsealing, the tubes direct a flow of water into the bottom of the corium layer. The water is forced up through the melt, cooling the melt and causing it to solidify in a form that allows continued permeation and heat removal by the water. Thus, the accident progression can be halted, and the debris may be permanently cooled. The key aspect of the passive ex-vessel core retention approach described above is the ability of water injected at the bottom of a corium melt layer to quench the melt forming a coolable debris bed in the process. This process has been tested using iron-alumina thermite as a corium simulant with promising results. As a part of a collaborative research agreement between FZK and the US DOE, two scoping tests are being conducted at Argonne National Laboratory to test the FZK core retention concept using real reactor materials. The second of these two tests, denoted COMET Test U2, was successfully conducted on December 17, 1997. The objectives of this data report are to: summarize the experiment facility and operating procedure for COMET Test U2, and present the test data.

  16. 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

    2015-07-01

    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. PMID:25911228

  17. Genomic functions of U2AF in constitutive and regulated splicing

    PubMed Central

    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. PMID:25901584

  18. Electron Correlations in Superconductor Rh17S15 Studied by 103Rh NMR and Specific Heat Measurements

    NASA Astrophysics Data System (ADS)

    Koyama, Takehide; Kanda, Keiji; Motoyama, Gaku; Mito, Takeshi; Ueda, Ko-ichi; Kohara, Takao; Nakamura, Hiroyuki; Harima, Hisatomo

    2010-11-01

    The electronic state of superconductor Rh17S15 has been investigated by 103Rh nuclear magnetic resonance (NMR) and specific heat measurements. We have identified the observed NMR lines corresponding to four inequivalent Rh sites in the cubic unit cell and obtained the site-selective information of each site. The spin-lattice relaxation rate 1/T1 indicates that the 4d electrons from the Rh 24m site are the most responsible for the large electronic specific heat coefficient γ. This conclusion is supported by the energy band calculation. Considering the experimental results and the band calculation, we concluded that the γ value is enhanced because of the electron correlations of Rh 4d bands. In the superconducting state, an exponential decrease of both 1/T1 and the electron specific heat are observed, revealing the isotropic superconducting gap with 2Δ/kBTc=4.0. In addition, the decrease of the spin part of the Knight shift indicates the spin-singlet Cooper pair formation. These results demonstrate that Rh17S15 is an s-wave superconductor with enhanced effective electron mass.

  19. Climbing the vertebrate branch of U1A/U2B″ protein evolution

    PubMed Central

    Delaney, Kimberly J.; Williams, Sandra G.; Lawler, Mariah; Hall, Kathleen B.

    2014-01-01

    In the vertebrate lineage of the U1A/U2B″/SNF protein family, the U1A and U2B″ proteins bind to RNA stem–loops in the U1 or U2 snRNPs, respectively. However, their specialization is fairly recent, as they evolved from a single ancestral protein. The progress of their specialization (subfunctionalization) can be monitored by the amino acid sequence changes that give rise to their modern RNA-binding specificity. Using ancestral sequence reconstruction to predict the intermediates on the evolutionary branch, a probable path of sequential changes is defined for U1A and U2B″. The RNA-binding affinity for U1A/U2B″ protein ancestors was measured using modern U1 and U2 snRNA stem–loops and RNA stem–loop variants to understand how the proteins’ RNA specificities evolved. PMID:24840944

  20. Dual Function for U2AF35 in AG-Dependent Pre-mRNA Splicing

    PubMed Central

    Guth, Sabine; Tange, Thomas O/.; Kellenberger, Esther; Valcárcel, Juan

    2001-01-01

    The splicing factor U2AF is required for the recruitment of U2 small nuclear RNP to pre-mRNAs in higher eukaryotes. The 65-kDa subunit of U2AF (U2AF65) binds to the polypyrimidine (Py) tract preceding the 3′ splice site, while the 35-kDa subunit (U2AF35) contacts the conserved AG dinucleotide at the 3′ end of the intron. It has been shown that the interaction between U2AF35 and the 3′ splice site AG can stabilize U2AF65 binding to weak Py tracts characteristic of so-called AG-dependent pre-mRNAs. U2AF35 has also been implicated in arginine-serine (RS) domain-mediated bridging interactions with splicing factors of the SR protein family bound to exonic splicing enhancers (ESE), and these interactions can also stabilize U2AF65 binding. Complementation of the splicing activity of nuclear extracts depleted of U2AF by chromatography in oligo(dT)-cellulose requires, for some pre-mRNAs, only the presence of U2AF65. In contrast, splicing of a mouse immunoglobulin M (IgM) M1-M2 pre-mRNA requires both U2AF subunits. In this report we have investigated the sequence elements (e.g., Py tract strength, 3′ splice site AG, ESE) responsible for the U2AF35 dependence of IgM. The results indicate that (i) the IgM substrate is an AG-dependent pre-mRNA, (ii) U2AF35 dependence correlates with AG dependence, and (iii) the identity of the first nucleotide of exon 2 is important for U2AF35 function. In contrast, RS domain-mediated interactions with SR proteins bound to the ESE appear to be dispensable, because the purine-rich ESE present in exon M2 is not essential for U2AF35 activity and because a truncation mutant of U2AF35 consisting only of the pseudo-RNA recognition motif domain and lacking the RS domain is active in our complementation assays. While some of the effects of U2AF35 can be explained in terms of enhanced U2AF65 binding, other activities of U2AF35 do not correlate with increased cross-linking of U2AF65 to the Py tract. Collectively, the results argue that

  1. A role for U2/U6 helix Ib in 5' splice site selection.

    PubMed Central

    Luukkonen, B G; Séraphin, B

    1998-01-01

    Selection of pre-mRNA splice sites is a highly accurate process involving many trans-acting factors. Recently, we described a role for U6 snRNA position G52 in selection of the first intron nucleotide (+1G). Because some U2 alleles suppress U6-G52 mutations, we investigated whether the corresponding U2 snRNA region also influenced 5' splice site selection. Our results demonstrate that U2 snRNAs mutated at position U23, but not adjacent nucleotides, specifically affect 5' splice site cleavage. Furthermore, all U2 position U23 mutations are synthetic lethal with the thermosensitive U6-G52U allele. Interestingly, the U2-U23C substitution has an unprecedented hyperaccurate splicing phenotype in which cleavage of introns with a +1G substitution is reduced, whereas the strain grows with wild-type kinetics. U2 position U23 forms the first base pair with U6 position A59 in U2/U6 helix Ib. Restoration of the helical structure suppresses 5' splice site cleavage defects, showing an important role for the helix Ib structure in 5' splice site selection. U2/U6 helix Ib and helix II have recently been described as being functionally redundant. This report demonstrates a unique role for helix Ib in 5' splice site selection that is not shared with helix II. PMID:9701283

  2. 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

  3. 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.

  4. 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.

  5. BRCA1 maps proximal to D17S579 on chromosome 17q21 by genetic analysis

    PubMed Central

    Chamberlain, Jeffrey S.; Boehnke, Michael; Frank, Thomas S.; Kiousis, Sam; Xu, Junxhe; Guo, Sun-Wei; Hauser, Elizabeth R.; Norum, Robert A.; Helmbold, Elizabeth A.; Markel, Dorene S.; Keshavarzi, Sima M.; Jackson, C. Eugene; Calzone, Kathleen; Garber, Judy; Collins, Francis S.; Weber, Barbara L.

    1993-01-01

    Previous studies have demonstrated linkage between early-onset breast cancer and ovarian cancer and genetic markers on chromosome 17q21. These markers define the location of a gene (BRCA1) which appears to be inherited as an autosomal dominant susceptibility allele. We analyzed five families with multiple affected individuals for evidence of linkage to the BRCA1 region. Two of the five families appear to be linked to BRCA1. One apparently linked family contains critical recombinants, suggesting that the gene is proximal to the marker D17S579 (Mfd188). These findings are consistent with the maximum-likelihood position estimated by the Breast Cancer Linkage Consortium and with recombination events detected in other linked families. Linkage analysis was greatly aided by PCR-based analysis of paraffin-embedded normal breast tissue from deceased family members, demonstrating the feasibility and importance of this approach. One of the two families with evidence of linkage between breast cancer and genetic markers flanking BRCA1 represents the first such family of African-American descent to be reported in detail. ImagesFigure 4 PMID:8460646

  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. Sequence and structure in double-stranded ribonucleic acid: (A-G-C-U)2 and (A-C-G-U)2.

    PubMed

    Bubienko, E; Uniack, M A; Borer, P N

    1981-11-24

    Comparative studies of the thermally induced helix--coil transition in ribosyl (A-G-C-U)2 and (A-C-G-U)2 are described. Ordered structures form at low temperatures where the ribofuranose rings adopt the 3'-endo conformation and both oligomer helices have base-paired stacking arrangements qualitatively similar to the A-RNA family configuration. Especially for (A-C-G-U)2, there is a lack of quantitative agreement between the A-family base overlap and the 1H NMR data; ring-current and atomic diamagnetic anisotropies using A-form structures fail to predict five of the seven aromatic C--H resonances within 0.2 ppm. The NMR results are in better agreement with the A form for (A-G-C-U)2. For both oligomers, the changes in chemical shift for the anomeric (H1') resonances indicate substantial (greater than or equal to 20 degrees) changes in the average glycosidic torsion angle upon base pairing and stacking for the adenosine and cytidine residues; this angle in uridine and guanosine residues must change only slightly. PMID:7317364

  8. 11. DETAILED INTERIOR VIEW OF WEB AT U2L2, SHOWING VERTICAL, ...

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

    11. DETAILED INTERIOR VIEW OF WEB AT U2L2, SHOWING VERTICAL, ARCH RIB WELDED/BOLTED GUSSET PLATE AND GUARDRAIL, LOOKING SOUTH - Cottonville Bridge, County Road D-61 at Farmer's Creek, Maquoketa, Jackson County, IA

  9. 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.

  10. 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

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

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 46 Shipping 2 2014-10-01 2014-10-01 false Scope (modifies U-1 and U-2). 54.01-5 Section 54.01-5 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) MARINE ENGINEERING PRESSURE VESSELS General Requirements § 54.01-5 Scope (modifies U-1 and U-2). (a) This part contains requirements for pressure vessels. table 54.01-5(a) gives...

  12. The Splicing Factor U2AF Small Subunit Is Functionally Conserved between Fission Yeast and Humans

    PubMed Central

    Webb, Christopher J.; Wise, Jo Ann

    2004-01-01

    The small subunit of U2AF, which functions in 3′ splice site recognition, is more highly conserved than its heterodimeric partner yet is less thoroughly investigated. Remarkably, we find that the small subunit of Schizosaccharomyces pombe U2AF (U2AFSM) can be replaced in vivo by its human counterpart, demonstrating that the conservation extends to function. Precursor mRNAs accumulate in S. pombe following U2AFSM depletion in a time frame consistent with a role in splicing. A comprehensive mutational analysis reveals that all three conserved domains are required for viability. Notably, however, a tryptophan in the pseudo-RNA recognition motif implicated in a key contact with the large subunit by crystallographic data is dispensable whereas amino acids implicated in RNA recognition are critical. Mutagenesis of the two zinc-binding domains demonstrates that they are neither equivalent nor redundant. Finally, two- and three-hybrid analyses indicate that mutations with effects on large-subunit interactions are rare whereas virtually all alleles tested diminished RNA binding by the heterodimer. In addition to demonstrating extraordinary conservation of U2AF small-subunit function, these results provide new insights into the roles of individual domains and residues. PMID:15121844

  13. Thermal and transport properties of U2Pt(x)Ir(1-x)C2.

    PubMed

    Kang, Mingu; Wakeham, N; Ni, Ni; Bauer, E D; Kim, Jeehoon; Ronning, F

    2015-09-16

    We report thermal and transport properties of U2Pt x Ir1-x C2 from which a magnetic phase diagram is obtained. Pure U2IrC2 is an antiferromagnet at 6.5 K, whose Néel temperature initially rises to 13.2 K at x = 0.2 and subsequently is suppressed to zero temperature with increasing Pt content near x = 0.6. Heat capacity divided by temperature at x = 0.6 shows an upturn at low temperature, consistent with the expectations of enhanced quantum fluctuations in the presence of an underlying quantum critical point. The entropy after the phonon contribution has been subtracted has a value of 0.24 Rln2 at the Néel temperature of U2IrC2, revealing an itinerant nature of the 5 f electrons in this compound. On the Pt rich side of the phase diagram, superconductivity is suppressed by x = 0.85. The residual resistivity increases by a factor of 10 from pure Pt (x = 1) to x = 0.85 where superconductivity is suppressed to zero. By comparing the phase diagram of Ir doped U2PtC2 with the phase diagram of pressure tuned and Rh doped U2PtC2 we demonstrate the role of electronic tuning in this system. PMID:26302330

  14. Molecular characterization of the spliceosomal proteins U1A and U2B" from higher plants.

    PubMed Central

    Simpson, G G; Clark, G P; Rothnie, H M; Boelens, W; van Venrooij, W; Brown, J W

    1995-01-01

    In addition to their role in pre-mRNA splicing, the human spliceosomal proteins U1A and U2B" are important models of how RNP motif-containing proteins execute sequence-specific RNA binding. Genes encoding U1A and U2B" have been isolated from potato and thereby provide the only evolutionary comparison available for both proteins and represent the only full-length genes encoding plant spliceosomal proteins to have been cloned and characterized. In vitro RNA binding experiments revealed the ability of potato U2B" to interact with human U2A' to enhance sequence-specific binding and to distinguish cognate RNAs of either plant or animal origin. A comparison of the sequence of U1A and U2B" proteins indicated that multiple residues which could affect RNP motif conformation probably govern the specific distinction in RNA binding by these proteins. Since human U1A modulates polyadenylation in vertebrates, the possibility that plant U1A might be exploited in the characterization of this process in plants was examined. However, unlike vertebrate U1A, neither U1A from potato nor Arabidopsis bound their own mRNA and no evidence for binding to upstream efficiency elements in polyadenylation signals was obtained, suggesting that plant U1A is not involved in polyadenylation. Images PMID:7556097

  15. Thermal and transport properties of U2Pt x Ir1-x C2

    NASA Astrophysics Data System (ADS)

    Kang, Mingu; Wakeham, N.; Ni, Ni; Bauer, E. D.; Kim, Jeehoon; Ronning, F.

    2015-09-01

    We report thermal and transport properties of U2Pt x Ir1-x C2 from which a magnetic phase diagram is obtained. Pure U2IrC2 is an antiferromagnet at 6.5 K, whose Néel temperature initially rises to 13.2 K at x = 0.2 and subsequently is suppressed to zero temperature with increasing Pt content near x = 0.6. Heat capacity divided by temperature at x = 0.6 shows an upturn at low temperature, consistent with the expectations of enhanced quantum fluctuations in the presence of an underlying quantum critical point. The entropy after the phonon contribution has been subtracted has a value of 0.24 Rln2 at the Néel temperature of U2IrC2, revealing an itinerant nature of the 5 f electrons in this compound. On the Pt rich side of the phase diagram, superconductivity is suppressed by x = 0.85. The residual resistivity increases by a factor of 10 from pure Pt (x = 1) to x = 0.85 where superconductivity is suppressed to zero. By comparing the phase diagram of Ir doped U2PtC2 with the phase diagram of pressure tuned and Rh doped U2PtC2 we demonstrate the role of electronic tuning in this system.

  16. The amino acid sequence of ribonuclease U2 from Ustilago sphaerogena.

    PubMed Central

    Sato, S; Uchida, T

    1975-01-01

    1. RNAase (ribonuclease) U2, a purine-specific RNAase, was reduced, aminoethylated and hydrolysed with trypsin, chymotrypsin and thermolysin. On the basis of the analyses of the resulting peptides, the complete amino acid sequence of RNAase U2 was determined, 2. When the sequence was compared with the amino acid sequence of RNAase T1 (EC 3.1.4.8), the following regions were found to be similar in the two enzymes; Tyr-Pro-His-Gln-Tyr (38-42) in RNAase U2 and Tyr-Pro-His-Lys-Tyr (38-42) in RNAase T1, Glu-Phe-Pro-Leu-Val (61-65) in RNAase U2 and Glu-Trp-Pro-Ile-Leu (58-62) in RNAase T1, Asp-Arg-Val-Ile-Tyr-Gln (83-88) in RNAase U2 and Asp-Arg-Val-Phe-Asn (76-81) in RNAase T1 and Val-Thr-His-Thr-Gly-Ala (98-103) in RNAase U2 and Ile-Thr-His-Thr-Gly-Ala (90-95) in RNAase T1. All of the amino acid residues, histidine-40, glutamate-58, arginine-77 and histidine-92, which were found to play a crucial role in the biological activity of RNAase T1, were included in the regions cited here. 3. Detailed evidence for the amino acid sequence of the sequence of the proteins has been deposited as Supplementary Publication SUP 50041 (33 PAGES) AT THE British Library (Lending Division)(formerly the National Lending Library for Science and Technology), Boston Spa, Yorks. LS23 7BQ, U.K., from whom copies can be obtained on the terms indicated in Biochem. J. (1975), 145, 5. PMID:1156364

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

    DOE PAGESBeta

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

    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

  18. White matter hyperintensities on MRI in high-altitude U-2 pilots

    PubMed Central

    Sherman, Paul; Profenna, Leonardo; Grogan, Patrick; Sladky, John; Brown, Anthony; Robinson, Andrew; Rowland, Laura; Hong, Elliot; Patel, Beenish; Tate, David; Kawano, Elaine S.; Fox, Peter; Kochunov, Peter

    2013-01-01

    Objective: To demonstrate that U-2 pilot occupational exposure to hypobaria leads to increased incidence of white matter hyperintensities (WMH) with a more uniform distribution throughout the brain irrespective of clinical neurologic decompression sickness history. Methods: We evaluated imaging findings in 102 U-2 pilots and 91 controls matched for age, health, and education levels. Three-dimensional, T2-weighted, high-resolution (1-mm isotropic) imaging data were collected using fluid-attenuated inversion recovery sequence on a 3-tesla MRI scanner. Whole-brain and regional WMH volume and number were compared between groups using a 2-tailed Wilcoxon rank sum test. Results: U-2 pilots demonstrated an increase in volume (394%; p = 0.004) and number (295%; p < 0.001) of WMH. Analysis of regional distribution demonstrated WMH more uniformly distributed throughout the brain in U-2 pilots compared with mainly frontal distribution in controls. Conclusion: Pilots with occupational exposure to hypobaria showed a significant increase in WMH lesion volume and number. Unlike the healthy controls with predominantly WMH in the frontal white matter, WMH in pilots were more uniformly distributed throughout the brain. This is consistent with our hypothesized pattern of damage produced by interaction between microemboli and cerebral tissue, leading to thrombosis, coagulation, inflammation, and/or activation of innate immune response, although further studies will be necessary to clarify the pathologic mechanisms responsible. PMID:23960192

  19. Thermal and Transport properties of U2Pt1-xIrxC2

    NASA Astrophysics Data System (ADS)

    Kang, Min Gu; Wakeham, Nick; Ni, Ni; Bauer, Eric; Kim, Jeehoon; Ronning, Filip

    2015-03-01

    We report thermal and transport properties of U2Pt1-xIrxC2 from which a magnetic phase diagram is obtained. Pure U2IrC2 is an antiferromagnet at 6.5 K, whose Neel temperature initially rises to 13.2 K at x=0.8 and subsequently is suppressed to zero temperature with increasing Pt content near x=0.4. Heat capacity data at x=0.4 shows an upturn at low temperature, which is consistent with proximity to a quantum critical point and considered as non-Fermi liquid behavior. The entropy after the phonon contribution has been subtracted has a value of 0.18 Rln 2 at the Neel temperature of U2IrC2, revealing an itinerant nature of the 5f electrons in this compound. On the Pt rich side of the phase diagram, superconductivity is suppressed by x=0.15. The residual resistivity increases by a factor of 10 from pure Pt (x=0) to x=0.15 where superconductivity is suppressed to zero. The phase diagram is compared to pressure tuned and Rh doped U2PtC2 demonstrating the role of electronic tuning in this system.

  20. 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

  1. 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.

  2. 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.

  3. Positions of S2, S13, S16, S17, S19 and S21 in the 30 S ribosomal subunit of Escherichia coli.

    PubMed

    Capel, M S; Kjeldgaard, M; Engelman, D M; Moore, P B

    1988-03-01

    Neutron scattering distance data are presented for 33 protein pairs in the 30 S ribosomal subunit from Escherichia coli, along with the methods used for measuring distances between its exchangeable components. When combined with prior data, these new results permit the positioning of S2, S13, S16, S17, S19 and S21 in the 30 S ribosomal subunit, completing the mapping of its proteins by neutron scattering. Comparisons with other data suggest that the neutron map is a reliable guide to the quaternary structure of the 30 S subunit. PMID:3288761

  4. Hydrogen isotope effect on storage behavior of U2Ti and UZr2.3

    NASA Astrophysics Data System (ADS)

    Jat, Ram Avtar; Sawant, S. G.; Rajan, M. B.; Dhanuskar, J. R.; Kaity, Santu; Parida, S. C.

    2013-11-01

    U2Ti and UZr2.3 alloys were prepared by arc melting method, vacuum annealed and characterized by XRD, SEM and EDX methods. Hydrogen isotope effect on the storage behavior of these alloys were studied by measuring the hydrogen/deuterium desorption pressure-composition-temperature (PCT) profiles in the temperature range of 573-678 K using a Sievert's type volumetric apparatus. It was observed that, in the temperature and pressure range of investigation, all the isotherms show a single desorption plateau. The PCT data reveals that both U2Ti and UZr2.3 alloys had normal isotope effects on hydrogen/deuterium desorption at all experimental temperatures. Thermodynamic parameters for dehydrogenation and dedeuteration reactions of the corresponding hydrides and deuterides of the above alloys were deduced from the PCT data.

  5. Quantum geometry and quantization on U(u(2)) background. Noncommutative Dirac monopole

    NASA Astrophysics Data System (ADS)

    Gurevich, Dimitri; Saponov, Pavel

    2016-08-01

    In our previous publications we introduced differential calculus on the enveloping algebras U(gl(m)) similar to the usual calculus on the commutative algebra Sym (gl(m)) . The main ingredients of our calculus are quantum partial derivatives which turn into the usual partial derivatives in the classical limit. In the particular case m = 2 we prolonged this calculus on a central extension A of the algebra U(gl(2)) . In the present paper we consider the problem of a further extension of the quantum partial derivatives on the skew-field of the algebra A and define the corresponding de Rham complex. As an application of the differential calculus we suggest a method of transferring dynamical models defined on an extended Sym (u(2)) to an extended algebra U(u(2)) . We call this procedure the quantization with noncommutative configuration space. In this sense we quantize the Dirac monopole and find a solution of this model.

  6. Erosion Analysis for the Misaligned U2 Nozzle and its Connector Block

    SciTech Connect

    Lee, S.Y.

    2002-11-19

    In support of an erosion evaluation for the misaligned mating surfaces of the U2 nozzle and its connector block in the 3H evaporator lift-separator jumper, the Engineering Modeling and Simulation Group (EMSG) has developed computational models to identify potential sites of high erosion. Two mechanisms were considered to evaluate high erosion locations representative of the actual flow process in the misaligned U2 nozzle, abrasive erosion which occurs by high wall shear of viscous liquid film, and chip-off erosion which is mainly governed by particle impingement. The results show that primary locations of the highest erosion due to particle impingement are at the occurrence of sudden change of flow direction, sudden contraction, and flow obstruction as expected. Potential damage sites due to the abrasive wall erosion are at the upstream and downstream regions of sudden changes of flow direction.

  7. 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.

  8. Thermodynamic and electrical transport properties of single-crystalline U2Cu4As5

    NASA Astrophysics Data System (ADS)

    Gnida, D.; Pikul, A. P.; Kaczorowski, D.

    2015-06-01

    High-quality single crystals of U2Cu4As5 were investigated by means of magnetic susceptibility, magnetization, specific heat, electrical resistivity, magnetoresistivity and Hall effect measurements, performed in wide ranges of temperature and magnetic field. The results revealed an antiferromagnetic ordering below TN = 190 K and very strong magnetocrystalline anisotropy. In the paramagnetic state, the charge transport is driven by Kondo spin-flip scattering. In the ordered region, it is governed by electron-magnon and electron-electron scattering processes with the latter ones being dominant at the lowest temperatures. The uniaxial character of the magnetic structure of U2Cu4As5 manifests itself in the temperature variations of the magnetic susceptibility and the electrical resistivity as well as in the characteristic response to the applied magnetic field.

  9. The TOR signaling pathway regulates starvation-induced pseudouridylation of yeast U2 snRNA.

    PubMed

    Wu, Guowei; Radwan, Mohamed K; Xiao, Mu; Adachi, Hironori; Fan, Jason; Yu, Yi-Tao

    2016-08-01

    Pseudouridine (Ψ) has been identified in various types of RNAs, including mRNA, rRNA, tRNA, snRNA, and many other noncoding RNAs. We have previously shown that RNA pseudouridylation, like DNA and protein modifications, can be induced by stress. For instance, growing yeast cells to saturation induces the formation of Ψ93 in U2 snRNA. Here, we further investigate this inducible RNA modification. We show that switching yeast cells from nutrient-rich medium to different nutrient-deprived media (including water) results in the formation of Ψ93 in U2 snRNA. Using gene deletion/conditional depletion as well as rapamycin treatment, we further show that the TOR signaling pathway, which controls cell entry into stationary phase, regulates Ψ93 formation. The RAS/cAMP signaling pathway, which parallels the TOR pathway, plays no role in this inducible modification. PMID:27268497

  10. 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.

  11. 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.

  12. Single Molecule Analysis of Protein Free U2/U6 snRNAs

    PubMed Central

    Guo, Zhuojun; Karunatilaka, Krishanthi S.; Rueda, David

    2009-01-01

    Spliceosomes catalyze the maturation of precursor mRNAs from yeast to humans. Their catalytic core comprises three small nuclear RNAs (U2, U5 and U6) involved in substrate positioning and catalysis. It has been postulated, but never shown experimentally, that the U2/U6 complex adopts at least two conformations that reflect different activation states. We have used single-molecule fluorescence to probe the structural dynamics of a protein-free RNA complex modeling U2/U6 from yeast and mutants of highly conserved regions. Our data show the presence of at least three distinct conformations in equilibrium. The minimal folding pathway consists of a two-step process with an obligatory intermediate. The first step is strongly magnesium dependent and we provide evidence suggesting the second corresponds to the formation of the genetically conserved helix IB. Site-specific mutations in the highly conserved AGC triad and the U80 base in U6 suggest that the observed conformational dynamics correlate with residues that play an important role in splicing. PMID:19881500

  13. 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.

  14. Accurate and efficient 3' processing of U2 small nuclear RNA precursor in a fractionated cytoplasmic extract.

    PubMed Central

    Kleinschmidt, A M; Pederson, T

    1987-01-01

    The small nuclear RNAs U1, U2, U4, and U5 are cofactors in mRNA splicing and, like the pre-mRNAs with which they interact, are transcribed by RNA polymerase II. Also like mRNAs, mature U1 and U2 RNAs are generated by 3' processing of their primary transcripts. In this study we have investigated the in vitro processing of an SP6-transcribed human U2 RNA precursor, the 3' end of which matches that of authentic human U2 RNA precursor molecules. Although the SP6-U2 RNA precursor was efficiently processed in an ammonium sulfate-fractionated HeLa cytoplasmic S100 extract, the product RNA was unstable. Further purification of the processing activity on glycerol gradients resolved a 7S activity that nonspecifically cleaved all RNAs tested and a 15S activity that efficiently processed the 3' end of pre-U2 RNA. The 15S activity did not process the 3' end of a tRNA precursor molecule. As demonstrated by RNase protection, the processed 3' end of the SP6-U2 RNA maps to the same nucleotides as does mature HeLa U2 RNA. Images PMID:3670307

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

    NASA Astrophysics Data System (ADS)

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

    2011-02-01

    We present the magnetic and transport properties of single crystalline U2PdSi3 measured with the magnetic field (H) (or measuring current, I) applied along two typical crystallographic directions, i.e. H\\perp c -axis and H\\parallel c -axis (or I\\perp c -axis and I\\parallel c -axis). For both directions, a spin-glass state is confirmed to form at low temperature with the same spin freezing temperature Tf (= 11.5 K), initial frequency shift δTf (= 0.023) and activation energy Ea/kB (= 90.15 K) in zero dc field. Strong anisotropy in magnetic and transport behavior is found to be a significant feature of U2PdSi3. The unusual ferromagnetic-like anomaly in ac susceptibility and dc magnetization curves around Tm = 71 K is observed in the case of H\\parallel c -axis but not in the cases of H \\perp c -axis. The characteristic temperature Tir, below which evident irreversible magnetism originated from random spin freezing can be observed, shows much stronger field dependence for H \\perp c -axis than for H\\parallel 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 \\perp c -axis, while the coherent-Kondo-effect-like behavior is obvious for I\\parallel 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 U2PdSi3 and other 2:1:3 intermetallic compounds.

  16. Magnetic Field and Pressure Phase Diagrams of Uranium Heavy-Fermion Compound U2Zn17

    NASA Astrophysics Data System (ADS)

    Tateiwa, Naoyuki; Ikeda, Shugo; Haga, Yoshinori; Matsuda, Tatsuma D.; Yamamoto, Etsuji; Sugiyama, Kiyohiro; Hagiwara, Masayuki; Kindo, Koichi; Ōnuki, Yoshichika

    2011-01-01

    We have performed magnetization measurements at high magnetic fields of up to 53 T on single crystals of a uranium heavy-fermion compound U2Zn17 grown by the Bridgman method. In the antiferromagnetic state below the Néel temperature TN=9.7 K, a metamagnetic transition is found at Hc≃ 32 T for the field along the [11\\bar{2}0] direction (a-axis). The magnetic phase diagram for the field along the [11\\bar{2}0] direction is given. The magnetization curve shows a nonlinear increase at Hm≃ 35 T in the paramagnetic state above TN up to a characteristic temperature Tχmax where the magnetic susceptibility or electrical resistivity shows a maximum value. This metamagnetic behavior of the magnetization at Hm is discussed in comparison with the metamagnetic magnetism of the heavy-fermion super conductors UPt3, URu2Si2, and UPd2Al3. We have also carried out high-pressure resistivity measurement on U2Zn17 using a diamond anvil cell up to 8.7 GPa. Noble gas argon was used as a pressure-transmitting medium to ensure a good hydrostatic environment. The Néel temperature TN is almost pressure-independent up to 4.7 GPa and starts to increase in the higher-pressure region. The pressure dependences of the coefficient of the T2 term in the electrical resistivity A, the antiferromagnetic gap Δ, and the characteristic temperature Tρmax are discussed. It is found that the effect of pressure on the electronic states in U2Zn17 is weak compared with those in the other heavy fermion compounds.

  17. 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.

  18. Ab initio calculation of mechanical and thermal properties of U2Mo intermetallic

    NASA Astrophysics Data System (ADS)

    Jaroszewicz, S.; Losada, E. L.; Garcés, J. E.; Mosca, H. O.

    2013-10-01

    We present a study of structural, elastic and thermodynamic properties of tetragonal (C11b) U2Mo by means of density-functional theory based calculations using full-potential linearized augmented plane wave method. In this approach the generalized gradient approximation were used for the exchange-correlation potential calculation. The optimized lattice parameters are in excellent agreement with the experimental data. Through the Debye-Grüneisen model the temperature and pressure dependence of equation of state, bulk modulus, thermal expansion and specific heat have been obtained and discussed in the range of pressure 0-20 GPa and the temperature 0-800 K.

  19. Sp6<=crSscrU2 symmetry of the fermion dynamical symmetry model

    NASA Astrophysics Data System (ADS)

    Chen, Jin-Quan; Chen, Xuan-Gen; Feng, Da Hsuan; Wu, Cheng-Li; Ginocchio, Joseph N.; Guidry, Mike W.

    1989-12-01

    The SP6×scrSscrU2 symmetry of the fermion dynamical symmetry model (FDSM) was studied. Analytic expressions are given for the wave functions and matrix elements of the pair creation operators S°, D°, and E2 transition operator for the heritage u=0, 1, 2 cases. Various Pauli effects which differentiate the FDSM SU3 from IBM SU3, as well as the relationship between the wave functions and matrix elements in the FDSM, the interacting boson model, the Sp (6,R) models, and the Elliott model are discussed. Extensive discussions of the physical implications of the model are presented.

  20. Molecular genetic analysis of U2AF59 in Schizosaccharomyces pombe: differential sensitivity of introns to mutational inactivation.

    PubMed Central

    Romfo, C M; Lakhe-Reddy, S; Wise, J A

    1999-01-01

    The large subunit of the mammalian U2AF heterodimer (U2AF65) is essential for splicing in vitro. To expand our understanding of how this protein functions in vivo, we have created a null allele of the gene encoding the Schizosaccharomyces pombe ortholog, U2AF59, and employed it in a variety of genetic complementation assays. First, analysis of an extensive series of double amino acid substitutions indicates that this splicing factor is surprisingly refractory to mutations. Second, despite extensive structural conservation, we find that metazoan large subunit orthologs cannot substitute in vivo for fission yeast U2AF59. Third, because the activity of U2AF65 in vitro involves binding to the 3' polypyrimidine tract, we examined the splicing of introns containing or lacking this feature in a U2AF59 mutant described here as well as a previously isolated temperature-sensitive mutant (Potashkin et al., 1993, Science 262:573-575). Our data indicate that all four introns tested, including two that lack extensive runs of pyrimidines between the branchpoint and 3' splice site, show splicing defects upon shifting to the nonpermissive condition. In all cases, splicing is blocked prior to the first transesterification reaction in the mutants, consistent with the role inferred for human U2AF65 based on in vitro experiments. PMID:9917066

  1. Pseudouridines in U2 snRNA stimulate the ATPase activity of Prp5 during spliceosome assembly.

    PubMed

    Wu, Guowei; Adachi, Hironori; Ge, Junhui; Stephenson, David; Query, Charles C; Yu, Yi-Tao

    2016-03-15

    Pseudouridine (Ψ) is the most abundant internal modification identified in RNA, and yet little is understood of its effects on downstream reactions. Yeast U2 snRNA contains three conserved Ψs (Ψ35, Ψ42, and Ψ44) in the branch site recognition region (BSRR), which base pairs with the pre-mRNA branch site during splicing. Here, we show that blocks to pseudouridylation at these positions reduce the efficiency of pre-mRNA splicing, leading to growth-deficient phenotypes. Restoration of pseudouridylation at these positions using designer snoRNAs results in near complete rescue of splicing and cell growth. These Ψs interact genetically with Prp5, an RNA-dependent ATPase involved in monitoring the U2 BSRR-branch site base-pairing interaction. Biochemical analysis indicates that Prp5 has reduced affinity for U2 snRNA that lacks Ψ42 and Ψ44 and that Prp5 ATPase activity is reduced when stimulated by U2 lacking Ψ42 or Ψ44 relative to wild type, resulting in inefficient spliceosome assembly. Furthermore, in vivo DMS probing analysis reveals that pseudouridylated U2, compared to U2 lacking Ψ42 and Ψ44, adopts a slightly different structure in the branch site recognition region. Taken together, our results indicate that the Ψs in U2 snRNA contribute to pre-mRNA splicing by directly altering the binding/ATPase activity of Prp5. PMID:26873591

  2. 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.

  3. 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.

  4. 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.

  5. 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

    2016-04-01

    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. PMID:26974702

  6. Magnetic structure of U2Rh3Si5 in external fields up to 14.5 T

    NASA Astrophysics Data System (ADS)

    Galli, F.; Feyerherm, R.; Prokes, K.; Nieuwenhuys, G. J.

    2000-03-01

    The intermetallic compound U2Rh3Si5 exhibits a first-order transition at 25 K into a noncollinear antiferromagnetic structure. At the lowest temperature the antiferromagnetic structure can be destroyed by a field of 14 T. Using the two-axis spectrometer E4 at the Hahn-Meitner-Institute, we have studied the magnetic structure of U2Rh3Si5 for various temperatures and magnetic fields around the magnetic phase boundary.

  7. 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.

  8. 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

  9. Combining recombinant ribonuclease U2 and protein phosphatase for RNA modification mapping by liquid chromatography-mass spectrometry.

    PubMed

    Houser, Whitney M; Butterer, Annika; Addepalli, Balasubrahmanym; Limbach, Patrick A

    2015-06-01

    Ribonuclease (RNase) mapping of modified nucleosides onto RNA sequences is limited by RNase availability. A codon-optimized gene for RNase U2, a purine selective RNase with preference for adenosine, has been designed for overexpression using Escherichia coli as the host. Optimal expression conditions were identified enabling generation of milligram-scale quantities of active RNase U2. RNase U2 digestion products were found to terminate in both 2',3'-cyclic phosphates and 3'-linear phosphates. To generate a homogeneous 3'-linear phosphate set of products, an enzymatic approach was investigated. Bacteriophage lambda protein phosphatase was identified as the optimal enzyme for hydrolyzing cyclic phosphates from RNase U2 products. The compatibility of this enzymatic approach with liquid chromatography-tandem mass spectrometry (LC-MS/MS) RNA modification mapping was then demonstrated. RNase U2 digestion followed by subsequent phosphatase treatment generated nearly 100% 3'-phosphate-containing products that could be characterized by LC-MS/MS. In addition, bacteriophage lambda protein phosphatase can be used to introduce (18)O labels within the 3'-phosphate of digestion products when incubated in the presence of H2(18)O, allowing prior isotope labeling methods for mass spectrometry to include digestion products from RNase U2. PMID:25797349

  10. Design, synthesis and biological activity of flavonoid derivatives as selective agonists for neuromedin U 2 receptor.

    PubMed

    Ma, Ming-Liang; Li, Ming; Gou, Jiao-Jiao; Ruan, Tian-Yu; Jin, Hai-Shan; Zhang, Ling-Hong; Wu, Liang-Chun; Li, Xiao-Yan; Hu, Ying-He; Wen, Ke; Zhao, Zheng

    2014-11-01

    Central neuromedin U 2 receptor (NMU2R) plays important roles in the regulation of food intake and body weight. Identification of NMU2R agonists may lead to the development of pharmaceutical agents to treat obesity. Based on the structure of rutin, a typical flavonoid and one of the NMU2R agonists we previously identified from an in-house made natural product library, 30 flavonoid derivatives have been synthesized and screened on a cell-based reporter gene assay. A number of compounds were found to be selective and highly potent to NMU2R. For example, the EC50 value of compound NRA 4 is very close to that of NMU, the endogenous peptide ligand of NMU2R. Structure-activity relationship analysis revealed that a 3-hydroxyl group in ring C and a 2'-fluoride group in ring B were essential for this class of compounds to be active against NMU2R. PMID:25262941

  11. 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

  12. Lepton flavor non-universality in B-meson decays from a U(2) flavor model

    NASA Astrophysics Data System (ADS)

    Falkowski, Adam; Nardecchia, Marco; Ziegler, Robert

    2015-11-01

    We address the recent anomalies in semi-leptonic B-meson decays using a model of fermion masses based on the U(2) flavor symmetry. The new contributions to b → sℓℓ transitions arise due to a tree-level exchange of a Z' vector boson gauging a U(1) subgroup of the flavor symmetry. They are controlled by a single parameter and are approximately aligned to the Standard Model prediction, with constructive interference in the e-channel and destructive interference in the μ-channel. The current experimental data on semi-leptonic B-meson decays can be very well reproduced without violating existing constraints from flavor violation in the quark and lepton sectors. Our model will be tested by new measurements of b → sℓℓ transitions and also by future electroweak precision tests, direct Z' searches, and μ- e conversion in nuclei.

  13. 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

  14. Unusual 5f magnetism in the U2Fe3Ge ternary Laves phase: a single crystal study.

    PubMed

    Henriques, M S; Gorbunov, D I; Waerenborgh, J C; Havela, L; Shick, A B; Diviš, M; Andreev, A V; Gonçalves, A P

    2013-02-13

    Magnetic properties of the intermetallic compound U(2)Fe(3)Ge were studied on a single crystal. The compound crystallizes in the hexagonal Mg(2)Cu(3)Si structure, an ordered variant of the MgZn(2) Laves structure (C14). U(2)Fe(3)Ge displays ferromagnetic order below the Curie temperature T(C) = 55 K and presents an exception to the Hill rule, as the nearest inter-uranium distances do not exceed 3.2 Å. Magnetic moments lie in the basal plane of the hexagonal lattice, with the spontaneous magnetic moment M(s) = 1.0 μ(B)/f.u. at T = 2 K. No anisotropy within the basal plane is detected. In contrast to typical U-based intermetallics, U(2)Fe(3)Ge exhibits very low magnetic anisotropy, whose field does not exceed 10 T. The dominance of U in the magnetism of U(2)Fe(3)Ge is suggested by the (57)Fe Mössbauer spectroscopy study, which indicates very low or even zero Fe moments. Electronic structure calculations are in agreement with the observed easy-plane anisotropy but fail to explain the lack of an Fe contribution to the magnetism of U(2)Fe(3)Ge. PMID:23315489

  15. An extended U2AF65–RNA-binding domain recognizes the 3′ splice site signal

    PubMed Central

    Agrawal, Anant A.; Salsi, Enea; Chatrikhi, Rakesh; Henderson, Steven; Jenkins, Jermaine L.; Green, Michael R.; Ermolenko, Dmitri N.; Kielkopf, Clara L.

    2016-01-01

    How the essential pre-mRNA splicing factor U2AF65 recognizes the polypyrimidine (Py) signals of the major class of 3′ splice sites in human gene transcripts remains incompletely understood. We determined four structures of an extended U2AF65–RNA-binding domain bound to Py-tract oligonucleotides at resolutions between 2.0 and 1.5 Å. These structures together with RNA binding and splicing assays reveal unforeseen roles for U2AF65 inter-domain residues in recognizing a contiguous, nine-nucleotide Py tract. The U2AF65 linker residues between the dual RNA recognition motifs (RRMs) recognize the central nucleotide, whereas the N- and C-terminal RRM extensions recognize the 3′ terminus and third nucleotide. Single-molecule FRET experiments suggest that conformational selection and induced fit of the U2AF65 RRMs are complementary mechanisms for Py-tract association. Altogether, these results advance the mechanistic understanding of molecular recognition for a major class of splice site signals. PMID:26952537

  16. A novel 3′ splice site recognition by the two zinc fingers in the U2AF small subunit

    PubMed Central

    Yoshida, Hisashi; Park, Sam-Yong; Oda, Takashi; Akiyoshi, Taeko; Sato, Mamoru; Shirouzu, Mikako; Tsuda, Kengo; Kuwasako, Kanako; Unzai, Satoru; Muto, Yutaka; Urano, Takeshi; Obayashi, Eiji

    2015-01-01

    The pre-mRNA splicing reaction of eukaryotic cells has to be carried out extremely accurately, as failure to recognize the splice sites correctly causes serious disease. The small subunit of the U2AF heterodimer is essential for the determination of 3′ splice sites in pre-mRNA splicing, and several single-residue mutations of the U2AF small subunit cause severe disorders such as myelodysplastic syndromes. However, the mechanism of RNA recognition is poorly understood. Here we solved the crystal structure of the U2AF small subunit (U2AF23) from fission yeast, consisting of an RNA recognition motif (RRM) domain flanked by two conserved CCCH-type zinc fingers (ZFs). The two ZFs are positioned side by side on the β sheet of the RRM domain. Further mutational analysis revealed that the ZFs bind cooperatively to the target RNA sequence, but the RRM domain acts simply as a scaffold to organize the ZFs and does not itself contact the RNA directly. This completely novel and unexpected mode of RNA-binding mechanism by the U2AF small subunit sheds light on splicing errors caused by mutations of this highly conserved protein. PMID:26215567

  17. Unusual 5f magnetism in the U2Fe3Ge ternary Laves phase: a single crystal study

    NASA Astrophysics Data System (ADS)

    Henriques, M. S.; Gorbunov, D. I.; Waerenborgh, J. C.; Havela, L.; Shick, A. B.; Diviš, M.; Andreev, A. V.; Gonçalves, A. P.

    2013-02-01

    Magnetic properties of the intermetallic compound U2Fe3Ge were studied on a single crystal. The compound crystallizes in the hexagonal Mg2Cu3Si structure, an ordered variant of the MgZn2 Laves structure (C14). U2Fe3Ge displays ferromagnetic order below the Curie temperature TC = 55 K and presents an exception to the Hill rule, as the nearest inter-uranium distances do not exceed 3.2 Å. Magnetic moments lie in the basal plane of the hexagonal lattice, with the spontaneous magnetic moment Ms = 1.0 μB/f.u. at T = 2 K. No anisotropy within the basal plane is detected. In contrast to typical U-based intermetallics, U2Fe3Ge exhibits very low magnetic anisotropy, whose field does not exceed 10 T. The dominance of U in the magnetism of U2Fe3Ge is suggested by the 57Fe Mössbauer spectroscopy study, which indicates very low or even zero Fe moments. Electronic structure calculations are in agreement with the observed easy-plane anisotropy but fail to explain the lack of an Fe contribution to the magnetism of U2Fe3Ge.

  18. Genetic polymorphism study at four minisatellite loci (D1S80, D17S5, D19S20, and APOB) among five Indian population groups.

    PubMed

    Das, Birajalaxmi; Ghosh, Anu; Chauhan, P S; Seshadri, M

    2002-06-01

    The present study reports the genetic variation observed among five anthropologically distinct population groups of India, using four highly polymorphic minisatellite loci (D1S80, D17S5, D19S20, and APOB 3' VNTR) in order to examine the effect of geographical and linguistic affiliations on the genetic affinities among these groups. Random individuals from five ethnic groups were studied; the sample size ranged from 235 to 364. The population groups belong to two geographically separated regions of India, the state of Maharashtra (western India) and the state of Kerala (southern India). The two Maharashtrian groups (Konkanastha Brahmins and Marathas) speak "Marathi," an Indo-European language, whereas the three Kerala population groups (Nairs, Ezhavas, and Muslims) speak "Malayalam," an Indo-Dravidian language. Genomic DNA was extracted from peripheral blood samples and analyzed using amplified fragment length polymorphism (Amp-FLP) technique. All four loci displayed high heterozygosity with average heterozygosity in the range of 0.82 to 0.84. The Polymorphic Information Content and Power of Discrimination were > or = 0.75 and > or = 0.80, respectively. The coefficient of gene differentiation was found to be low (average G(ST) = 1.2%; range between 0.6% at D1S80 locus to 1.6% at APOB 3' VNTR locus) across the loci, indicating close affinity among the population groups. The neighbor-joining tree revealed two clear clusters, one for the two Maharashtrian population groups and the other for the three Kerala population groups. The results obtained are in conformity with the geographical and linguistic backgrounds of the studied populations. PMID:12180760

  19. p-Synephrine: a novel agonist for neuromedin U2 receptor.

    PubMed

    Zheng, Xuxu; Guo, Lixia; Wang, Daoqing; Deng, Xiaohong

    2014-01-01

    In the brain, Neuromedin U2 receptor (NMU2R) is prominent in the hypothalamic regions and is known to be associated with regulation of several important physiological functions, including food intake, energy balance, stress response, and nociception. In this article, by random screening of compounds using the model of high-throughput screening for NMU2R stable expression, NMU2R negative and NMU2R short hairpin RNA (shRNA) knockdown HEK293 cell lines, for the first time, we discovered that p-synephrine, which is the primary protoalkaloid in Citrus aurantium (bitter orange) and is widely used in weight loss and weight management products, is a highly potent and selective NMU2R agonist. In NMU2R activating ability experiments, p-synephrine was found binding to NMU2R with high efficacy and potency; the efficacy, 50% of the maximum possible effect (EC50) and potency values were determined to be 7.207, 6.604 and 0.227 µmol/L for the NMU2R, respectively. Our researches have important theoretical value for elucidating the mechanisms of p-synephrine in body weight and energy balance regulation. These data provide further evidence for widespread roles for p-synephrine and its receptors in the brain. PMID:24598981

  20. Description of work for 216-U-1 and 216-U-2 stainless steel pipeline integrity testing

    SciTech Connect

    Wasemiller, M.A.

    1994-06-30

    The objectives of this integrity test are to (1) inspect the interior of this pipeline by in-line camera survey and (2) if required, conduct a pressure test on a section of the pipeline. The U-1 and U-2 Cribs were constructed in 1951. From March 1952 to June 1967, the site received cell drainage from Tank 5-2 in the 221-U Building nd waste from the 224-U Building via the overflow from the 241-U-361 Settling Tank. From June 1957 to July 1957, the site received waste from the 224-U Building via the overflow from the 241-U-361 Settling Tank and contaminated solvent from the 276-U Settling Tank solvent storage area. The discharge of 221-U waste was discontinued during shutdown of production operations. From July 1957 to May 1967, the site received waste from the 224-U Building and equipment decontamination and reclamation wastes from operations in the 221-U Building canyon. The scope of work is encompassed in five steps: (1) obtaining access to the pipeline in order to perform an in-line camera survey of the line to the greatest extent possible, (2) evaluating the need for further investigation of the pipeline, (3) blanking the line, as needed, to perform a pressure test, (4) conducting the pressure test, as needed, and (5) documenting the ability of the line to maintain pressure.

  1. NMR investigations on single crystals of U2Ru2Sn: A Kondo insulator

    NASA Astrophysics Data System (ADS)

    Rajarajan, A. K.; Rabis, A.; Baenitz, M.; Gippius, A. A.; Morozova, E. N.; Mydosh, J. A.; Steglich, F.

    2005-04-01

    U2Ru2Sn is unique among all Kondo insulators because of its tetragonal structure and an energy gap of about 150 K being the smallest of all the uranium-based Kondo insulators. We report Knight shift K(T) and relaxation rate T1-1 measurements from 119Sn(I={1}/{2})-NMR for the first time in single crystals and oriented micro-crystallites. At low temperatures the anisotropy in K(T) increases ( K∥/K⊥(4.2 K)≈2), a trend observed also in χ(T) and ρ(T). K(H⊥c) exhibits a smooth variation, whereas for K(H ∥ c) a change of slope occurs at 150 K with a more rapid decrease below. The anisotropy is not as prominent in T1-1(T). The hyperfine coupling constant exhibits a cross-over behaviour from one linear regime of K(T) vs. χ(T) to another around a characteristic temperature.

  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. 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.

  4. First Principles Study of a-U2N3 Surfaces and its Anti-oxidant Mechanism

    NASA Astrophysics Data System (ADS)

    Jin, Mengting; Zhang, Yanning

    With the advantages over oxides as fuel materials for fast nuclear reactors, actinide nitrides have been extensively studied in experiments. In particular, a-U2N3 is also the main composition of surface layer obtained by surface nitriding for the enhancement of oxidation resistance of uranium in ambient conditions.[1-4] However, the anti-oxidant mechanism behind is still unclear, which hinders the further development of surface treatment technologies for uranium. Here we perform extensive ab initio studies on the geometric, magnetic and electronic properties of a-U2N3 bulk and (001) surfaces. Then the adsorption and diffusion of O2 near the stable a-U2N3(001) surface will be discussed, focusing on the local atomic arrangements of U-N and U-N-O that cannot be observed easily in experiments. Our theoretical results may give some insights in understanding the anti-oxidant mechanism of surface nitriding.

  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. 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.

  7. Useful to Usable (U2U): Transforming climate information into usable tools to support Midwestern agricultural production

    NASA Astrophysics Data System (ADS)

    Prokopy, L. S.; Widhalm, M.

    2014-12-01

    There is a close connection between weather and climate patterns and successful agricultural production. Therefore, incorporating climate information into farm management is likely to reduce the risk of economic losses and increase profitability. While weather and climate information is becoming ever more abundant and accessible, the use of such information in the agricultural community remains limited. Useful to Usable (U2U): Transforming Climate Variability and Change Information for Cereal Crop Producers is a USDA-NIFA funded research and extension project focused on improving the use of climate information for agricultural production in the Midwestern United States by developing user-driven decision tools and training resources. The U2U team is a diverse and uniquely qualified group of climatologists, crop modelers, agronomists, and social scientists from 9 Midwestern universities and two NOAA Regional Climate Centers. Together, we strive to help producers 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. To ensure relevance and usability of U2U products, our social science team is using a number of techniques including surveys and focus groups to integrate stakeholder interests, needs, and concerns into all aspects of U2U research. It is through this coupling of physical and social science disciplines that we strive to transform existing climate information into actionable knowledge.

  8. High similarity of U2 snDNA sequence between A and B chromosomes in the grasshopper Abracris flavolineata.

    PubMed

    Menezes-de-Carvalho, Nahanna Zimmermann; Palacios-Gimenez, Octavio Manuel; Milani, Diogo; Cabral-de-Mello, Diogo Cavalcanti

    2015-10-01

    B chromosomes are frequently enriched for a wide variety of repetitive DNAs. Among grasshoppers in the species Abracris flavolineata (Ommatolampidinae) the B chromosomes are submetacentric, C-negative and harbor repetitive DNAs such as, U2 snDNA, C 0 t-1 DNA, two Mariner-like elements and some microsatellites. Here, we provide evidence showing the intragenome similarity between the B chromosome and the A complement in A. flavolineata, combining analysis of microdissection and chromosome painting and B chromosome-specific amplification through polymerase chain reaction (PCR) of U2 snDNA. Chromosome painting revealed signals spread through the C-negative regions, including the A and B chromosomes. Moreover, significant clustered signals forming bands were observed in some A chromosomes, and for the B chromosome, significant signals were located on both arms, which could be caused by accumulation of repetitive DNA sequences. The C-positive regions did not reveal any signals. Sequence comparison of U2 snDNA between that obtained from a genome without the B chromosome and that from µB-DNA revealed high similarity with the occurrence of four shared haplotypes, one of them (i.e., Hap1) being highly prevalent and putatively ancestral. The highest divergence from Hap1 was observed for Hap3, which was caused by only six mutational steps. These data support an intraspecific origin of the B chromosome in A. flavolineata that is highly similar with the A complement, and the low U2 snDNA sequence diversity observed in the B chromosome could be related to its recent origin, besides intrachromosomal concerted evolution for U2 snDNA repeats in the B chromosome. PMID:25846962

  9. First principles study of the electronic and magnetic structures of U2Ni2SnH2

    NASA Astrophysics Data System (ADS)

    Matar, S. F.; Alam, A. F. Al

    2008-08-01

    The electronic and magnetic properties and the chemical bonding in recently evidenced U2Ni2SnH2 are self-consistently calculated within the local spin density-functional (LSDF) theory using the scalar-relativistic augmented spherical wave (ASW) method. Trends of the magnetism are discussed in terms of the changes brought by hydrogen within the pure U2Ni2Sn alloy system from both the volume expansion simulating negative pressure and the bonding between H and lattice constituents U, Ni and Sn pointing to a larger Ni H bonding versus U H. The ground state is found to be antiferromagnetic in agreement with experiment. Considering the relativistic effects of spin orbit coupling an ordered magnetic moment, mU=1 μB is calculated for U(5f), close to the experimental magnitude of mU=0.83 μB.

  10. Human PSENEN and U2AF1L4 genes are concertedly regulated by a genuine bidirectional promoter.

    PubMed

    Didych, D A; Shamsutdinov, M F; Smirnov, N A; Akopov, S B; Monastyrskaya, G S; Uspenskaya, N Y; Nikolaev, L G; Sverdlov, E D

    2013-02-15

    Head-to-head genes with a short distance between their transcription start sites may constitute up to 10% of all genes in the genomes of various species. It was hypothesized that this intergenic space may represent bidirectional promoters which are able to initiate transcription of both genes, but the true bidirectionality was proved only for a few of them. We present experimental evidence that, according to several criteria, a 269 bp region located between the PSENEN and U2AF1L4 human genes is a genuine bidirectional promoter regulating a concerted divergent transcription of these genes. Concerted transcription of PSENEN and U2AF1L4 can be necessary for regulation of T-cell activity. PMID:23246698

  11. 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.

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

    DOE PAGESBeta

    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

  13. High-Pressure Synthesis and Characterization of the Actinide Borate Phosphate U2[BO4][PO4

    PubMed Central

    Hinteregger, Ernst; Wurst, Klaus; Perfler, Lukas; Kraus, Florian; Huppertz, Hubert

    2013-01-01

    A new actinide borate phosphate, U2[BO4][PO4], was synthesized in a Walker-type multianvil apparatus at 12.5 GPa and 1000 °C. The crystal structure was determined from single-crystal X-ray diffraction data collected at room temperature. U2[BO4][PO4] crystallizes in the monoclinic space group P21/c with four formula units per unit cell and the lattice parameters a = 854.6(2), b = 775.3(2), c = 816.3(2) pm, and β = 102.52(3)°. The structure consists of double layers of linked uranium–oxygen polyhedra parallel to [100]. The borate tetrahedra are located between the uranium–oxygen layers inside the double layer. The phosphate groups link the double layers. PMID:24611029

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

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

    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.

  15. 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.

  16. High-Pressure Synthesis and Characterization of the Actinide Borate Phosphate U2[BO4][PO4].

    PubMed

    Hinteregger, Ernst; Wurst, Klaus; Perfler, Lukas; Kraus, Florian; Huppertz, Hubert

    2013-10-14

    A new actinide borate phosphate, U2[BO4][PO4], was synthesized in a Walker-type multianvil apparatus at 12.5 GPa and 1000 °C. The crystal structure was determined from single-crystal X-ray diffraction data collected at room temperature. U2[BO4][PO4] crystallizes in the monoclinic space group P21/c with four formula units per unit cell and the lattice parameters a = 854.6(2), b = 775.3(2), c = 816.3(2) pm, and β = 102.52(3)°. The structure consists of double layers of linked uranium-oxygen polyhedra parallel to [100]. The borate tetrahedra are located between the uranium-oxygen layers inside the double layer. The phosphate groups link the double layers. PMID:24611029

  17. 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.

  18. 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. PMID:26556480

  19. 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

  20. Density functional theory investigation of the layered uranium oxides U3O8 and U2O5.

    PubMed

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

    2015-02-14

    Oxidation of UO(2) in the nuclear fuel cycle leads to formation of the layered uranium oxides. Here we present DFT simulations of U(2)O(5) and U(3)O(8) using the PBE + U functional to examine their structural, electronic and mechanical properties. We build on previous simulation studies of Amm2 α-U(3)O(8), P2(1)/m β-U(3)O(8) and P6[combining macron]2m γ-U(3)O(8) by including C222 α-U(3)O(8), Cmcm β-U(3)O(8) and Pnma δ-U(2)O(5). All materials are predicted to be insulators with no preference for ferromagnetic or antiferromagnetic ordering. We predict δ-U(2)O(5) contains exclusively U(5+) ions in an even mixture of distorted octahedral and pentagonal bipyramidal coordination sites. In each U(3)O(8) polymorph modelled we predict U(5+) ions in pentagonal bipyramidal coordination and U(6+) in octahedral coordination, with no U(4+) present. The elastic constants of each phase have been calculated and the bulk modulus is found to be inversely proportional to the volume per uranium ion. Finally, a number of thermodynamic properties are estimated, showing general agreement with available experiments; for example α- and β-U(3)O(8) are predicted to be stable at low temperatures but β-U(3)O(8) and γ-U(3)O(8) dominate at high temperature and high pressure respectively. PMID:25382599

  1. Circulating U2 small nuclear RNA fragments as a novel diagnostic biomarker for pancreatic and colorectal adenocarcinoma.

    PubMed

    Baraniskin, Alexander; Nöpel-Dünnebacke, Stefanie; Ahrens, Maike; Jensen, Steffen Grann; Zöllner, Hannah; Maghnouj, Abdelouahid; Wos, Alexandra; Mayerle, Julia; Munding, Johanna; Kost, Dennis; Reinacher-Schick, Anke; Liffers, Sven; Schroers, Roland; Chromik, Ansgar M; Meyer, Helmut E; Uhl, Waldemar; Klein-Scory, Susanne; Weiss, Frank U; Stephan, Christian; Schwarte-Waldhoff, Irmgard; Lerch, Markus M; Tannapfel, Andrea; Schmiegel, Wolff; Andersen, Claus Lindbjerg; Hahn, Stephan A

    2013-01-15

    Improved non-invasive strategies for early cancer detection are urgently needed to reduce morbidity and mortality. Non-coding RNAs, such as microRNAs and small nucleolar RNAs, have been proposed as biomarkers for non-invasive cancer diagnosis. Analyzing serum derived from nude mice implanted with primary human pancreatic ductal adenocarcinoma (PDAC), we identified 15 diagnostic microRNA candidates. Of those miR-1246 was selected based on its high abundance in serum of tumor carrying mice. Subsequently, we noted a cross reactivity of the established miR-1246 assays with RNA fragments derived from U2 small nuclear RNA (RNU2-1). Importantly, we found that the assay signal discriminating tumor from controls was derived from U2 small nuclear RNA (snRNA) fragments (RNU2-1f) and not from miR-1246. In addition, we observed a remarkable stability of RNU2-1f in serum and provide experimental evidence that hsa-miR-1246 is likely a pseudo microRNA. In a next step, RNU2-1f was measured by qRT-PCR and normalized to cel-54 in 191 serum/plasma samples from PDAC and colorectal carcinoma (CRC) patients. In comparison to 129 controls, we were able to classify samples as cancerous with a sensitivity and specificity of 97.7% [95% CI = (87.7, 99.9)] and 90.6% [95% CI = (80.7, 96.5)], respectively [area under the ROC curve 0.972]. Of note, patients with CRC were detected with our assay as early as UICC Stage II with a sensitivity of 81%. In conclusion, this is the first report showing that fragments of U2 snRNA are highly stable in serum and plasma and may serve as novel diagnostic biomarker for PDAC and CRC for future prospective screening studies. PMID:22907602

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

    PubMed

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

    2013-04-01

    Degenerate splice site sequences mark the intron boundaries of pre-mRNA transcripts in multicellular eukaryotes. The essential pre-mRNA splicing factor U2AF(65) 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 U2AF(65) recognizes degenerate Py tracts, we determined six crystal structures of human U2AF(65) 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 U2AF(65) 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 U2AF(65) 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 U2AF(65) conformations. Our results highlight both local and global conformational selection as a means for universal 3' splice site recognition by U2AF(65). PMID:23376934

  3. 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. PMID:27033598

  4. Prediction of an U2S3-type polymorph of Al2O3 at 3.7 Mbar.

    PubMed

    Umemoto, Koichiro; Wentzcovitch, Renata M

    2008-05-01

    We predict by first principles a phase transition in alumina at approximately 3.7 Mbar and room temperature from the CaIrO(3)-type polymorph to another with the U(2)S(3)-type structure. Because alumina is used as window material in shock-wave experiments, this transformation should be important for the analysis of shock data in this pressure range. Comparison of our results on all high-pressure phases of alumina with shock data suggests the presence of two phase transitions in shock experiments: the corundum to Rh(2)O(3)(II)-type structure and the Rh(2)O(3)(II)-type to CaIrO(3)-type structure. The transformation to the U(2)S(3)-type polymorph is in the pressure range reached in the mantle of recently discovered terrestrial exoplanets and suggests that the multi-megabar crystal chemistry of planet-forming minerals might be related to that of the rare-earth sulfides. PMID:18451030

  5. Transcription of the Schizosaccharomyces pombe U2 gene in vivo and in vitro is directed by two essential promoter elements

    PubMed Central

    Zhou, Dewang; Lobo-Ruppert, Susan M.

    2001-01-01

    As compared to the metazoan small nuclear RNAs (snRNAs), relatively little is known about snRNA synthesis in unicellular organisms. We have analyzed the transcription of the Schizosaccharomyces pombe U2 snRNA gene in vivo and in the homologous in vitro system. Deletion and linker-scanning analyses show that the S.pombe U2 promoter contains at least two elements: the spUSE centered at –55, which functions as an activator, and a TATA box at –26, which is essential for basal transcription. These data point to a similar architecture among S.pombe, plant and invertebrate snRNA promoters. Factors recognizing the spUSE can be detected in whole cell extracts by DNase I footprinting and competition studies show that the binding of these factors correlates with transcriptional activity. Electrophoretic mobility shift assays and gel-filtration chromatography revealed a native molecular mass of ∼200 kDa for the spUSE binding activity. Two polypeptides of molecular masses 25 and 65 kDa were purified by virtue of their ability to specifically bind the spUSE. PMID:11353068

  6. Low energy constants of S U (2 ) partially quenched chiral perturbation theory from Nf=2 +1 domain wall QCD

    NASA Astrophysics Data System (ADS)

    Boyle, P. A.; Christ, N. H.; Garron, N.; Jung, C.; Jüttner, A.; Kelly, C.; Mawhinney, R. D.; McGlynn, G.; Murphy, D. J.; Ohta, S.; Portelli, A.; Sachrajda, C. T.

    2016-03-01

    We have performed fits of the pseudoscalar masses and decay constants, from a variety of the RBC-UKQCD Collaboration's domain wall fermion ensembles, to S U (2 ) partially quenched chiral perturbation theory at next-to-leading order (NLO) and next-to-next-to-leading order (NNLO). We report values for nine NLO and eight linearly independent combinations of NNLO partially quenched low-energy constants, which we compare to other lattice and phenomenological determinations. We discuss the size of successive terms in the chiral expansion and use our large set of low-energy constants to make predictions for mass splittings due to QCD isospin-breaking effects and the S-wave π π scattering lengths. We conclude that, for the range of pseudoscalar masses explored in this work, 115 MeV ≲mPS≲430 MeV , the NNLO S U (2 ) expansion is quite robust and can fit lattice data with percent-scale accuracy.

  7. Prediction of an U2S3-type polymorph of Al2O3 at 3.7 Mbar

    PubMed Central

    Umemoto, Koichiro; Wentzcovitch, Renata M.

    2008-01-01

    We predict by first principles a phase transition in alumina at ≈3.7 Mbar and room temperature from the CaIrO3-type polymorph to another with the U2S3-type structure. Because alumina is used as window material in shock-wave experiments, this transformation should be important for the analysis of shock data in this pressure range. Comparison of our results on all high-pressure phases of alumina with shock data suggests the presence of two phase transitions in shock experiments: the corundum to Rh2O3(II)-type structure and the Rh2O3(II)-type to CaIrO3-type structure. The transformation to the U2S3-type polymorph is in the pressure range reached in the mantle of recently discovered terrestrial exoplanets and suggests that the multi-megabar crystal chemistry of planet-forming minerals might be related to that of the rare-earth sulfides. PMID:18451030

  8. THRA1 and D17S183 flank an interval of < 4 cM for the breast-ovarian cancer gene (BRCA1) on chromosome 17q21.

    PubMed Central

    Bowcock, A M; Anderson, L A; Friedman, L S; Black, D M; Osborne-Lawrence, S; Rowell, S E; Hall, J M; Solomon, E; King, M C

    1993-01-01

    In order to pinpoint the locale of the gene for early-onset familial breast and ovarian cancer (BRCA1), polymorphisms were developed within the locus for thyroid hormone receptor alpha (THRA1) and for several anonymous sequences at chromosome 17q12-q21. The THRA1 polymorphism is a dinucleotide repeat with 10 alleles and heterozygosity.79. Gene mapping in extended families with inherited, early-onset breast and ovarian cancer indicates that BRCA1 is distal to THRA1 and proximal to D17S183 (SCG43), an interval of < 4 cM. This locale excludes HER2, THRA1, WNT3, HOX2, NGFR, PHB, COLIA1, NME1, and NME2 as candidates for BRCA1 but does not exclude RARA or EDH17B. Resolving the remaining recombination events in these families by new polymorphisms in the THRA1-D17S183 interval will facilitate positional cloning of the breast-ovarian cancer gene on chromosome 17q12-q21. PMID:8460637

  9. 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 .

  10. THRA1 and D17S183 flank an interval of <4 cM for the breast-ovarian cancer gene (BRCA1) on chromosome 17q21

    SciTech Connect

    Bowcock, A.M.; Osborne-Lawrence, S. ); Anderson, L.A.; Friedman, L.S.; Rowell, S.E.; Hall, J.M.; King, M.C. ); Black, D.M.; Solomon, E. )

    1993-04-01

    In order to pinpoint the locale of the gene for early-onset familial breast and ovarian cancer (BRCA1), polymorphisms were developed within the locus for thyroid hormone receptor alpha (THRA1) and for several anonymous sequences at chromosome 17q12-q21. The THRA1 polymorphism is a dinucleotide repeat with 10 alleles and heterozygosity .79. Gene mapping in extended families with inherited, early-onset breast and ovarian cancer indicates that BRCA1 is distal to THRA1 and proximal to D17S183 (SCG43), an interval of <4 cM. This locale excludes HER2, THRA1, WNT3, HOX2, NGFR, PHB, COLIA1, NME1, and NME2 as candidates for BRCA1 but does not exclude RARA or EDH17B. Resolving the remaining recombination events in these families by new polymorphisms in the THRA1-D17S183 interval will facilitate positional cloning of the breast-ovarian cancer gene on chromosome 17q12-q21. 16 refs., 3 figs., 1 tab.

  11. Single crystal study of layered UnRhIn3n+2 materials: Case of the novel U2RhIn8 compound

    NASA Astrophysics Data System (ADS)

    Bartha, Attila; Kratochvílová, M.; Dušek, M.; Diviš, M.; Custers, J.; Sechovský, V.

    2015-05-01

    We report on the single crystal properties of the novel U2RhIn8 compound studied in the context of parent URhIn5 and UIn3 systems. The compounds were prepared by In self-flux method. U2RhIn8 adopts the Ho2CoGa8-type structure with lattice parameters a=4.6056(6) Å and c=11.9911(15) Å. The behavior of U2RhIn8 strongly resembles that of the related URhIn5 and UIn3 with respect to magnetization, specific heat and resistivity except for magnetocrystalline anisotropy developing with lowering dimensionality in the series UIn3 vs. U2RhIn8 and URhIn5. U2RhIn8 orders antiferromagnetically below TN=117 K and exhibits a slightly enhanced Sommerfeld coefficient γ=47 mJ mol-1 K-2. Magnetic field leaves the value of Néel temperature for both URhIn5 and U2RhIn8 unaffected up to 9 T. On the other hand, TN is increasing when applying hydrostatic pressure up to 3.2 GPa. The character of uranium 5f electron states of U2RhIn8 was studied by first principles calculations based on the density functional theory. The overall phase diagram of U2RhIn8 is discussed in the context of magnetism in the related URhX5 and UX3 (X=In, Ga) compounds.

  12. Pac1p, an RNase III homolog, is required for formation of the 3' end of U2 snRNA in Schizosaccharomyces pombe.

    PubMed Central

    Zhou, D; Frendewey, D; Lobo Ruppert, S M

    1999-01-01

    Like its homologs in higher eukaryotes, the U2 snRNA in Schizosaccharomyces pombe is transcribed by RNA polymerase II and is not polyadenylated. Instead, an RNA stem-loop structure located downstream of the U2 snRNA coding sequence and transcribed as part of a 3' extended precursor serves as a signal for 3'-end formation. We have identified three mutants that have temperature-sensitive defects in U2 snRNA 3'-end formation. In these mutants, the synthesis of the major snRNAs is also affected and unprocessed rRNA precursors accumulate at the restrictive temperature. Two of these mutants contain the same G-to-A transition within the pac1 gene, whereas the third contains a lesion outside the pac1 locus, indicating that at least two genes are involved. The pac1+ gene is codominant with the mutant allele and can rescue the temperature-sensitive phenotype and the defects in snRNA and rRNA synthesis, if overexpressed. In vitro, Pac1p, an RNase III homolog, can cleave a synthetic U2 precursor within the signal for 3'-end formation, generating a product that is a few nucleotides longer than mature U2 snRNA. In addition, U2 precursors are cleaved and trimmed to the mature size in extracts made from wild-type S. pombe cells. However, extracts made from pac1 mutant cells are unable to do so unless they are supplemented with purified recombinant Pac1p. Thus, the 3' end of S. pombe U2 snRNA is generated by a processing reaction that requires Pac1p and an additional component, and can be dissociated from transcription in vitro. PMID:10445882

  13. An activity specified by the osteosarcoma line U2OS can substitute functionally for ICP0, a major regulatory protein of herpes simplex virus type 1.

    PubMed Central

    Yao, F; Schaffer, P A

    1995-01-01

    Among the five immediate-early regulatory proteins of herpes simplex virus (HSV) type 1, only ICP0 is capable of activating all kinetic classes of viral genes. Consistent with its broad transactivating activity, ICP0 plays a major role in enhancing the reactivation of HSV from latency both in vivo and in vitro. Although not essential for viral replication, ICP0 confers a significant growth advantage on the virus, especially at low multiplicities of infection. In this report we describe the expression of a novel activity by the osteosarcoma cell line U2OS that can substitute functionally for ICP0. Compared with Vero cells, both U2OS cells and cells of the ICP0-expressing line 0-28 significantly enhanced the plating efficiency of an ICP0 null mutant, 7134. In contrast, the plating efficiencies of the wild-type virus in all three cell types were similar. Single-step growth experiments demonstrated that the yield of 7134 in U2OS cells was severalfold higher than that in 0-28 cells and about 100-fold higher than that in Vero cells. In order to identify the viral genes whose expression is enhanced by the activity in U2OS cells, levels of expression of selected viral proteins in extracts of Vero and U2OS cells were compared by Western blot (immunoblot) analysis following low-multiplicity infection. At a multiplicity of 0.1 PFU per cell, the levels of expression of the immediate-early protein ICP4 and the early protein gD in 7134-infected U2OS cells were significantly higher than those in 7134-infected Vero cells. When infections were carried out at a multiplicity of 1 PFU per cell, however, no major differences in the levels of expression of these proteins in U2OS and Vero cells were observed. Cycloheximide reversal experiments demonstrated that the cellular activity expressed in U2OS cells that promotes high-level expression of ICP4 is not synthesized de novo but appears to exist as a preformed protein(s). To confirm this observation and to determine whether, like

  14. Deep recombination centers in C u2ZnSnS e4 revealed by screened-exchange hybrid density functional theory

    NASA Astrophysics Data System (ADS)

    Yee, Ye Sheng; Magyari-Köpe, Blanka; Nishi, Yoshio; Bent, Stacey F.; Clemens, Bruce M.

    2015-11-01

    We present a comprehensive study of the thermodynamic and electronic properties of intrinsic point defects in the solar energy conversion materials C u2ZnSnS e4 and CuInS e2 based on the screened-exchange hybrid density functional theory. A comparison between the defect transition levels for C u2ZnSnS e4 and CuInS e2 reveals that in C u2ZnSnS e4 , the S nCu and S nZn antisite defects can be recombination centers with defect states close to midgap, while the I nCu antisite defect has a shallow defect level in CuInS e2 . The resultant higher Shockley-Read-Hall recombination rate in C u2ZnSnS e4 reduces the steady-state concentration of minority carriers and quasi-Fermi level separation under illumination. This may explain the origin of the low open-circuit voltage values for C u2ZnSnS e4 solar cells compared to CuInS e2 solar cells.

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

    DOE PAGESBeta

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

    2016-06-08

    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

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

    PubMed

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

    2016-02-29

    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

  17. 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.

  18. 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

  19. Single crystal growth and structural characterization of ternary transition-metal uranium oxides: MnUO4, FeUO4, and NiU2O6

    NASA Astrophysics Data System (ADS)

    Read, Cory M.; Smith, Mark D.; zur Loye, Hans-Conrad

    2014-11-01

    Single crystals of MnUO4, FeUO4, and NiU2O6 were grown for the first time. The use of chloride fluxes facilitated the crystal growth. MnUO4, a hexavalent uranium compound, crystallizes in the orthorhombic space group, Imma, with a = 6.6421(19) Å, b = 6.978(2) Å, and c = 6.748(2) Å, and exhibits typical uranyl, UO22+, coordination. FeUO4 and NiU2O6 contain pentavalent uranium and are structurally related, exhibiting three-dimensional connectivity. FeUO4 crystallizes in the orthorhombic space group, Pbcn, with a = 4.8844(2) Å, b = 11.9328(5) Å, c = 5.1070(2) Å. NiU2O6 crystallizes in the trigonal space group, P321, with a = 9.0148(3) Å, c = 5.0144(3) Å.

  20. 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.

  1. 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

  2. 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.

  3. Differential recognition of the polypyrimidine-tract by the general splicing factor U2AF65 and the splicing repressor sex-lethal.

    PubMed Central

    Singh, R; Banerjee, H; Green, M R

    2000-01-01

    The polypyrimidine-tract (Py-tract) adjacent to 3' splice sites is an essential splicing signal and is recognized by several proteins, including the general splicing factor U2AF65 and the highly specific splicing repressor Sex-lethal (SXL). They both contain ribonucleoprotein-consensus RNA-binding motifs. However, U2AF65 recognizes a wide variety of Py-tracts, whereas SXL recognizes specific Py-tracts such as the nonsex-specific Py-tract of the transformer pre-mRNA. It is not understood how these seemingly similar proteins differentially recognize the Py-tract. To define these interactions, we used chemical interference and protection assays, saturation mutagenesis, and RNAs containing modified nucleotides. We find that these proteins recognize distinct features of the RNA. First, although uracils within the Py-tract are protected from chemical modification by both of these proteins, modification of any one of seven uracils by hydrazine, or any of eight phosphates by ethylnitrosourea strongly interfered with the binding of SXL only. Second, the 2' hydroxyl groups or backbone conformation appeared important for the binding of SXL, but not U2AF65. Third, although any of the bases (cytosine >> adenine > guanine) could substitute for uracils for U2AF65 binding, only guanine partially substituted for certain uracils for SXL binding. The different dependence on individual contacts and nucleotide preference may provide a basis for the different RNA-binding specificities and thus functions of U2AF65 and SXL in 3' splice site choice. PMID:10864047

  4. 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. PMID:27488102

  5. Purification and characterization of salicylate 5-hydroxylase, a three-component monooxygenase from Ralstonia sp. strain U2.

    PubMed

    Fang, Ti; Zhou, Ning-Yi

    2014-01-01

    Salicylate is an important intermediate in the bacterial degradation of polycyclic aromatic hydrocarbons and salicylate hydroxylases play essential roles in linking the peripheral and ring-cleavage catabolic pathways. Unlike the well-characterized salicylate 1-hydroxylases, the rarely occurred salicylate 5-hydroxylase (S5H) has not been characterized in detail. In this study, the three-component Fe-S protein complex (NagAaGHAb) of S5H from Ralstonia sp. strain U2 was purified, and its biochemical and catalytic properties were characterized. The oxygenase component NagGH exhibited an α₃β₃ heterohexameric structure and contained one Rieske-type [2Fe-2S] cluster and one mononuclear iron per α subunit. NagAa is the ferredoxin-NADP⁺ reductase component containing flavin and plant type [2Fe-2S] cluster. The ferredoxin component NagAb was characterized as a [2Fe-2S] dimer which remains remarkably stable in denaturing gel electrophoresis after being heated at 100 °C for 1 h. Purified NagAa and NagAb, NagGH catalyzed the hydroxylation of salicylate to gentisate with a specific activity of 107.12 ± 14.38 U/g and showed an apparent K(m) for salicylate of 102.79 ± 27.20 μM and a similar K(m) value for both NADH and NADPH (59.76 ± 7.81 μM versus 56.41 ± 12.76 μM). The hydroxylase exhibited different affinities for two hydroxysalicylates (2,4-dihydroxybenzoate K(m) of 93.54 ± 18.50 μM versus 2,6-dihydroxybenzoate K(m) of 939.80 ± 199.46 μM). Interestingly, this S5H also showed catalytic activity to the pollutant 2-nitrophenol and exhibited steady-state kinetic data of the same order of magnitude as those for salicylate. This study will allow further comparative studies of structure-function relationships of the ring hydroxylating mono- and di-oxygenase systems. PMID:23624660

  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. Crude extract of Rheum palmatum L. Induces cell cycle arrest S phase and apoptosis through mitochondrial-dependent pathways in U-2 OS human osteosarcoma cells.

    PubMed

    Lin, Chin-Chung; Lee, Ming-Huei; Lin, Ju-Hwa; Lin, Meng-Liang; Chueh, Fu-Shin; Yu, Chien-Chih; Lin, Jing-Pin; Chou, Yu-Cheng; Hsu, Shu-Chun; Chung, Jing-Gung

    2016-08-01

    Cancer is the second cause of death in children. Osteosarcoma is the most common primary malignancy of solid bone cancer primarily affecting adolescents and young adults. In the Chinese population, the crude extract of Rheum palmatum L. (CERP) has been used for treating different diseases, including SARS, rheumatoid arthritis, coxsackievirus B3, and human colon cancer cell, pancreatic cancer. There are no reports on CERP and human osteosarcoma cells. The present study examined effects of CERP on cytotoxicity including cell cycle distribution and cell death (apoptosis) in U-2 OS human osteosarcoma cells. CERP significantly induced S phase arrest in U-2 OS cells in a dose-dependent. CERP produced DNA damage and DNA condensation. Other effects of CERP were stimulation of ROS and Ca(2+) , mitochondria impairment, and activation of caspase-3, -8, and -9. CERP increased the levels of Bax, Bak, Bad, cyclin B, Fas, PARP, GRP78, GADD153, AIF, Endo G, Calpain-2, p21, and p27, but decreased the levels of Bcl-2, BCL-X, XIAP, Akt, CDC25A, CDK2, Cyclin A, and Cyclin E of U-2 OS cells. It was also observed that CERP promoted the expression of AIF, Endo G, GADD153, and cytochrome c. These results indicate that CERP has anticancer effects in vitro and provide the foundation for in vivo studies of animal models of osteosarcoma. © 2015 Wiley Periodicals, Inc. Environ Toxicol 31: 957-969, 2016. PMID:25689151

  9. Receptor for advanced glycation end-products (RAGE) is overexpressed in human osteosarcoma and promotes the proliferation of osteosarcoma U-2OS cells in vitro.

    PubMed

    Zhang, Q; Jin, Y; Zhao, C F; Wang, W J; Liu, G Y

    2016-01-01

    Osteosarcoma (OS) is an aggressive cancer of the long bones, and usually affects children and young adults. The receptor for advanced glycation end-products (RAGE) has recently been recognized as an oncogenic receptor that binds to different ligands, and promotes the progression of various cancers. However, little is known about the association between RAGE and the pathogenesis of OS. In this study, we first examined the expression of RAGE in OS tissues using immunohistochemical staining, western blotting, and reverse transcription quantitative polymerase chain reaction. We then determined the influence of the overexpressed RAGE on the proliferation of U-2OS cells in vitro. The results showed that RAGE was overexpressed in OS tissues compared with peritumor tissues, at both the mRNA and protein levels, and there was a significant association between overexpressed RAGE and clinicopathological characteristics, such as clinical stage and distant metastasis. Moreover, the overexpression of RAGE in U-2OS cells significantly promoted their proliferation in vitro. In conclusion, this study indicated that RAGE is overexpressed in OS tissue and promotes the proliferation of U-2OS cells. These data imply that RAGE promotes the growth of OS, and is a potential diagnostic biomarker and therapeutic target for the disorder. PMID:27323159

  10. Synthesis, crystal structure, resistivity, and electronic structure of the U(V) quaternary polyselenide Ba8PdU2Se12(Se2)2

    NASA Astrophysics Data System (ADS)

    Prakash, Jai; Mesbah, Adel; Lebègue, Sébastien; Malliakas, Christos D.; Ibers, James A.

    2015-10-01

    A new quaternary uranium(V) selenide, Ba8PdU2Se12(Se2)2, has been synthesized by reaction of elements at 1173 K. A single-crystal X-ray diffraction study shows that the compound crystallizes in a new structure type with two formula units in space group D2h12 - Pnnm of the orthorhombic crystal system with cell constants of a=9.490(1), b=12.240(2), and c=13.780(3) Å. Its crystal structure consists of [PdU2 Se1212-] units where U atoms are coordinated to six Se atoms in octahedral geometry and Pd atoms are coordinated to four Se atoms in square-planar geometry. These [PdU2 Se1212-] units are separated by Ba to result in a salt-like crystal structure. This compound also contains Se22- dimers that are part of Ba coordination polyhedra. The formula charge balances as (Ba2+)8(Pd2+)(U5+)2(Se2-)12(Se22-)2. Theoretical calculations predict antiferromagnetic semiconducting behavior for this compound with a band gap of 1.6 eV. Temperature-dependent four-probe resistivity measurements on single crystal confirm the semiconducting nature with an activation energy of 0.18(1) eV.

  11. Phospho-MEK1/2 and uPAR Expression Determine Sensitivity of AML Blasts to a Urokinase-Activated Anthrax Lethal Toxin (PrAgU2/LF)1

    PubMed Central

    Bekdash, Amira; Darwish, Manal; Timsah, Zahra; Kassab, Elias; Ghanem, Hadi; Najjar, Vicky; Ghosn, Marwan; Nasser, Selim; El-Hajj, Hiba; Bazerbachi, Ali; Liu, Shihui; Leppla, Stephen H.; Frankel, Arthur E.; Abi-Habib, Ralph J.

    2015-01-01

    In this study, we attempt to target both the urokinase plasminogen activator and the mitogen-activated protein kinase pathway in acute myeloid leukemia (AML) cell lines and primary AML blasts using PrAgU2/LF, a urokinase-activated anthrax lethal toxin. PrAgU2/LF was cytotoxic to five out of nine AML cell lines. Cytotoxicity of PrAgU2/LF appeared to be nonapoptotic and was associated with MAPK activation and urokinase activity because all the PrAgU2/LF-sensitive cell lines showed both uPAR expression and high levels of MEK1/2 phosphorylation. Inhibition of uPAR or desensitization of cells to MEK1/2 inhibition blocked toxicity of PrAgU2/LF, indicating requirement for both uPAR expression and MAPK activation for activity. PrAgU2/LF was also cytotoxic to primary blasts from AML patients, with blasts from four out of five patients showing a cytotoxic response to PrAgU2/LF. Cytotoxicity of primary AML blasts was also dependent on uPAR expression and phos-MEK1/2 levels. CD34+ bone marrow blasts and peripheral blood mononuclear cells lacked uPAR expression and were resistant to PrAgU2/LF, demonstrating the lack of toxicity to normal hematological cells and, therefore, the tumor selectivity of this approach. Dose escalation in mice revealed that the maximal tolerated dose of PrAgU2/LF is at least 5.7-fold higher than that of the wild-type anthrax lethal toxin, PrAg/LF, further demonstrating the increased safety of this molecule. We have shown, in this study, that PrAgU2/LF is a novel, dual-specific molecule for the selective targeting of AML. PMID:26500025

  12. 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.

  13. 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.

  14. [Cytokine-mediated regulation of expression of Gfi1 and U2afll4 genes activated by T-cells with different differentiation status in vitro].

    PubMed

    Yurova, K A; Sokhonevich, N A; Khaziakhmatova, O G; Litvinova, L S

    2016-01-01

    The dose-dependent effects of cytokines (IL-2, IL-7, and IL-15), which have a common g-chain, on mRNA expression of U2afll4 and GFi1 genes involved in regulation of alternative splicing of the Ptprc gene, have been investigated in vitro using T-lymphocyte cultures with different degrees of differentiation. IL-2, IL-7, and IL-15 caused a similar unidirectional inhibitory effect of various severity on restimulated CD45RO+ T-cells exposed to an antigen-independent activation; they caused a dose-dependent decrease of the U2af1l4 gene expression, and an increase of Gfi1 gene expression. This may suggest formation of active forms of the CD45 receptor, and also limitation of the formation of low-molecular short splice variants of the CD45RO receptor. Under conditions of antigen-independent stimulation of naive CD45RA+-cells rIL-7 and IL-15 exhibited opposite effects on U2af1l4 and Gfi1 gene expression. The increase of IL-7 concentrations in the incubation medium of naive cells was accompanied by a decrease in expression of both genes. IL-15 IL-7 exhibited opposite effects. Cytokines possessing a common g-chain (IL-2, IL-7, and IL-15) prevented antigen-independent differentiation of naive T-cells, by preventing the formation of polyclonal "surrogate" cells. In general, the study of the molecular mechanisms of genetic control determining homeostatic processes of T-cells in response to exposure to antigenic or non-antigenic treatments may be important for construction of a general model of self-maintenance and differentiation of immune cells. PMID:27143377

  15. U(2Ω )⊃U(Ω)⊗SU(2) Wigner-Racah algebra for embedded Gaussian unitary ensemble of random matrices with spin

    NASA Astrophysics Data System (ADS)

    Kota, V. K. B.

    2007-05-01

    Exact results for embedded Gaussian unitary ensemble of two-body interactions for fermions with spin [EGUE(2)-s] are derived using the Wigner-Racah algebra of the embedding U(2Ω )⊃U(Ω)⊗SU(2) algebra. Explicit formulas, for systems with m fermions and spin S, are given for the lower order cross correlations, between states with (m,S) and (m',S'), generated by this ensemble and also, in terms of a SU(Ω ) Racah coefficient, for the fourth order shape parameter for the fixed-(m,S) density of states.

  16. Antiferromagnetism in R u2Mn Z (Z =Sn ,Sb ,Ge ,Si ) full Heusler alloys: Effects of magnetic frustration and chemical disorder

    NASA Astrophysics Data System (ADS)

    Khmelevskyi, Sergii; Simon, Eszter; Szunyogh, László

    2015-03-01

    We present systematic theoretical investigations to explore the microscopic mechanisms leading to the formation of antiferromagnetism in R u2Mn Z (Z =Sn ,Sb ,Ge ,Si ) full Heusler alloys. Our study is based on first-principles calculations of interatomic Mn-Mn exchange interactions to set up a suitable Heisenberg spin model and on subsequent Monte Carlo simulations of the magnetic properties at finite temperature. The exchange interactions are derived from the paramagnetic state, while a realistic account of long-range chemical disorder is made in the framework of the coherent potential approximation. We find that in the case of the highly ordered alloys (Z =Sn and Sb), the exchange interactions derived from the perfectly ordered L 21 structure lead to Néel temperatures in excellent agreement with the experiments, whereas, in particular in the case of Si, the consideration of chemical disorder is essential to reproduce the experimental Néel temperatures. Our numerical results suggest that by improving a heat treatment of the samples to suppress the intermixing between the Mn and Si atoms, the Néel temperature of the Si-based alloys can potentially be increased by more than 30%. Based on calculated biquadratic exchange couplings, we evidence a lifting of degeneracy of the antiferromagnetic ground states on a frustrated face-centered-cubic lattice in the fully ordered compounds. Furthermore, we show that in strongly disordered R u2MnSi alloys, a distinct change in the antiferromagnetic ordering occurs.

  17. Detection of a Spin-Triplet Superconducting Phase in Oriented Polycrystalline U2PtC2 Samples Using 195Pt Nuclear Magnetic Resonance

    NASA Astrophysics Data System (ADS)

    Mounce, A. M.; Yasuoka, H.; Koutroulakis, G.; Ni, N.; Bauer, E. D.; Ronning, F.; Thompson, J. D.

    2015-03-01

    Nuclear magnetic resonance (NMR) measurements on the 195Pt nucleus in an aligned powder of the moderately heavy-fermion material U2PtC2 are consistent with spin-triplet pairing in its superconducting state. Across the superconducting transition temperature and to much lower temperatures, the NMR Knight shift is temperature independent for field both parallel and perpendicular to the tetragonal c axis, expected for triplet equal-spin pairing superconductivity. The NMR spin-lattice relaxation rate 1 /T1, in the normal state, exhibits characteristics of ferromagnetic fluctuations, compatible with an enhanced Wilson ratio. In the superconducting state, 1 /T1 follows a power law with temperature without a coherence peak giving additional support that U2PtC2 is an unconventional superconductor. Bulk measurements of the ac susceptibility and resistivity indicate that the upper critical field exceeds the Pauli limiting field for spin-singlet pairing and is near the orbital limiting field, an additional indication for spin-triplet pairing.

  18. The monitoring of gene functions on a cell-defined siRNA microarray in human bone marrow stromal and U2OS cells

    PubMed Central

    Kim, Hi Chul; Kim, Gi-Hwan; Shum, David; Cho, Ssang-Goo; Lee, Eun Ju; Kwon, Yong-Jun

    2016-01-01

    Here, we developed a cell defined siRNA microarray (CDSM) for human bone marrow stromal cells (hBMSCs) designed to control the culture of cells inside the spot area without reducing the efficiency of siRNA silencing, “Development of a cell-defined siRNA microarray for analysis of gene functionin human bone marrow stromal cells” (Kim et al., 2016 [1]). First, we confirmed that p65 protein inhibition efficiency was maintained when hBMSCs were culture for 7 days on the siRNA spot, and siRNA spot activity remained in spite of long term storage (10 days and 2 months). Additionally, we confirmed p65 protein inhibition in U2OS cells after 48 h reverse transfection. PMID:27054175

  19. Functional dissection of an enhancer-like element located within the second intron of the human U2AF1L4 gene.

    PubMed

    Didych, D A; Smirnov, N A; Kotova, E S; Akopov, S B; Nikolaev, L G; Sverdlov, E D

    2011-08-01

    A detailed functional and evolutionary analysis of an enhancer element of the human genome (enhancer 12) located in the second intron of the U2AF1L4 gene, which we identified earlier, is presented. Overlapping fragments of the studied genome region were analyzed for enhancer activity, and the site responsible for the activity of this element was identified using transient transfections of HeLa cells. Comparison of the enhancer 12 sequence with orthologous sequences from seven primate species revealed the existence of evolutionarily conserved sequences within this element. One of the identified conservative regions is likely responsible for the enhancer activity and is able to specifically interact in vitro with proteins of HeLa cell nuclear extract. The ability of orthologous primate sequences to compete with enhancer 12 for binding with HeLa cell nuclear extract proteins and to enhance the activity of the reporter gene in transient transfection of HeLa cells is demonstrated. PMID:22022969

  20. Free-carrier dynamics and band tails in C u2ZnSn (SxSe1-x) 4 : Evaluation of factors determining solar cell efficiency

    NASA Astrophysics Data System (ADS)

    Phuong, Le Quang; Okano, Makoto; Yamashita, Genki; Nagai, Masaya; Ashida, Masaaki; Nagaoka, Akira; Yoshino, Kenji; Kanemitsu, Yoshihiko

    2015-09-01

    We investigated the composition-dependent photocarrier dynamics in C u2ZnSn (SxSe1-x) 4 (CZTSSe) single crystals using various types of steady-state and time-resolved optical spectroscopy. Photoluminescence spectroscopy shows that the band-tail states formed below the band edge decrease monotonically with increasing Se content. THz time-resolved spectroscopy clarifies that an increase in the Se content leads to a shorter lifetime of the free photocarriers. A trade-off between the composition-dependent band-tail density and the free-carrier lifetime occurs in CZTSSe single crystals. Our experimental results provide insights into the physics behind the low and composition-dependent conversion efficiency of CZTSSe-based solar cells.

  1. From the CKM matrix to the Maki-Nakagawa-Sakata matrix: A model based on supersymmetric SO(10)xU(2){sub F} symmetry

    SciTech Connect

    Chen, Mu-Chun; Mahanthappa, K. T.

    2000-12-01

    We construct a realistic model based on SUSY SO(10) with U(2) flavor symmetry. In contrast with the commonly used effective operator approach, 126-dimensional Higgs fields are used to construct the Yukawa sector. R-parity symmetry is thus preserved at low energies. The Dirac and right-handed Majorana mass matrices in our model have very small mixings and they combine with the seesaw mechanism resulting in large leptonic mixing. The symmetric mass textures arising from the left-right symmetry breaking chain of SO(10) give rise to very good predictions; 15 masses (including three right-handed Majorana neutrino masses) and six mixing angles are predicted by 11 parameters. Both the vacuum oscillation and LOW solutions are favored for the solar neutrino problem.

  2. 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

  3. 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. PMID:26716701

  4. Cinobufagin induces autophagy-mediated cell death in human osteosarcoma U2OS cells through the ROS/JNK/p38 signaling pathway

    PubMed Central

    MA, KUN; ZHANG, CHUAN; HUANG, MAN-YU; LI, WU-YIN; HU, GUO-QIANG

    2016-01-01

    The main objective of this study was to explore whether autophagy could be triggered by cinobufagin, and to clarify the role of autophagy in the antitumor effects of cinobufagin on U2OS cells and the underlying mechanisms. U2OS cells were exposed to 15, 30, 60 and 120 mg/l cinobufagin for 0, 12, 24 and 48 h. An MTT assay was used to measure cell viability. FITC-Annexin V/PI staining and flow cytometry were used to analyze the apoptotic ratio, while apoptotic morphological changes were assessed by PI and Hoechst 33258 viable cell staining. The effects of autophagy on the cells were investigated with GFP-LC3b green fluorescence plasmid transfection and transmission electron microscopy. The levels of caspase-3, -8, - 9, cleaved PARP, LC3-II/LC3-I, p62 and the activation of JNK/p-38 were detected by western blot analysis. Reactive oxygen species (ROS) fluorescence intensity was examined under fluorescence microscopy with an analysis software system. Cell proliferation was obviously inhibited by cinobufagin in a dose- and time-dependent manner. The apoptosis ratio was gradually increased with treatment time as evidenced by flow cytometric analysis and Hoechst 33258 staining. Exposure to cinobufagin resulted in the activation of caspase-3, -8, -9, as well as cleaved PARP which indicated that cinobufagin induced caspase-dependent apoptosis. Autophagy was confirmed in the cinobufagin-treated cells as evidenced by formation of autophagosomes, accumulation of GFP-LC3 fluorescence particles as well as the upregulation of LC3-II/LC3-I levels. Inhibition of autophagy diminished apoptosis as detected by the MTT assays. Moreover the percentage of apoptotic cells decreased following pretreatment with 3-MA, CQ and si-beclin-1. Cinobufagin also induced phosphorylation of the JNK and p38 signaling pathway as well as ROS generation. The JNK and p38 inhibitors significantly attenuated coexistence of apoptosis and autophagy-related proteins. The ROS scavenger also prevented

  5. Cinobufagin induces autophagy-mediated cell death in human osteosarcoma U2OS cells through the ROS/JNK/p38 signaling pathway.

    PubMed

    Ma, Kun; Zhang, Chuan; Huang, Man-Yu; Li, Wu-Yin; Hu, Guo-Qiang

    2016-07-01

    The main objective of this study was to explore whether autophagy could be triggered by cinobufagin, and to clarify the role of autophagy in the antitumor effects of cinobufagin on U2OS cells and the underlying mechanisms. U2OS cells were exposed to 15, 30, 60 and 120 mg/l cinobufagin for 0, 12, 24 and 48 h. An MTT assay was used to measure cell viability. FITC-Annexin Ⅴ/PI staining and flow cytometry were used to analyze the apoptotic ratio, while apoptotic morphological changes were assessed by PI and Hoechst 33258 viable cell staining. The effects of autophagy on the cells were investigated with GFP-LC3b green fluorescence plasmid transfection and transmission electron microscopy. The levels of caspase-3, -8, - 9, cleaved PARP, LC3-II/LC3-I, p62 and the activation of JNK/p-38 were detected by western blot analysis. Reactive oxygen species (ROS) fluorescence intensity was examined under fluorescence microscopy with an analysis software system. Cell proliferation was obviously inhibited by cinobufagin in a dose- and time-dependent manner. The apoptosis ratio was gradually increased with treatment time as evidenced by flow cytometric analysis and Hoechst 33258 staining. Exposure to cinobufagin resulted in the activation of caspase-3, -8, -9, as well as cleaved PARP which indicated that cinobufagin induced caspase-dependent apoptosis. Autophagy was confirmed in the cinobufagin-treated cells as evidenced by formation of autophagosomes, accumulation of GFP-LC3 fluorescence particles as well as the upregulation of LC3-II/LC3-I levels. Inhibition of autophagy diminished apoptosis as detected by the MTT assays. Moreover the percentage of apoptotic cells decreased following pretreatment with 3-MA, CQ and si-beclin-1. Cinobufagin also induced phosphorylation of the JNK and p38 signaling pathway as well as ROS generation. The JNK and p38 inhibitors significantly attenuated coexistence of apoptosis and autophagy-related proteins. The ROS scavenger also prevented

  6. Zoledronate blocks geranylgeranylation not farnesylation to suppress human osteosarcoma U2OS cells metastasis by EMT via Rho A activation and FAK-inhibited JNK and p38 pathways

    PubMed Central

    Cheng, Hsin-Lin; Lin, Chiao-Wen; Yang, Jia-Sin; Hsieh, Ming-Ju; Yang, Shun-Fa; Lu, Ko-Hsiu

    2016-01-01

    Zoledronate is a standard treatment for preventing skeletal complications of osteoporosis and some types of cancer associated with bone metastases, but we little know whether the effect of zoledronate on metastasis of osteosarcoma. Here, we investigated the inhibitory effects of zoledronate on cell viability, motility, migration and invasion of 4 osteosarcoma cell lines (Saos2, MG-63, HOS and U2OS) by affecting cell morphology, epithelial-mesenchymal transition (EMT) and cytoskeletal organization as well as induction of E-cadherin and reduction of N-cadherin with activation of transcription factors Slug and Twist, especially in U2OS cells. Zoledronate decreased JNK and p38 phosphorylation and upper streams of focal adhesion kinase (FAK) and Src to suppress the motility, invasiveness and migration of U2OS cells. In addition to zoledronate-inhibited Rho A and Cdc42 membrane translocation and GTPγS activities, the anti-metastatic effects in U2OS cells including inhibition of adhesion were reversed by geranylgeraniol, but not farnesol. In conclusion, Zoledronate blocks geranylgeranylation not farnesylation to suppress human osteosarcoma U2OS cell-matrix and cell-cell interactions, migration potential, the invasive activity, and the adhesive ability by EMT via Rho A activation and FAK-inhibited JNK and p38 pathways. PMID:26848867

  7. Zoledronate blocks geranylgeranylation not farnesylation to suppress human osteosarcoma U2OS cells metastasis by EMT via Rho A activation and FAK-inhibited JNK and p38 pathways.

    PubMed

    Cheng, Hsin-Lin; Lin, Chiao-Wen; Yang, Jia-Sin; Hsieh, Ming-Ju; Yang, Shun-Fa; Lu, Ko-Hsiu

    2016-03-01

    Zoledronate is a standard treatment for preventing skeletal complications of osteoporosis and some types of cancer associated with bone metastases, but we little know whether the effect of zoledronate on metastasis of osteosarcoma. Here, we investigated the inhibitory effects of zoledronate on cell viability, motility, migration and invasion of 4 osteosarcoma cell lines (Saos2, MG-63, HOS and U2OS) by affecting cell morphology, epithelial-mesenchymal transition (EMT) and cytoskeletal organization as well as induction of E-cadherin and reduction of N-cadherin with activation of transcription factors Slug and Twist, especially in U2OS cells. Zoledronate decreased JNK and p38 phosphorylation and upper streams of focal adhesion kinase (FAK) and Src to suppress the motility, invasiveness and migration of U2OS cells. In addition to zoledronate-inhibited Rho A and Cdc42 membrane translocation and GTPγS activities, the anti-metastatic effects in U2OS cells including inhibition of adhesion were reversed by geranylgeraniol, but not farnesol. In conclusion, Zoledronate blocks geranylgeranylation not farnesylation to suppress human osteosarcoma U2OS cell-matrix and cell-cell interactions, migration potential, the invasive activity, and the adhesive ability by EMT via Rho A activation and FAK-inhibited JNK and p38 pathways. PMID:26848867

  8. 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.

  9. 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

  10. A monoclonal antibody raised against bacterially expressed MPV17 sequences shows peroxisomal, endosomal and lysosomal localisation in U2OS cells.

    PubMed

    Weiher, Hans; Pircher, Haymo; Jansen-Dürr, Pidder; Hegenbarth, Silke; Knolle, Percy; Grunau, Silke; Vapola, Miia; Hiltunen, J Kalervo; Zwacka, Ralf M; Schmelzer, Elmon; Reumann, Kerstin; Will, Hans

    2016-01-01

    Recessive mutations in the MPV17 gene cause mitochondrial DNA depletion syndrome, a fatal infantile genetic liver disease in humans. Loss of function in mice leads to glomerulosclerosis and sensineural deafness accompanied with mitochondrial DNA depletion. Mutations in the yeast homolog Sym1, and in the zebra fish homolog tra cause interesting, but not obviously related phenotypes, although the human gene can complement the yeast Sym1 mutation. The MPV17 protein is a hydrophobic membrane protein of 176 amino acids and unknown function. Initially localised in murine peroxisomes, it was later reported to be a mitochondrial inner membrane protein in humans and in yeast. To resolve this contradiction we tested two new mouse monoclonal antibodies directed against the human MPV17 protein in Western blots and immunohistochemistry on human U2OS cells. One of these monoclonal antibodies showed specific reactivity to a protein of 20 kD absent in MPV17 negative mouse cells. Immunofluorescence studies revealed colocalisation with peroxisomal, endosomal and lysosomal markers, but not with mitochondria. This data reveal a novel connection between a possible peroxisomal/endosomal/lysosomal function and mitochondrial DNA depletion. PMID:26921094

  11. YB-1 binds to CAUC motifs and stimulates exon inclusion by enhancing the recruitment of U2AF to weak polypyrimidine tracts

    PubMed Central

    Wei, Wen-Juan; Mu, Shi-Rong; Heiner, Monika; Fu, Xing; Cao, Li-Juan; Gong, Xiu-Feng; Bindereif, Albrecht; Hui, Jingyi

    2012-01-01

    The human Y box-binding protein-1 (YB-1) is a deoxyribonucleic acid (DNA)/ribonucleic acid (RNA)-binding protein with pleiotropic functions. Besides its roles in the regulation of transcription and translation, several recent studies indicate that YB-1 is a spliceosome-associated protein and is involved in alternative splicing, but the underlying mechanism has remained elusive. Here, we define both CAUC and CACC as high-affinity binding motifs for YB-1 by systematic evolution of ligands by exponential enrichment (SELEX) and demonstrate that these newly defined motifs function as splicing enhancers. Interestingly, on the endogenous CD44 gene, YB-1 appears to mediate a network interaction to activate exon v5 inclusion via multiple CAUC motifs in both the alternative exon and its upstream polypyrimidine tract. We provide evidence that YB-1 activates splicing by facilitating the recruitment of U2AF65 to weak polypyrimidine tracts through direct protein–protein interactions. Together, these findings suggest a vital role of YB-1 in activating a subset of weak 3′ splice sites in mammalian cells. PMID:22730292

  12. Microarray and ChIP-seq data analysis revealed changes in p53-mediated transcriptional regulation in Nutlin-3-treated U2OS cells

    PubMed Central

    ZHAO, SONG; NIU, FENG; XU, CHANG-YAN; YE, LONG; BI, GUI-BIN; CHEN, LIN; GONG, PING; TIAN, GANG; NIE, TIAN-HONG

    2015-01-01

    Integrative analysis of chromatin immunoprecipitation-sequencing (ChIP-seq) data and microarray data was performed to illustrate the effect of Nutlin-3 on promoter selectivity and transcriptional regulation by the tumor suppressor p53 in U2OS human osteosarcoma cells. Raw data (accession number, GSE46642) were downloaded from Gene Expression Omnibus. Differential analyses were performed using package limma of R software. Gene ontology enrichment and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed for the differentially expressed genes (DEGs) using the Database for Annotation, Visualization and Integration Discovery. Integrative analysis of ChIP-seq data and microarray data were confirmed with ChIP-Array. A total of 565 DEGs were identified, including 373 upregulated genes and 192 downregulated genes. Genes involved in the p53 signaling pathway, cell cycle, DNA replication, cytokine-cytokine receptor interaction and melanoma were markedly over-represented in the DEGs. A total of 39 DEGs were directly regulated by p53 and two were the transcription factors (TFs), E2F2 and HOXA1. E2F2 regulated 25 DEGs, while HOXA1 regulated one DEG. The cell cycle, p53 signaling pathway, melanoma and pathways involved in cancer were enriched in the direct and indirect target genes. Changes in the p53-binding pattern induced by Nutlin-3 were described in the present study, which may advance the understanding of the regulatory network of p53 in osteosarcoma and aid in the development of novel therapies. PMID:26080812

  13. 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)

  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. Fine structure of the “PcG body” in human U-2 OS cells established by correlative light-electron microscopy

    PubMed Central

    Juda, Pavel; Cmarko, Dušan

    2011-01-01

    Polycomb group (PcG) proteins of the Polycomb repressive complex 1 (PRC1) are found to be diffusely distributed in nuclei of cells from various species. However they can also be localized in intensely fluorescent foci, whether imaged using GFP fusions to proteins of PRC1 complex, or by conventional immunofluorescence microscopy. Such foci are termed PcG bodies, and are believed to be situated in the nuclear intechromatin compartment. However, an ultrastructural description of the PcG body has not been reported to date. To establish the ultrastructure of PcG bodies in human U-2 OS cells stably expressing recombinant polycomb BMI1-GFP protein, we used correlative light-electron microscopy (CLEM) implemented with high-pressure freezing, cryosubstitution and on-section labeling of BMI1 protein with immunogold. This approach allowed us to clearly identify fluorescent PcG bodies, not as distinct nuclear bodies, but as nuclear domains enriched in separated heterochromatin fascicles. Importantly, high-pressure freezing and cryosubstitution allowed for a high and clear-cut immunogold BMI1 labeling of heterochromatin structures throughout the nucleus. The density of immunogold labeled BMI1 in the heterochromatin fascicles corresponding to fluorescent “PcG bodies” did not differ from the density of labeling of heterochromatin fascicles outside of the “PcG bodies”. Accordingly, an appearance of the fluorescent “PcG bodies” seems to reflect a local accumulation of the labeled heterochromatin structures in the investigated cells. The results of this study should allow expansion of the knowledge about the biological relevance of the “PcG bodies” in human cells. PMID:21818415

  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. Downregulation of microRNA-586 Inhibits Proliferation, Invasion and Metastasis and Promotes Apoptosis in Human Osteosarcoma U2-OS Cell Line.

    PubMed

    Yang, Lei; Liu, Zong-Ming; Rao, Yan-Wei; Cui, Shao-Qian; Wang, Huan; Jia, Xiao-Jing

    2015-01-01

    In this study, we aim to examine the association of microRNA-586 (miR-586) with osteosarcoma (OS) cell proliferation, apoptosis, invasion, and metastasis. U2-OS cell lines were divided into 4 groups: an miR-586 group, anti-miR-586 group, control group (empty plasmid) and blank group (no plasmid). qRT-PCR was used to detect miR-586 expression, cell counting kit-8 and EdU assays to detect cell proliferation, flow cytometry to detect cell cycle distribution, Annexin V/PI double staining to detect cell apoptosis, and the Transwell assay to detect cell invasion and metastasis. miR-586 expression was significantly higher in the miR-586 group but significantly lower in the anti-miR-586 group compared with the control and blank groups. Cell proliferation at 2-5 days after cell transfection and the EdU-positive cell number increased obviously in the miR-586 group but decreased clearly in the anti-miR-586 group. In the miR-586 group, cells at G0/G1 stage and apoptosis cells significantly decreased, while cells at G2/M and S stages and invasive and metastatic cells significantly increased compared to the control and blank groups; however, opposite trends were found in the anti-miR-586 group. Downregulation of miR-586 expression in OS may inhibit cell proliferation, invasion and metastasis, and promote cell apoptosis. PMID:26580004

  19. 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

  20. Chromosomal Mapping of Repetitive DNA Sequences in Five Species of Astyanax (Characiformes, Characidae) Reveals Independent Location of U1 and U2 snRNA Sites and Association of U1 snRNA and 5S rDNA.

    PubMed

    Silva, Duilio M Z A; Utsunomia, Ricardo; Pansonato-Alves, José C; Oliveira, Cláudio; Foresti, Fausto

    2015-01-01

    Astyanax is a genus of Characidae fishes currently composed of 155 valid species. Previous cytogenetic studies revealed high chromosomal diversification among them, and several studies have been performed using traditional cytogenetic techniques to investigate karyotypes and chromosomal locations of 18S and 5S rDNA genes. However, only a few studies are currently available about other repetitive sequences. Here, the chromosomal location of small nuclear RNA genes, identified as U1 and U2 snRNA clusters, was established and compared to the distribution of 5S rDNA and histone clusters in 5 Astyanax species (A. paranae, A. fasciatus, A. bockmanni, A. altiparanae, and A. jordani) using FISH. The cytogenetic mapping of U1 and U2 snRNA demonstrated a conserved pattern in the number of sites per genome independent of the location in Astyanax species. The location of the U1 snRNA gene was frequently associated with 5S rDNA sequences, indicating a possible interaction between the distinct repetitive DNA families. Finally, comparisons involving the location of U1 and U2 snRNA clusters in the chromosomes of Astyanax species revealed a very diverse pattern, suggesting that many rearrangements have occurred during the diversification process of this group. PMID:26329975

  1. Structures, sequence characteristics, and synteny relationships of the transcription factor E4TF1, the splicing factor U2AF35 and the cystathionine beta synthetase genes from Fugu rubripes.

    PubMed

    Tassone, F; Villard, L; Clancy, K; Gardiner, K

    1999-01-21

    A cosmid containing the beta-amyloid precursor protein (APP) from Fugu rubripes has been completely sequenced. In addition to APP, the cosmid contains the E4TF1-60 transcription factor, the U2AF35 pre-mRNA splicing factor, and the cystathionine beta synthetase (CBS) gene. The human homologues of all four genes map to human chromosome 21 but are not clustered; APP and E4TF1-60 map within 21q21, whereas U2AF35 and CBS map approximately 20Mb distal in 21q22. 3. The protein sequences of the Fugu genes vary in their overall level of similarity to their mammalian homologues, but several regions of functional importance are almost identical. As expected, the intron/exon structures of the homologous pairs of genes are highly conserved, but there are significant differences in the compaction ratios. The introns of APP and E4TF1-60 are 49- and 24-fold smaller in Fugu than in human, and the intergenic distance is compressed at least 100-fold. For U2AF35 and CBS, the introns are compressed only five- to eightfold. These size differences were compared with those for a number of previously reported Fugu genes; in general, levels of compaction of Fugu genes are consistent with the isochore locations of the human homologues. PMID:9931491

  2. Dryofragin inhibits the migration and invasion of human osteosarcoma U2OS cells by suppressing MMP-2/9 and elevating TIMP-1/2 through PI3K/AKT and p38 MAPK signaling pathways.

    PubMed

    Su, Yan; Wan, Daqian; Song, Wenqi

    2016-08-01

    Dryofragin, a phloroglucinol derivative extracted from Dryopteris fragrans (L.) Schott, was found to inhibit proliferation and induce apoptosis of tumor cells. However, the mechanism involved in the suppression of cancer cell metastasis by dryofragin remains unclear. Our study investigated the mechanisms for the antitumor properties of dryofragin on the migration and invasion of human osteosarcoma U2OS cells. Dryofragin suppressed the migration and invasive ability of U2OS cells, and it decreased the expression of MMP-2 and MMP-9 and elevated the expression of TIMP-1 and TIMP-2. Western blotting assays indicated that dryofragin was effective in suppressing the phosphorylation of phosphatidylinositide-3 kinase (PI3K), Akt, and p38 MAPK. These results suggest that dryofragin inhibited U2OS cell migration and invasion by reducing the expression of MMP-2 and MMP-9 and elevating the expression of TIMP-1 and TIMP-2 through the PI3K/AKT and p38 MAPK signaling pathways. Above all, we conclude that dryofragin represents an anti-invasive agent and may potentially be applicable in osteosarcoma therapy. PMID:27243922

  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. 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

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

    PubMed Central

    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

  6. 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

    2014-01-01

    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. PMID:24350659

  7. 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.

  8. Studies to investigate the in vivo therapeutic window of the gamma-secretase inhibitor N2-[(2S)-2-(3,5-difluorophenyl)-2-hydroxyethanoyl]-N1-[(7S)-5-methyl-6-oxo-6,7-dihydro-5H-dibenzo[b,d]azepin-7-yl]-L-alaninamide (LY411,575) in the CRND8 mouse.

    PubMed

    Hyde, Lynn A; McHugh, Nansie A; Chen, Joseph; Zhang, Qi; Manfra, Denise; Nomeir, Amin A; Josien, Hubert; Bara, Thomas; Clader, John W; Zhang, Lili; Parker, Eric M; Higgins, Guy A

    2006-12-01

    Accumulation of amyloid beta-peptide (Abeta) is considered a key step in the etiology of Alzheimer's disease. Abeta is produced by sequential cleavage of the amyloid precursor protein by beta- and gamma-secretase enzymes. Consequently, inhibition of gamma-secretase provides a promising therapeutic approach to treat Alzheimer's disease. Preclinically, several gamma-secretase inhibitors have been shown to reduce plasma and brain Abeta, although they also produce mechanism-based side effects, including thymus atrophy and intestinal goblet cell hyperplasia. The present studies sought to establish an efficient screen for determining the therapeutic window of gamma-secretase inhibitors and to test various means of maximizing this window. Six-day oral administration of the gamma-secretase inhibitor N(2)-[(2S)-2-(3,5-difluorophenyl)-2-hydroxyethanoyl]-N(1)-[(7S)-5-methyl-6-oxo-6,7-dihydro-5H-dibenzo[b,d]azepin-7-yl]-l-alaninamide (LY411,575) reduced cortical Abeta(40) in young (preplaque) transgenic CRND8 mice (ED(50) approximately 0.6 mg/kg) and produced significant thymus atrophy and intestinal goblet cell hyperplasia at higher doses (>3 mg/kg). The therapeutic window was similar after oral and subcutaneous administration and in young and aged CRND8 mice. Both the thymus and intestinal side effects were reversible after a 2-week washout period. Three-week treatment with 1 mg/kg LY411,575 reduced cortical Abeta(40) by 69% without inducing intestinal effects, although a previously unreported change in coat color was observed. These studies demonstrate that the 3- to 5-fold therapeutic window for LY411,575 can be exploited to obtain reduction in Abeta levels without induction of intestinal side effects, that intermittent treatment could be used to mitigate side effects, and that a 6-day dosing paradigm can be used to rapidly determine the therapeutic window of novel gamma-secretase inhibitors. PMID:16946102

  9. Efficient production of lignocellulolytic enzymes xylanase, β-xylosidase, ferulic acid esterase and β-glucosidase by the mutant strain Aspergillus awamori 2B.361 U2/1

    PubMed Central

    Gottschalk, Leda Maria Fortes; de Sousa Paredes, Raquel; Teixeira, Ricardo Sposina Sobral; da Silva, Ayla Sant’Ana; da Silva Bon, Elba Pinto

    2013-01-01

    The production of xylanase, β-xylosidase, ferulic acid esterase and β-glucosidase by Aspergillus awamori 2B.361 U2/1, a hyper producer of glucoamylase and pectinase, was evaluated using selected conditions regarding nitrogen nutrition. Submerged cultivations were carried out at 30 °C and 200 rpm in growth media containing 30 g wheat bran/L as main carbon source and either yeast extract, ammonium sulfate, sodium nitrate or urea, as nitrogen sources; in all cases it was used a fixed molar carbon to molar nitrogen concentration of 10.3. The use of poor nitrogen sources favored the accumulation of xylanase, β-xylosidase and ferulic acid esterase to a peak concentrations of 44,880; 640 and 118 U/L, respectively, for sodium nitrate and of 34,580, 685 and 170 U/L, respectively, for urea. However, the highest β-glucosidase accumulation of 10,470 U/L was observed when the rich organic nitrogen source yeast extract was used. The maxima accumulation of filter paper activity, xylanase, β-xylosidase, ferulic acid esterase and β-glucosidase by A. awamori 2B.361 U2/1 was compared to that produced by Trichoderma reesei Rut-C30. The level of β-glucosidase was over 17-fold higher for the Aspergillus strain, whereas the levels of xylanase and β-xylosidase were over 2-fold higher. This strain also produced ferulic acid esterase (170 U/L), which was not detected in the T. reesei culture. PMID:24294256

  10. PRMT9 is a Type II methyltransferase that methylates the splicing factor SAP145

    PubMed Central

    Yang, Yanzhong; Hadjikyriacou, Andrea; Xia, Zheng; Gayatri, Sitaram; Kim, Daehoon; Zurita-Lopez, Cecilia; Kelly, Ryan; Guo, Ailan; Li, Wei; Clarke, Steven G.; Bedford, Mark T.

    2015-01-01

    The human genome encodes a family of nine protein arginine methyltransferases (PRMT1-9), which members can catalyze three distinct types of methylation on arginine residues. Here, we identify two spliceosome-associated proteins – SAP145 and SAP49 – as PRMT9 binding partners, linking PRMT9 to U2snRNP maturation. We show that SAP145 is methylated by PRMT9 at arginine 508, which takes the form of monomethylated arginine (MMA) and symmetrically dimethylated arginine (SDMA). PRMT9 thus joins PRMT5 as the only mammalian enzymes capable of depositing the SDMA mark. Methylation of SAP145 on Arg508 generates a binding site for the Tudor domain of the Survival of Motor Neuron (SMN) protein, and RNA-seq analysis reveals gross splicing changes when PRMT9 levels are attenuated. These results identify PRMT9 as a non-histone methyltransferase that primes the U2snRNP for interaction with SMN. PMID:25737013

  11. Dealing with Climate Change and Variability in the Growing Season: a U2U Decision Support Tool for Central United States Corn Producers Based on Corn Growing Degree Days

    NASA Astrophysics Data System (ADS)

    Angel, J. R.; Todey, D.; Massey, R.; Widhalm, M.; Biehl, L. L.; Andresen, J.

    2014-12-01

    Climate extremes are a major challenge for corn producers in the central United States. Among those extremes are wet springs that lead to planting delays, late spring and early fall frosts that can damage crops, and extreme summer temperatures either too warm or too cool. A newly-operational corn growing degree-day (CGDD) tool helps producers manage and adapt to these extremes. For example, a challenge in recent years has been exceptionally wet springs that have led to significant planting delays. Producers have been forced to re-assess their planting strategies on short notice, such as switching to a faster-growing but lower-yielding hybrids. With this pattern of wetter springs projected to continue or worsen in the central United States, the problem will remain and likely get worse. Another example is helping producers identify the risk of early or late frost/freezes. The CGDD tool puts current conditions into a 30-year historical perspective and offers trend projections (based on climatology or forecasts) through the end of the calendar year. Corn, or sometimes called modified, growing degree-days use a temperature base of 10 C (50 F) and a ceiling of 30 C (86 F) and is strongly correlated with the development of the corn crop. This tool was developed as part of USDA-supported U2U Useful to Usable Project for transforming climate variability and change information for cereal crop producers.

  12. On the Quasi-linear Elliptic PDE {-nabla \\cdot ( nabla{u}/ sqrt{1-| nabla{u} |^2}) = 4 π sum_k a_k δ_{s_k}} in Physics and Geometry

    NASA Astrophysics Data System (ADS)

    Kiessling, Michael K.-H.

    2012-09-01

    It is shown that for each finite number N of Dirac measures {δ_{s_n}} supported at points {s_n in {R}^3} with given amplitudes {a_n in {R} backslash\\{0\\}} there exists a unique real-valued function {u in C^{0, 1}({R}^3)}, vanishing at infinity, which distributionally solves the quasi-linear elliptic partial differential equation of divergence form {-nabla \\cdot ( nabla{u}/ sqrt{1-| nabla{u} |^2}) = 4 π sum_{n=1}^N a_n δ_{s_n}}. Moreover, {u in C^{ω}({R}^3backslash \\{s_n\\}_{n=1}^N)}. The result can be interpreted in at least two ways: (a) for any number N of point charges of arbitrary magnitude and sign at prescribed locations s n in three-dimensional Euclidean space there exists a unique electrostatic field which satisfies the Maxwell-Born-Infeld field equations smoothly away from the point charges and vanishes as | s| → ∞; (b) for any number N of integral mean curvatures assigned to locations {s_n in {R}^3 subset{R}^{1, 3}} there exists a unique asymptotically flat, almost everywhere space-like maximal slice with point defects of Minkowski spacetime {{R}^{1, 3}}, having lightcone singularities over the s n but being smooth otherwise, and whose height function vanishes as | s| → ∞. No struts between the point singularities ever occur.

  13. ATP can be dispensable for prespliceosome formation in yeast

    PubMed Central

    Perriman, Rhonda; Ares, Manuel

    2000-01-01

    The first ATP-dependent step in pre-mRNA splicing involves the stable binding of U2 snRNP to form the prespliceosome. We show that a prespliceosome-like complex forms in the absence of ATP in yeast extracts lacking the U2 suppressor protein CUS2. These complexes display the same pre-mRNA and U snRNA requirements as authentic prespliceosomes and can be chased through the splicing pathway, indicating that they are a functional intermediate in the spliceosome assembly pathway. ATP-independent prespliceosome-like complexes are also observed in extracts containing a mutant U2 snRNA. Loss of CUS2 does not bypass the role of PRP5, an RNA helicase family member required for ATP-dependent prespliceosome formation. Genetic interactions between CUS2 and a heat-sensitive prp5 allele parallel those observed between CUS2 and U2, and suggest that CUS2 mediates functional interactions between U2 RNA and PRP5. We propose that CUS2 enforces ATP dependence during formation of the prespliceosome by brokering an interaction between PRP5 and the U2 snRNP that depends on correct U2 RNA structure. PMID:10640279

  14. Linking U (2U (2 ) to O (4 ) model via decoupling

    NASA Astrophysics Data System (ADS)

    Sato, Tomomi; Yamada, Norikazu

    2015-02-01

    The nature of chiral phase transition of massless two flavor QCD depends on the fate of flavor singlet axial symmetry UA(1 ) at the critical temperature (Tc ). Assuming that a finite UA(1 ) breaking remains at Tc , the corresponding three dimensional effective theory is composed of four massless and four massive scalar fields. We study the renormalization group flow of the effective theory in the ɛ -expansion, using a mass dependent renormalization scheme, and determine the region of the attractive basin flowing into the O (4 ) fixed point with a focus on its dependence on the size of the UA(1 ) breaking. The result is discussed from a perspective of the decoupling of massive fields. It is pointed out that, although the effective theory inside the attractive basin eventually reaches the O (4 ) fixed point, the approaching rate, one of the universal exponents, is different from that of the standard O (4 ) model. We present the reason for this peculiarity, and propose a novel possibility for chiral phase transition in two-flavor QCD.

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

    PubMed Central

    Labourier, E; Rio, D C

    2001-01-01

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

  16. Two distinct arginine methyltransferases are required for biogenesis of Sm-class ribonucleoproteins

    PubMed Central

    Gonsalvez, Graydon B.; Tian, Liping; Ospina, Jason K.; Boisvert, François-Michel; Lamond, Angus I.; Matera, A. Gregory

    2007-01-01

    Small nuclear ribonucleoproteins (snRNPs) are core components of the spliceosome. The U1, U2, U4, and U5 snRNPs each contain a common set of seven Sm proteins. Three of these Sm proteins are posttranslationally modified to contain symmetric dimethylarginine (sDMA) residues within their C-terminal tails. However, the precise function of this modification in the snRNP biogenesis pathway is unclear. Several lines of evidence suggest that the methyltransferase protein arginine methyltransferase 5 (PRMT5) is responsible for sDMA modification of Sm proteins. We found that in human cells, PRMT5 and a newly discovered type II methyltransferase, PRMT7, are each required for Sm protein sDMA modification. Furthermore, we show that the two enzymes function nonredundantly in Sm protein methylation. Lastly, we provide in vivo evidence demonstrating that Sm protein sDMA modification is required for snRNP biogenesis in human cells. PMID:17709427

  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. A protein map of the yeast activated spliceosome as obtained by electron microscopy.

    PubMed

    Sun, Chengfu; Rigo, Norbert; Fabrizio, Patrizia; Kastner, Berthold; Lührmann, Reinhard

    2016-09-01

    We have elucidated the spatial arrangement of proteins and snRNP subunits within the purified spliceosomal B(act) complex from Saccharomyces cerevisiae, using negative-stain immunoelectron microscopy. The B(act) spliceosome exhibits a mushroom-like shape with a main body connected to a foot and a steep and a shallow slope. The U5 core components, including proteins Snu114 and Prp8, are located in the main body and foot, while Brr2 is on the shallow slope. U2 snRNP components and the RNA helicase Prp2 were predominantly located in the upper regions of both slopes. While several proteins of the "nineteen complex" are located on the steep slope, Prp19, Cef1, and the U6 snRNA-binding protein Cwc2 are on the main body. Our results also indicate that the catalytic core RNP of the spliceosome resides in its main body. We thus assign distinct domains of the B(act) complex to its snRNP and protein components, and we provide first structural insights into the remodeling events at the spliceosome during its transformation from the B to the B(act) complex. PMID:27368340

  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. Purification and characterization of native spliceosomes suitable for three-dimensional structural analysis.

    PubMed Central

    Jurica, Melissa S; Licklider, Lawrence J; Gygi, Steven R; Grigorieff, Nikolaus; Moore, Melissa J

    2002-01-01

    We describe characterization of spliceosomes affinity purified under native conditions. These spliceosomes consist largely of C complex containing splicing intermediates. After C complex assembly on an MS2 affinity-tagged pre-mRNA substrate containing a 3' splice site mutation, followed by RNase H digestion of earlier complexes, spliceosomes were purified by size exclusion and affinity selection. This protocol yielded 40S C complexes in sufficient quantities to visualize in negative stain by electron microscopy. Complexes purified in this way contain U2, U5, and U6 snRNAs, but very little U1 or U4 snRNA. Analysis by tandem mass spectrometry confirmed the presence of core snRNP proteins (SM and LSM), U2 and U5 snRNP-specific proteins, and the second step factors Prp16, Prp17, Slu7, and Prp22. In contrast, proteins specific to earlier splicing complexes, such as U2AF and U1 snRNP components, were not detected in C complex, but were present in similarly purified H complex. Images of these spliceosomes revealed single particles with dimensions of approximately 270 x 240 A that assort into well-defined classes. These images represent an important first step toward attaining a comprehensive three-dimensional understanding of pre-mRNA splicing. PMID:11991638

  1. Mild hydrothermal crystal growth, structure, and magnetic properties of ternary U(IV) containing fluorides: LiUF5, KU2F9, K7U6F31, RbUF5, RbU2F9, and RbU3F13.

    PubMed

    Yeon, Jeongho; Smith, Mark D; Tapp, Joshua; Möller, Angela; zur Loye, Hans-Conrad

    2014-06-16

    Single crystals of several ternary alkali uranium fluorides, LiUF5, KU2F9, K7U6F31, RbUF5, RbU2F9, and RbU3F13, have been obtained in a mild hydrothermal process using UO2(CH3CO2)2(H2O)2 as the uranium source. Their crystal structures were determined by single crystal X-ray diffraction. The uranium in the starting reagent was successfully reduced from U(6+) to U(4+) in a dilute hydrofluoric acid environment, aided by the presence of a copper salt. All materials exhibit highly complex crystal structures that range from two-dimensional to three-dimensional. The U(4+) cations are found in high (UF8 and UF9) coordination environments. The magnetic susceptibility measurements yielded effective magnetic moments of 3.01-3.83 μB for the U(4+) cations. The temperature dependent magnetic susceptibility measurements confirmed that the U(4+) cation exhibits a nonmagnetic singlet ground state at low temperatures. No long-range magnetic order was observed for any of the above compositions down to 2 K. Optical and thermal behaviors of the fluorides were also investigated. PMID:24867234

  2. U(IV)/ Ln(III) unexpected mixed site in polymetallic oxalato complexes. Part I. Substitution of Ln(III) for U(IV) from the new oxalate (NH 4) 2U 2(C 2O 4) 5·0.7H 2O

    NASA Astrophysics Data System (ADS)

    Chapelet-Arab, Benedicte; Nowogrocki, Guy; Abraham, Francis; Grandjean, Stephane

    2005-10-01

    A new ammonium uranium (IV) oxalate (NH 4) 2U 2(C 2O 4) 5·0.7H 2O ( 1) and three mixed uranium (IV)-lanthanide (III) oxalates, (N 2H 5) 2.6U 1.4M0.6(C 2O 4) 5· xH 2O ( M=Nd ( 2) and M=Sm ( 3)), Na 2.56U 1.44Nd 0.56(C 2O 4) 5·7.6H 2O ( 4) and Na 3UCe(C 2O 4) 5·10.4H 2O ( 5), have been prepared. The crystal structures of compounds 1, 4 and 5 have been determined by single-crystal X-ray diffraction. The crystal structures were solved by the direct methods and Fourier difference techniques, and refined by a least square method on the basis of F2 for all unique reflections. Compounds 2 and 3 are isotypic with 1. Crystallographic data: 1, hexagonal, space group P6 3/ mmc, a=19.177(3), c=12.728(4) Å, Z=6, R1=0.0575 for 52 parameters with 1360 reflections with I⩾2 σ( I); 2, hexagonal, space group P6 3/ mmc, a=19.243(4), c=12.760(5) Å, Z=6; 3, hexagonal, space group P6 3/ mmc, a=19.211(3), c=12.274(4) Å, Z=6; 4, orthorhombic, space group Pbcn, a=18.79(3), b=11.46(1), c=12.77(2) Å, Z=4, R1=0.0511 for 183 parameters with 3026 reflections with I⩾2σ(I); 5, monoclinic, space group C2/ c, a=18.878(6), b=11.684(4), c=12.932(4) Å, β=95.97(1)°, Z=4, R1=0.0416 for 213 parameters with 4060 reflections with I⩾2 σ( I). The honeycomb-like structure of the five compounds is built from the same three-dimensional arrangement of metallic and oxalate ions. Similar hexagonal rings of alternating metallic and oxalate ions form layers parallel to the (001) plane that are pillared by another oxalate ion. Indeed, some torsions or rotations of the bridging oxalate ligands led to modifications of the network symmetry. The monovalent cations and the water molecules occupy the hexagonal tunnels running down the [001] direction. Starting from the uranium (IV) compound A 2U 2(C 2O 4) 5·0.7H 2O with A=NH 4+ ( 1), the mixed U(IV)/ Ln(III) oxalates are obtained by partial substitution of U(IV) by Ln(III) in a ten-coordinated site, the charge deficit being compensated by intercalation

  3. Genome-wide RNAi screens in human brain tumor isolates reveal a novel viability requirement for PHF5A

    PubMed Central

    Hubert, Christopher G.; Bradley, Robert K.; Ding, Yu; Toledo, Chad M.; Herman, Jacob; Skutt-Kakaria, Kyobi; Girard, Emily J.; Davison, Jerry; Berndt, Jason; Corrin, Philip; Hardcastle, Justin; Basom, Ryan; Delrow, Jeffery J.; Webb, Thomas; Pollard, Steven M.; Lee, Jeongwu; Olson, James M.; Paddison, Patrick J.

    2013-01-01

    To identify key regulators of human brain tumor maintenance and initiation, we performed multiple genome-wide RNAi screens in patient-derived glioblastoma multiforme (GBM) stem cells (GSCs). These screens identified the plant homeodomain (PHD)-finger domain protein PHF5A as differentially required for GSC expansion, as compared with untransformed neural stem cells (NSCs) and fibroblasts. Given PHF5A's known involvement in facilitating interactions between the U2 snRNP complex and ATP-dependent helicases, we examined cancer-specific roles in RNA splicing. We found that in GSCs, but not untransformed controls, PHF5A facilitates recognition of exons with unusual C-rich 3′ splice sites in thousands of essential genes. PHF5A knockdown in GSCs, but not untransformed NSCs, astrocytes, or fibroblasts, inhibited splicing of these genes, leading to cell cycle arrest and loss of viability. Notably, pharmacologic inhibition of U2 snRNP activity phenocopied PHF5A knockdown in GSCs and also in NSCs or fibroblasts overexpressing MYC. Furthermore, PHF5A inhibition compromised GSC tumor formation in vivo and inhibited growth of established GBM patient-derived xenograft tumors. Our results demonstrate a novel viability requirement for PHF5A to maintain proper exon recognition in brain tumor-initiating cells and may provide new inroads for novel anti-GBM therapeutic strategies. PMID:23651857

  4. Genome-wide RNAi screens in human brain tumor isolates reveal a novel viability requirement for PHF5A.

    PubMed

    Hubert, Christopher G; Bradley, Robert K; Ding, Yu; Toledo, Chad M; Herman, Jacob; Skutt-Kakaria, Kyobi; Girard, Emily J; Davison, Jerry; Berndt, Jason; Corrin, Philip; Hardcastle, Justin; Basom, Ryan; Delrow, Jeffery J; Webb, Thomas; Pollard, Steven M; Lee, Jeongwu; Olson, James M; Paddison, Patrick J

    2013-05-01

    To identify key regulators of human brain tumor maintenance and initiation, we performed multiple genome-wide RNAi screens in patient-derived glioblastoma multiforme (GBM) stem cells (GSCs). These screens identified the plant homeodomain (PHD)-finger domain protein PHF5A as differentially required for GSC expansion, as compared with untransformed neural stem cells (NSCs) and fibroblasts. Given PHF5A's known involvement in facilitating interactions between the U2 snRNP complex and ATP-dependent helicases, we examined cancer-specific roles in RNA splicing. We found that in GSCs, but not untransformed controls, PHF5A facilitates recognition of exons with unusual C-rich 3' splice sites in thousands of essential genes. PHF5A knockdown in GSCs, but not untransformed NSCs, astrocytes, or fibroblasts, inhibited splicing of these genes, leading to cell cycle arrest and loss of viability. Notably, pharmacologic inhibition of U2 snRNP activity phenocopied PHF5A knockdown in GSCs and also in NSCs or fibroblasts overexpressing MYC. Furthermore, PHF5A inhibition compromised GSC tumor formation in vivo and inhibited growth of established GBM patient-derived xenograft tumors. Our results demonstrate a novel viability requirement for PHF5A to maintain proper exon recognition in brain tumor-initiating cells and may provide new inroads for novel anti-GBM therapeutic strategies. PMID:23651857

  5. Crystal structure of a core spliceosomal protein interface.

    PubMed

    Schellenberg, Matthew J; Edwards, Ross A; Ritchie, Dustin B; Kent, Oliver A; Golas, Monika M; Stark, Holger; Lührmann, Reinhard; Glover, J N Mark; MacMillan, Andrew M

    2006-01-31

    The precise excision of introns from precursor mRNAs (pre-mRNAs) in eukaryotes is accomplished by the spliceosome, a complex assembly containing five small nuclear ribonucleoprotein (snRNP) particles. Human p14, a component of the spliceosomal U2 and U11/U12 snRNPs, has been shown to associate directly with the pre-mRNA branch adenosine early in spliceosome assembly and within the fully assembled spliceosome. Here we report the 2.5-A crystal structure of a complex containing p14 and a peptide derived from the p14-associated U2 snRNP component SF3b155. p14 contains an RNA recognition motif (RRM), the surface of which is largely occluded by a C-terminal alpha-helix and a portion of the SF3b155 peptide. An analysis of RNA.protein crosslinking to wild-type and mutant p14 shows that the branch adenosine directly interacts with a conserved aromatic within a pocket on the surface of the complex. This result, combined with a comparison of the structure with known RRMs and pseudoRRMs as well as model-building by using the electron cryomicroscopy structure of a spliceosomal U11/U12 di-snRNP, suggests that p14.SF3b155 presents a noncanonical surface for RNA recognition at the heart of the mammalian spliceosome. PMID:16432215

  6. Mass spectrometry and biochemical analysis of RNA polymerase II: targeting by protein phosphatase-1

    PubMed Central

    Jerebtsova, Marina; Klotchenko, Sergei A.; Artamonova, Tatiana O.; Ammosova, Tatiana; Washington, Kareem; Egorov, Vladimir V.; Shaldzhyan, Aram A.; Sergeeva, Maria V.; Zatulovskiy, Evgeny A.; Temkina, Olga A.; Petukhov, Mikhail G.; Vasin, Andrei V.; Khodorkovskii, Mikhail A.; Orlov, Yuri N.

    2011-01-01

    Transcription of eukaryotic genes is regulated by phosphorylation of serine residues of heptapeptide repeats of the carboxyterminal domain (CTD) of RNA polymerase II (RNAPII). We previously reported that protein phosphatase-1 (PP1) dephosphorylates RNAPII CTD in vitro and inhibition of nuclear PP1-blocked viral transcription. In this article, we analyzed the targeting of RNAPII by PP1 using biochemical and mass spectrometry analysis of RNAPII-associated regulatory subunits of PP1. Immunoblotting showed that PP1 co-elutes with RNAPII. Mass spectrometry approach showed the presence of U2 snRNP. Co-immunoprecipitation analysis points to NIPP1 and PNUTS as candidate regulatory subunits. Because NIPP1 was previously shown to target PP1 to U2 snRNP, we analyzed the effect of NIPP1 on RNAPII phosphorylation in cultured cells. Expression of mutant NIPP1 promoted RNAPII phosphorylation suggesting that the deregulation of cellular NIPP1/PP1 holoenzyme affects RNAPII phosphorylation and pointing to NIPP1 as a potential regulatory factor in RNAPII-mediated transcription. PMID:20941529

  7. The Origin of Hard X-rays in M17's Remarkable O4-O4 Binary

    NASA Astrophysics Data System (ADS)

    Gagne, Marc

    2008-09-01

    At 2 kpc M17 is the nearest giant HII region, with 10,000 stars younger than 1 Myr and a prominent X-ray champagne flow. At the heart of M17 are CEN 1A and 1B, a visual pair of O4 stars separated by only 1.8". A long series of ACIS observations show that each O4 star is a very hard time variable X-ray source. We suggest that one or both O4 stars are themselves colliding wind shock binaries or, alternatively, that one or both have strong magnetic fields. We propose to obtain time-resolved, spatially resolved HEG/MEG spectra of both stars to measure He-like line ratios and line profiles to directly test these two models. This roll-constrained 150-ks GO proposal is tied to a 25-ks GTO proposal (PI: Garmire) for the same target.

  8. The Translation Initiation Factor eIF4E Regulates the Sex-Specific Expression of the Master Switch Gene Sxl in Drosophila melanogaster

    PubMed Central

    Graham, Patricia L.; Yanowitz, Judith L.; Penn, Jill K. M.; Deshpande, Girish; Schedl, Paul

    2011-01-01

    In female fruit flies, Sex-lethal (Sxl) turns off the X chromosome dosage compensation system by a mechanism involving a combination of alternative splicing and translational repression of the male specific lethal-2 (msl-2) mRNA. A genetic screen identified the translation initiation factor eif4e as a gene that acts together with Sxl to repress expression of the Msl-2 protein. However, eif4e is not required for Sxl mediated repression of msl-2 mRNA translation. Instead, eif4e functions as a co-factor in Sxl-dependent female-specific alternative splicing of msl-2 and also Sxl pre-mRNAs. Like other factors required for Sxl regulation of splicing, eif4e shows maternal-effect female-lethal interactions with Sxl. This female lethality can be enhanced by mutations in other co-factors that promote female-specific splicing and is caused by a failure to properly activate the Sxl-positive autoregulatory feedback loop in early embryos. In this feedback loop Sxl proteins promote their own synthesis by directing the female-specific alternative splicing of Sxl-Pm pre-mRNAs. Analysis of pre-mRNA splicing when eif4e activity is compromised demonstrates that Sxl-dependent female-specific splicing of both Sxl-Pm and msl-2 pre-mRNAs requires eif4e activity. Consistent with a direct involvement in Sxl-dependent alternative splicing, eIF4E is associated with unspliced Sxl-Pm pre-mRNAs and is found in complexes that contain early acting splicing factors—the U1/U2 snRNP protein Sans-fils (Snf), the U1 snRNP protein U1-70k, U2AF38, U2AF50, and the Wilms' Tumor 1 Associated Protein Fl(2)d—that have been directly implicated in Sxl splicing regulation. PMID:21829374

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

    PubMed Central

    Jacewicz, Agata; Chico, Lidia; Smith, Paul

    2015-01-01

    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. PMID:25587180

  10. 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

  11. 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.

  12. Cross-Talk between Snurportin1 SubdomainsD⃞

    PubMed Central

    Ospina, Jason K.; Gonsalvez, Graydon B.; Bednenko, Janna; Darzynkiewicz, Edward; Gerace, Larry; Matera, A. Gregory

    2005-01-01

    The initial steps of spliceosomal small nuclear ribonucleoprotein (snRNP) maturation take place in the cytoplasm. After formation of an Sm-core and a trimethylguanosine (TMG) cap, the RNPs are transported into the nucleus via the import adaptor snurportin1 (SPN) and the import receptor importin-β. To better understand this process, we identified SPN residues that are required to mediate interactions with TMG caps, importin-β, and the export receptor, exportin1 (Xpo1/Crm1). Mutation of a single arginine residue within the importin-β binding domain (IBB) disrupted the interaction with importin-β, but preserved the ability of SPN to bind Xpo1 or TMG caps. Nuclear transport assays showed that this IBB mutant is deficient for snRNP import but that import can be rescued by addition of purified survival of motor neurons (SMN) protein complexes. Conserved tryptophan residues outside of the IBB are required for TMG binding. However, SPN can be imported into the nucleus without cargo. Interestingly, SPN targets to Cajal bodies when U2 but not U1 snRNPs are imported as cargo. SPN also relocalizes to Cajal bodies upon treatment with leptomycin B. Finally, we uncovered an interaction between the N- and C-terminal domains of SPN, suggesting an autoregulatory function similar to that of importin-α. PMID:16030253

  13. 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

  14. Materials Data on U2Mn12P7 (SG:174) 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

  15. Magnetism and superconductivity in U2PtxRh1-xC2

    DOE PAGESBeta

    Wakeham, N.; Ni, Ni; Bauer, E. D.; Thompson, J. D.; Tegtmeier, E.; Ronning, F.

    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

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

    SciTech Connect

    Kristin Persson

    2015-02-09

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

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... chapter must meet the requirements of this part or, as applicable, the requirements in 49 CFR parts 171... (incorporated by reference; see 46 CFR 54.01-1) and must be stamped with the ASME “U” symbol. These pressure... requirements, section VIII of the ASME Boiler and Pressure Vessel Code (incorporated by reference, see 46...

  18. 46 CFR 54.01-5 - Scope (modifies U-1 and U-2).

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... chapter must meet the requirements of this part or, as applicable, the requirements in 49 CFR parts 171... (incorporated by reference; see 46 CFR 54.01-1) and must be stamped with the ASME “U” symbol. These pressure... requirements, section VIII of the ASME Boiler and Pressure Vessel Code (incorporated by reference, see 46...

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

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... chapter must meet the requirements of this part or, as applicable, the requirements in 49 CFR parts 171... (incorporated by reference; see 46 CFR 54.01-1) and must be stamped with the ASME “U” symbol. These pressure... requirements, section VIII of the ASME Boiler and Pressure Vessel Code (incorporated by reference, see 46...

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

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... chapter must meet the requirements of this part or, as applicable, the requirements in 49 CFR parts 171... (incorporated by reference; see 46 CFR 54.01-1) and must be stamped with the ASME “U” symbol. These pressure... requirements, section VIII of the ASME Boiler and Pressure Vessel Code (incorporated by reference, see 46...

  1. Materials Data on CsU2F9 (SG:1) by Materials Project

    DOE Data Explorer

    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

  2. Materials Data on Rb6U2W4O21 (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

  3. Ampelopsin suppresses TNF-α-induced migration and invasion of U2OS osteosarcoma cells.

    PubMed

    Liu, Changying; Zhao, Pengfei; Yang, Yubao; Xu, Xiaodong; Wang, Liang; Li, Bo

    2016-06-01

    Ampelopsin has been suggested as a novel anticancer agent, however, there is no evidence regarding its direct effect on the migration and invasion of osteosarcoma cells. The aims of the present study were to investigate the influence of ampelopsin on the migration and invasion of osteosarcoma cells and to clarify the underlying mechanisms. Scratch wound healing and Transwell assays were used to measure the migratory and invasive activities of the cells, respectively. The protein and RNA levels of matrix metalloproteinase-2 (MMP-2) were detected with western blot and RT-qPCR, respectively, following stimulation with tumor necrosis factor‑α (TNF-α) and ampelopsin. The expression levels of phospho‑ and total-p38MAPK were detected using western blot analysis. Additionally, SB203580, an inhibitor of p38MAPK, was used to investigate the effect of TNF‑α and ampelopsin. The results demonstrated that TNF‑α upregulated the expression level of MMP‑2 and promoted the migration and invasion of osteosarcoma cells. TNF‑α also activated the p38MAPK pathway, and SB203580 significantly inhibited the effect of TNF‑α on MMP‑2 expression. The application of ampelopsin abolished the effects of TNF‑α on the activation of the p38MAPK pathway and the expression of MMP‑2, and downregulated the migration and invasion of the osteosarcoma cells. These results demonstrated that ampelopsin inhibits the TNF‑α‑induced migration and invasion of osteosarcoma cells, and that the effect of ampelopsin was mediated by p38MAPK/MMP‑2 signaling. PMID:27082056

  4. Materials Data on U2Ni2Sn (SG:127) by Materials Project

    SciTech Connect

    Kristin Persson

    2015-01-27

    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 U2Fe2Sn (SG:127) by Materials Project

    SciTech Connect

    Kristin Persson

    2015-02-09

    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

  6. Materials Data on U2SnRu2 (SG:127) by Materials Project

    SciTech Connect

    Kristin Persson

    2015-02-09

    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

  7. Materials Data on U2SnPd2 (SG:127) by Materials Project

    SciTech Connect

    Kristin Persson

    2015-02-09

    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

  8. Materials Data on U2Co2Sn (SG:127) by Materials Project

    SciTech Connect

    Kristin Persson

    2015-02-09

    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

  9. Materials Data on U2Se3 (SG:62) by Materials Project

    DOE Data Explorer

    Kristin Persson

    2015-01-27

    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 U2Bi2O7 (SG:51) 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

  11. Materials Data on U2Al3Os (SG:194) by Materials Project

    SciTech Connect

    Kristin Persson

    2015-02-09

    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

  12. Materials Data on U2Ni12P7 (SG:174) 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

  13. Critical experiments on low-enriched uranium oxide systems with H/U = 2. 03

    SciTech Connect

    Rothe, R E; Goebel, G R

    1982-02-01

    Seven critical experiments were performed on a horizontal split table machine using 4.48% enriched /sup 235/U uranium oxide (U/sub 3/O/sub 8/). The oxide was compacted to a density of 4.68 g/cm/sup 3/ and placed in 152-mm cubical aluminum cans. Water was added to achieve an H/U atomic ratio of 2.03. Various arrays of oxide cans were distributed on each half of the split table and the separation between halves reduced until criticality occurred. The critical table separation varied from 4.3 mm to 29.3 mm. These experiments were performed in both plastic and concrete reflectors. The first five experiments required the addition of a high-enriched (approx. 93% /sup 235/U) metal driver to achieve criticality. Critical uranium driver masses ranged from 2.765 kg to 13.730 kg for 5 x 5 x 5 arrays of uranium oxide cans. In all five cases, the center can of the array was deleted to accommodate the driver. The uranium oxide mass was 1859.6 kg. Two additional experiments in the plastic reflector contained either 9.3-mm- or 24.3-mm-thick plastic moderator material between the oxide cans. These latter experiments did not require a driver to achieve criticality; and the uranium oxide mass was 723.9 kg for the configuration having the thinner interstitial moderator and 452.4 kg for the other.

  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 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

  16. 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

  17. Materials Data on U2AlCo3 (SG:194) by Materials Project

    SciTech Connect

    Kristin Persson

    2015-03-08

    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 U2PS (SG:141) by Materials Project

    SciTech Connect

    Kristin Persson

    2015-04-12

    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 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

  20. 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

  1. The Stem-Loop Binding Protein (SLBP1) Is Present in Coiled Bodies of the Xenopus Germinal Vesicle

    PubMed Central

    Abbott, Jennifer; Marzluff, William F.; Gall, Joseph G.

    1999-01-01

    The stem-loop binding protein (SLBP1) binds the 3′ stem-loop of histone pre-mRNA and is required for efficient processing of histone transcripts in the nucleus. We examined the localization of SLBP1 in the germinal vesicle of Xenopus laevis oocytes. In spread preparations of germinal vesicle contents, an anti-SLBP1 antibody stained coiled bodies and specific chromosomal loci, including terminal granules, axial granules, and some loops. After injection of myc-tagged SLBP1 transcripts into the oocyte cytoplasm, newly translated myc-SLBP1 protein was detectable in coiled bodies within 4 h and in terminal and axial granules by 8 h. To identify the region(s) of SLBP1 necessary for subnuclear localization, we subcloned various parts of the SLBP1 cDNA and injected transcripts of these into the cytoplasm of oocytes. We determined that 113 amino acids at the carboxy terminus of SLBP1 are sufficient for coiled body localization and that disruption of a previously defined RNA-binding domain did not alter this localization. Coiled bodies also contain the U7 small nuclear ribonucleoprotein particle (snRNP), which participates in cleavage of the 3′ end of histone pre-mRNA. The colocalization of SLBP1 and the U7 snRNP in the coiled body suggests coordinated control of their functions, perhaps through a larger histone-processing particle. Some coiled bodies are attached to the lampbrush chromosomes at the histone gene loci, consistent with the view that coiled bodies in the oocyte recruit histone-processing factors to the sites of histone pre-mRNA transcription. The non-histone chromosomal sites at which SLBP1 is found include the genes coding for 5 S rRNA, U1 snRNA, and U2 snRNA, suggesting a wider role for SLBP1 in the biosynthesis of small non-spliced RNAs. PMID:9950690

  2. Structural model of the p14/SF3b155·branch duplex complex

    PubMed Central

    Schellenberg, Matthew J.; Dul, Erin L.; MacMillan, Andrew M.

    2011-01-01

    Human p14 (SF3b14), a component of the spliceosomal U2 snRNP, interacts directly with the pre-mRNA branch adenosine within the context of the bulged duplex formed between the pre-mRNA branch region and U2 snRNA. This association occurs early in spliceosome assembly and persists within the fully assembled spliceosome. Analysis of the crystal structure of a complex containing p14 and a peptide derived from p14-associated SF3b155 combined with the results of cross-linking studies has suggested that the branch nucleotide interacts with a pocket on a non-canonical RNA binding surface formed by the complex. Here we report a structural model of the p14•bulged duplex interaction based on a combination of X-ray crystallography of an adenine p14/SF3b155 peptide complex, biochemical comparison of a panel of disulfide cross-linked protein–RNA complexes, and small-angle X-ray scattering (SAXS). These studies reveal specific recognition of the branch adenosine within the p14 pocket and establish the orientation of the bulged duplex RNA bound on the protein surface. The intimate association of one surface of the bulged duplex with the p14/SF3b155 peptide complex described by this model buries the branch nucleotide at the interface and suggests that p14•duplex interaction must be disrupted before the first step of splicing. PMID:21062891

  3. 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

  4. 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

  5. A Targeted Oligonucleotide Enhancer of SMN2 Exon 7 Splicing Forms Competing Quadruplex and Protein Complexes in Functional Conditions

    PubMed Central

    Smith, Lindsay D.; Dickinson, Rachel L.; Lucas, Christian M.; Cousins, Alex; Malygin, Alexey A.; Weldon, Carika; Perrett, Andrew J.; Bottrill, Andrew R.; Searle, Mark S.; Burley, Glenn A.; Eperon, Ian C.

    2014-01-01

    Summary The use of oligonucleotides to activate the splicing of selected exons is limited by a poor understanding of the mechanisms affected. A targeted bifunctional oligonucleotide enhancer of splicing (TOES) anneals to SMN2 exon 7 and carries an exonic splicing enhancer (ESE) sequence. We show that it stimulates splicing specifically of intron 6 in the presence of repressing sequences in intron 7. Complementarity to the 5′ end of exon 7 increases U2AF65 binding, but the ESE sequence is required for efficient recruitment of U2 snRNP. The ESE forms at least three coexisting discrete states: a quadruplex, a complex containing only hnRNP F/H, and a complex enriched in the activator SRSF1. Neither hnRNP H nor quadruplex formation contributes to ESE activity. The results suggest that splicing limited by weak signals can be rescued by rapid exchange of TOES oligonucleotides in various complexes and raise the possibility that SR proteins associate transiently with ESEs. PMID:25263560

  6. 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.

  7. 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.

  8. Materials Data on CsU2H3(C2O7)2 (SG:11) 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

  9. Materials Data on RbU2H5C4O15 (SG:11) by Materials Project

    SciTech Connect

    Kristin Persson

    2014-10-02

    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

  10. Sound velocity measurement of nuclear-ordered U2D2 solid 3He along the melting curve

    NASA Astrophysics Data System (ADS)

    Nomura, R.; Suzuki, M.; Yamaguchi, M.; Sasaki, Y.; Mizusaki, T.

    2000-05-01

    The sound velocity of a single-domain 3He crystal was measured in the nuclear-ordered low-field phase and the paramagnetic phase along the melting curve, using 10.98 MHz longitudinal sound. The temperature dependence of the sound velocity along the melting curve was explained by a nuclear spin contribution and the molar volume change along the melting curve. By comparing the measured velocity with thermodynamic quantities, we extracted the Grüneizen constant for the exchange energy. The anisotropy of the velocity in the ordered phase was investigated for three samples and was found to be smaller than 2×10 -5 in Δ v/ v. The attenuation coefficient of the sound was much smaller than 0.2 cm-1.

  11. Materials Data on U2Si(H2O5)2 (SG:70) 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

  12. Materials Data on U2CuAs2(H4O5)4 (SG:85) 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

  13. Direct containment heating experiments in Zion Nuclear Power Plant Geometry using prototypic core materials, the U2 test

    SciTech Connect

    Binder, J.L.; McUmber, L.M.; Spencer, B.W.

    1993-05-01

    A third Direct Containment Heating (DCH) experiments has been completed which utilizes prototypic core materials. The reactor material tests are a follow on to the Integral Effects Testing (IET) DCH program. The IET series of tests primarily addressed the effect of scale on DCH phenomena. This was accomplished by completing a series of counterpart tests in 1/40 and 1/10th linear scale DCH facilities at Argonne National Laboratory (ANL) and Sandia National Laboratories (SNL), respectively. The IET experiments modeled the Zion Nuclear Power Plant Geometry. The scale models included representations of the primary system volume, RPV lower head, cavity and instrument tunnel, and the lower containment structures. The experiments were steam driven at nominally 6.2 MPa. Iron-alumina thermite with chromium was used as a core melt simulant in the IET experiments. While the IET experiments at ANL and SNL provided useful data on the effect of scale on DCH phenomena, a significant question concerns the potential experiment distortions introduced by the use of non-prototypic iron/alumina thermite. Therefore, further testing with prototypic materials has been carried out at ANL. A prototypic core melt was produced for the experiment by first mixing powders of uranium, zirconium, iron oxide (Fe{sub 2}O{sub 3}), and chromium trioxide (CrO{sub 3}). When ignited the powders react exothermically to produce a molten mixture. The amounts of each powder were selected to produce the anticipated composition for a core melt following a station blackout: 57.8 mass% UO{sub 2} 10.5 mass% ZrO{sub 2} 14.3 mass% Fe, 13.7 mass% Zr, and 3.7 mass% Cr. Development tests measured the initial melt temperature to be in the range of 2600 - 2700 K. The total thermal specific energy content of the melt at 2700 K is 1.2 MJ/kg compared to 2.25 MJ/kg for the iron-alumina simulant at its measured initial temperature of 2500 K.

  14. Recognition of Trimethylated Histone H3 Lysine 4 Facilitates the Recruitment of Transcription Post-Initiation Factors and pre-mRNA Splicing

    PubMed Central

    Sims, Robert J.; Millhouse, Scott; Chen, Chi-Fu; Lewis, Brian A.; Erdjument-Bromage, Hediye; Tempst, Paul; Manley, James L.; Reinberg, Danny

    2007-01-01

    Tri-methylation of histone H3 on lysine 4 (H3K4me3) localizes near the 5′ region of genes and is tightly associated with active loci. Several proteins, such as CHD1, BPTF, JMJD2A, and the ING tumor suppressor family, directly recognize this lysine methyl mark. However, how H3K4me3 recognition participates in active transcription remains poorly characterized. Here we identify specific CHD1-interacting proteins via H3K4me3 affinity purification, including numerous factors mediating post-initiation events. Conventional biochemical purification revealed a stable complex between CHD1 and components of the spliceosome. Depletion of CHD1 in extracts dramatically reduced splicing efficiency in vitro, indicating a functional link between CHD1 and the spliceosome. Knockdown of CHD1 and H3K4me3 levels by siRNA reduced association of U2 snRNP components with chromatin, and more importantly, altered the efficiency of pre-mRNA splicing on active genes in vivo. These findings suggest that methylated H3K4 serves to facilitate the competency of pre-mRNA maturation through the bridging of spliceosomal components to H3K4me3 via CHD1. PMID:18042460

  15. Structure of a yeast spliceosome at 3.6-angstrom resolution.

    PubMed

    Yan, Chuangye; Hang, Jing; Wan, Ruixue; Huang, Min; Wong, Catherine C L; Shi, Yigong

    2015-09-11

    Splicing of precursor messenger RNA (pre-mRNA) in yeast is executed by the spliceosome, which consists of five small nuclear ribonucleoproteins (snRNPs), NTC (nineteen complex), NTC-related proteins (NTR), and a number of associated enzymes and cofactors. Here, we report the three-dimensional structure of a Schizosaccharomyces pombe spliceosome at 3.6-angstrom resolution, revealed by means of single-particle cryogenic electron microscopy. This spliceosome contains U2 and U5 snRNPs, NTC, NTR, U6 small nuclear RNA, and an RNA intron lariat. The atomic model includes 10,574 amino acids from 37 proteins and four RNA molecules, with a combined molecular mass of approximately 1.3 megadaltons. Spp42 (Prp8 in Saccharomyces cerevisiae), the key protein component of the U5 snRNP, forms a central scaffold and anchors the catalytic center. Both the morphology and the placement of protein components appear to have evolved to facilitate the dynamic process of pre-mRNA splicing. Our near-atomic-resolution structure of a central spliceosome provides a molecular framework for mechanistic understanding of pre-mRNA splicing. PMID:26292707

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

    PubMed Central

    2014-01-01

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

  17. Pressure-induced electronic and magnetic phase transitions in a Mott insulator: Ti-doped C a3R u2O7 bilayer ruthenate

    NASA Astrophysics Data System (ADS)

    Zou, T.; Cao, H. B.; Liu, G. Q.; Peng, J.; Gottschalk, M.; Zhu, M.; Zhao, Y.; Leão, J. B.; Tian, W.; Mao, Z. Q.; Ke, X.

    2016-07-01

    We report the hydrostatic pressure-induced electronic and magnetic phase transitions in a Mott insulator, a bilayer ruthenate C a3(Ru0.97Ti0.03 ) 2O7 , via electronic transport and single crystal neutron diffraction measurements. The system undergoes an insulator-metal transition at a very small hydrostatic pressure ≈0.04 GPa, followed by a magnetic phase transition around 0.3 GPa, suggesting that the low energy charge fluctuation and magnetic ordering couple to the pressure separately in this compound. The a b initio calculations show that the suppressed Ru O6 flattening induced by the pressure reduces the orbital polarization and gives rise to an insulator-metal transition preceding the magnetic phase transition.

  18. 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

  19. Structure and novel functional mechanism of Drosophila SNF in sex-lethal splicing.

    PubMed

    Hu, Jicheng; Cui, Gaofeng; Li, Congmin; Liu, Cong; Shang, Erchang; Lai, Luhua; Jin, Changwen; Wang, Jiwu; Xia, Bin

    2009-01-01

    Sans-fille (SNF) is the Drosophila homologue of mammalian general splicing factors U1A and U2B'', and it is essential in Drosophila sex determination. We found that, besides its ability to bind U1 snRNA, SNF can also bind polyuridine RNA tracts flanking the male-specific exon of the master switch gene Sex-lethal (Sxl) pre-mRNA specifically, similar to Sex-lethal protein (SXL). The polyuridine RNA binding enables SNF directly inhibit Sxl exon 3 splicing, as the dominant negative mutant SNF(1621) binds U1 snRNA but not polyuridine RNA. Unlike U1A, both RNA recognition motifs (RRMs) of SNF can recognize polyuridine RNA tracts independently, even though SNF and U1A share very high sequence identity and overall structure similarity. As SNF RRM1 tends to self-associate on the opposite side of the RNA binding surface, it is possible for SNF to bridge the formation of super-complexes between two introns flanking Sxl exon 3 or between a intron and U1 snRNP, which serves the molecular basis for SNF to directly regulate Sxl splicing. Taken together, a new functional model for SNF in Drosophila sex determination is proposed. The key of the new model is that SXL and SNF function similarly in promoting Sxl male-specific exon skipping with SNF being an auxiliary or backup to SXL, and it is the combined dose of SXL and SNF governs Drosophila sex determination. PMID:19727396

  20. In vitro assembly of coiled bodies in Xenopus egg extract.

    PubMed Central

    Bauer, D W; Murphy, C; Wu, Z; Wu, C H; Gall, J G

    1994-01-01

    When demembranated sperm nuclei are placed in a Xenopus egg extract, they become surrounded by a nuclear envelope and then swell to form morphologically typical pronuclei. Granules ranging from < 1.0 to approximately 3.0 microns in diameter appear within such nuclei. Bell et al. identified four nucleolar proteins in these "prenucleolar bodies" by immunofluorescent staining (fibrillarin, nucleolin, B23/NO38, 180-kDa nucleolar protein). By in situ hybridization we show that these bodies also contain U3 and U8 small nuclear RNAs (snRNAs), known to be involved in pre-rRNA processing. Moreover, they contain all the snRNAs involved in pre-mRNA splicing (U1, U2, U4, U5, and U6), as well as U7, which is required for histone pre-mRNA 3' end formation. In addition to the nucleolar antigens previously identified, we demonstrated staining with antibodies against the Sm epitope, trimethylguanosine, and coilin. Because the composition of these prenucleolar bodies is closer to that of coiled bodies than to nucleoli, we propose that they be referred to as coiled bodies. The existence of large coiled bodies in transcriptionally inactive pronuclei suggests that they may play a role in the import, assembly, and storage of RNA processing components but are not themselves sites of processing. In transcriptionally active nuclei coiled bodies could serve as sites for initial preassembly and distribution of snRNP complexes for the three major RNA processing pathways: pre-mRNA splicing, pre-rRNA processing, and histone pre-mRNA 3' end formation. Images PMID:7949420

  1. 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.

  2. Analysis of spliceosomal proteins in Trypanosomatids reveals novel functions in mRNA processing.

    PubMed

    Tkacz, Itai Dov; Gupta, Sachin Kumar; Volkov, Vadim; Romano, Mali; Haham, Tomer; Tulinski, Pawel; Lebenthal, Ilana; Michaeli, Shulamit

    2010-09-01

    In trypanosomatids, all mRNAs are processed via trans-splicing, although cis-splicing also occurs. In trans-splicing, a common small exon, the spliced leader (SL), which is derived from a small SL RNA species, is added to all mRNAs. Sm and Lsm proteins are core proteins that bind to U snRNAs and are essential for both these splicing processes. In this study, SmD3- and Lsm3-associated complexes were purified to homogeneity from Leishmania tarentolae. The purified complexes were analyzed by mass spectrometry, and 54 and 39 proteins were purified from SmD3 and Lsm complexes, respectively. Interestingly, among the proteins purified from Lsm3, no mRNA degradation factors were detected, as in Lsm complexes from other eukaryotes. The U1A complex was purified and mass spectrometry analysis identified, in addition to U1 small nuclear ribonucleoprotein (snRNP) proteins, additional co-purified proteins, including the polyadenylation factor CPSF73. Defects observed in cells silenced for U1 snRNP proteins suggest that the U1 snRNP functions exclusively in cis-splicing, although U1A also participates in polyadenylation and affects trans-splicing. The study characterized several trypanosome-specific nuclear factors involved in snRNP biogenesis, whose function was elucidated in Trypanosoma brucei. Conserved factors, such as PRP19, which functions at the heart of every cis-spliceosome, also affect SL RNA modification; GEMIN2, a protein associated with SMN (survival of motor neurons) and implicated in selective association of U snRNA with core Sm proteins in trypanosomes, is a master regulator of snRNP assembly. This study demonstrates the existence of trypanosomatid-specific splicing factors but also that conserved snRNP proteins possess trypanosome-specific functions. PMID:20592024

  3. (1'S,12'R,13'S,17'S)-15',15'-Dimethyl-1,2-dihydro-11',14',16',18'-tetra-oxa-7'-aza-spiro-[indole-3,8'-penta-cyclo-[10.6.0.0(2,9).0(3,7).0(13,17)]octa-deca-ne]-2,10'-dione.

    PubMed

    Sabari, V; Ponnusamy, R; Prasanna, R; Raghunathan, R; Aravindhan, S

    2013-04-01

    In the title compound, C22H24N2O6, the indole ring has a twist conformation and the tetra-hydro-2H-pyran-2-one ring a half-chair conformation. One of the pyrrolidine rings adopts an envelope conformation on the N atom, while the other has a twist conformation; the 'butterfly' angle between their mean planes is 62.98 (11)°. The dioxolane ring adopts a twist conformation and the tetra-hydro-furan ring has an envelope conformation on the C atom in the fused tetra-hydro-2H-pyran-2-one ring adjacent to the O atom of the tetra-hydro-furan ring. The 'butterfly' angle between the mean planes of these two five-membered rings is 69.14 (10)°. In the crystal, mol-ecules are linked by N-H⋯O hydrogen bonds, forming chains along the a axis. PMID:23634025

  4. Crystallization and biochemical characterization of the human spliceosomal Aar2-Prp8(RNaseH) complex.

    PubMed

    Santos, Karine; Preussner, Marco; Heroven, Anna Christina; Weber, Gert

    2015-11-01

    In eukaryotes, the removal of nuclear noncoding sequences (pre-mRNA splicing) is catalyzed by the spliceosome, which consists of five ribonucleoprotein particles (U1, U2, U4, U5 and U6 snRNPs, each with a respective snRNA) and a plethora of protein factors that aid spliceosomal maturation, assembly, activation and disassembly. Recently, the U5 snRNP maturation factor Aar2p from baker's yeast has been characterized structurally and biochemically. Aar2p binds to the RNaseH (RH) and Jab1/MPN domains of the highly conserved U5-specific Prp8p, which forms a framework for the spliceosomal catalytic centre. Thereby, Aar2p sterically excludes Brr2p, a helicase essential for the catalytic activation of the spliceosome, from Prp8p binding. At the same time, Aar2p blocks U4/U6 di-snRNA binding to Prp8p. Aar2p therefore prevents premature spliceosome activation and its functions are regulated by reversible phosphorylation. To date, little is known about the hypothetical human Aar2 (hsAar2) orthologue C20ORF4. This study identifies C20ORF4 (i) as part of the HeLa proteome by Western blotting and (ii) as a true Aar2 orthologue which binds to the RH domain (hsRH) of Prp8 and corroborates an evolutionary link between yeast and human Aar2 function. An elaborate strategy was devised to crystallize hsAar2 in complex with hsRH. The analysis of initial weakly diffracting crystals obtained by in situ proteolysis and homology modelling guided the design of an hsAar2 construct in which an internal loop was replaced by three serines (hsAar2(Δloop)). A complex of hsAar2(Δloop) and hsRH crystallized in space group C2; the crystals diffracted to 2.35 Å resolution and were suitable for structure determination by molecular-replacement approaches. The study presented here suggests a connection between Aar2 and the spliceosome in human cells and paves the way for structural studies of human Aar2. PMID:26527271

  5. U1 small nuclear ribonucleoprotein complex and RNA splicing alterations in Alzheimer's disease.

    PubMed

    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

    2013-10-01

    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

  6. High-density genetic map of the BRCA1 region of chromosome 17q12-q21

    SciTech Connect

    Anderson, L.A.; Friedman, L.; Lynch, E.; King, M.C. ); Osborne-Lawrence, S.; Bowcock, A. ); Weissenbach, J. )

    1993-09-01

    To facilitate the positional cloning of the breast-ovarian cancer gene BRCA1, the authors constructed a high-density genetic map of the 8.3-cM interval between D17S250 and GIP on chromosome 17q12-q21. Markers were mapped by linkage in the CEPH and in extended kindreds in the breast cancer series. The map comprises 33 ordered polymorphisms, including 12 genes and 21 anonymous markers, yielding an average of one polymorphism every 250 kb. Twenty-five of the markers are PCR-based systems. The order of polymorphic genes and markers is cen-D17S250-D17S518-HER2-THRA1-RARA-D17S80-KRT10-[D17S800-D17S857]-GAS-D17S856-EDH17B-D17S855-D17S859-D17S858-[PPY-D17S78]-D17S183-EPB3-D17S579-D17S509-[D17S508-D17S190 = D17S810]-D17S791-[D17S181 = D17S806]-D17S797-HOX2B-GP3A-[D17S507 = GIP]-qter. BRCA1 lies in the middle of the interval, between THRA1 and D17S183. Markers from this map can be used to determine whether cancer is linked to BRCA1 in families, to evaluate whether tumors have lost heterozygosity at loci in the region, and to identify probes for characterizing chromosomal rearrangements from patients and from tumors. 21 refs., 1 fig., 3 tabs.

  7. Highly variable cancer subpopulations that exhibit enhanced transcriptome variability and metastatic fitness.

    PubMed

    Nguyen, Alexander; Yoshida, Mitsukuni; Goodarzi, Hani; Tavazoie, Sohail F

    2016-01-01

    Individual cells within a tumour can exhibit distinct genetic and molecular features. The impact of such diversification on metastatic potential is unknown. Here we identify clonal human breast cancer subpopulations that display different levels of morphological and molecular diversity. Highly variable subpopulations are more proficient at metastatic colonization and chemotherapeutic survival. Through single-cell RNA-sequencing, inter-cell transcript expression variability is identified as a defining feature of the highly variable subpopulations that leads to protein-level variation. Furthermore, we identify high variability in the spliceosomal machinery gene set. Engineered variable expression of the spliceosomal gene SNRNP40 promotes metastasis, attributable to cells with low expression. Clinically, low SNRNP40 expression is associated with metastatic relapse. Our findings reveal transcriptomic variability generation as a mechanism by which cancer subpopulations can diversify gene expression states, which may allow for enhanced fitness under changing environmental pressures encountered during cancer progression. PMID:27138336

  8. Highly variable cancer subpopulations that exhibit enhanced transcriptome variability and metastatic fitness

    PubMed Central

    Nguyen, Alexander; Yoshida, Mitsukuni; Goodarzi, Hani; Tavazoie, Sohail F.

    2016-01-01

    Individual cells within a tumour can exhibit distinct genetic and molecular features. The impact of such diversification on metastatic potential is unknown. Here we identify clonal human breast cancer subpopulations that display different levels of morphological and molecular diversity. Highly variable subpopulations are more proficient at metastatic colonization and chemotherapeutic survival. Through single-cell RNA-sequencing, inter-cell transcript expression variability is identified as a defining feature of the highly variable subpopulations that leads to protein-level variation. Furthermore, we identify high variability in the spliceosomal machinery gene set. Engineered variable expression of the spliceosomal gene SNRNP40 promotes metastasis, attributable to cells with low expression. Clinically, low SNRNP40 expression is associated with metastatic relapse. Our findings reveal transcriptomic variability generation as a mechanism by which cancer subpopulations can diversify gene expression states, which may allow for enhanced fitness under changing environmental pressures encountered during cancer progression. PMID:27138336

  9. Regulation of CDK9 activity by phosphorylation and dephosphorylation.

    PubMed

    Nekhai, Sergei; Petukhov, Michael; Breuer, Denitra

    2014-01-01

    HIV-1 transcription is regulated by CDK9/cyclin T1, which, unlike a typical cell cycle-dependent kinase, is regulated by associating with 7SK small nuclear ribonuclear protein complex (snRNP). While the protein components of this complex are well studied, the mechanism of the complex formation is still not fully understood. The association of CDK9/cyclin T1 with 7SK snRNP is, in part, regulated by a reversible CDK9 phosphorylation. Here, we present a comprehensive review of the kinases and phosphatases involved in CDK9 phosphorylation and discuss their role in regulation of HIV-1 replication and potential for being targeted for drug development. We propose a novel pathway of HIV-1 transcription regulation via CDK9 Ser-90 phosphorylation by CDK2 and CDK9 Ser-175 dephosphorylation by protein phosphatase-1. PMID:24524087

  10. The importin-β binding domain of snurportin1 is responsible for the Ran- and energy-independent nuclear import of spliceosomal U snRNPs in vitro

    PubMed Central

    Huber, Jochen; Dickmanns, Achim; Lührmann, Reinhard

    2002-01-01

    The nuclear localization signal (NLS) of spliceosomal U snRNPs is composed of the U snRNA's 2,2,7-trimethyl-guanosine (m3G)-cap and the Sm core domain. The m3G-cap is specifically bound by snurportin1, which contains an NH2-terminal importin-β binding (IBB) domain and a COOH-terminal m3G-cap–binding region that bears no structural similarity to known import adaptors like importin-α (impα). Here, we show that recombinant snurportin1 and importin-β (impβ) are not only necessary, but also sufficient for U1 snRNP transport to the nuclei of digitonin-permeabilized HeLa cells. In contrast to impα–dependent import, single rounds of U1 snRNP import, mediated by the nuclear import receptor complex snurportin1–impβ, did not require Ran and energy. The same Ran- and energy-independent import was even observed for U5 snRNP, which has a molecular weight of more than one million. Interestingly, in the presence of impβ and a snurportin1 mutant containing an impα IBB domain (IBBimpα), nuclear U1 snRNP import was Ran dependent. Furthermore, β-galactosidase (βGal) containing a snurportin1 IBB domain, but not IBBimpα-βGal, was imported into the nucleus in a Ran-independent manner. Our results suggest that the nature of the IBB domain modulates the strength and/or site of interaction of impβ with nucleoporins of the nuclear pore complex, and thus whether or not Ran is required to dissociate these interactions. PMID:11815630

  11. A Bidirectional SF2/ASF- and SRp40-Dependent Splicing Enhancer Regulates Human Immunodeficiency Virus Type 1 rev, env, vpu, and nef Gene Expression

    PubMed Central

    Caputi, Massimo; Freund, Marcel; Kammler, Susanne; Asang, Corinna; Schaal, Heiner

    2004-01-01

    The integrated human immunodeficiency virus type 1 (HIV-1) genome is transcribed in a single pre-mRNA that is alternatively spliced into more than 40 mRNAs. We characterized a novel bidirectional exonic splicing enhancer (ESE) that regulates the expression of the HIV-1 env, vpu, rev, and nef mRNAs. The ESE is localized downstream of the vpu-, env-, and nef-specific 3′ splice site no. 5. SF2/ASF and SRp40 activate the ESE and are required for efficient 3′ splice site usage and binding of the U1 snRNP to the downstream 5′ splice site no. 4. U1 snRNP binding to the 5′ splice site no. 4 is required for splicing of the rev and nef mRNAs and to increase expression of the partially spliced env mRNA. Finally, our results indicate that this ESE is necessary for the recruitment of the U1 snRNP to the 5′ splice site no. 4, even when the 5′ splice site and the U1 snRNA have been mutated to obtain a perfect complementary match. The ESE characterized here is highly conserved in most viral subtypes. PMID:15163745

  12. Crystal structure of (acetato-κO)(ethanol-κO)[(9S,17S,21S,29S)-9,17,21,29-tetra­hydroxy-18,30-dioxa­octa­cyclo­[18.10.0.02,7.08,19.09,17.011,16.021,29.023,28]triaconta-1,3,5,7,11(16),12,14,19,23(28),24,26-undeca­ene-10,22-dione-κ3 O 18,O 21,O 22]caesium ethanol monosolvate

    PubMed Central

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

    2016-01-01

    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 inter­molecular inter­actions with the multiple oxygen-containing functional groups of the ligand, as well as O—H⋯O hydrogen bonds involving the ethanol solvent mol­ecules, stabilize the complex, forming a chain along [100]. Additional parallel-displaced π–π stacking, with an inter­planar distance of 3.669 (1) Å, connect several unit cells in a three-dimensional supra­molecular 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. PMID:27555923

  13. 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. PMID:27555923

  14. Structural features important for the U12 snRNA binding and minor spliceosome assembly of Arabidopsis U11/U12-small nuclear ribonucleoproteins.

    PubMed

    Park, Su Jung; Jung, Hyun Ju; Nguyen Dinh, Sy; Kang, Hunseung

    2016-07-01

    Although seven proteins unique to U12 intron-specific minor spliceosomes, denoted as U11/U12-65K, -59K, -48K, -35K, -31K, -25K, and -20K, have been identified in humans and the roles of some of them have been demonstrated, the functional role of most of these proteins in plants is not understood. A recent study demonstrated that Arabidopsis U11/U12-65K is essential for U12 intron splicing and normal plant development. However, the structural features and sequence motifs important for 65 K binding to U12 snRNA and other spliceosomal proteins remain unclear. Here, we demonstrated by domain-deletion analysis that the C-terminal region of the 65 K protein bound specifically to the stem-loop III of U12 snRNA, whereas the N-terminal region of the 65 K protein was responsible for interacting with the 59 K protein. Analysis of the interactions between each snRNP protein using yeast two-hybrid analysis and in planta bimolecular fluorescence complementation and luciferase complementation imaging assays demonstrated that the core interactions among the 65 K, 59 K, and 48 K proteins were conserved between plants and animals, and multiple interactions were observed among the U11/U12-snRNP proteins. Taken together, these results reveal that U11/U12-65K is an indispensible component of the minor spliceosome complex by binding to both U11/U12-59K and U12 snRNA, and that multiple interactions among the U11/U12-snRNP proteins are necessary for minor spliceosome assembly. PMID:27232356

  15. Suppressors of a cold-sensitive mutation in yeast U4 RNA define five domains in the splicing factor Prp8 that influence spliceosome activation.

    PubMed Central

    Kuhn, A N; Brow, D A

    2000-01-01

    The highly conserved splicing factor Prp8 has been implicated in multiple stages of the splicing reaction. However, assignment of a specific function to any part of the 280-kD U5 snRNP protein has been difficult, in part because Prp8 lacks recognizable functional or structural motifs. We have used a large-scale screen for Saccharomyces cerevisiae PRP8 alleles that suppress the cold sensitivity caused by U4-cs1, a mutant U4 RNA that blocks U4/U6 unwinding, to identify with high resolution five distinct regions of PRP8 involved in the control of spliceosome activation. Genetic interactions between two of these regions reveal a potential long-range intramolecular fold. Identification of a yeast two-hybrid interaction, together with previously reported results, implicates two other regions in direct and indirect contacts to the U1 snRNP. In contrast to the suppressor mutations in PRP8, loss-of-function mutations in the genes for two other splicing factors implicated in U4/U6 unwinding, Prp44 (Brr2/Rss1/Slt22/Snu246) and Prp24, show synthetic enhancement with U4-cs1. On the basis of these results we propose a model in which allosteric changes in Prp8 initiate spliceosome activation by (1) disrupting contacts between the U1 snRNP and the U4/U6-U5 tri-snRNP and (2) orchestrating the activities of Prp44 and Prp24. PMID:10924465

  16. Studies of the 5' exonuclease and endonuclease activities of CPSF-73 in histone pre-mRNA processing.

    PubMed

    Yang, Xiao-cui; Sullivan, Kelly D; Marzluff, William F; Dominski, Zbigniew

    2009-01-01

    Processing of histone pre-mRNA requires a single 3' endonucleolytic cleavage guided by the U7 snRNP that binds downstream of the cleavage site. Following cleavage, the downstream cleavage product (DCP) is rapidly degraded in vitro by a nuclease that also depends on the U7 snRNP. Our previous studies demonstrated that the endonucleolytic cleavage is catalyzed by the cleavage/polyadenylation factor CPSF-73. Here, by using RNA substrates with different nucleotide modifications, we characterize the activity that degrades the DCP. We show that the degradation is blocked by a 2'-O-methyl nucleotide and occurs in the 5'-to-3' direction. The U7-dependent 5' exonuclease activity is processive and continues degrading the DCP substrate even after complete removal of the U7-binding site. Thus, U7 snRNP is required only to initiate the degradation. UV cross-linking studies demonstrate that the DCP and its 5'-truncated version specifically interact with CPSF-73, strongly suggesting that in vitro, the same protein is responsible for the endonucleolytic cleavage of histone pre-mRNA and the subsequent degradation of the DCP. By using various RNA substrates, we define important space requirements upstream and downstream of the cleavage site that dictate whether CPSF-73 functions as an endonuclease or a 5' exonuclease. RNA interference experiments with HeLa cells indicate that degradation of the DCP does not depend on the Xrn2 5' exonuclease, suggesting that CPSF-73 degrades the DCP both in vitro and in vivo. PMID:18955505

  17. U1 small nuclear RNA variants differentially form ribonucleoprotein particles in vitro.

    PubMed

    Somarelli, Jason A; Mesa, Annia; Rodriguez, Carol E; Sharma, Shalini; Herrera, Rene J

    2014-04-25

    The U1 small nuclear (sn)RNA participates in splicing of pre-mRNAs by recognizing and binding to 5' splice sites at exon/intron boundaries. U1 snRNAs associate with 5' splice sites in the form of ribonucleoprotein particles (snRNPs) that are comprised of the U1 snRNA and 10 core components, including U1A, U1-70K, U1C and the 'Smith antigen', or Sm, heptamer. The U1 snRNA is highly conserved across a wide range of taxa; however, a number of reports have identified the presence of expressed U1-like snRNAs in multiple species, including humans. While numerous U1-like molecules have been shown to be expressed, it is unclear whether these variant snRNAs have the capacity to form snRNPs and participate in splicing. The purpose of the present study was to further characterize biochemically the ability of previously identified human U1-like variants to form snRNPs and bind to U1 snRNP proteins. A bioinformatics analysis provided support for the existence of multiple expressed variants. In vitro gel shift assays, competition assays, and immunoprecipitations (IPs) revealed that the variants formed high molecular weight assemblies to varying degrees and associated with core U1 snRNP proteins to a lesser extent than the canonical U1 snRNA. Together, these data suggest that the human U1 snRNA variants analyzed here are unable to efficiently bind U1 snRNP proteins. The current work provides additional biochemical insights into the ability of the variants to assemble into snRNPs. PMID:24583175

  18. 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.

  19. 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.

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

    PubMed

    De Maio, Federico A; Risso, Guillermo; Iglesias, Nestor G; Shah, Priya; Pozzi, Berta; Gebhard, Leopoldo G; Mammi, Pablo; Mancini, Estefania; Yanovsky, Marcelo J; Andino, Raul; Krogan, Nevan; Srebrow, Anabella; Gamarnik, Andrea V

    2016-08-01

    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

  1. 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

  2. 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

  3. 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

    2016-01-01

    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

  4. Multiple myeloma–associated chromosomal translocation activates orphan snoRNA ACA11 to suppress oxidative stress

    PubMed Central

    Chu, Liang; Su, Mack Y.; Maggi, Leonard B.; Lu, Lan; Mullins, Chelsea; Crosby, Seth; Huang, Gaofeng; Chng, Wee Joo; Vij, Ravi; Tomasson, Michael H.

    2012-01-01

    The histone methyltransferase WHSC1 (also known as MMSET) is overexpressed in multiple myeloma (MM) as a result of the t(4;14) chromosomal translocation and in a broad variety of other cancers by unclear mechanisms. Overexpression of WHSC1 did not transform wild-type or tumor-prone primary hematopoietic cells. We found that ACA11, an orphan box H/ACA class small nucleolar RNA (snoRNA) encoded within an intron of WHSC1, was highly expressed in t(4;14)-positive MM and other cancers. ACA11 localized to nucleoli and bound what we believe to be a novel small nuclear ribonucleoprotein (snRNP) complex composed of several proteins involved in postsplicing intron complexes. RNA targets of this uncharacterized snRNP included snoRNA intermediates hosted within ribosomal protein (RP) genes, and an RP gene signature was strongly associated with t(4;14) in patients with MM. Expression of ACA11 was sufficient to downregulate RP genes and other snoRNAs implicated in the control of oxidative stress. ACA11 suppressed oxidative stress, afforded resistance to chemotherapy, and increased the proliferation of MM cells, demonstrating that ACA11 is a critical target of the t(4;14) translocation in MM and suggesting an oncogenic role in other cancers as well. PMID:22751105

  5. 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

  6. 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

  7. PKC phosphorylates HEXIM1 and regulates P-TEFb activity

    PubMed Central

    Fujinaga, Koh; Barboric, Matjaz; Li, Qintong; Luo, Zeping; Price, David H.; Peterlin, B. Matija

    2012-01-01

    The positive transcription elongation factor b (P-TEFb) regulates RNA polymerase II elongation. In cells, P-TEFb partitions between small active and larger inactive states. In the latter, HEXIM1 binds to 7SK snRNA and recruits as well as inactivates P-TEFb in the 7SK snRNP. Several stimuli can affect this P-TEFb equilibrium. In this study, we demonstrate that protein kinase C (PKC) phosphorylates the serine at position158 (S158) in HEXIM1. This phosphorylated HEXIM1 protein neither binds to 7SK snRNA nor inhibits P-TEFb. Phorbol esters or the engagement of the T cell antigen receptor, which activate PKC and the expression of the constitutively active (CA) PKCθ protein, which is found in T cells, inhibit the formation of the 7SK snRNP. All these stimuli increase P-TEFb-dependent transcription. In contrast, the kinase-negative PKCθ and the mutant HEXIM1 (S158A) proteins block effects of these PKC-activating stimuli. These results indicate that the phosphorylation of HEXIM1 by PKC represents a major regulatory step of P-TEFb activity in cells. PMID:22821562

  8. 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

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

    PubMed Central

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

    2009-01-01

    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. PMID:19773425

  10. Loss of heterozygosity and transcriptome analyses of a 1.2 Mb candidate ovarian cancer tumor suppressor locus region at 17q25.1-q25.2.

    PubMed

    Presneau, Nadège; Dewar, Ken; Forgetta, Vince; Provencher, Diane; Mes-Masson, Anne-Marie; Tonin, Patricia N

    2005-07-01

    Loss of heterozygosity (LOH) analysis was performed in epithelial ovarian cancers (EOC) to further characterize a previously identified candidate tumor suppressor gene (TSG) region encompassing D17S801 at chromosomal region 17q25.1. LOH of at least one informative marker was observed for 100 (71%) of 140 malignant EOC samples in an analysis of 6 polymorphic markers (cen-D17S1839-D17S785-D17S1817-D17S801-D17S751-D17S722-tel). The combined LOH analysis revealed a 453 kilobase (Kb) minimal region of deletion (MRD) bounded by D17S1817 and D17S751. Human and mouse genome assemblies were used to resolve marker inconsistencies in the D17S1839-D17S722 interval and identify candidates. The region contains 32 known and strongly predicted genes, 9 of which overlap the MRD. The reference genomic sequences share nearly identical gene structures and the organization of the region is highly collinear. Although, the region does not show any large internal duplications, a 1.5 Kb inverted duplicated sequence of 87% nucleotide identity was observed in a 13 Kb region surrounding D17S801. Transcriptome analysis by Affymetrix GeneChip and reverse transcription (RT)-polymerase chain reaction (PCR) methods of 3 well characterized EOC cell lines and primary cultures of normal ovarian surface epithelial (NOSE) cells was performed with 32 candidates spanning D17S1839-D17S722 interval. RT-PCR analysis of 8 known or strongly predicted genes residing in the MRD in 10 EOC samples, that exhibited LOH of the MRD, identified FLJ22341 as a strong candidate TSG. The proximal repeat sequence of D17S801 occurs 8 Kb upstream of the putative promoter region of FLJ22341. RT-PCR analysis of the EOC samples and cell lines identified DKFZP434P0316 that maps proximal to the MRD, as a candidate. While Affymetrix technology was useful for initially eliminating less promising candidates, subsequent RT-PCR analysis of well-characterized EOC samples was essential to prioritize TSG candidates for further study

  11. 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

  12. The Y3** ncRNA promotes the 3′ end processing of histone mRNAs

    PubMed Central

    Köhn, Marcel; Ihling, Christian; Sinz, Andrea; Krohn, Knut; Hüttelmaier, Stefan

    2015-01-01

    We demonstrate that the Y3/Y3** noncoding RNAs (ncRNAs) bind to the CPSF (cleavage and polyadenylation specificity factor) and that Y3** associates with the 3′ untranslated region (UTR) of histone pre-mRNAs. The depletion of Y3** impairs the 3′ end processing of histone pre-mRNAs as well as the formation and protein dynamics of histone locus bodies (HLBs), the site of histone mRNA synthesis and processing. HLB morphology is also disturbed by knockdown of the CPSF but not the U7-snRNP components. In conclusion, we propose that the Y3** ncRNA promotes the 3′ end processing of histone pre-mRNAs by enhancing the recruitment of the CPSF to histone pre-mRNAs at HLBs. PMID:26443846

  13. Network of coregulated spliceosome components revealed by zebrafish mutant in recycling factor p110

    PubMed Central

    Trede, Nikolaus S.; Medenbach, Jan; Damianov, Andrey; Hung, Lee-Hsueh; Weber, Gerhard J.; Paw, Barry H.; Zhou, Yi; Hersey, Candace; Zapata, Agustin; Keefe, Matthew; Barut, Bruce A.; Stuart, Andrew B.; Katz, Tammisty; Amemiya, Chris T.; Zon, Leonard I.; Bindereif, Albrecht

    2007-01-01

    The spliceosome cycle consists of assembly, catalysis, and recycling phases. Recycling of postspliceosomal U4 and U6 small nuclear ribonucleoproteins (snRNPs) requires p110/SART3, a general splicing factor. In this article, we report that the zebrafish earl grey (egy) mutation maps in the p110 gene and results in a phenotype characterized by thymus hypoplasia, other organ-specific defects, and death by 7 to 8 days postfertilization. U4/U6 snRNPs were disrupted in egy mutant embryos, demonstrating the importance of p110 for U4/U6 snRNP recycling in vivo. Surprisingly, expression profiling of the egy mutant revealed an extensive network of coordinately up-regulated components of the spliceosome cycle, providing a mechanism compensating for the recycling defect. Together, our data demonstrate that a mutation in a general splicing factor can lead to distinct defects in organ development and cause disease. PMID:17416673

  14. 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.

  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. PMID:26908624

  16. Expression of U1 small nuclear ribonucleoprotein 70K antisense transcript using APETALA3 promoter suppresses the development of sepals and petals.

    PubMed

    Golovkin, Maxim; Reddy, Anireddy S N

    2003-08-01

    U1 small nuclear ribonucleoprotein (snRNP)-70K (U1-70K), a U1 snRNP-specific protein, is involved in the early stages of spliceosome formation. In non-plant systems, it is involved in constitutive and alternative splicing. It has been shown that U1snRNP is dispensable for in vitro splicing of some animal pre-mRNAs, and inactivation of U1-70K in yeast (Saccharomyces cerevisiae) is not lethal. As in yeast and humans (Homo sapiens), plant U1-70K is coded by a single gene. In this study, we blocked the expression of Arabidopsis U1-70K in petals and stamens by expressing U1-70K antisense transcript using the AP3 (APETALA3) promoter specific to these floral organs. Flowers of transgenic Arabidopsis plants expressing U1-70K antisense transcript showed partially developed stamens and petals that are arrested at different stages of development. In some transgenic lines, flowers have rudimentary petals and stamens and are male sterile. The severity of the phenotype is correlated with the level of the antisense transcript. Molecular analysis of transgenic plants has confirmed that the observed phenotype is not due to disruption of whorl-specific homeotic genes, AP3 or PISTILLATA, responsible for petal and stamen development. The AP3 transcript was not detected in transgenic flowers with severe phenotype. Flowers of Arabidopsis plants transformed with a reporter gene driven by the same promoter showed no abnormalities. These results show that U1-70K is necessary for the development of sepals and petals and is an essential gene in plants. PMID:12913145

  17. 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.

  18. Structure-function analysis and genetic interactions of the yeast branchpoint binding protein Msl5.

    PubMed

    Chang, Jonathan; Schwer, Beate; Shuman, Stewart

    2012-05-01

    Saccharomyces cerevisiae Msl5 (branchpoint binding protein) orchestrates spliceosome assembly by binding the branchpoint sequence 5'-UACUAAC and establishing cross intron-bridging interactions with other components of the splicing machinery. Reciprocal tandem affinity purifications verify that Msl5 exists in vivo as a heterodimer with Mud2 and that the Msl5-Mud2 complex is associated with the U1 snRNP. By gauging the ability of mutants of Msl5 to complement msl5Δ, we find that the Mud2-binding (amino acids 35-54) and putative Prp40-binding (PPxY(100)) elements of the Msl5 N-terminal domain are inessential, as are the C-terminal proline-rich domain (amino acids 382-476) and two zinc-binding CxxCxxxxHxxxxC motifs (amino acids 273-286 and 299-312). A subset of conserved branchpoint RNA-binding amino acids in the central KH-QUA2 domain (amino acids 146-269) are essential pairwise (Ile198-Arg190; Leu256-Leu259) or in trios (Leu169-Arg172-Leu176), whereas other pairs of RNA-binding residues are dispensable. We used our collection of viable Msl5 mutants to interrogate synthetic genetic interactions, in cis between the inessential structural elements of the Msl5 polypeptide and in trans between Msl5 and yeast splicing factors (Mud2, Nam8 and Tgs1) that are optional for vegetative growth. The results suggest a network of important but functionally buffered protein-protein and protein-RNA interactions between the Mud2-Msl5 complex at the branchpoint and the U1 snRNP at the 5' splice site. PMID:22287628

  19. Gemin4. A novel component of the SMN complex that is found in both gems and nucleoli.

    PubMed

    Charroux, B; Pellizzoni, L; Perkinson, R A; Yong, J; Shevchenko, A; Mann, M; Dreyfuss, G

    2000-03-20

    The survival of motor neurons (SMN) protein, the product of the neurodegenerative disease spinal muscular atrophy (SMA) gene, is localized both in the cytoplasm and in discrete nuclear bodies called gems. In both compartments SMN is part of a large complex that contains several proteins including Gemin2 (formerly SIP1) and the DEAD box protein Gemin3. In the cytoplasm, the SMN complex is associated with snRNP Sm core proteins and plays a critical role in spliceosomal snRNP assembly. In the nucleus, SMN is required for pre-mRNA splicing by serving in the regeneration of spliceosomes. These functions are likely impaired in cells of SMA patients because they have reduced levels of functional SMN. Here, we report the identification by nanoelectrospray mass spectrometry of a novel component of the SMN complex that we name Gemin4. Gemin4 is associated in vivo with the SMN complex through a direct interaction with Gemin3. The tight interaction of Gemin4 with Gemin3 suggests that it could serve as a cofactor of this DEAD box protein. Gemin4 also interacts directly with several of the Sm core proteins. Monoclonal antibodies against Gemin4 efficiently immunoprecipitate the spliceosomal U snRNAs U1 and U5 from Xenopus oocytes cytoplasm. Immunolocalization experiments show that Gemin4 is colocalized with SMN in the cytoplasm and in gems. Interestingly, Gemin4 is also detected in the nucleoli, suggesting that the SMN complex may also function in preribosomal RNA processing or ribosome assembly. PMID:10725331

  20. Molecular genetics of cone-rod dystrophy in Chinese patients: New data from 61 probands and mutation overview of 163 probands.

    PubMed

    Huang, Li; Xiao, Xueshan; Li, Shiqiang; Jia, Xiaoyun; Wang, Panfeng; Sun, Wenmin; Xu, Yan; Xin, Wei; Guo, Xiangming; Zhang, Qingjiong

    2016-05-01

    Cone-rod dystrophy (CORD) is a common form of inherited retinal degeneration. Previously, we have conducted serial mutational analysis in probands with CORD either by Sanger sequencing or whole exome sequencing (WES). In the current study, variants in all genes from RetNet were selected from the whole exome sequencing data of 108 CORD probands (including 61 probands reported here for the first time) and were analyzed by multistep bioinformatics analysis, followed by Sanger sequencing and segregation validation. Data from the previous studies and new data from this study (163 probands in total) were summarized to provide an overview of the molecular genetics of CORD. The following potentially pathogenic mutations were identified in 93 of the 163 (57.1%) probands: CNGA3 (32.5%), ABCA4 (3.8%), ALMS1 (3.1%), GUCY2D (3.1%), CACNA1F (2.5%), CRX (1.8%), PDE6C (1.8%), CNGB3 (1.8%), GUCA1A (1.2%), UNC119 (0.6%), RPGRIP1 (1.2%), RDH12 (0.6%), KCNV2 (0.6%), C21orf2 (0.6%), CEP290 (0.6%), USH2A (0.6%) and SNRNP200 (0.6%). The 17 genes with mutations included 12 known CORD genes and five genes (ALMS1, RDH12, CEP290, USH2A, and SNRNP200) associated with other forms of retinal degeneration. Mutations in CNGA3 is most common in this cohort. This is a systematic molecular genetic analysis of Chinese patients with CORD. PMID:26992781

  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. 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.

  3. Sorption and degradation of 17ß-estradiol-17-sulfate in sterilized soil-water systems

    Technology Transfer Automated Retrieval System (TEKTRAN)

    To identify abiotic processes that govern the fate of a sulfate conjugated estrogen, 17ß-estradiol-17-sulfate (E2-17S), soil batch experiments were conducted to investigate the dissipation, sorption, and degradation of radiolabeled E2-17S under sterilized conditions. The aqueous dissipation half-liv...

  4. 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.

  5. 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.

  6. A new locus for autosomal dominant retinitis pigmentosa on the short arm of chromosome 17.

    PubMed

    Greenberg, J; Goliath, R; Beighton, P; Ramesar, R

    1994-06-01

    Retinitis pigmentosa (RP) is a group of genetically and clinically heterogeneous retinopathies, some of which have been shown to result from mutations in two different known retinal genes, rhodopsin (3q) and peripherin-rds (6p). Three additional anonymous loci at 7p, 7q and pericentric 8 have been implicated by linkage studies. There are still, however, a few families in which all known loci have been excluded. In this report we present data indicating a location, on the short arm of chromosome 17, for the autosomal dominant RP (ADRP) locus in a large South African (SA) family of British ancestry. Positive two-point lod scores have been obtained for nine markers (D17S938, Z = 5.43; D17S796, Z = 4.82; D17S849, Z = 3.6; D17S786, Z = 3.55; TP53, Z = 3.55; D17S578, Z = 3.29; D17S960, Z = 3.16; D17S926, Z = 1.51; D17S804, Z = 0.47 all at theta = 0.10 except D17S804 and D17S926, theta = 0.20). These data provide definitive evidence for the localization of an ADRP gene on chromosome 17p. The human recoverin gene has been localized to 17p13.1 and was consequently a prime candidate for ADRP in the family studied. However, mutation screening of the three exons of this gene failed to produce any evidence of recoverin being the gene involved in the pathogenesis of ADRP in this SA family. PMID:7951236

  7. Nuclear Ribonucleoprotein Complexes Containing Polyadenylate from Mouse Ascites Cells

    PubMed Central

    Quinlan, Thomas J.; Billings, Peter B.; Martin, Terence E.

    1974-01-01

    Nuclear poly(A)-containing RNA of mouse ascites cells can be extracted in the form of 15-17S ribonucleoprotein complexes under conditions in which the bulk of the heterogeneous nuclear RNA is released as 30S complexes. The poly(A)-containing fraction of nuclear extracts has been resolved into two distinct components, 15 and 17 S; neither contains the two polypeptides of 30S ribonucleoprotein. The 17S particle contains approximately six polypeptide species of molecular masses 17,000-30,000 daltons. The 15S complex has four distinct polypeptides of higher molecular mass, including a prominent 80,000-dalton species. PMID:4368966

  8. 27 CFR 9.139 - Santa Lucia Highlands.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... boundary of section 28, T. 16S., R. 4E. The boundary is as follows: (1) From the beginning point the... sections 29, 19, 13, and 11, to the northwest corner of section 11, T. 17S., R. 4E on the Rana Creek, California U.S.G.S. map. (19) Then north along the western boundary of section 2, T. 17S., R. 4E., to...

  9. 27 CFR 9.139 - Santa Lucia Highlands.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... boundary of section 28, T. 16S., R. 4E. The boundary is as follows: (1) From the beginning point the... sections 29, 19, 13, and 11, to the northwest corner of section 11, T. 17S., R. 4E on the Rana Creek, California U.S.G.S. map. (19) Then north along the western boundary of section 2, T. 17S., R. 4E., to...

  10. 27 CFR 9.139 - Santa Lucia Highlands.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... boundary of section 28, T. 16S., R. 4E. The boundary is as follows: (1) From the beginning point the... sections 29, 19, 13, and 11, to the northwest corner of section 11, T. 17S., R. 4E on the Rana Creek, California U.S.G.S. map. (19) Then north along the western boundary of section 2, T. 17S., R. 4E., to...

  11. 27 CFR 9.139 - Santa Lucia Highlands.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... boundary of section 28, T. 16S., R. 4E. The boundary is as follows: (1) From the beginning point the... sections 29, 19, 13, and 11, to the northwest corner of section 11, T. 17S., R. 4E on the Rana Creek, California U.S.G.S. map. (19) Then north along the western boundary of section 2, T. 17S., R. 4E., to...

  12. Mutation analysis of pre-mRNA splicing genes in Chinese families with retinitis pigmentosa

    PubMed Central

    Pan, Xinyuan; Chen, Xue; Liu, Xiaoxing; Gao, Xiang; Kang, Xiaoli; Xu, Qihua; Chen, Xuejuan; Zhao, Kanxing; Zhang, Xiumei; Chu, Qiaomei; Wang, Xiuying

    2014-01-01

    Purpose Seven genes involved in precursor mRNA (pre-mRNA) splicing have been implicated in autosomal dominant retinitis pigmentosa (adRP). We sought to detect mutations in all seven genes in Chinese families with RP, to characterize the relevant phenotypes, and to evaluate the prevalence of mutations in splicing genes in patients with adRP. Methods Six unrelated families from our adRP cohort (42 families) and two additional families with RP with uncertain inheritance mode were clinically characterized in the present study. Targeted sequence capture with next-generation massively parallel sequencing (NGS) was performed to screen mutations in 189 genes including all seven pre-mRNA splicing genes associated with adRP. Variants detected with NGS were filtered with bioinformatics analyses, validated with Sanger sequencing, and prioritized with pathogenicity analysis. Results Mutations in pre-mRNA splicing genes were identified in three individual families including one novel frameshift mutation in PRPF31 (p.Leu366fs*1) and two known mutations in SNRNP200 (p.Arg681His and p.Ser1087Leu). The patients carrying SNRNP200 p.R681H showed rapid disease progression, and the family carrying p.S1087L presented earlier onset ages and more severe phenotypes compared to another previously reported family with p.S1087L. In five other families, we identified mutations in other RP-related genes, including RP1 p. Ser781* (novel), RP2 p.Gln65* (novel) and p.Ile137del (novel), IMPDH1 p.Asp311Asn (recurrent), and RHO p.Pro347Leu (recurrent). Conclusions Mutations in splicing genes identified in the present and our previous study account for 9.5% in our adRP cohort, indicating the important role of pre-mRNA splicing deficiency in the etiology of adRP. Mutations in the same splicing gene, or even the same mutation, could correlate with different phenotypic severities, complicating the genotype–phenotype correlation and clinical prognosis. PMID:24940031

  13. 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.

  14. The Spliceosomal Phosphopeptide P140 Controls the Lupus Disease by Interacting with the HSC70 Protein and via a Mechanism Mediated by γδ T Cells

    PubMed Central

    Page, Nicolas; Schall, Nicolas; Strub, Jean-Marc; Quinternet, Marc; Chaloin, Olivier; Décossas, Marion; Cung, Manh Thong; Van Dorsselaer, Alain; Briand, Jean-Paul; Muller, Sylviane

    2009-01-01

    The phosphopeptide P140 issued from the spliceosomal U1-70K snRNP protein is recognized by lupus CD4+ T cells, transiently abolishes T cell reactivity to other spliceosomal peptides in P140-treated MRL/lpr mice, and ameliorates their clinical features. P140 modulates lupus patients' T cell response ex vivo and is currently included in phase IIb clinical trials. Its underlying mechanism of action remains elusive. Here we show that P140 peptide binds a unique cell-surface receptor, the constitutively-expressed chaperone HSC70 protein, known as a presenting-protein. P140 induces apoptosis of activated MRL/lpr CD4+ T cells. In P140-treated mice, it increases peripheral blood lymphocyte apoptosis and decreases B cell, activated T cell, and CD4−CD8−B220+ T cell counts via a specific mechanism strictly depending on γδ T cells. Expression of inflammation-linked genes is rapidly regulated in CD4+ T cells. This work led us to identify a powerful pathway taken by a newly-designed therapeutic peptide to immunomodulate lupus autoimmunity. PMID:19390596

  15. Non-coding RNAs, the cutting edge of histone messages.

    PubMed

    Köhn, Marcel; Hüttelmaier, Stefan

    2016-04-01

    In metazoan the 3'-end processing of histone mRNAs is a conserved process involving the concerted action of many protein factors and the non-coding U7 snRNA. Recently, we identified that the processing of histone pre-mRNAs is promoted by an additional ncRNA, the Y3-derived Y3** RNA. U7 modulates the association of the U7 snRNP whereas Y3** promotes recruitment of CPSF (cleavage and polyadenylation specific factor) proteins to nascent histone transcripts at histone locus bodies (HLBs) in mammals. This enhances the 3'-end cleavage of nascent histone pre-mRNAs and modulates HLB assembly. Here we discuss new insights in the role of ncRNAs in the spatiotemporal control of histone synthesis. We propose that ncRNAs scaffold the formation of functional protein-RNA complexes and their sequential deposition on nascent histone pre-mRNAs at HLBs. These findings add to the multiple roles of ncRNAs in controlling gene expression and may provide new avenues for targeting histone synthesis in cancer. PMID:26909464

  16. Activities of the Sex-lethal protein in RNA binding and protein:protein interactions.

    PubMed Central

    Samuels, M; Deshpande, G; Schedl, P

    1998-01-01

    The Drosophila sex determination gene Sex-lethal (Sxl) controls its own expression, and the expression of downstream target genes such as transformer , by regulating pre-mRNA splicing and mRNA translation. Sxl codes an RNA-binding protein that consists of an N-terminus of approximately 100 amino acids, two 90 amino acid RRM domains, R1 and R2, and an 80 amino acid C-terminus. In the studies reported here we have examined the functional properties of the different Sxl protein domains in RNA binding and in protein:protein interactions. The two RRM domains are responsible for RNA binding. Specificity in the recognition of target RNAs requires both RRM domains, and proteins which consist of the single domains or duplicated domains have anomalous RNA recognition properties. Moreover, the length of the linker between domains can affect RNA recognition properties. Our results indicate that the two RRM domains mediate Sxl:Sxl protein interactions, and that these interactions probably occur both in cis and trans. We speculate that cis interactions between R1 and R2 play a role in RNA recognition by the Sxl protein, while trans interactions stabilize complex formation on target RNAs that contain two or more closely spaced binding sites. Finally, we show that the interaction of Sxl with the snRNP protein Snf is mediated by the R1 RRM domain. PMID:9592147

  17. NUFIP and the HSP90/R2TP chaperone bind the SMN complex and facilitate assembly of U4-specific proteins.

    PubMed

    Bizarro, Jonathan; Dodré, Maxime; Huttin, Alexandra; Charpentier, Bruno; Schlotter, Florence; Branlant, Christiane; Verheggen, Céline; Massenet, Séverine; Bertrand, Edouard

    2015-10-15

    The Sm proteins are loaded on snRNAs by the SMN complex, but how snRNP-specific proteins are assembled remains poorly characterized. U4 snRNP and box C/D snoRNPs have structural similarities. They both contain the 15.5K and proteins with NOP domains (PRP31 for U4, NOP56/58 for snoRNPs). Biogenesis of box C/D snoRNPs involves NUFIP and the HSP90/R2TP chaperone system and here, we explore the function of this machinery in U4 RNP assembly. We show that yeast Prp31 interacts with several components of the NUFIP/R2TP machinery, and that these interactions are separable from each other. In human cells, PRP31 mutants that fail to stably associate with U4 snRNA still interact with components of the NUFIP/R2TP system, indicating that these interactions precede binding of PRP31 to U4 snRNA. Knock-down of NUFIP leads to mislocalization of PRP31 and decreased association with U4. Moreover, NUFIP is associated with the SMN complex through direct interactions with Gemin3 and Gemin6. Altogether, our data suggest a model in which the NUFIP/R2TP system is connected with the SMN complex and facilitates assembly of U4 snRNP-specific proteins. PMID:26275778

  18. Splicing diversity revealed by reduced spliceosomes in C. merolae and other organisms

    PubMed Central

    Hudson, Andrew J; Stark, Martha R; Fast, Naomi M; Russell, Anthony G; Rader, Stephen D

    2015-01-01

    Pre-mRNA splicing has been considered one of the hallmarks of eukaryotes, yet its diversity is astonishing: the number of substrate introns for splicing ranges from hundreds of thousands in humans to a mere handful in certain parasites. The catalytic machinery that carries out splicing, the spliceosome, is similarly diverse, with over 300 associated proteins in humans to a few tens in other organisms. In this Point of View, we discuss recent work characterizing the reduced spliceosome of the acidophilic red alga Cyanidioschyzon merolae, which further highlights the diversity of splicing in that it does not possess the U1 snRNP that is characteristically responsible for 5′ splice site recognition. Comparisons to other organisms with reduced spliceosomes, such as microsporidia, trypanosomes, and Giardia, help to identify the most highly conserved splicing factors, pointing to the essential core of this complex machine. These observations argue for increased exploration of important biochemical processes through study of a wider ranger of organisms. PMID:26400738

  19. 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. PMID:24461387

  20. A Stochastic View of Spliceosome Assembly and Recycling in the Nucleus

    PubMed Central

    Desterro, Joana M. P; Lührmann, Reinhard; Carmo-Fonseca, Maria

    2007-01-01

    How splicing factors are recruited to nascent transcripts in the nucleus in order to assemble spliceosomes on newly synthesised pre-mRNAs is unknown. To address this question, we compared the intranuclear trafficking kinetics of small nuclear ribonucleoprotein particles (snRNP) and non-snRNP proteins in the presence and absence of splicing activity. Photobleaching experiments clearly show that spliceosomal proteins move continuously throughout the entire nucleus independently of ongoing transcription or splicing. Using quantitative experimental data, a mathematical model was applied for spliceosome assembly and recycling in the nucleus. The model assumes that splicing proteins move by Brownian diffusion and interact stochastically with binding sites located at different subnuclear compartments. Inhibition of splicing, which reduces the number of pre-mRNA binding sites available for spliceosome assembly, was modeled as a decrease in the on-rate binding constant in the nucleoplasm. Simulation of microscopy experiments before and after splicing inhibition yielded results consistent with the experimental observations. Taken together, our data argue against the view that spliceosomal components are stored in nuclear speckles until a signal triggers their recruitment to nascent transcripts. Rather, the results suggest that splicing proteins are constantly diffusing throughout the entire nucleus and collide randomly and transiently with pre-mRNAs. PMID:17967051

  1. NUFIP and the HSP90/R2TP chaperone bind the SMN complex and facilitate assembly of U4-specific proteins

    PubMed Central

    Bizarro, Jonathan; Dodré, Maxime; Huttin, Alexandra; Charpentier, Bruno; Schlotter, Florence; Branlant, Christiane; Verheggen, Céline; Massenet, Séverine; Bertrand, Edouard

    2015-01-01

    The Sm proteins are loaded on snRNAs by the SMN complex, but how snRNP-specific proteins are assembled remains poorly characterized. U4 snRNP and box C/D snoRNPs have structural similarities. They both contain the 15.5K and proteins with NOP domains (PRP31 for U4, NOP56/58 for snoRNPs). Biogenesis of box C/D snoRNPs involves NUFIP and the HSP90/R2TP chaperone system and here, we explore the function of this machinery in U4 RNP assembly. We show that yeast Prp31 interacts with several components of the NUFIP/R2TP machinery, and that these interactions are separable from each other. In human cells, PRP31 mutants that fail to stably associate with U4 snRNA still interact with components of the NUFIP/R2TP system, indicating that these interactions precede binding of PRP31 to U4 snRNA. Knock-down of NUFIP leads to mislocalization of PRP31 and decreased association with U4. Moreover, NUFIP is associated with the SMN complex through direct interactions with Gemin3 and Gemin6. Altogether, our data suggest a model in which the NUFIP/R2TP system is connected with the SMN complex and facilitates assembly of U4 snRNP-specific proteins. PMID:26275778

  2. 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.

  3. 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

  4. Spinal muscular atrophy and a model for survival of motor neuron protein function in axonal ribonucleoprotein complexes.

    PubMed

    Rossoll, Wilfried; Bassell, Gary J

    2009-01-01

    Spinal muscular atrophy (SMA) is a neurodegenerative disease that results from loss of function of the SMN1 gene, encoding the ubiquitously expressed survival of motor neuron (SMN) protein, a protein best known for its housekeeping role in the SMN-Gemin multiprotein complex involved in spliceosomal small nuclear ribonucleoprotein (snRNP) assembly. However, numerous studies reveal that SMN has many interaction partners, including mRNA binding proteins and actin regulators, suggesting its diverse role as a molecular chaperone involved in mRNA metabolism. This review focuses on studies suggesting an important role of SMN in regulating the assembly, localization, or stability of axonal messenger ribonucleoprotein (mRNP) complexes. Various animal models for SMA are discussed, and phenotypes described that indicate a predominant function for SMN in neuronal development and synapse formation. These models have begun to be used to test different therapeutic strategies that have the potential to restore SMN function. Further work to elucidate SMN mechanisms within motor neurons and other cell types involved in neuromuscular circuitry hold promise for the potential treatment of SMA. PMID:19343312

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

    PubMed Central

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

    2014-01-01

    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. PMID:24914973

  6. 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

  7. 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. PMID:26818120

  8. CstF64: Cell Cycle Regulation and Functional Role in 3′ End Processing of Replication-Dependent Histone mRNAs

    PubMed Central

    Romeo, Valentina; Griesbach, Esther

    2014-01-01

    The 3′ end processing of animal replication-dependent histone mRNAs is activated during G1/S-phase transition. The processing site is recognized by stem-loop binding protein and the U7 snRNP, but cleavage additionally requires a heat-labile factor (HLF), composed of cleavage/polyadenylation specificity factor, symplekin, and cleavage stimulation factor 64 (CstF64). Although HLF has been shown to be cell cycle regulated, the mechanism of this regulation is unknown. Here we show that levels of CstF64 increase toward the S phase and its depletion affects histone RNA processing, S-phase progression, and cell proliferation. Moreover, analyses of the interactions between CstF64, symplekin, and the U7 snRNP-associated proteins FLASH and Lsm11 indicate that CstF64 is important for recruiting HLF to histone precursor mRNA (pre-mRNA)-resident proteins. Thus, CstF64 is central to the function of HLF and appears to be at least partly responsible for its cell cycle regulation. Additionally, we show that misprocessed histone transcripts generated upon CstF64 depletion mainly accumulate in the nucleus, where they are targets of the exosome machinery, while a small cytoplasmic fraction is partly associated with polysomes. PMID:25266659

  9. The exosome controls alternative splicing by mediating the gene expression and assembly of the spliceosome complex

    PubMed Central

    Zhang, Lin; Wan, Yufeng; Huang, Guobin; Wang, Dongni; Yu, Xinyang; Huang, Guocun; Guo, Jinhu

    2015-01-01

    The exosome is a complex with exoribonuclease activity that regulates RNA surveillance and turnover. The exosome also plays a role in regulating the degradation of precursor mRNAs to maintain the expression of splicing variants. In Neurospora, the silencing of rrp44, which encodes the catalytic subunit of the exosome, changed the expression of a set of spliceosomal snRNA, snRNP genes and SR protein related genes. The knockdown of rrp44 also affected the assembly of the spliceosome. RNA-seq analysis revealed a global change in bulk splicing events. Exosome-mediated splicing may regulate alternative splicing of NCU05290, NCU07421 and the circadian clock gene frequency (frq). The knockdown of rrp44 led to an increased ratio of splicing variants without intron 6 (I-6) and shorter protein isoform small FRQ (s-FRQ) as a consequence. These findings suggest that the exosome controls splicing events by regulating the degradation of precursor mRNAs and the gene expression, assembly and function of the spliceosome. PMID:26306464

  10. 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

  11. Gemin5 Binds to the Survival Motor Neuron mRNA to Regulate SMN Expression.

    PubMed

    Workman, Eileen; Kalda, Caitlin; Patel, Aalapi; Battle, Daniel J

    2015-06-19

    Reduced expression of SMN causes spinal muscular atrophy, a severe neurodegenerative disease. Despite the importance of maintaining SMN levels, relatively little is known about the mechanisms by which SMN levels are regulated. We show here that Gemin5, the snRNA-binding protein of the SMN complex, binds directly to the SMN mRNA and regulates SMN expression. Gemin5 binds with high specificity, both in vitro and in vivo, to sequence and structural elements in the SMN mRNA 3'-untranslated region that are reminiscent of the snRNP code to which Gemin5 binds on snRNAs. Reduction of Gemin5 redistributes the SMN mRNA from heavy polysomes to lighter polysomes and monosomes, suggesting that Gemin5 functions as an activator of SMN translation. SMN protein is not stoichiometrically present on the SMN mRNA with Gemin5, but the mRNA-binding activity of Gemin5 is dependent on SMN levels, providing a feedback mechanism for SMN to regulate its own expression via Gemin5. This work both reveals a new autoregulatory pathway governing SMN expression, and identifies a new mechanism through which SMN can modulate specific mRNA expression via Gemin5. PMID:25911097

  12. 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.

  13. 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. PMID:22591583

  14. 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. PMID:26720152

  15. Molecular Basis and Therapeutic Strategies to Rescue Factor IX Variants That Affect Splicing and Protein Function.

    PubMed

    Tajnik, Mojca; Rogalska, Malgorzata Ewa; Bussani, Erica; Barbon, Elena; Balestra, Dario; Pinotti, Mirko; Pagani, Franco

    2016-05-01

    Mutations that result in amino acid changes can affect both pre-mRNA splicing and protein function. Understanding the combined effect is essential for correct diagnosis and for establishing the most appropriate therapeutic strategy at the molecular level. We have identified a series of disease-causing splicing mutations in coagulation factor IX (FIX) exon 5 that are completely recovered by a modified U1snRNP particle, through an SRSF2-dependent enhancement mechanism. We discovered that synonymous mutations and missense substitutions associated to a partial FIX secretion defect represent targets for this therapy as the resulting spliced-corrected proteins maintains normal FIX coagulant specific activity. Thus, splicing and protein alterations contribute to define at the molecular level the disease-causing effect of a number of exonic mutations in coagulation FIX exon 5. In addition, our results have a significant impact in the development of splicing-switching therapies in particular for mutations that affect both splicing and protein function where increasing the amount of a correctly spliced protein can circumvent the basic functional defects. PMID:27227676

  16. Dual function of C/D box small nucleolar RNAs in rRNA modification and alternative pre-mRNA splicing.

    PubMed

    Falaleeva, Marina; Pages, Amadis; Matuszek, Zaneta; Hidmi, Sana; Agranat-Tamir, Lily; Korotkov, Konstantin; Nevo, Yuval; Eyras, Eduardo; Sperling, Ruth; Stamm, Stefan

    2016-03-22

    C/D box small nucleolar RNAs (SNORDs) are small noncoding RNAs, and their best-understood function is to target the methyltransferase fibrillarin to rRNA (for example, SNORD27 performs 2'-O-methylation of A27 in 18S rRNA). Unexpectedly, we found a subset of SNORDs, including SNORD27, in soluble nuclear extract made under native conditions, where fibrillarin was not detected, indicating that a fraction of the SNORD27 RNA likely forms a protein complex different from canonical snoRNAs found in the insoluble nuclear fraction. As part of this previously unidentified complex,SNORD27 regulates the alternative splicing of the transcription factor E2F7p re-mRNA through direct RNA-RNA interaction without methylating the RNA, likely by competing with U1 small nuclear ribonucleoprotein (snRNP). Furthermore, knockdown of SNORD27 activates previously "silent" exons in several other genes through base complementarity across the entire SNORD27 sequence, not just the antisense boxes. Thus, some SNORDs likely function in both rRNA and pre-mRNA processing, which increases the repertoire of splicing regulators and links both processes. PMID:26957605

  17. Structural bioinformatics of the human spliceosomal proteome

    PubMed Central

    Korneta, Iga; Magnus, Marcin; Bujnicki, Janusz M.

    2012-01-01

    In this work, we describe the results of a comprehensive structural bioinformatics analysis of the spliceosomal proteome. We used fold recognition analysis to complement prior data on the ordered domains of 252 human splicing proteins. Examples of newly identified domains include a PWI domain in the U5 snRNP protein 200K (hBrr2, residues 258–338), while examples of previously known domains with a newly determined fold include the DUF1115 domain of the U4/U6 di-snRNP protein 90K (hPrp3, residues 540–683). We also established a non-redundant set of experimental models of spliceosomal proteins, as well as constructed in silico models for regions without an experimental structure. The combined set of structural models is available for download. Altogether, over 90% of the ordered regions of the spliceosomal proteome can be represented structurally with a high degree of confidence. We analyzed the reduced spliceosomal proteome of the intron-poor organism Giardia lamblia, and as a result, we proposed a candidate set of ordered structural regions necessary for a functional spliceosome. The results of this work will aid experimental and structural analyses of the spliceosomal proteins and complexes, and can serve as a starting point for multiscale modeling of the structure of the entire spliceosome. PMID:22573172

  18. Non-coding RNAs, the cutting edge of histone messages

    PubMed Central

    Köhn, Marcel; Hüttelmaier, Stefan

    2016-01-01

    ABSTRACT In metazoan the 3′-end processing of histone mRNAs is a conserved process involving the concerted action of many protein factors and the non-coding U7 snRNA. Recently, we identified that the processing of histone pre-mRNAs is promoted by an additional ncRNA, the Y3-derived Y3** RNA. U7 modulates the association of the U7 snRNP whereas Y3** promotes recruitment of CPSF (cleavage and polyadenylation specific factor) proteins to nascent histone transcripts at histone locus bodies (HLBs) in mammals. This enhances the 3′-end cleavage of nascent histone pre-mRNAs and modulates HLB assembly. Here we discuss new insights in the role of ncRNAs in the spatiotemporal control of histone synthesis. We propose that ncRNAs scaffold the formation of functional protein-RNA complexes and their sequential deposition on nascent histone pre-mRNAs at HLBs. These findings add to the multiple roles of ncRNAs in controlling gene expression and may provide new avenues for targeting histone synthesis in cancer. PMID:26909464

  19. Genetic Interactions between the Members of the SMN-Gemins Complex in Drosophila

    PubMed Central

    Borg, Rebecca M.; Bordonne, Rémy; Vassallo, Neville; Cauchi, Ruben J.

    2015-01-01

    The SMN-Gemins complex is composed of Gemins 2–8, Unrip and the survival motor neuron (SMN) protein. Limiting levels of SMN result in the neuromuscular disorder, spinal muscular atrophy (SMA), which is presently untreatable. The most-documented function of the SMN-Gemins complex concerns the assembly of spliceosomal small nuclear ribonucleoproteins (snRNPs). Despite multiple genetic studies, the Gemin proteins have not been identified as prominent modifiers of SMN-associated mutant phenotypes. In the present report, we make use of the Drosophila model organism to investigate whether viability and motor phenotypes associated with a hypomorphic Gemin3 mutant are enhanced by changes in the levels of SMN, Gemin2 and Gemin5 brought about by various genetic manipulations. We show a modifier effect by all three members of the minimalistic fly SMN-Gemins complex within the muscle compartment of the motor unit. Interestingly, muscle-specific overexpression of Gemin2 was by itself sufficient to depress normal motor function and its enhanced upregulation in all tissues leads to a decline in fly viability. The toxicity associated with increased Gemin2 levels is conserved in the yeast S. pombe in which we find that the cytoplasmic retention of Sm proteins, likely reflecting a block in the snRNP assembly pathway, is a contributing factor. We propose that a disruption in the normal stoichiometry of the SMN-Gemins complex depresses its function with consequences that are detrimental to the motor system. PMID:26098872

  20. A new interaction between the mouse 5' external transcribed spacer of pre-rRNA and U3 snRNA detected by psoralen crosslinking.

    PubMed Central

    Tyc, K; Steitz, J A

    1992-01-01

    The first cleavage in mammalian pre-rRNA processing occurs within the 5' external transcribed spacer (ETS). We have recently shown that the U3 snRNP is required for this cleavage reaction, binds to the rRNA precursor, and remains complexed with the downstream processing product after the reaction has been completed (1). Using psoralen crosslinking in mouse cell extract we have detected a new interaction between U3 RNA and the mouse ETS processing substrate and its processed product. The crosslinked sites on both U3 and ETS RNAs have been mapped by RNase H cleavage and primer extension analyses. The crosslinked sites in U3 RNA map to C5, U6, and U8. U8 lies within and C5 and U6 are adjacent to an evolutionarily conserved U3 sequence termed box A'. In the ETS the crosslinked sites are U1012 and U1013, 362 nucleotides downstream from the processing site. Although the crosslinked site is dispensable for the primary processing reaction in vitro, a short conserved sequence just 3' to the cleavage site (nucleotides 650-668) is absolutely required for crosslink formation. We conclude that the interaction between U3 RNA and the 5' ETS detected by psoralen crosslinking may play a role in subsequent step(s) of pre-rRNA processing. Images PMID:1437554

  1. Analysis of the splicing machinery in fission yeast: a comparison with budding yeast and mammals

    PubMed Central

    Käufer, Norbert F.; Potashkin, Judith

    2000-01-01

    Based on genetic and bioinformatic analysis, 80 proteins from the newly sequenced Schizosaccharomyces pombe genome appear to be splicing factors. The fission yeast splicing factors were compared to those of Homo sapiens and Saccharomyces cerevisiae in order to determine the extent of conservation or divergence that has occurred over the billion years of evolution that separate these organisms. Our results indicate that many of the factors present in all three organisms have been well conserved throughout evolution. It is calculated that 38% of the fission yeast splicing factors are more similar to the human proteins than to the budding yeast proteins (>10% more similar or similar over a greater region). Many of the factors in this category are required for recognition of the 3′ splice site. Ten fission yeast splicing factors, including putative regulatory factors, have human homologs, but no apparent budding yeast homologs based on sequence data alone. Many of the budding yeast factors that are absent in fission yeast are associated with the U1 and U4/U6.U5 snRNP. Collectively the data presented in this survey indicate that of the two yeasts, S.pombe contains a splicing machinery more closely reflecting the archetype of a spliceosome. PMID:10931913

  2. Spectrum of splicing errors caused by CHRNE mutations affecting introns and intron/exon boundaries

    PubMed Central

    Ohno, K; Tsujino, A; Shen, X; Milone, M; Engel, A

    2005-01-01

    Background: Mutations in CHRNE, the gene encoding the muscle nicotinic acetylcholine receptor ε subunit, cause congenital myasthenic syndromes. Only three of the eight intronic splice site mutations of CHRNE reported to date have had their splicing consequences characterised. Methods: We analysed four previously reported and five novel splicing mutations in CHRNE by introducing the entire normal and mutant genomic CHRNEs into COS cells. Results and conclusions: We found that short introns (82–109 nucleotides) favour intron retention, whereas medium to long introns (306–1210 nucleotides) flanking either or both sides of an exon favour exon skipping. Two mutations are of particular interest. Firstly, a G→T substitution at the 3' end of exon 8 predicts an R286M missense mutation, but instead results in skipping of exon 8. In human genes, a mismatch of the last exonic nucleotide to U1 snRNP is frequently compensated by a matching nucleotide at intron position +6. CHRNE intron 8 has a mismatch at position +6, and accordingly fails to compensate for the exonic mutation at position –1. Secondly, a 16 bp duplication, giving rise to two 3' splice sites (g.IVS10-9_c.1167dup16), results in silencing of the downstream 3' splice site. This conforms to the scanning model of recognition of the 3' splice site, which predicts that the first "ag" occurring after the branch point is selected for splicing. PMID:16061559

  3. 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

  4. 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. PMID:27097027

  5. An intronic (A/U)GGG repeat enhances the splicing of an alternative intron of the chicken beta-tropomyosin pre-mRNA.

    PubMed Central

    Sirand-Pugnet, P; Durosay, P; Brody, E; Marie, J

    1995-01-01

    Computer analysis of human intron sequences have revealed a 50 nucleotide (nt) GC-rich region downstream of the 5' splice site; the trinucleotide GGG occurs almost four times as frequently as it would in a random sequence. The 5' part of a beta-tropomyosin intron exhibits six repetitions of the motif (A/U)GGG. In order to test whether these motifs play a role in the splicing process we have mutated some or all of them. Mutated RNAs show a lower in vitro splicing efficiency when compared with the wild-type, especially when all six motifs are mutated (> 70% inhibition). Assembly of the spliceosome complex B and, to a lesser extent, of the pre-spliceosome complex A also appears to be strongly affected by this mutation. A 55 kDa protein within HeLa cell nuclear extract is efficiently cross-linked to the G-rich region. This protein is present in the splicing complexes and its cross-linking to the pre-mRNA requires the presence of one or several snRNP. Altogether our results suggest that the G-rich sequences present in the 5' part of introns may act as an enhancer of the splicing reaction at the level of spliceosome assembly. Images PMID:7567462

  6. The spliceosomal PRP19 complex of trypanosomes

    PubMed Central

    Ambrósio, Daniela L.; Badjatia, Nitika; Günzl, Arthur

    2015-01-01

    Summary In trypanosomes, mRNAs are processed by spliced leader (SL) trans splicing, in which a capped SL, derived from SL RNA, is spliced onto the 5′ end of each mRNA. This process is mediated by the spliceosome, a large and dynamic RNA-protein machinery consisting of small nuclear ribonucleoproteins (snRNPs) and non-snRNP proteins. Due to early evolutionary divergence, the amino acid sequences of trypanosome splicing factors exhibit limited similarity to those of their eukaryotic orthologs making their bioinformatic identification challenging. Most of the ~ 60 protein components that have been characterized thus far are snRNP proteins because, in contrast to individual snRNPs, purification of intact spliceosomes has not been achieved yet. Here, we characterize the non-snRNP PRP19 complex of Trypanosoma brucei. We identified a complex that contained the core subunits PRP19, CDC5, PRL1, and SPF27, as well as PRP17, SKIP and PPIL1. Three of these proteins were newly annotated. The PRP19 complex was associated primarily with the activated spliceosome and, accordingly, SPF27 silencing blocked the first splicing step. Interestingly, SPF27 silencing caused an accumulation of SL RNA with a hypomethylated cap that closely resembled the defect observed previously upon depletion of the cyclin-dependent kinase CRK9, indicating that both proteins may function in spliceosome activation. PMID:25524563

  7. 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. PMID:25115866

  8. Molecular Basis and Therapeutic Strategies to Rescue Factor IX Variants That Affect Splicing and Protein Function

    PubMed Central

    Bussani, Erica; Barbon, Elena; Pinotti, Mirko; Pagani, Franco

    2016-01-01

    Mutations that result in amino acid changes can affect both pre-mRNA splicing and protein function. Understanding the combined effect is essential for correct diagnosis and for establishing the most appropriate therapeutic strategy at the molecular level. We have identified a series of disease-causing splicing mutations in coagulation factor IX (FIX) exon 5 that are completely recovered by a modified U1snRNP particle, through an SRSF2-dependent enhancement mechanism. We discovered that synonymous mutations and missense substitutions associated to a partial FIX secretion defect represent targets for this therapy as the resulting spliced-corrected proteins maintains normal FIX coagulant specific activity. Thus, splicing and protein alterations contribute to define at the molecular level the disease-causing effect of a number of exonic mutations in coagulation FIX exon 5. In addition, our results have a significant impact in the development of splicing-switching therapies in particular for mutations that affect both splicing and protein function where increasing the amount of a correctly spliced protein can circumvent the basic functional defects. PMID:27227676

  9. U1 small nuclear ribonucleoprotein immune complexes induce type I interferon in plasmacytoid dendritic cells through TLR7.

    PubMed

    Savarese, Emina; Chae, Ohk-wha; Trowitzsch, Simon; Weber, Gert; Kastner, Berthold; Akira, Shizuo; Wagner, Hermann; Schmid, Roland M; Bauer, Stefan; Krug, Anne

    2006-04-15

    Plasmacytoid dendritic cells (PDCs), which produce IFN-alpha in response to autoimmune complexes containing nuclear antigens, are thought to be critically involved in the pathogenesis of systemic lupus erythematosus (SLE). One of the immunostimulatory components of SLE immune complexes (SLE-ICs) is self DNA, which is recognized through Tlr9 in PDCs and B cells. Small nuclear ribonucleoproteins (snRNPs) are another major component of SLE-ICs in 30% to 40% of patients. In this study, we show that murine PDCs are activated by purified U1snRNP/anti-Sm ICs to produce IFN-alpha and proinflammatory cytokines and to up-regulate costimulatory molecules. The induction of IFN-alpha and IL-6 by U1snRNPs in murine bone marrow-derived PDCs required the presence of intact U1RNA and was largely dependent on Tlr7 but independent of Tlr3. Intracellularly delivered isolated U1snRNA and oligoribonucleotides derived from the stem loop regions and the Sm-binding site of U1snRNA efficiently induced IFN-alpha and IL-6 in Flt3L-cultured DCs in a Tlr7-dependent manner. The U1snRNA component of U1snRNP immune complexes, found in patients with SLE, acts as an endogenous "self" ligand for Tlr7 and triggers IFN-alpha and IL-6 production in PDCs. PMID:16368889

  10. GEMINs: potential therapeutic targets for spinal muscular atrophy?

    PubMed Central

    Borg, Rebecca; Cauchi, Ruben J.

    2014-01-01

    The motor neuron degenerative disease spinal muscular atrophy (SMA) remains one of the most frequently inherited causes of infant mortality. Afflicted patients loose the survival motor neuron 1 (SMN1) gene but retain one or more copies of SMN2, a homolog that is incorrectly spliced. Primary treatment strategies for SMA aim at boosting SMN protein levels, which are insufficient in patients. SMN is known to partner with a set of diverse proteins collectively known as GEMINs to form a macromolecular complex. The SMN-GEMINs complex is indispensible for chaperoning the assembly of small nuclear ribonucleoproteins (snRNPs), which are key for pre-mRNA splicing. Pharmaceutics that alleviate the neuromuscular phenotype by restoring the fundamental function of SMN without augmenting its levels are also crucial in the development of an effective treatment. Their use as an adjunct therapy is predicted to enhance benefit to patients. Inspired by the surprising discovery revealing a premier role for GEMINs in snRNP biogenesis together with in vivo studies documenting their requirement for the correct function of the motor system, this review speculates on whether GEMINs constitute valid targets for SMA therapeutic development. PMID:25360080

  11. 3'-end-dependent formation of U6 small nuclear ribonucleoprotein particles in Xenopus laevis oocyte nuclei.

    PubMed Central

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

    1992-01-01

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

  12. Trichostatin A increases SMN expression and survival in a mouse model of spinal muscular atrophy

    PubMed Central

    Avila, Amy M.; Burnett, Barrington G.; Taye, Addis A.; Gabanella, Francesca; Knight, Melanie A.; Hartenstein, Parvana; Cizman, Ziga; Di Prospero, Nicholas A.; Pellizzoni, Livio; Fischbeck, Kenneth H.; Sumner, Charlotte J.

    2007-01-01

    The inherited motor neuron disease spinal muscular atrophy (SMA) is caused by mutation of the telomeric survival motor neuron 1 (SMN1) gene with retention of the centromeric SMN2 gene. We sought to establish whether the potent and specific hydroxamic acid class of histone deacetylase (HDAC) inhibitors activates SMN2 gene expression in vivo and modulates the SMA disease phenotype when delivered after disease onset. Single intraperitoneal doses of 10 mg/kg trichostatin A (TSA) in nontransgenic and SMA model mice resulted in increased levels of acetylated H3 and H4 histones and modest increases in SMN gene expression. Repeated daily doses of TSA caused increases in both SMN2-derived transcript and SMN protein levels in neural tissues and muscle, which were associated with an improvement in small nuclear ribonucleoprotein (snRNP) assembly. When TSA was delivered daily beginning on P5, after the onset of weight loss and motor deficit, there was improved survival, attenuated weight loss, and enhanced motor behavior. Pathological analysis showed increased myofiber size and number and increased anterior horn cell size. These results indicate that the hydroxamic acid class of HDAC inhibitors activates SMN2 gene expression in vivo and has an ameliorating effect on the SMA disease phenotype when administered after disease onset. PMID:17318264

  13. Mechanisms and Developmental Roles of Promoter-proximal Pausing of RNA Polymerase II

    PubMed Central

    Robinson, Christine; Lowe, Matthew; Schwartz, Amanda; Kikyo, Nobuaki

    2016-01-01

    RNA polymerase II (Pol II) temporarily stops transcription after synthesizing 30–50 bases, and resumes elongation only after stimulations by various signaling molecules and developmental cues. This phenomenon, called promoter-proximal pausing, is observed in 10–50% of the entire genes from Drosophila embryos to human cells. Release of paused Pol II is primarily mediated by the activated form of positive transcription elongation factor b (P-TEFb) initially sequestered in the inhibitory 7SK small nuclear ribonucleoprotein (7SK snRNP) complex. Many proteins and RNAs have been discovered and studied in detail to explain the process of the pausing and release of Pol II in relation to P-TEFb. At the functional level, promoter-proximal pausing regulates genes involved in stimulus-response and development in Drosophila. In mammalian stem cell biology, pausing is important for proliferation and signaling in embryonic stem cells and the formation of induced pluripotent stem cells. Other than this, however, little is known about the biological significance of pausing in mammalian cell differentiation. Further study on pausing mechanisms as well as its functions will contribute to the development of stem cell biology and its clinical applications. PMID:27158559

  14. The reciprocal regulation between splicing and 3'-end processing.

    PubMed

    Kaida, Daisuke

    2016-07-01

    Most eukaryotic precursor mRNAs are subjected to RNA processing events, including 5'-end capping, splicing and 3'-end processing. These processing events were historically studied independently; however, since the early 1990s tremendous efforts by many research groups have revealed that these processing factors interact with each other to control each other's functions. U1 snRNP and its components negatively regulate polyadenylation of precursor mRNAs. Importantly, this function is necessary for protecting the integrity of the transcriptome and for regulating gene length and the direction of transcription. In addition, physical and functional interactions occur between splicing factors and 3'-end processing factors across the last exon. These interactions activate or inhibit splicing and 3'-end processing depending on the context. Therefore, splicing and 3'-end processing are reciprocally regulated in many ways through the complex protein-protein interaction network. Although interesting questions remain, future studies will illuminate the molecular mechanisms underlying the reciprocal regulation. WIREs RNA 2016, 7:499-511. doi: 10.1002/wrna.1348 For further resources related to this article, please visit the WIREs website. PMID:27019070

  15. Gemin3 Is an Essential Gene Required for Larval Motor Function and Pupation in Drosophila

    PubMed Central

    Shpargel, Karl B.; Praveen, Kavita; Rajendra, T. K.

    2009-01-01

    The assembly of metazoan Sm-class small nuclear ribonucleoproteins (snRNPs) is an elaborate, step-wise process that takes place in multiple subcellular compartments. The initial steps, including formation of the core RNP, are mediated by the survival motor neuron (SMN) protein complex. Loss-of-function mutations in human SMN1 result in a neuromuscular disease called spinal muscular atrophy. The SMN complex is comprised of SMN and a number of tightly associated proteins, collectively called Gemins. In this report, we identify and characterize the fruitfly ortholog of the DEAD box protein, Gemin3. Drosophila Gemin3 (dGem3) colocalizes and interacts with dSMN in vitro and in vivo. RNA interference for dGem3 codepletes dSMN and inhibits efficient Sm core assembly in vitro. Transposon insertion mutations in Gemin3 are larval lethals and also codeplete dSMN. Transgenic overexpression of dGem3 rescues lethality, but overexpression of dSMN does not, indicating that loss of dSMN is not the primary cause of death. Gemin3 mutant larvae exhibit motor defects similar to previously characterized Smn alleles. Remarkably, appreciable numbers of Gemin3 mutants (along with one previously undescribed Smn allele) survive as larvae for several weeks without pupating. Our results demonstrate the conservation of Gemin3 protein function in metazoan snRNP assembly and reveal that loss of either Smn or Gemin3 can contribute to neuromuscular dysfunction. PMID:18923150

  16. 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

  17. Developing therapies for spinal muscular atrophy.

    PubMed

    Wertz, Mary H; Sahin, Mustafa

    2016-02-01

    Spinal muscular atrophy is an autosomal-recessive pediatric neurodegenerative disease characterized by loss of spinal motor neurons. It is caused by mutation in the gene survival of motor neuron 1 (SMN1), leading to loss of function of the full-length SMN protein. SMN has a number of functions in neurons, including RNA splicing and snRNP biogenesis in the nucleus, and RNA trafficking in neurites. The expression level of full-length SMN protein from the SMN2 locus modifies disease severity. Increasing full-length SMN protein by a small amount can lead to significant improvements in the neurological phenotype. Currently available interventions for spinal muscular atrophy patients are physical therapy and orthopedic, nutritional, and pulmonary interventions; these are palliative or supportive measures and do not address the etiology of the disease. In the past decade, there has been a push for developing therapeutics to improve motor phenotypes and increase life span of spinal muscular atrophy patients. These therapies are aimed primarily at restoration of full-length SMN protein levels, but other neuroprotective treatments have been investigated as well. Here, we discuss recent advances in basic and clinical studies toward finding safe and effective treatments of spinal muscular atrophy using gene therapy, antisense oligonucleotides, and other small molecule modulators of SMN expression. PMID:26173388

  18. Vent Processes and Deposits of a Hiatus in a Violent Eruption: Quilotoa Volcano, Ecuador

    NASA Astrophysics Data System (ADS)

    Best, J. A.; Bustillos, J.; Ort, M. H.; Cashman, K. V.; Mothes, P. A.; di Muro, A.; Rosi, M.

    2010-12-01

    The 800 BP eruption of Quilotoa volcano, Ecuador, produced two plinian eruptions separated by a short (days-weeks) hiatus. Units 1 and 3 (U1 and U3) of the eruption correspond to the first and second Plinian eruptions, respectively, and produced fallout and pyroclastic density currents. Unit 2 (U2) records processes during the hiatus and consists of three subunits: U2a, U2b, and U2c. 147 tephra samples of U1, U2, and U3 were collected from 25 sites from around the volcano. Thickness and grain-size features were described, with particular attention paid to U2, in order to characterize the processes that occurred during the eruptive hiatus. Grain-size and componentry analysis of a subset of these samples reveals a number of trends. The upper part of U1 is massive and normally graded at its top, 32-45 % dominantly vitric ash ≤ 3.0 φ, and likely represents the clearing of the air at the end of the first plinian eruption. U2a, present out to a maximum of 7 km from the vent, has a polymodal distribution with a large fraction of 4.0 φ and finer vitric material. Dune forms occur in this unit, which are interpreted to be the product of surges. The areal distribution of U2a is constrained by topography, whereas U2b is not. U2b is coarser overall with alternating fine- (2-3φ) and coarse- (1-2φ) grained layers. The beds, both coarse and fine, have a near-bimodal grain-size distribution and normal grading. U2b is interpreted as a fall deposit. The U2a/U2b contact is gradational in that 0-2 beds of U2b material occur within the uppermost U2a beds at proximal localities, indicating vent conditions for both briefly coexisted. U2c is a <2-cm-thick vitric ash bed with sparse dense juvenile vitric lapilli. These lapilli also occur in the overlying basal U3 fallout, which has a polymodal grain-size distribution. U2b is characteristically orange in color due to the dust that loosely covers the grains. Hydrothermal activity within the vent is likely the source of this staining

  19. Detailed deletion mapping in sporadic breast cancer at chromosomal region 17p13 distal to the TP53 gene: association with clinicopathological parameters.

    PubMed

    Seitz, S; Poppe, K; Fischer, J; Nothnagel, A; Estévez-Schwarz, L; Haensch, W; Schlag, P M; Scherneck, S

    2001-07-01

    Chromosome 17p is among the most frequently deleted regions in a variety of human malignancies including breast cancer. This study has further refined the localization of a putative tumour suppressor gene (TSG) at 17p13 distal to the TP53 gene in breast carcinomas. It was found that 73% (37 of 51) of the breast tumours exhibited loss of heterozygosity (LOH) at one or more loci at 17p13. The allelic loss patterns of these tumours suggest the presence of at least seven commonly deleted regions on 17p13. The three most frequently deleted regions were mapped at chromosomal location 17p13.3-17p13.2 between the markers D17S831 and D17S1845 (56% LOH), at 17p13.1 between D17S1810 and D17S1832 (53% LOH), and at 17p13.1 between D17S938 and TP53 (55% LOH). A significant correlation was found between loss at 17p13 and tumour grade, size, proliferative activity, and oestrogen receptor (ER) status. Losses at 17p13 were seen more frequently in large and poorly differentiated tumours with high proliferative activity. These data support and extend previous reports on the presence of a putative TSG(s) at chromosomal region 17p13 distal to the TP53 gene and show that different subsets of LOH are associated with more aggressive tumour behaviour. PMID:11439364

  20. 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.

  1. 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.

  2. 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...

  3. 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...

  4. 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...

  5. 40 CFR 98.214 - Monitoring and QA/QC requirements.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 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, 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...

  7. 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

  8. 49 CFR 572.183 - Neck assembly.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... CFR 572.33) at the time the pendulum makes contact with the decelerating mechanism. The velocity-time... 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)...

  9. 49 CFR 572.183 - Neck assembly.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... CFR 572.33) at the time the pendulum makes contact with the decelerating mechanism. The velocity-time... 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)...

  10. 49 CFR 572.183 - Neck assembly.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... CFR 572.33) at the time the pendulum makes contact with the decelerating mechanism. The velocity-time... 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)...

  11. 49 CFR 572.183 - Neck assembly.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... CFR 572.33) at the time the pendulum makes contact with the decelerating mechanism. The velocity-time... 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)...

  12. 49 CFR 572.183 - Neck assembly.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... CFR 572.33) at the time the pendulum makes contact with the decelerating mechanism. The velocity-time... 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)...

  13. Vent Processes and Deposits of a Hiatus in a Violent Eruption: Quilotoa Volcano, Ecuador

    NASA Astrophysics Data System (ADS)

    Best, J. A.; Bustillos, J.; Ort, M. H.; Cashman, K. V.; Mothes, P. A.; di Muro, A.; Rosi, M.

    2009-12-01

    The 800 BP eruption of Quilotoa volcano, Ecuador, produced two plinian eruptions separated by a short (days-weeks) hiatus. We examine the tephra produced both during this hiatus and erupted at the onset of the second Plinian eruption. Units 1 and 3 (U1 and U3) of the eruption correspond to the first and second Plinian eruptions, respectively, and produced fallout and pyroclastic density currents. Unit 2 (U2) records processes during the hiatus and consists of two subunits: U2a, a vitric ashfall, and U2b, a crystal and lithic-rich fallout. 130 individual tephra samples of U1, U2, and U3 were collected from 24 sites along three radial transects from the volcano in January 2009. Thickness and grain-size features were described, with particular attention paid to U2. Grain-size and componentry analysis of a subset of these samples reveals a number of trends. The upper part of U1 is massive and normally graded at its top. This part of U1 is dominantly vitric ash smaller than 3.0 φ and likely represents the clearing of the air at the end of the first plinian eruption. U2a has a polymodal distribution with a large fraction of 4.0 φ and finer vitric material. Dune forms occur in this unit, which is interpreted to be the product of surges. U2b is coarser overall with alternating fine- (2-3φ) and coarse- (1-2φ) grained layers. The beds have a unimodal grain-size distribution and normal grading. U2b is interpreted as a fall deposit. The U2a/U2b contact is gradational in that 0-2 beds of U2b material occur within the uppermost U2a beds, indicating vent conditions for both briefly coexisted. U2c is a <2-cm-thick vitric ash with sparse crystal-rich lava lapilli. These lapilli also occur in the overlying basal U3 fallout, which has a polymodal grain-size distribution. Some U2b pumice fragments and crystals are stained orange, which gives U2b its characteristic color. Stained grains are also present but rare in other units and may have been sourced from the conduit walls. The

  14. One-step, regioselective synthesis of up to 50-mers of RNA oligomers by montmorillonite catalysis.

    PubMed

    Huang, Wenhua; Ferris, James P

    2006-07-12

    5'-Nucleotides of A and U with the phosphate activated with 1-methyladenine generate RNA oligomers containing 40-50 monomers in 1 day in reactions catalyzed by montmorillonite. The corresponding monomers of C give oligomers that are 20-25-mers in length after a 9-day reaction. It was not possible to determine the chain lengths of the oligomers of G since they did not give well-defined bands on gel electrophoresis. Co-oligomers of A and U as well as A, U, G, and C were also prepared. The oligo(A)s formed were separated by gel electrophoresis, and the bands of the 7-39-mers were isolated, the 3',5'-phosphodiester bonds were cleaved by RNase T(2), and the terminal phosphate groups were cleaved with alkaline phosphatase. HPLC analysis revealed that the proportions of A(5)'pp(5)'A, A, A(2)'pA, and A(2)'pA(2)'pA formed were almost the same for the long and shorter oligomers. A similar structure analysis performed on the oligo(U)s established that the proportions of U(5)'pp(5)'U, U, U(2)'pU, U(2)'pU(2)'pU, U(2)'pU(2)'pU(2)'pU, and U(2)'pU(2)'pU(2)'pU(2)'pU did not vary with chain length. The structural analysis of the oligomers of A revealed that 74% of the phosphodiester bonds were 3',5'-linked a value slightly greater than 67% observed when imidazole was the activating group. 61% of the bonds in the U oligomers were 3',5'-linked, which is almost 3 times greater than the 20% measured when imidazole was the activating group. The potential significance of these data to the origin and early evolution of life is discussed. PMID:16819887

  15. 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.

  16. 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.

  17. The importance of wall-normal Reynolds stress in turbulent rough channel flows

    NASA Astrophysics Data System (ADS)

    Orlandi, P.

    2013-11-01

    In this paper, it is demonstrated by DNS of turbulent rough channels that a proportionality between widetilde{u}_2^' |_w (the wall-normal Reynolds stress widetilde{u}_2^' =< u_2^' 2} rangle ^{1/2} at the top of the roughness elements) and the roughness function does exist. This observation confirmed by experiments allows the derivation of a simple expression for the velocity profile in the log-region. This parameterization of rough walls through widetilde{u}_2^' |_w is suggested by the direct link between wall structures and partial ^2 widetilde{u_2^' }}^2/partial x^22. Identification of the wall structures, near smooth and different kinds of rough surfaces, demonstrates flow isotropization near rough walls, corroborated by profiles of partial ^2 widetilde{u_2^' }}^2/partial x^22, is depicted by visualizations of ∇2p. The relationship between the roughness function and widetilde{u}_2^' |_w allows the derivation of a new kind of Moody diagram, useful in the prediction of friction factors of rough flows at high Reynolds numbers.

  18. 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].

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

    PubMed

    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

    2015-12-15

    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

  20. Extensive genetic interactions between PRP8 and PRP17/CDC40, two yeast genes involved in pre-mRNA splicing and cell cycle progression.

    PubMed Central

    Ben-Yehuda, S; Russell, C S; Dix, I; Beggs, J D; Kupiec, M

    2000-01-01

    Biochemical and genetic experiments have shown that the PRP17 gene of the yeast Saccharomyces cerevisiae encodes a protein that plays a role during the second catalytic step of the splicing reaction. It was found recently that PRP17 is identical to the cell division cycle CDC40 gene. cdc40 mutants arrest at the restrictive temperature after the completion of DNA replication. Although the PRP17/CDC40 gene product is essential only at elevated temperatures, splicing intermediates accumulate in prp17 mutants even at the permissive temperature. In this report we describe extensive genetic interactions between PRP17/CDC40 and the PRP8 gene. PRP8 encodes a highly conserved U5 snRNP protein required for spliceosome assembly and for both catalytic steps of the splicing reaction. We show that mutations in the PRP8 gene are able to suppress the temperature-sensitive growth phenotype and the splicing defect conferred by the absence of the Prp17 protein. In addition, these mutations are capable of suppressing certain alterations in the conserved PyAG trinucleotide at the 3' splice junction, as detected by an ACT1-CUP1 splicing reporter system. Moreover, other PRP8 alleles exhibit synthetic lethality with the absence of Prp17p and show a reduced ability to splice an intron bearing an altered 3' splice junction. On the basis of these findings, we propose a model for the mode of interaction between the Prp8 and Prp17 proteins during the second catalytic step of the splicing reaction. PMID:10628969

  1. 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.

  2. Structure and interactions of the first three RNA recognition motifs of splicing factor Prp24

    PubMed Central

    Bae, Euiyoung; Reiter, Nicholas J.; Bingman, Craig A.; Kwan, Sharon S.; Lee, Donghan; Phillips, George N.; Butcher, Samuel E.; Brow, David A.

    2007-01-01

    Summary The essential Saccharomyces cerevisiae pre-messenger RNA splicing protein 24 (Prp24) has four RNA recognition motifs (RRMs) and facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 is a component of the free U6 small nuclear ribonucleoprotein particle (snRNP) but not the U4/U6 bi-snRNP, and so is thought to be displaced from U6 by U4/U6 base-pairing. The interaction partners of each of the four RRMs of Prp24 and how these interactions direct U4/U6 pairing are not known. Here we report the crystal structure of the first three RRMs and the solution structure of the first two RRMs of Prp24. Strikingly, RRM 2 forms extensive inter-domain contacts with RRMs 1 and 3. These contacts occupy much of the canonical RNA-binding faces (β-sheets) of RRMs 1 and 2, but leave the β-sheet of RRM 3 exposed. Previously identified substitutions in Prp24 that suppress mutations in U4 and U6 spliceosomal RNAs cluster primarily in the β-sheet of RRM 3, but also in a conserved loop of RRM 2. RNA binding assays and chemical shift mapping indicate that a large basic patch evident on the surface of RRMs 1 and 2 is part of a high affinity U6 RNA binding site. Our results suggest that Prp24 binds free U6 RNA primarily with RRMs 1 and 2, which may remodel the U6 secondary structure. The β-sheet of RRM 3 then influences U4/U6 pairing through interaction with an unidentified ligand. PMID:17320109

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

    PubMed Central

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

    2015-01-01

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

  4. Supraspliceosomes at Defined Functional States Portray the Pre-Assembled Nature of the Pre-mRNA Processing Machine in the Cell Nucleus

    PubMed Central

    Kotzer-Nevo, Hani; de Lima Alves, Flavia; Rappsilber, Juri; Sperling, Joseph; Sperling, Ruth

    2014-01-01

    When isolated from mammalian cell nuclei, all nuclear pre-mRNAs are packaged in multi-subunit large ribonucleoprotein complexes—supraspliceosomes—composed of four native spliceosomes interconnected by the pre-mRNA. Supraspliceosomes contain all five spliceosomal U snRNPs, together with other splicing factors, and are functional in splicing. Supraspliceosomes studied thus far represent the steady-state population of nuclear pre-mRNAs that were isolated at different stages of the splicing reaction. To analyze specific splicing complexes, here, we affinity purified Pseudomonas aeruginosa phage 7 (PP7)-tagged splicing complexes assembled in vivo on Adenovirus Major Late (AdML) transcripts at specific functional stages, and characterized them using molecular techniques including mass spectrometry. First, we show that these affinity purified splicing complexes assembled on PP7-tagged AdML mRNA or on PP7-tagged AdML pre-mRNA are assembled in supraspliceosomes. Second, similar to the general population of supraspliceosomes, these defined supraspliceosomes populations are assembled with all five U snRNPs at all splicing stages. This study shows that dynamic changes in base-pairing interactions of U snRNA:U snRNA and U snRNA:pre-mRNA that occur in vivo during the splicing reaction do not require changes in U snRNP composition of the supraspliceosome. Furthermore, there is no need to reassemble a native spliceosome for the splicing of each intron, and rearrangements of the interactions will suffice. PMID:24983480

  5. 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. PMID:8018391

  6. Crystal structure, mutational analysis and RNA-dependent ATPase activity of the yeast DEAD-box pre-mRNA splicing factor Prp28

    DOE PAGESBeta

    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 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

  7. The 3.8 Å structure of the U4/U6.U5 tri-snRNP: Insights into spliceosome assembly and catalysis.

    PubMed

    Wan, Ruixue; Yan, Chuangye; Bai, Rui; Wang, Lin; Huang, Min; Wong, Catherine C L; Shi, Yigong

    2016-01-29

    Splicing of precursor messenger RNA is accomplished by a dynamic megacomplex known as the spliceosome. Assembly of a functional spliceosome requires a preassembled U4/U6.U5 tri-snRNP complex, which comprises the U5 small nuclear ribonucleoprotein (snRNP), the U4 and U6 small nuclear RNA (snRNA) duplex, and a number of protein factors. Here we report the three-dimensional structure of a Saccharomyces cerevisiae U4/U6.U5 tri-snRNP at an overall resolution of 3.8 angstroms by single-particle electron cryomicroscopy. The local resolution for the core regions of the tri-snRNP reaches 3.0 to 3.5 angstroms, allowing construction of a refined atomic model. Our structure contains U5 snRNA, the extensively base-paired U4/U6 snRNA, and 30 proteins including Prp8 and Snu114, which amount to 8495 amino acids and 263 nucleotides with a combined molecular mass of ~1 megadalton. The catalytic nucleotide U80 from U6 snRNA exists in an inactive conformation, stabilized by its base-pairing interactions with U4 snRNA and protected by Prp3. Pre-messenger RNA is bound in the tri-snRNP through base-pairing interactions with U6 snRNA and loop I of U5 snRNA. This structure, together with that of the spliceosome, reveals the molecular choreography of the snRNAs in the activation process of the spliceosomal ribozyme. PMID:26743623

  8. 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

  9. Structure, dynamics and RNA binding of the multi-domain splicing factor TIA-1

    PubMed Central

    Wang, Iren; Hennig, Janosch; Jagtap, Pravin Kumar Ankush; Sonntag, Miriam; Valcárcel, Juan; Sattler, Michael

    2014-01-01

    Alternative pre-messenger ribonucleic acid (pre-mRNA) splicing is an essential process in eukaryotic gene regulation. The T-cell intracellular antigen-1 (TIA-1) is an apoptosis-promoting factor that modulates alternative splicing of transcripts, including the pre-mRNA encoding the membrane receptor Fas. TIA-1 is a multi-domain ribonucleic acid (RNA) binding protein that recognizes poly-uridine tract RNA sequences to facilitate 5′ splice site recognition by the U1 small nuclear ribonucleoprotein (snRNP). Here, we characterize the RNA interaction and conformational dynamics of TIA-1 by nuclear magnetic resonance (NMR), isothermal titration calorimetry (ITC) and small angle X-ray scattering (SAXS). Our NMR-derived solution structure of TIA-1 RRM2–RRM3 (RRM2,3) reveals that RRM2 adopts a canonical RNA recognition motif (RRM) fold, while RRM3 is preceded by an non-canonical helix α0. NMR and SAXS data show that all three RRMs are largely independent structural modules in the absence of RNA, while RNA binding induces a compact arrangement. RRM2,3 binds to pyrimidine-rich FAS pre-mRNA or poly-uridine (U9) RNA with nanomolar affinities. RRM1 has little intrinsic RNA binding affinity and does not strongly contribute to RNA binding in the context of RRM1,2,3. Our data unravel the role of binding avidity and the contributions of the TIA-1 RRMs for recognition of pyrimidine-rich RNAs. PMID:24682828

  10. Nuclear speckles are involved in nuclear aggregation of PABPN1 and in the pathophysiology of oculopharyngeal muscular dystrophy.

    PubMed

    Bengoechea, Rocío; Tapia, Olga; Casafont, Iñigo; Berciano, José; Lafarga, Miguel; Berciano, María T

    2012-04-01

    Nuclear speckles are essential nuclear compartments involved in the assembly, delivery and recycling of pre-mRNA processing factors, and in the post-transcriptional processing of pre-mRNAs. Oculopharyngeal muscular dystrophy (OPMD) is caused by a small expansion of the polyalanine tract in the poly(A)-binding protein nuclear 1 (PABPN1). Aggregation of expanded PABPN1 into intranuclear inclusions (INIs) in skeletal muscle fibers is the pathological hallmark of OPMD. In this study what we have analyzed in muscle fibers of OPMD patients and in primary cultures of human myoblasts are the relationships between nuclear speckles and INIs, and the contribution of the former to the biogenesis of the latter. While nuclear speckles concentrate snRNP splicing factors and PABPN1 in control muscle fibers, they are depleted of PABPN1 and appear closely associated with INIs in muscle fibers of OPMD patients. The induction of INI formation in human myoblasts expressing either wild type GFP-PABPN1 or expanded GFP-PABPN1-17ala demonstrates that the initial aggregation of PABPN1 proteins and their subsequent growth in INIs occurs at the edges of the nuclear speckles. Moreover, the growing of INIs gradually depletes PABPN1 proteins and poly(A) RNA from nuclear speckles, although the existence of these nuclear compartments is preserved. Time-lapse experiments in cultured myoblasts confirm nuclear speckles as biogenesis sites of PABPN1 inclusions. Given the functional importance of nuclear speckles in the post-transcriptional processing of pre-mRNAs, the INI-dependent molecular reorganization of these nuclear compartments in muscle fibers may cause a severe dysfunction in nuclear trafficking and processing of polyadenylated mRNAs, thereby contributing to the molecular pathophysiology of OPMD. Our results emphasize the potential importance of nuclear speckles as nuclear targets of neuromuscular disorders. PMID:22249111

  11. A role for complexes of survival of motor neurons (SMN) protein with gemins and profilin in neurite-like cytoplasmic extensions of cultured nerve cells

    SciTech Connect

    Sharma, Aarti; Lambrechts, Anja; Le thi Hao; Le, Thanh T.; Sewry, Caroline A.; Ampe, Christophe; Burghes, Arthur H.M.; Morris, Glenn E. . E-mail: glenn.morris@rjah.nhs.uk

    2005-09-10

    Spinal muscular atrophy (SMA) is caused by reduced levels of SMN (survival of motor neurons protein) and consequent loss of motor neurons. SMN is involved in snRNP transport and nuclear RNA splicing, but axonal transport of SMN has also been shown to occur in motor neurons. SMN also binds to the small actin-binding protein, profilin. We now show that SMN and profilin II co-localise in the cytoplasm of differentiating rat PC12 cells and in neurite-like extensions, especially at their growth cones. Many components of known SMN complexes were also found in these extensions, including gemin2 (SIP-1), gemin6, gemin7 and unrip (unr-interacting protein). Coilin p80 and Sm core protein immunoreactivity, however, were seen only in the nucleus. SMN is known to associate with {beta}-actin mRNA and specific hnRNPs in axons and in neurite extensions of cultured nerve cells, and SMN also stimulates neurite outgrowth in cultures. Our results are therefore consistent with SMN complexes, rather than SMN alone, being involved in the transport of actin mRNPs along the axon as in the transport of snRNPs into the nucleus by similar SMN complexes. Antisense knockdown of profilin I and II isoforms inhibited neurite outgrowth of PC12 cells and caused accumulation of SMN and its associated proteins in cytoplasmic aggregates. BIAcore studies demonstrated a high affinity interaction of SMN with profilin IIa, the isoform present in developing neurons. Pathogenic missense mutations in SMN, or deletion of exons 5 and 7, prevented this interaction. The interaction is functional in that SMN can modulate actin polymerisation in vitro by reducing the inhibitory effect of profilin IIa. This suggests that reduced SMN in SMA might cause axonal pathfinding defects by disturbing the normal regulation of microfilament growth by profilins.

  12. 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. PMID:27421219

  13. 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.

  14. Phosphoregulation of the human SMN complex.

    PubMed

    Husedzinovic, Alma; Oppermann, Felix; Draeger-Meurer, Stefanie; Chari, Ashwin; Fischer, Utz; Daub, Henrik; Gruss, Oliver J

    2014-03-01

    The survival motor neuron (SMN) complex is a macromolecular machine comprising 9 core proteins: SMN, Gemins2-8 and unrip in vertebrates. It performs tasks in RNA metabolism including the cytoplasmic assembly of spliceosomal small nuclear ribonucleoprotein particles (snRNPs). The SMN complex also localizes to the nucleus, where it accumulates in Cajal Bodies (CB) and may function in transcription and/or pre-mRNA splicing. The SMN complex is subject to extensive phosphorylation. Detailed understanding of SMN complex regulation necessitates a comprehensive analysis of these post-translational modifications. Here, we report on the first comprehensive phosphoproteome analysis of the intact human SMN complex, which identify 48 serine/threonine phosphosites in the complex. We find that 7 out of 9 SMN components of the intact complex are phosphoproteins and confidently place 29 phosphorylation sites, 12 of them in SMN itself. By the generation of multi non-phosphorylatable or phosphomimetic variants of SMN, respectively, we address to which extent phosphorylation regulates SMN complex function and localization. Both phosphomimetic and non-phosphorylatable variants assemble into intact SMN complexes and can compensate the loss of endogenous SMN in snRNP assembly at least to some extent. However, they partially or completely fail to target to nuclear Cajal bodies. Moreover, using a mutant of SMN, which cannot be phosphorylated on previously reported tyrosine residues, we provide first evidence that this PTM regulates SMN localization and nuclear accumulation. Our data suggest complex regulatory cues mediated by phosphorylation of serine/threonine and tyrosine residues, which control the subcellular localization of the SMN complex and its accumulation in nuclear CB. PMID:24602413

  15. RBP45 and RBP47, two oligouridylate-specific hnRNP-like proteins interacting with poly(A)+ RNA in nuclei of plant cells.

    PubMed Central

    Lorković, Z J; Wieczorek Kirk, D A; Klahre, U; Hemmings-Mieszczak, M; Filipowicz, W

    2000-01-01

    Introns in plant nuclear pre-mRNAs are highly enriched in U or U + A residues and this property is essential for efficient splicing. Moreover, 3'-untranslated regions (3'-UTRs) in plant pre-mRNAs are generally UA-rich and contain sequences that are important for the polyadenylation reaction. Here, we characterize two structurally related RNA-binding proteins (RBPs) from Nicotiana plumbaginifolia, referred to as RBP45 and RBP47, having specificity for oligouridylates. Both proteins contain three RBD-type RNA-binding domains and a glutamine-rich N-terminus, and share similarity with Nam8p, a protein associated with U1 snRNP in the yeast Saccharomyces cerevisiae. Deletion analysis of RBP45 and RBP47 indicated that the presence of at least two RBD are required for interaction with RNA and that domains other than RBD do not significantly contribute to binding. mRNAs for RBP45 and RBP47 and mRNAs encoding six related proteins in Arabidopsis thaliana are constitutively expressed in different plant organs. Indirect immunofluorescence and fractionation of cell extracts showed that RBP45 and RBP47 are localized in the nucleus. In vivo UV crosslinking experiments demonstrated their association with the nuclear poly(A)+ RNA. In contrast to UBP1, another oligouridylate-binding nuclear three-RBD protein of N. plumbaginifolia (Lambermon et al., EMBO J, 2000, 19:1638-1649), RBP45 and RBP47 do not stimulate mRNA splicing and accumulation when transiently overexpressed in protoplasts. Properties of RBP45 and RBP47 suggest they represent hnRNP-proteins participating in still undefined steps of pre-mRNA maturation in plant cell nuclei. PMID:11105760

  16. The sequence complementarity between HIV-1 5' splice site SD4 and U1 snRNA determines the steady-state level of an unstable env pre-mRNA.

    PubMed Central

    Kammler, S; Leurs, C; Freund, M; Krummheuer, J; Seidel, K; Tange, T O; Lund, M K; Kjems, J; Scheid, A; Schaal, H

    2001-01-01

    HIV-1 env expression from certain subgenomic vectors requires the viral regulatory protein Rev, its target sequence RRE, and a 5' splice site upstream of the env open reading frame. To determine the role of this splice site in the 5'-splice-site-dependent Rev-mediated env gene expression, we have subjected the HIV-1 5' splice site, SD4, to a mutational analysis and have analyzed the effect of those mutations on env expression. The results demonstrate that the overall strength of hydrogen bonding between the 5' splice site, SD4, and the free 5' end of the U1 snRNA correlates with env expression efficiency, as long as env expression is suboptimal, and that a continuous stretch of 14 hydrogen bonds can lead to full env expression, as a result of stabilizing the pre-mRNA. The U1 snRNA-mediated stabilization is independent of functional splicing, as a mismatch in position +1 of the 5' splice site that led to loss of detectable amounts of spliced transcripts did not preclude stabilization and expression of the unspliced env mRNA, provided that Rev enables its nuclear export. The nucleotides capable of participating in U1 snRNA:pre-mRNA interaction include positions -3 to +8 of the 5' splice site and all 11 nt constituting the single-stranded 5' end of U1 snRNA. Moreover, env gene expression is significantly decreased upon the introduction of point mutations in several upstream GAR nucleotide motifs, which are mediating SF2/ASF responsiveness in an in vitro splicing assay. This suggests that the GAR sequences may play a role in stabilizing the pre-mRNA by sequestering U1 snRNP to SD4. PMID:11333022

  17. Estrogen receptor alpha (ESR1)-signaling regulates the expression of the taxane-response biomarker PRP4K.

    PubMed

    Lahsaee, Sara; Corkery, Dale P; Anthes, Livia E; Holly, Alice; Dellaire, Graham

    2016-01-01

    The pre-mRNA splicing factor 4 kinase PRP4K (PRPF4B), is an essential kinase that is a component of the U5 snRNP and functions in spliceosome assembly. We demonstrated that PRP4K is a novel biological marker for taxane response in ovarian cancer patients and reduced levels of PRP4K correlate with intrinsic and acquired taxane resistance in both breast and ovarian cancer. Breast cancer treatments are chosen based on hormone and growth factor receptor status, with HER2 (ERBB2) positive breast cancer patients receiving anti-HER2 agents and taxanes and estrogen receptor alpha (ESR1) positive (ER+) breast cancer patients receiving anti-estrogen therapies such as tamoxifen. Here we demonstrate that PRP4K is expressed in the normal mammary duct epithelial cells of the mouse, and that estrogen induces PRP4K gene and protein expression in ER+ human MCF7 breast cancer cells. Estrogen acts through ESR1 to regulate PRP4K expression, as over-expression of ESR1 in the ER-negative MDA-MB-231 breast cancer cell line increased the expression of this kinase, and knock-down of ESR1 in ER+ T47D breast cancer cells reduced PRP4K levels. Furthermore, treatment with 4-hydroxytamoxifen (4-OHT) resulted in a dose-dependent decrease in PRP4K protein expression in MCF7 cells. Consistent with our previous studies identifying PRP4K as a taxane-response biomarker, reduced PRP4K expression in 4-OHT-treated cells correlated with reduced sensitivity to paclitaxel. Thus, PRP4K is novel estrogen regulated kinase, and its levels can be reduced by 4-OHT in ER+ breast cancer cells altering their response to taxanes. PMID:26712520

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

    PubMed Central

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

    2015-01-01

    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. PMID:25838544

  19. 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.

  20. Temporal Profiling of Lapatinib-suppressed Phosphorylation Signals in EGFR/HER2 Pathways*

    PubMed Central

    Imami, Koshi; Sugiyama, Naoyuki; Imamura, Haruna; Wakabayashi, Masaki; Tomita, Masaru; Taniguchi, Masatoshi; Ueno, Takayuki; Toi, Masakazu; Ishihama, Yasushi

    2012-01-01

    Lapatinib is a clinically potent kinase inhibitor for breast cancer patients because of its outstanding selectivity for epidermal growth factor receptor (EGFR) and EGFR2 (also known as HER2). However, there is only limited information about the in vivo effects of lapatinib on EGFR/HER2 and downstream signaling targets. Here, we profiled the lapatinib-induced time- and dose-dependent phosphorylation dynamics in SKBR3 breast cancer cells by means of quantitative phosphoproteomics. Among 4953 identified phosphopeptides from 1548 proteins, a small proportion (5–7%) was regulated at least twofold by 1–10 μm lapatinib. We obtained a comprehensive phosphorylation map of 21 sites on EGFR/HER2, including nine novel sites on HER2. Among them, serine/threonine phosphosites located in a small region of HER2 (amino acid residues 1049–1083) were up-regulated by the drug, whereas all other sites were down-regulated. We show that cAMP-dependent protein kinase is involved in phosphorylation of this particular region of HER2 and regulates HER2 tyrosine kinase activity. Computational analyses of quantitative phosphoproteome data indicated for the first time that protein-protein networks related to cytoskeletal organization and transcriptional/translational regulation, such as RNP complexes (i.e. hnRNP, snRNP, telomerase, ribosome), are linked to EGFR/HER2 signaling networks. To our knowledge, this is the first report to profile the temporal response of phosphorylation dynamics to a kinase inhibitor. The results provide new insights into EGFR/HER2 regulation through region-specific phosphorylation, as well as a global view of the cellular signaling networks associated with the anti-breast cancer action of lapatinib. PMID:22964224

  1. The missing puzzle piece: splicing mutations

    PubMed Central

    Lewandowska, Marzena A

    2013-01-01

    Proper gene splicing is highly dependent on the correct recognition of exons. Among the elements allowing this process are the “cis” (conserved sequences) and “trans” (snRNP, splicing factors) elements. Splicing mutations are related with a number of genetic disorders and usually induce exon skipping, form new exon/intron boundaries or activate new cryptic exons as a result of alterations at donor/acceptor sites. They constitute more than 9% of the currently published mutations, but this value is highly underestimated as many of the potential mutations are located in the “cis” elements and should be confirmed experimentally. The most commonly detected splicing mutations are located at donor (5’) and acceptor (3’) sites. Mutations at the branch point are rare (only over a dozen are known to date), and are mostly searched and detected when no alteration has been detected in the sequenced exons and UTRs. Polypyrimidine tract mutations are equally rare. High throughput technologies, as well as traditional Sanger sequencing, allow detection of many changes in intronic sequences and intron/exon boundaries. However, the assessment whether a mutation affects exon recognition and results in a genetic disorder has to be conducted using molecular biology methods: in vitro transcription of the sequence of interest cloned into a plasmid, with and without alterations, or mutation analysis via a hybrid minigene system. Even though microarrays and new generation sequencing methods pose difficulties in detecting novel branch point mutations, these tools seem appropriate to expand the mutation detection panel especially for diagnostic purposes. PMID:24294354

  2. 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…

  3. 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...

  4. MASTER: PSN in interacting galaxy, dwarf nova and possible YSO objects

    NASA Astrophysics Data System (ADS)

    Gress, O.; Shurpakov, S.; Pogrosheva, T.; Lipunov, V.; Lopez, R. Rebolo; Buckley, D.; Tlatov, A.; Gorbovskoy, E.; Tiurina, N.; Balanutsa, P.; Kuznetsov, A.; Kornilov, V.; Vlasenko, D.; Popova, E.; Ricart, M. Serra; Israelian, G.; Lodieu, N.; Potter, S.; Kniazev, A.; Senik, V.; Dormidontov, D.; Parkhomenko, A.; Kochutina, N.; Shumkov, V.

    2016-07-01

    MASTER-IAC auto-detection system ( Lipunov et al., "MASTER Global Robotic Net", Advances in Astronomy, 2010, 349171 ) discovered OT source at (RA, Dec) = 15h 16m 47.17s +28d 37m 42.8s on 2016-06-28.97168 UT. The OT unfiltered magnitude is 17.8m (limit 20.2m).

  5. 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., Jr.

    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

  6. A radiation hybrid map of the BRCA1 region of chromosome 17q12-q21

    SciTech Connect

    Abel, K.J.; Boehnke, M.; Prahalad, M.; Flejter, W.L.; Watkins, M.; Chandrasekharappa, S.C.; Glover, T.W. Howard Hughes Medical Institute, Ann Arbor, MI ); Ho, P.; VanderStoep, J.; Weber, B.L. ); Collins, F.S. Michigan Human Genome Center, Ann Arbor, MI Howard Hughes Medical Institute, Ann Arbor, MI )

    1993-09-01

    The chromosomal region 17q12-q21 contains a gene (BRCA1) conferring susceptibility to early-onset familial breast and ovarian cancer. An 8000-rad radiation-reduced hybrid (RH) panel was constructed to provide a resource for long-range mapping of this region. A large fraction of the hybrids ([approximately]90%) retained detectable human chromosome 17 sequences. The complete panel of 76 hybrids was scored for the presence or absence of 22 markers from this chromosomal region, including 14 cloned genes, seven microsatellite repeats, and one anonymous DNA segment. Statistical analysis of the marker retention data employing multipoint methods provided both comprehensive and framework maps of this chromosomal region, including distance estimates between adjacent markers. The comprehensive RH map includes 17 loci and spans 179 cRays[sub (8000)]. Likelihood ratios of at least 1000:1 support the 10-locus framework order: cen-D17S250-ERBB2-(THRA1, TOP2A)-D17S855-PPY-D17S190-MTBT1-GP3A-BTR-D17S588-tel. The order obtained from RH mapping, when used in conjunction with other methods, will be useful in linkage analysis of breast cancer families and will facilitate the development of a physical map of this region. 42 refs., 3 figs., 2 tabs.

  7. Local discrimination scheme for some unitary operations

    NASA Astrophysics Data System (ADS)

    Cao, TianQing; Gao, Fei; Tian, GuoJing; Xie, ShuCui; Wen, QiaoYan

    2016-09-01

    It has been shown that for two different multipartite unitary operations U 1 and U 2, when tr( U 1 † U 2) = 0, they can always be perfectly distinguished by local operations and classical communication in the single-run scenario. However, how to find the detailed scheme to complete the local discrimination is still a fascinating problem. In this paper, aiming at some U 1 and U 2 acting on the bipartite and tripartite space respectively, especially for U 1 † U 2 locally unitary equivalent to the high dimensional X-type hermitian unitary matrix V with tr V = 0, we put forward the explicit local distinguishing schemes in the single-run scenario.

  8. Evolution of dimerized phase in a one-dimensional correlated electron system

    NASA Astrophysics Data System (ADS)

    Ding, Hanqin; Zhang, Jun

    2015-02-01

    The one-dimensional half-filled correlated electron system with on-site (U), nearest-neighbor (V) and pair hopping (Y) repulsions is studied analytically at weak coupling, combined the Abelian bosonization with renormalization group methods. The corresponding ground-state phase diagram consists of three insulating phases, a charge-density-wave (CDW) phase for U - 2V< - 2Y, a spin-density-wave (SDW) phase for U - 2V> 2Y, and a bond-charge-density-wave (BOW) phase for | U - 2V | < 2Y. The pair hopping, which breaks an accident symmetry and splits the frustrating line U - 2V = 0, provides a possibility for the dimerized BOW phase between the CDW and SDW phases. In the phenomenological parameter regime, the superconducting (SC) and bond-spin-density-wave (BSDW) phases are briefly discussed.

  9. Evolution of dimerized phase in a one-dimensional correlated electron system

    NASA Astrophysics Data System (ADS)

    Ding, Hanqin; Zhang, Jun

    2015-02-01

    The one-dimensional half-filled correlated electron system with on-site ( U), nearest-neighbor ( V) and pair hopping ( Y) repulsions is studied analytically at weak coupling, combined the Abelian bosonization with renormalization group methods. The corresponding ground-state phase diagram consists of three insulating phases, a charge-density-wave (CDW) phase for U - 2 V< - 2 Y, a spin-density-wave (SDW) phase for U - 2 V> 2 Y, and a bond-charge-density-wave (BOW) phase for | U - 2 V | < 2 Y. The pair hopping, which breaks an accident symmetry and splits the frustrating line U - 2 V = 0, provides a possibility for the dimerized BOW phase between the CDW and SDW phases. In the phenomenological parameter regime, the superconducting (SC) and bond-spin-density-wave (BSDW) phases are briefly discussed.

  10. 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.

  11. 77 FR 53876 - Proposed Subsequent Arrangement

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-09-04

    ... arrangement concerns the retransfer of 2,959,580 kg of U.S.-origin natural uranium hexafluoride (UF6) (67.60% U), 2,000,000 kg of which is uranium, from Cameco Corporation (Cameco) in Saskatoon,...

  12. 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%.

  13. Caesium diuranium hexa­telluride

    PubMed Central

    Mesbah, Adel; Ibers, James A.

    2012-01-01

    Single crystals of CsU2Te6 were synthesized from the reaction of U, Te, and Cs2Te3 at 1273 K. CsU2Te6 crystallizes in the space group Cmcm in the CsTh2Te6 structure type. The asymmetric unit comprises one U (site symmetry m2m), one Cs (m2m; half-occupancy) and two Te atoms (m.. and m2m). The structure of CsU2Te6 consists of infinite [U2Te6] layers perpendicular to [010] separated by Cs atoms. There are infinite Te—Te—Te linear chains along [001]. PMID:23125566

  14. 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.

  15. Haplotype analysis of BRCA1 intragenic markers in Iranian patients with familial breast and ovarian cancer

    PubMed Central

    Miresmaeili, Seyed Mohsen; Kordi Tamandani, Dor Mohammad; Kalantar, Seyed Mehdi; Moshtaghioun, Seyed Mohammad

    2016-01-01

    Background: Breast cancer is the most common malignancy in women. Breast Cancer Type 1 Susceptibility gene (BRCA1) is a tumor suppressor gene, involved in DNA damage repair and in 81% of the breast-ovarian cancer families were due to BRCA1. In some clinically investigated genes, the intragenic marker polymorphism is important and the screening of such mutations is faster by using short tandem repeat (STR) polymorphism. Individual polymorphism of STR is a good evidence for following inheritance of repeat polymorphism. Objective: The aim of this study was to evaluate three intragenic BRCA1 marker polymorphisms in families, which have two or more patients with breast/ovarian cancer in comparison to healthy women. Materials and Methods: A total of 107 breast and/or ovarian cancer patients and 93 unrelated healthy women with no clinical phenotype of any malignancy or familial cancer history constitute the study groups. Haplotyping analysis, at 3 intragenic BRCA1 microsatellite markers (D17S855, D17S1322 and D17S1323), were performed for all subject and control groups using labeled primers. Results: After fragment analysis, significance differences were observed as follows: two alleles of D17S855; allele 146 (p=0.02) and 150 (p=0.006), and two alleles of D17S1322, allele 121 (p=0.015) and 142 (p=0.043). These differences were compared with control group. There was significance difference in 8 di/tri allelic haplotypes in present experimental subjects. Some haplotypes were observed to have approximately twice the relation risk for breast cancer. Conclusion: According to recent results, assessment of presence or absence of mentioned alleles in BRCA1 microsatellite can be used for prognosis in individuals, suspected of having or not having the breast cancer. PMID:27351029

  16. 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.

  17. Forest Fire Observation

    NASA Technical Reports Server (NTRS)

    1982-01-01

    Conditions on the perimeter of a forest fire can be obtained by use of airborne remote sensing techniques demonstrated by Ames Research Center. An Ames U-2 high-altitude survey aircraft served as an aerial fire observation system. Equipped with two types of sensors, the U-2 produces real-time infrared images of fireground scenes. Information acquired by the U-2's scanners defines the fire boundary and aids fire management decisions by showing the size, shape and direction of burn and the locations of hot spots in the fire zone. U-2 sends sensor date in digital form to an antenna at Ames Research Center. There the data is computer processed into images which are overlaid on U.S. Geological Survey topographical maps of the fire area. Maps are then transmitted by telecopy machine directly to fire control center. Whole process takes less than 10 minutes and the U-2 can provide information for up to five hours. Ames antenna can pick up signals from the U-2 anywhere within a 300 mile radius from Ames.

  18. 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.

  19. Impact of allogeneic hematopoietic cell transplant in patients with myeloid neoplasms carrying spliceosomal mutations.

    PubMed

    Hamilton, Betty Ky; Visconte, Valeria; Jia, Xuefei; Tabarroki, Ali; Makishima, Hideki; Hasrouni, Edy; Abounader, Donna; Kalaycio, Matt; Sekeres, Mikkael A; Sobecks, Ronald; Duong Liu, Hien; Bolwell, Brian; Maciejewski, Jaroslaw P; Copelan, Edward; Tiu, Ramon V

    2016-06-01

    Molecular predictors of outcome are increasingly important in determining optimal therapy for myeloid neoplasms. Mutations in the spliceosomal genes (U2AF1 and SRSF2) predict for poor outcomes in myelodysplastic syndromes (MDS) and related diseases. We investigated the effect of hematopoietic cell transplant (HCT) on the negative prognostic impact of U2AF1 and SRSF2 mutations. In total, 122 patients with MDS (30%), acute myeloid leukemia (51%), myeloproliferative neoplasms (MPN) (11%), and MDS/MPN (8%) receiving a HCT from 2003 to 2012 were evaluated for mutations in U2AF1 and SRSF2 by direct sequencing. Median time of follow up was 24 months (range 0.46-110). SRSF2 mutations were detected in 11 (10%) patients and U2AF1 in 3 (3%) patients. There were no significant differences in baseline characteristics between mutated and wild-type (WT) patients. Patients carrying SRSF2 and U2AF1 mutations had similar overall survival (P = 0.84), relapse mortality (P = 0.50), and non-relapse mortality (P = 0.72) compared to WT patients. However, taking into account disease status and cytogenetics in a subset of AML patients, SRSF2 and U2AF1 mutations were associated with worse survival (HR 3.71, P = 0.035). Am. J. Hematol. 91:406-409, 2016. © 2016 Wiley Periodicals, Inc. PMID:26799334

  20. Systematic search for markers linked to insulin-dependent diabetes on chromosome 17

    SciTech Connect

    Williams, S.R.; Shephard, J.M.; Berger, J.S.

    1994-09-01

    We tested 19 microsatellite markers on chromosome 17 for linkage with insulin-dependent diabetes mellitus (IDDM). Nuclear families (N = 235) with at least two affected offspring were provided by the British Diabetic Association, Human Biological Data Interchange, and our own lab. The mean interval ({plus_minus}sd) between markers was 8 {plus_minus} 3 cM. For each parent heterozygous at the marker locus being studied, we determined whether the same or different alleles were transmitted to the two affected sibs. The {open_quotes}degree of sharing{close_quotes} for each marker is the frequency with which the same parental allele is transmitted to both affected sibs. Linkage with IDDM susceptibility leads to values higher than 0.50 for degree of sharing. Unlike lods, this approach makes no assumption about mode of inheritance. Mean sharing for the 19 markers was 0.51 (range 0.460 to 0.557; sd = .03). Three markers on 17q (all mutually unlinked) showed sharing of {approximately}0.55. The degree of sharing was 228/414 = 0.551 for D17A807 ({chi}{sup 2} = 4.26, p = .04), 172/309 = 0.557 for D17S784 ({chi}{sup 2} = 3.96, p = .04), and 218/398 = 0.548 for D17S798 ({chi}{sup 2} = 3.63, p =.06). We also looked for evidence of linkage disequilibrium between IDDM and alleles of each of these markers, by means of the transmission/disequilibrium test of Spielman. No significant linkage disequilibrium was found for D17S784 or D17S798. However, allele 6 of D17S807 was transmitted from heterozygous parents to IDDM offspring with frequency 131/230 = 0.57 ({chi}{sup 2} = 4.45, p = .035), supporting linkage with IDDM. We are currently investigating other markers and candidate genes in the region of D17S807.

  1. 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.

  2. The mass concentration phenomenon for L 2-critical constrained problems related to Kirchhoff equations

    NASA Astrophysics Data System (ADS)

    Ye, Hongyu

    2016-04-01

    In this paper, we study the concentration behavior of critical points with a minimax characterization to the following functional I(u)=a/2 intlimits_{R}^N}|nabla u|^2+b/4 ( intlimits_{R}^N}|nabla u|^2)^2-N/2N+8 intlimits_{R}^N}|u|^{2N+8/N} constrain on {S_c={uin H^1({R}^N)| |u|_2=c,c > 0}} when {c→ (c^*)^+}, where {c^*=(2^{-1}b|Q|_2^{8/N} )^{N/8-2N}}, {N=1,2,3,} and {Q} is up to translations, the unique positive solution of {-2Δ Q+(4/N-1)Q=|Q|^{8/N} Q} in R^N. As such constraint problem is {L^2}-critical, it seems impossible to benefit from natural constraints {V_c= {uin S_c| aintlimits_{R}^N}|nabla u|^2+b( intlimits_{R}^N}|nabla u|^2)^2=2N/N+4 intlimits_{R}^N}|u|^{2N+8/N} }}. We show that the mountain pass energy level {γ(c)=inflimits_{uin M_c}I(u)} for some submanifold {M_csubset V_c} and then prove the strict monotonicity of {γ(c)} on {(c^*,+∞)}. We obtained that the critical point {u_c} behaves like u_c(x)≈(a^2/2b(c^*)^2[({c/{c^*})^{8-2N/N}-1]^2})^{N/8}Q((a/b(c^*)^2[({c/{c^*})^{8-2N/N}-1]} )^{1/2}(x-y_c)) for some {y_cin{R}^N} as {c} approaches {c^*} from above.

  3. Hypoxia promotes drug resistance in osteosarcoma cells via activating AMP-activated protein kinase (AMPK) signaling

    PubMed Central

    Zhao, Changfu; Zhang, Qiao; Yu, Tao; Sun, Shudong; Wang, Wenjun; Liu, Guangyao

    2016-01-01

    Purpose Drug resistance has been recognized to be a major obstacle to the chemotherapy for osteosarcoma. And the potential importance of hypoxia as a target to reverse drug resistance in osteosarcoma has been indicated, though the mechanism underlining such role is not clarified. The present study aims to investigate the role of hypoxia in the drug resistance in osteosarcoma cells via activating AMP-activated protein kinase (AMPK) signaling. Experimental design We investigated the promotion of the resistance to doxorubicin of osteosarcoma MG-63 and U2-os cells in vitro, and then determined the role of hypoxia-inducible factor-1 (HIF-1)α and HIF-1β, the activation and regulatory role of AMPK in the osteosarcoma U2-os cells which were treated with doxorubicin under hypoxia. Results It was demonstrated that hypoxia significantly reduced the sensitivity of MG-63 and U2-os cells to doxorubicin, indicating an inhibited viability reduction and a reduced apoptosis promotion. And such reduced sensitivity was not associated with HIF-1α, though it was promoted by hypoxia in U2-os cells. Interestingly, the AMPK signaling was significantly promoted by hypoxia in the doxorubicin-treated U2-os cells, with a marked upregulation of phosphorylated AMPK (Thr 172) and phosphorylated acetyl-CoA carboxylase (ACC) (Ser 79), which were sensitive to the AMPK activator, AICAR and the AMPK inhibitor, Compound C. Moreover, the promoted AMPK activity by AICAR or the downregulated AMPK activity by Compound C significantly reduced or promoted the sensitivity of U2-os cells to doxorubicin. Conclusion The present study confirmed the AMPK signaling activation in the doxorubicin-treated osteosarcoma cells, in response to hypoxia, and the chemical upregulation or downregulation of AMPK signaling reduced or increased the chemo-sensitivity of osteosarcoma U2-os cells in vitro. Our study implies that AMPK inhibition might be a effective strategy to sensitize osteocarcoma cells to chemotherapy. PMID

  4. 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.

  5. 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.

  6. Genome sequences of copper resistant and sensitive Enterococcus faecalis strains isolated from copper-fed pigs in Denmark

    PubMed Central

    2015-01-01

    Six strains of Enterococcus faecalis (S1, S12, S17, S18, S19 and S32) were isolated from copper fed pigs in Denmark. These Gram-positive bacteria within the genus Enterococcus are able to survive a variety of physical and chemical challenges by the acquisition of diverse genetic elements. The genome of strains S1, S12, S17, S18, S19 and S32 contained 2,615, 2,769, 2,625, 2,804, 2,853 and 2,935 protein-coding genes, with 41, 42, 27, 42, 32 and 44 genes encoding antibiotic and metal resistance, respectively. Differences between Cu resistant and sensitive E. faecalis strains, and possible co-transfer of Cu and antibiotic resistance determinants were detected through comparative genome analysis. PMID:26203344

  7. Heterologous expression and localization of gentisate transporter Ncg12922 from Corynebacterium glutamicum ATCC 13032

    SciTech Connect

    Xu Ying; Yan Dazhong; Zhou Ningyi . E-mail: n.zhou@pentium.whiov.ac.cn

    2006-07-28

    Ralstonia sp. strain U2 metabolizes naphthalene via gentisate (2,5-dihydroxybenzoate) to central metabolites, but it was found unable to utilize gentisate as growth substrate. A putative gentisate transporter encoded by ncg12922 from Corynebacterium glutamicum ATCC 13032 was functionally expressed in Ralstonia sp. strain U2, converting strain U2 to a gentisate utilizer. After ncg12922 was inserted into plasmid pGFPe with green fluorescence protein gene gfp, the expressed fusion protein Ncg12922-GFP could be visualized in the periphery of Escherichia coli cells under confocal microscope, consistent with a cytoplasmic membrane location. In contrast, GFP was ubiquitous in the cytoplasm of E. coli cells carrying pGFPe only. Gentisate 1,2-dioxygenase activity was present in the cell extract from strain U2 induced with gentisate but at a much lower level (one-fifth) than that obtained with salicylate. However, it exhibited a similar level in strain U2 containing Ncg12922 induced either by salicylate or gentisate.

  8. 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)

  9. Gauged twistor formulation of a massive spinning particle in four dimensions

    NASA Astrophysics Data System (ADS)

    Deguchi, Shinichi; Okano, Satoshi

    2016-02-01

    We present a gauged twistor model of a free massive spinning particle in four-dimensional Minkowski space. This model is governed by an action, referred to here as the gauged generalized Shirafuji (GGS) action, that consists of twistor variables, auxiliary variables, and U (1 ) and S U (2 ) gauge fields on the one-dimensional parameter space of a particle's worldline. The GGS action remains invariant under reparametrization and the local U (1 ) and S U (2 ) transformations of the relevant variables, although the S U (2 ) symmetry is nonlinearly realized. We consider the canonical Hamiltonian formalism based on the GGS action in the unitary gauge by following Dirac's recipe for constrained Hamiltonian systems. It is shown that just sufficient constraints for the twistor variables are consistently derived by virtue of the gauge symmetries of the GGS action. In the subsequent quantization procedure, these constraints turn into simultaneous differential equations for a twistor function. We perform the Penrose transform of this twistor function to define a massive spinor field of arbitrary rank, demonstrating that the spinor field satisfies generalized Dirac-Fierz-Pauli equations with S U (2 ) indices. We also investigate the rank-one spinor fields in detail to clarify the physical meanings of the U (1 ) and S U (2 ) symmetries.

  10. A relativistic DFT probe of polypyrrolic macrocyclic diuranium(III) complexes with terminal solvents and iodines.

    PubMed

    Su, Dong-Mei; Zheng, Xiu-Jun; Guo, Yuan-Ru; Pan, Qing-Jiang

    2016-08-01

    Relativistic density functional theory finds that two isomers of a diuranium(III) complex of a polypyrrolic macrocycle (H4L) feature active sites on uranium moieties, allowing for their potential application in activating industrially and economically important small molecules. To address this, a series of adducts [(X)nU2(L)]((2-m)+) (X = THF, I(-) and HI; n = 1 and 2; m = 0, 1 and 2) have been examined. The coordination from X to the exposed uranium(s) changes the general geometry and electronic structure slightly. Thermodynamic calculations reveal that iodine termination is energetically favored over THF/HI coordination. Graphical abstract Scalar and spin-orbit coupling relativistic DFT calculation reveals that the active sites on the uranium moieties of [U2(L)](2+) lead to formation of adducts [(THF)nU2(L)](2+), [InU2(L)]((2-n)+) and [(HI)nU2(L)](2+) (n = 1 and 2). Coordination to the exposed uranium(s) changes geometrical and electronic properties slightly, but iodine termination is the most energetically favored. PMID:27469391

  11. Three-dimensional evaluation of maxillary anterior alveolar bone for optimal placement of miniscrew implants

    PubMed Central

    Choi, Jin Hwan; Lee, Kee Joon; Park, Young Chel

    2014-01-01

    Objective This study aimed to propose clinical guidelines for placing miniscrew implants using the results obtained from 3-dimensional analysis of maxillary anterior interdental alveolar bone by cone-beam computed tomography (CBCT). Methods By using CBCT data from 52 adult patients (17 men and 35 women; mean age, 27.9 years), alveolar bone were measured in 3 regions: between the maxillary central incisors (U1-U1), between the maxillary central incisor and maxillary lateral incisor (U1-U2), and between the maxillary lateral incisor and the canine (U2-U3). Cortical bone thickness, labio-palatal thickness, and interdental root distance were measured at 4 mm, 6 mm, and 8 mm apical to the interdental cementoenamel junction (ICEJ). Results The cortical bone thickness significantly increased from the U1-U1 region to the U2-U3 region (p < 0.05). The labio-palatal thickness was significantly less in the U1-U1 region (p < 0.05), and the interdental root distance was significantly less in the U1-U2 region (p < 0.05). Conclusions The results of this study suggest that the interdental root regions U2-U3 and U1-U1 are the best sites for placing miniscrew implants into maxillary anterior alveolar bone. PMID:24696821

  12. Role of HIV-1 matrix protein p17 variants in lymphoma pathogenesis

    PubMed Central

    Dolcetti, Riccardo; Giagulli, Cinzia; He, Wangxiao; Selleri, Marina; Caccuri, Francesca; Eyzaguirre, Lindsay M.; Mazzuca, Pietro; Corbellini, Silvia; Campilongo, Federica; Marsico, Stefania; Giombini, Emanuela; Muraro, Elena; Rozera, Gabriella; De Paoli, Paolo; Carbone, Antonino; Capobianchi, Maria Rosaria; Ippolito, Giuseppe; Fiorentini, Simona; Blattner, William A.; Lu, Wuyuan; Gallo, Robert C.; Caruso, Arnaldo

    2015-01-01

    Although in decline after successful anti-HIV therapy, B-cell lymphomas are still elevated in HIV-1-seropositive (HIV+) persons, and the mechanisms are obscure. The HIV-1 matrix protein p17 persists in germinal centers long after HIV-1 drug suppression, and some p17 variants (vp17s) activate Akt signaling and promote growth of transformed B cells. Here we show that vp17s derived from four of five non-Hodgkin lymphoma (NHL) tissues from HIV+ subjects display potent B-cell growth-promoting activity. They are characterized by amino acid insertions at position 117–118 (Ala–Ala) or 125–126 (Gly–Asn or Gly–Gln–Ala–Asn–Gln–Asn) among some other mutations throughout the sequence. Identical dominant vp17s are found in both tumor and plasma. Three of seven plasma samples from an independent set of NHL cases manifested multiple Ala insertions at position 117–118, and one with the Ala–Ala profile also promoted B-cell growth and activated Akt signaling. Ultradeep pyrosequencing showed that vp17s with C-terminal insertions are more frequently detected in plasma of HIV+ subjects with than without NHL. Insertion of Ala–Ala at position 117–118 into reference p17 (refp17) was sufficient to confer B-cell growth-promoting activity. In contrast, refp17 bearing the Gly–Asn insertion at position 125–126 did not, suggesting that mutations not restricted to the C terminus can also account for this activity. Biophysical analysis revealed that the Ala–Ala insertion mutant is destabilized compared with refp17, whereas the Gly–Asn form is stabilized. This finding provides an avenue for further exploration of structure function relationships and new treatment strategies in combating HIV-1–related NHL. PMID:26578780

  13. Molecular analyses of 17p11.2 deletions in 62 Smith-Magenis syndrome patients.

    PubMed Central

    Juyal, R. C.; Figuera, L. E.; Hauge, X.; Elsea, S. H.; Lupski, J. R.; Greenberg, F.; Baldini, A.; Patel, P. I.

    1996-01-01

    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 (i) FISH analysis, (ii)PCR and Southern analysis of somatic cell hybrids retaining the deleted chromosome 17 from selected patients, and (iii) 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. Images Figure 2 PMID:8651284

  14. AIPL1 implicated in the pathogenesis of two cases of autosomal recessive retinal degeneration

    PubMed Central

    Li, David; Jin, Chongfei; Jiao, Xiaodong; Li, Lin; Bushra, Tahmina; Naeem, Muhammad Asif; Butt, Nadeem H.; Husnain, Tayyab; Sieving, Paul A.; Riazuddin, Sheikh; Riazuddin, S. Amer

    2014-01-01

    Purpose To localize and identify the gene and mutations causing autosomal recessive retinal dystrophy in two consanguineous Pakistani families. Methods Consanguineous families from Pakistan were ascertained to be affected with autosomal recessive retinal degeneration. All affected individuals underwent thorough ophthalmologic examinations. Blood samples were collected, and genomic DNA was extracted using a salting out procedure. Genotyping was performed using microsatellite markers spaced at approximately 10 cM intervals. Two-point linkage analysis was performed with the lod score method. Direct DNA sequencing of amplified genomic DNA was performed for mutation screening of candidate genes. Results Genome-wide linkage scans yielded a lod score of 3.05 at θ=0 for D17S1832 and 3.82 at θ=0 for D17S938, localizing the disease gene to a 12.22 cM (6.64 Mb) region flanked by D17S1828 and D17S1852 for family 61032 and family 61227, which contains aryl hydrocarbon receptor interacting protein-like 1 (AIPL1), a gene previously implicated in recessive Leber congenital amaurosis and autosomal dominant cone-rod dystrophy. Sequencing of AIPL1 showed a homozygous c.773G>C (p.Arg258Pro) sequence change in all affected individuals of family 61032 and a homozygous c.465G>T (p.(H93_Q155del)) change in all affected members of family 61227. Conclusions The results strongly suggest that the c.773G>C (p.R258P) and c.465G>T (p.(H93_Q155del)) mutations in AIPL1 cause autosomal recessive retinal degeneration in these consanguineous Pakistani families. PMID:24426771

  15. 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.

  16. Cipacinoids A-D, Four Limonoids with Spirocyclic Skeletons from Cipadessa cinerascens.

    PubMed

    Yu, Jin-Hai; Liu, Qun-Fang; Sheng, Li; Wang, Guo-Cai; Li, Jia; Yue, Jian-Min

    2016-02-01

    Four limonoids, cipacinoids A-D (1-4), with spirocyclic skeletons were isolated from Cipadessa cinerascens. It is particularly notable that compounds 1-3 had a 17S-configuration for the first time in the limonoid family. Their structures with absolute configurations were assigned by spectroscopic data, X-ray crystallography, and CD analysis. Compound 1 showed moderate protein tyrosine phosphatase 1B (PTP1B) inhibition. PMID:26760061

  17. WITHDRAWN: (438) Efficacy of CL-108 compared to hydrocodone 7.5 mg/acetaminophen 325 mg in preventing vomiting and the use of anti-emetics, Opioid-Induced Nausea and Vomiting (OINV).

    PubMed

    Hersh, Elliot; Schachtel, Bernard; Kozarek, William; Schachtel, Emily; Marino, Mark

    2016-04-01

    The Publisher regrets that this abstract is an accidental duplication of abstract (431), also published in the 2016 American Pain Society Scientific Meeting abstracts supplement: J Pain 17:S82, 2016, http://dx.doi.org/10.1016/j.jpain.2016.01.408. The duplicate abstract (438) has therefore been withdrawn. The full Elsevier Policy on Article Withdrawal can be found at http://www.elsevier.com/locate/withdrawalpolicy. PMID:27105853

  18. WITHDRAWN: (440) Opioid-Induced Nausea and Vomiting (OINV) in Post-Operative Patients: A Comparison of CL-108 to Hydrocodone 7.5 mg/Acetaminophen 325 mg.

    PubMed

    Richardson, Stephen; Patrick, Kyle; Daniels, Stephen; Royall, Steven; Schachtel, Emily; Zhang, Bing; Marino, Mark; Schachtel, Bernard

    2016-04-01

    The Publisher regrets that this abstract is an accidental duplication of abstract (436), also published in the 2016 American Pain Society Scientific Meeting abstracts supplement: J Pain 17:S83, 2016, http://dx.doi.org/10.1016/j.jpain.2016.01.413. The duplicate abstract (440) has therefore been withdrawn. The full Elsevier Policy on Article Withdrawal can be found at http://www.elsevier.com/locate/withdrawalpolicy. PMID:27105852

  19. 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.

  20. 33 CFR 117.501 - Teche Bayou.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... bridge, mile 48.7 at Olivier. (14) S3195 bridge, mile 50.4 at New Iberia. (15) S87 Spur bridge, mile 52.5 at New Iberia. (16) S86 bridge, mile 53.0 at New Iberia. (17) S3156 bridge, mile 53.3 at New Iberia. (18) S44 bridge, mile 56.7 at Morbihan. (19) Iberia Parish bridge, mile 58.0 at New Iberia....

  1. A missense mutation (p.G274R) in gene ASPA causes Canavan disease in a Pakistani family.

    PubMed

    Hussain, Rashida; Daud, Shakeela; Kakar, Naseebullah; Ahmad, Adeel; Baloch, Abdul Hameed; Tareen, Abdul Malik; Kakar, Muhammad Azam; Ahmad, Jamil

    2012-05-01

    Canavan disease (OMIM 271900) is an autosomal recessive lethal neurodegenerative disorder characterized by spongy degeneration of the brain. A highly consanguineous Pakistani family with Canavan disease was enrolled on the basis of diagnosis. All the affected individuals have mental retardation, megalocephaly and degradation of motor skills, poor head control, partial vision loss, weakness of the muscles and raised urinary concentration of N-acetyl aspartic acid in the urine. Blood samples were collected from affected as well as normal siblings and processed for DNA purification. Linkage analysis was performed by typing three short tandem repeat markers D17S1583 (7.19 cM), D17S1828 (10.02 cM) and D17S919 (14.69 cM) for an already-reported gene/locus ASPA at chromosome 17p13.2 causing Canavan disease. During linkage analysis, all the affected individuals were homozygous for short tandem repeat markers while the normal siblings were heterozygous showing co-segregation of the disease. Gene ASPA (NM_000049) was undertaken to sequence for mutation analysis. As a result of sequence analysis, we found missense substitution 740A→G (p.G274R) in exon 6 of gene ASPA. To our knowledge, this is the first report about Canavan disease on a Pakistani family. PMID:22219087

  2. Phosphorylation of CDK9 at Ser175 Enhances HIV Transcription and Is a Marker of Activated P-TEFb in CD4+ T Lymphocytes

    PubMed Central

    Mbonye, Uri R.; Gokulrangan, Giridharan; Datt, Manish; Dobrowolski, Curtis; Cooper, Maxwell; Chance, Mark R.; Karn, Jonathan

    2013-01-01

    The HIV transactivator protein, Tat, enhances HIV transcription by recruiting P-TEFb from the inactive 7SK snRNP complex and directing it to proviral elongation complexes. To test the hypothesis that T-cell receptor (TCR) signaling induces critical post-translational modifications leading to enhanced interactions between P-TEFb and Tat, we employed affinity purification–tandem mass spectrometry to analyze P-TEFb. TCR or phorbal ester (PMA) signaling strongly induced phosphorylation of the CDK9 kinase at Ser175. Molecular modeling studies based on the Tat/P-TEFb X-ray structure suggested that pSer175 strengthens the intermolecular interactions between CDK9 and Tat. Mutations in Ser175 confirm that this residue could mediate critical interactions with Tat and with the bromodomain protein BRD4. The S175A mutation reduced CDK9 interactions with Tat by an average of 1.7-fold, but also completely blocked CDK9 association with BRD4. The phosphomimetic S175D mutation modestly enhanced Tat association with CDK9 while causing a 2-fold disruption in BRD4 association with CDK9. Since BRD4 is unable to compete for binding to CDK9 carrying S175A, expression of CDK9 carrying the S175A mutation in latently infected cells resulted in a robust Tat-dependent reactivation of the provirus. Similarly, the stable knockdown of BRD4 led to a strong enhancement of proviral expression. Immunoprecipitation experiments show that CDK9 phosphorylated at Ser175 is excluded from the 7SK RNP complex. Immunofluorescence and flow cytometry studies carried out using a phospho-Ser175-specific antibody demonstrated that Ser175 phosphorylation occurs during TCR activation of primary resting memory CD4+ T cells together with upregulation of the Cyclin T1 regulatory subunit of P-TEFb, and Thr186 phosphorylation of CDK9. We conclude that the phosphorylation of CDK9 at Ser175 plays a critical role in altering the competitive binding of Tat and BRD4 to P-TEFb and provides an informative molecular marker for

  3. 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'.

  4. Condensation nuclei measurement in the stratosphere for the NASA ACE program. Final report, 1 February 1980-31 January 1987

    SciTech Connect

    Wilson, J.C.

    1994-11-01

    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.

  5. 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.

  6. The Domain Geometry and the Bubbling Phenomenon of Rank Two Gauge Theory

    NASA Astrophysics Data System (ADS)

    Huang, Hsin-Yuan; Zhang, Lei

    2016-06-01

    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.

  7. Dynamical generation of a nontrivial index on the fuzzy 2-sphere

    SciTech Connect

    Aoki, Hajime; Iso, Satoshi; Nagao, Keiichi; Maeda, Toshiharu

    2005-02-15

    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.

  8. Effects of polydeoxyribonucleotides (PDRN) on wound healing: Electric cell-substrate impedance sensing (ECIS).

    PubMed

    Koo, Youngmi; Yun, Yeoheung

    2016-12-01

    Polydeoxyribonucleotides (PDRN) have been explored as an effective treatment for tissue repair in peripheral artery occlusive disease, diabetic foot ulcers, and eye lotion. We report on the effect of polydeoxyribonucleotides (PDRN) on wound healing by using the electric cell-substrate impedance sensing (ECIS) system and viability testing. Human osteoblasts (U2OS) and primary human dermal fibroblasts (HDF) were used to study the effect of PDRN on migration and proliferation. ECIS allowed the creation of a wound by applying high current, and then monitoring the healing process by measuring impedance in real time. The traditional culture-insert gap-closure migration assay was performed and compared with the ECIS wound assay. PDRN-treated U2OS and HDF cells affected cell motilities to wounding site. Viability test results show that HDF and U2OS proliferation depended on PDRN concentration. Based on the results, a PDRN compound can be useful in wound healing associated with bone and skin. PMID:27612747

  9. 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.

  10. Actin-dependent intranuclear repositioning of an active gene locus in vivo

    PubMed Central

    Dundr, Miroslav; Ospina, Jason K.; Sung, Myong-Hee; John, Sam; Upender, Madhvi; Ried, Thomas; Hager, Gordon L.; Matera, A. Gregory

    2007-01-01

    Although bulk chromatin is thought to have limited mobility within the interphase eukaryotic nucleus, directed long-distance chromosome movements are not unknown. Cajal bodies (CBs) are nuclear suborganelles that nonrandomly associate with small nuclear RNA (snRNA) and histone gene loci in human cells during interphase. However, the mechanism responsible for this association is uncertain. In this study, we present an experimental system to probe the dynamic interplay of CBs with a U2 snRNA target gene locus during transcriptional activation in living cells. Simultaneous four-dimensional tracking of CBs and U2 genes reveals that target loci are recruited toward relatively stably positioned CBs by long-range chromosomal motion. In the presence of a dominant-negative mutant of β-actin, the repositioning of activated U2 genes is markedly inhibited. This supports a model in which nuclear actin is required for these rapid, long-range chromosomal movements. PMID:18070915

  11. 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

  12. On the steady-state solutions of a nonlinear photonic lattice model

    NASA Astrophysics Data System (ADS)

    Liu, Chungen; Ren, Qiang

    2015-03-01

    In this paper, we consider the steady-state solutions of the following equation related with nonlinear photonic lattice model Δ u = /P u 1 + |u|2 + |v|2 + λ u , Δ v = /Q v 1 + |u|2 + |v|2 + λ v , where u, v are real-value function defined on R/(τ1Z) × R/(τ2Z). The existence and non-existence of non-constant semi-trivial (with only one component zero) solutions are considered.

  13. LLNL's Response to 9/9/2009 Annual Inspection Report Comments B113 Issue #1 and B271 Issue #2

    SciTech Connect

    Schwartz, W W

    2009-11-19

    This is LLNL's responses to comments in the 9/9/2009 Annual Inspection Report concerning Underground Storage Tank (UST) 113-D1U2 (Issue No.1) at Building 113 and UST 271-D2U1 (Issue No.2) at Building 271. Also provided is the required Application for Underground Storage Tank Modification for USTs 113-D1U2 and 271-D2U1 and the specification sheet for the Phil-Tite spill bucket that is proposed to be installed in the 271-D2U1 sump.

  14. Chiral Lagrangians from lattice gauge theories in the strong coupling limit

    SciTech Connect

    Nagao, Taro; Nishigaki, Shinsuke M.

    2001-07-01

    We derive nonlinear {sigma} models (chiral Lagrangians) over symmetric spaces U(n), U(2n)/Sp(2n), and U(2n)/O(2n) from U(N), O(N), and Sp(2N) lattice gauge theories coupled to n flavors of staggered fermions, in the large-N and g{sup 2}N limit. To this end, we employ Zirnbauer{close_quote}s color-flavor transformation. We prove the spatial homogeneity of the vacuum configurations of mesons by explicitly solving the large-N saddle point equations, and thus establish these patterns of spontaneous chiral symmetry breaking in the above limit.

  15. Director fluctuations in nematic liquid crystals induced by an ultrasonic wave

    NASA Astrophysics Data System (ADS)

    Sátiro, Caio; Vitoriano, Carlindo

    2012-07-01

    The director-density coupling theory was formulated with two parameters (u1 and u2) to explain the acousto-optic effect in nematic liquid crystals. The assumption that the director is not able to accompany rapid oscillations of the sound wave, so that it actually couples to the time-averaged interaction, renders it effectively a u1-independent theory. In this paper, we investigate a route in which the time average is postponed to the end of the calculation. This approach allows us to derive measurable quantities that depend on both u1 and u2.

  16. Approximate formula for the escape function for nearly conservative scattering

    NASA Astrophysics Data System (ADS)

    Yanovitskij, E. G.

    2002-02-01

    The escape function u(μ) (i.e., the boundary solution of the Milne problem for a semi-infinite atmosphere) is considered. It is presented in the form u(μ) = u0 (μ ) + √ {1 - λ}u1(μ) + (1-λ)u2(μ) + ldots, where λ is the single-scattering albedo. A rather accurate approximate formula for a the function u0 (μ) is obtained for not highly elongated phase function. An approximate expression for the function u2 (μ) is also derived, it is exact in the case of the most simple anisotropic scattering.

  17. Pilot James Barrilleaux with ER-2 aircraft on ramp

    NASA Technical Reports Server (NTRS)

    1998-01-01

    James Barrilleaux is the assistant chief pilot for ER-2s in the Flight Crew Branch of NASA's Dryden Flight Research Center, Edwards, California. The ER-2s--civilian variants of the military U-2S reconnaissance aircraft--are part of NASA's Airborne Science program. The ER-2s can carry airborne scientific payloads of up to 2,600 pounds to altitudes of about 70,000 feet to investigate such matters as earth resources, celestial phenomena, atmospheric chemistry and dynamics, and oceanic processes. Barrilleaux has held his current position since February 1998. Barrilleaux joined NASA in 1986 as a U-2/ER-2 pilot with NASA's Airborne Science program at Ames Research Center, Moffett Field, California. He flew both the U-2C (until 1989) and the ER-2 on a wide variety of missions both domestic and international. Barrilleaux flew high-altitude operations over Antarctica in which scientific instruments aboard the ER-2 defined the cause of ozone depletion over the continent, known as the ozone hole. He has also flown the ER-2 over the North Pole. Barrilleaux served for 20 years in the U.S. Air Force before he joined NASA. He completed pilot training at Reese Air Force Base, Lubbock, Texas, in 1966. He flew 120 combat missions as a F-4 fighter pilot over Laos and North Vietnam in 1970 and 1971. He joined the U-2 program in 1974, becoming the commander of an overseas U-2 operation in 1982. In 1983, he became commander of the squadron responsible for training all U-2 pilots and SR-71 crews located at Beale Air Force Base, Marysville, California. He retired from the Air Force as a lieutenant colonel in 1986. On active duty, he flew the U-2, F-4 Phantom, the T-38, T-37, and the T-33. His decorations included two Distinguished Flying Crosses, 12 Air Medals, two Meritorious Service Medals, and other Air Force and South Vietnamese awards. Barrilleaux earned a bachelor of science degree in chemical engineering from Texas A&M University, College Station, in 1964 and a master of science

  18. A parity breaking Ising chain Hamiltonian as a Brownian motor

    NASA Astrophysics Data System (ADS)

    Cornu, F.; Hilhorst, H. J.

    2014-10-01

    We consider the translationally invariant but parity (left-right symmetry) breaking Ising chain Hamiltonian {\\cal H} =-{U_2}\\sumk sksk+1 - {U_3}\\sumk sksk+1sk+3 and let this system evolve by Kawasaki spin exchange dynamics. Monte Carlo simulations show that perturbations forcing this system off equilibrium make it act as a Brownian molecular motor which, in the lattice gas interpretation, transports particles along the chain. We determine the particle current under various different circumstances, in particular as a function of the ratio {U_3}/{U_2} and of the conserved magnetization M=\\sum_ksk . The symmetry of the U3 term in the Hamiltonian is discussed.

  19. A search variability in the UV spectrum of Pi Aquarii and Fe 3 shell lines of Be stars

    NASA Technical Reports Server (NTRS)

    1984-01-01

    Several short U1 and U2 observations of Be stars are obtained with the Copernicus satellite. Pi Aquarii (B1 IV-Ve) is observed with the U1 and U2 spectrometers. These scans are compared with earlier observations. Variations in the strengths and profiles of selected shell and photospheric features are examined. In order to study possible changes in the temperature of the circumstellar envelope, features covering a wide range in ionization are observed. Included in the observing program are lines of O VI, N V, Si IV, Si III, S III, Fe III, and N I.

  20. Experimental and theoretical study of s 2p and c 1s spectroscopyin cs2

    SciTech Connect

    Eustatiu, I.G.; Tyliszczak, Tolek; Cooper, G.; Hitchcock, Adam; Turci, C.C.; Rocha, A.B.; Barbatti, M.; Bielschowsky, C.E.

    2006-12-01

    The generalized oscillator strength profiles in the momentumtransfer range (K) of (2 a.u.- 2u.-2) for the mostintense resolved S 2p, and C 1s transitions of carbon disulfide (CS2) arepresented. Optical oscillator strengths and generalized oscillatorstrength profiles have been calculated for vertical excitation from theground X1SIGMAg+ electronic state to several C(1s) and S(2p) inner-shellelectronic excited states of CS2, using high level ab initio (HF-CI)calculations. The experimental and computed GOS profiles of CS2 arecompared and found to be generally in reasonable agreement.