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Sample records for analisis terhadap tata

  1. Entamoeba histolytica TATA-box binding protein binds to different TATA variants in vitro.

    PubMed

    de Dios-Bravo, Guadalupe; Luna-Arias, Juan Pedro; Riverón, Ana María; Olivares-Trejo, José J; López-Camarillo, César; Orozco, Esther

    2005-03-01

    The ability of Entamoeba histolytica TATA binding protein (EhTBP) to interact with different TATA boxes in gene promoters may be one of the key factors to perform an efficient transcription in this human parasite. In this paper we used several TATA variants to study the in vitro EhTBP DNA-binding activity and to determine the TATA-EhTBP dissociation constants. The presence of EhTBP in complexes formed by nuclear extracts (NE) and the TATTTAAA oligonucleotide, which corresponds to the canonical TATA box for E. histolytica, was demonstrated by gel-shift assays. In these experiments a single NE-TATTTAAA oligonucleotide complex was detected. Complex was retarded by anti-EhTBP Igs in supershift experiments and antibodies also recognized the cross-linked complex in Western blot assays. Recombinant EhTBP formed specific complexes with TATA variants found in E. histolytica gene promoters and other TATA variants generated by mutation of TATTTAAA sequence. The dissociation constants of recombinant EhTBP for TATA variants ranged between 1.04 (+/-0.39) x 10(-11) and 1.60 (+/-0.37) x 10(-10) m. TATTTAAA and TAT_ _AAA motifs presented the lowest KD values. Intriguingly, the recombinant EhTBP affinity for TATA variants is stronger than other TBPs reported. In addition, EhTBP is more promiscuous than human and yeast TBPs, probably due to modifications in amino acids involved in TBP-DNA binding. PMID:15752353

  2. 75 FR 21352 - Tata Technologies Incorporated; A Subsidiary of Tata Technologies Limited: Formally Known As...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-04-23

    ... engineering design and product lifecycle management. Information reports that before April 2009, Tata... subject firm who were adversely affected by an affiliated vendor acquiring engineering design and product lifecycle management in India. The amended notice applicable to TA-W-71,414 is hereby issued as follows:...

  3. 75 FR 24747 - TATA Technologies Incorporated, a Subsidiary of TATA Technologies Limited, Formally Known as...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-05-05

    ... engineering design and product lifecycle management. Information reports that before April 2009, Tata... subject firm who were adversely affected by an affiliated vendor acquiring engineering design and product lifecycle management in India. The amended notice applicable to TA-W-71,414 is hereby issued as follows:...

  4. Functional significance of the TATA element major groove in transcription initiation by RNA polymerase II.

    PubMed Central

    Lee, D K; Wang, K C; Roeder, R G

    1997-01-01

    The binding of TFIID to the TATA element initiates assembly of a preinitiation complex and thus represents one of the most important steps for transcriptional regulation. The fact that the TATA binding protein (TBP), a subunit of TFIID, exclusively contacts the minor groove of the TATA element led us to ask whether the major groove of the TATA element plays any role in transcription initiation or its regulation. Our results show that modifications of the major groove of the TATA element in the adenovirus major late promoter have no effect on TFIID binding affinity or on transcription in a cell-free system reconstituted with purified factors. However, major groove modifications do decrease the levels of both basal and activator-mediated transcription in unfractionated nuclear extracts, indicating that the intact structure of the major groove of the TATA element is functionally important for transcription initiation in a more physiological context. PMID:9336466

  5. Dynamics of TBP binding to the TATA box

    NASA Astrophysics Data System (ADS)

    Schluesche, Peter; Heiss, Gregor; Meisterernst, Michael; Lamb, Don C.

    2008-02-01

    Gene expression is highly controlled and regulated in living cells. One of the first steps in gene transcription is recognition of the promoter site by the TATA box Binding Protein (TBP). TBP recruits other transcriptions factors and eventually the RNA polymerase II to transcribe the DNA in mRNA. We developed a single pair Förster Resonance Energy Transfer (spFRET) assay to investigate the mechanism of gene regulation. Here, we apply this assay to investigate the initial binding process of TBP to the adenovirus major late (AdML) promoter site. From the spFRET measurements, we were able to identify two conformations of the TBP-DNA complex that correspond to TBP bound in the correct and the opposite orientation. Increased incubation times or the presence of the transcription factor TFIIA improved the alignment of TBP on the promoter site. Binding of TBP to the TATA box shows a rich dynamics with abrupt transitions between multiple FRET states. A frame-wise histogram analysis revealed the presence of at least six discrete states, showing that TBP binding is more complicated than previously thought. Hence, the spFRET assay is very sensitive to the conformation of the TBP-DNA complex and is very promising tool for investigating the pathway of TBP binding in detail.

  6. Transcription Factor Binding Site Positioning in Yeast: Proximal Promoter Motifs Characterize TATA-Less Promoters

    PubMed Central

    Erb, Ionas; van Nimwegen, Erik

    2011-01-01

    The availability of sequence specificities for a substantial fraction of yeast's transcription factors and comparative genomic algorithms for binding site prediction has made it possible to comprehensively annotate transcription factor binding sites genome-wide. Here we use such a genome-wide annotation for comprehensively studying promoter architecture in yeast, focusing on the distribution of transcription factor binding sites relative to transcription start sites, and the architecture of TATA and TATA-less promoters. For most transcription factors, binding sites are positioned further upstream and vary over a wider range in TATA promoters than in TATA-less promoters. In contrast, a group of ‘proximal promoter motifs’ (GAT1/GLN3/DAL80, FKH1/2, PBF1/2, RPN4, NDT80, and ROX1) occur preferentially in TATA-less promoters and show a strong preference for binding close to the transcription start site in these promoters. We provide evidence that suggests that pre-initiation complexes are recruited at TATA sites in TATA promoters and at the sites of the other proximal promoter motifs in TATA-less promoters. TATA-less promoters can generally be classified by the proximal promoter motif they contain, with different classes of TATA-less promoters showing different patterns of transcription factor binding site positioning and nucleosome coverage. These observations suggest that different modes of regulation of transcription initiation may be operating in the different promoter classes. In addition we show that, across all promoter classes, there is a close match between nucleosome free regions and regions of highest transcription factor binding site density. This close agreement between transcription factor binding site density and nucleosome depletion suggests a direct and general competition between transcription factors and nucleosomes for binding to promoters. PMID:21931670

  7. UV cross-linking identifies four polypeptides that require the TATA box to bind to the Drosophila hsp70 promoter

    SciTech Connect

    Gilmour, D.S.; Dietz, T.J.; Elgin, S.C. )

    1990-08-01

    A protein fraction that requires the TATA sequence to bind to the hsp70 promoter has been partially purified from nuclear extracts of Drosophila embryos. This TATA factor produces a large DNase I footprint that extends from -44 to +35 on the promoter. A mutation that changes TATA to TATG interferes both with the binding of this complex and with the transcription of the hsp70 promoter in vitro, indicating that this interaction is important for transcriptional activity. Using a highly specific protein-DNA cross-linking assay, we have identified four polypeptides that require the TATA sequence to bind to the hsp70 promoter. Polypeptides of 26 and 42 kilodaltons are in intimate contact with the TATA sequence. Polypeptides of 150 and 60 kilodaltons interact within the region from +24 to +47 in a TATA-dependent manner. Both the extended footprint and the polypeptides identified by UV cross-linking indicate that the Drosophila TATA factor is a multicomponent complex.

  8. The adenovirus E1A repression domain disrupts the interaction between the TATA binding protein and the TATA box in a manner reversible by TFIIB.

    PubMed Central

    Song, C Z; Loewenstein, P M; Toth, K; Tang, Q; Nishikawa, A; Green, M

    1997-01-01

    The human adenovirus E1A 243 amino acid oncoprotein possesses a transcription repression function that appears to be linked with its ability to induce cell cycle progression and to inhibit cell differentiation. The molecular mechanism of E1A repression has been poorly understood. Recently, we reported that the TATA binding protein (TBP) is a cellular target of E1A repression. Here we demonstrate that the interaction between TBP and the E1A repression domain is direct and specific. The TBP binding domain within E1A 243R maps to E1A N-terminal residues approximately 1 to 35 and is distinct from the TBP binding domain within conserved region 3 unique to the E1A 289R transactivator. An E1A protein fragment consisting of only the E1A N-terminal 80 amino acids (E1A 1-80) and containing the E1A repression function was found to block the interaction between TBP and the TATA box element as shown by gel mobility and DNase protection analysis. Interestingly, a preformed TBP-TATA box promoter complex can be dissociated by E1A 1-80. Further, TFIIB can prevent E1A disruption of TBP-TATA box interaction. TFIIB, like TBP, can overcome E1A repression of transcription in vitro. The ability of the E1A repression domain to block TBP interaction with the TATA box and the ability of TFIIB to reverse E1A disruption of the TBP-TATA box complex implies a mechanism for E1A repression distinct from those of known cellular repressors that target TBP. PMID:9121468

  9. Upstream box/TATA box order is the major determinant of the direction of transcription.

    PubMed Central

    Xu, L C; Thali, M; Schaffner, W

    1991-01-01

    Mammalian gene promoters for transcription by RNA polymerase II are typically organized in the following order: upstream sequence motif(s)/TATA box/initiation site. Here we report studies in which the order, orientation and DNA sequences of these three elements are varied to determine how these affect polarity of transcription. We have constructed promoters with an 'octamer' upstream sequence ATTTGCAT (or its complement ATGCAAAT) in combination with several different TATA boxes and initiation (cap) sites, and tested these promoters in transfection experiments with cultured cells. TATA boxes derived from the adenovirus major late promoter (TATAAAA), immunoglobulin kappa light chain (TTATATA) and heavy chain (TAAATATA) promoter functioned equally well or even better when inverted. Only the beta-globin TATA box (CATAAAA) was poorly active when inverted. In addition, a symmetrical TATA box (TATATATA) derived from a casein gene was very active. Our results suggest that the asymmetry of most TATA boxes (consensus TATAAAA) is not a primary determinant of the polarity of transcription. We also found that the initiation (cap) site, which usually consists of an adenine embedded in a pyrimidine-rich region (PyPyCAPyPyPyPyPy), was permissive towards sequence alterations; even a randomly composed sequence worked well. However, an inverted, hence purine-rich, cap site reduced transcript levels to 1/7th, as did an oligo G sequence. Irrespective of the presence of a cap site, the configuration: 'TATA box/octamer' yielded a strong leftward, rather than rightward transcription. From this, we conclude that the polarity of transcription is primarily determined by the linear order of an upstream sequence relative to a TATA box, rather than by the individual orientations of either of these two elements. Images PMID:1762900

  10. Cellular microRNAs up-regulate transcription via interaction with promoter TATA-box motifs

    PubMed Central

    Zhang, Yijun; Fan, Miaomiao; Zhang, Xue; Huang, Feng; Wu, Kang; Zhang, Junsong; Liu, Jun; Huang, Zhuoqiong; Luo, Haihua; Tao, Liang; Zhang, Hui

    2014-01-01

    The TATA box represents one of the most prevalent core promoters where the pre-initiation complexes (PICs) for gene transcription are assembled. This assembly is crucial for transcription initiation and well regulated. Here we show that some cellular microRNAs (miRNAs) are associated with RNA polymerase II (Pol II) and TATA box-binding protein (TBP) in human peripheral blood mononuclear cells (PBMCs). Among them, let-7i sequence specifically binds to the TATA-box motif of interleukin-2 (IL-2) gene and elevates IL-2 mRNA and protein production in CD4+ T-lymphocytes in vitro and in vivo. Through direct interaction with the TATA-box motif, let-7i facilitates the PIC assembly and transcription initiation of IL-2 promoter. Several other cellular miRNAs, such as mir-138, mir-92a or mir-181d, also enhance the promoter activities via binding to the TATA-box motifs of insulin, calcitonin or c-myc, respectively. In agreement with the finding that an HIV-1–encoded miRNA could enhance viral replication through targeting the viral promoter TATA-box motif, our data demonstrate that the interaction with core transcription machinery is a novel mechanism for miRNAs to regulate gene expression. PMID:25336585

  11. Binding of TATA Binding Protein to a Naturally Positioned Nucleosome Is Facilitated by Histone Acetylation

    PubMed Central

    Sewack, Gerald F.; Ellis, Thomas W.; Hansen, Ulla

    2001-01-01

    The TATA sequence of the human, estrogen-responsive pS2 promoter is complexed in vivo with a rotationally and translationally positioned nucleosome (NUC T). Using a chromatin immunoprecipitation assay, we demonstrate that TATA binding protein (TBP) does not detectably interact with this genomic binding site in MCF-7 cells in the absence of transcriptional stimuli. Estrogen stimulation of these cells results in hyperacetylation of both histones H3 and H4 within the pS2 chromatin encompassing NUC T and the TATA sequence. Concurrently, TBP becomes associated with the pS2 promoter region. The relationship between histone hyperacetylation and the binding of TBP was assayed in vitro using an in vivo-assembled nucleosomal array over the pS2 promoter. With chromatin in its basal state, the binding of TBP to the pS2 TATA sequence at the edge of NUC T was severely restricted, consistent with our in vivo data. Acetylation of the core histones facilitated the binding of TBP to this nucleosomal TATA sequence. Therefore, we demonstrate that one specific, functional consequence of induced histone acetylation at a native promoter is the alleviation of nucleosome-mediated repression of the binding of TBP. Our data support a fundamental role for histone acetylation at genomic promoters in transcriptional activation by nuclear receptors and provide a general mechanism for rapid and reversible transcriptional activation from a chromatin template. PMID:11158325

  12. Direct stimulation of transcription by negative cofactor 2 (NC2) through TATA-binding protein (TBP)

    PubMed Central

    Cang, Yong; Prelich, Gregory

    2002-01-01

    Negative cofactor 2 (NC2) is an evolutionarily conserved transcriptional regulator that was originally identified as an inhibitor of basal transcription. Its inhibitory mechanism has been extensively characterized; NC2 binds to the TATA-binding protein (TBP), blocking the recruitment of TFIIA and TFIIB, and thereby inhibiting preinitiation complex assembly. NC2 is also required for expression of many yeast genes in vivo and stimulates TATA-less transcription in a Drosophila in vitro transcription system, but the mechanism responsible for the NC2-mediated stimulation of transcription is not understood. Here we establish that yeast NC2 can directly stimulate activated transcription from TATA-driven promoters both in vivo and in vitro, and moreover that this positive role requires the same surface of TBP that mediates the NC2 repression activity. On the basis of these results, we propose a model to explain how NC2 can mediate both repression and activation through the same surface of TBP. PMID:12237409

  13. Two distinct factors bind to the rabbit uteroglobin TATA-box region and are required for efficient transcription.

    PubMed Central

    Klug, J; Knapp, S; Castro, I; Beato, M

    1994-01-01

    The rabbit uteroglobin gene is expressed in a variety of epithelial cell types like the lung Clara cells and the glandular and luminal epithelial cells of the endometrium. Expression in Clara cells is on a high constitutive level, whereas expression in the rabbit endometrium is under tight hormonal control. One important element of the rabbit uteroglobin gene mediating its efficient transcription in two epithelial cell lines from human endometrium (Ishikawa) and lung (NCI-H441) is its noncanonical TATA box (TACA). Here, we show that two factors (TATA core factor [TCF] and TATA palindrome factor [TPF]) different from the TATA-box binding protein bind to the DNA major groove at two adjacent sites within the uteroglobin TATA-box region and that one of them (TCF) is specifically expressed in cell lines derived from uteroglobin-expressing tissues. The binding sites for TCF and TPF, respectively, are both required for efficient transcription in Ishikawa and NCI-H441 cells. Mutation of the TACA box, which we show is a poor TATA box in functional terms, to a canonical TATA motif does not affect TCF and TPF binding. Therefore, we suggest that the function of the unusual cytosine could be to reduce rabbit uteroglobin expression in cells lacking TCF and that the interaction of TATA-box binding protein with the weak TACA site is facilitated in TCF- and TPF-positive cells. Images PMID:8065353

  14. TATA-less promoters of some Ets-family genes are efficiently repressed by wild-type p53.

    PubMed

    Iotsova, V; Crépieux, P; Montpellier, C; Laudet, V; Stehelin, D

    1996-12-01

    p53 has been reported to repress a number of TATA-containing promoters in transient transfection assays. TATA-less promoters are generally believed to be refractive to p53 repression. We report here that the TATA-less promoters of Ets-family genes (Ets-1 and Ets-2) are efficiently repressed by wild-type but not mutant p53 in transient co-transfection assays. Moreover, p53 was immunologically detected in protein complexes formed on oligonucleotides from both the TATA-containing and TATA-less promoters. Our data suggest that p53 is involved in the regulation of the expression of both promoter types, most probably by protein-protein interaction. A model for p53 function in promoter repression is proposed. PMID:8957074

  15. Human immunodeficiency virus type 1 LTR TATA and TAR region sequences required for transcriptional regulation.

    PubMed Central

    Garcia, J A; Harrich, D; Soultanakis, E; Wu, F; Mitsuyasu, R; Gaynor, R B

    1989-01-01

    The human immunodeficiency virus (HIV) type 1 LTR is regulated at the transcriptional level by both cellular and viral proteins. Using HeLa cell extracts, multiple regions of the HIV LTR were found to serve as binding sites for cellular proteins. An untranslated region binding protein UBP-1 has been purified and fractions containing this protein bind to both the TAR and TATA regions. To investigate the role of cellular proteins binding to both the TATA and TAR regions and their potential interaction with other HIV DNA binding proteins, oligonucleotide-directed mutagenesis of both these regions was performed followed by DNase I footprinting and transient expression assays. In the TATA region, two direct repeats TC/AAGC/AT/AGCTGC surround the TATA sequence. Mutagenesis of both of these direct repeats or of the TATA sequence interrupted binding over the TATA region on the coding strand, but only a mutation of the TATA sequence affected in vivo assays for tat-activation. In addition to TAR serving as the site of binding of cellular proteins, RNA transcribed from TAR is capable of forming a stable stem-loop structure. To determine the relative importance of DNA binding proteins as compared to secondary structure, oligonucleotide-directed mutations in the TAR region were studied. Local mutations that disrupted either the stem or loop structure were defective in gene expression. However, compensatory mutations which restored base pairing in the stem resulted in complete tat-activation. This indicated a significant role for the stem-loop structure in HIV gene expression. To determine the role of TAR binding proteins, mutations were constructed which extensively changed the primary structure of the TAR region, yet left stem base pairing, stem energy and the loop sequence intact. These mutations resulted in decreased protein binding to TAR DNA and defects in tat-activation, and revealed factor binding specifically to the loop DNA sequence. Further mutagenesis which inverted

  16. Search for DNA conformational features for functional sites. Investigation of the TATA box

    SciTech Connect

    Ponomarenko, M.P.; Ponomarenko, J.V.; Kel, A.E.; Kolchanov, N.A.

    1996-12-31

    A method for searching for DNA conformational features significant for functional sites is developed. The method uses helical angles averaged for known X-ray structures. Nucleotide sequences are assigned mean angles in a given region. Choice of the significant angles is based on their capabilities to discriminate functional sites from random sequences. The yeast, invertebrate, and vertebrate TATA boxes are analyzed using this method. Regions neighboring the TATA boxes are found to have smaller helical twist and roll angles. The results agree with the experimental data on Dickerson-Drew dodecamers. There is a significant decrease in the length of a small roll angle region with increasing complexity of taxon organization. 28 refs., 3 figs., 3 tabs.

  17. Upstream regulatory regions required to stabilize binding to the TATA sequence in an adenovirus early promoter.

    PubMed

    Garcia, J; Wu, F; Gaynor, R

    1987-10-26

    Of the five early adenovirus promoters, the early region 3 (E3) promoter is one of the most strongly induced by the E1A protein. To identify cellular proteins involved in both the basal and E1A-induced transcriptional regulation of the E3 promoter, DNase I footprinting using partially purified Hela cell extracts was performed. Four regions of the E3 promoter serve as binding domains for cellular proteins. These regions are found between -156 to -179 (site IV), -83 to -103 (site III), -47 to -67 (site II), and -16 to -37 (site I), relative to the start of transcription. Examination of the DNA sequences in each binding domain suggests that site III likely serves as a binding site for activator protein 1 (AP-1), site II for the cyclic AMP regulatory element binding protein (CREB), and site I for a TATA binding factor. The factors binding to either site II or III were sufficient to stabilize binding to the TATA sequence (site I). Mutagenesis studies indicated that both sites II and III, in addition to site I, are needed for complete basal and E1A-induced transcription. These results suggest that multiple cellular factors are involved in both the basal and E1A-induced transcriptional regulation of the E3 promoter, and that either of two upstream regions are capable of stabilizing factor binding to the TATA sequence. PMID:2959908

  18. Upstream regulatory regions required to stabilize binding to the TATA sequence in an adenovirus early promoter.

    PubMed Central

    Garcia, J; Wu, F; Gaynor, R

    1987-01-01

    Of the five early adenovirus promoters, the early region 3 (E3) promoter is one of the most strongly induced by the E1A protein. To identify cellular proteins involved in both the basal and E1A-induced transcriptional regulation of the E3 promoter, DNase I footprinting using partially purified Hela cell extracts was performed. Four regions of the E3 promoter serve as binding domains for cellular proteins. These regions are found between -156 to -179 (site IV), -83 to -103 (site III), -47 to -67 (site II), and -16 to -37 (site I), relative to the start of transcription. Examination of the DNA sequences in each binding domain suggests that site III likely serves as a binding site for activator protein 1 (AP-1), site II for the cyclic AMP regulatory element binding protein (CREB), and site I for a TATA binding factor. The factors binding to either site II or III were sufficient to stabilize binding to the TATA sequence (site I). Mutagenesis studies indicated that both sites II and III, in addition to site I, are needed for complete basal and E1A-induced transcription. These results suggest that multiple cellular factors are involved in both the basal and E1A-induced transcriptional regulation of the E3 promoter, and that either of two upstream regions are capable of stabilizing factor binding to the TATA sequence. Images PMID:2959908

  19. The TATA-less promoter of VP1, a plant gene controlling seed germination.

    PubMed

    Carrari, F; Frankel, N; Lijavetzky, D; Benech-Arnold, R; Sánchez, R; Iusem, N D

    2001-01-01

    Vp1 is a seed-specific gene involved in the control of dormancy and germination. We here present the complete sequence of the sorghum vp1 promoter/enhancer region highlighting its main features, especially the lack of canonical TATA and CAAT boxes and the presence of elements responsive to abscisic acid and light. The region closest to the start of transcription is highly homologous to the partial proximal sequence reported for the maize vp1 promoter. This region is interrupted by a 57-nt stretch containing 14 CT microsatellite repeats. We observed a poor overall homology to the promoter from abi3 gene, the Arabidopsis counterpart bearing a similar coding sequence. However, there exists a high degree of homology (89%) between a TATA-rich 103-bp stretch of the sorghum vp1 promoter located about 700 nt upstream of the startpoint and miniature inverted transposable elements (MITEs) interspersed within the sorghum seed-specific kafirin cluster. This sorghum MITE-like element displays considerable homology (68%) to the TATA-less promoter from the sorghum NADP-malate dehydrogenase gene and lesser similarity to the Tourist, Pilgrim and Batuta MITEs previously identified within the promoter from the maize Abp1 (auxin-binding protein) gene. PMID:11761708

  20. Stepwise Bending of DNA by a Single TATA-Box Binding Protein

    NASA Astrophysics Data System (ADS)

    Tolicnorrelykke, S.; Rasmussen, M.; Pavone, F.; Bergsorensen, K.; Oddershede, L.

    2006-05-01

    The TATA-box Binding Protein (TBP) is required by all three eukaryotic RNA polymerases for the initiation of transcription from most promoters. TBP recognizes, binds to, and bends promoter sequences called ``TATA-boxes'' in the DNA. We present results from the study of individual Saccharomyces cerevisia TBPs interacting with single DNA molecules containing a TATA-box. Using video microscopy, we observed the Brownian motion of beads tethered by short surface-bound DNA. When TBP binds to and bends the DNA, the conformation of the DNA changes and the amplitude of Brownian motion of the tethered bead is reduced compared to that of unbent DNA. We detected individual binding and dissociation events and derived kinetic parameters for the process. Dissociation was induced by increasing the salt concentration or by directly pulling on the tethered bead using optical tweezers. In addition to the well-defined free and bound classes of Brownian motion, we observed another two classes of motion. These extra classes were identified with intermediate states on a three-step, linear binding pathway. Biological implications of the intermediate states are discussed.

  1. Interaction of the Dr1 inhibitory factor with the TATA binding protein is disrupted by adenovirus E1A.

    PubMed Central

    Kraus, V B; Inostroza, J A; Yeung, K; Reinberg, D; Nevins, J R

    1994-01-01

    Past experiments have shown that the adenovirus E1A12S product activates the hsp70 promoter, dependent on the TATA element and dependent on N-terminal E1A sequences. Other experiments have identified a factor termed Dr1 that interacts with and inhibits the transcriptional activity of the TATA-binding protein (TBP). We now find that the E1A12S protein can disrupt the interaction of the Dr1 factor with the TATA-specific TBP factor, allowing the productive interaction of TBP with TFIIA. This E1A-mediated disruption is dependent on N-terminal sequences that are also essential for the TATA-dependent trans-activation of the hsp70 promoter. Moreover, we also find that Dr1 expression in transfected cells can inhibit transcription from the hsp70 promoter and that this can be overcome by coexpression of the wild-type E1A protein, dependent on N-terminal sequences. We conclude that the activation of hsp70 through the TATA element may be mechanistically similar to the activation of the E2 promoter via E2F, in each case involving a release of a transcription factor from an inactive complex. Images PMID:8022773

  2. The TATA-binding protein as a regulator of cellular transformation.

    PubMed

    Johnson, Sandra A S; Dubeau, Louis; White, Robert J; Johnson, Deborah L

    2003-01-01

    The TATA-binding protein, TBP, is used by all three RNA polymerases and is therefore central to the process of gene expression. TBP associates with several subsets of proteins, called TATA-binding protein-associated factors (TAFs). This results in the formation of at least three distinct complexes, SL1, TFIID, and TFIIIB, which dictates whether TBP functions in RNA polymerase (pol) I, pol II, or pol III transcription, respectively. The regulation of gene expression has focused largely on proteins that serve to modulate the efficiency by which the general transcription components, such as TBP, interact with promoters. The possibility of a basal transcription factor, itself, being regulated, and influencing cellular homeostasis, has not been extensively considered. However, recent studies have indicated that TBP is indeed regulated, and that modulation of its cellular concentration has a profound, and surprisingly selective, impact on gene expression that can mediate the normal proliferative responses of cells to growth stimuli as well as the transformation potential of cells. PMID:12963838

  3. Molecular Cloning of a cDNA Encoding for Taenia solium TATA-Box Binding Protein 1 (TsTBP1) and Study of Its Interactions with the TATA-Box of Actin 5 and Typical 2-Cys Peroxiredoxin Genes.

    PubMed

    Rodríguez-Lima, Oscar; García-Gutierrez, Ponciano; Jiménez, Lucía; Zarain-Herzberg, Ángel; Lazzarini, Roberto; Landa, Abraham

    2015-01-01

    TATA-box binding protein (TBP) is an essential regulatory transcription factor for the TATA-box and TATA-box-less gene promoters. We report the cloning and characterization of a full-length cDNA that encodes a Taenia solium TATA-box binding protein 1 (TsTBP1). Deduced amino acid composition from its nucleotide sequence revealed that encodes a protein of 238 residues with a predicted molecular weight of 26.7 kDa, and a theoretical pI of 10.6. The NH2-terminal domain shows no conservation when compared with to pig and human TBP1s. However, it shows high conservation in size and amino acid identity with taeniids TBP1s. In contrast, the TsTBP1 COOH-terminal domain is highly conserved among organisms, and contains the amino acids involved in interactions with the TATA-box, as well as with TFIIA and TFIIB. In silico TsTBP1 modeling reveals that the COOH-terminal domain forms the classical saddle structure of the TBP family, with one α-helix at the end, not present in pig and human. Native TsTBP1 was detected in T. solium cysticerci´s nuclear extract by western blot using rabbit antibodies generated against two synthetic peptides located in the NH2 and COOH-terminal domains of TsTBP1. These antibodies, through immunofluorescence technique, identified the TBP1 in the nucleus of cells that form the bladder wall of cysticerci of Taenia crassiceps, an organism close related to T. solium. Electrophoretic mobility shift assays using nuclear extracts from T. solium cysticerci and antibodies against the NH2-terminal domain of TsTBP1 showed the interaction of native TsTBP1 with the TATA-box present in T. solium actin 5 (pAT5) and 2-Cys peroxiredoxin (Ts2-CysPrx) gene promoters; in contrast, when antibodies against the anti-COOH-terminal domain of TsTBP1 were used, they inhibited the binding of TsTBP1 to the TATA-box of the pAT5 promoter gene. PMID:26529408

  4. Molecular Cloning of a cDNA Encoding for Taenia solium TATA-Box Binding Protein 1 (TsTBP1) and Study of Its Interactions with the TATA-Box of Actin 5 and Typical 2-Cys Peroxiredoxin Genes

    PubMed Central

    Rodríguez-Lima, Oscar; García-Gutierrez, Ponciano; Jiménez, Lucía; Zarain-Herzberg, Ángel; Lazzarini, Roberto; Landa, Abraham

    2015-01-01

    TATA-box binding protein (TBP) is an essential regulatory transcription factor for the TATA-box and TATA-box-less gene promoters. We report the cloning and characterization of a full-length cDNA that encodes a Taenia solium TATA-box binding protein 1 (TsTBP1). Deduced amino acid composition from its nucleotide sequence revealed that encodes a protein of 238 residues with a predicted molecular weight of 26.7 kDa, and a theoretical pI of 10.6. The NH2-terminal domain shows no conservation when compared with to pig and human TBP1s. However, it shows high conservation in size and amino acid identity with taeniids TBP1s. In contrast, the TsTBP1 COOH-terminal domain is highly conserved among organisms, and contains the amino acids involved in interactions with the TATA-box, as well as with TFIIA and TFIIB. In silico TsTBP1 modeling reveals that the COOH-terminal domain forms the classical saddle structure of the TBP family, with one α-helix at the end, not present in pig and human. Native TsTBP1 was detected in T. solium cysticerci´s nuclear extract by western blot using rabbit antibodies generated against two synthetic peptides located in the NH2 and COOH-terminal domains of TsTBP1. These antibodies, through immunofluorescence technique, identified the TBP1 in the nucleus of cells that form the bladder wall of cysticerci of Taenia crassiceps, an organism close related to T. solium. Electrophoretic mobility shift assays using nuclear extracts from T. solium cysticerci and antibodies against the NH2-terminal domain of TsTBP1 showed the interaction of native TsTBP1 with the TATA-box present in T. solium actin 5 (pAT5) and 2-Cys peroxiredoxin (Ts2-CysPrx) gene promoters; in contrast, when antibodies against the anti-COOH-terminal domain of TsTBP1 were used, they inhibited the binding of TsTBP1 to the TATA-box of the pAT5 promoter gene. PMID:26529408

  5. Identification and characterization of the activation domain of Ifh1, an activator of model TATA-less genes.

    PubMed

    Zhong, Peipei; Melcher, Karsten

    2010-01-29

    In yeast, TATA box-binding protein TBP can be delivered to protein-coding genes by direct interactions with two different coactivators: TFIID, which delivers TBP preferentially to TATA-less promoters, and SAGA, which strongly favors TATA box-containing promoters. Transcriptional activators of SAGA-dependant genes are characterized by prototypic acidic activation domains (ADs) that efficiently recruit SAGA, but not TFIID, to UAS elements even in the absence of a core promoter. In contrast to the well-studied acidic activation domains, little is known about the activation domains of activators of TFIID-dependent genes, even though these genes constitute more than 80% of eukaryotic protein-coding genes. The paradigm for TATA-less genes are the ribosomal protein genes (RPGs). Here we have identified the AD of the RPG activator Ifh1p and demonstrate that a minimal Ifh1 AD represents a new class of AD that significantly differs from acidic ADs in amino acid signature, relative coactivator affinities, and core promoter selectivity. PMID:20059977

  6. FOXM1c transactivates the human c-myc promoter directly via the two TATA boxes P1 and P2.

    PubMed

    Wierstra, Inken; Alves, Jürgen

    2006-10-01

    FOXM1c transactivates the c-myc promoter via the P1 and P2 TATA boxes using a new mechanism. Whereas the P1 TATA box TATAATGC requires its sequence context to be FOXM1c responsive, the P2 TATA box TATAAAAG alone is sufficient to confer FOXM1c responsiveness to any minimal promoter. FOXM1c transactivates by binding to the TATA box as well as directly to TATA-binding protein, transcription factor IIB and transcription factor IIA. This new transactivation mechanism is clearly distinguished from the function of FOXM1c as a conventional transcription factor. The central domain of FOXM1c functions as an essential domain for activation via the TATA box, but as an inhibitory domain (retinoblastoma protein-independent transrepression domain and retinoblastoma protein-recruiting negative regulatory domain) for transactivation via conventional FOXM1c-binding sites. Each promoter with the P2 TATA box TATAAAAG is postulated to be transactivated by FOXM1c. This was demonstrated for the promoters of c-fos, hsp70 and histone H2B/a. A database search revealed almost 300 probable FOXM1c target genes, many of which function in proliferation and tumorigenesis. Accordingly, dominant-negative FOXM1c proteins reduced cell growth approximately threefold, demonstrating a proliferation-stimulating function for wild-type FOXM1c. PMID:16965535

  7. TATA-binding protein and associated factors in polymerase II and polymerase III transcription.

    PubMed Central

    Meyers, R E; Sharp, P A

    1993-01-01

    Transcription by RNA polymerase I (pol I), pol II, and pol III requires the TATA-binding protein (TBP). This protein functions in association with distinct TBP-associated factors (TAFs) which may specify the nature of the polymerase selected for initiation at a promoter site. In the pol III transcription system, the TBP-TAF complex is a component of the TFIIIB factor. This factor has been resolved into a TBP-TAF complex and another component, both of which are required for reconstitution of transcription by pol III. Neither the TBP-TAF complexes B-TFIID and D-TFIID, which were previously characterized as active for pol II transcription, nor TBP alone can complement pol III transcription reactions that are dependent upon the TBP-TAF subcomponent of TFIIIB. Surprisingly, the TBP-TAF subcomponent of TFIIIB is active in reconstitution of pol II transcription. Images PMID:8247010

  8. It takes two to tango: two TatA paralogues and two redox enzyme-specific chaperones are involved in the localization of twin-arginine translocase substrates in Campylobacter jejuni

    PubMed Central

    Liu, Yang-Wei; Hitchcock, Andrew; Salmon, Robert C.

    2014-01-01

    The food-borne zoonotic pathogen Campylobacter jejuni has complex electron transport chains required for growth in the host, many of which contain cofactored periplasmic enzymes localized by the twin-arginine translocase (TAT). We report here the identification of two paralogues of the TatA translocase component in C. jejuni strain NCTC 11168, encoded by cj1176c (tatA1) and cj0786 (tatA2). Deletion mutants constructed in either or both of the tatA1 and tatA2 genes displayed distinct growth and enzyme activity phenotypes. For sulphite oxidase (SorAB), the multi-copper oxidase (CueO) and alkaline phosphatase (PhoX), complete dependency on TatA1 for correct periplasmic activity was observed. However, the activities of nitrate reductase (NapA), formate dehydrogenase (FdhA) and trimethylamine N-oxide reductase (TorA) were significantly reduced in the tatA2 mutant. In contrast, the specific rate of fumarate reduction catalysed by the flavoprotein subunit of the methyl menaquinone fumarate reductase (MfrA) was similar in periplasmic fractions of both the tatA1 and the tatA2 mutants and only the deletion of both genes abolished activity. Nevertheless, unprocessed MfrA accumulated in the periplasm of the tatA1 (but not tatA2) mutant, indicating aberrant signal peptide cleavage. Surprisingly, TatA2 lacks two conserved residues (Gln8 and Phe39) known to be essential in Escherichia coli TatA and we suggest it is unable to function correctly in the absence of TatA1. Finally, only two TAT chaperones (FdhM and NapD) are encoded in strain NCTC 11168, which mutant studies confirmed are highly specific for formate dehydrogenase and nitrate reductase assembly, respectively. Thus, other TAT substrates must use general chaperones in their biogenesis. PMID:24961951

  9. Construction of Hunveyor-9 and Experiments with its Magnetic Carpet Observing Dust Mixtures at Eötvös High School, Tata, Hungary

    NASA Astrophysics Data System (ADS)

    Magyar, I.; Varga, T.; Bérczi, Sz.; Hegyi, S.; Hudoba, Gy.; Almády, B.; Badics, A.; Bakonyi, I.; Franko, M.; Gyürky, A.; Héricz, M.; Ikonga, R.; Németh, A.; Pardy, T.; Varga, T.; Végh, Gy.

    2008-03-01

    We report about the construction of the ninth Hungarian University Surveyor (Hunveyor-9) and its experiment with magnetic dust observation by carpet containing small discs of magnets at Tata, Eötvös József High School, Hungary.

  10. A novel TATA-box-binding factor from the silk glands of the mulberry silkworm, Bombyx mori.

    PubMed Central

    Srinivasan, Lakshmi; Gopinathan, Karumathil P

    2002-01-01

    The presence of one or more TATATAA motifs in the flanking sequences of individual members of a multi-gene tRNA(Gly)(1) family from the mulberry silkworm, Bombyx mori, negatively modulated the transcription of the gene copies. Characterization of proteins from posterior silk gland nuclear extracts, binding to the TATATAA motif, identified a novel 43 kD protein, designated here as P43 TATA-box-binding factor (TBF). The protein was purified to homogeneity. P43 TBF binding was highly sequence-specific and showed a 100-fold-higher affinity for binding than the TATA-box-binding protein (TBP). The protein also showed binding to the TATAAA sequence of the actin5C promoter. P43 TBF inhibited transcription of all the tRNA genes examined, as well as RNA polymerase II transcription from the actin5C promoter. The amino acid sequence of eleven peptides generated from P43 TBF did not share homology with proteins that bind the TATA box, such as TBP, TRF (TBP-related factor) or TLFs (TBP-like factors) reported from other sources. Inhibition of transcription of tRNA genes by P43 TBF could not be reversed by TBP. The inhibitory effect appeared to be exerted through sequestration of the associated transcription factors. PMID:11964150

  11. Operation of Cryogenic Facility in e-way at Tata Institute of Fundamental Research, Mumbai, India.

    NASA Astrophysics Data System (ADS)

    Srinivasan, K. V.

    2012-12-01

    In an attempt towards the development of modern, model and paperless cryogenic facility, the Low Temperature Facility of Tata Institute of Fundamental Research, at Mumbai, India; carried out many automation works using programmable logic controller (PLC) and other modern electronic tools, with the objective of bringing the entire plant operation to your palm whenever and wherever you are. Efficiency in the plant operation by keeping a watch on the plant healthiness, advance indication about the possible plant problem by means of pre-warning alarms, so that the remedial action can be taken well prior to the actual failure affects the plant operation, reduction in plant down time were achieved by the automation works. Large size in our cryogen production, controlling the complicated helium liquefier, meeting the uninterrupted supply of cryogen to the users on “any time availability basis,” safety in handling cryogens and high pressure gas, effective usage of limited skilled manpower etc., all these requirements call for the definite need of modern electronic gears and gadgets. This paper will describe in details about the automation works carried out at our cryogenic facility at TIFR.

  12. Differential stability of TATA box binding proteins from archaea with different optimal growth temperatures

    NASA Astrophysics Data System (ADS)

    Kopitz, Annette; Soppa, Jörg; Krejtschi, Carsten; Hauser, Karin

    2009-09-01

    The TATA box binding protein (TBP) is involved in promoter recognition, the first step of transcription initiation. TBP is universally conserved and essential in archaea and eukaryotes. In archaea, TBPs have to be stable and to function in species that cover an extremely wide range of optimal growth temperatures (OGTs), from below 0 °C to more than 100 °C. Thus, the archaeal TBP family is ideally suited to study the evolutionary adaptation of proteins to an extremely wide range of temperatures. We characterized the thermostability of one mesophilic and one thermophilic TBP by infrared spectroscopy. Transition temperatures ( Tms) of thermal unfolding have been determined using TBPs from Methanosarcina mazei (OGT 37 °C) and from Methanothermobacter thermautotrophicus (OGT 65 °C). Furthermore, the influence of protein and salt concentration on thermostability has been characterized. Together with previous studies, our results reveal that the Tms of archaeal TBPs are closely correlated with the OGTs of the respective species. Noteworthy, this is also true for the TBP from M. mazei representing the first characterized TBP from a mesophilic archaeon. In contrast, the only characterized eukaryotic TBP of the mesophilic plant Arabidopsis thaliana has a Tm more than 40 °C above the OGT.

  13. Yeast RNA polymerase II initiates transcription in vitro at TATA sequences proximal to potential non-B forms of the DNA template.

    PubMed Central

    Lescure, B; Arcangioli, B

    1984-01-01

    Pure yeast RNA polymerase II selectively initiates an abortive in vitro transcript within a TATA box of the yeast iso-1 cytochrome c gene promoter. Using a series of promoter deletions we show that a DNA sequence located upstream of the TATA box is needed for an efficient in vitro transcription. Supercoiling of the DNA template is an absolute requirement for the specific in vitro transcription. Examination of the DNA structure near several in vitro initiation sites shows that the common features observed are the presence of a TATA sequence in which RNA synthesis is initiated, and which is proximal to a potential non-B form of the DNA (a B to Z transition or a cruciform structure). Images Fig. 2. Fig. 3. Fig. 4. Fig. 5. Fig. 6. PMID:6376116

  14. TATA-binding protein and transcription factor IIB induce transcript slipping during early transcription by RNA polymerase II.

    PubMed

    Gilman, Benjamin; Drullinger, Linda F; Kugel, Jennifer F; Goodrich, James A

    2009-04-01

    To better understand the mechanism of steps in early transcription by RNA polymerase II (pol II), we investigated the molecular determinants of transcript slipping within complexes assembled on promoters containing a pre-melted transcription bubble from -9 to +3. Transcript slippage occurs when an RNA transcript contains a repetitive sequence that allows the transcript to slip back and pair with the template strand of the DNA at a new register before transcription continues. We established the contributions of individual transcription factors, DNA elements, and RNA length to slipping on a heteroduplex template using a highly purified human pol II transcription system. We found that transcripts slip at a very defined point in the transcription reaction, after pol II completes phosphodiester bond synthesis at register +5. This point is set by the position of the polymerase active site on the DNA template, as opposed to the length of the transcript, as well as by a repetitive CUCU sequence that must occur from +2 to +5. Interestingly, slipping at this juncture is induced by TATA-binding protein and transcription factor IIB and requires a TATA box but not a transcription factor IIB recognition sequence. We propose a model in which transcribing complexes, upon completing phosphodiester bond synthesis at register +5, enter one of two branches in which they either complete productive synthesis of the transcript or undergo multiple rounds of transcript slipping. PMID:19193635

  15. The gene for human TATA-binding-protein-associated factor (TAFII) 170: structure, promoter and chromosomal localization.

    PubMed Central

    Van Der Knaap, J A; Van Den Boom, V; Kuipers, J; Van Eijk, M J; Van Der Vliet, P C; Timmers, H T

    2000-01-01

    The TATA-binding protein (TBP) plays a central role in eukaryotic transcription and forms protein complexes with TBP-associated factors (TAFs). The genes encoding TAF(II) proteins frequently map to chromosomal regions altered in human neoplasias. TAF(II)170 of B-TFIID is a member of the SF2 superfamily of putative helicases. Members of this superfamily have also been implicated in several human genetic disorders. In this study we have isolated human genomic clones encoding TAF(II)170 and we show that the gene contains 37 introns. Ribonuclease-protection experiments revealed that TAF(II)170 has multiple transcription start sites, consistent with the observation that the promoter lacks a canonical TATA box and initiator element. Deletion analysis of the promoter region showed that a fragment of 264 bp is sufficient to direct transcription. In addition, we determined the chromosomal localization by two independent methods which mapped the gene to human chromosome 10q22-q23 between the markers D10S185 and WI-1183. The region surrounding these markers has been implicated in several human disorders. PMID:10642510

  16. SPN1, a conserved gene identified by suppression of a postrecruitment-defective yeast TATA-binding protein mutant.

    PubMed Central

    Fischbeck, Julie A; Kraemer, Susan M; Stargell, Laurie A

    2002-01-01

    Little is known about TATA-binding protein (TBP) functions after recruitment to the TATA element, although several TBP mutants display postrecruitment defects. Here we describe a genetic screen for suppressors of a postrecruitment-defective TBP allele. Suppression was achieved by a single point mutation in a previously uncharacterized Saccharomyces cerevisiae gene, SPN1 (suppresses postrecruitment functions gene number 1). SPN1 is an essential yeast gene that is highly conserved throughout evolution. The suppressing mutation in SPN1 substitutes an asparagine for an invariant lysine at position 192 (spn1(K192N)). The spn1(K192N) strain is able to suppress additional alleles of TBP that possess postrecruitment defects, but not a TBP allele that is postrecruitment competent. In addition, Spn1p does not stably associate with TFIID in vivo. Cells containing the spn1(K192N) allele exhibit a temperature-sensitive phenotype and some defects in activated transcription, whereas constitutive transcription appears relatively robust in the mutant background. Consistent with an important role in postrecruitment functions, transcription from the CYC1 promoter, which has been shown to be regulated by postrecruitment mechanisms, is enhanced in spn1(K192N) cells. Moreover, we find that SPN1 is a member of the SPT gene family, further supporting a functional requirement for the SPN1 gene product in transcriptional processes. PMID:12524336

  17. Using FRET to Measure the Angle at Which a Protein Bends DNA: TBP Binding a TATA Box as a Model System

    ERIC Educational Resources Information Center

    Kugel, Jennifer F.

    2008-01-01

    An undergraduate biochemistry laboratory experiment that will teach the technique of fluorescence resonance energy transfer (FRET) while analyzing protein-induced DNA bending is described. The experiment uses the protein TATA binding protein (TBP), which is a general transcription factor that recognizes and binds specific DNA sequences known as…

  18. TATA boxes in gene transcription and poly (A) tails in mRNA stability: New perspective on the effects of berberine

    PubMed Central

    Yuan, Zhi-Yi; Lu, Xi; Lei, Fan; Chai, Yu-Shuang; Wang, Yu-Gang; Jiang, Jing-Fei; Feng, Tian-Shi; Wang, Xin-Pei; Yu, Xuan; Yan, Xiao-Jin; Xing, Dong-Ming; Du, Li-Jun

    2015-01-01

    Berberine (BBR) is a natural compound with variable pharmacological effects and a broad panel of target genes. We investigated berberine’s pharmacological activities from the perspective of its nucleotide-binding ability and discovered that BBR directly regulates gene expression by targeting TATA boxes in transcriptional regulatory regions as well as the poly adenine (poly (A)) tail at the mRNA terminus. BBR inhibits gene transcription by binding the TATA boxes in the transcriptional regulatory region, but it promotes higher levels of expression by targeting the poly (A) tails of mRNAs. The present study demonstrates that TATA boxes and poly (A) tails are the first and second primary targets by which BBR regulates gene expression. The final outcome of gene regulation by BBR depends on the structure of the individual gene. This is the first study to reveal that TATA boxes and poly (A) tails are direct targets for BBR in its regulation of gene expression. Our findings provide a novel explanation for the complex activities of a small molecule compound in a biological system and a novel horizon for small molecule-compound pharmacological studies. PMID:26671652

  19. Asian-American Mental Health and Help-Seeking Behavior: Comment on Solberg et al. (1994), Tata and Leong (1994), and Lin (1994).

    ERIC Educational Resources Information Center

    Sue, Derald Wing

    1994-01-01

    Comments on previous articles (this issue) by Solberg et al., Tata and Leong, and Lin on help-seeking behaviors of Asian Americans. Sees articles as dispelling false images and stereotypes about mental health needs of Asian Americans. Suggests that future research focus on diversity of Asian American population and development of theories and…

  20. DNA and Protein Footprinting Analysis of the Modulation of DNA Binding by the N-Terminal Domain of the Saccharomyces cervisiae TATA Binding Protein

    SciTech Connect

    Gupta,S.; Cheng, H.; Mollah, A.; Jamison, E.; Morris, S.; Chance, M.; Khrapunov, S.; Brenowitz, M.

    2007-01-01

    Recombinant full-length Saccharomyces cerevisiae TATA binding protein (TBP) and its isolated C-terminal conserved core domain (TBPc) were prepared with measured high specific DNA-binding activities. Direct, quantitative comparison of TATA box binding by TBP and TBPc reveals greater affinity by TBPc for either of two high-affinity sequences at several different experimental conditions. TBPc associates more rapidly than TBP to TATA box bearing DNA and dissociates more slowly. The structural origins of the thermodynamic and kinetic effects of the N-terminal domain on DNA binding by TBP were explored in comparative studies of TBPc and TBP by 'protein footprinting' with hydroxyl radical ({center_dot}OH) side chain oxidation. Some residues within TBPc and the C-terminal domain of TBP are comparably protected by DNA, consistent with solvent accessibility changes calculated from core domain crystal structures. In contrast, the reactivity of some residues located on the top surface and the DNA-binding saddle of the C-terminal domain differs between TBP and TBPc in both the presence and absence of bound DNA; these results are not predicted from the crystal structures. A strikingly different pattern of side chain oxidation is observed for TBP when a nonionic detergent is present. Taken together, these results are consistent with the N-terminal domain actively modulating TATA box binding by TBP and nonionic detergent modulating the interdomain interaction.

  1. Interaction identification of Zif268 and TATA(ZF) proteins with GC-/AT-rich DNA sequence: A theoretical study.

    PubMed

    Yang, Bo; Zhu, Yanyan; Wang, Yan; Chen, Guangju

    2011-02-01

    Molecular dynamics (MD) simulations for Zif268 (a zinc-finger-protein binding specifically to the GC-rich DNA)-d(A(1) G(2) C(3) G(4) T(5) G(6) G(7) G(8) C(9) A(10) C(11) )(2) and TATA(ZF) (a zinc-finger-protein recognizing the AT-rich DNA)-d(A(1) C(2) G(3) C(4) T(5) A(6) T(7) A(8) A(9) A(10) A(11) G(12) G(13) )(2) complexes have been performed for investigating the DNA binding affinities and specific recognitions of zinc fingers to GC-rich and AT-rich DNA sequences. The binding free energies for the two systems have been further analyzed by using the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method. The calculations of the binding free energies reveal that the affinity energy of Zif268-DNA complex is larger than that of TATA(ZF) -DNA one. The affinity between the zinc-finger-protein and DNA is mainly driven by more favorable van-der-Waals and nonpolar/solvation interactions in both complexes. However, the affinity energy difference of the two binding systems is mainly caused by the difference of van-der-Waals interactions and entropy components. The decomposition analysis of MM-PBSA free energies on each residue of the proteins predicts that the interactions between the residues with the positive charges and DNA favor the binding process; while the interactions between the residues with the negative charges and DNA behave in the opposite way. The interhydrogen-bonds at the protein-DNA interface and the induced intrafinger hydrogen bonds between the residues of protein for the Zif268-DNA complex have been identified at some key contact sites. However, only the interhydrogen-bonds between the residues of protein and DNA for TATA(ZF) -DNA complex have been found. The interactions of hydrogen-bonds, electrostatistics and van-der-Waals type at some new contact sites have been identified. Moreover, the recognition characteristics of the two studied zinc-finger-proteins have also been discussed. PMID:20658568

  2. Is capillary electrophoresis on microchip devices able to genotype uridine diphosphate glucuronosyltransferase 1A1 TATA-box polymorphisms?

    PubMed

    Minucci, Angelo; Canu, Giulia; De Bonis, Maria; Delibato, Elisabetta; Capoluongo, Ettore

    2014-06-01

    In this commentary, we focused our attention on capillary electrophoresis. It achieves the efficient separation of molecular species by the application of high voltages to samples in solution. Actually, capillary electrophoresis can be performed on microchip devices, based on an automated and miniaturized electrophoresis system, based on lab-on-a-chip technology. By this technology it is possible to separate nucleic acid fragments (DNA or RNA) with respect to sizing accuracy and sizing resolution. Currently, two automated capillary electrophoresis on microchips devices are available: the Agilent 2100 Bioanalyzer and the Experion™ Automated Electrophoresis System. In this study, we evaluated if the CE is able to distinguish the three uridine diphosphate glucuronosyltransferase 1A1 TATA-box genotypes. PMID:24687976

  3. A role for the TATA-box-binding protein component of the transcription factor IID complex as a general RNA polymerase III transcription factor.

    PubMed Central

    White, R J; Jackson, S P; Rigby, P W

    1992-01-01

    The major class of vertebrate genes transcribed by RNA polymerase (EC 2.7.7.6) III, which includes 5S rRNA genes, tRNA genes, and the adenovirus VA genes, is characterized by split internal promoters and no absolute dependence upon specific upstream sequences. Fractionation experiments have shown that transcription of such genes requires two general RNA polymerase III-specific factors, TFIIIB and TFIIIC. We now demonstrate that a third general factor is also employed by these genes. This is the TATA-box-binding protein originally identified as being a component of the general RNA polymerase II transcription factor TFIID. This protein is involved in the transcription by RNA polymerase III of every template tested, even though the promoters of VA and most vertebrate tRNA and 5S rRNA genes do not contain recognizable TATA elements. Images PMID:1542692

  4. Mechanism of initiator-mediated transcription: evidence for a functional interaction between the TATA-binding protein and DNA in the absence of a specific recognition sequence.

    PubMed Central

    Zenzie-Gregory, B; Khachi, A; Garraway, I P; Smale, S T

    1993-01-01

    Promoters containing Sp1 binding sites and an initiator element but lacking a TATA box direct high levels of accurate transcription initiation by using a mechanism that requires the TATA-binding protein (TBP). We have begun to address the role of TBP during transcription from Sp1-initiator promoters by varying the nucleotide sequence between -14 and -33 relative to the start site. With each of several promoters containing different upstream sequences, we detected accurate transcription both in vitro and in vivo, but the promoter strengths varied widely, particularly with the in vitro assay. The variable promoter activities correlated with, but were not proportional to, the abilities of the upstream sequences to function as TATA boxes, as assessed by multiple criteria. These results confirm that accurate transcription can proceed in the presence of an initiator, regardless of the sequence present in the -30 region. However, the results reveal a role for this upstream region, most consistent with a model in which initiator-mediated transcription requires binding of TBP to the upstream DNA in the absence of a specific recognition sequence. Moreover, in vivo it appears that the promoter strength is modulated less severely by altering the -30 sequence, consistent with a previous suggestion that TBP is not rate limiting in vivo for TATA-less promoters. Taken together, these results suggest that variations in the structure of a core promoter might alter the rate-limiting step for transcription initiation and thereby alter the potential modes of transcriptional regulation, without severely changing the pathway used to assemble a functional preinitiation complex. Images PMID:8321191

  5. Interaction between TATA-Binding Protein (TBP) and Multiprotein Bridging Factor-1 (MBF1) from the Filamentous Insect Pathogenic Fungus Beauveria bassiana

    PubMed Central

    Song, Chi; Ortiz-Urquiza, Almudena; Ying, Sheng-Hua; Zhang, Jin-Xia; Keyhani, Nemat O.

    2015-01-01

    TATA-binding protein (TBP) is a ubiquitous component of eukaryotic transcription factors that acts to nucleate assembly and position pre-initiation complexes. Multiprotein bridging factor 1 (MBF1) is thought to interconnect TBP with gene specific transcriptional activators, modulating transcriptional networks in response to specific signal and developmental programs. The insect pathogen, Beauveria bassiana, is a cosmopolitan fungus found in most ecosystems where it acts as an important regulator of insect populations and can form intimate associations with certain plants. In order to gain a better understanding of the function of MBF1 in filamentous fungi, its interaction with TBP was demonstrated. The MBF1 and TBP homologs in B. bassiana were cloned and purified from a heterologous E. coli expression system. Whereas purified BbTBP was shown to be able to bind oligonucleotide sequences containing the TATA-motif (Kd ≈ 1.3 nM) including sequences derived from the promoters of the B. bassiana chitinase and protease genes. In contrast, BbMBF1 was unable to bind to these same target sequences. However, the formation of a ternary complex between BbMBF1, BbTBP, and a TATA-containing target DNA sequence was seen in agarose gel electrophoretic mobility shift assays (EMSA). These data indicate that BbMBF1 forms direct interactions with BbTBP, and that the complex is capable of binding to DNA sequences containing TATA-motifs, confirming that BbTBP can link BbMBF1 to target sequences as part of the RNA transcriptional machinery in fungi. PMID:26466369

  6. Interaction between TATA-Binding Protein (TBP) and Multiprotein Bridging Factor-1 (MBF1) from the Filamentous Insect Pathogenic Fungus Beauveria bassiana.

    PubMed

    Song, Chi; Ortiz-Urquiza, Almudena; Ying, Sheng-Hua; Zhang, Jin-Xia; Keyhani, Nemat O

    2015-01-01

    TATA-binding protein (TBP) is a ubiquitous component of eukaryotic transcription factors that acts to nucleate assembly and position pre-initiation complexes. Multiprotein bridging factor 1 (MBF1) is thought to interconnect TBP with gene specific transcriptional activators, modulating transcriptional networks in response to specific signal and developmental programs. The insect pathogen, Beauveria bassiana, is a cosmopolitan fungus found in most ecosystems where it acts as an important regulator of insect populations and can form intimate associations with certain plants. In order to gain a better understanding of the function of MBF1 in filamentous fungi, its interaction with TBP was demonstrated. The MBF1 and TBP homologs in B. bassiana were cloned and purified from a heterologous E. coli expression system. Whereas purified BbTBP was shown to be able to bind oligonucleotide sequences containing the TATA-motif (Kd ≈ 1.3 nM) including sequences derived from the promoters of the B. bassiana chitinase and protease genes. In contrast, BbMBF1 was unable to bind to these same target sequences. However, the formation of a ternary complex between BbMBF1, BbTBP, and a TATA-containing target DNA sequence was seen in agarose gel electrophoretic mobility shift assays (EMSA). These data indicate that BbMBF1 forms direct interactions with BbTBP, and that the complex is capable of binding to DNA sequences containing TATA-motifs, confirming that BbTBP can link BbMBF1 to target sequences as part of the RNA transcriptional machinery in fungi. PMID:26466369

  7. The gene for the TATA binding protein (TBP) that contains a highly polymorphic protein coding CAG repeat maps to 6q27

    SciTech Connect

    Imbert, G.; Trottier, Y.; Mandel, J.L.

    1994-06-01

    The gene for TATA binding protein (TBP, an important general transcription initiation factor) was shown to contain a long polymorphic imperfect CAG repeat in the form (CAG){sub 3} (CAA){sub 3} (CAG){sub 7-11} CAA CAG CAA (CAG){sub 9-21} CAA CAG. The gene was tentatively assigned to chromosome 6 using a somatic cell hybrid panel.

  8. How to Use SNP_TATA_Comparator to Find a Significant Change in Gene Expression Caused by the Regulatory SNP of This Gene's Promoter via a Change in Affinity of the TATA-Binding Protein for This Promoter

    PubMed Central

    Ponomarenko, Mikhail; Rasskazov, Dmitry; Arkova, Olga; Ponomarenko, Petr; Suslov, Valentin; Savinkova, Ludmila; Kolchanov, Nikolay

    2015-01-01

    The use of biomedical SNP markers of diseases can improve effectiveness of treatment. Genotyping of patients with subsequent searching for SNPs more frequent than in norm is the only commonly accepted method for identification of SNP markers within the framework of translational research. The bioinformatics applications aimed at millions of unannotated SNPs of the “1000 Genomes” can make this search for SNP markers more focused and less expensive. We used our Web service involving Fisher's Z-score for candidate SNP markers to find a significant change in a gene's expression. Here we analyzed the change caused by SNPs in the gene's promoter via a change in affinity of the TATA-binding protein for this promoter. We provide examples and discuss how to use this bioinformatics application in the course of practical analysis of unannotated SNPs from the “1000 Genomes” project. Using known biomedical SNP markers, we identified 17 novel candidate SNP markers nearby: rs549858786 (rheumatoid arthritis); rs72661131 (cardiovascular events in rheumatoid arthritis); rs562962093 (stroke); rs563558831 (cyclophosphamide bioactivation); rs55878706 (malaria resistance, leukopenia), rs572527200 (asthma, systemic sclerosis, and psoriasis), rs371045754 (hemophilia B), rs587745372 (cardiovascular events); rs372329931, rs200209906, rs367732974, and rs549591993 (all four: cancer); rs17231520 and rs569033466 (both: atherosclerosis); rs63750953, rs281864525, and rs34166473 (all three: malaria resistance, thalassemia). PMID:26516624

  9. An RNA polymerase II transcription factor has an associated DNA-dependent ATPase (dATPase) activity strongly stimulated by the TATA region of promoters.

    PubMed Central

    Conaway, R C; Conaway, J W

    1989-01-01

    A transcription factor required for synthesis of accurately initiated run-off transcripts by RNA polymerase II has been purified and shown to have an associated DNA-dependent ATPase (dATPase) activity that is strongly stimulated by the TATA region of promoters. This transcription factor, designated delta, was purified more than 3000-fold from extracts of crude rat liver nuclei and has a native molecular mass of approximately 230 kDa. DNA-dependent ATPase (dATPase) and transcription activities copurify when delta is analyzed by hydrophobic interaction and ion-exchange HPLC, arguing that transcription factor delta possesses an ATPase (dATPase) activity. ATPase (dATPase) is specific for adenine nucleotides; ATP and dATP, but not CTP, UTP, or GTP, are hydrolyzed. ATPase (dATPase) is stimulated by both double-stranded and single-stranded DNAs, including pUC18, ssM13, and poly(dT); however, DNA fragments containing the TATA region of either the adenovirus 2 major late or mouse interleukin 3 promoters stimulate ATPase as much as 10-fold more effectively than DNA fragments containing nonpromoter sequences. These data suggest the intriguing possibility that delta plays a critical role in the ATP (dATP)-dependent activation of run-off transcription through a direct interaction with the TATA region of promoters. Images PMID:2552440

  10. Functional roles for the TATA promoter and enhancers in basal and Tat-induced expression of the human immunodeficiency virus type 1 long terminal repeat.

    PubMed Central

    Berkhout, B; Jeang, K T

    1992-01-01

    We have analyzed the contributory role of the human immunodeficiency virus type 1 (HIV-1) promoter and enhancers in basal and Tat-induced transcription. We found that a minimal promoter competent for basal expression is contained within sequences spanning nucleotides -43 to +80. Basal expression from this HIV-1 promoter was boosted more by the additional presence of the NF-kappa B elements than by the Sp1 elements. The minimal long terminal repeat promoter (-43 to +80), while having an intact TAR sequence, was not Tat inducible. However, the simple addition of short synthetic enhancer motifs (AP1, Oct, Sp1, and NF-kappa B) conferred Tat responsiveness. This ability to respond to Tat was in part dependent on the presence of the HIV-1 promoter. Changing the HIV-1 TATA to other eucaryotic TATA or non-TATA initiators minimally affected basal expression but altered Tat inducibility. Our findings suggest a specific context of functional promoter and enhancer elements that is optimal for Tat trans activation of the HIV-1 long terminal repeat. Our results do not allow conclusions about whether Tat acts at the level of initiation or at the level of elongation to be drawn. Images PMID:1727476

  11. STD1 (MSN3) interacts directly with the TATA-binding protein and modulates transcription of the SUC2 gene of Saccharomyces cerevisiae.

    PubMed Central

    Tillman, T S; Ganster, R W; Jiang, R; Carlson, M; Schmidt, M C

    1995-01-01

    STD1 (MSN3) was isolated independently as a multicopy suppressor of mutations in the TATA-binding protein and in SNF4, suggesting that STD1 might couple the SNF1 kinase signaling pathway to the transcriptional machinery. We report here a direct physical interaction between STD1 and the TATA-binding protein (TBP), observed in vivo by the two-hybrid system and in vitro by binding studies. STD1 bound both native TBP in yeast cell-free extracts and purified recombinant TBP. This interaction was altered when TBP delta 57 was used, suggesting a role for the non-conserved N-terminal domain of TBP in mediating protein-protein interactions. We also show that perturbation of STD1-TBP stoichiometry alters SUC2 expression in vivo and that this effect is dependent on the N-terminal domain of TBP. The activation of SUC2 expression by increased copy number of STD1 occurs at the level of mRNA accumulation and it requires the same TATA element and uses the same transcription start site as does activation of SUC2 by glucose limitation. Taken together, these results suggest that STD1 modulates SUC2 transcription through direct interactions with TBP. Images PMID:7667094

  12. Linkage of TATA-binding protein and proteasome subunit C5 genes in mice and humans reveals synteny conserved between mammals and invertebrates.

    PubMed

    Trachtulec, Z; Hamvas, R M; Forejt, J; Lehrach, H R; Vincek, V; Klein, J

    1997-08-15

    The TATA-binding protein (TBP) is a factor required for the transcription of all classes of eukaryotic genes. Here, we demonstrate that in the mouse the TBP-encoding gene (Tbp) resides next to the proteasomal subunit C5-encoding gene (Psmb1). The genes are located on mouse chromosome 17 in the t complex within the Hybrid sterility 1 (Hst1) region. We demonstrate that the homologous human genes (TBP AND PSMB1) are tightly linked on the long arm of chromosome 6, in a region syntenic with the proximal part of mouse chromosome 17. The mouse Tbp and Psmb1 and the human TBP and PSMB1 genes are transcribed in the opposite orientation. The TATA-binding protein and proteasomal subunit C5 genes are also linked on chromosome III of Caenorhabditis elegans, and together they are linked to other genes whose homologs map to human chromosome 6 and mouse chromosome 17. In the Drosophila genome, the housekeeping TATA-binding protein gene maps close to two other genes with homologs in the mammalian major histocompatibility complex. There thus exists conserved synteny of unrelated genes between mammals and invertebrates. PMID:9286694

  13. The Saccharomyces cerevisiae RNA polymerase III recruitment factor subunits Brf1 and Bdp1 impose a strict sequence preference for the downstream half of the TATA box.

    PubMed

    Tsihlis, Nick D; Grove, Anne

    2006-01-01

    Association of the TATA-binding protein (TBP) with its cognate site within eukaryotic promoters is key to accurate and efficient transcriptional initiation. To achieve recruitment of Saccharomyces cerevisiae RNA polymerase III, TBP is associated with two additional factors, Brf1 and Bdp1, to form the initiation factor TFIIIB. Previous data have suggested that the structure or dynamics of the TBP-DNA complex may be altered upon entry of Brf1 and Bdp1 into the complex. We show here, using the altered specificity TBP mutant TBPm3 and an iterative in vitro selection assay, that entry of Brf1 and Bdp1 into the complex imposes a strict sequence preference for the downstream half of the TATA box. Notably, the selected sequence (TGTAAATA) is a perfect match to the TATA box of the RNA polymerase III-transcribed U6 small nuclear RNA (SNR6) gene. We suggest that the selected T*A base pair step at the downstream end of the 8 bp TBP site may provide a DNA flexure that promotes TFIIIB-DNA complex formation. PMID:17028095

  14. Repeat expansion in spinocerebellar ataxia type 17 alleles of the TATA-box binding protein gene: an evolutionary approach.

    PubMed

    Tomiuk, Jürgen; Bachmann, Lutz; Bauer, Claudia; Rolfs, Arndt; Schöls, Ludger; Roos, Christian; Zischler, Hans; Schuler, Mathias M; Bruntner, Silke; Riess, Olaf; Bauer, Peter

    2007-01-01

    The variability and mutational changes of the CAG microsatellite in the TATA-box binding protein gene (TBP) were studied. We sequenced the microsatellite of the TBP gene of 25 unrelated individuals from northern Germany (10 SCA17 patients and 15 unaffected control individuals). In addition, the microsatellites were sequenced from individuals of 10 northern German families with at least one family member affected by SCA17. To study also the evolutionary history of this CAG/CAA microsatellite in nonhuman primates, the homologous regions were analysed from Pan troglodytes, Gorilla gorilla, Pongo pygmaeus, P. abellii, Hylobates lar, Nomascus leucogenys, Symphalangus syndactylus, Macaca mulatta, Papio hamadryas, Colobus polykomos and Callithrix jacchus. Three major conclusions were drawn: (i) Patterns of synonymous CAA interruptions in the microsatellite are characteristic and likely to result from selection for stabilizing the repetitive region; (ii) Interspecific comparisons indicate that SCA17 is likely to be a human trait. The most common allele in humans (37 repeats) is close to the threshold value upon which neurodegenerative changes can occur and may act as a repository for expanded, pathogenic alleles; (iii) The cassette-like structure of five out of 17 expanded alleles can be attributed to unequal crossing over. This can explain the rare and sporadic de novo generation of SCA17 alleles. PMID:17033685

  15. Effect of temperature on the structure and hydration layer of TATA-box DNA: A molecular dynamics simulation study.

    PubMed

    Samanta, Sudipta; Raghunathan, Devanathan; Mukherjee, Sanchita

    2016-05-01

    DNA within the living cells experiences a diverse range of temperature, ranging from freezing condition to hot spring water. How the structure, the mechanical properties of DNA, and the solvation dynamics around DNA changes with the temperature is important to understand the functionality of DNA under those acute temperature conditions. In that notion, we have carried out molecular dynamics simulations of a DNA oligomer, containing TATA-box sequence for three different temperatures (250K, 300K and 350K). We observed that the structure of the DNA, in terms of backbone torsion angles, sugar pucker, base pair parameters, and base pair step parameters, did not show any unusual properties within the studied range of temperatures, but significant structural alteration was noticed between BI and BII forms at higher temperature. As expected, the flexibility of the DNA, in terms of the torsional rigidity and the bending rigidity is highly temperature dependent, confirming that flexibility increases with increase in temperature. Additionally, the groove widths of the studied DNA showed temperature sensitivity, specifically, the major groove width decreases and the minor groove width increases, respectively, with the increase in temperature. We observed that at higher temperature, water around both the major and the minor groove of the DNA is less structured. However, the water dynamics around the minor groove of the DNA is more restricted as compared to the water around the major groove throughout the studied range of temperatures, without any anomalous behavior. PMID:27017424

  16. TRF3, a TATA-box-binding protein-related factor, is vertebrate-specific and widely expressed.

    PubMed

    Persengiev, Stephan P; Zhu, Xiaochun; Dixit, Bharat L; Maston, Glenn A; Kittler, Ellen L W; Green, Michael R

    2003-12-01

    TATA-box-binding protein (TBP) is a highly conserved RNA polymerase II general transcription factor that binds to the core promoter and initiates assembly of the preinitiation complex. Two proteins with high homology to TBP have been found: TBP-related factor 1 (TRF1), described only in Drosophila melanogaster, and TRF2, which is broadly distributed in metazoans. Here, we report the identification and characterization of an additional TBP-related factor, TRF3. TRF3 is virtually identical to TBP in the C-terminal core domain, including all residues involved in DNA binding and interaction with other general transcription factors. Like other TBP family members, the N-terminal region of TRF3 is divergent. The TRF3 gene is present and expressed in vertebrates, from fish through humans, but absent from the genomes of the urochordate Ciona intestinalis and the lower eukaryotes D. melanogaster and Caenorhabditis elegans. TRF3 is a nuclear protein that is present in all human and mouse tissues and cell lines examined. Despite the highly homologous TBP-like C-terminal core domain, gel filtration analysis indicates that the native molecular weight of TRF3 is substantially less than that of TFIID. Interestingly, after mitosis, reimport of TRF3 into the nucleus occurs subsequent to TBP and other basal transcription factors. In summary, TRF3 is a highly conserved vertebrate-specific TRF whose phylogenetic conservation, expression pattern, and other properties are distinct from those of TBP and all other TRFs. PMID:14634207

  17. Reconstruction of the mandible with vascularized iliac crest flap--initial experience at the Tata Memorial Hospital.

    PubMed

    Savant, D N; Patel, S G; Verghese, T; Bhathena, H M; Kavarana, N M

    1995-01-01

    Resection of the mandible for cancer of the oral cavity can result in gross functional and aesthetic deformity. Inspite of technological advances, reconstruction of mandibular defects remains one of the most challenging procedures in head and neck surgery. Conventional methods like alloplastic implants and bone grafting have a high rate of failure. The advent of microvascular techniques for mandibular reconstruction has revolutionised the management of these patients. We present our initial experience based on 18 patients who underwent vascularised iliac creast transfer at the Tata Memorial Hospital between November, 1992 and January, 1994. The operative technique of raising, shaping and fixation of the iliac crest flap as well as advantages and disadvantages are discussed. Postoperative graft viability was assessed using 99mTc-MDP scans during the 1st, 3rd and 12th weeks after surgery. We lost 3 flaps (16.4%) due to uncontrolled infection and vessel thrombosis. All of the remaining patients demonstrated good uptake on bone scans and satisfactory bony union on OPG. We conclude that mandibular reconstruction using the vascularised iliac crest is reliable and produces acceptable postoperative functional results with 88% of patients having no swallowing difficulty, 83% with normal speech and excellent cosmesis in 83% (15/18) of the patients. PMID:8525747

  18. Doubly Spliced RNA of Hepatitis B Virus Suppresses Viral Transcription via TATA-Binding Protein and Induces Stress Granule Assembly

    PubMed Central

    Tsai, Kuen-Nan; Chong, Chin-Liew; Chou, Yu-Chi; Huang, Chien-Chiao; Wang, Yi-Ling; Wang, Shao-Win; Chen, Mong-Liang

    2015-01-01

    ABSTRACT The risk of liver cancer in patients infected with the hepatitis B virus (HBV) and their clinical response to interferon alpha therapy vary based on the HBV genotype. The mechanisms underlying these differences in HBV pathogenesis remain unclear. In HepG2 cells transfected with a mutant HBVG2335A expression plasmid that does not transcribe the 2.2-kb doubly spliced RNA (2.2DS-RNA) expressed by wild-type HBV genotype A, the level of HBV pregenomic RNA (pgRNA) was higher than that in cells transfected with an HBV genotype A expression plasmid. By using cotransfection with HBV genotype D and 2.2DS-RNA expression plasmids, we found that a reduction of pgRNA was observed in the cells even in the presence of small amounts of the 2.2DS-RNA plasmid. Moreover, ectopic expression of 2.2DS-RNA in the HBV-producing cell line 1.3ES2 reduced the expression of pgRNA. Further analysis showed that exogenously transcribed 2.2DS-RNA inhibited a reconstituted transcription in vitro. In Huh7 cells ectopically expressing 2.2DS-RNA, RNA immunoprecipitation revealed that 2.2DS-RNA interacted with the TATA-binding protein (TBP) and that nucleotides 432 to 832 of 2.2DS-RNA were required for efficient TBP binding. Immunofluorescence experiments showed that 2.2DS-RNA colocalized with cytoplasmic TBP and the stress granule components, G3BP and poly(A)-binding protein 1 (PABP1), in Huh7 cells. In conclusion, our study reveals that 2.2DS-RNA acts as a repressor of HBV transcription through an interaction with TBP that induces stress granule formation. The expression of 2.2DS-RNA may be one of the viral factors involved in viral replication, which may underlie differences in clinical outcomes of liver disease and responses to interferon alpha therapy between patients infected with different HBV genotypes. IMPORTANCE Patients infected with certain genotypes of HBV have a lower risk of hepatocellular carcinoma and exhibit a more favorable response to antiviral therapy than patients

  19. Transcriptional activation requires protection of the TATA-binding protein Tbp1 by the ubiquitin-specific protease Ubp3.

    PubMed

    Chew, Boon Shang; Siew, Wee Leng; Xiao, Benjamin; Lehming, Norbert

    2010-11-01

    Tbp1, the TATA-binding protein, is essential for transcriptional activation, and Gal4 and Gcn4 are unable to fully activate transcription in a Saccharomyces cerevisiae TBP1E86D mutant strain. In the present study we have shown that the Tbp1E186D mutant protein is proteolytically instable, and we have isolated intragenic and extragenic suppressors of the transcription defects of the TBP1E186D mutant strain. The TBP1R6S mutation stabilizes the Tbp1E186D mutant protein and suppresses the defects of the TBP1E186D mutant strain. Furthermore, we found that the overexpression of the de-ubiquitinating enzyme Ubp3 (ubiquitin-specific protease 3) also stabilizes the Tbp1E186D mutant protein and suppresses of the defects of the TBP1E186D mutant strain. Importantly, the deletion of UBP3 and its cofactor BRE5 lead to increased degradation of wild-type Tbp1 protein and to defects in transcriptional activation by Gal4 and Gcn4. Purified GST (glutathione transferase)-Ubp3 reversed Tbp1 ubiquitination, and the deletion of UBP3 lead to the accumulation of poly-ubiquitinated species of Tbp1 in a proteaseome-deficient genetic background, demonstrating that Ubp3 reverses ubiquitination of Tbp1 in vitro and in vivo. Chromatin immunoprecipitation showed that Ubp3 was recruited to the GAL1 and HIS3 promoters upon the induction of the respective gene, indicating that protection of promoter-bound Tbp1 by Ubp3 is required for transcriptional activation. PMID:20738257

  20. TATA-Binding Protein Mutants That Are Lethal in the Absence of the Nhp6 High-Mobility-Group Protein

    PubMed Central

    Eriksson, Peter; Biswas, Debabrata; Yu, Yaxin; Stewart, James M.; Stillman, David J.

    2004-01-01

    The Saccharomyces cerevisiae Nhp6 protein is related to the high-mobility-group B family of architectural DNA-binding proteins that bind DNA nonspecifically but bend DNA sharply. Nhp6 is involved in transcriptional activation by both RNA polymerase II (Pol II) and Pol III. Our previous genetic studies have implicated Nhp6 in facilitating TATA-binding protein (TBP) binding to some Pol II promoters in vivo, and we have used a novel genetic screen to isolate 32 new mutations in TBP that are viable in wild-type cells but lethal in the absence of Nhp6. The TBP mutations that are lethal in the absence of Nhp6 cluster in three regions: on the upper surface of TBP that may have a regulatory role, near residues that contact Spt3, or near residues known to contact either TFIIA or Brf1 (in TFIIIB). The latter set of mutations suggests that Nhp6 becomes essential when a TBP mutant compromises its ability to interact with either TFIIA or Brf1. Importantly, the synthetic lethality for some of the TBP mutations is suppressed by a multicopy plasmid with SNR6 or by an spt3 mutation. It has been previously shown that nhp6ab mutants are defective in expressing SNR6, a Pol III-transcribed gene encoding the U6 splicing RNA. Chromatin immunoprecipitation experiments show that TBP binding to SNR6 is reduced in an nhp6ab mutant. Nhp6 interacts with Spt16/Pob3, the yeast equivalent of the FACT elongation complex, consistent with nhp6ab cells being extremely sensitive to 6-azauracil (6-AU). However, this 6-AU sensitivity can be suppressed by multicopy SNR6 or BRF1. Additionally, strains with SNR6 promoter mutations are sensitive to 6-AU, suggesting that decreased SNR6 RNA levels contribute to 6-AU sensitivity. These results challenge the widely held belief that 6-AU sensitivity results from a defect in transcriptional elongation. PMID:15226442

  1. In vitro transcription of a Drosophila U1 small nuclear RNA gene requires TATA box-binding protein and two proximal cis-acting elements with stringent spacing requirements.

    PubMed Central

    Zamrod, Z; Tyree, C M; Song, Y; Stumph, W E

    1993-01-01

    Transcription of a Drosophila U1 small nuclear RNA gene was functionally analyzed in cell extracts derived from 0- to 12-h embryos. Two promoter elements essential for efficient initiation of transcription in vitro by RNA polymerase II were identified. The first, termed PSEA, is located between positions -41 and -61 relative to the transcription start site, is crucial for promoter activity, and is the dominant element for specifying the transcription initiation site. PSEA thus appears to be functionally homologous to the proximal sequence element of vertebrate small nuclear RNA genes. The second element, termed PSEB, is located at positions -25 to -32 and is required for an efficient level of transcription initiation because mutation of PSEB, or alteration of the spacing between PSEA and PSEB, severely reduced transcriptional activity relative to that of the wild-type promoter. Although the PSEB sequence does not have any obvious sequence similarity to a TATA box, conversion of PSEB to the canonical TATA sequence dramatically increased the efficiency of the U1 promoter and simultaneously relieved the requirement for the upstream PSEA. Despite these effects, introduction of the TATA sequence into the U1 promoter had no effect on the choice of start site or on the RNA polymerase II specificity of the promoter. Finally, evidence is presented that the TATA box-binding protein is required for transcription from the wild-type U1 promoter as well as from the TATA-containing U1 promoter. Images PMID:8355718

  2. Candidate SNP Markers of Chronopathologies Are Predicted by a Significant Change in the Affinity of TATA-Binding Protein for Human Gene Promoters

    PubMed Central

    Ponomarenko, Petr; Rasskazov, Dmitry; Suslov, Valentin; Sharypova, Ekaterina; Savinkova, Ludmila; Podkolodnaya, Olga; Podkolodny, Nikolay L.; Tverdokhleb, Natalya N.; Chadaeva, Irina; Kolchanov, Nikolay

    2016-01-01

    Variations in human genome (e.g., single nucleotide polymorphisms, SNPs) may be associated with hereditary diseases, their complications, comorbidities, and drug responses. Using Web service SNP_TATA_Comparator presented in our previous paper, here we analyzed immediate surroundings of known SNP markers of diseases and identified several candidate SNP markers that can significantly change the affinity of TATA-binding protein for human gene promoters, with circadian consequences. For example, rs572527200 may be related to asthma, where symptoms are circadian (worse at night), and rs367732974 may be associated with heart attacks that are characterized by a circadian preference (early morning). By the same method, we analyzed the 90 bp proximal promoter region of each protein-coding transcript of each human gene of the circadian clock core. This analysis yielded 53 candidate SNP markers, such as rs181985043 (susceptibility to acute Q fever in male patients), rs192518038 (higher risk of a heart attack in patients with diabetes), and rs374778785 (emphysema and lung cancer in smokers). If they are properly validated according to clinical standards, these candidate SNP markers may turn out to be useful for physicians (to select optimal treatment for each patient) and for the general population (to choose a lifestyle preventing possible circadian complications of diseases).

  3. The TATA-box-binding protein (TBP) of Halobacterium salinarum. Cloning of the tbp gene, heterologous production of TBP and folding of TBP into a native conformation.

    PubMed

    Soppa, J; Link, T A

    1997-10-01

    The TATA-box binding protein (TBP) is a basal transcription factor involved in transcription initiation in Eucarya and Archaea. Using a tbp-specific probe, a 4.5-kbp genomic fragment from Halobacterium salinarum was cloned and sequenced. It contained the tbp gene and the 5'-ends of two additional open reading frames, but surprisingly, 70% of the cloned fragment (3.2 kbp) was devoid of coding capacity or similarity to database sequences. The deduced halobacterial TBP exhibits sequence similarities to other archaeal (41-43%) as well as to eucaryal (27-38%) TBP. A comparative analysis showed that the archaeal and eucaryal TBP form two related monophylic protein families, and the archaeal TBP possess features which separate them from eucaryal TBP. Compared with the other TBP, the halobacterial TBP is unique in having a high excess of negatively charged residues. A histidine-tagged version of the halobacterial TBP was produced in Escherichia coli in a denatured conformation and purified by means of Ni-chelating chromatography. CD spectroscopy was used to monitor TBP secondary structure and the conditions necessary for folding it into a native conformation. In the absence of denaturating agents, the folded as well as the unfolded state were found to be stable over a wide range of salt concentrations. Properly folded TBP was shown to bind to a halobacterial TATA-box-containing DNA fragment, indicating that the fusion protein can be used to characterize DNA recognition by the halobacterial TBP. PMID:9363785

  4. Reconfiguring the connectivity of a multiprotein complex: fusions of yeast TATA-binding protein with Brf1, and the function of transcription factor IIIB.

    PubMed

    Kassavetis, George A; Soragni, Elisabetta; Driscoll, Robert; Geiduschek, E Peter

    2005-10-25

    Transcription factor (TF) IIIB, the central transcription initiation factor of RNA polymerase III (pol III), is composed of three subunits, Bdp1, Brf1 and TATA-binding protein (TBP), all essential for normal function in vivo and in vitro. Brf1 is a modular protein: Its N-proximal half is related to TFIIB and binds similarly to the C-terminal stirrup of TBP; its C-proximal one-third provides most of the affinity for TBP by binding along the entire length of the convex surface and N-terminal lateral face of TBP. A structure-informed triple fusion protein, with TBP core placed between the N- and C-proximal domains of Brf1, has been constructed. The Brf1-TBP triple fusion protein effectively replaces both Brf1 and TBP in TFIIIC-dependent and -independent transcription in vitro, and forms extremely stable TFIIIB-DNA complexes that are indistinguishable from wild-type TFIIIB-DNA complexes by chemical nuclease footprinting. Unlike Brf1 and TBP, the triple fusion protein is able to recruit pol III for TATA box-directed transcription of linear and supercoiled DNA in the absence of Bdp1. The Brf1-TBP triple fusion protein also effectively replaces Brf1 function in vivo as the intact protein, creating a TBP paralogue in yeast that is privatized for pol III transcription. PMID:16227432

  5. The high mobility group protein HMG1 can reversibly inhibit class II gene transcription by interaction with the TATA-binding protein.

    PubMed

    Ge, H; Roeder, R G

    1994-06-24

    Regulation of transcription by RNA polymerase II in eukaryotic cells requires both basal and accessory factors, which interact through specific protein-DNA or protein-protein interactions. The high mobility group 1 protein (HMG1) was previously demonstrated to be a nonhistone chromatin-associated protein, which selectively recognizes cruciform DNA rather than a specific primary sequence element. During our investigations of proteins that interact with TFIID, we found that purified mammalian HMG1, as well as recombinant human HMG1, can interact with TATA-binding protein (TBP) in the presence of a TATA box-containing oligonucleotide to form a specific HMG1.TBP.promoter complex. This complex prevents TFIIB binding to TBP and consequently blocks formation of the preinitiation complex. In contrast, TFIIA can compete with HMG1 for binding to TBP. In an in vitro transcription assay reconstituted with highly purified or recombinant general factors, HMG1 is able to inhibit transcription by RNA polymerase II over 30-fold. As expected, addition of TFIIA can partially reverse this repression in a concentration-dependent manner. These results demonstrate that HMG1, a chromatin-associated protein, has the potential to act as a TBP-dependent negative transcription factor and may provide an important link between chromatin structure and the modulation of class II gene transcription. PMID:8006019

  6. Analysis of TFIIA Function In Vivo: Evidence for a Role in TATA-Binding Protein Recruitment and Gene-Specific Activation

    PubMed Central

    Liu, Qing; Gabriel, Scott E.; Roinick, Kelli L.; Ward, Robert D.; Arndt, Karen M.

    1999-01-01

    Activation of transcription can occur by the facilitated recruitment of TFIID to promoters by gene-specific activators. To investigate the role of TFIIA in TFIID recruitment in vivo, we exploited a class of yeast TATA-binding protein (TBP) mutants that is activation and DNA binding defective. We found that co-overexpression of TOA1 and TOA2, the genes that encode yeast TFIIA, overcomes the activation defects caused by the TBP mutants. Using a genetic screen, we isolated a new class of TFIIA mutants and identified three regions on TFIIA that are likely to be involved in TBP recruitment or stabilization of the TBP-TATA complex in vivo. Amino acid replacements in only one of these regions enhance TFIIA-TBP-DNA complex formation in vitro, suggesting that the other regions are involved in regulatory interactions. To determine the relative importance of TFIIA in the regulation of different genes, we constructed yeast strains to conditionally deplete TFIIA levels prior to gene activation. While the activation of certain genes, such as INO1, was dramatically impaired by TFIIA depletion, activation of other genes, such as CUP1, was unaffected. These data suggest that TFIIA facilitates DNA binding by TBP in vivo, that TFIIA may be regulated by factors that target distinct regions of the protein, and that promoters vary significantly in the degree to which they require TFIIA for activation. PMID:10567590

  7. A new class of transcription initiation factors, intermediate between TATA box-binding proteins (TBPs) and TBP-like factors (TLFs), is present in the marine unicellular organism, the dinoflagellate Crypthecodinium cohnii.

    PubMed

    Guillebault, Delphine; Sasorith, Souphatta; Derelle, Evelyne; Wurtz, Jean-Marie; Lozano, Jean-Claude; Bingham, Scott; Tora, Laszlo; Moreau, Hervé

    2002-10-25

    Dinoflagellates are marine unicellular eukaryotes that exhibit unique features including a very low level of basic proteins bound to the chromatin and the complete absence of histones and nucleosomal structure. A cDNA encoding a protein with a strong homology to the TATA box-binding proteins (TBP) has been isolated from an expressed sequence tag library of the dinoflagellate Crypthecodinium cohnii. The typical TBP repeat signature and the amino acid motives involved in TFIIA and TFIIB interactions were conserved in this new TBP-like protein. However, the four phenylalanines known to interact with the TATA box were substituted with hydrophilic residues (His(77), Arg(94), Tyr(171), Thr(188)) as has been described for TBP-like factors (TLF)/TBP-related proteins (TRP). A phylogenetic analysis showed that cTBP is intermediate between TBP and TLF/TRP protein families, and the structural similarity of cTBP with TLF was confirmed by low affinity binding to a consensus' TATA box in an equivalent manner to that usually observed for TLFs. Six 5'-upstream gene regions of dinoflagellate genes have been analyzed and neither a TATA box nor a consensus-promoting element could be found within these different sequences. Our results showed that cTBP could bind stronger to a TTTT box sequence than to the canonical TATA box, especially at high salt concentration. Same binding results were obtained with a mutated cTBP (mcTBP), in which the four phenylalanines were restored. To our knowledge, this is the first description of a TBP-like protein in a unicellular organism, which also appears as the major form of TBP present in C. cohnii. PMID:12154093

  8. Differential Utilization of TATA Box-binding Protein (TBP) and TBP-related Factor 1 (TRF1) at Different Classes of RNA Polymerase III Promoters*

    PubMed Central

    Verma, Neha; Hung, Ko-Hsuan; Kang, Jin Joo; Barakat, Nermeen H.; Stumph, William E.

    2013-01-01

    In the fruit fly Drosophila melanogaster, RNA polymerase III transcription was found to be dependent not upon the canonical TATA box-binding protein (TBP) but instead upon the TBP-related factor 1 (TRF1) (Takada, S., Lis, J. T., Zhou, S., and Tjian, R. (2000) Cell 101, 459–469). Here we confirm that transcription of fly tRNA genes requires TRF1. However, we unexpectedly find that U6 snRNA gene promoters are occupied primarily by TBP in cells and that knockdown of TBP, but not TRF1, inhibits U6 transcription in cells. Moreover, U6 transcription in vitro effectively utilizes TBP, whereas TBP cannot substitute for TRF1 to promote tRNA transcription in vitro. Thus, in fruit flies, different classes of RNA polymerase III promoters differentially utilize TBP and TRF1 for the initiation of transcription. PMID:23955442

  9. Obesity-related known and candidate SNP markers can significantly change affinity of TATA-binding protein for human gene promoters

    PubMed Central

    2015-01-01

    Background Obesity affects quality of life and life expectancy and is associated with cardiovascular disorders, cancer, diabetes, reproductive disorders in women, prostate diseases in men, and congenital anomalies in children. The use of single nucleotide polymorphism (SNP) markers of diseases and drug responses (i.e., significant differences of personal genomes of patients from the reference human genome) can help physicians to improve treatment. Clinical research can validate SNP markers via genotyping of patients and demonstration that SNP alleles are significantly more frequent in patients than in healthy people. The search for biomedical SNP markers of interest can be accelerated by computer-based analysis of hundreds of millions of SNPs in the 1000 Genomes project because of selection of the most meaningful candidate SNP markers and elimination of neutral SNPs. Results We cross-validated the output of two computer-based methods: DNA sequence analysis using Web service SNP_TATA_Comparator and keyword search for articles on comorbidities of obesity. Near the sites binding to TATA-binding protein (TBP) in human gene promoters, we found 22 obesity-related candidate SNP markers, including rs10895068 (male breast cancer in obesity); rs35036378 (reduced risk of obesity after ovariectomy); rs201739205 (reduced risk of obesity-related cancers due to weight loss by diet/exercise in obese postmenopausal women); rs183433761 (obesity resistance during a high-fat diet); rs367732974 and rs549591993 (both: cardiovascular complications in obese patients with type 2 diabetes mellitus); rs200487063 and rs34104384 (both: obesity-caused hypertension); rs35518301, rs72661131, and rs562962093 (all: obesity); and rs397509430, rs33980857, rs34598529, rs33931746, rs33981098, rs34500389, rs63750953, rs281864525, rs35518301, and rs34166473 (all: chronic inflammation in comorbidities of obesity). Using an electrophoretic mobility shift assay under nonequilibrium conditions, we

  10. Synergistic Transcriptional Activation by TATA-Binding Protein and hTAFII28 Requires Specific Amino Acids of the hTAFII28 Histone Fold

    PubMed Central

    Lavigne, Anne-Claire; Gangloff, Yann-Gaël; Carré, Lucie; Mengus, Gabrielle; Birck, Catherine; Poch, Olivier; Romier, Christophe; Moras, Dino; Davidson, Irwin

    1999-01-01

    Coexpression of the human TATA-binding protein (TBP)-associated factor 28 (hTAFII28) with the altered-specificity mutant TBP spm3 synergistically enhances transcriptional activation by the activation function 2 of the nuclear receptors (NRs) for estrogen and vitamin D3 from a reporter plasmid containing a TGTA element in mammalian cells. This synergy is abolished by mutation of specific amino acids in the α2-helix of the histone fold in the conserved C-terminal region of hTAFII28. Critical amino acids are found on both the exposed hydrophilic face of this helix and the hydrophobic interface with TAFII18. This α-helix of hTAFII28 therefore mediates multiple interactions required for coactivator activity. We further show that mutation of specific residues in the H1′ α-helix of TBP either reduces or increases interactions with hTAFII28. The mutations which reduce interactions with hTAFII28 do not affect functional synergy, whereas the TBP mutation which increases interaction with hTAFII28 is defective in its ability to synergistically enhance activation by NRs. However, this TBP mutant supports activation by other activators and is thus specifically defective for its ability to synergize with hTAFII28. PMID:10373554

  11. The Ability to Associate with Activation Domains in vitro is not Required for the TATA Box-Binding Protein to Support Activated Transcription in vivo

    NASA Astrophysics Data System (ADS)

    Tansey, William P.; Herr, Winship

    1995-11-01

    The TATA box-binding protein (TBP) interacts in vitro with the activation domains of many viral and cellular transcription factors and has been proposed to be a direct target for transcriptional activators. We have examined the functional relevance of activator-TBP association in vitro to transcriptional activation in vivo. We show that alanine substitution mutations in a single loop of TBP can disrupt its association in vitro with the activation domains of the herpes simplex virus activator VP16 and of the human tumor suppressor protein p53; these mutations do not, however, disrupt the transcriptional response of TBP to either activation domain in vivo. Moreover, we show that a region of VP16 distinct from its activation domain can also tightly associate with TBP in vitro, but fails to activate transcription in vivo. These data suggest that the ability of TBP to interact with activation domains in vitro is not directly relevant to its ability to support activated transcription in vivo.

  12. Species-specific interaction of the glutamine-rich activation domains of Sp1 with the TATA box-binding protein.

    PubMed Central

    Emili, A; Greenblatt, J; Ingles, C J

    1994-01-01

    We have used protein-blotting and protein affinity chromatography to demonstrate that each of the two glutamine-rich activation domains of the human transcription factor Sp1 can bind specifically and directly to the C-terminal evolutionarily conserved domain of the human TATA box-binding protein (TBP). These activation domains of Sp1 also bind directly to Drosophila TBP but bind much less strongly to TBP from the yeast Saccharomyces cerevisiae. The abilities of the Sp1 activation domains to interact directly with the TBPs of various species correlate well with their abilities to activate transcription in extracts derived from the same species. We also show that a glutamine-rich transcriptional activating region of the Drosophila protein Antennapedia binds directly to TBP in a species-specific manner that reflects its ability to activate transcription in vivo. These results support the notion that TBP is a direct and important target of glutamine-rich transcriptional activators. Images PMID:8114696

  13. Transcriptional corepression in vitro: a Mot1p-associated form of TATA-binding protein is required for repression by Leu3p.

    PubMed Central

    Wade, P A; Jaehning, J A

    1996-01-01

    Signals from transcriptional activators to the general mRNA transcription apparatus are communicated by factors associated with RNA polymerase II or the TATA-binding protein (TBP). Currently, little is known about how gene-specific transcription repressors communicate with RNA polymerase II. We have analyzed the requirements for repression by the saccharomyces cerevisiae Leu3 protein (Leu3p) in a reconstituted transcription system. We have identified a complex form of TBP which is required for communication of the repressing signal. This TFIID-like complex contains a known TBP-associated protein, Mot1p, which has been implicated in the repression of a subset of yeast genes by genetic analysis. Leu3p-dependent repression can be reconstituted with purified Mot1p and recombinant TBP. In addition, a mutation in the Mot1 gene leads to partial derepression of the Leu3p-dependent LEU2 promoter. These in vivo and in vitro observations define a role for Mot1p as a transcriptional corepressor. PMID:8657139

  14. Transcription factor IID in the Archaea: sequences in the Thermococcus celer genome would encode a product closely related to the TATA-binding protein of eukaryotes

    NASA Technical Reports Server (NTRS)

    Marsh, T. L.; Reich, C. I.; Whitelock, R. B.; Olsen, G. J.; Woese, C. R. (Principal Investigator)

    1994-01-01

    The first step in transcription initiation in eukaryotes is mediated by the TATA-binding protein, a subunit of the transcription factor IID complex. We have cloned and sequenced the gene for a presumptive homolog of this eukaryotic protein from Thermococcus celer, a member of the Archaea (formerly archaebacteria). The protein encoded by the archaeal gene is a tandem repeat of a conserved domain, corresponding to the repeated domain in its eukaryotic counterparts. Molecular phylogenetic analyses of the two halves of the repeat are consistent with the duplication occurring before the divergence of the archael and eukaryotic domains. In conjunction with previous observations of similarity in RNA polymerase subunit composition and sequences and the finding of a transcription factor IIB-like sequence in Pyrococcus woesei (a relative of T. celer) it appears that major features of the eukaryotic transcription apparatus were well-established before the origin of eukaryotic cellular organization. The divergence between the two halves of the archael protein is less than that between the halves of the individual eukaryotic sequences, indicating that the average rate of sequence change in the archael protein has been less than in its eukaryotic counterparts. To the extent that this lower rate applies to the genome as a whole, a clearer picture of the early genes (and gene families) that gave rise to present-day genomes is more apt to emerge from the study of sequences from the Archaea than from the corresponding sequences from eukaryotes.

  15. Msx1 homeodomain transcription factor and TATA-binding protein interact to repress the expression of the glycoprotein hormone α subunit gene.

    PubMed

    Park, Ki-Sun; Kim, Kee K; Kim, Kyoon Eon

    Studying the regulatory mechanism of the glycoprotein hormone α subunit (αGSU) gene in thyrotropes is essential for understanding the synthesis of functional thyroid-stimulating hormone (TSH). Here, we investigated the influence of a homeodomain transcription factor Msx1 (Msh homeobox 1) on αGSU expression in thyrotropes. The transient expression of Msx1 inhibited the activity of an αGSU reporter gene, as well as its endogenous mRNA level in thyrotrope-derived αTSH cells. Luciferase reporter assays with serial deletion constructs and a close examination of the sequences revealed that the putative Msx1 binding site (PMS) in the αGSU promoter is not responsible for Msx1-mediated transcriptional repression. We also identified the TATA-box binding protein (TBP) as an interacting protein in thyrotropes. Interaction of TBP with Msx1 attenuates the inhibitory effect of Msx1 on αGSU gene expression in a DNA binding-independent manner. Furthermore, transient transfection studies with mutant Msx1 revealed that the interaction of TBP and Msx1 is critical for Msx1-mediated transcriptional repression of the αGSU. These results suggest that Msx1 functions as a transcriptional repressor of αGSU and that its interaction with TBP is an integral part of the mechanism by which Msx1 regulates the inhibition of αGSU gene expression. PMID:26505791

  16. Analysis of polyglutamine-coding repeats in the TATA-binding protein in different human populations and in patients with schizophrenia an bipolar affective disorder

    SciTech Connect

    Rubinsztein, D.C.; Leggo, J.; Crow, T.J.

    1996-09-20

    A new class of disease (including Huntington disease, Kennedy disease, and spinocerebellar ataxias types 1 and 3) results from abnormal expansions of CAG trinucleotides in the coding regions of genes. In all of these diseases the CAG repeats are thought to be translated into polyglutamine tracts. There is accumulating evidence arguing for CAG trinucleotide expansions as one of the causative disease mutations in schizophrenia and bipolar affective disorder. We and others believe that the TATA-binding protein (TBP) is an important candidate to investigate in these diseases as it contains a highly polymorphic stretch of glutamine codons, which are close to the threshold length where the polyglutamine tracts start to be associated with disease. Thus, we examined the lengths of this polyglutamine repeat in normal unrelated East Anglians, South African Blacks, sub-Saharan Africans mainly from Nigeria, and Asian Indians. We also examined 43 bipolar affective disorder patients and 65 schizophrenic patients. The range of polyglutamine tract-lengths that we found in humans was from 26-42 codons. No patients with bipolar affective disorder and schizophrenia had abnormal expansions at this locus. 22 refs., 1 tab.

  17. U-Pb zircon geochronology of the Paleoproterozoic Tagragra de Tata inlier and its Neoproterozoic cover, western Anti-Atlas, Morocco

    USGS Publications Warehouse

    Walsh, G.J.; Aleinikoff, J.N.; Benziane, F.; Yazidi, A.; Armstrong, T.R.

    2002-01-01

    New U-Pb zircon data obtained by sensitive high resolution ion microprobe (SHRIMP) from the Tagragra de Tata inlier in the western Anti-Atlas, Morocco establish Paleoproterozoic ages for the basement schists, granites, and metadolerites, and a Neoproterozoic age for an ignimbrite of the Ouarzazate Series in the cover sequence. The age of interbedded felsic metatuff in the metasedimentary and metavolcanic sequence of the basement schists is 2072 ?? 8 Ma. This date represents: (1) the first reliable age from the metasedimentary and metavolcanic sequence; (2) the oldest reliable age for the basement of the Anti-Atlas; (3) the first date on the timing of deposition of the sediments on the northern edge of the Paleoproterozoic West African craton; (4) a lower age limit on deformation during the Eburnean orogeny; and (5) the first date obtained from the non-granitic Paleoproterozoic basement of Morocco. Ages of 2046 ?? 7 Ma (Targant granite) and 2041 ?? 6 Ma (Oudad granite) support earlier interpretations of a Paleoproterozoic Eburnean igneous event in the Anti-Atlas. The granites post-date the Eburnean D1 deformation event in the Paleoproterozoic schist sequence, and place a ???2046 Ma limit on short-lived Eburnean deformation in the area. Cross-cutting metadolerite is 2040 ?? 6 Ma; this is the first date from a metadolerite in the western Anti-Atlas. All of the dolerites in the area post-date emplacement of the two granites and the new age constrains the onset of late- or post-Eburnean extension. Ignimbrite of the Ouarzazate Series, immediately above the Paleoproterozoic basement is 565 ?? 7 Ma. This Neoproterozoic age agrees with ages of similar volcanic rocks elsewhere from the Ouarzazate Series. The date also agrees with the ages of associated hypabyssal intrusions, and marks the second and final stage of Pan-African orogenic activity in the western Anti-Atlas. ?? 2002 Elsevier Science B.V. All rights reserved.

  18. Impaired uptake and/or utilization of leucine by Saccharomyces cerevisiae is suppressed by the SPT15-300 allele of the TATA-binding protein gene.

    PubMed

    Baerends, Richard J S; Qiu, Jin-Long; Rasmussen, Simon; Nielsen, Henrik Bjørn; Brandt, Anders

    2009-10-01

    Successful fermentations to produce ethanol require microbial strains that have a high tolerance to glucose and ethanol. Enhanced glucose/ethanol tolerance of the laboratory yeast Saccharomyces cerevisiae strain BY4741 under certain growth conditions as a consequence of the expression of a dominant mutant allele of the SPT15 gene (SPT15-300) corresponding to the three amino acid changes F177S, Y195H, and K218R has been reported (H. Alper, J. Moxley, E. Nevoigt, G. R. Fink, and G. Stephanopoulos, Science 314:1565-1568, 2006). The SPT15 gene codes for the TATA-binding protein. This finding prompted us to examine the effect of expression of the SPT15-300 allele in various yeast species of industrial importance. Expression of SPT15-300 in leucine-prototrophic strains of S. cerevisiae, Saccharomyces bayanus, or Saccharomyces pastorianus (lager brewing yeast), however, did not improve tolerance to ethanol on complex rich medium (yeast extract-peptone-dextrose). The enhanced growth of the laboratory yeast strain BY4741 expressing the SPT15-300 mutant allele was seen only on defined media with low concentrations of leucine, indicating that the apparent improved growth in the presence of ethanol was indeed associated with enhanced uptake and/or utilization of leucine. Reexamination of the microarray data published by Alper and coworkers likewise suggested that expression of genes coding for the leucine permeases, Tat1p and Bap3p, were upregulated in the SPT15-300 mutant, as was expression of the genes ARO10, ADH3, ADH5, and SFA1, involved in leucine degradation. PMID:19666729

  19. Regulation of RNA Polymerase I-Dependent Promoters by the Hepatitis B Virus X Protein via Activated Ras and TATA-Binding Protein

    PubMed Central

    Wang, Horng-Dar; Trivedi, Alpa; Johnson, Deborah L.

    1998-01-01

    The hepatitis B virus (HBV) X protein is essential for viral infectivity, and evidence indicates that it is a strong contributor to HBV-mediated oncogenesis. X has been shown to transactivate a wide variety of RNA polymerase (Pol) II-dependent, as well as RNA Pol III-dependent, promoters. In this study, we have investigated the possibility that X modulates RNA Pol I-dependent rRNA transcription. In both human hepatoma Huh7 and Drosophila Schneider S2 cell lines, X expression stimulated rRNA promoter activity. Extracts prepared from X-expressing cells stably transfected with an X gene also exhibited an increased ability to transcribe the rRNA promoter. The mechanism for X transactivation was examined by determining whether this regulatory event was dependent on Ras activation and increased TATA-binding protein (TBP) levels. Our previous studies have demonstrated that X, and the activation of Ras, produces an increase in the cellular levels of TBP (H.-D. Wang, A. Trivedi, and D. L. Johnson, Mol. Cell. Biol. 17:6838–6846, 1997). Expression of a dominant negative form of Ras blocked the X-mediated induction of the rRNA promoters, whereas expression of a constitutively activated form of Ras mimicked the enhancing effect of X on rRNA promoter activity. When TBP was overexpressed in either Huh7 or S2 cells, a dose-dependent increase in rRNA promoter activity was observed. To analyze whether the increase in TBP was modulating rRNA promoter activity indirectly, by increasing activity of RNA Pol II-dependent promoters, a Drosophila TBP cDNA was constructed with a mutation that eliminated its ability to stimulate RNA Pol II-dependent promoters. Transient expression of wild-type TBP in S2 cells increased the activities of specific RNA Pol I- and Pol II-dependent promoters. Expression of the mutant TBP protein failed to enhance the activity of the RNA Pol II-dependent promoters, yet the protein completely retained its ability to stimulate the rRNA promoter. Furthermore, the

  20. Association of Transcription Factor IIA with TATA Binding Protein Is Required for Transcriptional Activation of a Subset of Promoters and Cell Cycle Progression in Saccharomyces cerevisiae

    PubMed Central

    Ozer, Josef; Lezina, Larissa E.; Ewing, Joshua; Audi, Salma; Lieberman, Paul M.

    1998-01-01

    The general transcription factor IIA (TFIIA) interacts with the TATA binding protein (TBP) and promoter DNA to mediate transcription activation in vitro. To determine if this interaction is generally required for activation of all class II genes in vivo, we have constructed substitution mutations in yeast TFIIA which compromise its ability to bind TBP. Substitution mutations in the small subunit of TFIIA (Toa2) at residue Y69 or W76 significantly impaired the ability of TFIIA to stimulate TBP-promoter binding in vitro. Gene replacement of wild-type TOA2 with a W76E or Y69A/W76A mutant was lethal in Saccharomyces cerevisiae, while the Y69F/W76F mutant exhibited extremely slow growth at 30°C. Both the Y69A and W76A mutants were conditionally lethal at higher temperatures. Light microscopy indicated that viable toa2 mutant strains accumulate as equal-size dumbbells and multibudded clumps. Transcription of the cell cycle-regulatory genes CLB1, CLB2, CLN1, and CTS1 was significantly reduced in the toa2 mutant strains, while the noncycling genes PMA1 and ENO2 were only modestly affected, suggesting that these toa2 mutant alleles disrupt cell cycle progression. The differential effect of these toa2 mutants on gene transcription was examined for a number of other genes. toa2 mutant strains supported high levels of CUP1, PHO5, TRP3, and GAL1 gene activation, but the constitutive expression of DED1 was significantly reduced. Activator-induced start site expression for HIS3, GAL80, URA1, and URA3 promoters was defective in toa2 mutant strains, suggesting that the TFIIA-TBP complex is important for promoters which require an activator-dependent start site selection from constitutive to regulated expression. We present evidence to indicate that transcription defects in toa2 mutants can be both activator and promoter dependent. These results suggest that the association of TFIIA with TBP regulates activator-induced start site selection and cell cycle progression in S

  1. Impairment of the DNA binding activity of the TATA-binding protein renders the transcriptional function of Rvb2p/Tih2p, the yeast RuvB-like protein, essential for cell growth.

    PubMed

    Ohdate, Hidezumi; Lim, Chun Ren; Kokubo, Tetsuro; Matsubara, Kenichi; Kimata, Yukio; Kohno, Kenji

    2003-04-25

    In Saccharomyces cerevisiae, two highly conserved proteins, Rvb1p/Tih1p and Rvb2p/Tih2p, have been demonstrated to be major components of the chromatin-remodeling INO80 complex. The mammalian orthologues of these two proteins have been shown to physically associate with the TATA-binding protein (TBP) in vitro but not clearly in vivo. Here we show that yeast proteins interact with TBP under both conditions. To assess the functional importance of these interactions, we examined the effect of mutating both TIH2/RVB2 and SPT15, which encodes TBP, on yeast cell growth. Intriguingly, only those spt15 mutations that affected the ability of TBP to bind to the TATA box caused synthetic growth defects in a tih2-ts160 background. This suggests that Tih2p might be important in recruiting TBP to the promoter. A DNA microarray technique was used to identify genes differentially expressed in the tih2-ts160 strain grown at the restrictive temperature. Only 34 genes were significantly and reproducibly affected; some up-regulated and others down-regulated. We compared the transcription of several of these Tih2p target genes in both wild type and various mutant backgrounds. We found that the transcription of some genes depends on functions possessed by both Tih2p and TBP and that these functions are substantially impaired in the spt15/tih2-ts160 double mutants that confer synthetic growth defects. PMID:12576485

  2. B1-induced caspase-independent apoptosis in MCF-7 cells is mediated by down-regulation of Bcl-2 via p53 binding to P2 promoter TATA box

    SciTech Connect

    Liang Xin; Xu Ke; Xu Yufang; Liu Jianwen Qian Xuhong

    2011-10-01

    The Bcl-2 family contains a panel of proteins which are conserved regulators of apoptosis in mammalian cells, like the anti-apoptotic protein Bcl-2. According to its significant role in altering susceptibility to apoptosis, the deciphering of the mechanism of Bcl-2 expression modulation may be crucial for identifying therapeutics strategies for cancer. Treatment with naphthalimide-based DNA intercalators, including M2-A and R16, generally leads to a decrease in Bcl-2 intracellular amounts. Whereas the interest for these chemotherapeutics is accompanied by advances in the fundamental understanding of their anticancer properties, the molecular mechanism underlying changes in Bcl-2 expression remains poorly understood. We report here that p53 contributes to Bcl-2 down-regulation induced by B1, a novel naphthalimide-based DNA intercalating agent. Indeed, the decrease in Bcl-2 protein levels observed during B1-induced apoptosis was correlated to the decrease in mRNA levels, as a result of the inhibition of Bcl-2 transcription and promoter activity. In this context, we evaluated p53 contribution in the Bcl-2 transcriptional down-regulation. We found a significant increase of p53 binding to P{sub 2} promoter TATA box in MCF7 cells by chromatin immunoprecipitation. These data suggest that B1-induced caspase-independent apoptosis in MCF-7 cells is associated with the activation of p53 and the down-regulation of Bcl-2. Our study strengthens the links between p53 and Bcl-2 at a transcriptional level, upon naphthalimide-based DNA intercalator treatment. - Research Highlights: > B1 induced apoptosis in MCF-7 cells, following a transcriptional decrease in Bcl-2. > B1 treatment triggered p53 activation and leads to a p53-dependent down-regulation of Bcl-2. > B1 induced significant increase of p53 binding to Bcl-2 P{sub 2} promoter TATA box.

  3. The distal upstream promoter in Ly49 genes, Pro1, is active in mature NK cells and T cells, does not require TATA boxes, and displays enhancer activity1

    PubMed Central

    Gays, Frances; Taha, Sally; Brooks, Colin G.

    2016-01-01

    Missing self recognition of MHC class I molecules is mediated in murine species through the stochastic expression of CD94/NKG2 and Ly49 receptors on NK cells. Previous studies have suggested that the stochastic expression of Ly49 receptors is achieved through the use of an alternate upstream promoter, designated Pro1, that is active only in immature NK cells, and operates via the mutually exclusive binding of transcription initiation complexes to closely opposed forward and reverse TATA boxes, forward transcription being transiently required to activate the downstream promoters, Pro2/Pro3, that are subsequently responsible for transcription in mature NK cells. Here we report that Pro1 transcripts are not restricted to immature NK cells but are also found in mature NK cells and T cells, and that Pro1-fragments display strong promoter activity in mature NK cell and T cell lines as well as in immature NK cells. However, the strength of promoter activity in vitro does not correlate well with Ly49 expression in vivo and forward promoter activity is generally weak or undetectable, suggesting that components outside of Pro1 are required for efficient forward transcription. Indeed, conserved sequences immediately upstream and downstream of the core Pro1 region were found to inhibit or enhance promoter activity. Most surprisingly, promoter activity does not require either the forward or reverse TATA boxes, but is instead dependent on residues in the largely invariant central region of Pro1. Importantly, Pro1 displays strong enhancer activity suggesting that this may be its principal function in vivo. PMID:25926675

  4. Candidate SNP Markers of Gender-Biased Autoimmune Complications of Monogenic Diseases Are Predicted by a Significant Change in the Affinity of TATA-Binding Protein for Human Gene Promoters

    PubMed Central

    Ponomarenko, Mikhail P.; Arkova, Olga; Rasskazov, Dmitry; Ponomarenko, Petr; Savinkova, Ludmila; Kolchanov, Nikolay

    2016-01-01

    Some variations of human genome [for example, single nucleotide polymorphisms (SNPs)] are markers of hereditary diseases and drug responses. Analysis of them can help to improve treatment. Computer-based analysis of millions of SNPs in the 1000 Genomes project makes a search for SNP markers more targeted. Here, we combined two computer-based approaches: DNA sequence analysis and keyword search in databases. In the binding sites for TATA-binding protein (TBP) in human gene promoters, we found candidate SNP markers of gender-biased autoimmune diseases, including rs1143627 [cachexia in rheumatoid arthritis (double prevalence among women)]; rs11557611 [demyelinating diseases (thrice more prevalent among young white women than among non-white individuals)]; rs17231520 and rs569033466 [both: atherosclerosis comorbid with related diseases (double prevalence among women)]; rs563763767 [Hughes syndrome-related thrombosis (lethal during pregnancy)]; rs2814778 [autoimmune diseases (excluding multiple sclerosis and rheumatoid arthritis) underlying hypergammaglobulinemia in women]; rs72661131 and rs562962093 (both: preterm delivery in pregnant diabetic women); and rs35518301, rs34166473, rs34500389, rs33981098, rs33980857, rs397509430, rs34598529, rs33931746, rs281864525, and rs63750953 (all: autoimmune diseases underlying hypergammaglobulinemia in women). Validation of these predicted candidate SNP markers using the clinical standards may advance personalized medicine. PMID:27092142

  5. Investigation of reference gene expression during human herpesvirus 6B infection indicates peptidylprolyl isomerase A as a stable reference gene and TATA box binding protein as a gene up-regulated by this virus.

    PubMed

    Engdahl, Elin; Dunn, Nicky; Fogdell-Hahn, Anna

    2016-01-01

    When using relative gene expression for quantification of RNA it is crucial that the reference genes used for normalization do not change with the experimental condition. We aimed at investigating the expressional stability of commonly used reference genes during Human herpesvirus 6B (HHV-6B) infection. Expression of eight commonly used reference genes were investigated with quantitative PCR in a T-cell line infected with HHV-6B. The stability of genes was investigated using the 2(-ΔΔCT) method and the algorithms BestKeeper, GeNorm and NormFinder. Our results indicate that peptidylprolyl isomerase A (PPIA) is the most stably expressed gene while TATA box binding protein (TBP) is the least stably expressed gene during HHV-6B infection. In a confirmatory experiment, TBP was demonstrated to be dose and time dependently upregulated by HHV-6B. The stability of PPIA is in line with other studies investigating different herpesvirus infections whereas the finding that HHV-6B significantly upregulates TBP is novel and most likely specific to HHV-6B. PMID:26542463

  6. TATA-binding protein-related factor 2 is localized in the cytoplasm of mammalian cells and much of it migrates to the nucleus in response to genotoxic agents.

    PubMed

    Park, Kyoung-ae; Tanaka, Yuji; Suenaga, Yusuke; Tamura, Taka-aki

    2006-10-31

    TBP (TATA-binding protein)-related factor 2 (TRF2) regulates transcription during a nuber of cellular processes. We previously demonstrated that it is localized in the cytoplasm and is translocated to the nucleus by DNA-damaging agents. However, the cytoplasmic localization of TRF2 is controversial. In this study, we reconfirmed its cytoplasmic localization in various ways and examined its nuclear migration. Stresses such as heat shock, redox agents, heavy metals, and osmotic shock did not affect localization whereas genotoxins such as methyl methanesulfonate (MMS), cisplatin, etoposide, and hydroxyurea caused it to migrate to the nucleus. Adriamycin, mitomycin C and gamma-rays had no obvious effect. We determined optimal conditions for the nuclear migration. The proportions of cells with nuclei enriched for TRF2 were 25-60% and 5-10% for stressed cells and control cells, respectively. Nuclear translocation was observed after 1 h, 4 h and 12 h for cisplatin, etoposide and MMS and hydroxyurea, respectively. The association of TRF2 with the chromatin and promoter region of the proliferating cell nuclear antigen (PCNA) gene, a putative target of TRF2, was increased by MMS treatment. Thus TRF2 may be involved in genotoxin-induced transcriptional regulation. PMID:17085973

  7. A point mutation in the putative TATA box, detected in nondiseased individuals and patients with hereditary breast cancer, decreases promoter activity of the 17{beta}-hydroxysteroid dehydrogenase type 1 gene 2 (EDH17B2) in vitro

    SciTech Connect

    Peltoketo, H.; Piao, Y.; Isomaa, V.

    1994-09-01

    EDH17B2, the gene encoding 17{beta}-hydroxysteroid dehydrogenase type 1, has been suggested as a candidate for the familial breast cancer gene, BRCA1, located on 17q12-q21. We analyzed the promoter region of EDH17B2 in DNA from 20 control individuals and 40 patients with familial breast cancer. Two frequent (designated vI and vIII) and two rare (vII and vIV) nucleotide variations were present in both the breast cancer patients and the controls, except the alteration vII, which was found only in one patient. Although the data do not support the identification of EDH17B2 as the BRCA1 gene, it is of interest that point mutation vIV (A {yields} C) was located in the putative TATA box of the EDH17B2 gene. Reporter gene analysis showed that the mutation vIV decreases EDH17B2 promoter activity by an average of 45% in in vitro assays, suggesting that nucleotide A at position -27 is significant for efficient transcription. 12 refs., 2 figs., 1 tab.

  8. A critical role for heat shock transcription factor in establishing a nucleosome-free region over the TATA-initiation site of the yeast HSP82 heat shock gene.

    PubMed Central

    Gross, D S; Adams, C C; Lee, S; Stentz, B

    1993-01-01

    Heat shock genes are poised for rapid transcriptional activation in response to environmental stress. A universal structural characteristic of such genes is the presence of a nucleosome-free, DNase I hypersensitive promoter region. Here we investigate the structural and functional effects of mutating HSE1, the preferred heat shock factor (HSF) binding site upstream of the yeast HSP82 gene. In situ deletion or substitution of this sequence reduces both basal and induced transcription by at least two orders of magnitude. Moreover, such mutations lead to a dramatic transition in chromatin structure: the DNase I hypersensitive region is replaced by two stable, sequence-positioned nucleosomes. One of these is centered over the mutated heat shock element, while the other--as revealed by DNase I genomic footprinting--is precisely positioned in a rotational sense over the TATA-initiation site. Overexpression of yeast HSF strongly suppresses the null phenotype of the induced hsp82-delta HSE1 gene and re-establishes DNase I hypersensitivity over its promoter. Such suppression is mediated through sequence disposed immediately upstream of HSE1 and containing two low affinity heat shock elements. These data imply a critical role for HSF in displacing stably positioned nucleosomes in Saccharomyces cerevisiae and suggest that HSF transcriptionally activates HSP82 at least partly through its ability to alleviate nucleosome repression of the core promoter. Images PMID:8404861

  9. Guidelines for locoregional therapy in primary breast cancer in developing countries: The results of an expert panel at the 8th Annual Women's Cancer Initiative – Tata Memorial Hospital (WCI-TMH) Conference

    PubMed Central

    Munshi, Anusheel; Gupta, Sudeep; Anderson, Benjamin; Yarnold, John; Parmar, Vani; Jalali, Rakesh; Sharma, Suresh Chander; Desai, Sangeeta; Thakur, Meenakshi; Baijal, Gunjan; Sarin, Rajiv; Mittra, Indraneel; Ghosh, Jaya; Badwe, Rajendra

    2012-01-01

    Background: Limited guidelines exist for breast cancer management in developing countries. In this context, the Women's Cancer Initiative - Tata Memorial Hospital (WCI-TMH) organised its 8th Annual Conference to update guidelines in breast cancer. Materials and Methods: Appropriately formulated guideline questions on each topic and subtopic in the surgical, radiation and systemic management of primary breast cancer were developed by the scientific committee and shared with the guest faculty of the Conference. Majority of the questions had multiple choice answers. The opinion of the audience, comprising academic and community oncologists, was electronically cumulated, followed by focussed presentations by eminent national and international experts on each topic. The guidelines were finally developed through an expert panel that voted on each guideline question after all talks had been delivered and audience opinion elicited. Separate panels were constituted for locoregional and systemic therapy in primary breast cancer. Results: Based on the voting results of the expert panel, guidelines for locoregional therapy of breast cancer have been formulated. Voting patterns for each question are reported. Conclusions: The updated guidelines on locoregional management of primary breast cancer in the context of developing countries are presented in this article. These recommendations have been designed to allow centers in the developing world to improve the quality of care for breast cancer patients. PMID:22988354

  10. [open quotes]Cryptic[close quotes] repeating triplets of purines and pyrimidines (cRRY(i)) are frequent and polymorphic: Analysis of coding cRRY(i) in the proopiomelanocortin (POMC) and TATA-binding protein (TBP) genes

    SciTech Connect

    Gostout, B.; Qiang Liu; Sommer, S.S. )

    1993-06-01

    Triplets of the form of purine, purine, pyrimidine (RRY(i)) are enhanced in frequency in the genomes of primates, rodents, and bacteria. Some RRY(i) are [open quotes]cryptic[close quotes] repeats (cRRY(i)) in which no one tandem run of a trinucleotide predominates. A search of human GenBank sequence revealed that the sequences of cRRY(i) are highly nonrandom. Three randomly chosen human cRRY(i) were sequenced in search of polymorphic alleles. Multiple polymorphic alleles were found in cRRY(i) in the coding regions of the genes for proopiomelanocortin (POMC) and TATA-binding protein (TBP). The highly polymorphic TBP cRRY(i) was characterized in detail. Direct sequencing of 157 unrelated human alleles demonstrated the presence of 20 different alleles which resulted in 29--40 consecutive glutamines in the amino-terminal region of TBP. These alleles are differently distributed among the races. PCR was used to screen 1,846 additional alleles in order to characterize more fully the range of variation in the population. Three additional alleles were discovered, but there was no example of a substantial sequence amplification as is seen in the repeat sequences associated with X-linked spinal and bulbar muscular atrophy, myotonic dystrophy, or the fragile-X syndrome. The structure of the TBP cRRY(i) is conserved in the five monkey species examined. In the chimpanzee, examination of four individuals revealed that the cRRY(i) was highly polymorphic, but the pattern of polymorphism differed from that in humans. The TBP cRRY(i) displays both similarities with and differences from the previously described RRY(i) in the coding sequence of the androgen receptor. The data suggest how simple tandem repeats could evolve from cryptic repeats. 18 refs., 3 figs., 6 tabs.

  11. Mutational analysis of the D1/E1 core helices and the conserved N-terminal region of yeast transcription factor IIB (TFIIB): identification of an N-terminal mutant that stabilizes TATA-binding protein-TFIIB-DNA complexes.

    PubMed Central

    Bangur, C S; Pardee, T S; Ponticelli, A S

    1997-01-01

    The general transcription factor IIB (TFIIB) plays an essential role in transcription of protein-coding genes by RNA polymerase II. We have used site-directed mutagenesis to assess the role of conserved amino acids in several important regions of yeast TFIIB. These include residues in the highly conserved amino-terminal region and basic residues in the D1 and E1 core domain alpha-helices. Acidic substitutions of residues K190 (D1) and K201 (E1) resulted in growth impairments in vivo, reduced basal transcriptional activity in vitro, and an inability to form stable TFIIB-TATA-binding protein-DNA (DB) complexes. Significantly, these mutants retained the ability to respond to acidic activators in vivo and to the Gal4-VP16 activator in vitro, supporting the view that these basic residues play a role in basal transcription. In addition, 14 single-amino-acid substitutions were introduced in the conserved amino-terminal region. Three of these mutants, the L50D, R64E, and R78L mutants, displayed altered growth properties in vivo and were compromised for supporting transcription in vitro. The L50D mutant was impaired for RNA polymerase II interaction, while the R64E mutant exhibited altered transcription start site selection both in vitro and in vivo and, surprisingly, was more active than the wild type in the formation of stable DB complexes. These results support the view that the amino-terminal domain is involved in the direct interaction between yeast TFIIB and RNA polymerase II and suggest that this domain may interact with DNA and/or modulate the formation of a DB complex. PMID:9372909

  12. The TATA-containing core promoter of the type II collagen gene (COL2A1) is the target of interferon-gamma-mediated inhibition in human chondrocytes: requirement for Stat1 alpha, Jak1 and Jak2.

    PubMed Central

    Osaki, Makoto; Tan, Lujian; Choy, Bob K; Yoshida, Yasuhiro; Cheah, Kathryn S E; Auron, Philip E; Goldring, Mary B

    2003-01-01

    Interferon-gamma (IFN-gamma) inhibits the synthesis of the cartilage-specific extracellular matrix protein type II collagen, and suppresses the expression of the type II collagen gene ( COL2A1 ) at the transcriptional level. To further examine this mechanism, the responses of COL2A1 regulatory sequences to IFN-gamma and the role of components of the Janus kinase/signal transducer and activators of transcription (JAK/STAT) pathway were examined in the immortalized human chondrocyte cell line, C-28/I2. IFN-gamma inhibited the mRNA levels of COL2A1 and aggrecan, but not Sox9, L-Sox5 and Sox6, all of which were expressed by these cells as markers of the differentiated phenotype. IFN-gamma suppressed the expression of luciferase reporter constructs containing sequences of the COL2A1 promoter spanning -6368 to +125 bp in the absence and presence of the intronic enhancer and stimulated activity of the gamma-interferon-activated site (GAS) luciferase reporter vector, associated with induction of Stat1 alpha-binding activity in nuclear extracts. These responses to IFN-gamma were blocked by overexpression of the JAK inhibitor, JAK-binding protein (JAB), or reversed by dominant-negative Stat1 alpha Y701F containing a mutation at Tyr-701, the JAK phosphorylation site. IFN-gamma had no effect on COL2A1 promoter expression in Jak1 (U4A)-, Jak2 (gamma 2A)- and Stat1 alpha (U3A)-deficient cell lines. In the U3A cell line, the response to IFN-gamma was rescued by overexpression of Stat1 alpha, but not by either Stat1 alpha Y701F or Stat1 beta. Functional analysis using deletion constructs showed that the IFN-gamma response was retained in the COL2A1 core promoter region spanning -45 to +11 bp, containing the TATA-box and GC-rich sequences but no Stat1-binding elements. Inhibition of COL2A1 promoter activity by IFN-gamma persisted in the presence of multiple deletions within the -45/+11 bp region. Our results indicate that repression of COL2A1 gene transcription by IFN

  13. Les structures de la couverture Néoprotérozoïque terminal et Paléozoïque de la région de Tata, Anti-Atlas centre-occidental, Maroc: déformation polyphasée, ou interactions socle/couverture pendant l'orogenèse hercynienne?The structures of the Late Neoproterozoic and Early Palæozoic cover of the Tata area, western Anti-Atlas, Morocco: polyphased deformation or basement/cover interactions during the Variscan orogeny?

    NASA Astrophysics Data System (ADS)

    Faik, F.; Belfoul, M. A.; Bouabdelli, M.; Hassenforder, B.

    2001-05-01

    The western Anti-Atlas was formed by a Precambrian basement in the core of anticlines, surrounded by a Neoproterozoic and Palæozoic cover. The structural study of the Tata regional rocks shows a heterogeneous deformation, characterised especially by two types of folds in two orthogonal directions: north-south to north-northeast-south-southwest-trending and east-west-trending. The north-south structures are present in all of the Palæozoic cover and belong to the major Variscan compression of Late Carboniferous age by a comparison of the other domains of the western Anti-Atlas. Alternatively, east-west folding is assigned only to the lower part of the cover and consists of a ductile heterogeneous deformation, especially marked at the basement-cover interface. These folds are associated with a subhorizontal cleavage, indicating a southern vergence of the structures. A discussion of the age and the tectonic style of these structures is proposed, as well as their significance within the Variscan belt along the northern margin of the West African Craton.

  14. Analisis del contenido curricular de los Documentos Normativos del Programa de Ciencias en el area de biologia para la escuela superior del sistema de educacion publica de Puerto Rico: 1993-2012

    NASA Astrophysics Data System (ADS)

    Davila Montanez, Melissa

    Esta investigacion de naturaleza cualitativa se ocupo de realizar un analisis de contenido documental de los Documentos Normativos del Programa de Ciencias en el area de biologia de la escuela superior del sistema de educacion publica de Puerto Rico del periodo 1993-2012. Los documentos analizados fueron: Guia Curricular, 1995; Marco Curricular, 2003; Estandares de Excelencia, 1996, 2000 y Estandares de Contenido y Expectativas de Grado, 2007. Se indago si hubo cambios en significados en los Componentes Estructurales: Naturaleza de la ciencia, Paradigmas para la ensenanza de la ciencia, Funcion del curriculo formal, Mision de la ensenanza de la ciencia; Contenidos, destrezas y competencias, Estrategias de ensenanza y Evaluacion/Assessment del aprendizaje. El analisis sugiere que no hubo cambios sustanciales en los significados de los Componentes Estructurales. Los documentos estudiados muestran mayormente caracteristicas similares, aunque los documentos mas recientes eran mas descriptivos, explicativos y especificos.

  15. Revision curricular a partir de un analisis comparativo de las discrepancias en los curriculos de una escuela de optometria en Puerto Rico con las competencias requeridas para las agencias de revalida y acreditacion 2004

    NASA Astrophysics Data System (ADS)

    Rivera Pacheco, Andres

    El proposito de esta investigacion, un estudio cualitativo de caso, fue comparar y contrastar el curriculo vigente de la Escuela de Optometria de la UIAPR con las competencias y estandares requeridos por las agencias de acreditacion y de revalida. Con este proposito, decidimos realizar una revision y un analisis de documentos: el prontuario de cada uno de los cursos de los curriculos implantados en el 1993 y en el 2001; las competencias y estandares establecidos por las agencias de revalida y de acreditacion; y las estadisticas en las que se analiza el porcentaje de estudiantes que aprueban cada una de las partes de los examenes de revalida entre el 1998 al 2003. Se realizaron entrevistas dirigidas para dar apoyo y complementar la revision y el analisis de estos documentos. Los participantes de las entrevistas fueron tres estudiantes de la clase de optometria del 2004 (ultima clase del curriculo del 1993); tres estudiantes de la clase de optometria del 2005 (primera clase graduanda del curriculo vigente) y tres profesores y/o directores de los Departamentos de Ciencias Basicas, Ciencias Clinicas y Cuidado al Paciente. Esta investigacion se enmarco en el modelo de evaluacion curricular de discrepancia de Malcolm Provus y en el modelo de desarrollo basado en competencias. Uno de los hallazgos mas importantes del estudio es que los cambios que se implantaron al curriculo del 2001 no han logrado que los estudiantes mejoren su ejecucion en los examenes de revalida. Por otro lado, se encontro que el curriculo vigente atiende completamente los estandares de la practica de Optometria, pero no las competencias. Esta informacion fue validada mediante el uso de una tabla de cotejo para el analisis de los cursos y de la informacion obtenida de las entrevistas. El estudio determina y concluye que existen discrepancias entre los prontuarios de los cursos del curriculo y las competencias requeridas por la agencia de revalida. Segundo, que el Departamento de Ciencias Basicas es el

  16. DISCRETE TATA BOXES WITHIN THE PROMOTERS OF TWO PEACH DEHYDRIN GENES CONTROL DIFFERENTIAL EXPRESSION

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A genomic clone encoding two dehydrin genes, Ppdhn1 and Ppdhn2, has been isolated from peach (Prunus persica [L.] Batsch.). Ppdhn1, previously described, can be classified as a Y2K9-type dehydrin that exhibits considerable identity with Arabidopsis Xero2 (a K6 dehydrin). Ppdhn2 represents a dehydr...

  17. A high speed digital data acquisition system for the Indian National Gamma Array at Tata Institute of Fundamental Research

    NASA Astrophysics Data System (ADS)

    Palit, R.; Saha, S.; Sethi, J.; Trivedi, T.; Sharma, S.; Naidu, B. S.; Jadhav, S.; Donthi, R.; Chavan, P. B.; Tan, H.; Hennig, W.

    2012-07-01

    A digital data acquisition system for the Compton suppressed clover detector array has been implemented at the TIFR-BARC accelerator facility for the high resolution gamma ray spectroscopy using the Pixie-16 Digital Gamma Finder modules by XIA LLC. This system has a provision for simultaneous digitization of 96 preamplifier signals of high purity germanium crystals. The energy and timing characteristics of the clover detectors have been investigated in detail. In-beam data has been collected both in singles and in the coincidence mode. The system has been tested with 64 channels with each of the 64 crystals having an event rate up to 5 kHz and 2-fold clover coincidence rate up to 15 kHz. The use of the digital data acquisition system has improved the high counting rate handling capabilities for the clover array. Conventional systems with analog shaping are being replaced by digital system that provides higher throughput, better energy resolution and better stability for the multi-detector Compton suppressed clover array.

  18. The hepatitis B virus X protein increases the cellular level of TATA-binding protein, which mediates transactivation of RNA polymerase III genes

    SciTech Connect

    Wang, Horng-Dar; Johnson, D.L.; Yuh, Chio-Hwa

    1995-12-01

    This report decribes the mechanism by which the hepatitis B virus X gene product induces RNA polymerase III genes. The RNA pol III transcription system serves as model for understanding the mechanism of X in the transactivation of cellular genes in both Drosophila and rat cell lines. 53 refs., 7 figs., 1 tab.

  19. Dental Wings CAD/CAM system precision: an internal and marginal fit sperimental analisys

    PubMed Central

    SANNINO, G.; GLORIA, F.; SCHIAVETTI, R.; OTTRIA, L.; BARLATTANI, A.

    2010-01-01

    SUMMARY Statement of problem. The CAD-CAM technology has been developed to design and manufacture prosthetic structures with constant quality characteristics; in fact procedures are codified, manageable and repeatable. Purpose. The purpose of this in vitro study is to evaluate the internal and marginal gap of zirconia casts made with a new CAD-CAM systematic that use Dental Wings laser scanner and Yenamak milling machine. Material and methods. 6 analogs of solid abutments of Straumann implants were used, fixed in plexiglass bases. The samples were scanned by Dental Wings laser; the file obtained by scanning of each probe was sent to the Yenamak D40 milling machine, then the casts were sintered in Protherm furnace. Then 6 samples were cemented with resin luting agent capsules (Relyx Unicem, 3M ESPE). The samples were incorporated in transparent epoxy resin. After resin hardening, the cylinders obtained were cut with a microtomes. These slices thus obtained were then polished with a Polisher sander with alumina dust decreasing grain. Each section was observed and photographed in reflected light with the aid of an optic microscope type, first at low magnification and then at higher magnification. Results. The overall average fitting of copings on the abutments was 32,87 μ. No differences were found in marginal fit on buccal and lingual sides, it was easily predictable because of the standard form of the used stumps. The recorded values for the marginal fit were lower than those of axial walls. The accuracy of adaptation was always achieved within the limits of clinical acceptability. Conclusions. Within the limitations of this study, the system evaluated represents a valuable alternative to conventional prosthetic rehabilitation techniques. PMID:23285364

  20. Analisis de las Condiciones de Salud del Nino de 0-6 anos en Honduras.

    ERIC Educational Resources Information Center

    Matamoros, Douglas Alberto

    1987-01-01

    Examines the National Pediatric Service and the research program of the Maternity-Infant-Hospital-School in Honduras. Reports that health conditions of young children (birth to six years) in Honduras are appalling and that available funds for health services are inadequate, reflecting the country's economic and social crisis. (NH)

  1. Peripheral Desmoplastic Ameloblastoma in Adolescent Age: Clinico-Pathological and Immunohistochemical Analisys of a Case

    PubMed Central

    Oteri, Giacomo; Lentini, Maria; Pisano, Michele; Cicciù, Marco

    2014-01-01

    The Extraosseous or Peripheral Ameloblastoma (PA) is a rare and benign odontogenic tumour, representing 1% to 5% of all ameloblastomas. It is usually localized in the soft oral tissues, without deep bone involvement. Its biological behaviour is specific, and several authors define PA as a non-infiltrating hamartomatous lesion. Indeed, recurrences rarely occur and progression in malignant tumors appears to be rare. The PA originates from the tooth-forming apparatus and it consists of proliferating odontogenic epithelium, exhibiting the same histological cell types and patterns of the intraosseous counterpart or infiltrating ameloblastoma. The peripheral desmoplastic ameloblastoma (PDA) can be classified as a newly recognized and very rare histological variant. To our knowledge, only a few cases of adult patients affected by PDA have been published. The aim of this paper is to report a case of PDA affecting an adolescent patient. The clinical-pathological and immunohistological features are discussed in order to improve knowledge regarding a correct diagnosis and to differentiate PDA lesions from similar diseases. PMID:25317210

  2. Photoelastic analisys in the lower region of vertebral body L4

    PubMed Central

    Fakhouri, Sarah Fakher; Zamarioli, Ariane; Shimano, Marcos Massao; Defino, Helton Luiz Aparecido; Araujo, Cleudmar Amaral; Shimano, Antonio Carlos

    2012-01-01

    Objective To analyze the shear forces on the vertebral body L4 when submitted to a compression force by means of transmission photoelasticity. Methods Twelve photoelastic models were divided into three groups, with four models per group, according to the positioning of the sagittal section vertebrae L4-L5 (sections A, B and C). The simulation was performed using a 15N compression force, and the fringe orders were evaluated in the vertebral body L4 by the Tardy compensation method. Results Photoelastic analysis showed, in general, a homogeneous distribution in the vertebral bodies. The shear forces were higher in section C than B, and higher in B than A. Conclusion The posterior area of L4, mainly in section C, showed higher shear concentrations, corresponding to a more susceptible area for bone fracture and spondylolisthesis. Economic and Decision Analyses - Development of an Economic or Decision Model. Level I PMID:24453574

  3. Mapping wildfire effects on Ca2+ and Mg2+ released from ash. A microplot analisis.

    NASA Astrophysics Data System (ADS)

    Pereira, Paulo; Úbeda, Xavier; Martin, Deborah

    2010-05-01

    Wildland fires have important implications in ecosystems dynamic. Their effects depends on many biophysical components, mainly burned specie, ecosystem affected, amount and spatial distribution of the fuel, relative humidity, slope, aspect and time of residence. These parameters are heterogenic across the landscape, producing a complex mosaic of severities. Wildland fires have a heterogenic impact on ecosystems due their diverse biophysical features. It is widely known that fire impacts can change rapidly even in short distances, producing at microplot scale highly spatial variation. Also after a fire, the most visible thing is ash and his physical and chemical properties are of main importance because here reside the majority of the available nutrients available to the plants. Considering this idea, is of major importance, study their characteristics in order to observe the type and amount of elements available to plants. This study is focused on the study of the spatial variability of two nutrients essential to plant growth, Ca2+ and Mg2+, released from ash after a wildfire at microplot scale. The impacts of fire are highly variable even small distances. This creates many problems at the hour of map the effects of fire in the release of the studied elements. Hence is of major priority identify the less biased interpolation method in order to predict with great accuracy the variable in study. The aim of this study is map the effects of wildfire on the referred elements released from ash at microplot scale, testing several interpolation methods. 16 interpolation techniques were tested, Inverse Distance to a Weight (IDW), with the with the weights of 1,2, 3, 4 and 5, Local Polynomial, with the power of 1 (LP1) and 2 (LP2), Polynomial Regression (PR), Radial Basis Functions, especially, Spline With Tension (SPT), Completely Regularized Spline (CRS), Multiquadratic (MTQ), Inverse Multiquadratic (MTQ), and Thin Plate Spline (TPS). Also geostatistical methods were tested from Kriging family, mainly Ordinary Kriging (OK), Simple Kriging (SK) and Universal Kriging (UK). Interpolation techniques were assessed throughout the Mean Error (ME) and Root Mean Square (RMSE), obtained from the cross validation procedure calculated in all methods. The fire occurred in Portugal, near an urban area and inside the affected area we designed a grid with the dimensions of 9 x 27 m and we collected 40 samples. Before modelling data, we tested their normality with the Shapiro Wilk test. Since the distributions of Ca2+ and Mg2+ did not respect the gaussian distribution we transformed data logarithmically (Ln). With this transformation, data respect the normality and spatial distribution was modelled with the transformed data. On average in the entire plot the ash slurries contained 4371.01 mg/l of Ca2+, however with a higher coefficient of variation (CV%) of 54.05%. From all the tested methods LP1 was the less biased and hence the most accurate to interpolate this element. The most biased was LP2. In relation to Mg2+, considering the entire plot, the ash released in solution on average 1196.01 mg/l, with a CV% of 52.36%, similar to the identified in Ca2+. The best interpolator in this case was SK and the most biased was LP1 and TPS. Comparing all methods in both elements, the quality of the interpolations was higher in Ca2+. These results allowed us to conclude that to achieve the best prediction it is necessary test a wide range of interpolation methods. The best accuracy will permit us to understand with more precision where the studied elements are more available and accessible to plant growth and ecosystem recovers. This spatial pattern of both nutrients is related with ash pH and burned severity evaluated from ash colour and CaCO3 content. These aspects will be also discussed in the work.

  4. Coastal morphodynamic features/patterns analisys through a video-based system and image processing

    NASA Astrophysics Data System (ADS)

    Santos, Fábio; Pais-Barbosa, Joaquim; Teodoro, Ana C.; Gonçalves, Hernâni; Baptista, Paolo; Moreira, António; Veloso-Gomes, Fernando; Taveira-Pinto, Francisco; Gomes-Costa, Paulo; Lopes, Vítor; Neves-Santos, Filipe

    2012-10-01

    The Portuguese coastline, like many other worldwide coastlines, is often submitted to several types of extreme events resulting in erosion, thus, acquisition of high quality field measurements has become a common concern. The nearshore survey systems have been traditionally based on in situ measurements or in the use of satellite or aircraft mounted remote sensing systems. As an alternative, video-monitoring systems proved to be an economic and efficient way to collect useful and continuous data, and to document extreme events. In this context, is under development the project MoZCo (Advanced Methodologies and Techniques Development for Coastal Zone Monitoring), which intends to develop and implement monitoring techniques for the coastal zone based on a low cost video monitoring system. The pilot study area is Ofir beach (north of Portugal), a critical coastal area. In the beginning of this project (2010) a monitoring video station was developed, collecting snapshots and 10 minutes videos every hour. In order to process the data, several video image processing algorithms were implemented in Matlab®, allowing achieve the main video-monitoring system products, such as, the shoreline detection. An algorithm based on image processing techniques was developed, using the HSV color space, the idea is to select a study and a sample area, containing pixels associated with dry and wet regions, over which a thresholding and some morphological operators are applied. After comparing the results with manual digitalization, promising results were achieved despite the method's simplicity, which is in continuous development in order to optimize the results.

  5. [Analisys of work-related accidents and incidents in an oil refinery in Rio de Janeiro].

    PubMed

    de Souza, Carlos Augusto Vaz; de Freitas, Carlos Machado

    2003-01-01

    Accidents in the chemical industry can have serious consequences for workers, communities, and the environment and are thus highly relevant to public health. This article is the result of an occupational surveillance project involving several public institutions. We analyze 800 work-related accidents that resulted in injuries, environmental damage, or loss of production in 1997 in an oil refinery located in Rio de Janeiro, Brazil. The methodology was based on managerial and organizational approaches to accident investigation, with the European Union reporting system as the reference. The results highlight various limitations in the process of reporting and investigating accidents, as well as a certain hierarchy of accidents, with more attention given to accidents involving loss of production and less to those resulting in injuries, particularly among outsourced workers. PMID:14666211

  6. Forest fire risk estimation from time series analisys of NOAA NDVI data

    NASA Astrophysics Data System (ADS)

    Gabban, Andrea; Liberta, Giorgio; San-Miguel-Ayanz, Jesus; Barbosa, Paulo

    2004-02-01

    The values of the Normalized Difference Vegetation Index obtained from NOAA Advanced Very High Resolution Radiometer (AVHRR) have often been used for forestry application, including the assessment of fire risk. Forest fire risk estimates were based mainly on the decrease of NDVI values during the summer in areas subject to summer drought. However, the inter-annual variability of the vegetation response has never been extensively taken into account. The present work was based on the assumption that Mediterranean vegetation is adapted to summer drought and one possible estimator of the vegetation stress was the inter-annual variability of the vegetation status, as reflected by NDVI values. This article presents a novel methodology for the assessment of fire risk based on the comparison of the current NDVI values, on a given area, with the historical values along a time series of 13 years. The first part of the study is focused on the characterization of the Minimum and Maximum long term daily images. The second part is centered on the best method to compare the long term Maximum and Minimum with the current NDVI. A statistical index, Dynamic Relative Greenness, DRG, was tested on as a novel potential fire risk indicator.

  7. [Analisys of nursing diagnosis risk of falls in adults and children].

    PubMed

    Hernando Mate, Alba; Meneses Monroy, Alfonso

    2013-05-01

    Falls are a problem for all age groups but it affects children and the elderly in particular. Falls are a major public health problem as they not only have physical, social and economic consequences but also they are associated to high mortality rates. It has been proven that the cause of falls is multifactorial. Therefore, the implementation of a Multifactorial Fall Prevention Program is extremely important. For these reasons, this research study is done based on other studies already published. Falls linked to specific factors are analyzed in order to prove through evidence risk factors established by the NANDA for Risk Fall Diagnosis or if some of them can not be justified and, therefore, should not be classified as risk factors. PMID:23815056

  8. Wireless optical transceiver design, link analisys and alignment control for mobile communication

    NASA Astrophysics Data System (ADS)

    Zhou, Dayong

    Pointing, acquisition and tracking of a free-space optical node in a mobile network experiencing misalignment due to adverse factors including vibration, motion and atmospheric turbulence requires a different approach than traditional free-space optical transceivers. A recent fiber-bundle approach for beam steering at the transmitter was investigated to provide continuous beam coverage at the receiver without the application of mechanical devices. Utilizing multiple fibers-lenses sets at the receiver was also proposed to enhance the tolerance of optical link misalignment. In this work, both laboratory experiments and software simulation were implemented to evaluate the optical link performance for different fiber-bundle-based transceiver setups as the link parameters were varied. The performance was evaluated in terms of the coverage area at the receiver, which is a measure of misalignment tolerance and is dependent not only on wavelength but on other key parameters such as link length, transmitted power, the pattern of transmitters, beam divergence, and the receiver construction. The results showed that fiber-bindle-based transceivers reveal significant potential to maximize the up time of the link, and the results also provide guidance on the further development of the overall system. To incorporate the proposed transceiver designs, an alignment control system was developed and evaluated as well. The laboratory results show that the optical control system successfully recovered and maintained the link while the receiver was in motion and the signal coverage at the target area was enhanced significantly.

  9. Ppp Analisys with GPS and Glonass Integration in Periods Under Ionospheric Scintillation Effects

    NASA Astrophysics Data System (ADS)

    Marques, H. A. S.

    2015-12-01

    The GNSS is widely used nowadays either for geodetic positioning or scientific purposes. The GNSS currently includes GPS, GLONASS, Galileo among other emerging systems. The GPS and GLONASS are currently operational with a full satellite constellation. The GPS is still the most used nowadays and both GPS and GLONASS are under a modernization process. The geodetic positioning by using data from multi-constellation can provide better accuracy in positioning and also more reliability. The PPP is benefited once the satellite geometry is crucial in this method, mainly for kinematic scenarios. The satellite geometry can change suddenly for data collected in urban areas or in conditions of strong atmospheric effects such as Ionospheric Scintillation (IS) that causes weakening of signals with cycle slips and even loss of lock. The IS is caused by small irregularities in the ionosphere layer and is characterized by rapid change in amplitude and phase of the signal being stronger in equatorial and high latitudes regions. In this work the PPP is evaluated with GPS and GLONASS data collected by monitoring receivers from Brazilian CIGALA/CALIBRA network under IS conditions. The PPP processing was accomplished by using the GPSPPP software provided by Natural Resources Canadian (NRCAN). The IS effects were analyzed taking account the S4 and PHI60 indices. Considering periods with moderate IS effects, the use of only GPS data in the PPP presented several peaks in the coordinate time series due to cycle slips and loos of lock. In cycle slip conditions the ambiguity parameter are reinitialized by GPSPPP and considering loss of lock few satellites can be available in some epochs affecting the positioning geometry and consequently decreasing accuracy. In such situations, the PPP using GPS and GLONASS data presented improvements in positioning accuracy of the order to 70% in height component when compared with PPP using only GPS data. Analyses of GDOP and ambiguities parameters were also performed.

  10. Una Metodologia de Analisis de la Interaccion Alumno-Orgendaor en la Investigacion Sobre Informatica Educativa.

    ERIC Educational Resources Information Center

    Estepa, A.; And Others

    1992-01-01

    The recording of the interaction between pupil and computer is one of the data sources frequently used in research on the use of computers in teaching. Describes the analysis methodology of these recordings to determine the use of computers in statistics and its adaptation to other research work on the use of computers in education. (Author/MDH)

  11. Analisis de Alteraciones EN la Imagen Debidas a Descolimacion de un Telescopio

    NASA Astrophysics Data System (ADS)

    Cobos, F. J.; Galan, M. J.

    1987-05-01

    Podemos considerar, en términos generales, que los espejos de un telescopio tienen una calidad óptica intrínseca, entendiendo por ésta la que se ha obtenido como resultado, fundamentalmente, de la destreza del personal del Taller Optico, que considerará terminadas las superficies ópticas cuando éstas satisfagan los requisitos de diseño y las pruebas de evaluación pertinentes. Debemos esperar que, una vez instalados los espejos en el telescopio, no se altere esta calidad de la óptica por un funcionamiento inadecuado de partes mecánicas del mismo. En los últimos años, en la medida que los problemas de infraestructuratura de nuestros Observatorios se han ido resolviendo, se ha hecho más patente la necesidad de llevar a la instrumentación existente al máximo de su potencial y parte esencial de ésta la conforman los mismos te lescopios. Mejorar la calidad óptica de las imágenes obtenidas con ellos ha hecho que sea prioritario el realizar una investigación más sistemática de sus características. Este trabajo ha tenido como objetivo primordial el usar un programa de diseño óptico, en el caso particular del telescopio UNAM212, con el fin de calcular y obtener gráficamente los diagramas de manchas de imagenes en foco y extrafocales, tanto con la óptica perfectamente alineada como descolimándola (mediante pequenos giros y descentramientos de los espejos). De esta manera, se hizo una evaluación de los efectos que estas alteraciones simuladas producirían en las imágenes focales y extra focales para así poder compararlas con las que realmente se han observado. Asimismo, se ha buscado información bibliográfica, en particular sobre los efectos de giros y descentramientos en las imágenes extrafocales, en lo que se ref iere a la falta de concentricidad de los círculos que forman la "dona" y a la distribución de intensidad luminosa en la misma. De ésta, l futuro un proceso que, haciendo uso de los detectores bidimensionales, nos permita Ilevar a cabo una alineación más rigurosa de la óptica del telescopio y evaluar con precisión Si variaciones en el posicionado del misesperamos desarrollar en emo producen efectos de descolimación.

  12. Analisys of pectoralis major tendon in weightlifting athletes using ultrasonography and elastography

    PubMed Central

    Pochini, Alberto de Castro; Ferretti, Mario; Kawakami, Eduardo Felipe Kin Ito; Fernandes, Artur da Rocha Corrêa; Yamada, Andre Fukunishi; de Oliveira, Gabriela Clemente; Cohen, Moisés; Andreoli, Carlos Vicente; Ejnisman, Benno

    2015-01-01

    ABSTRACT Objective To evaluate tendinopathy of the pectoralis major muscle in weightlifting athletes using ultrasound and elastography. Methods This study included 20 patients, 10 with rupture of the pectoralis major muscle and 10 control patients. We evaluated pectoralis major muscle contralateral tendon with ultrasonographic and elastography examinations. The ultrasonographic examinations were performed using a high-resolution B mode ultrasound device. The elastography evaluation was classified into three patterns: (A), if stiff (more than 50% area with blue staining); (B), if intermediate (more than 50% green); and (C), if softened (more than 50% red). Results Patients’ mean age was 33±5.3 years. The presence of tendinous injury measured by ultrasound had a significant different (p=0.0055), because 80% of cases had tendinous injury versus 10% in the Control Group. No significant differences were seen between groups related with change in elastography (p=0.1409). Conclusion Long-term bodybuilders had ultrasound image with more tendinous injury than those in Control Group. There was no statistical significance regarding change in tendon elasticity compared with Control Group. PMID:26761551

  13. Identification of Rocks on Planetary Surface Using Husar-9 Rover Camera: Field Work Simulations with Hunveyor-9 Space Probe Model System at Eötvös High School, Tata, Hungary

    NASA Astrophysics Data System (ADS)

    Magyar, I.; Badics, A.; Bakonyi, I.; Csiszár, Á.; Franko, M.; Gyürki, Á.; Héricz, M.; Marschall, B.; Nagyházi, Á.; Varga, T. N.; Végh, Gy.; Varga, T. P.; Bérczi, Sz.

    2009-03-01

    We studied the rock types along the Husar-9 rover’s path and identified them on the basis of their shape, color and surface textures: komatiite, basalt, granite, conglomerate, schist rock, porphyritic granite, suevite breccia, and vesicular basalt.

  14. Estudio general de la region del Lago Titicaca evaluando en forma preliminar un sistema de analisis interactivo de imagenes multiespectrales

    USGS Publications Warehouse

    Brockmann, C.E.; Carter, William D.

    1976-01-01

    ERTS-1 digital data in the form of computer compatible tapes provide the geoscientist with an unusual opportunity to test the maximum flexibility of the satellite system using interactive computers, such as the General Electric Image 100 System. Approximately 9 hours of computer and operator time were used to analyze the Lake Titicaca image, 1443-14073, acquired 9 October 1973. The total area of the lake and associate wetlands was calculated and found to be within 3 percent of previous measurements. The area was subdivided by reflectance characteristics employing cluster analysis of all 4 bands and later compared with density values of band 4. Reflectance variations may be attributed to surface roughness, water depth and bottom characteristics, turbidity, and floating matter. Wetland marsh vegetation, vegetation related to ground-water effluents, natural grasses, and farm crops were separated by cluster analysis. Sandstone, limestone, sand dunes, and several volcanic rock types were similarly separated and displayed by assigned colors and extended through the entire scene. Waste dumps of the Matilde Zinc Mine and smaller mine workings were tentatively identified by signature analysis. Histograms of reflectance values and map printouts were automatically obtained as a record of each of the principal themes. These themes were also stored on a work tape for later display and photographic record as well as to serve in training. The Image 100 System is rapid, extremely flexible and very useful to the investigator in identifying subtle features that may not be noticed by conventional image analysis. The entire scene, which covers 34,225 km2, was analyzed at a scale of 1:600,000, and portions at 1:98,000 and 1:25,000, during a 9-hour period at a rental cost of $250 per hour. Costs to the user can be reduced by restricting its uses to specific areas, objectives, and procedures, rather than undertaking a complete analysis of a total scene.

  15. Analisis parametrico de las variables que influyen en el comportamiento adherente de las armaduras pretesas en el hormigon

    NASA Astrophysics Data System (ADS)

    Arbelaez Jaramillo, Cesar Augusto

    Prestressed concrete technique through the use of prestressed reinforcement is extended in the precast concrete industry. This technique consists on casting a concrete element over a previously prestressed reinforcement, proceeding to release once the concrete has reached a determined strength so the prestressed stress introduced to the reinforcement be transmitted, by bond, to concrete. The bond behaviour of prestressed reinforcement includes two phenomena: prestress transmission from the reinforcement to concrete and anchorage of the reinforcement. This bond behaviour is characterized by mean of two lengths: transmission length and anchorage length. The good design of these lengths is a basic and fundamental aspect in the project of precast prestressed concrete elements to guaranty the appropriate transmission of prestress and to allow the anchorage of the reinforcement along the structural element service life. The influence of the parameters related to the concrete dosage on the transmission and anchorage lengths of prestressing strands have been analyzed. The ECADA test method has been applied. With this method the operations of transmission of prestress and anchorage of the reinforcement are sequentially done. The transmission and anchorage lengths are determined from the force control supported by the reinforcement testing series of specimens with different embedment lengths. The differentiation of the concepts of anchorage length without slips and with slips has been proposed. The relationship of the parameters of dosage with the bond stress and the registered slips during the processes of transmission and anchorage has been studied. Expressions to value the slips distribution of the reinforcement in the transmission zone and in the anchorage zone have been proposed. A study on the determination of the transmission length from the free reinforcement slip end has been done and the viability to experimentally determine the transmission length from the slips sequence in the pull-out end as a function of the embedment length has been verified. The experimental results have been compared with results and predictions from other authors and standards, and an expression to calculate the transmission length have been proposed. Finally, the bond behaviour of self-compacting concretes has been compared with the bond behaviour of traditional concretes.

  16. Analisys of the therapeutic factors in the Therapeutic Community Podsused among the war related diagnosis and the others.

    PubMed

    Martic-Biocina, Sanja; Sakoman, Mirna Pandzic; Bosak, Josipa; Stipic, N

    2015-09-01

    Therapeutic community/TC/ is a sociotherapeutic method that uses sociotherapeutic and psychotherapeutic techniques for various mental disorders. In Croatia, during and after the war many war veterans have been in treatment through TC and many of them still participate in it. Majority of them were diagnosed with PTSD diagnosis, but some of them also had other diagnosis, e.g. depression, paranoid delusion, etc. In this paper we describe principles of TC that we use in Croatia and we also try to find out which curative factors of TC are the most important for this population. We applied semistructured intervju based on Yalom book of practice and theory of psychotherapy to explore what factors do war veterans find the most important and relevant for their resilience and better coping with everyday issues. PMID:26417803

  17. Solution Processable White Organic Light-Emitting Diodes Using New Blue Host Material Including Substituent Group.

    PubMed

    Lee, Jaehyun; Shin, Hwangyu; Park, Jongwook

    2016-02-01

    New host material of T-TATa isomer substituted t-butyl group was investigated in solution process WOLED device compared with 4-(10-(3',5'-diphenylbiphenyl-4-yl)anthracen-9-yl)-N,N-diphenylaniline [TATa]. A two-color WOLED of a co-host system using solution process method was demonstrated. The device configuration was ITO/PEDOT:PSS (40 nm)/emitting layer (50 nm)/TPBi (20 nm)/LiF (1 nm)/AI. The emitting layer consisted of TATa or T-TATa isomer, NPB, DPAVBi (blue dopant), and rubrene (yellow dopant). NPB was used as not only blue host but also helping hole carrier transport. The device using T-TATa compound as a co-host exhibited a luminance efficiency of 3.39 cd/A, which is about twice higher than TATa device of 1.58 cd/A at 10 mA/cm2. PMID:27433738

  18. TRF2: TRansForming the view of general transcription factors.

    PubMed

    Zehavi, Yonathan; Kedmi, Adi; Ideses, Diana; Juven-Gershon, Tamar

    2015-01-01

    Transcriptional regulation is pivotal for development and differentiation of organisms. Transcription of eukaryotic protein-coding genes by RNA polymerase II (Pol II) initiates at the core promoter. Core promoters, which encompass the transcription start site, may contain functional core promoter elements, such as the TATA box, initiator, TCT and downstream core promoter element. TRF2 (TATA-box-binding protein-related factor 2) does not bind TATA box-containing promoters. Rather, it is recruited to core promoters via sequences other than the TATA box. We review the recent findings implicating TRF2 as a basal transcription factor in the regulation of diverse biological processes and specialized transcriptional programs. PMID:25588059

  19. A New-Anthracene Derivative Containing t-Butyl Group for Solution Process Organic Light-Emitting Diodes.

    PubMed

    Lee, Jaehyun; Kim, Seungho; Kim, Jee-Hwan; Park, Jongwook

    2015-10-01

    4-(10-(3',5'-diphenylbiphenyl-4-yl)anthracen-9-yl)-N,N-diphenylaniline [TATa] and a new anthracene derivative of 4-(2 or 3-tert-butyl-10-(3',5'-diphenylbiphenyl-4-yl)anthracen-9-yl)-N,N-diphenylaniline [T-TATa] isomer by introduced t-butyl group were synthesized. OLED devices of TATa and T-TATa were fabricated by solution process. Its physical properties such as optical, electrochemical, and electroluminescent properties were also investigated. Two compounds were used as emitting layer (EML) in OLED device: ITO/PEDOT (40 nm)/synthesized materials (60 nm)/TPBi (20 nm)/LiF (1 nm)/Al (200 nm). The luminance efficiency of the synthesized compounds at 10 mA/cm2 were measured 0.85 cd/A for TATa and 1.49 cd/A for T-TATa, respectively. Moreover, the power efficiency of T-TATa is 1.08 lm/W. Its value is almost two times higher than 0.56 lm/W of TATa. As a result, more improved efficiency was shown with the device in a compound including t-butyl group to TATa core part, when the deivces were prepared by solution process. PMID:26726504

  20. Books and DVDs Offer Excellent Resources for Childbirth Education Classes

    PubMed Central

    Shilling, Teri

    2006-01-01

    In this column, reviewers offer perspectives and comments on the second edition of The Labor Progress Handbook, a book by Penny Simkin and Ruth Ancheta; What Babies Want, a documentary directed by Debby Takikawa; A Pleasing Birth, a book by Raymond De Vries; and Baby Tata, a DVD production by Baby Tata LLC.

  1. Triazatriangulene as binding group for molecular electronics.

    PubMed

    Wei, Zhongming; Wang, Xintai; Borges, Anders; Santella, Marco; Li, Tao; Sørensen, Jakob Kryger; Vanin, Marco; Hu, Wenping; Liu, Yunqi; Ulstrup, Jens; Solomon, Gemma C; Chi, Qijin; Bjørnholm, Thomas; Nørgaard, Kasper; Laursen, Bo W

    2014-12-16

    The triazatriangulene (TATA) ring system was investigated as a binding group for tunnel junctions of molecular wires on gold surfaces. Self-assembled monolayers (SAMs) of TATA platforms with three different lengths of phenylene wires were fabricated, and their electrical conductance was recorded by both conducting probe-atomic force microscopy (CP-AFM) and scanning tunneling microscopy (STM). Similar measurements were performed for phenylene SAMs with thiol anchoring groups as references. It was found that, despite the presence of a sp(3) hybridized carbon atom in the conduction path, the TATA platform displays a contact resistance only slightly larger than the thiols. This surprising finding has not been reported before and was analyzed by theoretical computations of the transmission functions of the TATA anchored molecular wires. The relatively low contact resistance of the TATA platform along with its high stability and directionality make this binding group very attractive for molecular electronic measurements and devices. PMID:25426950

  2. Mapa Sociolinguistico. Analisis demolinguistico de la Comunidad Autonoma Vasca derivado del padron de 1986 (Sociolinguistic Map. Demolinguistic analysis of the Autonomous Basque Community derived from the 1986 Census).

    ERIC Educational Resources Information Center

    Basque Autonomous Community, Vitoria (Spain). General Secretariat of Linguistic Policy.

    Sociolinguistic data are presented in the form of sophisticated maps and tables in this pioneering study on the status of the Basque language. Based on information collected from the 1986 census, the major demographic characteristics of Basque are examined in order to ascertain the factors and processes that have contributed to its current status.…

  3. L'organizzazione di una lezione di traduzione basata sull'approccio dell'analisi testuale (The Organization of a Translation Lesson Based on a Textual Analysis Approach).

    ERIC Educational Resources Information Center

    Horrakh, Livio

    1988-01-01

    Describes a three-phase approach to teaching translation: (1) decoding the "macro" (beyond sentence level) and the "micro" (sentence or phrase level) elements of the passage; (2) coordinating the elements of the original language text with the target language text; and (3) producing the text in the target language. (CFM)

  4. [Influence of tobacco smoking on newborn's birth weight--analisys of dates concerning births from Maternity Hospital named. Dr S. Mossor's in Opole City].

    PubMed

    Guzikowski, Wojciech; Pirogowicz, Iwona

    2008-01-01

    Despite wide education, tobacco smoking while being pregnant is very important issue in perinatology. It is important problem because of life style of polish society, including pregnant women. Clinical observation of this issue is pointing on risk of occurring pathology in pregnancy, unfavorable consequences for neonate also many distant pathological effects among children. Purpose of this was getting an answer for question: whether in current social and economic situation there is connection between low birth mass and smoking tobacco during pregnancy. Under analysis were found births between 38th and 40th one hundred successive births (according to book of birth-room from 2860 labors in hospital in Opol, 2007) of mothers are smoking up to 10 cigarettes a day (group I), mothers smoking 11-20 cigarettes a day (group II) and mothers that are not smoking. This works affirms that smoking has negative influence on child birth mass. It is also displayed that higher the number of smoked cigarettes the higher percent of newborns with low birth mass and higher number o fetus with intrauterine growth retardation. Among mothers that are smoking the biggest group were young women (mean. 24, years) and multipara female (58%). PMID:19189515

  5. Analisys, processing and validation data from eolic stations of SONDA project (National Organization System of Environmental Data) at Brazilian National Institute for Space Research (CPTEC/INPE) .

    NASA Astrophysics Data System (ADS)

    Junior, A. B.; Nogueira, J. M.; Garcia, S. G.; Andrade, E. S.

    2007-05-01

    Asiel Bomfin Jr. LIM/CPTEC/INPE, Cachoeira Paulista, S.P., Brazil; Eliana Soares de Andrade; Jorge Luiz Martins Nogueira and Silvia Garcia de Castro. The Center for Weather Forecast and Climatic Analysis (CPTEC), a division of INPE, the Brazilian National Institute for Space Research. Several of the INPE´s departments and centers, like the CPTEC, have a variety of valuable datasets, many of them freely available and eolic data from SONDA project are also part of them at Meteorological Instrumental Laboratory (LIM). This paper presents the Analiys, processing and validation method applied to the eolic data in a temporal time of ten minutes, to be used in a PC IBM computer. This method is divided in tree separated programs. The first software called "separa.c" has the capability of divide the ingest data set in mensal files, identified by each station group. The second software called "minuto.c" does a syntactical analysis, verifying and correcting eventual lost data with NAN values. The third one called "validacode.c" generates two principal files, one containing the original data and the other with the codes of each variable for each minute analyzed. These codes is based on BSRN (Baseline Surface Radiation Network), but with some differences in their analyzed method. This method followed the Webmet.com, The Meteorological Resource Center. Table 1:Validation Codes Code Meaning 0 Quality check procedure is not avaiable for this level 2 The data is suspect 5 Quality check procedure is avaiable for this level, but not can be done 9 The data is correct Table 2: Validation levels for WIND SPEED: Validation Levels Quality check procedure for suspect data 0 Maximum and Minimum values of 25 m/s and 0 m/s 1 Can not vary more than 0,1 m/s for 03 consecutive hours 2 Can not vary more than 0,5 m/s for 12 consecutive hours 3 - Table 3: Validation levels for WIND DRECTION: Validation Levels Quality check procedure for suspect data 0 Maximum and Minimum values of 360 and 0 degrees 1 Can not vary more than 01 degree for 03 consecutive hours 2 Can not vary more than 10 degrees for 18 consecutive hours 3 - Table 4: Validation levels for TEMPERATURE: Validation Levels Quality check procedure for suspect data 0 Maximum and Minimum values of local data 1 Must vary more than 5 °C with reference to1 hour before 2 Can not vary more than 0, 5°C for 12 consecutive hours 3 - Output code examples according with the validation levels : Table 5: Output code examples Level 0 (Limit) Level 1 Level 2 Level 3 (final output) 0009 0029 0529 0529 0009 0099 0999 ou 0299 0999 ou 0299 0002 0052 0552 0552 6 Bibliographical references Stull, R. B., Introduction to Boundary Layer Meteorology, Dordrecht: Kluwer, 666 p, 1988. Vickers, D.; Mahrt, L. Quality control and flux sampling problems for tower and aircraft data. Journal of Atmospheric and Oceanic Technology, v. 14, n. 3, p. 512-526, June 1997.. 7 Electronical references National Organization System of Environmental Data Site http:www.cptec.inpe.br/~sonda/ The Meteorological Resource Center -Webmet.com Site http:www.webmet.com/

  6. Psicolinguistica, psicologia del linguaggio e "Analisi elettroacustica del linguaggio" di P. Agostino Gemelli (Psycholinguistics, Psychology of Language and P. Agostino Gemelli's "Electric-Acoustical Analysis of Language").

    ERIC Educational Resources Information Center

    Titone, Renzo

    1987-01-01

    Discusses the contribution of the little-known linguist Gemelli who favors a holistic approach to human language emphasizing the human personality as an essential factor in the expression of speech. Gemelli makes clear the breadth of the field of language psychology in contrast with the narrowness of psycholinguistics. (CFM)

  7. Reducing time delay in the thrombolysis of myocardial infarction: an internal quality improvement project. ARIAM Project Group. Analisis del Retraso en Infarto Agudo de Miocardio.

    PubMed

    Saturno, P J; Felices, F; Segura, J; Vera, A; Rodriguez, J J

    2000-01-01

    The objectives of this study were to improve thrombolytic therapy in acute myocardial infarction by reducing the "door-to-needle" time in a 285-bed university hospital in Spain. A quality management approach was used involving all the relevant staff. Target standard was set at 35 minutes. Baseline data, intervention effect, and continuous monitoring were analyzed using x control charts. Analysis of baseline data showed a wide out-of-control variation and 72 minutes' average delay. Cause analysis revealed organizational and clinical problems that were subjected to intervention. Postintervention data showed a stable process, with an average of 30 minutes. Continuous monitoring showed further improvement in average time and predictable variation. The template of the current control chart has an average of 26 minutes. Quality management methods, particularly staff involvement in problem analysis and intervention design, and the use of control charts were useful to understand, solve, and continuously monitor an important clinical problem whose existence was evident only after it was measured. PMID:10872258

  8. Analisi dell'Interazione Verbale Nella Discussione Matematica: Un Approccio Vygotskiano (A Verbal Analysis of Interaction in Mathematics Discussion: The Vygotskiano Approach).

    ERIC Educational Resources Information Center

    Bussi, Maria G. Bartolini; Boni, Mara

    1995-01-01

    Presents a methodology for analyzing verbal interaction in mathematical discussion which is both a product and an instrument of a research project in grades one through eight. Analyzes an example of discussion from a first-grade classroom about point of view. (Author/MKR)

  9. Truncated abrin A chain expressed in Escherichia coli: A promising vaccine candidate

    PubMed Central

    Zhang, Tao; Kang, Lin; Gao, Shan; Yang, Hao; Xin, Wenwen; Wang, Junhong; Guo, Maowen; Wang, Jinglin

    2014-01-01

    Abrin toxin (AT) is a highly potent toxin, and is classified as one of the most important biological warfare and bioterrorism agents. There is currently no approved vaccine for AT. Therefore, the development of an effective vaccine is important in the prevention of intoxication by abrin. In this study, five vectors containing different gene of truncated abrin toxin A chain (tATA) fragments were constructed, and two of them (tATA11-126, tATA41-188) were successfully expressed as a soluble form in E.coli strain. Both of the two tATA retained most of their immunogenicity with either low or no toxic effects as determined by both in vitro and in vivo assays. They were used to immunize BALB/c mice three times at an interval of three weeks apart. As a result, the tATA1 can elicite 80% protective efficacy against i.p. challenge of 5 × LD50 of abrin, and the tATA4 provides a better protection, which can elicite 100% protective efficacy against intraperitoneal challenge of 40 × LD50 of abrin. The superior fragment (tATA41-188) should be considered as a promising vaccine candidate for further investigations. PMID:25483485

  10. TatBC-Independent TatA/Tat Substrate Interactions Contribute to Transport Efficiency

    PubMed Central

    Taubert, Johannes; Hou, Bo; Risselada, H. Jelger; Mehner, Denise; Lünsdorf, Heinrich; Grubmüller, Helmut; Brüser, Thomas

    2015-01-01

    The Tat system can transport folded, signal peptide-containing proteins (Tat substrates) across energized membranes of prokaryotes and plant plastids. A twin-arginine motif in the signal peptide of Tat substrates is recognized by TatC-containing complexes, and TatA permits the membrane passage. Often, as in the model Tat systems of Escherichia coli and plant plastids, a third component – TatB – is involved that resembles TatA but has a higher affinity to TatC. It is not known why most TatA dissociates from TatBC complexes in vivo and distributes more evenly in the membrane. Here we show a TatBC-independent substrate-binding to TatA from Escherichia coli, and we provide evidence that this binding enhances Tat transport. First hints came from in vivo cross-linking data, which could be confirmed by affinity co-purification of TatA with the natural Tat substrates HiPIP and NrfC. Two positions on the surface of HiPIP could be identified that are important for the TatA interaction and transport efficiency, indicating physiological relevance of the interaction. Distributed TatA thus may serve to accompany membrane-interacting Tat substrates to the few TatBC spots in the cells. PMID:25774531

  11. TFIIIB subunit locations on U6 gene promoter DNA mapped by site-specific protein-DNA photo-cross-linking.

    PubMed

    Kang, Jin Joo; Kang, Yoon Soon; Stumph, William E

    2016-05-01

    RNA polymerase III-transcribed U6 snRNA genes have gene-external promoters that contain TATA boxes. U6 TATA sequences are bound by TFIIIB that in Drosophila contains the three subunits TBP, Brf1, and Bdp1. The overall structure of TFIIIB is still not well understood. We have therefore studied the mode of TFIIIB binding to DNA by site-specific protein-DNA photo-cross-linking. The results indicate that a portion of Brf1 is sandwiched between Bdp1 and TBP upstream of the TATA box. Furthermore, Bdp1 traverses the DNA under the N-terminal stirrup of TBP to interact with the DNA (and very likely Brf1) downstream of the TATA sequence. PMID:27112515

  12. 75 FR 25281 - Center for Scientific Review; Amended Notice of Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-05-07

    ... Panel, May 19, 2010, 12 p.m. to May 19, 2010, 5 p.m., Tata Communications, 2355 Dulles Corner Boulevard, 7th Floor, Herndon, VA 20171 which was published in the Federal Register on April 26, 2010, 75...

  13. Army Strong, Superintendent Savvy

    ERIC Educational Resources Information Center

    Mellon, Ericka

    2011-01-01

    Brigadier General Anthony "Tony" Tata of the U.S. Army had one of those "ah-ha" moments in April 2006 when, on the eve of an operation he was heading in Afghanistan, an Al Qaeda rocket shattered a nearby school. The attack killed a teacher and seven students and wounded dozens more. The rocket incident eventually nudged Tata toward a new mission:…

  14. Structural model for the protein-translocating element of the twin-arginine transport system

    PubMed Central

    Rodriguez, Fernanda; Rouse, Sarah L.; Tait, Claudia E.; Harmer, Jeffrey; De Riso, Antonio; Timmel, Christiane R.; Sansom, Mark S. P.; Berks, Ben C.; Schnell, Jason R.

    2013-01-01

    The twin-arginine translocase (Tat) carries out the remarkable process of translocating fully folded proteins across the cytoplasmic membrane of prokaryotes and the thylakoid membrane of plant chloroplasts. Tat is required for bacterial pathogenesis and for photosynthesis in plants. TatA, the protein-translocating element of the Tat system, is a small transmembrane protein that assembles into ring-like oligomers of variable size. We have determined a structural model of the Escherichia coli TatA complex in detergent solution by NMR. TatA assembly is mediated entirely by the transmembrane helix. The amphipathic helix extends outwards from the ring of transmembrane helices, permitting assembly of complexes with variable subunit numbers. Transmembrane residue Gln8 points inward, resulting in a short hydrophobic pore in the center of the complex. Simulations of the TatA complex in lipid bilayers indicate that the short transmembrane domain distorts the membrane. This finding suggests that TatA facilitates protein transport by sensitizing the membrane to transient rupture. PMID:23471988

  15. Protein translocation without specific quality control in a computational model of the Tat system

    NASA Astrophysics Data System (ADS)

    Nayak, Chitra R.; Brown, Aidan I.; Rutenberg, Andrew D.

    2014-10-01

    The twin-arginine translocation (Tat) system transports folded proteins of various sizes across both bacterial and plant thylakoid membranes. The membrane-associated TatA protein is an essential component of the Tat translocon, and a broad distribution of different sized TatA-clusters is observed in bacterial membranes. We assume that the size dynamics of TatA clusters are affected by substrate binding, unbinding, and translocation to associated TatBC clusters, where clusters with bound translocation substrates favour growth and those without associated substrates favour shrinkage. With a stochastic model of substrate binding and cluster dynamics, we numerically determine the TatA cluster size distribution. We include a proportion of targeted but non-translocatable (NT) substrates, with the simplifying hypothesis that the substrate translocatability does not directly affect cluster dynamical rate constants or substrate binding or unbinding rates. This amounts to a translocation model without specific quality control. Nevertheless, NT substrates will remain associated with TatA clusters until unbound and so will affect cluster sizes and translocation rates. We find that the number of larger TatA clusters depends on the NT fraction f. The translocation rate can be optimized by tuning the rate of spontaneous substrate unbinding, {{\\Gamma }_{U}}. We present an analytically solvable three-state model of substrate translocation without cluster size dynamics that follows our computed translocation rates, and that is consistent with in vitro Tat-translocation data in the presence of NT substrates.

  16. La semantica dei colori: Aspetti teorici e analisi dei cromonimi in italiano e neerlandese (Semantics of Colors: Theoretical Aspects and Analysis of Names of Colors in Italian and Dutch).

    ERIC Educational Resources Information Center

    Ross, Delores

    1989-01-01

    Presents a review of the literature dealing with the theory of the naming of colors. A comparison is made between the names of colors in Italian and Dutch, discussing the differences between languages in terms of the influence of the sociocultural context. (61 references) (CFM)

  17. Veicolarita e linguaggio scientifico--analisi del primo "Progetto italiano per studenti universitari somali" (Languages for Special Purposes and Scientific Usage--An Analysis of the First "Italian Project for Somali University Students").

    ERIC Educational Resources Information Center

    Amato, Antonio

    1979-01-01

    The development of an intensive Italian course for science students attending Somalia's National University is described. The historical background for this project, sponsored by the Italian Government and staffed by Italian teachers, is outlined. Course objectives, methods, and organization are illustrated by samples of instructional materials,…

  18. Presupposti teorici per un progetto di insegnamento della traduzione dalla lingua straniera basato sull'analisi testuale (Theoretical Presuppositions for a Project to Teach Translation from a Foreign Language Based on Textual Analysis).

    ERIC Educational Resources Information Center

    Horrakh, Livio

    1987-01-01

    Discusses an approach to translation based on textual linguistics. The student/translator first looks at the foreign language text as a whole, then analyzes its parts, and finally arrives at a new synthesis (the translation) that is comparable to the original text. (CFM)

  19. Primera Reunion de la Comision Nacional de Analisis y Evaluacion del Sistema Educativo: Informe Final (The First Meeting of the National Committee for Analysis and Evaluation of the Educational System: Final Report).

    ERIC Educational Resources Information Center

    Ministerio de Cultura y Educacion, Buenos Aires (Argentina). Centro National de Documentacion e Informacion Educativa.

    This document contains the legislation creating the National Committee for Analysis and Evaluation of the Educational System and the final report of that committee's first meeting. The report deals with each level from elementary to higher education. For each level it describes and considers curriculum, school buildings, human resources, current…

  20. La mejora de la educacion infantil desde el analisis del pensamiento practico de sus educadores. [The Improvement of Early Childhood Education from an Analysis of the Practical Thinking of Early Childhood Educators.

    ERIC Educational Resources Information Center

    Argos, Javier

    2000-01-01

    Discusses proposals for the innovation and development of early childhood education practice, based on findings from case studies on the practical knowledge of four experienced female early childhood educators. Argues that improving early childhood education should be based on its reasons and purposes rather than content or method. (JPB)

  1. The different positioning of the proximal sequence element in the Xenopus RNA polymerase II and III snRNA promoters is a key determinant which confers RNA polymerase III specificity.

    PubMed Central

    Lescure, A; Carbon, P; Krol, A

    1991-01-01

    We and others have previously described the TATA motif as a major determinant for Pol III specificity of the U6 promoter. Surprisingly, however, the data documented here show that the sole introduction of a TATA sequence into a U1 Pol II snRNA gene is not sufficient to confer Pol III transcription. Rather, this promoter element can mediate optimal Pol III transcription only if the PSE, the second promoter element, is shifted 4 bp upstream of the position it occupies in Pol II snRNA genes. As a result, the PSE-TATA-start site spacing introduced into the U1 Pol II gene is identical to that of the U6 gene and is strictly required to produce properly initiated Pol III transcripts. Thus, Pol II and Pol III PSEs, although similar in sequence, are not positionally equivalent. Competitive experiments raise the possibility that vertebrate U6 genes contain other, as yet unidentified, promoter elements. Images PMID:2011518

  2. Phenotypic consequences of promoter-mediated transcriptional noise: Experiment and computational modeling

    NASA Astrophysics Data System (ADS)

    Balazsi, Gabor; Blake, William; Kohanski, Michael; Murphy, Kevin; Collins, James

    2007-03-01

    A more complete understanding of the causes and effects of gene expression noise is needed to elucidate whether the resulting phenotypes are disadvantageous or confer some adaptive advantage. We introduce mutations within the promoter region of an engineered, repressible Saccharomyces cerevisiae GAL1 promoter to show that the level of gene expression noise is affected by the sequence of the TATA box. Through computer simulations, we identify transcription scaffold stability as a critical noise-mediating factor. We demonstrate that TATA box-dependent, increased gene expression noise can be beneficial after an acute change in environmental conditions. First, we illustrate computationally how a stable transcription scaffold can enable increased cell-cell variability at steady state. Second, we experimentally verify our computational prediction that the increased gene expression noise enabled by TATA-containing promoters confers a clear benefit in the face of an acute environmental stress.

  3. The downstream core promoter element, DPE, is conserved from Drosophila to humans and is recognized by TAFII60 of Drosophila

    PubMed Central

    Burke, Thomas W.; Kadonaga, James T.

    1997-01-01

    We analyzed the function of the downstream promoter element (DPE), a distinct 7-nucleotide core promoter element that is ∼30 nucleotides downstream of the transcription start site of many TATA-box-deficient (TATA-less) promoters in Drosophila. There is a strict requirement for spacing between the Inr and DPE motifs, as an increase or decrease of 3 nucleotides in the distance between the Inr and DPE causes a seven- to eightfold reduction in transcription as well as a significant reduction in the binding of purified TFIID. These results suggest a specific and somewhat rigid interaction of TFIID with the Inr and DPE sequences. Photo-cross-linking analysis of purified TFIID with a TATA-less DPE-containing promoter revealed specific cross-linking of dTAFII60 and dTAFII40 to the DPE, with a higher efficiency of cross-linking to dTAFII60 than to dTAFII40. These data, combined with the previously well-characterized interactions between the two TAFs and their homology to histones H4 and H3, suggest that a dTAFII60–dTAFII40 heterotetramer binds to the DPE. Human and Drosophila transcription factors exhibit essentially the same requirements for DPE sequence and for Inr–DPE spacing. In addition, the TATA-less promoter of the human interferon regulatory factor-1 (IRF-1) gene contains a DPE that is important for transcriptional activity both in vitro and in cultured cells. Hence, these studies provide evidence for a direct role of TAFs in basal transcription of TATA-less DPE-containing genes and collectively indicate that the DPE is, in many respects, a downstream counterpart to the TATA box that is present in Drosophila to humans. PMID:9367984

  4. A genetic analysis of Adhl regulation. Progress report, June 1991--May 1993

    SciTech Connect

    Freeling, M.

    1992-12-01

    Several separate but related studies are reported on the mechanism of alcohol dehydrogenase (Adh-1) are reported. A study of a deletion mutation in the TATA box region which resulted in an increase from 6--60% of wildtype Adh-1 expression in the revertant has led to a focus on trans-acting protein factors that bind the TATA box. Analysis of another revertant has led to study of cis-acting sequences in Adh-1 expression. Screening efforts aimed at defining different mutants affecting Adh-1 expression are reported.

  5. A genetic analysis of Adhl regulation

    SciTech Connect

    Freeling, M.

    1992-01-01

    Several separate but related studies are reported on the mechanism of alcohol dehydrogenase (Adh-1) are reported. A study of a deletion mutation in the TATA box region which resulted in an increase from 6--60% of wildtype Adh-1 expression in the revertant has led to a focus on trans-acting protein factors that bind the TATA box. Analysis of another revertant has led to study of cis-acting sequences in Adh-1 expression. Screening efforts aimed at defining different mutants affecting Adh-1 expression are reported.

  6. Search for TeV gamma rays from Geninga. [2CG 195+04

    SciTech Connect

    Fegan, D.J. ); Akerlof, C.W. ); Breslin, A.C. ); Cawley, M.F. ); Chantell, M. ); Fennell, S. Whipple Observatory, Harvard-Smithsonian CfA, Amado, Arizona ); Gaidos, J.A.; Hagan, J. ); Hillas, A.M. ); Kerrick, A.D.; Lamb, R.C. ); Lawrence, M.A. ); Lewis, D.A. (Physics Department, Io

    1993-07-05

    Recently the Tata group have reported (1) the detection of TeV [gamma]-rays from Geminga. Results of a search by the Whipple observatory Collaboration are presented here, based on observations made during 1989--90 and 1990--91, using the 10 m high resolution imaging cerenkov camera.

  7. 76 FR 77775 - Certain Hot-Rolled Carbon Steel Flat Products From India: Amended Final Results of Countervailing...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-12-14

    ..., 75 FR 43448 (July 26, 2010) (Final Results), and accompanying Issues and Decision Memorandum. Tata... International Trade Administration Certain Hot-Rolled Carbon Steel Flat Products From India: Amended Final... administrative review of the countervailing duty order on certain ] hot-rolled carbon steel flat products...

  8. 75 FR 43488 - Certain Hot-Rolled Carbon Steel Flat Products From India: Final Results of Countervailing Duty...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-07-26

    ... Hot-Rolled Carbon Steel Flat Products from India, 66 FR 60198 (December 3, 2001). On February 2, 2009...; 75 FR 1495 (January 11, 2010) (Preliminary Results). We preliminarily found that Tata Steel Limited... Countervailing Duty Administrative Reviews and Requests for Revocation in Part, 74 FR 5821 (February 2,...

  9. Caudal, a key developmental regulator, is a DPE-specific transcriptional factor

    PubMed Central

    Juven-Gershon, Tamar; Hsu, Jer-Yuan; Kadonaga, James T.

    2008-01-01

    The regulation of gene transcription is critical for the proper development and growth of an organism. The transcription of protein-coding genes initiates at the RNA polymerase II core promoter, which is a diverse module that can be controlled by many different elements such as the TATA box and downstream core promoter element (DPE). To understand the basis for core promoter diversity, we explored potential biological functions of the DPE. We found that nearly all of the Drosophila homeotic (Hox) gene promoters, which lack TATA-box elements, contain functionally important DPE motifs that are conserved from Drosophila melanogaster to Drosophila virilis. We then discovered that Caudal, a sequence-specific transcription factor and key regulator of the Hox gene network, activates transcription with a distinct preference for the DPE relative to the TATA box. The specificity of Caudal activation for the DPE is particularly striking when a BREu core promoter motif is associated with the TATA box. These findings show that Caudal is a DPE-specific activator and exemplify how core promoter diversity can be used to establish complex regulatory networks. PMID:18923080

  10. Drosophila TRF2 is a preferential core promoter regulator.

    PubMed

    Kedmi, Adi; Zehavi, Yonathan; Glick, Yair; Orenstein, Yaron; Ideses, Diana; Wachtel, Chaim; Doniger, Tirza; Waldman Ben-Asher, Hiba; Muster, Nemone; Thompson, James; Anderson, Scott; Avrahami, Dorit; Yates, John R; Shamir, Ron; Gerber, Doron; Juven-Gershon, Tamar

    2014-10-01

    Transcription of protein-coding genes is highly dependent on the RNA polymerase II core promoter. Core promoters, generally defined as the regions that direct transcription initiation, consist of functional core promoter motifs (such as the TATA-box, initiator [Inr], and downstream core promoter element [DPE]) that confer specific properties to the core promoter. The known basal transcription factors that support TATA-dependent transcription are insufficient for in vitro transcription of DPE-dependent promoters. In search of a transcription factor that supports DPE-dependent transcription, we used a biochemical complementation approach and identified the Drosophila TBP (TATA-box-binding protein)-related factor 2 (TRF2) as an enriched factor in the fractions that support DPE-dependent transcription. We demonstrate that the short TRF2 isoform preferentially activates DPE-dependent promoters. DNA microarray analysis reveals the enrichment of DPE promoters among short TRF2 up-regulated genes. Using primer extension analysis and reporter assays, we show the importance of the DPE in transcriptional regulation of TRF2 target genes. It was previously shown that, unlike TBP, TRF2 fails to bind DNA containing TATA-boxes. Using microfluidic affinity analysis, we discovered that short TRF2-bound DNA oligos are enriched for Inr and DPE motifs. Taken together, our findings highlight the role of short TRF2 as a preferential core promoter regulator. PMID:25223897

  11. Rapid molecular diagnosis of the Gilbert's syndrome-associated exon 1 mutation within the UGT1A1 gene.

    PubMed

    Hsieh, T-Y; Shiu, T-Y; Chu, N-F; Chao, T-Y; Chu, H-C; Chang, W-K; Chao, Y-C; Huang, H-H

    2014-01-01

    Gilbert's syndrome is suspected in patients with unconjugated hyperbilirubinemia caused by decreased activity of the UDP-glucuronosyltransferase 1A1 (UGT1A1) gene in the absence of abnormal liver function and hemolysis. The major genetic variants underlying Gilbert's syndrome are TATA-box repeats of the promoter region and exon 1 G211A of the coding region, particularly in Asians. The efficacy of DNA melting curve analysis, however, has not been established for the G211A mutation. For rapid and accurate molecular diagnosis of Gilbert's syndrome, DNA melting curve analysis was evaluated for its genotyping capability not only for TATA-box repeats of the UGT1A1 promoter, but also for G211A of UGT1A1 exon 1. TA repeats within the TATA-box sequence and the exon 1 G211A mutation of the UGT1A1 gene were analyzed by DNA melting curve analysis. To evaluate the assay reliability, direct sequencing or polyacrylamide gel electrophoresis was used as a comparative method. All homozygous and heterozygous polymorphisms of A(TA)7TAA within the TATA-box allele and of exon 1 G211A mutants of the UGT1A1 gene were successfully identified with DNA melting curve analysis. DNA melting curve analysis is, therefore, an effective molecular method for the rapid diagnosis of Gilbert's syndrome, as it detects not only TATA-box polymorphisms but also the exon 1 G211A mutation located within the UGT1A1 gene. PMID:24615032

  12. In simple synthetic promoters YY1-induced DNA bending is important in transcription activation and repression.

    PubMed Central

    Kim, J; Shapiro, D J

    1996-01-01

    Depending on promoter context, YY1 can activate or repress transcription, or provide a site for transcription initiation. To investigate whether the ability of YY1 to induce DNA bending influenced its ability to activate and repress transcription, simple synthetic promoters were constructed in which the YY1 binding site was inserted between the TATA box and either the NF1 or AP1 recognition sequences. In transient transfections of COS cells, the NF1YY1TATA and NF1RYY1TATA promoters exhibited a dramatic 15-20-fold increase in correctly initiated transcription. These promoters exhibited even larger 60-80-fold increases in transcription in HeLa cells. Neither multiple copies of the YY1 binding site alone, nor placement of a YY1 site upstream of the NF1 site activated transcription. Deletion of 4 bp between the NF1 and YY1 sites, which changes the phase of the DNA bends, abolished the 16-fold activation of transcription by NF1YY1TATA. Insertion of the YY1 site between the AP1 site and the TATA box decreased transcription approximately 3-fold. Replacing the YY1 binding site with an intrinsic DNA bending sequence mimicked this transcription repression. Sequences of similar length which do not bend DNA fail to repress AP1-mediated transcription. Gel mobility shift assays were used to show that binding of YY1 to its recognition sequence did not repress binding of AP1 to its recognition sequences. Our data indicate that YY1-induced DNA bending may activate and repress transcription by changing the spatial relationships between transcription activators and components of the basal transcription apparatus. PMID:8932392

  13. Elaborazione dei dati sperimentali

    NASA Astrophysics Data System (ADS)

    Dapor, M.; Ropele, M.

    L'analisi statistica dei dati sperimentali, la loro elaborazione ed una corretta stima degli errori sono conoscenze necessarie agli studenti di fisica, biologia, chimica, ingegneria e dei corsi di specializzazione tecnico-scientifici in cui a di laboratorio. Chi si occupa di problemi tecnici e di misure, per studio o per lavoro, deve possedere gli strumenti matematici di calcolo e di analisi necessari ad una corretta interpretazione dei dati sperimentali. Il testo fornisce in modo sintetico, chiaro ed esaustivo, tutte le nozioni e le conoscenze utili allo scopo.

  14. Homogeneity and Entropy

    NASA Astrophysics Data System (ADS)

    Tignanelli, H. L.; Vazquez, R. A.; Mostaccio, C.; Gordillo, S.; Plastino, A.

    1990-11-01

    RESUMEN. Presentamos una metodologia de analisis de la homogeneidad a partir de la Teoria de la Informaci6n, aplicable a muestras de datos observacionales. ABSTRACT:Standard concepts that underlie Information Theory are employed in order design a methodology that enables one to analyze the homogeneity of a given data sample. Key : DATA ANALYSIS

  15. Biomedical applications in EELA.

    PubMed

    Cardenas, Miguel; Hernández, Vicente; Mayo, Rafael; Blanquer, Ignacio; Perez-Griffo, Javier; Isea, Raul; Nuñez, Luis; Mora, Henry Ricardo; Fernández, Manuel

    2006-01-01

    The current demand for Grid Infrastructures to bring collabarating groups between Latina America and Europe has created the EELA proyect. This e-infrastructure is used by Biomedical groups in Latina America and Europe for the studies of ocnological analisis, neglected diseases, sequence alignments and computation plygonetics. PMID:16823158

  16. Dunkerque-Falklands: Due eventi storico-politici attraverso l'analisi linguistica dei discorsi di Winston Churchill e Margaret Thatcher (Dunkirk-Falklands: Two Historical-Political Events through the Linguistic Analysis of the Speeches of Winston Churchill and Margaret Thatcher).

    ERIC Educational Resources Information Center

    Arcaini, Giovanna

    1988-01-01

    The political speech is a unique kind of document that reflects the socio-historic climate of its time. Two historical events (Dunkirk and the Falkland Islands Crisis) and a principal protagonist from each are discussed, and the speeches of these two individuals are analyzed in order to find similarities and differences, and to find their basic…

  17. Affinity and competition for TBP are molecular determinants of gene expression noise

    PubMed Central

    Ravarani, Charles N. J.; Chalancon, Guilhem; Breker, Michal; de Groot, Natalia Sanchez; Babu, M. Madan

    2016-01-01

    Cell-to-cell variation in gene expression levels (noise) generates phenotypic diversity and is an important phenomenon in evolution, development and disease. TATA-box binding protein (TBP) is an essential factor that is required at virtually every eukaryotic promoter to initiate transcription. While the presence of a TATA-box motif in the promoter has been strongly linked with noise, the molecular mechanism driving this relationship is less well understood. Through an integrated analysis of multiple large-scale data sets, computer simulation and experimental validation in yeast, we provide molecular insights into how noise arises as an emergent property of variable binding affinity of TBP for different promoter sequences, competition between interaction partners to bind the same surface on TBP (to either promote or disrupt transcription initiation) and variable residence times of TBP complexes at a promoter. These determinants may be fine-tuned under different conditions and during evolution to modulate eukaryotic gene expression noise. PMID:26832815

  18. MEF2 Is an In Vivo Immune-Metabolic Switch

    PubMed Central

    Clark, Rebecca I.; Tan, Sharon W.S.; Péan, Claire B.; Roostalu, Urmas; Vivancos, Valérie; Bronda, Kévin; Pilátová, Martina; Fu, Jingqi; Walker, David W.; Berdeaux, Rebecca; Geissmann, Frédéric; Dionne, Marc S.

    2013-01-01

    Summary Infections disturb metabolic homeostasis in many contexts, but the underlying connections are not completely understood. To address this, we use paired genetic and computational screens in Drosophila to identify transcriptional regulators of immunity and pathology and their associated target genes and physiologies. We show that Mef2 is required in the fat body for anabolic function and the immune response. Using genetic and biochemical approaches, we find that MEF2 is phosphorylated at a conserved site in healthy flies and promotes expression of lipogenic and glycogenic enzymes. Upon infection, this phosphorylation is lost, and the activity of MEF2 changes—MEF2 now associates with the TATA binding protein to bind a distinct TATA box sequence and promote antimicrobial peptide expression. The loss of phosphorylated MEF2 contributes to loss of anabolic enzyme expression in Gram-negative bacterial infection. MEF2 is thus a critical transcriptional switch in the adult fat body between metabolism and immunity. PMID:24075010

  19. Archaeal promoter architecture and mechanism of gene activation.

    PubMed

    Peng, Nan; Ao, Xiang; Liang, Yun Xiang; She, Qunxin

    2011-01-01

    Sulfolobus solfataricus and Sulfolobus islandicus contain several genes exhibiting D-arabinose-inducible expression and these systems are ideal for studying mechanisms of archaeal gene expression. At sequence level, only two highly conserved cis elements are present on the promoters: a regulatory element named ara box directing arabinose-inducible expression and the basal promoter element TATA, serving as the binding site for the TATA-binding protein. Strikingly, these promoters possess a modular structure that allows an essentially inactive basal promoter to be strongly activated. The invoked mechanisms include TFB (transcription factor B) recruitment by the ara-box-binding factor to activate gene expression and modulation of TFB recruitment efficiency to yield differential gene expression. PMID:21265754

  20. MEF2 is an in vivo immune-metabolic switch.

    PubMed

    Clark, Rebecca I; Tan, Sharon W S; Péan, Claire B; Roostalu, Urmas; Vivancos, Valérie; Bronda, Kévin; Pilátová, Martina; Fu, Jingqi; Walker, David W; Berdeaux, Rebecca; Geissmann, Frédéric; Dionne, Marc S

    2013-10-10

    Infections disturb metabolic homeostasis in many contexts, but the underlying connections are not completely understood. To address this, we use paired genetic and computational screens in Drosophila to identify transcriptional regulators of immunity and pathology and their associated target genes and physiologies. We show that Mef2 is required in the fat body for anabolic function and the immune response. Using genetic and biochemical approaches, we find that MEF2 is phosphorylated at a conserved site in healthy flies and promotes expression of lipogenic and glycogenic enzymes. Upon infection, this phosphorylation is lost, and the activity of MEF2 changes--MEF2 now associates with the TATA binding protein to bind a distinct TATA box sequence and promote antimicrobial peptide expression. The loss of phosphorylated MEF2 contributes to loss of anabolic enzyme expression in Gram-negative bacterial infection. MEF2 is thus a critical transcriptional switch in the adult fat body between metabolism and immunity. PMID:24075010

  1. Finding human promoter groups based on DNA physical properties

    NASA Astrophysics Data System (ADS)

    Zeng, Jia; Cao, Xiao-Qin; Zhao, Hongya; Yan, Hong

    2009-10-01

    DNA rigidity is an important physical property originating from the DNA three-dimensional structure. Although the general DNA rigidity patterns in human promoters have been investigated, their distinct roles in transcription are largely unknown. In this paper, we discover four highly distinct human promoter groups based on similarity of their rigidity profiles. First, we find that all promoter groups conserve relatively rigid DNAs at the canonical TATA box [a consensus TATA(A/T)A(A/T) sequence] position, which are important physical signals in binding transcription factors. Second, we find that the genes activated by each group of promoters share significant biological functions based on their gene ontology annotations. Finally, we find that these human promoter groups correlate with the tissue-specific gene expression.

  2. Identifying Dyads and their conservation in Drosphila.

    NASA Astrophysics Data System (ADS)

    Dan, Debasis

    2007-03-01

    Core promoter regions in Drosophila are enriched with binding sites like TATA, Inr, DPE, MTE, etc. They have very strict spacing between each other in promoters where they occur together. For example, in Drosophila melanogaster TATA-Inr has a spacing of 25-30 bp. Our aim in this work is to identify all such pair of motifs having strict positional constraint in the core promoters of all Drosophila species. We discover how these motifs and the spacing between them evolve within Drosophila species. For this we analyze 700 bp upstream and 300 bp downstream of TSS in D. melanogaster and the corresponding orthologous region in other Drosophila species. For each species, this 1000 bp region is searched for statistically over-represented compound words of the form W1NLW2, where L is the spacing between words W1 and W2. These compound words are systematically clustered for further analysis.

  3. GAGA mediates the enhancer blocking activity of the eve promoter in the Drosophila embryo

    PubMed Central

    Ohtsuki, Sumio; Levine, Michael

    1998-01-01

    Insulator DNAs and promoter competition regulate enhancer–promoter interactions within complex genetic loci. A transgenic embryo assay was used to obtain evidence that the Drosophila eve promoter possesses an insulator activity that can be uncoupled from the core elements that mediate competition. The eve promoter contains an optimal TATA element and a GAGA sequence. The analysis of various chimeric promoters provides evidence that TATA is essential for promoter competition, whereas GAGA mediates enhancer blocking. The Trithorax-like (Trl) protein interacts with GAGA, and mutations in trl attenuate eve promoter insulator activity. We suggest that Trl–GAGA increases the stability of enhancer–promoter interactions by creating an open chromatin configuration at the core promoter. PMID:9808619

  4. In vitro characterization of the fibroin gene promoter by the use of single-base substitution mutants.

    PubMed Central

    Hirose, S; Takeuchi, K; Suzuki, Y

    1982-01-01

    A highly efficient method for segment-directed mutagenesis has been developed. The method relies on the deamination by sodium nitrite of the bases in the separated strands of a small DNA restriction fragment. The mutagen-treated strands produce transition mutations by the following sequence: (i) hybridization with the complementary strand of the wild-type DNA that had been cloned into a phage fl vector, (ii) repair synthesis in vitro, and (iii) transfection of Escherichia coli. Using this method, we have isolated 14 single-point mutants within a 31-base-pair stretch of the fibroin gene (from the T-A-T-A box at the nucleotide position -30 to the cap site at +1). In vitro transcription experiments with the HeLa cell or the silk gland cell extract show that single-base transitions at the T-A-T-A box (T to C at -30, A to G at -29, and T to C at -28) and at the -20 region (G to A at -21, T to C at -20, and A to G at -17) result in decreased promoter activities, whereas those at the cap site and the -10 regions have no effect. The initiation site of transcription is the same for five "down" (reduced activity) mutants (T to C at -30, T to C at -28, G to A at -21, T to C at -20, and A to G at -17), the cap site mutant (A to G at +1), and the wild-type genes--position +1. However, the A-to-G transition at -29 (the second base of the T-A-T-A box) induces an additional transcription start from position +4. Functions of the T-A-T-A box and the -20 regions are discussed. Images PMID:6961405

  5. Efficient chimeric promoters derived from full-length and sub-genomic transcript promoters of Figwort mosaic virus (FMV).

    PubMed

    Ranjan, Rajiv; Patro, Sunita; Kumari, Sangeeta; Kumar, Deepak; Dey, Nrisingha; Maiti, Indu B

    2011-03-10

    Addition of multiple repeats of the FS3 upstream activation sequence (FS3-UAS, -270 to -60) intra-molecularly to the TATA containing core-domain of the FS3 (-151 to +31) promoter resulted in 2-3-folds enhanced promoter activity. The chimeric promoter, FS3-UAS-3X with maximum activity, showed 3.31 times stronger activity in root vascular tissue compared to FS3 promoter and could be used efficiently in translational research. PMID:21262279

  6. Structure and expression of a pea nuclear gene encoding a chlorophyll a/b-binding polypeptide

    SciTech Connect

    Cashmore, A.R.

    1984-05-01

    A nuclear gene AB80 has been isolated from a phage lambda Charon 4 library of pea DNA. The sequence of the gene has been determined and it has been shown to contain an interrupted reading frame of 269 amino acids, corresponding to a precursor to a constituent polypeptide of the light-harvesting chlorophyll a/b-protein complex. Primer extension and S1 nuclease studies defined a cap site for AB80. The first methionine codon 3' from this site is 69 nucleotides away and is the initiating codon of the open reading frame. A TATA sequence occurs 31 nucleotides 5' from the cap site. A second TATA sequence is found 7 nucleotides on the 5' side of the initiating methionine codon and the sequences surrounding this TATA sequence are strikingly similar to those surrounding the first TATA sequence. The mature polypeptide encoded by AB80 differs by 5 amino acids from the polypeptide corresponding to a previously characterized cDNA sequence pAB96. This result is indicative of heterogeneity within the constituent polypeptides of the light-harvesting chlorophyll a/b-protein complex. The sequence Arg-Lys-Ser-Ala-Thr-Thr-Lys-Lys occurs at, or near, the NH/sub 2/-terminus of the mature polypeptide encoded by AB80. This basic peptide is of interest because of its apparent involvement in changes in excitation-energy distribution in chloroplast membranes. Some general similarities, but no extensive sequence homology, is found on comparing the transit sequence for the precursor to the chlorophyll a/b-binding polypeptide with the transit sequences previously determined for the precursors to the small subunit of ribulose-1,5-bisphosphate carboxylase. 40 references, 3 figures.

  7. Basal core promoters control the equilibrium between negative cofactor 2 and preinitiation complexes in human cells

    PubMed Central

    2010-01-01

    Background The general transcription factor TFIIB and its antagonist negative cofactor 2 (NC2) are hallmarks of RNA polymerase II (RNAPII) transcription. Both factors bind TATA box-binding protein (TBP) at promoters in a mutually exclusive manner. Dissociation of NC2 is thought to be followed by TFIIB association and subsequent preinitiation complex formation. TFIIB dissociates upon RNAPII promoter clearance, thereby providing a specific measure for steady-state preinitiation complex levels. As yet, genome-scale promoter mapping of human TFIIB has not been reported. It thus remains elusive how human core promoters contribute to preinitiation complex formation in vivo. Results We compare target genes of TFIIB and NC2 in human B cells and analyze associated core promoter architectures. TFIIB occupancy is positively correlated with gene expression, with the vast majority of promoters being GC-rich and lacking defined core promoter elements. TATA elements, but not the previously in vitro defined TFIIB recognition elements, are enriched in some 4 to 5% of the genes. NC2 binds to a highly related target gene set. Nonetheless, subpopulations show strong variations in factor ratios: whereas high TFIIB/NC2 ratios select for promoters with focused start sites and conserved core elements, high NC2/TFIIB ratios correlate to multiple start-site promoters lacking defined core elements. Conclusions TFIIB and NC2 are global players that occupy active genes. Preinitiation complex formation is independent of core elements at the majority of genes. TATA and TATA-like elements dictate TFIIB occupancy at a subset of genes. Biochemical data support a model in which preinitiation complex but not TBP-NC2 complex formation is regulated. PMID:20230619

  8. Bangalore looks to new interdisciplinary science centre

    NASA Astrophysics Data System (ADS)

    Ramachandran, Ramaseshan

    2008-09-01

    A new centre to boost interdisciplinary research in India is being established in Bangalore - India's IT and software capital. The International Centre for Theoretical Sciences (ICTS) will be led by Spenta Wadia, a theoretical physicist from the Tata Institute of Fundamental Research (TIFR) in Mumbai, which is setting up the new centre. He expects construction of the ICTS, the first of its kind in India, to start by November 2009.

  9. No detection of L-band radio emission from SN 2007gr by GMRT

    NASA Astrophysics Data System (ADS)

    Ray, Alak K.

    2007-08-01

    Sayan Chakraborti (Tata Institute of Fundamental Research, Mumbai, (TIFR)), Poonam Chandra (Univ Virginia and National Radio Astronomical Observatory, Charlottesville), Nirupam Roy (National Centre for Radio Astrophysics (NCRA-TIFR), Pune, and Alak Ray (TIFR) report on the Target of Opportunity observation of SN 2007gr on 2007 Aug 24 by the Giant Metrewave Radio Telescope (GMRT) in the L-band between UT 0200 to 0400.

  10. A Tat ménage à trois--The role of Bacillus subtilis TatAc in twin-arginine protein translocation.

    PubMed

    Goosens, Vivianne J; De-San-Eustaquio-Campillo, Alba; Carballido-López, Rut; van Dijl, Jan Maarten

    2015-10-01

    The twin-arginine translocation system (Tat) is a protein transport system that moves fully folded and cofactor-containing proteins across membranes of bacteria, archaea and thylakoids. The minimal Tat pathway is composed of two subunits, TatA and TatC. In some organisms TatA has been duplicated and evolved to form a third specialized subunit, TatB. The Bacillus subtilis genome encodes two TatC subunits (TatCd and TatCy) and three TatA subunits (TatAd, TatAy and TatAc). These subunits combine to form two parallel minimal pathways, TatAy-TatCy and TatAd-TatCd. The purpose and role of the third TatA component, TatAc, has remained ambiguous. In this study we examined the translocation of two natively expressed TatAy-TatCy-dependent substrates, EfeB and QcrA, in various Tat-deficient genetic backgrounds. More specifically, we examined the ability of different mutated TatAy subunits to complement for the absence of wild-type TatAy. We further detailed a graded growth phenotype associated with the functional translocation of EfeB. We found that in various instances where specific amino acid substitutions were made in TatAy, a definite TatAc-associated growth phenotype occurred in genetic backgrounds lacking TatAc. Altogether, our findings show that TatAy and TatAc interact and that this TatAy-TatAc interaction, although not essential, supports the translocation of the Tat substrate EfeB when TatAy function is compromised. This implies that the third TatA-like protein in B. subtilis could represent an intermediate evolutionary step in TatA-TatB specialization. PMID:26239117

  11. Analyses of alpha/beta-type gliadin genes from diploid and hexaploid wheats.

    PubMed

    Reeves, C D; Okita, T W

    1987-01-01

    The alpha/beta-gliadin genes isolated from both hexaploid wheat (cv. Yamhill) and the diploid A genome progenitor Triticum urartu had remarkably similar sequences and differ by only a few point mutations. Primer extension analysis indicated that the transcriptional start points for individual genes in the family cluster within a few nucleotides. Comparison of the promoter region of several alpha/beta-gliadin and B-hordein genes reveals two conserved regions at about -130 and -250 bp. DNA from the hexaploid cultivars, Cheyenne and Chinese Spring, and the diploid progenitors T. urartu and Aegilops squarrosa was analysed by Southern blotting. Restriction fragment lengths of the alpha/beta-gliadin genes varied only slightly between the various wheats, although the overall copy number varied significantly. A region between approx. -1700 and -700 bp upstream from the TATA box was highly repeated in all three wheat genomes. For the hexaploid-derived gene, over 1700 bp of sequence upstream from the TATA box was determined, revealing an additional open reading frame between approx. -1550 and -1250 bp relative to the gliadin TATA box. Northern blot analysis indicated that RNA homologous to this repeated sequence family was present only in developing seed and accumulated to a maximum at late stages of maturation. PMID:3038689

  12. TBP binds the transcriptionally inactive TA5 sequence but the resulting complex is not efficiently recognised by TFIIB and TFIIA.

    PubMed Central

    Bernués, J; Carrera, P; Azorin, F

    1996-01-01

    The binding of TBP (TFIID) to the TATA box has been considered to direct promoter recognition and pre-initiation complex formation because it is the first event leading to basal transcription by RNA polymerase II. Here, we analyse the binding of yeast TBP to a consensus TATAAA box and two point mutations, TAAAAA (inactive) and TATATA (active). Despite the fact that the TAAAAA sequence does not support transcription in vitro, yeast TBP binds the three sequences showing, in this sense, only a limited sequence specificity. However, the TBP-TAAAAA complex cannot be recognised by other basal transcription factors, in particular by TFIIB. DNase I footprinting patterns of the TBP-TAAAAA complex are different from those observed in functional TBP-TATA box complexes, indicating that, most likely, it is a different spatial arrangement of the TBP-DNA complex that prevents formation of the TFIIB-TBP-TAAAAA complex, also seriously impairing entry of TFIIA to the complex. DNA deformability of the A/T-rich sequences appears to be an important determinant in the formation of a productive TBP-TATA complex. These results indicate that the transcriptional competence of A/T-rich sequences is determined not only by TBP binding, but also by the ability of other basal transcription factors to recognise the preformed TBP-DNA complexes. PMID:8760879

  13. Binding sites of HeLa cell nuclear proteins on the upstream region of adenovirus type 5 E1A gene.

    PubMed Central

    Yoshida, K; Narita, M; Fujinaga, K

    1989-01-01

    Twenty one binding sites of HeLa cell nuclear proteins were identified on the upstream region of adenovirus type 5 E1A gene using DNase I footprint assay. The proximal promoter region contained five binding sites that overlapped the cap site, TATA box, TATA-like sequence, CCAAT box, and -100 region relative to the E1A cap site(+1). The -190 region was a potential site for octamer-motif binding proteins, such as NFIII and OBP100. An upstream copy of the E1A enhancer element 1 was the site for a factor (E1A-F) with the binding specificity of XGGAYGT (X = A, C; Y = A, T). E1A-F factor also bound to three other sites, one of which coincided with the distal E1A enhancer element. The distal element also contained a potential site for ATF factor. The adenovirus minimal origin of DNA replication competed for DNA-protein complex formation on the CCAAT and TATA box region and the -190 region, suggesting that these regions interacted with a common or related factor. Images PMID:2532319

  14. DNase1 footprints suggest the involvement of at least three types of transcription factors in the regulation of alpha-Amy2/A by gibberellin.

    PubMed

    Willmott, R L; Rushton, P J; Hooley, R; Lazarus, C M

    1998-11-01

    To elucidate the mechanisms by which alpha-amylase genes are expressed in wild oat aleurone, two genes, alpha-Amy2/A and alpha-Amy2/D, were isolated. Both were shown to be positively regulated by gibberellin (GA) during germination and both contain the conserved cis-acting elements Box 2, GA-response element (TAACAGA) and TATCSATSS (where S is C or G). In addition, they possess a conserved initiator element (CATCA) that is present in both alpha-Amy2 and alpha-Amy1 genes, and also in a number of other plant TATA-containing and TATA-less promoters. DNase 1 footprint analysis showed the alpha-Amy2/A promoter to be a complex array of binding sites for a number of different classes of DNA-binding proteins. Our data suggest that the area around the initiator element (Inr) is bound by a large complex of general transcription factors, that the TATA box is bound by the TFIID complex, that Box 2 is bound by one or more WRKY proteins and that the GA-response element is bound by one or more MYBs. Two other elements containing the core sequence CCATGG/C are bound by nuclear protein and this sequence is the core of the Sph element. The regulation of alpha-Amy2 genes by GA therefore involves an interplay of at least three different types of transcription factor. PMID:9862499

  15. Redundant cooperative interactions for assembly of a human U6 transcription initiation complex.

    PubMed

    Ma, Beicong; Hernandez, Nouria

    2002-11-01

    The core human U6 promoter consists of a proximal sequence element (PSE) located upstream of a TATA box. The PSE is recognized by the snRNA-activating protein complex (SNAP(c)), which consists of five types of subunits, SNAP190, SNAP50, SNAP45, SNAP43, and SNAP19. The TATA box is recognized by TATA box binding protein (TBP). In addition, basal U6 transcription requires the SANT domain protein Bdp1 and the transcription factor IIB-related factor Brf2. SNAP(c) and mini-SNAP(c), which consists of just SNAP43, SNAP50, and the N-terminal third of SNAP190, bind cooperatively with TBP to the core U6 promoter. By generating complexes smaller than mini-SNAP(c), we have identified a 50-amino-acid region within SNAP190 that is (i) required for cooperative binding with TBP in the context of mini-SNAP(c) and (ii) sufficient for cooperative binding with TBP when fused to a heterologous DNA binding domain. We show that derivatives of mini-SNAP(c) lacking this region are active for transcription and that with such complexes, TBP can still be recruited to the U6 promoter through cooperative interactions with Brf2. Our results identify complexes smaller than mini-SNAP(c) that are transcriptionally active and show that there are at least two redundant mechanisms to stably recruit TBP to the U6 transcription initiation complex. PMID:12391172

  16. Redundant Cooperative Interactions for Assembly of a Human U6 Transcription Initiation Complex

    PubMed Central

    Ma, Beicong; Hernandez, Nouria

    2002-01-01

    The core human U6 promoter consists of a proximal sequence element (PSE) located upstream of a TATA box. The PSE is recognized by the snRNA-activating protein complex (SNAPc), which consists of five types of subunits, SNAP190, SNAP50, SNAP45, SNAP43, and SNAP19. The TATA box is recognized by TATA box binding protein (TBP). In addition, basal U6 transcription requires the SANT domain protein Bdp1 and the transcription factor IIB-related factor Brf2. SNAPc and mini-SNAPc, which consists of just SNAP43, SNAP50, and the N-terminal third of SNAP190, bind cooperatively with TBP to the core U6 promoter. By generating complexes smaller than mini-SNAPc, we have identified a 50-amino-acid region within SNAP190 that is (i) required for cooperative binding with TBP in the context of mini-SNAPc and (ii) sufficient for cooperative binding with TBP when fused to a heterologous DNA binding domain. We show that derivatives of mini-SNAPc lacking this region are active for transcription and that with such complexes, TBP can still be recruited to the U6 promoter through cooperative interactions with Brf2. Our results identify complexes smaller than mini-SNAPc that are transcriptionally active and show that there are at least two redundant mechanisms to stably recruit TBP to the U6 transcription initiation complex. PMID:12391172

  17. Applying Thymine Isostere 2,4-Difluoro-5-Methylbenzene as a NMR Assignment Tool and Probe of Homopyrimidine/Homopurine Tract Structural Dynamics.

    PubMed

    Brinson, Robert G; Miller, Jennifer T; Kahn, Jason D; Le Grice, Stuart F J; Marino, John P

    2016-01-01

    Proton assignment of nuclear magnetic resonance (NMR) spectra of homopyrimidine/homopurine tract oligonucleotides becomes extremely challenging with increasing helical length due to severe cross-peak overlap. As an alternative to the more standard practice of (15)N and (13)C labeling of oligonucleotides, here, we describe a method for assignment of highly redundant DNA sequences that uses single-site substitution of the thymine isostere 2,4-difluoro-5-methylbenzene (dF). The impact of this approach in facilitating the assignment of intractable spectra and analyzing oligonucleotide structure and dynamics is demonstrated using A-tract and TATA box DNA and two polypurine tract-containing RNA:DNA hybrids derived from HIV-1 and the Saccharomyces cerevisiae long-terminal repeat-containing retrotransposon Ty3. Only resonances proximal to the site of dF substitution exhibit sizable chemical shift changes, providing spectral dispersion while still allowing chemical shift mapping of resonances from unaffected residues distal to the site of modification directly back to the unmodified sequence. It is further illustrated that dF incorporation can subtly alter the conformation and dynamics of homopyrimidine/homopurine tract oligonucleotides, and how these NMR observations can be correlated, in the cases of the TATA box DNA, with modulation in the TATA box-binding protein interaction using an orthogonal gel assay. PMID:26791977

  18. Transcriptional activation in yeast cells lacking transcription factor IIA.

    PubMed Central

    Chou, S; Chatterjee, S; Lee, M; Struhl, K

    1999-01-01

    The general transcription factor IIA (TFIIA) forms a complex with TFIID at the TATA promoter element, and it inhibits the function of several negative regulators of the TATA-binding protein (TBP) subunit of TFIID. Biochemical experiments suggest that TFIIA is important in the response to transcriptional activators because activation domains can interact with TFIIA, increase recruitment of TFIID and TFIIA to the promoter, and promote isomerization of the TFIID-TFIIA-TATA complex. Here, we describe a double-shut-off approach to deplete yeast cells of Toa1, the large subunit of TFIIA, to <1% of the wild-type level. Interestingly, such TFIIA-depleted cells are essentially unaffected for activation by heat shock factor, Ace1, and Gal4-VP16. However, depletion of TFIIA causes a general two- to threefold decrease of transcription from most yeast promoters and a specific cell-cycle arrest at the G2-M boundary. These results indicate that transcriptional activation in vivo can occur in the absence of TFIIA. PMID:10581267

  19. [Governance and health: the rise of the managerialism in public sector reform].

    PubMed

    Denis, Jean L; Lamothe, Lise; Langley, Ann; Stéphane, Guérard

    2010-01-01

    The article examines various healthcare systems reform projects in Canada and some Canadian provinces and reveals some tendencies in governance renewal. The analisis is based on the hypothesis that reform is an exercise aiming at the renewal of governance conception and practices. In renewing governance, reform leaders hope to use adequate and effective levers to attain announced reform objectives. The article shows that the conceptions and operational modalities of governance have changed over time and that they reveal tensions inherent to the transformation and legitimation process of public healthcare systems. The first section discusses the relationships between reform and change. The second section defines the conception of gouvernance used for the analisis. Based on a content analisis of the various reform reports, the third section reveals the evolution of the conception of governance in healthcare systems in Canada. In order to expose the new tendencies, ideologies and operational principles at the heart of the reform projects are analysed. Five ideologies are identified: the democratic ideology, the "population health" ideology, the business ideology, the managerial ideology and the ideology of equity and humanism. This leads to a discussion on the dominant influence of the managerial ideology in the current reform projects. PMID:20963305

  20. Association of Neonatal Hyperbilirubinemia with UGT1A1 Gene Polymorphisms: A Meta-Analysis

    PubMed Central

    Yu, Zibi; Zhu, Kaichang; Wang, Li; Liu, Ying; Sun, Jianmei

    2015-01-01

    Background The results of studies on association between the polymorphisms in the coding region and the promoter of uridine diphosphateglucuronosyl transferase 1A1 (UGT1A1) and neonatal hyperbilirubinemia are controversial. This study aimed to determine whether the UGT1A1 gene polymorphisms of Gly71Arg and TATA promoter were significant risk factors associated with neonatal hyperbilirubinemia. Material/Methods The PubMed, Cochrane Library, and Embase databases were searched for papers that describe the association between UGT1A1 polymorphisms and neonatal hyperbilirubinemia. Summary odds ratios and 95% confidence intervals (CI) were estimated based on a fixed-effects model or random-effects model, depending on the absence or presence of significant heterogeneity. Results A total of 32 eligible studies and 6520 participants were identified. Among them, 24 studies focused on the association of neonatal hyperbilirubinemia with UGT1A1 Gly71Arg polymorphisms, and a significant difference was found for the comparison of AA vs. AG+GG (OR=3.47, 95% CI=2.29–5.28, P<0.0001). We included 19 studies on the association of neonatal hyperbilirubinemia with UGT1A1 TATA promoter polymorphism, which also found a statistically significant difference between 7/7 and 6/7 + 6/6 (OR=2.24, 95% CI=1.29–3.92, P=0.004). Conclusions This meta-analysis demonstrated that UGT1A1 polymorphisms (Gly71Arg and TATA promoter) significantly increase the risk of neonatal hyperbilirubinemia. PMID:26467199

  1. Diversification and Molecular Evolution of ATOH8, a Gene Encoding a bHLH Transcription Factor

    PubMed Central

    Balakrishnan-Renuka, Ajeesh; Leese, Florian; Schempp, Werner; Schaller, Felix; Hoffmann, Michael M.; Morosan-Puopolo, Gabriela; Yusuf, Faisal; Bisschoff, Izak Johannes; Chankiewitz, Verena; Xue, Jinglun; Chen, Jingzhong; Ying, Kang; Brand-Saberi, Beate

    2011-01-01

    ATOH8 is a bHLH domain transcription factor implicated in the development of the nervous system, kidney, pancreas, retina and muscle. In the present study, we collected sequence of ATOH8 orthologues from 18 vertebrate species and 24 invertebrate species. The reconstruction of ATOH8 phylogeny and sequence analysis showed that this gene underwent notable divergences during evolution. For those vertebrate species investigated, we analyzed the gene structure and regulatory elements of ATOH8. We found that the bHLH domain of vertebrate ATOH8 was highly conserved. Mammals retained some specific amino acids in contrast to the non-mammalian orthologues. Mammals also developed another potential isoform, verified by a human expressed sequence tag (EST). Comparative genomic analyses of the regulatory elements revealed a replacement of the ancestral TATA box by CpG-islands in the eutherian mammals and an evolutionary tendency for TATA box reduction in vertebrates in general. We furthermore identified the region of the effective promoter of human ATOH8 which could drive the expression of EGFP reporter in the chicken embryo. In the opossum, both the coding region and regulatory elements of ATOH8 have some special features, such as the unique extended C-terminus encoded by the third exon and absence of both CpG islands and TATA elements in the regulatory region. Our gene mapping data showed that in human, ATOH8 was hosted in one chromosome which is a fusion product of two orthologous chromosomes in non-human primates. This unique chromosomal environment of human ATOH8 probably subjects its expression to the regulation at chromosomal level. We deduce that the great interspecific differences found in both ATOH8 gene sequence and its regulatory elements might be significant for the fine regulation of its spatiotemporal expression and roles of ATOH8, thus orchestrating its function in different tissues and organisms. PMID:21857980

  2. Substrate-Dependent Assembly of the Tat Translocase as Observed in Live Escherichia coli Cells

    PubMed Central

    Rose, Patrick; Fröbel, Julia; Graumann, Peter L.; Müller, Matthias

    2013-01-01

    The twin-arginine translocation (Tat) pathway guides fully folded proteins across membranes of bacteria, archaea and plant chloroplasts. In Escherichia coli, Tat-specific transport is executed in a still largely unknown manner by three functionally diverse membrane proteins, termed TatA, TatB, and TatC. In order to follow the intracellular distribution of the TatABC proteins in live E. coli cells, we have individually expressed fluorophore-tagged versions of each Tat protein in addition to a set of chromosomally encoded TatABC proteins. In this way, a Tat translocase could form from the native TatABC proteins and be visualized via the association of a fluorescent Tat variant. A functionally active TatA-green fluorescent protein fusion was found to re-locate from a uniform distribution in the membrane into a few clusters preferentially located at the cell poles. Clustering was absolutely dependent on the co-expression of functional Tat substrates, the proton-motive force, and the cognate TatBC subunits. Likewise, polar cluster formation of a functional TatB-mCherry fusion required TatA and TatC and that of a functional TatC-mCherry fusion a functional Tat substrate. Furthermore we directly demonstrate the co-localization of TatA and TatB in the same fluorescent clusters. Our collective results are consistent with distinct Tat translocation sites dynamically forming in vivo in response to newly synthesized Tat substrates. PMID:23936332

  3. Subunit composition and in vivo substrate-binding characteristics of Escherichia coli Tat protein complexes expressed at native levels.

    PubMed

    McDevitt, Christopher A; Buchanan, Grant; Sargent, Frank; Palmer, Tracy; Berks, Ben C

    2006-12-01

    The Tat system transports folded proteins across the bacterial cytoplasmic membrane and the thylakoid membrane of plant chloroplasts. Substrates are targeted to the Tat pathway by signal peptides containing a pair of consecutive arginine residues. The membrane proteins TatA, TatB and TatC are the essential components of this pathway in Escherichia coli. The complexes that these proteins form at native levels of expression have been investigated by the use of affinity tag-coding sequences fused to chromosomal tat genes. Distinct TatA and TatBC complexes were identified using size-exclusion chromatography and shown to have apparent molecular masses of approximately 700 and 500 kDa, respectively. Following in vivo expression, the Tat substrate protein SufI was found to copurify with the TatBC, but not the TatA, complex. This binding required the SufI signal peptide. Substitution of the twin-arginine residues in the SufI signal peptide by either twin lysine or twin alanine residues abolished export. However, both variant SufI proteins still copurified with the TatBC complex. These data show that the twin-arginine residues of the Tat consensus motif are not essential for binding of precursor to the TatBC complex but are required for the successful entry of the precursor into the transport cycle. The effect on substrate binding of single amino acid substitutions in TatC that affect Tat transport were studied using TatC variants Phe94Ala, Glu103Ala, Glu103Arg and Asp211Ala. Only variant Glu103Arg showed reduced copurification of SufI with TatBC. The transport defects associated with the other TatC variants do not, therefore, arise from an inability to bind substrate proteins. PMID:17212781

  4. Postproliferative transcription of the rat osteocalcin gene is reflected by vitamin D-responsive developmental modifications in protein-DNA interactions at basal and enhancer promoter elements.

    PubMed Central

    Owen, T A; Bortell, R; Shalhoub, V; Heinrichs, A; Stein, J L; Stein, G S; Lian, J B

    1993-01-01

    In the osteocalcin (OC) gene promoter, both independent positive and negative regulatory elements, as well as others with contiguous [TATA/glucocorticoid-responsive elements (GRE)] or overlapping [TATA/GRE, vitamin D-responsive enhancer elements (VDRE)/AP-1, and OC box/AP-1] domains, are sites for modifications in protein-DNA interactions. In the present studies, we have examined nuclear protein extracts from fetal rat calvarial cells that undergo a developmental sequence of bone cell differentiation. Our results demonstrate modifications in protein-DNA interactions that relate to the developmental stages of the osteoblast and support developmental regulation of OC gene transcription. Basal expression of the OC gene is associated with sequence-specific protein-DNA interactions at the OC box, VDRE, and TATA/GRE box. Distinct differences are observed in proliferating osteoblasts, where the OC gene is not transcribed compared to postproliferative, differentiated osteoblasts that transcribe the OC gene. Furthermore, the protein-DNA complexes that reflect hormonal control are also developmentally regulated, mediating both the transcriptionally active and repressed states of the OC gene. For example, in proliferating osteoblasts, a vitamin D receptor-antibody-sensitive complex is formed that is different from the DNA binding complex induced by vitamin D postproliferatively when the OC gene is transcribed. Mutational analysis of the steroid hormone binding domain and the overlapping AP-1 site at the VDRE supports mutually exclusive occupancy by Fos-Jun heterodimers and vitamin D receptor. Such protein-DNA interactions at the VDRE are consistent with repression of competency for vitamin D-mediated transcriptional enhancement in proliferating osteoblasts expressing high levels of Fos and Jun. Images PMID:8381969

  5. Genome-wide identification and characterization of transcription start sites and promoters in the tunicate Ciona intestinalis.

    PubMed

    Yokomori, Rui; Shimai, Kotaro; Nishitsuji, Koki; Suzuki, Yutaka; Kusakabe, Takehiro G; Nakai, Kenta

    2016-01-01

    The tunicate Ciona intestinalis, an invertebrate chordate, has recently emerged as a powerful model organism for gene regulation analysis. However, few studies have been conducted to identify and characterize its transcription start sites (TSSs) and promoters at the genome-wide level. Here, using TSS-seq, we identified TSSs at the genome-wide scale and characterized promoters in C. intestinalis. Specifically, we identified TSS clusters (TSCs), high-density regions of TSS-seq tags, each of which appears to originate from an identical promoter. TSCs were found not only at known TSSs but also in other regions, suggesting the existence of many unknown transcription units in the genome. We also identified candidate promoters of 79 ribosomal protein (RP) genes, each of which had the major TSS in a polypyrimidine tract and showed a sharp TSS distribution like human RP gene promoters. Ciona RP gene promoters, however, did not appear to have typical TATA boxes, unlike human RP gene promoters. In Ciona non-RP promoters, two pyrimidine-purine dinucleotides, CA and TA, were frequently used as TSSs. Despite the absence of CpG islands, Ciona TATA-less promoters showed low expression specificity like CpG-associated human TATA-less promoters. By using TSS-seq, we also predicted trans-spliced gene TSSs and found that their downstream regions had higher G+T content than those of non-trans-spliced gene TSSs. Furthermore, we identified many putative alternative promoters, some of which were regulated in a tissue-specific manner. Our results provide valuable information about TSSs and promoter characteristics in C. intestinalis and will be helpful in future analysis of transcriptional regulation in chordates. PMID:26668163

  6. RNA aptamers directed to discrete functional sites on a single protein structural domain

    PubMed Central

    Shi, Hua; Fan, Xiaochun; Sevilimedu, Aarti; Lis, John T.

    2007-01-01

    Cellular regulatory networks are organized such that many proteins have few interactions, whereas a few proteins have many. These densely connected protein “hubs” are critical for the system-wide behavior of cells, and the capability of selectively perturbing a subset of interactions at these hubs is invaluable in deciphering and manipulating regulatory mechanisms. SELEX-generated RNA aptamers are proving to be highly effective reagents for inhibiting targeted proteins, but conventional methods generate one or several aptamer clones that usually bind to a single target site most preferred by a nucleic acid ligand. We advance a generalized scheme for isolating aptamers to multiple sites on a target molecule by reducing the ability of the preferred site to select its cognate aptamer. We demonstrate the use of this scheme by generating aptamers directed to discrete functional surfaces of the yeast TATA-binding protein (TBP). Previously we selected “class 1” RNA aptamers that interfere with the TBP's binding to TATA-DNA. By masking TBP with TATA-DNA or an unamplifiable class 1 aptamer, we isolated a new aptamer class, “class 2,” that can bind a TBP·DNA complex and is in competition with binding another general transcription factor, TFIIA. Moreover, we show that both of these aptamers inhibit RNA polymerase II-dependent transcription, but analysis of template-bound factors shows they do so in mechanistically distinct and unexpected ways that can be attributed to binding either the DNA or TFIIA recognition sites. These results should spur innovative approaches to modulating other highly connected regulatory proteins. PMID:17360423

  7. Schistosoma haematobium detection in snails by DraI PCR and Sh110/Sm-Sl PCR: further evidence of the interruption of schistosomiasis transmission in Morocco

    PubMed Central

    2014-01-01

    Background This is the first study in Morocco to estimate snail infection rates at the last historic transmission sites of schistosomiasis, known to be free from new infection among humans since 2004. Screening of large numbers of snails for infection is one way to confirm that Schistosoma haematobium transmission has stopped and does not resurge. Methods A total of 2703 Bulinus truncatus snails were collected from 24 snail habitats in five provinces of Morocco: Errachidia, El Kelaa des Sraghna, Tata, Beni Mellal, and Chtouka Ait Baha. All visible snails were collected with a scoop net or by hand. We used waders and gloves as simple precautions. Snails were morphologically identified according to Moroccan Health Ministry guide of schistosomiasis (1982). All snails were analyzed in pools by molecular tool, using primers from the newly identified repeated DNA sequence, termed DraI, in the S. haematobium group. To distinguish S. bovis and S. haematobium, the snails were analyzed by Sh110/Sm-Sl PCR that was specific of S. haematobium. Results The results showed that snails from Errachidia, Chtouka Ait Baha, sector of Agoujgal in Tata and sector of Mbarkiya in El kelaa des Sraghna were negative for DraI PCR; but, snails from remaining snail habitats of El Kelaa des Sraghna, Tata and Beni Mellal were positive. This led to suggest the presence of circulating schistosome species (S. haematobium, S. bovis or others) within these positive snail habitats. Subsequently, confirmation with S. haematobium species specific molecular assay, Sh110/Sm-Sl PCR, showed that none of the collected snails were infected by S. haematobium in all historic endemic areas. Conclusion The absence of S. haematobium infection in snails supports the argument of S. haematobium transmission interruption in Morocco. PMID:24962624

  8. Interferon regulatory factors and TFIIB cooperatively regulate interferon-responsive promoter activity in vivo and in vitro.

    PubMed Central

    Wang, I M; Blanco, J C; Tsai, S Y; Tsai, M J; Ozato, K

    1996-01-01

    Interferon regulatory factors (IRFs) bind to the interferon-stimulated response element (ISRE) and regulate interferon- and virus-mediated gene expression. IRF-1 acts as a transcriptional activator, while IRF-2 acts as a repressor. Here we show that IRF-1 and IRF-2 bind to both cellular TFIIB, a component of the basal transcription machinery, and recombinant TFIIB (rTFIIB) and that this protein-protein interaction facilitates binding of IRFs to the ISRE. A functional interaction between TFIIB and IRF was assessed by a newly established in vitro transcription assay in which recombinant IRF-1 (rIRF-1) stimulated transcription specifically from an ISRE-containing template. With this assay we show that rIRF-1 and rTFIIB cooperatively enhance the ISRE promoter in vitro. We found that the activity of an ISRE-containing promoter was cooperatively enhanced upon cotransfection of TFIIB and IRF-1 cDNAs into P19 embryonal carcinoma cells, further demonstrating functional interactions in vivo. The cooperative enhancement by TFIIB and IRF-1 was independent of the TATA sequence in the ISRE promoter but dependent on the initiator sequence (Inr) and was abolished when P19 cells were induced to differentiate by retinoic acid treatment. In contrast, cotransfection of TFIIB and IRF-1 into NIH 3T3 cells resulted in a dose-dependent repression of promoter activation which occurred in a TATA-dependent manner. Our results indicate the presence of a cell type-specific factor that mediates the functional interaction between IRFs and TFIIB and that acts in conjunction with the requirement of TATA and Inr for promoter activation. PMID:8887661

  9. Genome-wide identification and characterization of transcription start sites and promoters in the tunicate Ciona intestinalis

    PubMed Central

    Yokomori, Rui; Shimai, Kotaro; Nishitsuji, Koki; Suzuki, Yutaka; Kusakabe, Takehiro G.; Nakai, Kenta

    2016-01-01

    The tunicate Ciona intestinalis, an invertebrate chordate, has recently emerged as a powerful model organism for gene regulation analysis. However, few studies have been conducted to identify and characterize its transcription start sites (TSSs) and promoters at the genome-wide level. Here, using TSS-seq, we identified TSSs at the genome-wide scale and characterized promoters in C. intestinalis. Specifically, we identified TSS clusters (TSCs), high-density regions of TSS-seq tags, each of which appears to originate from an identical promoter. TSCs were found not only at known TSSs but also in other regions, suggesting the existence of many unknown transcription units in the genome. We also identified candidate promoters of 79 ribosomal protein (RP) genes, each of which had the major TSS in a polypyrimidine tract and showed a sharp TSS distribution like human RP gene promoters. Ciona RP gene promoters, however, did not appear to have typical TATA boxes, unlike human RP gene promoters. In Ciona non-RP promoters, two pyrimidine-purine dinucleotides, CA and TA, were frequently used as TSSs. Despite the absence of CpG islands, Ciona TATA-less promoters showed low expression specificity like CpG-associated human TATA-less promoters. By using TSS-seq, we also predicted trans-spliced gene TSSs and found that their downstream regions had higher G+T content than those of non-trans-spliced gene TSSs. Furthermore, we identified many putative alternative promoters, some of which were regulated in a tissue-specific manner. Our results provide valuable information about TSSs and promoter characteristics in C. intestinalis and will be helpful in future analysis of transcriptional regulation in chordates. PMID:26668163

  10. Imine-Functionalized Triazatriangulenium Platforms: Towards an Artificial Ciliated Epithelium.

    PubMed

    Hammerich, Melanie; Rusch, Talina; Krekiehn, Nicolai R; Bloedorn, Andreas; Magnussen, Olaf M; Herges, Rainer

    2016-06-17

    Triazatriangulenium (TATA) platforms have been used to prepare highly ordered, self-assembled monolayers of free- and vertically standing imines on Au(111) surfaces. Upon irradiation, the imines undergo trans-cis isomerization and a fast thermal reaction (t1/2 =0.58 s at 20 °C) back to the more stable trans form. It is known that the photochemical reaction proceeds through rotation of the C=N bond and the thermochemical reaction through inversion at the N atom. The imine motors, therefore, should be able to induce a net displacement of particles above the surface similar to cilia epithelia in nature. PMID:27016909

  11. Differential regulation of RNA polymerases I, II, and III by the TBP-binding repressor Dr1.

    PubMed

    White, R J; Khoo, B C; Inostroza, J A; Reinberg, D; Jackson, S P

    1994-10-21

    RNA polymerases I, II, and III each use the TATA-binding protein (TBP). Regulators that target this shared factor may therefore provide a means to coordinate the activities of the three nuclear RNA polymerases. The repressor Dr1 binds to TBP and blocks the interaction of TBP with polymerase II- and polymerase III-specific factors. This enables Dr1 to coordinately regulate transcription by RNA polymerases II and III. Under the same conditions, Dr1 does not inhibit polymerase I transcription. By selectively repressing polymerases II and III, Dr1 may shift the physiological balance of transcriptional output in favor of polymerase I. PMID:7939686

  12. Homoatomic clustering in T4Ga5 (T = Ta, Nb, Ta/Mo): a story of reluctant intermetallics crystallizing in a new binary structure type.

    PubMed

    Fredrickson, Rie T; Kilduff, Brandon J; Fredrickson, Daniel C

    2015-02-01

    In the formation of binary compounds, heteroatomic interactions are generally expected to play the leading role in providing stability. In this Article, we present a series of gallides, T(4)Ga(5) (T = Ta, Nb, and Ta/Mo), which appear to defy this expectation. Their complex crystal structures represent a new binary structure type (to the best of our knowledge),, which can be visualized in terms of a host lattice of T@T(8) body centered cubic (bcc) clusters linked through face-capping Ga(2) dumbbells to form a primitive cubic framework. The cubic spaces that result are alternately filled by distorted T pentagonal dodecahedra (sharing atoms with the host lattice) and dimers of bcc fragments, leading to a √2 × √2 × 2 supercell of the host framework structure. Ga tetrahedra and icosahedral units fill the remaining void spaces. Underlying these structural features is a strong tendency for homoatomic clustering of Ta and Ga, which is evident in all of the coordination polyhedra. Electronic structure calculations using density functional theory (DFT) and DFT-calibrated Hückel models reveal possible origins for this elemental segregation and the factors stabilizing the structure as a whole. A deep pseudogap is present at the Fermi energy of Ta(4)Ga(5) (as well as at that of Nb(4)Ga(5)), corresponding to the near-optimization of Ta-Ta and Ta-Ga interactions. This pseudogap emerges as a result of the ability of extensive Ta-Ta bonding to provide local 18-electron configurations to the Ta atoms, despite the electron concentration being only 8.75 electrons per Ta atom. Support for these Ta-Ta interactions is provided by Ga bridging atoms, whose valence orbitals' low number of angular nodes confers preferential stabilization to Ta-Ta bonding functions over antibonding ones. The observed spatial separation of the structure into Ta and Ga domains occurs as a consequence of the Ga atoms being pushed toward the periphery of the Ta clusters to play this supporting role. PMID

  13. Nucleotide sequence of a cluster of early and late genes in a conserved segment of the vaccinia virus genome.

    PubMed Central

    Plucienniczak, A; Schroeder, E; Zettlmeissl, G; Streeck, R E

    1985-01-01

    The nucleotide sequence of a 7.6 kb vaccinia DNA segment from a genomic region conserved among different orthopox virus has been determined. This segment contains a tight cluster of 12 partly overlapping open reading frames most of which can be correlated with previously identified early and late proteins and mRNAs. Regulatory signals used by vaccinia virus have been studied. Presumptive promoter regions are rich in A, T and carry the consensus sequences TATA and AATAA spaced at 20-24 base pairs. Tandem repeats of a CTATTC consensus sequence are proposed to be involved in the termination of early transcription. PMID:2987815

  14. A TatABC-Type Tat Translocase Is Required for Unimpaired Aerobic Growth of Corynebacterium glutamicum ATCC13032

    PubMed Central

    Oertel, Dan; Schmitz, Sabrina; Freudl, Roland

    2015-01-01

    The twin-arginine translocation (Tat) system transports folded proteins across the cytoplasmic membrane of bacteria and the thylakoid membrane of plant chloroplasts. Escherichia coli and other Gram-negative bacteria possess a TatABC-type Tat translocase in which each of the three inner membrane proteins TatA, TatB, and TatC performs a mechanistically distinct function. In contrast, low-GC Gram-positive bacteria, such as Bacillus subtilis, use a TatAC-type minimal Tat translocase in which the TatB function is carried out by a bifunctional TatA. In high-GC Gram-positive Actinobacteria, such as Mycobacterium tuberculosis and Corynebacterium glutamicum, tatA, tatB, and tatC genes can be identified, suggesting that these organisms, just like E. coli, might use TatABC-type Tat translocases as well. However, since contrary to this view a previous study has suggested that C. glutamicum might in fact use a TatAC translocase with TatB only playing a minor role, we reexamined the requirement of TatB for Tat-dependent protein translocation in this microorganism. Under aerobic conditions, the misassembly of the Rieske iron-sulfur protein QcrA was identified as a major reason for the severe growth defect of Tat-defective C. glutamicum mutant strains. Furthermore, our results clearly show that TatB, besides TatA and TatC, is strictly required for unimpaired aerobic growth. In addition, TatB was also found to be essential for the secretion of a heterologous Tat-dependent model protein into the C. glutamicum culture supernatant. Together with our finding that expression of the C. glutamicum TatB in an E. coli ΔtatB mutant strain resulted in the formation of an active Tat translocase, our results clearly indicate that a TatABC translocase is used as the physiologically relevant functional unit for Tat-dependent protein translocation in C. glutamicum and, most likely, also in other TatB-containing Actinobacteria. PMID:25837592

  15. Thematic mapper studies of Andean volcanoes

    NASA Technical Reports Server (NTRS)

    Francis, P. W.

    1986-01-01

    The primary objective was to identify all the active volcanoes in the Andean region of Bolivia. Morphological features of the Tata Sabaya volcano, Bolivia, were studied with the thematic mapper. Details include marginal levees on lava and pyroclastic flows, and summit crater structure. Valley glacier moraine deposits, not easily identified on the multispectral band scanner, were also unambiguous, and provide useful marker horizons on large volcanic edifices which were built up in preglacial times but which were active subsequently. With such high resolution imagery, it is not only possible to identify potentially active volcanoes, but also to use standard photogeological interpretation to outline the history of individual volcanoes.

  16. Molecular structure of r/GCG/d/TATACGC/ - A DNA-RNA hybrid helix joined to double helical DNA

    NASA Technical Reports Server (NTRS)

    Wang, A. H.-J.; Fujii, S.; Rich, A.; Van Boom, J. H.; Van Der Marel, G. A.; Van Boeckel, S. A. A.

    1982-01-01

    The molecule r(GCG)d(TATACGC) is self-complementary and forms two DNA-RNA hybrid segments surrounding a central region of double helical DNA; its molecular structure has been solved by X-ray analysis. All three parts of the molecule adopt a conformation which is close to that seen in the 11-fold RNA double helix. The conformation of the ribonucleotides is partly determined by water molecules bridging between the ribose O2' hydroxyl group and cytosine O2. The hybrid-DNA duplex junction contains no structural discontinuities. However, the central DNA TATA sequence has some structural irregularities.

  17. Homi Jehangir Bhabha: remembering a scientist and celebrating his contributions to science, technology, and education in India

    NASA Astrophysics Data System (ADS)

    Vaidya, Sheila

    2010-06-01

    The focus of this paper is on the current developments in science education occurring in the posthumously built Homi Bhabha Centre for Science Education in Mumbai and to offer context for various indigenous developments that are shaping science education in India today. In this paper, I describe the story of Homi Bhabha and his rich legacy of India's atomic energy program. Specifically, I focus on the institutions built by Homi Bhabha, including the Tata Institute of Fundamental Research and the Bhabha Atomic Research Centre (BARC) and I examine how these institutions have enabled Indian scientists to contribute to the advancement of science knowledge in the world.

  18. VizieR Online Data Catalog: JHK photometry in 2 star-forming regions (Anandarao+, 2008)

    NASA Astrophysics Data System (ADS)

    Anandarao, B. G.; Venkata Raman, V.; Ghosh, S. K.; Ojha, D. K.; Kumar, M. S. N.

    2009-05-01

    Subarcsec resolution JHK photometry was performed at UKIRT during 2005 July 17 on the two objects under excellent seeing conditions (~0.5arcsec) using the UFTI (HAWAII- 1 1024x1024 ) camera. The radio continuum observations in the 1.280-GHz frequency band (with a bandwidth of 16MHz) were made on 2003 August 1 at the Giant Metrewave Radio Telescope (GMRT), operated by National Centre for Radio Astrophysics (NCRA), Tata Institute of Fundamental Research (TIFR) near Pune (India). (3 data files).

  19. a New Study on the Energy Spectrum and Composition of Primary Cosmic Ray Flux at Energies ~ 1014 - 1016 EV Using the GRAPES-3 Array at Ooty

    NASA Astrophysics Data System (ADS)

    Tonwar, S. C.; Gupta, S. K.; Mohanty, D. K.; Mohanty, P. K.; Sivaprasad, K.; Sreekantan, B. V.; Hayashi, Y.; Ito, N.; Kawakami, S.; Nonaka, T.; Tanaka, H.; Yoshikoshi, T.

    Data collected with the 217-detector air shower array and the 560 m2 area tracking muon detector, being operated at Ooty in southern India by the India-Japan (Tata Institute-Osaka City University) collaboration, GRAPES, have been analyzed to study the shape of the energy spectrum and the composition around the knee. It is shown that the muon multiplicity distribution, observed with the highly modular muon detector, permits a relatively reliable measurement on the composition of primary flux which then helps in a more accurate reconstruction of the energy spectrum from the observed shower size spectrum. The highlights of the GRAPES array, the analysis procedure and the results are presented.

  20. Electrochemical Patterning and Detection of DNA Arrays on a Two-Electrode Platform

    PubMed Central

    Furst, Ariel; Landefeld, Sally; Hill, Michael G.; Barton, Jacqueline K.

    2014-01-01

    We report a novel method of DNA array formation that is electrochemically formed and addressed with a two-electrode platform. Electrochemical activation of a copper catalyst, patterned with one electrode, enables precise placement of multiple sequences of DNA onto a second electrode surface. The two-electrode patterning and detection platform allows for both spatial resolution of the patterned DNA array and optimization of detection through DNA-mediated charge transport with electrocatalysis. This two-electrode platform has been used to form arrays that enable differentiation between well-matched and mismatched sequences, the detection of TATA-binding protein, and sequence-selective DNA hybridization. PMID:24328227

  1. Electrochemical patterning and detection of DNA arrays on a two-electrode platform.

    PubMed

    Furst, Ariel; Landefeld, Sally; Hill, Michael G; Barton, Jacqueline K

    2013-12-26

    We report a novel method of DNA array formation that is electrochemically formed and addressed with a two-electrode platform. Electrochemical activation of a copper catalyst, patterned with one electrode, enables precise placement of multiple sequences of DNA onto a second electrode surface. The two-electrode patterning and detection platform allows for both spatial resolution of the patterned DNA array and optimization of detection through DNA-mediated charge transport with electrocatalysis. This two-electrode platform has been used to form arrays that enable differentiation between well-matched and mismatched sequences, the detection of TATA-binding protein, and sequence-selective DNA hybridization. PMID:24328227

  2. A genetic analysis of Adh1 regulation. Progress report, June 1991--February 1992

    SciTech Connect

    Freeling, M.

    1992-03-01

    The overall goal of our research proposal is to understand the meaning of the various cis-acting sites responsible for AdH1 expression in the entire maize plant. Progress is reported in the following areas: Studies on the TATA box and analysis of revertants of the Adh1-3F1124 allele; screening for more different mutants that affect Adh1 expression differentially; studies on cis-acting sequences required for root-specific Adh1 expression; refinement of the use of the particle gun; and functional analysis of a non- glycolytic anaerobic protein.

  3. A genetic analysis of Adh1 regulation

    SciTech Connect

    Freeling, M.

    1992-01-01

    The overall goal of our research proposal is to understand the meaning of the various cis-acting sites responsible for AdH1 expression in the entire maize plant. Progress is reported in the following areas: Studies on the TATA box and analysis of revertants of the Adh1-3F1124 allele; screening for more different mutants that affect Adh1 expression differentially; studies on cis-acting sequences required for root-specific Adh1 expression; refinement of the use of the particle gun; and functional analysis of a non- glycolytic anaerobic protein.

  4. Diversity and Evolution of Bacterial Twin Arginine Translocase Protein, TatC, Reveals a Protein Secretion System That Is Evolving to Fit Its Environmental Niche

    PubMed Central

    Simone, Domenico; Bay, Denice C.; Leach, Thorin; Turner, Raymond J.

    2013-01-01

    Background The twin-arginine translocation (Tat) protein export system enables the transport of fully folded proteins across a membrane. This system is composed of two integral membrane proteins belonging to TatA and TatC protein families and in some systems a third component, TatB, a homolog of TatA. TatC participates in substrate protein recognition through its interaction with a twin arginine leader peptide sequence. Methodology/Principal Findings The aim of this study was to explore TatC diversity, evolution and sequence conservation in bacteria to identify how TatC is evolving and diversifying in various bacterial phyla. Surveying bacterial genomes revealed that 77% of all species possess one or more tatC loci and half of these classes possessed only tatC and tatA genes. Phylogenetic analysis of diverse TatC homologues showed that they were primarily inherited but identified a small subset of taxonomically unrelated bacteria that exhibited evidence supporting lateral gene transfer within an ecological niche. Examination of bacilli tatCd/tatCy isoform operons identified a number of known and potentially new Tat substrate genes based on their frequent association to tatC loci. Evolutionary analysis of these Bacilli isoforms determined that TatCy was the progenitor of TatCd. A bacterial TatC consensus sequence was determined and highlighted conserved and variable regions within a three dimensional model of the Escherichia coli TatC protein. Comparative analysis between the TatC consensus sequence and Bacilli TatCd/y isoform consensus sequences revealed unique sites that may contribute to isoform substrate specificity or make TatA specific contacts. Synonymous to non-synonymous nucleotide substitution analyses of bacterial tatC homologues determined that tatC sequence variation differs dramatically between various classes and suggests TatC specialization in these species. Conclusions/Significance TatC proteins appear to be diversifying within particular bacterial

  5. Transient expression of a mouse alpha-fetoprotein minigene: deletion analyses of promoter function.

    PubMed Central

    Scott, R W; Tilghman, S M

    1983-01-01

    The constitutive transcription of a mouse alpha-fetoprotein (AFP) minigene was examined during the transient expression of AFP-simian virus 40-pBR322 recombinant DNAs introduced into HeLa cells by Ca3(PO4)2 precipitation. We tested three constructs, each of which contains the AFP minigene and pBR322 DNAs inserted in the late region of simian virus 40 and found that the relative efficiency of AFP gene expression was dependent on the arrangement of the three DNA elements in the vector. The transcripts begin at the authentic AFP cap site and are properly spliced and polyadenylated. To define a sequence domain in the 5' flanking region of the AFP gene required for constitutive expression, sequential 5' deletion mutants of the AFP minigene were constructed and introduced into HeLa cells. All AFP deletion mutants which retained at least the TATA motif located 30 base pairs upstream from the cap site were capable of directing accurate and efficient AFP transcription. However, when the TATA sequence was deleted, no accurately initiated AFP transcripts were detected. These results are identical to those obtained from in vitro transcription of truncated AFP 5' deletion mutant templates assayed in HeLa cell extracts. The rate of AFP transcription in vivo was unaffected by deletion of DNA upstream of the AFP TATA box but was greatly affected by the distance between the simian virus 40 control region and the 5' end of the gene. The absence of any promoter activity upstream of the TATA box in this assay system is in contrast to what has been reported for several other eucaryotic structural genes in a variety of in vivo systems. A sequence comparison between the 5' flanking region of the AFP gene and these genes suggested that the AFP gene lacks those structural elements found to be important for constitutive transcription in vivo. Either the AFP gene lacks upstream promoter function in the 5' flanking DNA contained within the minigene, or the use of a viral vector in a

  6. A new Epstein-Barr virus transactivator, R, induces expression of a cytoplasmic early antigen.

    PubMed Central

    Hardwick, J M; Lieberman, P M; Hayward, S D

    1988-01-01

    Several Epstein-Barr virus (EBV) early promoters respond to a new EBV transactivator encoded by BRLF1, designated R. Transactivation was measured in chloramphenicol acetyltransferase assays on Raji, BHK, and Vero cells that were cotransfected with the transactivator and target promoters linked to the cat gene. The divergent promoter of BamHI-H was particularly responsive to R transactivation. This large promoter region consists of a leftward TATA box for the NotI repeat gene (BHLF1) and a probable rightward TATA box for the EA-R gene (BHRF1) separated by 940 base pairs of unusual sequence complexity. Sequences within this divergent promoter region appear to confer inducibility by EBV transactivators R and Z (BZLF1). The Z transactivator stimulated expression in both the leftward and rightward directions, and R stimulated expression primarily in the rightward direction, but the MS transactivator (BMLF1) had no activity in either direction. The adenovirus E3 promoter also responded to the R transactivator, but several other herpesvirus and human promoters were nonresponsive. When the divergent promoter was linked to the EA-R gene as it is in the EBV genome, the R and Z transactivators also induced the expression of EA-R in cotransfected cells. This cytoplasmic early antigen is encoded by BHRF1 and may be anchored in intracellular membranes by a carboxy-terminal transmembrane region. Images PMID:2836611

  7. Population and family planning in developing countries: the employer's role.

    PubMed

    Tata, N H

    1974-01-01

    The overall population problem of the world is discussed briefly. The author asserts that rapid population growth has serious social and political implications and imposes serious restraints on economic progress. It is also linked to problems of urbanization. Family planning is a way out. The state alone is not enough to make family planning successful, it must be supported by the different segments of society. Employers have a major social responsibility in this respect. After this general introduction, and the assertion of the basic role of the employer in family planning programs, the author deals with the specific situation in India in terms of 1) its population problem, 2) progress and impact of the Indian family planning program, and 3) the role of employers in the promotion of family planning in India; a detailed section is devoted to the family planning centers of the Tata group of companies (Tata textile units, chemicals, iron and steel, engineering and locomotive, etc.). The author enumerates the measures to promote effective participation by employers, which include 1) an organized framework, 2) assistance to employers, and 3) removal of disincentives. The author concludes by saying that the efforts of employers to limit population growth need to be supplemented by international cooperation and action. PMID:12257448

  8. TFIIF, a basal eukaryotic transcription factor, is a substrate for poly(ADP-ribosyl)ation.

    PubMed Central

    Rawling, J M; Alvarez-Gonzalez, R

    1997-01-01

    We have examined the susceptibility of some of the basal eukaryotic transcription factors as covalent targets for poly(ADP-ribosyl)ation. Human recombinant TATA-binding protein, transcription factor (TF)IIB and TFIIF (made up of the 30 and 74 kDa RNA polymerase II-associated proteins RAP30 and RAP74) were incubated with calf thymus poly(ADP-ribose) polymerase and [32P]NAD+ at 37 degrees C. On lithium dodecyl sulphate/PAGE and autoradiography, two bands of radioactivity, coincident with RAP30 and RAP74, were observed. No radioactivity co-migrated with TATA-binding protein or TFIIB. The phenomenon was dependent on the presence of nicked DNA, which is essential for poly(ADP-ribose) polymerase activity. Covalent modification of TFIIF increased with time of incubation, with increasing TFIIF concentration and with increasing NAD+ concentration. High-resolution PAGE confirmed that the radioactive species associated with RAP30 and RAP74 were ADP-ribose polymers. From these observations, we conclude that both TFIIF subunits are highly specific substrates for covalent poly(ADP-ribosyl)ation. PMID:9164864

  9. Allosteric regulation of rhomboid intramembrane proteolysis

    PubMed Central

    Arutyunova, Elena; Panwar, Pankaj; Skiba, Pauline M; Gale, Nicola; Mak, Michelle W; Lemieux, M Joanne

    2014-01-01

    Proteolysis within the lipid bilayer is poorly understood, in particular the regulation of substrate cleavage. Rhomboids are a family of ubiquitous intramembrane serine proteases that harbour a buried active site and are known to cleave transmembrane substrates with broad specificity. In vitro gel and Förster resonance energy transfer (FRET)-based kinetic assays were developed to analyse cleavage of the transmembrane substrate psTatA (TatA from Providencia stuartii). We demonstrate significant differences in catalytic efficiency (kcat/K0.5) values for transmembrane substrate psTatA (TatA from Providencia stuartii) cleavage for three rhomboids: AarA from P. stuartii, ecGlpG from Escherichia coli and hiGlpG from Haemophilus influenzae demonstrating that rhomboids specifically recognize this substrate. Furthermore, binding of psTatA occurs with positive cooperativity. Competitive binding studies reveal an exosite-mediated mode of substrate binding, indicating allostery plays a role in substrate catalysis. We reveal that exosite formation is dependent on the oligomeric state of rhomboids, and when dimers are dissociated, allosteric substrate activation is not observed. We present a novel mechanism for specific substrate cleavage involving several dynamic processes including positive cooperativity and homotropic allostery for this interesting class of intramembrane proteases. PMID:25009246

  10. Rat hepatic glutaminase: identification of the full coding sequence and characterization of a functional promoter.

    PubMed Central

    Chung-Bok, M I; Vincent, N; Jhala, U; Watford, M

    1997-01-01

    Glutamine catabolism in mammalian liver is catalysed by a unique isoenzyme of phosphate-activated glutaminase. The full coding and 5' untranslated sequence for rat hepatic glutaminase was isolated by screening lambda ZAP cDNA libraries and a Charon 4a rat genomic library. The sequence produces a mRNA 2225 nt in length, encoding a polypeptide of 535 amino acid residues with a calculated molecular mass of 59.2 kDa. The deduced amino acid sequence of rat liver glutaminase shows 86% similarity to that of rat kidney glutaminase and 65% similarity to a putative glutaminase from Caenorhabditis elegans. A genomic clone to rat liver glutaminase was isolated that contains 3.5 kb of the gene and 7.5 kb of the 5' flanking region. The 1 kb immediately upstream of the hepatic glutaminase gene (from -1022 to +48) showed functional promoter activity in HepG2 hepatoma cells. This promoter region did not respond to treatment with cAMP, but was highly responsive (10-fold stimulation) to the synthetic glucocorticoid dexamethasone. Subsequent 5' deletion analysis indicated that the promoter region between -103 and +48 was sufficient for basal promoter activity. This region does not contain an identifiable TATA element, indicating that transcription of the glutaminase gene is driven by a TATA-less promoter. The region responsive to glucocorticoids was mapped to -252 to -103 relative to the transcription start site. PMID:9164856

  11. Adjacent proline residues in the inhibitory domain of the Oct-2 transcription factor play distinct functional roles.

    PubMed Central

    Liu, Y Z; Lee, I K; Locke, I; Dawson, S J; Latchman, D S

    1998-01-01

    A 40 amino acid region of Oct-2 from amino acids 142 to 181 functions as an active repressor domain capable of inhibiting both basal activity and activation of promoters containing a TATA box, but not of those that contain an initiator element. Based on our observation that the equivalent region of the closely related Oct-1 factor does not act as an inhibitory domain, we have mutated specific residues in the Oct-2 domain in an attempt to probe their importance in repressor domain function. Although mutations of several residues have no or minimal effect, mutation of proline 175 to arginine abolishes the ability to inhibit both basal and activated transcription. In contrast, mutation of proline 174 to arginine confers upon the domain the ability to repress activation of an initiator-containing promoter by acidic activation domains, and also suppresses the effect of the proline 175 mutation. Hence, adjacent proline residues play key roles in the functioning of the inhibitory domain and in limiting its specificity to TATA-box-containing promoters. PMID:9580701

  12. Theoretical estimates of exposure timescales of protein binding sites on DNA regulated by nucleosome kinetics.

    PubMed

    Parmar, Jyotsana J; Das, Dibyendu; Padinhateeri, Ranjith

    2016-02-29

    It is being increasingly realized that nucleosome organization on DNA crucially regulates DNA-protein interactions and the resulting gene expression. While the spatial character of the nucleosome positioning on DNA has been experimentally and theoretically studied extensively, the temporal character is poorly understood. Accounting for ATPase activity and DNA-sequence effects on nucleosome kinetics, we develop a theoretical method to estimate the time of continuous exposure of binding sites of non-histone proteins (e.g. transcription factors and TATA binding proteins) along any genome. Applying the method to Saccharomyces cerevisiae, we show that the exposure timescales are determined by cooperative dynamics of multiple nucleosomes, and their behavior is often different from expectations based on static nucleosome occupancy. Examining exposure times in the promoters of GAL1 and PHO5, we show that our theoretical predictions are consistent with known experiments. We apply our method genome-wide and discover huge gene-to-gene variability of mean exposure times of TATA boxes and patches adjacent to TSS (+1 nucleosome region); the resulting timescale distributions have non-exponential tails. PMID:26553807

  13. Conserved enhancer and silencer elements responsible for differential Adh transcription in Drosophila cell lines.

    PubMed Central

    Ayer, S; Benyajati, C

    1990-01-01

    The distal promoter of Adh is differentially expressed in Drosophila tissue culture cell lines. After transfection with an exogenous Adh gene, there was a specific increase in distal alcohol dehydrogenase (ADH) transcripts in ADH-expressing (ADH+) cells above the levels observed in transfected ADH-nonexpressing (ADH-) cells. We used deletion mutations and a comparative transient-expression assay to identify the cis-acting elements responsible for enhanced Adh distal transcription in ADH+ cells. DNA sequences controlling high levels of distal transcription were localized to a 15-base-pair (bp) region nearly 500 bp upstream of the distal RNA start site. In addition, a 61-bp negative cis-acting element was found upstream from and adjacent to the enhancer. When this silencer element was deleted, distal transcription increased only in the ADH+ cell line. These distant upstream elements must interact with the promoter elements, the Adf-1-binding site and the TATA box, as they only influenced transcription when at least one of these two positive distal promoter elements was present. Internal deletions targeted to the Adf-1-binding site or the TATA box reduced transcription in both cell types but did not affect the transcription initiation site. Distal transcription in transfected ADH- cells appears to be controlled primarily through these promoter elements and does not involve the upstream regulatory elements. Evolutionary conservation in distantly related Drosophila species suggests the importance of these upstream elements in correct developmental and tissue-specific expression of ADH. Images PMID:1694013

  14. Biochemical and genetic characterization of a yeast TFIID mutant that alters transcription in vivo and DNA binding in vitro.

    PubMed Central

    Arndt, K M; Ricupero, S L; Eisenmann, D M; Winston, F

    1992-01-01

    A mutation in the gene that encodes Saccharomyces cerevisiae TFIID (SPT15), which was isolated in a selection for mutations that alter transcription in vivo, changes a single amino acid in a highly conserved region of the second direct repeat in TFIID. Among eight independent spt15 mutations, seven cause this same amino acid change, Leu-205 to Phe. The mutant TFIID protein (L205F) binds with greater affinity than that of wild-type TFIID to at least two nonconsensus TATA sites in vitro, showing that the mutant protein has altered DNA binding specificity. Site-directed mutations that change Leu-205 to five different amino acids cause five different phenotypes, demonstrating the importance of this amino acid in vivo. Virtually identical phenotypes were observed when the same amino acid changes were made at the analogous position, Leu-114, in the first repeat of TFIID. Analysis of these mutations and additional mutations in the most conserved regions of the repeats, in conjunction with our DNA binding results, suggests that these regions of the repeats play equivalent roles in TFIID function, possibly in TATA box recognition. Images PMID:1569955

  15. Cyclin E/Cdk2, P/CAF, and E1A regulate the transactivation of the c-myc promoter by FOXM1

    SciTech Connect

    Wierstra, Inken Alves, Juergen

    2008-03-28

    FOXM1c transactivates the c-myc promoter by binding directly to its TATA-boxes. The present study demonstrates that the transactivation of the c-myc promoter by FOXM1c is enhanced by the key proliferation signal cyclin E/Cdk2, but repressed by P/CAF and the adenoviral oncoprotein E1A. Furthermore, FOXM1c interacts with the coactivator and histone acetyltransferase P/CAF. This study shows that, on the c-myc-P1 TATA-box, FOXM1c does not function simply as normal transcription factor just binding to an unusual site. Moreover, the inhibitory N-terminus of FOXM1c does not inhibit its transrepression domain or its EDA. Others reported that a cyclin/Cdk-binding LXL-motif of the splice variant FoxM1b is required for its interaction with Cdk2, Cdk1, and p27, its phosphorylation by Cdk1 and its activation by Cdc25B. In contrast, we now demonstrate that this LXL-motif is not required for the activation of FOXM1c by cyclin D1/Cdk4, cyclin E/Cdk and cyclin A/Cdk2 or for the repression of FOXM1c by p27.

  16. DNA sequence preferences of several AT-selective minor groove binding ligands.

    PubMed Central

    Abu-Daya, A; Brown, P M; Fox, K R

    1995-01-01

    We have examined the interaction of distamycin, netropsin, Hoechst 33258 and berenil, which are AT-selective minor groove-binding ligands, with synthetic DNA fragments containing different arrangements of AT base pairs by DNase I footprinting. For fragments which contain multiple blocks of (A/T)4 quantitative DNase I footprinting reveals that AATT and AAAA are much better binding sites than TTAA and TATA. Hoechst 33258 shows that greatest discrimination between these sites with a 50-fold difference in affinity between AATT and TATA. Alone amongst these ligands, Hoechst 33258 binds to AATT better than AAAA. These differences in binding to the various AT-tracts are interpreted in terms of variations in DNA minor groove width and suggest that TpA steps within an AT-tract decrease the affinity of these ligands. The behaviour of each site also depends on the flanking sequences; adjacent pyrimidine-purine steps cause a decrease in affinity. The precise ranking order for the various binding sites is not the same for each ligand. Images PMID:7567447

  17. Characteristics of a strong promoter from figwort mosaic virus: comparison with the analogous 35S promoter from cauliflower mosaic virus and the regulated mannopine synthase promoter.

    PubMed

    Sanger, M; Daubert, S; Goodman, R M

    1990-03-01

    A segment of DNA from the genome of figwort mosaic virus (FMV) strain M3 possesses promoter activity when tested in electroporated protoplasts from, and transgenic plants of, Nicotiana tabacum cv. Xanthi nc. The 1.1 kb DNA segment, designated the '34S' promoter, is derived from a position on the FMV genome comparable to the position on the cauliflower mosaic virus (CaMV) genome containing the 35S promoter. The 34S and 35S promoters show approximately 63% nucleotide homology in the TATA, CCACT, and -18 to +1 domains, but in sequences further upstream the homology drops below 50%. Promoter activities were estimated using beta-glucuronidase and neomycin phosphotransferase II reporter gene systems. The activity of the 34S promoter segment approximates that of the 35S promoter in both protoplast transient expression assays and in stably transformed tobacco plants. Truncation of 5' sequences from the 34S promoter indicates that promoter strength depends upon DNA sequences located several hundred nucleotides upstream from the TATA box. In leaf tissue the 34S promoter is 20-fold more active than the mannopine synthase (MAS) promoter from Agrobacterium tumefaciens T-DNA. The 34S promoter lacks the root-specific and wound-stimulated expression of the MAS promoter, showing relatively uniform root, stem, leaf, and floral activities. PMID:2102823

  18. Structural analysis of substrate binding by the TatBC component of the twin-arginine protein transport system.

    PubMed

    Tarry, Michael J; Schäfer, Eva; Chen, Shuyun; Buchanan, Grant; Greene, Nicholas P; Lea, Susan M; Palmer, Tracy; Saibil, Helen R; Berks, Ben C

    2009-08-11

    The Tat system transports folded proteins across the bacterial cytoplasmic membrane and the thylakoid membrane of plant chloroplasts. In Escherichia coli substrate proteins initially bind to the integral membrane TatBC complex which then recruits the protein TatA to effect translocation. Overproduction of TatBC and the substrate protein SufI in the absence of TatA led to the accumulation of TatBC-SufI complexes that could be purified using an affinity tag on the substrate. Three-dimensional structures of the TatBC-SufI complexes and unliganded TatBC were obtained by single-particle electron microscopy and random conical tilt reconstruction. Comparison of the structures shows that substrate molecules bind on the periphery of the TatBC complex and that substrate binding causes a significant reduction in diameter of the TatBC part of the complex. Although the TatBC complex contains multiple copies of the signal peptide-binding TatC protomer, purified TatBC-SufI complexes contain only 1 or 2 SufI molecules. Where 2 substrates are present in the TatBC-SufI complex, they are bound at adjacent sites. These observations imply that only certain TatC protomers within the complex interact with substrate or that there is a negative cooperativity of substrate binding. Similar TatBC-substrate complexes can be generated by an alternative in vitro reconstitution method and using a different substrate protein. PMID:19666509

  19. Mapping precursor-binding site on TatC subunit of twin arginine-specific protein translocase by site-specific photo cross-linking.

    PubMed

    Zoufaly, Stefan; Fröbel, Julia; Rose, Patrick; Flecken, Tobias; Maurer, Carlo; Moser, Michael; Müller, Matthias

    2012-04-13

    A number of secreted precursor proteins of bacteria, archaea, and plant chloroplasts stand out by a conserved twin arginine-containing sequence motif in their signal peptides. Many of these precursor proteins are secreted in a completely folded conformation by specific twin arginine translocation (Tat) machineries. Tat machineries are high molecular mass complexes consisting of two types of membrane proteins, a hexahelical TatC protein, and usually one or two single-spanning membrane proteins, called TatA and TatB. TatC has previously been shown to be involved in the recognition of twin arginine signal peptides. We have performed an extensive site-specific cross-linking analysis of the Escherichia coli TatC protein under resting and translocating conditions. This strategy allowed us to map the recognition site for twin arginine signal peptides to the cytosolic N-terminal region and first cytosolic loop of TatC. In addition, discrete contact sites between TatC, TatB, and TatA were revealed. We discuss a tentative model of how a twin arginine signal sequence might be accommodated in the Tat translocase. PMID:22362773

  20. Differential interactions between a twin-arginine signal peptide and its translocase in Escherichia coli.

    PubMed

    Alami, Meriem; Lüke, Iris; Deitermann, Sandra; Eisner, Gottfried; Koch, Hans-Georg; Brunner, Joseph; Müller, Matthias

    2003-10-01

    The twin-arginine translocation (Tat) machinery of the Escherichia coli inner membrane is dedicated to the export of proteins harboring a conserved SRRxFLK motif in their signal sequence. TatA, TatB, and TatC are the functionally essential constituents of the Tat machinery, but their precise function is unknown. Using site-specific crosslinking, we have analyzed interactions of the twin-arginine precursor preSufI with the Tat proteins upon targeting to inner membrane vesicles. TatA association is observed only in the presence of a transmembrane H(+) gradient. TatB is found in contact with the entire signal sequence and adjacent parts of mature SufI. Interaction of TatC with preSufI is, however, restricted to a discrete area around the consensus motif. The results reveal a hierarchy in targeting of a Tat substrate such that for the primary interaction, TatC is both necessary and sufficient while a subsequent association with TatB likely mediates transfer from TatC to the actual Tat pore. PMID:14580344

  1. A new RHQT Nb3Al superconducting wire with a Ta/Cu/Ta three-layer filament-barrier structure

    NASA Astrophysics Data System (ADS)

    Takeuchi, Takao; Tsuchiya, Kiyosumi; Nakagawa, Kazuhiko; Nimori, Shigeki; Banno, Nobuya; Iijima, Yasuo; Kikuchi, Akihiro; Nakamoto, Tatsushi

    2012-06-01

    To suppress the low-magnetic-field instability (flux jumps in low magnetic fields) of a rapid-heating, quenching and transformation (RHQT) processed Nb3Al superconductor, we had previously modified the cross-sectional design of an RHQT Nb3Al by adopting a Ta filament-barrier structure. Unlike Nb barriers, Ta barriers are not superconducting in magnetic fields at 4.2 K so that they electromagnetically decouple filaments. However, small flux jumps still occurred at 1.8 K, which is a typical operating temperature for the magnets used in high-energy particle accelerators. Furthermore, poor bonding at the Ta/Ta interface between neighboring Ta-coated jelly-roll (JR) filaments frequently caused precursor wires to break during drawing. To overcome these problems, we fabricated a new RHQT Nb3Al wire with a Ta/Cu/Ta three-layer filament-barrier structure for which an internal stabilization technique (Cu rods encased in Ta are dispersed in the wire cross section) was extended. Removing the Ta/Ta interface in the interfilamentary barrier (JR filament/Ta/Cu/Ta/JR filament) allowed precursor wires to be drawn without breaking. Furthermore, the Cu filament barrier electromagnetically decoupled filaments to suppress flux jumps at 1.8 K. The ductile Cu layer also improved the bending strain tolerance of RHQT Nb3Al.

  2. Insertional activation of a promoterless thymidine kinase gene

    SciTech Connect

    Hiller, S.; Hengstler, M.; Kunze, M.; Knippers, R.

    1988-08-01

    A plasmid carrying a promoterless herpes complex virus thymidine kinase gene was transfected via calcium phosphate precipitation into LM (tk/sup -/) mouse fibroblast cells. The transfected gene was efficiently expressed, as the transfected cells grew perfectly well in selective hypoxanthine-aminopterin-thymidine medium, suggesting that the thymidine kinase-coding region became linked to a promoterlike element on integration into the recipient genome. To investigate the structure of the surrogate promoter, the authors first isolated the integrated gene from a genomic library. The nucleotide sequence of the DNA adjacent to the thymidine kinase-coding sequence was then determined. They found, first, that the integration of the transfected DNA apparently occurred by a blunt end ligation mechanism involving no obvious sequence similarities between integrated and recipient DNA and, second, that the 5'-flanking region included a TATA box, to CCAAT boxes, and a GC box element. However, the TATA box motif and the most proximal CCAAT box appeared to be sufficient of full promoter activity, as determined by the transfection efficiencies of appropriate plasmid constructs. Except for these canonical promoter elements, the surrogate promoter had no obvious similarities to known thymidine kinase gene promoters.

  3. Chromatin remodeling during Saccharomyces cerevisiae ADH2 gene activation.

    PubMed

    Verdone, L; Camilloni, G; Di Mauro, E; Caserta, M

    1996-05-01

    We have analyzed at both low and high resolution the distribution of nucleosomes over the Saccharomyces cerevisiae ADH2 promoter region in its chromosomal location, both under repressing (high-glucose) conditions and during derepression. Enzymatic treatments (micrococcal nuclease and restriction endonucleases) were used to probe the in vivo chromatin structure during ADH2 gene activation. Under glucose-repressed conditions, the ADH2 promoter was bound by a precise array of nucleosomes, the principal ones positioned at the RNA initiation sites (nucleosome +1), at the TATA box (nucleosome -1), and upstream of the ADR1-binding site (UAS1) (nucleosome -2). The UAS1 sequence and the adjacent UAS2 sequence constituted a nucleosome-free region. Nucleosomes -1 and +1 were destabilized soon after depletion of glucose and had become so before the appearance of ADH2 mRNA. When the transcription rate was high, nucleosomes -2 and +2 also underwent rearrangement. When spheroplasts were prepared from cells grown in minimal medium, detection of this chromatin remodeling required the addition of a small amount of glucose. Cells lacking the ADR1 protein did not display any of these chromatin modifications upon glucose depletion. Since the UAS1 sequence to which Adr1p binds is located immediately upstream of nucleosome -1, Adr1p is presumably required for destabilization of this nucleosome and for aiding the TATA-box accessibility to the transcription machinery. PMID:8628264

  4. Architecture of a yeast U6 RNA gene promoter.

    PubMed Central

    Eschenlauer, J B; Kaiser, M W; Gerlach, V L; Brow, D A

    1993-01-01

    The promoters of vertebrate and yeast U6 small nuclear RNA genes are structurally dissimilar, although both are recognized by RNA polymerase III. Vertebrate U6 RNA genes have exclusively upstream promoters, while the U6 RNA gene from the yeast Saccharomyces cerevisiae (SNR6) has internal and downstream promoter elements that match the tRNA gene intragenic A- and B-block elements, respectively. Substitution of the SNR6 A or B block greatly diminished U6 RNA accumulation in vivo, and a subcellular extract competent for RNA polymerase III transcription generated nearly identical DNase I protection patterns over the SNR6 downstream B block and a tRNA gene intragenic B block. We conclude that the SNR6 promoter is functionally similar to tRNA gene promoters, although the effects of extragenic deletion mutations suggest that the downstream location of the SNR6 B block imposes unique positional constraints on its function. Both vertebrate and yeast U6 RNA genes have an upstream TATA box element not normally found in tRNA genes. Substitution of the SNR6 TATA box altered the site of transcription initiation in vivo, while substitution of sequences further upstream had no effect on SNR6 transcription. We present a model for the SNR6 transcription complex that explains these results in terms of their effects on the binding of transcription initiation factor TFIIIB. Images PMID:8474459

  5. Selection of Reference Genes for Expression Analysis Using Quantitative Real-Time PCR in the Pea Aphid, Acyrthosiphon pisum (Harris) (Hemiptera, Aphidiae)

    PubMed Central

    Liu, Yong; Zhou, Xuguo

    2014-01-01

    To facilitate gene expression study and obtain accurate qRT-PCR analysis, normalization relative to stable expressed housekeeping genes is required. In this study, expression profiles of 11 candidate reference genes, including actin (Actin), elongation factor 1 α (EF1A), TATA-box-binding protein (TATA), ribosomal protein L12 (RPL12), β-tubulin (Tubulin), NADH dehydrogenase (NADH), vacuolar-type H+-ATPase (v-ATPase), succinate dehydrogenase B (SDHB), 28S ribosomal RNA (28S), 16S ribosomal RNA (16S), and 18S ribosomal RNA (18S) from the pea aphid Acyrthosiphon pisum, under different developmental stages and temperature conditions, were investigated. A total of four analytical tools, geNorm, Normfinder, BestKeeper, and the ΔCt method, were used to evaluate the suitability of these genes as endogenous controls. According to RefFinder, a web-based software tool which integrates all four above-mentioned algorithms to compare and rank the reference genes, SDHB, 16S, and NADH were the three most stable house-keeping genes under different developmental stages and temperatures. This work is intended to establish a standardized qRT-PCR protocol in pea aphid and serves as a starting point for the genomics and functional genomics research in this emerging insect model. PMID:25423476

  6. Analysis of selected transcript levels in porcine spermatozoa, oocytes, zygotes and two-cell stage embryos.

    PubMed

    Kempisty, Bartosz; Antosik, Paweł; Bukowska, Dorota; Jackowska, Marta; Lianeri, Margarita; Jaśkowski, Jedrzej M; Jagodziński, Paweł P

    2008-01-01

    It has been suggested that spermatozoa can deliver mRNAs to the oocyte during fertilisation. Using reverse transcription and real-time quantitative polymerase chain reaction analysis (RQ-PCR), we evaluated the presence of clusterin (CLU), protamine 2 (PRM2), calmegin (CLGN), cAMP-response element modulator protein (CREM), methyltransferase 1 (DNMT1), linker histone 1 (H1), protamine 1 (PRM1), TATA box-binding protein associated factor 1 (TAF1) and TATA box-binding protein (TBP) in porcine mature oocytes, zygotes and two-cell stage embryos. Spermatozoa isolated from semen samples of boars contained all transcripts investigated, whereas oocytes contained only CREM, H1, TAF1, and TBP mRNAs. The zygote and two-cell stage embryos contained CLU, CREM, H1, PRM1, PRM2, TAF1 and TBP transcripts. Our observations suggest that porcine spermatozoa may delivery CLU, PRM1 and PRM2 mRNAs to the oocyte, which may contribute to zygotic and early embryonic development. PMID:18462614

  7. Molecular cloning and characterization of GbDXS and GbGGPPS gene promoters from Ginkgo biloba.

    PubMed

    Xu, F; Huang, X H; Li, L L; Deng, G; Cheng, H; Rong, X F; Li, J B; Cheng, S Y

    2013-01-01

    Ginkgolides are key pharmaceutical components in Ginkgo biloba leaves. 1-Deoxy-D-xylulose-5-phosphate synthase (GbDXS) and geranylgeranyl pyrophosphate (GbGGPPS) genes are critical genes involved in ginkgolide biosynthesis. In this study, the promoters of GbDXS and GGPPS, with 676 and 570 bp in length, respectively, were cloned by chromosome walking. The cis-elements of GbDXS and GbGGPPS promoters were predicted and analyzed by the plant cis-acting regulatory element (CARE) database. We found some major cis-elements in the sequence of GbDXS and GbGGPPS promoters. The GbDXS promoter has 3 TATA boxes, 10 CAAT boxes, 6 GATA boxes, and 1 I box. The GbGGPPS promoter has 1 TATA box, 6 CAAT boxes, 6 GATA boxes, and 4 I boxes. Furthermore, some stress-related cis-elements in the promoters of GbDXS and GbGGPPS were found to be light-regulated elements, including sequences over-represented in light-induced promoters (SORLIP1- AT), GATA box, and I box, a gibberellin-responsive element (WRKY), salicylic acid-induced (GT-1), cold- and dehydration-responsive (MYC-Core), and copper-inducible (CURE-Core). Further analyses of these cis-elements will aid in elucidating the molecular mechanisms regulating the expression of the GbDXS and GbGGPPS genes during ginkgolide accumulation in G. biloba. PMID:23408416

  8. Bromodomain factor 1 corresponds to a missing piece of yeast TFIID

    PubMed Central

    Matangkasombut, Oranart; Buratowski, Robin M.; Swilling, Nathan W.; Buratowski, Stephen

    2000-01-01

    The basal transcription factor TFIID consists of the TATA-binding protein (TBP) and TBP-associated factors (TAFs). Yeast Taf67 is homologous to mammalian TAFII55. Using a yeast two-hybrid screen to identify proteins that interact with Taf67, we isolated Bromodomain factor 1 (Bdf1) and its homolog (Bdf2). The Bdf proteins are genetically redundant, as cells are inviable without at least one of the two BDF genes. Both proteins contain two bromodomains, a motif found in several proteins involved in transcription and chromatin modification. The BDF genes interact genetically with TAF67. Furthermore, Bdf1 associates with TFIID and is recruited to a TATA-containing promoter. Deletion of Bdf1 or the Taf67 Bdf-interacting domain leads to defects in gene expression. Interestingly, the higher eukaryotic TAFII250 has an acetyltransferase activity, two bromodomains, and an associated kinase activity. Its yeast homolog, Taf145, has acetyltransferase activity but lacks the bromodomains and kinase. Bdf1, like TAFII250, has a kinase activity that maps carboxy-terminal to the bromodomains. The structural and functional similarities suggest that Bdf1 corresponds to the carboxy-terminal region of higher eukaryotic TAFII250 and that the interaction between TFIID and Bdf1 is important for proper gene expression. PMID:10783167

  9. Complete architecture of the archaeal RNA polymerase open complex from single-molecule FRET and NPS

    NASA Astrophysics Data System (ADS)

    Nagy, Julia; Grohmann, Dina; Cheung, Alan C. M.; Schulz, Sarah; Smollett, Katherine; Werner, Finn; Michaelis, Jens

    2015-01-01

    The molecular architecture of RNAP II-like transcription initiation complexes remains opaque due to its conformational flexibility and size. Here we report the three-dimensional architecture of the complete open complex (OC) composed of the promoter DNA, TATA box-binding protein (TBP), transcription factor B (TFB), transcription factor E (TFE) and the 12-subunit RNA polymerase (RNAP) from Methanocaldococcus jannaschii. By combining single-molecule Förster resonance energy transfer and the Bayesian parameter estimation-based Nano-Positioning System analysis, we model the entire archaeal OC, which elucidates the path of the non-template DNA (ntDNA) strand and interaction sites of the transcription factors with the RNAP. Compared with models of the eukaryotic OC, the TATA DNA region with TBP and TFB is positioned closer to the surface of the RNAP, likely providing the mechanism by which DNA melting can occur in a minimal factor configuration, without the dedicated translocase/helicase encoding factor TFIIH.

  10. Complete architecture of the archaeal RNA polymerase open complex from single-molecule FRET and NPS.

    PubMed

    Nagy, Julia; Grohmann, Dina; Cheung, Alan C M; Schulz, Sarah; Smollett, Katherine; Werner, Finn; Michaelis, Jens

    2015-01-01

    The molecular architecture of RNAP II-like transcription initiation complexes remains opaque due to its conformational flexibility and size. Here we report the three-dimensional architecture of the complete open complex (OC) composed of the promoter DNA, TATA box-binding protein (TBP), transcription factor B (TFB), transcription factor E (TFE) and the 12-subunit RNA polymerase (RNAP) from Methanocaldococcus jannaschii. By combining single-molecule Förster resonance energy transfer and the Bayesian parameter estimation-based Nano-Positioning System analysis, we model the entire archaeal OC, which elucidates the path of the non-template DNA (ntDNA) strand and interaction sites of the transcription factors with the RNAP. Compared with models of the eukaryotic OC, the TATA DNA region with TBP and TFB is positioned closer to the surface of the RNAP, likely providing the mechanism by which DNA melting can occur in a minimal factor configuration, without the dedicated translocase/helicase encoding factor TFIIH. PMID:25635909

  11. Single molecule microscopy reveals mechanistic insight into RNA polymerase II preinitiation complex assembly and transcriptional activity

    PubMed Central

    Horn, Abigail E.; Kugel, Jennifer F.; Goodrich, James A.

    2016-01-01

    Transcription by RNA polymerase II (Pol II) is a complex process that requires general transcription factors and Pol II to assemble on DNA into preinitiation complexes that can begin RNA synthesis upon binding of NTPs (nucleoside triphosphate). The pathways by which preinitiation complexes form, and how this impacts transcriptional activity are not completely clear. To address these issues, we developed a single molecule system using TIRF (total internal reflection fluorescence) microscopy and purified human transcription factors, which allows us to visualize transcriptional activity at individual template molecules. We see that stable interactions between polymerase II (Pol II) and a heteroduplex DNA template do not depend on general transcription factors; however, transcriptional activity is highly dependent upon TATA-binding protein, TFIIB and TFIIF. We also found that subsets of general transcription factors and Pol II can form stable complexes that are precursors for functional transcription complexes upon addition of the remaining factors and DNA. Ultimately we found that Pol II, TATA-binding protein, TFIIB and TFIIF can form a quaternary complex in the absence of promoter DNA, indicating that a stable network of interactions exists between these proteins independent of promoter DNA. Single molecule studies can be used to learn how different modes of preinitiation complex assembly impact transcriptional activity. PMID:27112574

  12. Structure and chromosomal localization of the human gene of the phosphotyrosyl phosphatase activator (PTPA) of protein phosphatase 2A

    SciTech Connect

    Van Hoof, C.; Cayla, X.; Merlevede, W.; Goris, J.

    1995-07-20

    The PTPA gene encodes a specific phosphotyrosyl phosphatase activator of the dimeric form of protein phosphatase 2A. PTPA, cloned from human genomic libraries, is encoded by one single-copy gene, composed of 10 exons and 9 introns with a total length of about 60 kb. The transcription start site was determined, and the 5{prime} flanking sequence was analyzed for its potential as a promotor. This region lacks a TATA sequence in the appropriate position relative to the transcription start, is very GC-rich, and contains upstream of the transcription start four Sp1 sites, a feature common to many TATA-less promotors. Based on the homology with DNA binding consensus sequences of transcription factors, we identified in this promotor region several putative DNA binding sites for transcription factors, such as NF-{kappa}B, Myb, Ets-1, Myc, and ATF. Transfection experiments with a construct containing the PTPA promotor region inserted 5{prime} of a luciferase reporter gene revealed that the 5{prime} flanking sequence of the PTPA gene indeed displayed promotor activity that seems to be cell-line dependent. By fluorescence in situ hybridization and G-banding, the PTPA gene was localized to the 9q34 region. The PTPA gene is positioned centromeric of c-abl in a region embracing several genes implicated in oncogenesis. 28 refs., 8 figs., 1 tab.

  13. Structure of promoter-bound TFIID and model of human pre-initiation complex assembly.

    PubMed

    Louder, Robert K; He, Yuan; López-Blanco, José Ramón; Fang, Jie; Chacón, Pablo; Nogales, Eva

    2016-03-31

    The general transcription factor IID (TFIID) plays a central role in the initiation of RNA polymerase II (Pol II)-dependent transcription by nucleating pre-initiation complex (PIC) assembly at the core promoter. TFIID comprises the TATA-binding protein (TBP) and 13 TBP-associated factors (TAF1-13), which specifically interact with a variety of core promoter DNA sequences. Here we present the structure of human TFIID in complex with TFIIA and core promoter DNA, determined by single-particle cryo-electron microscopy at sub-nanometre resolution. All core promoter elements are contacted by subunits of TFIID, with TAF1 and TAF2 mediating major interactions with the downstream promoter. TFIIA bridges the TBP-TATA complex with lobe B of TFIID. We also present the cryo-electron microscopy reconstruction of a fully assembled human TAF-less PIC. Superposition of common elements between the two structures provides novel insights into the general role of TFIID in promoter recognition, PIC assembly, and transcription initiation. PMID:27007846

  14. Regulatory elements mediating transcription from the Drosophila melanogaster actin 5C proximal promoter.

    PubMed Central

    Chung, Y T; Keller, E B

    1990-01-01

    The major cytoskeletal actin gene of Drosophila melanogaster, the actin 5C gene, has two promoters, the proximal one of which controls constitutive synthesis of actin in all growing tissues. To locate regulatory elements required for constitutive activity of the proximal promoter, mutants of this promoter were fused to the bacterial chloramphenicol acetyltransferase gene and assayed for transient expression activity in cultured Drosophila embryonic Schneider line 2 cells. An essential regulatory element has been located 313 base pairs upstream from the cap site. Deletion of this element lowered expression to one-third of the wild-type level. The element has the sequence AAGTTGTAGTTG, as shown by protein-binding footprinting with the reagent methidiumpropyl-EDTA-Fe(II). This element is probably not a general one, since it was not detected in a search of the published 5'-flanking sequences of 27 Drosophila genes. In addition to this regulatory element, there are five GAGA elements in the actin 5C proximal promoter, some or all of which are essential for the promoter activity as shown by an in vivo competition assay. Although this promoter has no classical TATA element, there is an essential promoter region about 35 base pairs upstream from the cap site that could be a TATA surrogate. The promoter also shows sequences homologous to the alcohol dehydrogenase factor 1-binding site and to the core of the vertebrate serum response element, but mutations of these sites did not affect promoter activity in transient expression assays. Images PMID:2104658

  15. Genomic organization and transcriptional analysis of the human l-glutaminase gene.

    PubMed Central

    Pérez-Gómez, Cristina; Matés, José M; Gómez-Fabre, Pedro M; del Castillo-Olivares, Antonio; Alonso, Francisco J; Márquez, Javier

    2003-01-01

    In mammals, glutaminase (GA) is expressed in most tissues, but the regulation of organ-specific expression is largely unknown. Therefore, as an essential step towards studying the regulation of GA expression, the human liver-type GA (hLGA) gene has been characterized. LGA genomic sequences were isolated using the genome walking technique. Analysis and comparison of these sequences with two LGA cDNA clones and the Human Genome Project database, allowed the determination of the genomic organization of the LGA gene. The gene has 18 exons and is approx. 18 kb long. All exon/intron junction sequences conform to the GT/AG rule. Progressive deletion analysis of LGA promoter-luciferase constructs indicated that the core promoter is located between nt -141 and +410, with several potential regulatory elements: CAAT, GC, TATA-like, Ras-responsive element binding protein and specificity protein 1 (Sp1) sites. The minimal promoter was mapped within +107 and +410, where only an Sp1 binding site is present. Mutation experiments suggested that two CAAT recognition elements near the transcription-initiation site (-138 and -87), play a crucial role for optimal promoter activity. Electrophoretic mobility-shift assays confirmed the importance of CAAT- and TATA-like boxes to enhance basal transcription, and demonstrated that HNF-1 motif is a significant distal element for transcriptional regulation of the hLGA gene. PMID:12444921

  16. Regulation of tryptophan operon expression in the archaeon Methanothermobacter thermautotrophicus.

    PubMed

    Xie, Yunwei; Reeve, John N

    2005-09-01

    Conserved trp genes encode enzymes that catalyze tryptophan biosynthesis in all three biological domains, and studies of their expression in Bacteria and eukaryotes have revealed a variety of different regulatory mechanisms. The results reported here provide the first detailed description of an archaeal trp gene regulatory system. We have established that the trpEGCFBAD operon in Methanothermobacter thermautotrophicus is transcribed divergently from a gene (designated trpY) that encodes a tryptophan-sensitive transcription regulator. TrpY binds to TRP box sequences (consensus, TGTACA) located in the overlapping promoter regions between trpY and trpE, inhibiting trpY transcription in the absence of tryptophan and both trpY and trpEGCFBAD transcription in the presence of tryptophan. TrpY apparently inhibits trpY transcription by blocking RNA polymerase access to the site of trpY transcription initiation and represses trpEGCFBAD transcription by preventing TATA box binding protein (TBP) binding to the TATA box sequence. Given that residue 2 (W2) is the only tryptophan in TrpY and in TrpY homologues in other Euryarchaea and that there is only one tryptophan codon in the entire trpEGCFBAD operon (trpB encodes W175), expression of the trp operon may also be regulated in vivo by the supply of charged tRNA(Trp) available to translate the second codon of the trpY mRNA. PMID:16159776

  17. RNA Polymerase III promoter screen uncovers a novel noncoding RNA family conserved in Caenorhabditis and other clade V nematodes.

    PubMed

    Gruber, Andreas R

    2014-07-10

    RNA Polymerase III is a highly specialized enzyme complex responsible for the transcription of a very distinct set of housekeeping noncoding RNAs including tRNAs, 7SK snRNA, Y RNAs, U6 snRNA, and the RNA components of RNaseP and RNaseMRP. In this work we have utilized the conserved promoter structure of known RNA Polymerase III transcripts consisting of characteristic sequence elements termed proximal sequence elements (PSE) A and B and a TATA-box to uncover a novel RNA Polymerase III-transcribed, noncoding RNA family found to be conserved in Caenorhabditis as well as other clade V nematode species. Homology search in combination with detailed sequence and secondary structure analysis revealed that members of this novel ncRNA family evolve rapidly, and only maintain a potentially functional small stem structure that links the 5' end to the very 3' end of the transcript and a small hairpin structure at the 3' end. This is most likely required for efficient transcription termination. In addition, our study revealed evidence that canonical C/D box snoRNAs are also transcribed from a PSE A-PSE B-TATA-box promoter in Caenorhabditis elegans. PMID:24792899

  18. Initial assembly steps of a translocase for folded proteins

    PubMed Central

    Blümmel, Anne-Sophie; Haag, Laura A.; Eimer, Ekaterina; Müller, Matthias; Fröbel, Julia

    2015-01-01

    The so-called Tat (twin-arginine translocation) system transports completely folded proteins across cellular membranes of archaea, prokaryotes and plant chloroplasts. Tat-directed proteins are distinguished by a conserved twin-arginine (RR-) motif in their signal sequences. Many Tat systems are based on the membrane proteins TatA, TatB and TatC, of which TatB and TatC are known to cooperate in binding RR-signal peptides and to form higher-order oligomeric structures. We have now elucidated the fine architecture of TatBC oligomers assembled to form closed intramembrane substrate-binding cavities. The identification of distinct homonymous and heteronymous contacts between TatB and TatC suggest that TatB monomers coalesce into dome-like TatB structures that are surrounded by outer rings of TatC monomers. We also show that these TatBC complexes are approached by TatA protomers through their N-termini, which thereby establish contacts with TatB and membrane-inserted RR-precursors. PMID:26068441

  19. Engineering Promoter Architecture in Oleaginous Yeast Yarrowia lipolytica.

    PubMed

    Shabbir Hussain, Murtaza; Gambill, Lauren; Smith, Spencer; Blenner, Mark A

    2016-03-18

    Eukaryotic promoters have a complex architecture to control both the strength and timing of gene transcription spanning up to thousands of bases from the initiation site. This complexity makes rational fine-tuning of promoters in fungi difficult to predict; however, this very same complexity enables multiple possible strategies for engineering promoter strength. Here, we studied promoter architecture in the oleaginous yeast, Yarrowia lipolytica. While recent studies have focused on upstream activating sequences, we systematically examined various components common in fungal promoters. Here, we examine several promoter components including upstream activating sequences, proximal promoter sequences, core promoters, and the TATA box in autonomously replicating expression plasmids and integrated into the genome. Our findings show that promoter strength can be fine-tuned through the engineering of the TATA box sequence, core promoter, and upstream activating sequences. Additionally, we identified a previously unreported oleic acid responsive transcription enhancement in the XPR2 upstream activating sequences, which illustrates the complexity of fungal promoters. The promoters engineered here provide new genetic tools for metabolic engineering in Y. lipolytica and provide promoter engineering strategies that may be useful in engineering other non-model fungal systems. PMID:26635071

  20. Using DNA mechanics to predict intrinsic and extrinsic nucleosome positioning signals

    NASA Astrophysics Data System (ADS)

    Morozov, Alexandre

    2008-03-01

    In eukaryotic genomes, nucleosomes function to compact DNA and to regulate access to it both by simple physical occlusion and by providing the substrate for numerous covalent epigenetic tags. While nucleosome positions in vitro are determined by sequence alone, in vivo competition with other DNA-binding factors and action of chromatin remodeling enzymes play a role that needs to be quantified. We developed a biophysical, DNA mechanics-based model for the sequence dependence of DNA bending energies, and validated it against a collection of in vitro free energies of nucleosome formation and a nucleosome crystal structure; we also successfully designed both strong and poor histone binding sequences ab initio. For in vivo data from S.cerevisiae, the strongest positioning signal came from the competition with other factors rather than intrinsic nucleosome sequence preferences. Based on sequence alone, our model predicts that functional transcription factor binding sites tend to be covered by nucleosomes, yet are uncovered in vivo because functional sites cluster within a single nucleosome footprint and thus make transcription factors bind cooperatively. Similarly a weak enhancement of nucleosome binding in the TATA region becomes a strong depletion when the TATA-binding protein is included, in quantitative agreement with experiment. Our model distinguishes multiple ways in which genomic sequence influences nucleosome positions, and thus provides alternative explanations for several genome-wide experimental findings. In the future our approach will be used to rationally alter gene expression levels in model systems through redesign of nucleosome occupancy profiles.

  1. New Mars meteorite fall in Morocco: collecting observations and determining the spatial distribution in the strewnfield

    NASA Astrophysics Data System (ADS)

    Ibhi, Abderrahmane

    2013-01-01

    The existence of Martian meteorites in the region of Tissint (Tata, Morocco) dropped by a very bright fireball on July 18, 2011, had been notified to a group of scientists of the Ibn Zohr University of Agadir, Morocco, at the beginning of January 2012, by a nomad of Tata who had found a small fragment in the region. As soon as a scientific expedition arrived at the place of the meteorite fall, the members of the laboratory of Geo-heritage and Geo-materials Science started gathering information and collecting the debris of this Martian meteorite. The Tissint fireball has been observed and reported by numerous witnesses across the southeastern Morocco. The event was extremely valuable to the scientific community: it was the brightest and most comprehensively observed fireball in Morocco's known astronomical history. We are now in a position to draw the distribution ellipse of the fall, which starts at Jbel Al Gallab and continues in east-southeastern direction, above big rocky plateaus.

  2. Monolayers and Langmuir-Blodgett films of luminescent 1,3,5-triazine derivatives containing naphthalene or anthracene chromophores

    NASA Astrophysics Data System (ADS)

    Cai, Ya-Qi; Wu, Wei; Wang, Hua; Miyake, Jun; Qian, Dong-Jin

    2011-02-01

    Monolayer behaviors and Langmuir-Blodgett (LB) films of three luminescent aryl triazines, 2,4,6-tri(naphthalen-1-yl)-1,3,5-triazine (TN 1Ta), 2,4,6-tri(naphthalen-2-yl)-1,3,5-triazine (TN 2Ta), and 2,4,6-tri(anthracen-9-yl)-1,3,5-triazine (TATa) have been investigated. Surface pressure-area isotherms indicated that pure aryl triazines were difficult to form stable monolayers, while their mixtures with arachidic acid (AA) could be stabilized at the air-water interface. The mixed LB films of triazine-AA were deposited on substrate surfaces and analyzed by using UV-vis and infrared absorption spectra, X-ray photoelectron spectra, as well as scanning electron microscopy. Morphologies of the LB films and molecular aggregates were closely dependent on the structure of triazines and the surface pressures of deposition. Under UV radiation, TN 1Ta and TN 2Ta emitted at 410-460 nm while TATa emitted at 500-510 nm, with the emission lifetime falling into the range of 0.29 to 10.8 ns. Compared with those in solutions, the emissions of aryl triazines were red shifted in the LB films, especially for the TN 1Ta-AA and TN 2Ta-AA, which was attributed to the closely packed arrangement for the molecules in the LB films.

  3. Sequence-directed nucleosome-depletion is sufficient to activate transcription from a yeast core promoter in vivo.

    PubMed

    Ichikawa, Yuichi; Morohashi, Nobuyuki; Tomita, Nobuyuki; Mitchell, Aaron P; Kurumizaka, Hitoshi; Shimizu, Mitsuhiro

    2016-07-22

    Nucleosome-depleted regions (NDRs) (also called nucleosome-free regions or NFRs) are often found in the promoter regions of many yeast genes, and are formed by multiple mechanisms, including the binding of activators and enhancers, the actions of chromatin remodeling complexes, and the specific DNA sequences themselves. However, it remains unclear whether NDR formation per se is essential for transcriptional activation. Here, we examined the relationship between nucleosome organization and gene expression using a defined yeast reporter system, consisting of the CYC1 minimal core promoter and the lacZ gene. We introduced simple repeated sequences that should be either incorporated in nucleosomes or excluded from nucleosomes in the site upstream of the TATA boxes. The (CTG)12, (GAA)12 and (TGTAGG)6 inserts were incorporated into a positioned nucleosome in the core promoter region, and did not affect the reporter gene expression. In contrast, the insertion of (CGG)12, (TTAGGG)6, (A)34 or (CG)8 induced lacZ expression by 10-20 fold. Nucleosome mapping analyses revealed that the inserts that induced the reporter gene expression prevented nucleosome formation, and created an NDR upstream of the TATA boxes. Thus, our results demonstrated that NDR formation dictated by DNA sequences is sufficient for transcriptional activation from the core promoter in vivo. PMID:27208777

  4. Structure of silent transcription intervals and noise characteristics of mammalian genes

    PubMed Central

    Zoller, Benjamin; Nicolas, Damien; Molina, Nacho; Naef, Felix

    2015-01-01

    Mammalian transcription occurs stochastically in short bursts interspersed by silent intervals showing a refractory period. However, the underlying processes and consequences on fluctuations in gene products are poorly understood. Here, we use single allele time-lapse recordings in mouse cells to identify minimal models of promoter cycles, which inform on the number and durations of rate-limiting steps responsible for refractory periods. The structure of promoter cycles is gene specific and independent of genomic location. Typically, five rate-limiting steps underlie the silent periods of endogenous promoters, while minimal synthetic promoters exhibit only one. Strikingly, endogenous or synthetic promoters with TATA boxes show simplified two-state promoter cycles. Since transcriptional bursting constrains intrinsic noise depending on the number of promoter steps, this explains why TATA box genes display increased intrinsic noise genome-wide in mammals, as revealed by single-cell RNA-seq. These findings have implications for basic transcription biology and shed light on interpreting single-cell RNA-counting experiments. PMID:26215071

  5. [Effect of environmental and individual factors in renal lithiasis].

    PubMed

    Vasilescu, L; Ciochină, Al D; Corciovă, C

    2011-01-01

    The large number of cases with renal lithiasis occurring in the population of the south-east region of Iasi county has determined us to make a study in this region for the identification of environmental and individual factors involved in the etiopathogenesis of this disease. This study is performed to assert the corelation between the clinical and paraclinical patients data with those obtained through water and soil chemical analisys for identification of determinant environmental and individual factors involved in etiopathogenesis of this disease. This study indicates that the environment factors (water, soil) correlated with personal factors, especially the diet and standard of living are the favouring factors of renal lithiasis. PMID:21688574

  6. [Features of morbidity community-acquired pneumonia among young recruits].

    PubMed

    Serdukov, D U; Gordienko, A V; Kozlov, M S; Mikhailov, A A; Davydov, P A

    2015-10-01

    Were examined 3338 military personnel of the combined training center. 183 of them diagnosed community-acquired pneumonia, in 3155 focal and infiltrative changes in lung tissue were not identified. The analisys of prevalence been made among young recruits of the acute respiratory illness before arriving in part and at the assembly point, foci of chronic infection, smoking, low body weight. 511 military personnel arrived at the training center in the disease state with symptoms of acute respiratory illness. Examined the relationship these risk factor to the development of community-acquired pneumonia in this category of servicemen. PMID:26827502

  7. Cerebellar neurones: Differentiation and modulation of sensitivity to excitotoxic treatment.

    PubMed

    Mercanti, D; Angelini, A; Ciotti, M; Eboli, M; Galli, C; Battistini, L; Merlo, D; Calissano, P

    1993-01-01

    The neurite outgrowth and adhesion complex (NOAC), isolated from rabbit sera has been dissociated in its major components by reverse-phase chromatography in HPLC by using a C(18) column. SDS-PAGE analisys of the active fractions revealed the presence of three major bands of approximately 100, 70 and 50 kDa. Studies on the biological activity of NOAC were carried out on rat cerebellar granule cells. NOAC-cultured cells exhibit a marked resistance to excitotoxic stimuli carried by glutamate. PMID:22358672

  8. El rol de Ia colaboracion y el Modelo de Aprendizaje Basado en Proyectos (ABPr) mediante el lente de la Teoria de Actividad (CHAT): un estudio de caso con estudiantes de 9no grado

    NASA Astrophysics Data System (ADS)

    Delgado, Isabel C.

    Los modelos de eensenanza y aprendizaje constructivistas conceptualizan el aprendizaje como un proceso activo. El modelo de Aprendizaje Basado en Proyectos (ABPr) se distingue por una serie de componentes, entre los cuales se destaca el aspecto colaborativo y cooperativo como un reto al momento de su implantacion. Son pocas las investigaciones que se concentran en este aspecto del modelo. En este estudio, se analizaron las diversas interacciones que surgen durante la implantacion de una unidad curricular sobre el tema de Geologia de Puerto Rico, la cual se diseno con el modelo ABPr cuyo enfoque es orientacion a proyectos. Particularmente, se examinaron las interacciones sociales que surgen entre los pares y entre pares y docente durante el proceso de planificacion y desarrollo de los productos finales, al igual que las interacciones entre los estudiantes y el material didactico en estas etapas del modelo. La investigacion es de tipo cualitativo e incorpora como diseno el estudio de caso. Las diversas interacciones constituyen la unidad de analisis. En el estudio participaron 19 estudiantes de 9no grado, a quienes se organizaron en 5 grupos colaborativos por temas de interes (Pangea, Placas tectonicas, Volcanes, Tsunamis y Terremotos). Las tecnicas que se utilizaron para recopilar los datos fueron: observaciones participativas, grupos focales y analisis de documentos (cuadernos reflexivos y respuestas de los estudiantes a la pregunta central del proyecto). Para el analisis de los datos se aplico la teoria de actividad (CHAT) que concentra la unidad de analisis en la actividad humana en un contexto particular. Los resultados del estudio senalan que las interacciones entre pares, entre pares y docente, asi como entre estudiantes y material didactico son fundamentales en el proceso de aprendizaje. Una mayor interaccion entre pares durante las etapas de planificar y desarrollar los productos finales de la unidad, promueve una mejor comprension de los conceptos de la

  9. Comparative study of analysis methods in biospeckle phenomenon

    NASA Astrophysics Data System (ADS)

    da Silva, Emerson Rodrigo; Muramatsu, Mikiya

    2008-04-01

    In this work we present a review of main statistical properties of speckle patterns and accomplish a comparative study of the more used methods for analysis and extraction of information from optical grainy. The first and second order space-time statistics are dicussed in an overview perspective. The biospeckle phenomenon has detailed attention, specially in its application on monitoring of activity in tissues. The main techniques used to obtain information from speckle patterns are presented, with special prominence to autocorrelation function, co-occurrence matrices, Fujii's method, Briers' contrast and spatial and temporal contrast analisys (LASCA and LASTCA). An incipient method for analysis, based on the study of sucessive correlations contrast, is introduced. Numerical simulations, using diferent probability density functions for velocities of scatterers, were made with two objectives: to test the analysis methods and to give subsidies for interpretation of in vivo results. Vegetable and animal tissues are investigated, achieving the monitoring of senescence process and vascularization maps on leaves, the accompaniment of fungi contamined fruits, the mapping of activity in flowers and the analisys of healing in rats subjected to abdominal surgery. Experiments using the biospeckle phenomenon in microscopy are carried out. At last, it is evaluated the potentiality of biospeckle as diagnosis tool in chronic vein ulcer cared with low intensity laser therapy and the better analysis methods for each kind of tissue are pointed.

  10. National Serologic Survey of Haematobium Schistosomiasis in Morocco: Evidence for Elimination

    PubMed Central

    Amarir, Fatima; El Mansouri, Bouchra; Fellah, Hajiba; Sebti, Faiza; Mohammed, Lakranbi; Handali, Sukwan; Wilkins, Patricia; El Idrissi, Abderrahman Laamrani; Sadak, Abderrahim; Rhajaoui, Mohamed

    2011-01-01

    The Moroccan Health Ministry launched a Process of Eliminating Schistosomiasis in 1994. During 2005–2009, the epidemiologic status showed a clear interruption of disease transmission at the national level; only a few residual cases were recorded. Our present study is the first systematic serologic survey to evaluate the transmission status in remaining disease-endemic foci. A study population of 2,382 children born after the date of the last autochthonous cases were selected from provinces with histories of high schistosomiasis transmission (Tata, Chtouka Ait Baha, Errachidia, El Kelaa Des Sraghna, and Beni Mellal). To identify the presence of disease, specific antibodies directed against Schistosoma haematobium adult worm microsomal antigens were detected by using an enzyme-linked immunoelectrotransfer blot assay. The results showed an absence of antibodies in all serum samples. Consequently, our findings confirm either a low transmission status or an interruption of schistosomiasis transmission within the last disease endemic foci. PMID:21212195