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Sample records for terminal gap gene

  1. Gene circuit analysis of the terminal gap gene huckebein.

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    Maksat Ashyraliyev

    2009-10-01

    Full Text Available The early embryo of Drosophila melanogaster provides a powerful model system to study the role of genes in pattern formation. The gap gene network constitutes the first zygotic regulatory tier in the hierarchy of the segmentation genes involved in specifying the position of body segments. Here, we use an integrative, systems-level approach to investigate the regulatory effect of the terminal gap gene huckebein (hkb on gap gene expression. We present quantitative expression data for the Hkb protein, which enable us to include hkb in gap gene circuit models. Gap gene circuits are mathematical models of gene networks used as computational tools to extract regulatory information from spatial expression data. This is achieved by fitting the model to gap gene expression patterns, in order to obtain estimates for regulatory parameters which predict a specific network topology. We show how considering variability in the data combined with analysis of parameter determinability significantly improves the biological relevance and consistency of the approach. Our models are in agreement with earlier results, which they extend in two important respects: First, we show that Hkb is involved in the regulation of the posterior hunchback (hb domain, but does not have any other essential function. Specifically, Hkb is required for the anterior shift in the posterior border of this domain, which is now reproduced correctly in our models. Second, gap gene circuits presented here are able to reproduce mutants of terminal gap genes, while previously published models were unable to reproduce any null mutants correctly. As a consequence, our models now capture the expression dynamics of all posterior gap genes and some variational properties of the system correctly. This is an important step towards a better, quantitative understanding of the developmental and evolutionary dynamics of the gap gene network.

  2. 76 FR 32316 - Gap in Termination Provisions

    Science.gov (United States)

    2011-06-06

    ... example, the Software and Information Industry Association (SIIA) stated that the better practice would be... Copyright Office 37 CFR Part 201 Gap in Termination Provisions AGENCY: Copyright Office, Library of Congress. ACTION: Final rule. SUMMARY: The Copyright Office is amending its regulations governing notices of...

  3. GAP: A computer program for gene assembly

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    Eisnstein, J.R.; Uberbacher, E.C.; Guan, X.; Mural, R.J.; Mann, R.C.

    1991-09-01

    A computer program, GAP (Gene Assembly Program), has been written to assemble and score hypothetical genes, given a DNA sequence containing the gene, and the outputs of several other programs which analyze the sequence. These programs include the codign-recognition and splice-junction-recognition modules developed in this laboratory. GAP is a prototype of a planned system in which it will be integrated with an expert system and rule base. Initial tests of GAP have been carried out with four sequences, the exons of which have been determined by biochemcial methods. The highest-scoring hypothetical genes for each of the four sequences had percent correct splice junctions ranging from 50 to 100% (average 81%) and percent correct bases ranging from 92 to 100% (average 96%). 9 refs., 1 tab.

  4. 75 FR 27248 - Gap in Termination Provisions; Inquiry

    Science.gov (United States)

    2010-05-14

    ... Title 17 provides a termination right to authors (and other persons specified by statute) when the grant... run sold out slowly, but because the author's subsequent works were critically acclaimed, it was released with an updated cover last year and is now a best seller. The rights remained with the publisher...

  5. Adeno-associated virus inverted terminal repeats stimulate gene editing

    OpenAIRE

    Hirsch, ML

    2014-01-01

    Advancements in genome editing have relied on technologies to specifically damage DNA which, in turn, stimulates DNA repair including homologous recombination (HR). As off-target concerns complicate the therapeutic translation of site-specific DNA endonucleases, an alternative strategy to stimulate gene editing based on fragile DNA was investigated. To do this, an episomal gene-editing reporter was generated by a disruptive insertion of the adeno-associated virus (AAV) inverted terminal repea...

  6. Interfering amino terminal peptides and functional implications for heteromeric gap junction formation

    Directory of Open Access Journals (Sweden)

    Richard David Veenstra

    2013-05-01

    Full Text Available Connexin43 (Cx43 is widely expressed in many different tissues of the human body. In cells of some organs, Cx43 is co-expressed with other connexins (Cx, including Cx46 and Cx50 in lens, Cx40 in atrium, Purkinje fibers, and the blood vessel wall, Cx45 in heart, and Cx37 in the ovary. Interactions with the co-expressed connexins may have profound functional implications. The abilities of Cx37, Cx45, Cx46, and Cx50 to function in heteromeric gap junction combinations with Cx43 are well documented. Different studies disagree regarding the ability of Cx43 and Cx40 to produce functional heteromeric gap junctions with each other. We review previous studies regarding the heteromeric interactions of Cx43. The possibility of negative functional interactions between the cytoplasmic pore-forming amino terminal (NT domains of these connexins was assessed using pentameric connexin sequence-specific NT domain (iNT peptides applied to cells expressing homomeric Cx40, Cx37, Cx45, Cx46, and Cx50 gap junctions. A Cx43 iNT peptide corresponding to amino acids 9 to 13 (Ac-KLLDK-NH2 specifically inhibited the electrical coupling of Cx40 gap junctions in a transjunctional (Vj voltage-dependent manner without affecting the function of homologous Cx37, Cx46, Cx50, and Cx45 gap junctions. A Cx40 iNT (Ac-EFLEE-OH peptide counteracted the Vj-dependent block of Cx40 gap junctions, whereas a similarly charged Cx50 iNT (Ac-EEVNE-OH peptide did not, suggesting that these NT domain interactions are not solely based on electrostatics. These data are consistent with functional Cx43 heteromeric gap junction formation with Cx37, Cx45, Cx46, and Cx50 and suggest that Cx40 uniquely experiences functional suppressive interactions with a Cx43 NT domain sequence. These findings present unique functional implications about the heteromeric interactions between Cx43 and Cx40 that may influence cardiac conduction in atrial myocardium and the specialized conduction system.

  7. The GapA/B gene duplication marks the origin of Streptophyta (charophytes and land plants).

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    Petersen, Jörn; Teich, René; Becker, Burkhard; Cerff, Rüdiger; Brinkmann, Henner

    2006-06-01

    Independent evidence from morphological, ultrastructural, biochemical, and molecular data have shown that land plants originated from charophycean green algae. However, the branching order within charophytes is still unresolved, and contradictory phylogenies about, for example,the position of the unicellular green alga Mesostigma viride are difficult to reconcile. A comparison of nuclear-encoded Calvin cycle glyceraldehyde-3-phosphate dehydrogenases (GAPDH) indicates that a crucial duplication of the GapA gene occurred early in land plant evolution. The duplicate called GapB acquired a characteristic carboxy-terminal extension (CTE) from the general regulator of the Calvin cycle CP12. This CTE is responsible for thioredoxin-dependent light/dark regulation. In this work, we established GapA, GapB, and CP12 sequences from bryophytes, all orders of charophyte as well as chlorophyte green algae, and the glaucophyte Cyanophora paradoxa. Comprehensive phylogenetic analyses of all available plastid GAPDH sequences suggest that glaucophytes and green plants are sister lineages and support a positioning of Mesostigma basal to all charophycean algae. The exclusive presence of GapB in terrestrial plants, charophytes, and Mesostigma dates the GapA/B gene duplication to the common ancestor of Streptophyta. The conspicuously high degree of GapB sequence conservation suggests an important metabolic role of the newly gained regulatory function. Because the GapB-mediated protein aggregation most likely ensures the complete blockage of the Calvin cycle at night, we propose that this mechanism is also crucial for efficient starch mobilization. This innovation may be one prerequisite for the development of storage tissues in land plants.

  8. Electronic properties of graphene nano-flakes: Energy gap, permanent dipole, termination effect, and Raman spectroscopy

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    Singh, Sandeep Kumar, E-mail: SandeepKumar.Singh@uantwerpen.be; Peeters, F. M., E-mail: Francois.Peeters@uantwerpen.be [Department of Physics, University of Antwerpen, Groenenborgerlaan 171, B-2020 Antwerpen (Belgium); Neek-Amal, M., E-mail: neekamal@srttu.edu [Department of Physics, University of Antwerpen, Groenenborgerlaan 171, B-2020 Antwerpen (Belgium); Department of Physics, Shahid Rajaee Teacher Training University, Lavizan, Tehran 16788 (Iran, Islamic Republic of)

    2014-02-21

    The electronic properties of graphene nano-flakes (GNFs) with different edge passivation are investigated by using density functional theory. Passivation with F and H atoms is considered: C{sub N{sub c}} X{sub N{sub x}} (X = F or H). We studied GNFs with 10 < N{sub c} < 56 and limit ourselves to the lowest energy configurations. We found that: (i) the energy difference Δ between the highest occupied molecular orbital and the lowest unoccupied molecular orbital decreases with N{sub c}, (ii) topological defects (pentagon and heptagon) break the symmetry of the GNFs and enhance the electric polarization, (iii) the mutual interaction of bilayer GNFs can be understood by dipole-dipole interaction which were found sensitive to the relative orientation of the GNFs, (iv) the permanent dipoles depend on the edge terminated atom, while the energy gap is independent of it, and (v) the presence of heptagon and pentagon defects in the GNFs results in the largest difference between the energy of the spin-up and spin-down electrons which is larger for the H-passivated GNFs as compared to F-passivated GNFs. Our study shows clearly the effect of geometry, size, termination, and bilayer on the electronic properties of small GNFs. This study reveals important features of graphene nano-flakes which can be detected using Raman spectroscopy.

  9. Electronic properties of graphene nano-flakes: Energy gap, permanent dipole, termination effect, and Raman spectroscopy

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    Singh, Sandeep Kumar; Neek-Amal, M.; Peeters, F. M.

    2014-02-01

    The electronic properties of graphene nano-flakes (GNFs) with different edge passivation are investigated by using density functional theory. Passivation with F and H atoms is considered: C_{N_c} X_{N_x} (X = F or H). We studied GNFs with 10 interaction of bilayer GNFs can be understood by dipole-dipole interaction which were found sensitive to the relative orientation of the GNFs, (iv) the permanent dipoles depend on the edge terminated atom, while the energy gap is independent of it, and (v) the presence of heptagon and pentagon defects in the GNFs results in the largest difference between the energy of the spin-up and spin-down electrons which is larger for the H-passivated GNFs as compared to F-passivated GNFs. Our study shows clearly the effect of geometry, size, termination, and bilayer on the electronic properties of small GNFs. This study reveals important features of graphene nano-flakes which can be detected using Raman spectroscopy.

  10. Adeno-associated virus inverted terminal repeats stimulate gene editing.

    Science.gov (United States)

    Hirsch, M L

    2015-02-01

    Advancements in genome editing have relied on technologies to specifically damage DNA which, in turn, stimulates DNA repair including homologous recombination (HR). As off-target concerns complicate the therapeutic translation of site-specific DNA endonucleases, an alternative strategy to stimulate gene editing based on fragile DNA was investigated. To do this, an episomal gene-editing reporter was generated by a disruptive insertion of the adeno-associated virus (AAV) inverted terminal repeat (ITR) into the egfp gene. Compared with a non-structured DNA control sequence, the ITR induced DNA damage as evidenced by increased gamma-H2AX and Mre11 foci formation. As local DNA damage stimulates HR, ITR-mediated gene editing was investigated using DNA oligonucleotides as repair substrates. The AAV ITR stimulated gene editing >1000-fold in a replication-independent manner and was not biased by the polarity of the repair oligonucleotide. Analysis of additional human DNA sequences demonstrated stimulation of gene editing to varying degrees. In particular, inverted yet not direct, Alu repeats induced gene editing, suggesting a role for DNA structure in the repair event. Collectively, the results demonstrate that inverted DNA repeats stimulate gene editing via double-strand break repair in an episomal context and allude to efficient gene editing of the human chromosome using fragile DNA sequences.

  11. Gap Gene Regulatory Dynamics Evolve along a Genotype Network

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    Crombach, Anton; Wotton, Karl R.; Jiménez-Guri, Eva; Jaeger, Johannes

    2016-01-01

    Developmental gene networks implement the dynamic regulatory mechanisms that pattern and shape the organism. Over evolutionary time, the wiring of these networks changes, yet the patterning outcome is often preserved, a phenomenon known as “system drift.” System drift is illustrated by the gap gene network—involved in segmental patterning—in dipteran insects. In the classic model organism Drosophila melanogaster and the nonmodel scuttle fly Megaselia abdita, early activation and placement of gap gene expression domains show significant quantitative differences, yet the final patterning output of the system is essentially identical in both species. In this detailed modeling analysis of system drift, we use gene circuits which are fit to quantitative gap gene expression data in M. abdita and compare them with an equivalent set of models from D. melanogaster. The results of this comparative analysis show precisely how compensatory regulatory mechanisms achieve equivalent final patterns in both species. We discuss the larger implications of the work in terms of “genotype networks” and the ways in which the structure of regulatory networks can influence patterns of evolutionary change (evolvability). PMID:26796549

  12. Canalization of gene expression in the Drosophila blastoderm by gap gene cross regulation.

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    Manu

    2009-03-01

    Full Text Available Developing embryos exhibit a robust capability to reduce phenotypic variations that occur naturally or as a result of experimental manipulation. This reduction in variation occurs by an epigenetic mechanism called canalization, a phenomenon which has resisted understanding because of a lack of necessary molecular data and of appropriate gene regulation models. In recent years, quantitative gene expression data have become available for the segment determination process in the Drosophila blastoderm, revealing a specific instance of canalization. These data show that the variation of the zygotic segmentation gene expression patterns is markedly reduced compared to earlier levels by the time gastrulation begins, and this variation is significantly lower than the variation of the maternal protein gradient Bicoid. We used a predictive dynamical model of gene regulation to study the effect of Bicoid variation on the downstream gap genes. The model correctly predicts the reduced variation of the gap gene expression patterns and allows the characterization of the canalizing mechanism. We show that the canalization is the result of specific regulatory interactions among the zygotic gap genes. We demonstrate the validity of this explanation by showing that variation is increased in embryos mutant for two gap genes, Krüppel and knirps, disproving competing proposals that canalization is due to an undiscovered morphogen, or that it does not take place at all. In an accompanying article in PLoS Computational Biology (doi:10.1371/journal.pcbi.1000303, we show that cross regulation between the gap genes causes their expression to approach dynamical attractors, reducing initial variation and providing a robust output. These results demonstrate that the Bicoid gradient is not sufficient to produce gap gene borders having the low variance observed, and instead this low variance is generated by gap gene cross regulation. More generally, we show that the complex

  13. Proteome analysis of a Lactococcus lactis strain overexpressing gapA suggests that the gene product is an auxiliary glyceraldehyde 3-phosphate dehydrogenase

    DEFF Research Database (Denmark)

    Willemoes, Martin; Kilstrup, Mogens; Roepstorff, P.

    2002-01-01

    The sequence of the genome from the Lactococcus lactis subspecies lactis strain IL1403 shows the presence of two reading frames, gapA and gapB, putatively encoding glyceraldehyde 3-phosphate dehydrogenase (GAPDH). Previous proteomic analysis of the L. lactis subspecies cremoris strain MG1363 has...... revealed two neighbouring protein spots, GapBI and GapBII, with amino terminal sequences identical to the product of gapA from the L. lactis subspecies cremoris strain LM0230 and that of the two IL1403 sequences. In order to assign the two protein spots to their respective genes we constructed an L. lactis...... strain that overexpessed the gapA gene derived from MG1363 upon nisin induction. Compared to the wild-type, the overexpressing strain had a 3.4-fold elevated level of specific GAPDH activity when grown in the presence of nisin. In both MG 1363 and the gapA overexpressing strain the GAPDH activity...

  14. Characterization of Escherichia coli strains with gapA and gapB genes deleted.

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    Seta, F D; Boschi-Muller, S; Vignais, M L; Branlant, G

    1997-08-01

    We obtained a series of Escherichia coli strains in which gapA, gapB, or both had been deleted. Delta gapA strains do not revert on glucose, while delta gapB strains grow on glycerol or glucose. We showed that gapB-encoded protein is expressed but at a very low level. Together, these results confirm the essential role for gapA in glycolysis and show that gapB is dispensable for both glycolysis and the pyridoxal biosynthesis pathway.

  15. Characterization of Escherichia coli strains with gapA and gapB genes deleted.

    OpenAIRE

    Seta, F D; Boschi-Muller, S; Vignais, M L; Branlant, G

    1997-01-01

    We obtained a series of Escherichia coli strains in which gapA, gapB, or both had been deleted. Delta gapA strains do not revert on glucose, while delta gapB strains grow on glycerol or glucose. We showed that gapB-encoded protein is expressed but at a very low level. Together, these results confirm the essential role for gapA in glycolysis and show that gapB is dispensable for both glycolysis and the pyridoxal biosynthesis pathway.

  16. Proteome analysis of a Lactococcus lactis strain overexpressing gapA suggests that the gene product is an auxiliary glyceraldehyde 3-phosphate dehydrogenase.

    Science.gov (United States)

    Willemoës, Martin; Kilstrup, Mogens; Roepstorff, Peter; Hammer, Karin

    2002-08-01

    The sequence of the genome from the Lactococcus lactis subspecies lactis strain IL1403 shows the presence of two reading frames, gapA and gapB, putatively encoding glyceraldehyde 3-phosphate dehydrogenase (GAPDH). Previous proteomic analysis of the L. lactis subspecies cremoris strain MG1363 has revealed two neighbouring protein spots, GapBI and GapBII, with amino terminal sequences identical to the product of gapA from the L. lactis subspecies cremoris strain LM0230 and that of the two IL1403 sequences. In order to assign the two protein spots to their respective genes we constructed an L. lactis strain that overexpessed the gapA gene derived from MG1363 upon nisin induction. Compared to the wild-type, the overexpressing strain had a 3.4-fold elevated level of specific GAPDH activity when grown in the presence of nisin. In both MG1363 and the gapA overexpressing strain the GAPDH activity was specific for NAD. No NADP dependent activity was detected. Proteome analysis of the gapA overexpressing strain revealed two new protein spots, GapAI and GapAII, not previously detected in proteome analysis of MG1363. Results from mass spectrometry analysis of GapA and GapB and comparison with the deduced protein sequences for the GAPDH isozymes from the genome sequence of strain IL1403 allowed us to assign GapA and GapB to their apparent IL1403 homologues encoded by gapA and gapB, respectively. Furthermore, we suggest that a homologue of a gapB product, represented by GapB, is the main source of GAPDH activity in L. lactis during normal growth.

  17. Functional roles of the amino terminal domain in determining biophysical properties of Cx50 gap junction channels

    Directory of Open Access Journals (Sweden)

    Li eXin

    2013-12-01

    Full Text Available Communication through gap junction channels is essential for synchronized and coordinated cellular activities. The gap junction channel pore size, its switch control for opening/closing, and the modulations by chemicals can be different depending on the connexin subtypes that compose the channel. Recent structural and functional studies provide compelling evidence that the amino terminal (NT domains of several connexins line the pore of gap junction channels and play an important role in single channel conductance (γj and transjunctional voltage-dependent gating (Vj-gating. This article reviews recent studies conducted on a series of mutations/chimeras in the NT domain of connexin50 (Cx50. Functional examination of the gap junction channels formed by these mutants/chimeras shows the net charge number at the NT domain to be an important factor in γj and in Vj-gating. Furthermore, with an increase in the net negative charge at the NT domain, we observed an increase in the γj, as well as changes in the parameters of the Boltzmann fit of the normalized steady-state conductance and Vj relationship. Our data are consistent with a structural model where the NT domain of Cx50 lines the gap junction pore and plays an important role in sensing Vj and in the subsequent conformational changes leading to gating, as well as in limiting the rate of ion permeation.

  18. Proteome analysis of a Lactococcus lactis strain overexpressing gapA suggests that the gene product is an auxiliary glyceraldehyde 3-phosphate dehydrogenase

    DEFF Research Database (Denmark)

    Willemoës, Martin; Kilstrup, Mogens; Roepstorff, Peter

    2002-01-01

    revealed two neighbouring protein spots, GapBI and GapBII, with amino terminal sequences identical to the product of gapA from the L. lactis subspecies cremoris strain LM0230 and that of the two IL1403 sequences. In order to assign the two protein spots to their respective genes we constructed an L. lactis...... strain that overexpessed the gapA gene derived from MG1363 upon nisin induction. Compared to the wild-type, the overexpressing strain had a 3.4-fold elevated level of specific GAPDH activity when grown in the presence of nisin. In both MG1363 and the gapA overexpressing strain the GAPDH activity...

  19. The Drosophila gap gene network is composed of two parallel toggle switches.

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    Dmitri Papatsenko

    Full Text Available Drosophila "gap" genes provide the first response to maternal gradients in the early fly embryo. Gap genes are expressed in a series of broad bands across the embryo during first hours of development. The gene network controlling the gap gene expression patterns includes inputs from maternal gradients and mutual repression between the gap genes themselves. In this study we propose a modular design for the gap gene network, involving two relatively independent network domains. The core of each network domain includes a toggle switch corresponding to a pair of mutually repressive gap genes, operated in space by maternal inputs. The toggle switches present in the gap network are evocative of the phage lambda switch, but they are operated positionally (in space by the maternal gradients, so the synthesis rates for the competing components change along the embryo anterior-posterior axis. Dynamic model, constructed based on the proposed principle, with elements of fractional site occupancy, required 5-7 parameters to fit quantitative spatial expression data for gap gradients. The identified model solutions (parameter combinations reproduced major dynamic features of the gap gradient system and explained gap expression in a variety of segmentation mutants.

  20. Transcription termination between polo and snap, two closely spaced tandem genes of D. melanogaster

    Science.gov (United States)

    Henriques, Telmo; Ji, Zhe; Tan-Wong, Sue Mei; Carmo, Alexandre M.; Tian, Bin; Proudfoot, Nicholas J.; Moreira, Alexandra

    2012-01-01

    Transcription termination of RNA polymerase II between closely spaced genes is an important, though poorly understood, mechanism. This is true, in particular, in the Drosophila genome, where approximately 52% of tandem genes are separated by less than 1 kb. We show that a set of Drosophila tandem genes has a negative correlation of gene expression and display several molecular marks indicative of promoter pausing. We find that an intergenic spacing of 168 bp is sufficient for efficient transcription termination between the polo-snap tandem gene pair, by a mechanism that is independent of Pcf11 and Xrn2. In contrast, analysis of a tandem gene pair containing a longer intergenic region reveals that termination occurs farther downstream of the poly(A) signal and is, in this case, dependent on Pcf11 and Xrn2. For polo-snap, displacement of poised polymerase from the snap promoter by depletion of the initiation factor TFIIB results in an increase of polo transcriptional read-through. This suggests that poised polymerase is necessary for transcription termination. Interestingly, we observe that polo forms a TFIIB dependent gene loop between its promoter and terminator regions. Furthermore, in a plasmid containing the polo-snap locus, deletion of the polo promoter causes an increase in snap expression, as does deletion of polo poly(A) signals. Taken together, our results indicate that polo forms a gene loop and polo transcription termination occurs by an Xrn2 and Pcf11 independent mechanism that requires TFIIB. PMID:22992452

  1. Modules for C-terminal epitope tagging of Tetrahymena genes

    OpenAIRE

    Kataoka, Kensuke; Schoeberl, Ursula E.; Mochizuki, Kazufumi

    2010-01-01

    Although epitope tagging has been widely used for analyzing protein function in many organisms, there are few genetic tools for epitope tagging in Tetrahymena. In this study, we describe several C-terminal epitope tagging modules that can be used to express tagged proteins in Tetrahymena cells by both plasmid- and PCR-based strategies.

  2. Modules for C-terminal epitope tagging of Tetrahymena genes.

    Science.gov (United States)

    Kataoka, Kensuke; Schoeberl, Ursula E; Mochizuki, Kazufumi

    2010-09-01

    Although epitope tagging has been widely used for analyzing protein function in many organisms, there are few genetic tools for epitope tagging in Tetrahymena. In this study, we describe several C-terminal epitope tagging modules that can be used to express tagged proteins in Tetrahymena cells by both plasmid- and PCR-based strategies. (c) 2010 Elsevier B.V. All rights reserved.

  3. A second Escherichia coli gene with similarity to gapA.

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    Hidalgo, E; Limón, A; Aguilar, J

    1996-03-01

    An open reading frame has been found downstream of the ald gene at 31 min in the Escherichia coli chromosome and has been designated gapC because of its high similarity with gapA (min 39, encoding glyceraldehyde-3-phosphate dehydrogenase), and with gapB (min 62, a gene with high similarity to gapA, encoding erythrose-4-phosphate dehydrogenase). The gapC gene (min 31) encodes a polypeptide of 204 amino acids, 126 residues shorter than glyceraldehyde-3-phosphate dehydrogenase. In this 204-codon open reading frame several amino acids important for catalysis are conserved. However, the cofactor binding site is lost. The results illustrate a case of a gene, encoding a glycolytic enzyme, for which at least three copies maintaining a certain degree of similarity are apparent in the E. coli genome. It seems likely that the genes encode products with different cellular functions. The origin of these three copies of the gap gene by horizontal transfer or by duplication of an ancestral gene is discussed.

  4. Gene induction and repression during terminal erythropoiesis are mediated by distinct epigenetic changes.

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    Wong, Piu; Hattangadi, Shilpa M; Cheng, Albert W; Frampton, Garrett M; Young, Richard A; Lodish, Harvey F

    2011-10-20

    It is unclear how epigenetic changes regulate the induction of erythroid-specific genes during terminal erythropoiesis. Here we use global mRNA sequencing (mRNA-seq) and chromatin immunoprecipitation coupled to high-throughput sequencing (CHIP-seq) to investigate the changes that occur in mRNA levels, RNA polymerase II (Pol II) occupancy, and multiple posttranslational histone modifications when erythroid progenitors differentiate into late erythroblasts. Among genes induced during this developmental transition, there was an increase in the occupancy of Pol II, the activation marks H3K4me2, H3K4me3, H3K9Ac, and H4K16Ac, and the elongation methylation mark H3K79me2. In contrast, genes that were repressed during differentiation showed relative decreases in H3K79me2 levels yet had levels of Pol II binding and active histone marks similar to those in erythroid progenitors. We also found that relative changes in histone modification levels, in particular, H3K79me2 and H4K16ac, were most predictive of gene expression patterns. Our results suggest that in terminal erythropoiesis both promoter and elongation-associated marks contribute to the induction of erythroid genes, whereas gene repression is marked by changes in histone modifications mediating Pol II elongation. Our data map the epigenetic landscape of terminal erythropoiesis and suggest that control of transcription elongation regulates gene expression during terminal erythroid differentiation.

  5. The gap junction inhibitor 2-aminoethoxy-diphenyl-borate protects against acetaminophen hepatotoxicity by inhibiting cytochrome P450 enzymes and c-jun N-terminal kinase activation

    Energy Technology Data Exchange (ETDEWEB)

    Du, Kuo; Williams, C. David; McGill, Mitchell R.; Xie, Yuchao [Department of Pharmacology, Toxicology and Therapeutics, University of Kansas Medical Center, Kansas City, KS (United States); Farhood, Anwar [Department of Pathology, St. David' s North Austin Medical Center, Austin, TX 78756 (United States); Vinken, Mathieu [Department of Toxicology, Center for Pharmaceutical Sciences, Vrije Universiteit Brussels, 1090 Brussels (Belgium); Jaeschke, Hartmut, E-mail: hjaeschke@kumc.edu [Department of Pharmacology, Toxicology and Therapeutics, University of Kansas Medical Center, Kansas City, KS (United States)

    2013-12-15

    Acetaminophen (APAP) hepatotoxicity is the leading cause of acute liver failure in the US. Although many aspects of the mechanism are known, recent publications suggest that gap junctions composed of connexin32 function as critical intercellular communication channels which transfer cytotoxic mediators into neighboring hepatocytes and aggravate liver injury. However, these studies did not consider off-target effects of reagents used in these experiments, especially the gap junction inhibitor 2-aminoethoxy-diphenyl-borate (2-APB). In order to assess the mechanisms of protection of 2-APB in vivo, male C56Bl/6 mice were treated with 400 mg/kg APAP to cause extensive liver injury. This injury was prevented when animals were co-treated with 20 mg/kg 2-APB and was attenuated when 2-APB was administered 1.5 h after APAP. However, the protection was completely lost when 2-APB was given 4–6 h after APAP. Measurement of protein adducts and c-jun-N-terminal kinase (JNK) activation indicated that 2-APB reduced both protein binding and JNK activation, which correlated with hepatoprotection. Although some of the protection was due to the solvent dimethyl sulfoxide (DMSO), in vitro experiments clearly demonstrated that 2-APB directly inhibits cytochrome P450 activities. In addition, JNK activation induced by phorone and tert-butylhydroperoxide in vivo was inhibited by 2-APB. The effects against APAP toxicity in vivo were reproduced in primary cultured hepatocytes without use of DMSO and in the absence of functional gap junctions. We conclude that the protective effect of 2-APB was caused by inhibition of metabolic activation of APAP and inhibition of the JNK signaling pathway and not by blocking connexin32-based gap junctions. - Highlights: • 2-APB protected against APAP-induced liver injury in mice in vivo and in vitro • 2-APB protected by inhibiting APAP metabolic activation and JNK signaling pathway • DMSO inhibited APAP metabolic activation as the solvent of 2-APB

  6. Unprecedented enhancement of transient gene expression from minimal cassettes using a double terminator.

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    Beyene, Getu; Buenrostro-Nava, Marco T; Damaj, Mona B; Gao, San-Ji; Molina, Joe; Mirkov, T Erik

    2011-01-01

    The potential of using vector-free minimal gene cassettes (MGCs) with a double terminator for the enhancement and stabilization of transgene expression was tested in sugarcane biolistic transformation. The MGC system used consisted of the enhanced yellow fluorescent protein (EYFP) reporter gene driven by the maize ubiquitin-1 (Ubi) promoter and a single or double terminator from nopaline synthase (Tnos) or/and Cauliflower mosaic virus 35S (35ST). Transient EYFP expression from Tnos or 35ST single terminator MGC was very low and unstable, typically peaking early (8-16 h) and diminishing rapidly (48-72 h) after bombardment. Addition of a ~260 bp vector sequence (VS) to the single MGC downstream of Tnos (Tnos + VS) or 35ST (35ST + VS) enhanced EYFP expression by 1.25- to 25-fold. However, a much more significant increase in EYFP expression was achieved when the VS in 35ST + VS was replaced by Tnos to generate a 35ST-Tnos double terminator MGC, reaching its maximum at 24 h post-bombardment. The enhanced EYFP expression from the double terminator MGC was maintained for a long period of time (168 h), resulting in an overall increase of 5- to 65-fold and 10- to 160-fold as compared to the 35ST and Tnos single terminator MGCs, respectively. The efficiency of the double terminator MGC in enhancing EYFP expression was also demonstrated in sorghum and tobacco, suggesting that the underlying mechanism is highly conserved among monocots and dicots. Our results also suggest the involvement of posttranscriptional gene silencing in the reduced and unstable transgene expression from single terminator MGCs in plants.

  7. Genes in the terminal regions of orthopoxvirus genomes experience adaptive molecular evolution.

    Science.gov (United States)

    Esteban, David J; Hutchinson, Anne P

    2011-05-23

    Orthopoxviruses are dsDNA viruses with large genomes, some encoding over 200 genes. Genes essential for viral replication are located in the center of the linear genome and genes encoding host response modifiers and other host interacting proteins are located in the terminal regions. The central portion of the genome is highly conserved, both in gene content and sequence, while the terminal regions are more diverse. In this study, we investigated the role of adaptive molecular evolution in poxvirus genes and the selective pressures that act on the different regions of the genome. The relative fixation rates of synonymous and non-synonymous mutations (the d(N)/d(S) ratio) are an indicator of the mechanism of evolution of sequences, and can be used to identify purifying, neutral, or diversifying selection acting on a gene. Like highly conserved residues, amino acids under diversifying selection may be functionally important. Many genes experiencing diversifying selection are involved in host-pathogen interactions, such as antigen-antibody interactions, or the "host-pathogen arms race." We analyzed 175 gene families from orthopoxviruses for evidence of diversifying selection. 79 genes were identified as experiencing diversifying selection, 25 with high confidence. Many of these genes are located in the terminal regions of the genome and function to modify the host response to infection or are virion-associated, indicating a greater role for diversifying selection in host-interacting genes. Of the 79 genes, 20 are of unknown function, and implicating diversifying selection as an important mechanism in their evolution may help characterize their function or identify important functional residues. We conclude that diversifying selection is an important mechanism of orthopoxvirus evolution. Diversifying selection in poxviruses may be the result of interaction with host defense mechanisms.

  8. DNA sequence of the lactose operon: the lacA gene and the transcriptional termination region.

    OpenAIRE

    Hediger, M A; Johnson, D F; Nierlich, D P; Zabin, I

    1985-01-01

    The lac operon of Escherichia coli spans approximately 5300 base pairs and includes the lacZ, lacY, and lacA genes in addition to the operator, promoter, and transcription termination regions. We report here the sequence of the lacA gene and the region distal to it, confirming the sequence of thiogalactoside transacetylase and completing the sequence of the lac operon. The lacA gene is characterized by use of rare codons, suggesting an origin from a plasmid, transposon, or virus gene. UUG is ...

  9. Codon usage bias in 5' terminal coding sequences reveals distinct enrichment of gene functions.

    Science.gov (United States)

    Liu, Huiling; Rahman, Siddiq Ur; Mao, Yuanhui; Xu, Xiaodong; Tao, Shiheng

    2017-10-01

    Codon bias at the 5' terminal of coding sequence (CDS) is known to be distinct from the rest of the CDS. A number of events occur in this short region to regulate early translation elongation and co-translational translocation. In the genes encoding secretory proteins, there is a special signal sequence which has a higher occurrence of rare codons. In this study, we analyzed codon bias of secretory genes in several eukaryotes. The results showed that secretory genes in the species except mammals had a higher occurrence of rare codons in the 5' terminal of CDS, and the bias was greater than the same region of non-secretory genes. GO analysis revealed that secretory genes containing rare codon clusters in different regions were responsible for various roles in gene functions. Moreover, codon bias in the region encoding the hydrophobic region of protein is similar in secretory and non-secretory genes, indicating that codon bias in secretory genes was partly influenced by amino acid bias. Rare codon clusters are found more frequently in specific regions, and continuous rare codons are not favoured probably because they will increase the probability of ribosome collision and drop-off. Based on ribosome profiling data, there is no significant difference in the average translation efficiencies between rare and optimal codons. Higher ribosomal density in the 5' terminal may result from ribosome pausing which could be involved in different translation events. These findings collectively provided rich information on codon bias in secretory genes, which may shed light on the co-effect of codon bias, mRNA structure and tRNA abundance in translational regulations. Copyright © 2017. Published by Elsevier Inc.

  10. Identification of Staphylococcus spp. by PCR-Restriction Fragment Length Polymorphism of gap Gene

    OpenAIRE

    Yugueros, Javier; Temprano, Alejandro; Sánchez, María; Luengo, José María; Naharro, Germán

    2001-01-01

    Oligonucleotide primers specific for the Staphylococcus aureus gap gene were previously designed to identify 12 Staphylococcus spp. by PCR. In the present study, AluI digestion of PCR-generated products rendered distinctive restriction fragment length polymorphism patterns that allowed 24 Staphylococcus spp. to be identified with high specificity.

  11. Identification of Staphylococcus spp. by PCR-Restriction Fragment Length Polymorphism of gap Gene

    Science.gov (United States)

    Yugueros, Javier; Temprano, Alejandro; Sánchez, María; Luengo, José María; Naharro, Germán

    2001-01-01

    Oligonucleotide primers specific for the Staphylococcus aureus gap gene were previously designed to identify 12 Staphylococcus spp. by PCR. In the present study, AluI digestion of PCR-generated products rendered distinctive restriction fragment length polymorphism patterns that allowed 24 Staphylococcus spp. to be identified with high specificity. PMID:11574593

  12. Gene delivery systems: Bridging the gap between recombinant viruses and artificial vectors.

    Science.gov (United States)

    Navarro; Oudrhiri; Fabrega; Lehn

    1998-03-02

    Although most research in the field of somatic gene therapy has investigated the use of recombinant viruses for transferring genes into somatic target cells, various methods for nonviral gene delivery have also been proposed. Both types of gene delivery systems have advantages and drawbacks. Schematically, viral vectors are particularly efficient for gene delivery, whereas nonviral systems are free of the difficulties associated with the use of recombinant viruses but need to be further optimized to reach their full potential. In order to bridge the gap between viral vectors and synthetic reagents, we discuss here some specific features of the viral vector systems of today that could advantageously be taken into account for the design of improved nonviral gene delivery systems. Indeed, although nonviral systems differ fundamentally from viral systems, one possible approach towards enhanced artificial reagents aims at developing 'artificial viruses' that mimic the highly efficient processes of viral infection.

  13. GAP1, a novel selection and counter-selection marker for multiple gene disruptions in Saccharomyces cerevisiae

    DEFF Research Database (Denmark)

    Regenberg, Birgitte; Hansen, J.

    2000-01-01

    We report on the use of a new homologous marker for use in multiple gene deletions in S, cerevisiae, the general amino acid permease gene (GAP1), A GAP1 strain can utilize L-citrulline as the sole nitrogen source but cannot grow in the presence of the toxic amino acid D-histidine, L-citrulline as......We report on the use of a new homologous marker for use in multiple gene deletions in S, cerevisiae, the general amino acid permease gene (GAP1), A GAP1 strain can utilize L-citrulline as the sole nitrogen source but cannot grow in the presence of the toxic amino acid D-histidine, L...... flanked by short (60 bp) stretches of the gene in question. Through homologous recombination, the cassette will integrate into the target gene, which is thus replaced by GAP1, and mutants are selected for on minimal L-citrulline medium. When propagated under non-selective conditions, some cells will lose...... the GAP1 gene. This is caused by recombination between two Salmonella typuimurium hisG direct repeats embracing GAP1, and will result in a sub-population of gap1 cells. Such cells are selected on a medium containing D-histidine, and may subsequently be used for a second gene disruption. Hence, multiple...

  14. In Silico Identification and Characterization of N-Terminal Acetyltransferase Genes of Poplar (Populus trichocarpa

    Directory of Open Access Journals (Sweden)

    Hang-Yong Zhu

    2014-01-01

    Full Text Available N-terminal acetyltransferase (Nats complex is responsible for protein N-terminal acetylation (Nα-acetylation, which is one of the most common covalent modifications of eukaryotic proteins. Although genome-wide investigation and characterization of Nat catalytic subunits (CS and auxiliary subunits (AS have been conducted in yeast and humans they remain unexplored in plants. Here we report on the identification of eleven genes encoding eleven putative Nat CS polypeptides, and five genes encoding five putative Nat AS polypeptides in Populus. We document that the expansion of Nat CS genes occurs as duplicated blocks distributed across 10 of the 19 poplar chromosomes, likely only as a result of segmental duplication events. Based on phylogenetic analysis, poplar Nat CS were assigned to six subgroups, which corresponded well to the Nat CS types (CS of Nat A–F, being consistent with previous reports in humans and yeast. In silico analysis of microarray data showed that in the process of normal development of the poplar, their Nat CS and AS genes are commonly expressed at one relatively low level but share distinct tissue-specific expression patterns. This exhaustive survey of Nat genes in poplar provides important information to assist future studies on their functional role in poplar.

  15. DNA sequence of the lactose operon: the lacA gene and the transcriptional termination region.

    Science.gov (United States)

    Hediger, M A; Johnson, D F; Nierlich, D P; Zabin, I

    1985-10-01

    The lac operon of Escherichia coli spans approximately 5300 base pairs and includes the lacZ, lacY, and lacA genes in addition to the operator, promoter, and transcription termination regions. We report here the sequence of the lacA gene and the region distal to it, confirming the sequence of thiogalactoside transacetylase and completing the sequence of the lac operon. The lacA gene is characterized by use of rare codons, suggesting an origin from a plasmid, transposon, or virus gene. UUG is the translation initiation codon. A preliminary examination of 3' end of the lac messenger in the region distal to the lacA gene indicates several endpoints. A predominant one is located at the 3' end of a G + C-rich hairpin structure, which may be involved in termination of transcription or in post-transcriptional processing. An open reading frame of 702 base pairs is present on the complementary strand downstream from lacA.

  16. In silico identification and characterization of N-Terminal acetyltransferase genes of poplar (Populus trichocarpa).

    Science.gov (United States)

    Zhu, Hang-Yong; Li, Chun-Ming; Wang, Li-Feng; Bai, Hui; Li, Yan-Ping; Yu, Wen-Xi; Xia, De-An; Liu, Chang-Cai

    2014-01-27

    N-terminal acetyltransferase (Nats) complex is responsible for protein N-terminal acetylation (Nα-acetylation), which is one of the most common covalent modifications of eukaryotic proteins. Although genome-wide investigation and characterization of Nat catalytic subunits (CS) and auxiliary subunits (AS) have been conducted in yeast and humans they remain unexplored in plants. Here we report on the identification of eleven genes encoding eleven putative Nat CS polypeptides, and five genes encoding five putative Nat AS polypeptides in Populus. We document that the expansion of Nat CS genes occurs as duplicated blocks distributed across 10 of the 19 poplar chromosomes, likely only as a result of segmental duplication events. Based on phylogenetic analysis, poplar Nat CS were assigned to six subgroups, which corresponded well to the Nat CS types (CS of Nat A-F), being consistent with previous reports in humans and yeast. In silico analysis of microarray data showed that in the process of normal development of the poplar, their Nat CS and AS genes are commonly expressed at one relatively low level but share distinct tissue-specific expression patterns. This exhaustive survey of Nat genes in poplar provides important information to assist future studies on their functional role in poplar.

  17. Establishment of a Cre/loxP recombination system for N-terminal epitope tagging of genes in Tetrahymena

    OpenAIRE

    Mochizuki Kazufumi; Vogt Alexander; Busch Clara

    2010-01-01

    Abstract Background Epitope tagging is a powerful strategy to study the function of proteins. Although tools for C-terminal protein tagging in the ciliated protozoan Tetrahymena thermophila have been developed, N-terminal protein tagging in this organism is still technically demanding. Results In this study, we have established a Cre/loxP recombination system in Tetrahymena and have applied this system for the N-terminal epitope tagging of Tetrahymena genes. Cre can be expressed in Tetrahymen...

  18. Identification of Novel Short C-Terminal Transcripts of Human SERPINA1 Gene.

    Science.gov (United States)

    Matamala, Nerea; Aggarwal, Nupur; Iadarola, Paolo; Fumagalli, Marco; Gomez-Mariano, Gema; Lara, Beatriz; Martinez, Maria Teresa; Cuesta, Isabel; Stolk, Jan; Janciauskiene, Sabina; Martinez-Delgado, Beatriz

    2017-01-01

    Human SERPINA1 gene is located on chromosome 14q31-32.3 and is organized into three (IA, IB, and IC) non-coding and four (II, III, IV, V) coding exons. This gene produces α1-antitrypsin (A1AT), a prototypical member of the serpin superfamily of proteins. We demonstrate that human peripheral blood leukocytes express not only a product corresponding to the transcript coding for the full-length A1AT protein but also two short transcripts (ST1C4 and ST1C5) of A1AT. In silico sequence analysis revealed that the last exon of the short transcripts contains an Open Reading Frame (ORF) and thus putatively can produce peptides. We found ST1C4 expression across different human tissues whereas ST1C5 was mainly restricted to leukocytes, specifically neutrophils. A high up-regulation (10-fold) of short transcripts was observed in isolated human blood neutrophils after activation with lipopolysaccharide. Parallel analyses by liquid chromatography-mass spectrometry identified peptides corresponding to C-terminal region of A1AT in supernatants of activated but not naïve neutrophils. Herein we report for the first time a tissue specific expression and regulation of short transcripts of SERPINA1 gene, and the presence of C-terminal peptides in supernatants from activated neutrophils, in vitro. This gives a novel insight into the studies on the transcription of SERPINA1 gene.

  19. Arrays in rays: terminal addition in echinoderms and its correlation with gene expression.

    Science.gov (United States)

    Mooi, Rich; David, Bruno; Wray, Gregory A

    2005-01-01

    The echinoderms are deuterostomes that superimpose radial symmetry upon bilateral larval morphology. Consequently, they are not the first animals that come to mind when the concepts of segmentation and terminal addition are being discussed. However, it has long been recognized that echinoderms have serial elements along their radii formed in accordance with the ocular plate rule (OPR). The OPR is a special case of terminal growth, forming elements of the ambulacra that define the rays in echinoderms. New elements are added at the terminus of the ray, which may or may not be marked by a calcified element called the terminal plate (the "ocular" of sea urchins). The OPR operates in every echinoderm, from the occasionally bizarre fossils of the Cambrian to the most familiar extant taxa. Using the OPR and other criteria of recognition, echinoderm body wall can be divided into two main regions: extraxial components are associated with the somatocoels, axial components (formed in accordance with the OPR) with the hydrocoel. We compare patterns of development in axial regions of echinoderms with those found in the anterior-posterior axes of the earliest echinoderms as well as other invertebrates. Although axial and extraxial skeletons appear to be composed of the same biomineral matrix, the genes involved in patterning these two skeletal components are likely distinct. During development of the axial skeleton, for instance, the genes engrailed and orthodenticle are expressed in spatial and temporal patterns consistent with the OPR. Other genes such as distal-less seem to demarcate early ontogenetic boundaries between the axial rudiment and the extraxial larval body. There is a complex and pervasive reorganization of gene expression domains to produce the highly divergent morphologies seen in the Echinodermata. We integrate morphological and genetic information, particularly with respect to the origins of radial symmetry in the rudiment, and the concomitant development of

  20. Lysis gene of bacteriophage MS2 is activated by translation termination at the overlapping coat gene

    NARCIS (Netherlands)

    Berkhout, B.; Schmidt, B. F.; van Strien, A.; van Boom, J.; van Westrenen, J.; van Duin, J.

    1987-01-01

    The 3' boundary of the coat gene of the RNA bacteriophage MS2 lies 46 nucleotides downstream from the beginning of the lysis (L) cistron. The translation of both reading frames is coupled; the synthesis of the lysis protein does not occur unless translation of the overlapping coat gene takes place.

  1. Establishment of a Cre/loxP recombination system for N-terminal epitope tagging of genes in Tetrahymena.

    Science.gov (United States)

    Busch, Clara Jana-Lui; Vogt, Alexander; Mochizuki, Kazufumi

    2010-07-13

    Epitope tagging is a powerful strategy to study the function of proteins. Although tools for C-terminal protein tagging in the ciliated protozoan Tetrahymena thermophila have been developed, N-terminal protein tagging in this organism is still technically demanding. In this study, we have established a Cre/loxP recombination system in Tetrahymena and have applied this system for the N-terminal epitope tagging of Tetrahymena genes. Cre can be expressed in Tetrahymena and localizes to the macronucleus where it induces precise recombination at two loxP sequences in direct orientation in the Tetrahymena macronuclear chromosome. This Cre/loxP recombination can be used to remove a loxP-flanked drug-resistance marker from an N-terminal tagging construct after it is integrated into the macronucleus. The system established in this study allows us to express an N-terminal epitope tagged gene from its own endogenous promoter in Tetrahymena.

  2. Synthesis and Gene Silencing Properties of siRNAs Containing Terminal Amide Linkages

    Directory of Open Access Journals (Sweden)

    Maria Gaglione

    2014-01-01

    Full Text Available The active components of the RNAi are 21 nucleotides long dsRNAs containing a 2 nucleotide overhang at the 3′ end, carrying 5′-phosphate and 3′-hydroxyl groups (siRNAs. Structural analysis revealed that the siRNA is functionally bound at both ends to RISC. Terminal modifications are considered with interest as the introduction of chemical moieties interferes with the 3′ overhang recognition by the PAZ domain and the 5′-phosphate recognition by the MID and PIWI domains of RISC. Herein, we report the synthesis of modified siRNAs containing terminal amide linkages by introducing hydroxyethylglycine PNA (hegPNA moieties at 5′, and at 3′ positions and on both terminals. Results of gene silencing studies highlight that some of these modifications are compatible with the RNAi machinery and markedly increase the resistance to serum-derived nucleases even after 24 h of incubation. Molecular docking simulations were attained to give at atomistic level a clearer picture of the effect of the most performing modifications on the interactions with the human Argonaute 2 PAZ, MID, and PIWI domains. This study adds another piece to the puzzle of the heterogeneous chemical modifications that can be attained to enhance the silencing efficiency of siRNAs.

  3. Synthesis and Gene Silencing Properties of siRNAs Containing Terminal Amide Linkages

    Science.gov (United States)

    Gaglione, Maria; Mercurio, M. Emilia; Mosca, Nicola; Novellino, Ettore; Messere, Anna

    2014-01-01

    The active components of the RNAi are 21 nucleotides long dsRNAs containing a 2 nucleotide overhang at the 3′ end, carrying 5′-phosphate and 3′-hydroxyl groups (siRNAs). Structural analysis revealed that the siRNA is functionally bound at both ends to RISC. Terminal modifications are considered with interest as the introduction of chemical moieties interferes with the 3′ overhang recognition by the PAZ domain and the 5′-phosphate recognition by the MID and PIWI domains of RISC. Herein, we report the synthesis of modified siRNAs containing terminal amide linkages by introducing hydroxyethylglycine PNA (hegPNA) moieties at 5′, and at 3′ positions and on both terminals. Results of gene silencing studies highlight that some of these modifications are compatible with the RNAi machinery and markedly increase the resistance to serum-derived nucleases even after 24 h of incubation. Molecular docking simulations were attained to give at atomistic level a clearer picture of the effect of the most performing modifications on the interactions with the human Argonaute 2 PAZ, MID, and PIWI domains. This study adds another piece to the puzzle of the heterogeneous chemical modifications that can be attained to enhance the silencing efficiency of siRNAs. PMID:24791003

  4. Bridging the gap between genes and language deficits in schizophrenia: an oscillopathic approach

    Directory of Open Access Journals (Sweden)

    Elliot Murphy

    2016-08-01

    Full Text Available Schizophrenia is characterised by marked language deficits, but it is not clear how these deficits arise from the alteration of genes related to the disease. The goal of this paper is to aid the bridging of the gap between genes and schizophrenia and, ultimately, give support to the view that the abnormal presentation of language in this condition is heavily rooted in the evolutionary processes that brought about modern language. To that end we will focus on how the schizophrenic brain processes language and, particularly, on its distinctive oscillatory profile during language processing. Additionally, we will show that candidate genes for schizophrenia are overrepresented among the set of genes that are believed to be important for the evolution of the human faculty of language. These genes crucially include (and are related to genes involved in brain rhythmicity. We will claim that this translational effort and the links we uncover may help develop an understanding of language evolution, along with the aetiology of schizophrenia, its clinical/linguistic profile, and its high prevalence among modern populations.

  5. Bridging the Gap between Genes and Language Deficits in Schizophrenia: An Oscillopathic Approach.

    Science.gov (United States)

    Murphy, Elliot; Benítez-Burraco, Antonio

    2016-01-01

    Schizophrenia is characterized by marked language deficits, but it is not clear how these deficits arise from the alteration of genes related to the disease. The goal of this paper is to aid the bridging of the gap between genes and schizophrenia and, ultimately, give support to the view that the abnormal presentation of language in this condition is heavily rooted in the evolutionary processes that brought about modern language. To that end we will focus on how the schizophrenic brain processes language and, particularly, on its distinctive oscillatory profile during language processing. Additionally, we will show that candidate genes for schizophrenia are overrepresented among the set of genes that are believed to be important for the evolution of the human faculty of language. These genes crucially include (and are related to) genes involved in brain rhythmicity. We will claim that this translational effort and the links we uncover may help develop an understanding of language evolution, along with the etiology of schizophrenia, its clinical/linguistic profile, and its high prevalence among modern populations.

  6. Bridging the Gap between Genes and Language Deficits in Schizophrenia: An Oscillopathic Approach

    Science.gov (United States)

    Murphy, Elliot; Benítez-Burraco, Antonio

    2016-01-01

    Schizophrenia is characterized by marked language deficits, but it is not clear how these deficits arise from the alteration of genes related to the disease. The goal of this paper is to aid the bridging of the gap between genes and schizophrenia and, ultimately, give support to the view that the abnormal presentation of language in this condition is heavily rooted in the evolutionary processes that brought about modern language. To that end we will focus on how the schizophrenic brain processes language and, particularly, on its distinctive oscillatory profile during language processing. Additionally, we will show that candidate genes for schizophrenia are overrepresented among the set of genes that are believed to be important for the evolution of the human faculty of language. These genes crucially include (and are related to) genes involved in brain rhythmicity. We will claim that this translational effort and the links we uncover may help develop an understanding of language evolution, along with the etiology of schizophrenia, its clinical/linguistic profile, and its high prevalence among modern populations. PMID:27601987

  7. Quantitative system drift compensates for altered maternal inputs to the gap gene network of the scuttle fly Megaselia abdita.

    Science.gov (United States)

    Wotton, Karl R; Jiménez-Guri, Eva; Crombach, Anton; Janssens, Hilde; Alcaine-Colet, Anna; Lemke, Steffen; Schmidt-Ott, Urs; Jaeger, Johannes

    2015-01-05

    The segmentation gene network in insects can produce equivalent phenotypic outputs despite differences in upstream regulatory inputs between species. We investigate the mechanistic basis of this phenomenon through a systems-level analysis of the gap gene network in the scuttle fly Megaselia abdita (Phoridae). It combines quantification of gene expression at high spatio-temporal resolution with systematic knock-downs by RNA interference (RNAi). Initiation and dynamics of gap gene expression differ markedly between M. abdita and Drosophila melanogaster, while the output of the system converges to equivalent patterns at the end of the blastoderm stage. Although the qualitative structure of the gap gene network is conserved, there are differences in the strength of regulatory interactions between species. We term such network rewiring 'quantitative system drift'. It provides a mechanistic explanation for the developmental hourglass model in the dipteran lineage. Quantitative system drift is likely to be a widespread mechanism for developmental evolution.

  8. Evolutionary genomics of plant genes encoding N-terminal-TM-C2 domain proteins and the similar FAM62 genes and synaptotagmin genes of metazoans

    Directory of Open Access Journals (Sweden)

    Craxton Molly

    2007-07-01

    Full Text Available Abstract Background Synaptotagmin genes are found in animal genomes and are known to function in the nervous system. Genes with a similar domain architecture as well as sequence similarity to synaptotagmin C2 domains have also been found in plant genomes. The plant genes share an additional region of sequence similarity with a group of animal genes named FAM62. FAM62 genes also have a similar domain architecture. Little is known about the functions of the plant genes and animal FAM62 genes. Indeed, many members of the large and diverse Syt gene family await functional characterization. Understanding the evolutionary relationships among these genes will help to realize the full implications of functional studies and lead to improved genome annotation. Results I collected and compared plant Syt-like sequences from the primary nucleotide sequence databases at NCBI. The collection comprises six groups of plant genes conserved in embryophytes: NTMC2Type1 to NTMC2Type6. I collected and compared metazoan FAM62 sequences and identified some similar sequences from other eukaryotic lineages. I found evidence of RNA editing and alternative splicing. I compared the intron patterns of Syt genes. I also compared Rabphilin and Doc2 genes. Conclusion Genes encoding proteins with N-terminal-transmembrane-C2 domain architectures resembling synaptotagmins, are widespread in eukaryotes. A collection of these genes is presented here. The collection provides a resource for studies of intron evolution. I have classified the collection into homologous gene families according to distinctive patterns of sequence conservation and intron position. The evolutionary histories of these gene families are traceable through the appearance of family members in different eukaryotic lineages. Assuming an intron-rich eukaryotic ancestor, the conserved intron patterns distinctive of individual gene families, indicate independent origins of Syt, FAM62 and NTMC2 genes. Resemblances

  9. Likelihood-based gene annotations for gap filling and quality assessment in genome-scale metabolic models.

    Directory of Open Access Journals (Sweden)

    Matthew N Benedict

    2014-10-01

    Full Text Available Genome-scale metabolic models provide a powerful means to harness information from genomes to deepen biological insights. With exponentially increasing sequencing capacity, there is an enormous need for automated reconstruction techniques that can provide more accurate models in a short time frame. Current methods for automated metabolic network reconstruction rely on gene and reaction annotations to build draft metabolic networks and algorithms to fill gaps in these networks. However, automated reconstruction is hampered by database inconsistencies, incorrect annotations, and gap filling largely without considering genomic information. Here we develop an approach for applying genomic information to predict alternative functions for genes and estimate their likelihoods from sequence homology. We show that computed likelihood values were significantly higher for annotations found in manually curated metabolic networks than those that were not. We then apply these alternative functional predictions to estimate reaction likelihoods, which are used in a new gap filling approach called likelihood-based gap filling to predict more genomically consistent solutions. To validate the likelihood-based gap filling approach, we applied it to models where essential pathways were removed, finding that likelihood-based gap filling identified more biologically relevant solutions than parsimony-based gap filling approaches. We also demonstrate that models gap filled using likelihood-based gap filling provide greater coverage and genomic consistency with metabolic gene functions compared to parsimony-based approaches. Interestingly, despite these findings, we found that likelihoods did not significantly affect consistency of gap filled models with Biolog and knockout lethality data. This indicates that the phenotype data alone cannot necessarily be used to discriminate between alternative solutions for gap filling and therefore, that the use of other information

  10. Cryptic Transcription and Early Termination in the Control of Gene Expression

    Directory of Open Access Journals (Sweden)

    Jessie Colin

    2011-01-01

    Full Text Available Recent studies on yeast transcriptome have revealed the presence of a large set of RNA polymerase II transcripts mapping to intergenic and antisense regions or overlapping canonical genes. Most of these ncRNAs (ncRNAs are subject to termination by the Nrd1-dependent pathway and rapid degradation by the nuclear exosome and have been dubbed cryptic unstable transcripts (CUTs. CUTs are often considered as by-products of transcriptional noise, but in an increasing number of cases they play a central role in the control of gene expression. Regulatory mechanisms involving expression of a CUT are diverse and include attenuation, transcriptional interference, and alternative transcription start site choice. This review focuses on the impact of cryptic transcription on gene expression, describes the role of the Nrd1-complex as the main actor in preventing nonfunctional and potentially harmful transcription, and details a few systems where expression of a CUT has an essential regulatory function. We also summarize the most recent studies concerning other types of ncRNAs and their possible role in regulation.

  11. Parameter estimation and determinability analysis applied to Drosophila gap gene circuits

    Directory of Open Access Journals (Sweden)

    Jaeger Johannes

    2008-09-01

    Full Text Available Abstract Background Mathematical modeling of real-life processes often requires the estimation of unknown parameters. Once the parameters are found by means of optimization, it is important to assess the quality of the parameter estimates, especially if parameter values are used to draw biological conclusions from the model. Results In this paper we describe how the quality of parameter estimates can be analyzed. We apply our methodology to assess parameter determinability for gene circuit models of the gap gene network in early Drosophila embryos. Conclusion Our analysis shows that none of the parameters of the considered model can be determined individually with reasonable accuracy due to correlations between parameters. Therefore, the model cannot be used as a tool to infer quantitative regulatory weights. On the other hand, our results show that it is still possible to draw reliable qualitative conclusions on the regulatory topology of the gene network. Moreover, it improves previous analyses of the same model by allowing us to identify those interactions for which qualitative conclusions are reliable, and those for which they are ambiguous.

  12. Establishment of a Cre/loxP recombination system for N-terminal epitope tagging of genes in Tetrahymena

    Directory of Open Access Journals (Sweden)

    Mochizuki Kazufumi

    2010-07-01

    Full Text Available Abstract Background Epitope tagging is a powerful strategy to study the function of proteins. Although tools for C-terminal protein tagging in the ciliated protozoan Tetrahymena thermophila have been developed, N-terminal protein tagging in this organism is still technically demanding. Results In this study, we have established a Cre/loxP recombination system in Tetrahymena and have applied this system for the N-terminal epitope tagging of Tetrahymena genes. Cre can be expressed in Tetrahymena and localizes to the macronucleus where it induces precise recombination at two loxP sequences in direct orientation in the Tetrahymena macronuclear chromosome. This Cre/loxP recombination can be used to remove a loxP-flanked drug-resistance marker from an N-terminal tagging construct after it is integrated into the macronucleus. Conclusions The system established in this study allows us to express an N-terminal epitope tagged gene from its own endogenous promoter in Tetrahymena.

  13. Polymerase read-through at the first transcription termination site contributes to regulation of borna disease virus gene expression.

    Science.gov (United States)

    Poenisch, Marion; Wille, Sandra; Staeheli, Peter; Schneider, Urs

    2008-10-01

    An unusually long noncoding sequence is located between the N gene of Borna disease virus (BDV) and the genes for regulatory factor X and polymerase cofactor P. Most of these nucleotides are transcribed and seem to control translation of the bicistronic X/P mRNA. We report here that Vero cells persistently infected with mutant viruses containing minor alterations in this control region showed almost normal levels of N, X, and P proteins but exhibited greatly reduced levels of mRNAs coding for these viral gene products. Surprisingly, cells infected with these BDV mutants accumulated a viral transcript 1.9 kb in length that represents a capped and polyadenylated mRNA containing the coding regions of the N, X, and P genes. Cells infected with wild-type BDV also contained substantial amounts of this read-through mRNA, which yielded both N and P protein when translated in vitro. Viruses carrying mutations that promoted read-through transcription at the first gene junction failed to replicate in the brain of adult rats. In the brains of newborn rats, these mutant viruses were able to replicate after acquiring second-site mutations in or near the termination signal located downstream of the N gene. Thus, sequence elements adjacent to the core termination signal seem to regulate the frequency by which the polymerase terminates transcription after the N gene. We conclude from these observations that BDV uses read-through transcription for fine-tuning the expression of the N, X, and P genes which, in turn, influence viral polymerase activity.

  14. Polymerase Read-Through at the First Transcription Termination Site Contributes to Regulation of Borna Disease Virus Gene Expression ▿

    Science.gov (United States)

    Poenisch, Marion; Wille, Sandra; Staeheli, Peter; Schneider, Urs

    2008-01-01

    An unusually long noncoding sequence is located between the N gene of Borna disease virus (BDV) and the genes for regulatory factor X and polymerase cofactor P. Most of these nucleotides are transcribed and seem to control translation of the bicistronic X/P mRNA. We report here that Vero cells persistently infected with mutant viruses containing minor alterations in this control region showed almost normal levels of N, X, and P proteins but exhibited greatly reduced levels of mRNAs coding for these viral gene products. Surprisingly, cells infected with these BDV mutants accumulated a viral transcript 1.9 kb in length that represents a capped and polyadenylated mRNA containing the coding regions of the N, X, and P genes. Cells infected with wild-type BDV also contained substantial amounts of this read-through mRNA, which yielded both N and P protein when translated in vitro. Viruses carrying mutations that promoted read-through transcription at the first gene junction failed to replicate in the brain of adult rats. In the brains of newborn rats, these mutant viruses were able to replicate after acquiring second-site mutations in or near the termination signal located downstream of the N gene. Thus, sequence elements adjacent to the core termination signal seem to regulate the frequency by which the polymerase terminates transcription after the N gene. We conclude from these observations that BDV uses read-through transcription for fine-tuning the expression of the N, X, and P genes which, in turn, influence viral polymerase activity. PMID:18653450

  15. Functional angucycline-like antibiotic gene cluster in the terminal inverted repeats of the Streptomyces ambofaciens linear chromosome.

    Science.gov (United States)

    Pang, Xiuhua; Aigle, Bertrand; Girardet, Jean-Michel; Mangenot, Sophie; Pernodet, Jean-Luc; Decaris, Bernard; Leblond, Pierre

    2004-02-01

    Streptomyces ambofaciens has an 8-Mb linear chromosome ending in 200-kb terminal inverted repeats. Analysis of the F6 cosmid overlapping the terminal inverted repeats revealed a locus similar to type II polyketide synthase (PKS) gene clusters. Sequence analysis identified 26 open reading frames, including genes encoding the beta-ketoacyl synthase (KS), chain length factor (CLF), and acyl carrier protein (ACP) that make up the minimal PKS. These KS, CLF, and ACP subunits are highly homologous to minimal PKS subunits involved in the biosynthesis of angucycline antibiotics. The genes encoding the KS and ACP subunits are transcribed constitutively but show a remarkable increase in expression after entering transition phase. Five genes, including those encoding the minimal PKS, were replaced by resistance markers to generate single and double mutants (replacement in one and both terminal inverted repeats). Double mutants were unable to produce either diffusible orange pigment or antibacterial activity against Bacillus subtilis. Single mutants showed an intermediate phenotype, suggesting that each copy of the cluster was functional. Transformation of double mutants with a conjugative and integrative form of F6 partially restored both phenotypes. The pigmented and antibacterial compounds were shown to be two distinct molecules produced from the same biosynthetic pathway. High-pressure liquid chromatography analysis of culture extracts from wild-type and double mutants revealed a peak with an associated bioactivity that was absent from the mutants. Two additional genes encoding KS and CLF were present in the cluster. However, disruption of the second KS gene had no effect on either pigment or antibiotic production.

  16. Ras GAP-related and C-terminal domain-dependent localization and tumorigenic activities of IQGAP1 in melanoma cells.

    Directory of Open Access Journals (Sweden)

    Michael Reimer

    Full Text Available IQGAP1 interacts with a number of binding partners through a calponin homology domain (CHD, a WW motif, IQ repeats, a Ras GAP-related domain (GRD, and a conserved C-terminal (CT domain. Among various biological and cellular functions, IQGAP1 is known to play a role in actin cytoskeleton dynamics during membrane ruffling and lamellipodium protrusion. In addition, phosphorylation near the CT domain is thought to control IQGAP1 activity through regulation of intramolecular interaction. In a previous study, we discovered that IQGAP1 preferentially localizes to retracting areas in B16F10 mouse melanoma cells, not areas of membrane ruffling and lamellipodium protrusion. Nothing is known of the domains needed for retraction localization and very little is known of IQGAP1 function in the actin cytoskeleton of melanoma cells. Thus, we examined localization of IQGAP1 mutants to retracting areas, and characterized knock down phenotypes on tissue culture plastic and physiologic-stiffness hydrogels. Localization of IQGAP1 mutants (S1441E/S1443D, S1441A/S1443A, ΔCHD, ΔGRD or ΔCT to retracting and protruding cell edges were measured. In retracting areas there was a decrease in S1441A/S1443A, ΔGRD and ΔCT localization, a minor decrease in ΔCHD localization, and normal localization of the S1441E/S1443D mutant. In areas of cell protrusion just behind the lamellipodium leading edge, we surprisingly observed both ΔGRD and ΔCT localization, and increased number of microtubules. IQGAP1 knock down caused loss of cell polarity on laminin-coated glass, decreased proliferation on tissue culture polystyrene, and abnormal spheroid growth on laminin-coated hydrogels. We propose that the GRD and CT domains regulate IQGAP1 localization to retracting actin networks to promote a tumorigenic role in melanoma cells.

  17. Premature termination codons in the Type VII collagen gene (COL7A1) underlie severe, mutilating recessive dystrophic epidermolysis bullosa

    Energy Technology Data Exchange (ETDEWEB)

    Christiano, A.M.; Uitto, J. (Thomas Jefferson Univ., Philadelphia, PA (United States)); Anhalt, G. (Johns Hopkins School of Medicine, Baltimore, MD (United States)); Gibbons, S.; Bauer, E.A. (Stanford Univ. School of Medicine, CA (United States))

    1994-05-01

    Epidermolysis bullosa (EB) is a group of heritable mechano-bullous skin diseases classified into three major categories on the basis of the level of tissue separation within the dermal-epidermal basement membrane zone. The most severe, dystrophic (scarring) forms of EB demonstrate blister formation below the cutaneous basement membrane at the level of the anchoring fibrils. Ultrastructural observations of altered anchoring fibrils and genetic linkage to the gene encoding type VII collagen (COL7A1), the major component of anchoring fibrils, have implicated COL7A1 as the candidate gene in the dystrophic forms of EB. The authors have recently cloned the entire cDNA and gene for human COL7A1, which has been mapped to 3p21. In this study, they describe mutations in four COL7A1 alleles in three patients with severe, mutilating recessive dystrophic EB (Hallopeau-Siemens type, HS-RDEB). Each of these mutations resulted in a premature termination codon (PTC) in the amino-terminal portion of COL7A1. One of the patients was a compound heterozygote for two different mutations. The heterozygous carriers showed an [approximately] 50% reduction in anchoring fibrils, yet were clinically unaffected. Premature termination codons in both alleles of COL7A1 may thus be a major underlying cause of the severe, recessive dystrophic forms of EB. 40 refs., 8 figs.

  18. Cleavage-induced termination in U2 snRNA gene expression

    Energy Technology Data Exchange (ETDEWEB)

    Nabavi, Sadeq [Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada N1G 2W1 (Canada); Nazar, Ross N., E-mail: rnnazar@uoguelph.ca [Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada N1G 2W1 (Canada)

    2010-03-12

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

  19. Sugar-mediated transcriptional regulation of the Gap gene system and concerted photosystem II functional modulation in the microalga Scenedesmus vacuolatus.

    Science.gov (United States)

    Valverde, Federico; Ortega, José M; Losada, Manuel; Serrano, Aurelio

    2005-08-01

    Partial cDNAs corresponding to the GapA, GapC and GapN genes that encode the three different glyceraldehyde-3-phosphate dehydrogenases (GAPDHs) of the green microalga Scenedesmus vacuolatus SAG 211-8b have been cloned and characterized. Northern blot experiments, as well as immunoblots and activity measurements, demonstrate a differential regulation by sugars of the components of the algal Gap gene system. Addition of glucose or other metabolizable sugars to photoautotrophic cultures promoted a drastic repression of the GapA gene and depletion to negligible levels of the corresponding GAPDHA, a chloroplastic protein involved in photosynthetic CO2 assimilation. By contrast, expression of the GapC and GapN genes encoding their cytosolic counterparts involved in glycolysis was enhanced. However, no down-regulation of the GapA gene by glucose took place in the dark, indicating that the observed effect is associated with sugar assimilation in the light. Likewise, glucose promoted in illuminated algal cultures a severe decrease of photosystem II functionality, estimated by O2 evolution activity, thermoluminescence emission and D1 protein level, while again, no effect was observed in the dark. On the basis of the correlation found between photosystem II performance and sugar transcriptional regulation of the GapA gene, a scenario of sugar-mediated regulation of photosynthetic metabolism in microalgae is proposed that will help to explain the so-called glucose bleaching effect in photosynthetic eukaryotes.

  20. Adenoviral vector-mediated expression of B-50/GAP-43 induces alterations in the membrane organization of olfactory axon terminals in vivo

    NARCIS (Netherlands)

    Holtmaat, Anthony J D G; Hermens, W.T.J.M.C.; Sonnemans, M.A.F.; Giger, Roman J; Van Leeuwen, F W; Kaplitt, M G; Oestreicher, A B; Gispen, Willem Hendrik; Verhaagen, J

    1997-01-01

    B-50/GAP-43 is an intraneuronal membrane-associated growth cone protein with an important role in axonal growth and regeneration. By using adenoviral vector-directed expression of B-50/GAP-43 we studied the morphogenic action of B-50/GAP-43 in mature primary olfactory neurons that have established

  1. The carboxy-terminal domain of Dictyostelium C-module-binding factor is an independent gene regulatory entity.

    Directory of Open Access Journals (Sweden)

    Jörg Lucas

    Full Text Available The C-module-binding factor (CbfA is a multidomain protein that belongs to the family of jumonji-type (JmjC transcription regulators. In the social amoeba Dictyostelium discoideum, CbfA regulates gene expression during the unicellular growth phase and multicellular development. CbfA and a related D. discoideum CbfA-like protein, CbfB, share a paralogous domain arrangement that includes the JmjC domain, presumably a chromatin-remodeling activity, and two zinc finger-like (ZF motifs. On the other hand, the CbfA and CbfB proteins have completely different carboxy-terminal domains, suggesting that the plasticity of such domains may have contributed to the adaptation of the CbfA-like transcription factors to the rapid genome evolution in the dictyostelid clade. To support this hypothesis we performed DNA microarray and real-time RT-PCR measurements and found that CbfA regulates at least 160 genes during the vegetative growth of D. discoideum cells. Functional annotation of these genes revealed that CbfA predominantly controls the expression of gene products involved in housekeeping functions, such as carbohydrate, purine nucleoside/nucleotide, and amino acid metabolism. The CbfA protein displays two different mechanisms of gene regulation. The expression of one set of CbfA-dependent genes requires at least the JmjC/ZF domain of the CbfA protein and thus may depend on chromatin modulation. Regulation of the larger group of genes, however, does not depend on the entire CbfA protein and requires only the carboxy-terminal domain of CbfA (CbfA-CTD. An AT-hook motif located in CbfA-CTD, which is known to mediate DNA binding to A+T-rich sequences in vitro, contributed to CbfA-CTD-dependent gene regulatory functions in vivo.

  2. N-ICE plasmids for generating N-terminal 3 × FLAG tagged genes that allow inducible, constitutive or endogenous expression in Saccharomyces cerevisiae.

    Science.gov (United States)

    Zhang, Yueping; Serratore, Nina D; Briggs, Scott D

    2017-05-01

    PCR-mediated homologous recombination is a powerful approach to introduce epitope tags into the chromosomal loci at the N-terminus or the C-terminus of targeted genes. Although strategies of C-terminal epitope tagging of target genes at their loci are simple and widely used in yeast, C-terminal epitope tagging is not practical for all proteins. For example, a C-terminal tag may affect protein function or a protein may get cleaved or processed, resulting in the loss of the epitope tag. Therefore, N-terminal epitope tagging may be necessary to resolve these problems. In some cases, an epitope tagging strategy is used to introduce a heterologous promoter with the epitope tag at the N-terminus of a gene of interest. The potential issue with this strategy is that the tagged gene is not expressed at the endogenous level. Another strategy after integration is to excise the selection marker, using the Cre-LoxP system, leaving the epitope tagged gene expressed from the endogenous promoter. However, N-terminal epitope tagging of essential genes using this strategy requires a diploid strain followed by tetrad dissection. Here we present 14 new plasmids for N-terminal tagging, which combines two previous strategies for epitope tagging in a haploid strain. These 'N-ICE' plasmids were constructed so that non-essential and essential genes can be N-terminally 3 × FLAG tagged and expressed from an inducible promoter (GAL1), constitutive promoters (CYC1 or PYK1) or the endogenous promoter. We have validated the N-ICE plasmid system by N-terminal tagging two non-essential genes (SET1 and SET2) and two essential genes (ERG11 and PKC1). Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

  3. A Large Number of Nuclear Genes in the Human Parasite Blastocystis Require mRNA Polyadenylation to Create Functional Termination Codons

    OpenAIRE

    Klimeš, Vladimír; Gentekaki, Eleni; Roger, Andrew J.; Eliáš, Marek

    2014-01-01

    Termination codons in mRNA molecules are typically specified directly by the sequence of the corresponding gene. However, in mitochondria of a few eukaryotic groups, some mRNAs contain the termination codon UAA deriving one or both adenosines from transcript polyadenylation. Here, we show that a similar phenomenon occurs for a substantial number of nuclear genes in Blastocystis spp., divergent unicellular eukaryote gut parasites. Our analyses of published genomic data from Blastocystis sp. su...

  4. Conserved function of the Krüppel gap gene in the blowfly Lucilia sericata, despite anterior shift of expression.

    Science.gov (United States)

    Blechert, O; Douglas, D; Baumgartner, S

    2011-04-01

    To determine whether expression patterns of segmentation genes found in Drosophila melanogaster can be scaled to pattern larger insects, we studied the expression of the Krüppel (Kr) gene in the blowfly Lucilia sericata. Compared with Drosophila Kr, L. sericata Kr showed an unexpected 10% shift of expression towards the anterior pole. Furthermore, expression domains not found in D. melanogaster were present at the blastoderm stage of L. sericata. To compare Kr activity and function, we employed RNA interference-mediated gene silencing. We found Kr phenotypes in L. sericata comparable with those observed in D. melanogaster, demonstrating that L. sericata Kr functions as a gap gene as it does in Drosophila. Our results show that, despite an anterior shift in expression, Kr function has remained conserved during the evolution of the blowflies. © 2010 Lund University. Insect Molecular Biology © 2010 The Royal Entomological Society.

  5. Expression of the gapA gene encoding glyceraldehyde-3-phosphate dehydrogenase of Corynebacterium glutamicum is regulated by the global regulator SugR.

    Science.gov (United States)

    Toyoda, Koichi; Teramoto, Haruhiko; Inui, Masayuki; Yukawa, Hideaki

    2008-11-01

    Regulation of expression of the gapA gene encoding glyceraldehyde-3-phosphate dehydrogenase essential for glycolysis in Corynebacterium glutamicum was studied. We applied DNA affinity beads to isolate proteins binding to the promoter region of the gapA gene and obtained SugR, which has been shown to be a repressor of pts genes involved in sugar transport system. The results of electrophoretic mobility shift assays revealed that SugR specifically bound to the gapA promoter and the consensus sequence TGTTTG in the promoter region was required for its binding. We examined expression of the gapA gene in a sugR deletion mutant. Effect of mutation in the SugR binding site on gapA-lacZ fusion expression was also examined. These assays revealed that SugR acts as a negative transcriptional regulator of the gapA gene in the absence of sugar, and repression by SugR is alleviated in the presence of sugar, i.e., fructose and sucrose. Fructose-1-phosphate and fructose-1,6-bisphosphate revealed negative effects on binding of SugR to the gapA promoter, indicating that the sugar metabolites are involved in the derepression of gapA expression.

  6. Analysis of bacteriophage phi X174 gene A protein-mediated termination and reinitiation of phi X DNA synthesis. I. Characterization of the termination and reinitiation reactions.

    Science.gov (United States)

    Brown, D R; Roth, M J; Reinberg, D; Hurwitz, J

    1984-08-25

    The phi X174 (phi X) gene A protein-mediated termination and reinitiation of single-stranded circular (SS(c] phi X viral DNA synthesis in vitro were directly and independently analyzed. Following incubation together with purified DNA replication enzymes from Escherichia coli, ATP, [alpha-32P]dNTPs, and either the phi X A protein and phi X replicative form I (RF I) DNA, or the purified RF II X A complex, the phi X A protein was detected covalently linked to newly synthesized 32P-labeled DNA. Formation of the phi X A protein-[32P]DNA covalent complex required all the factors necessary for phi X (+) SS(c) DNA synthesis in vitro. Thus, it was a product of the reinitiation reaction and an intermediate of the replication cycle. Identification of this complex provided direct evidence that reinitiation of phi X (+) strand DNA synthesis involved regeneration of the RF II X A complex. Substitution of 2',3'-dideoxyguanosine triphosphate (ddGTP) for dGTP in reaction mixtures resulted in the formation of covalent phi X A protein 32P-oligonucleotide complexes; these complexes were trapped analogues of the regenerated RF II X A complex. They could not act catalytically due to the presence of ddGMP residues at the 3'-termini of the oligonucleotide moieties. Reaction mixtures containing ddGTP also yielded nonradioactive (+) SS(c) DNA products derived from circularization of the displaced (+) strand of the input parental template DNA. The formation of the phi X A protein-32P-oligonucleotide complexes and nonradioactive (+) SS(c) DNA were used to assay both reinitiation and termination reactions, respectively. Both reactions required DNA synthesis from the 3'-hydroxyl primer at nucleotide residue 4305 which was formed by cleavage of phi X RF I DNA by the phi X A protein. Elongation of this primer by 18, but not 11 nucleotides was sufficient to support each reaction. Reinitiation reactions proceeded rapidly and were essentially complete after 90 s. In contrast, when ddGTP was replaced

  7. Effect of Mefloquine, a Gap Junction Blocker, on Circadian Period2 Gene Oscillation in the Mouse Suprachiasmatic Nucleus

    Directory of Open Access Journals (Sweden)

    Jinmi Koo

    2015-09-01

    Full Text Available BackgroundIn mammals, the master circadian pacemaker is localized in an area of the ventral hypothalamus known as the suprachiasmatic nucleus (SCN. Previous studies have shown that pacemaker neurons in the SCN are highly coupled to one another, and this coupling is crucial for intrinsic self-sustainability of the SCN central clock, which is distinguished from peripheral oscillators. One plausible mechanism underlying the intercellular communication may involve direct electrical connections mediated by gap junctions.MethodsWe examined the effect of mefloquine, a neuronal gap junction blocker, on circadian Period 2 (Per2 gene oscillation in SCN slice cultures prepared from Per2::luciferase (PER2::LUC knock-in mice using a real-time bioluminescence measurement system.ResultsAdministration of mefloquine causes instability in the pulse period and a slight reduction of amplitude in cyclic PER2::LUC expression. Blockade of gap junctions uncouples PER2::LUC-expressing cells, in terms of phase transition, which weakens synchrony among individual cellular rhythms.ConclusionThese findings suggest that neuronal gap junctions play an important role in synchronizing the central pacemaker neurons and contribute to the distinct self-sustainability of the SCN master clock.

  8. Abrupt onset of mutations in a developmentally regulated gene during terminal differentiation of post-mitotic photoreceptor neurons in mice.

    Directory of Open Access Journals (Sweden)

    Ivette M Sandoval

    Full Text Available For sensitive detection of rare gene repair events in terminally differentiated photoreceptors, we generated a knockin mouse model by replacing one mouse rhodopsin allele with a form of the human rhodopsin gene that causes a severe, early-onset form of retinitis pigmentosa. The human gene contains a premature stop codon at position 344 (Q344X, cDNA encoding the enhanced green fluorescent protein (EGFP at its 3' end, and a modified 5' untranslated region to reduce translation rate so that the mutant protein does not induce retinal degeneration. Mutations that eliminate the stop codon express a human rhodopsin-EGFP fusion protein (hRho-GFP, which can be readily detected by fluorescence microscopy. Spontaneous mutations were observed at a frequency of about one per retina; in every case, they gave rise to single fluorescent rod cells, indicating that each mutation occurred during or after the last mitotic division. Additionally, the number of fluorescent rods did not increase with age, suggesting that the rhodopsin gene in mature rod cells is less sensitive to mutation than it is in developing rods. Thus, there is a brief developmental window, coinciding with the transcriptional activation of the rhodopsin locus, in which somatic mutations of the rhodopsin gene abruptly begin to appear.

  9. Kissing loops hide premature termination codons in pre-mRNAof selenoprotein genes and in genes containing programmedribosomal frameshifts

    DEFF Research Database (Denmark)

    Knudsen, Steen; Brunak, Søren

    1997-01-01

    A novel RNA secondary structure that places the selenocysteine codon UGA in one hairpin and a donor splice site in another, has been discovered in selenoprotein genes. The presence of the structure resolves the discrepancy that the selenocysteine triplet, UGA, should block splicing. Without...... a specific signal such as the novel RNA secondary structure, selenoproteins could not be produced from genes containing intervening sequences....

  10. The Escherichia coli gapA gene is transcribed by the vegetative RNA polymerase holoenzyme E sigma 70 and by the heat shock RNA polymerase E sigma 32.

    Science.gov (United States)

    Charpentier, B; Branlant, C

    1994-02-01

    Escherichia coli D-glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is produced by the gapA gene and is structurally related to eukaryotic GAPDHs. These facts led to the proposal that the gapA gene originated by a horizontal transfer of genetic information. The yields and start sites of gapA mRNAs produced in various fermentation conditions and genetic contexts were analyzed by primer extension. The transcriptional regulatory region of the gapA gene was found to contain four promoter sequences, three recognized by the vegetative RNA polymerase E sigma 70 and one recognized by the heat shock RNA polymerase E sigma 32. Transcription of gapA by E sigma 32 is activated in the logarithmic phase under conditions of starvation and of heat shock. Using a GAPDH- strain, we found that GAPDH production has a positive effect on cell growth at 43 degrees C. Thus, E. coli GAPDH displays some features of heat shock proteins. One of the gapA promoter sequences transcribed by E sigma 70 is subject to catabolic repression. Another one has growth phase-dependent efficiency. This complex area of differentially regulated promoters allows the production of large amounts of gapA transcripts in a wide variety of environmental conditions. On the basis of these data, the present view of E sigma 32 RNA polymerase function has to be enlarged, and the various hypotheses on E. coli gapA gene origin have to be reexamined.

  11. COOH-terminal deletion of HBx gene is a frequent event in HBV-associated hepatocellular carcinoma

    Science.gov (United States)

    Liu, Xiao-Hong; Lin, Jing; Zhang, Shu-Hui; Zhang, Shun-Min; Feitelson, Mark A; Gao, Heng-Jun; Zhu, Ming-Hua

    2008-01-01

    AIM: To investigate the hepatitis B virus (HBV) x gene (HBx) state in the tissues of HBV-related hepatocellular carcinoma (HCC) in Chinese patients and whether there were particular HBx mutations. METHODS: HBx gene was amplified and direct sequencing was used in genomic DNA samples from 20 HCC and corresponding non-cancerous liver tissues from HBsAg-positive patients. HBV DNA integration and HBx deleted mutation were validated in 45 HCC patients at different stages by Southern blot analysis and polymerase chain reaction methods. RESULTS: The frequencies of HBx point mutations were significantly lower in HCC than their corresponding non-cancerous liver tissues (11/19 vs 18/19, P = 0.019). In contrast, deletions in HBx gene were significantly higher in HCC than their non-cancerous liver tissues (16/19 vs 4/19, P < 0.001). The deletion of HBx COOH-terminal was detected in 14 HCC tissues. A specific integration of HBx at 17p13 locus was also found in 8 of 16 HCC, and all of them also exhibited full-length HBx deletions. Integrated or integrated coexistence with replicated pattern was obtained in 45.5% (20/45) - 56.8% (25/45) tumors and 40.9% (18/45) - 52.3% (23/45) non-tumor tissues. CONCLUSION: HBx deletion, especially the COOH-terminal deletion of HBx is a frequent event in HBV-associated HCC tissues in China. HBV integration had also taken place in partial HCC tissues. This supporting the hypothesis that deletion and probably integrated forms of the HBx gene may be implicated in liver carcinogenesis. PMID:18322946

  12. Candida albicans AGE3, the ortholog of the S. cerevisiae ARF-GAP-encoding gene GCS1, is required for hyphal growth and drug resistance.

    Directory of Open Access Journals (Sweden)

    Thomas Lettner

    Full Text Available BACKGROUND: Hyphal growth and multidrug resistance of C. albicans are important features for virulence and antifungal therapy of this pathogenic fungus. METHODOLOGY/PRINCIPAL FINDINGS: Here we show by phenotypic complementation analysis that the C. albicans gene AGE3 is the functional ortholog of the yeast ARF-GAP-encoding gene GCS1. The finding that the gene is required for efficient endocytosis points to an important functional role of Age3p in endosomal compartments. Most C. albicans age3Delta mutant cells which grew as cell clusters under yeast growth conditions showed defects in filamentation under different hyphal growth conditions and were almost completely disabled for invasive filamentous growth. Under hyphal growth conditions only a fraction of age3Delta cells shows a wild-type-like polarization pattern of the actin cytoskeleton and lipid rafts. Moreover, age3Delta cells were highly susceptible to several unrelated toxic compounds including antifungal azole drugs. Irrespective of the AGE3 genotype, C-terminal fusions of GFP to the drug efflux pumps Cdr1p and Mdr1p were predominantly localized in the plasma membrane. Moreover, the plasma membranes of wild-type and age3Delta mutant cells contained similar amounts of Cdr1p, Cdr2p and Mdr1p. CONCLUSIONS/SIGNIFICANCE: The results indicate that the defect in sustaining filament elongation is probably caused by the failure of age3Delta cells to polarize the actin cytoskeleton and possibly of inefficient endocytosis. The high susceptibility of age3Delta cells to azoles is not caused by inefficient transport of efflux pumps to the cell membrane. A possible role of a vacuolar defect of age3Delta cells in drug susceptibility is proposed and discussed. In conclusion, our study shows that the ARF-GAP Age3p is required for hyphal growth which is an important virulence factor of C. albicans and essential for detoxification of azole drugs which are routinely used for antifungal therapy. Thus, it

  13. Dexamethasone Induces Cardiomyocyte Terminal Differentiation via Epigenetic Repression of Cyclin D2 Gene

    National Research Council Canada - National Science Library

    Gay, Maresha S; Dasgupta, Chiranjib; Li, Yong; Kanna, Angela; Zhang, Lubo

    2016-01-01

    .... Yet mechanisms remain undetermined. The present study tested the hypothesis that the direct effect of glucocorticoid receptor-mediated epigenetic repression of cyclin D2 gene in the cardiomyocyte plays a key role in the dexamethasone...

  14. Role of connexin (gap junction) genes in cell growth control and carcinogenesis; Role des jonctions intercellulaires dans la cancerogenese

    Energy Technology Data Exchange (ETDEWEB)

    Yamasaki, H.; Krutovskikh, V.; Mesnil, M.; Tanaka, T.; Zaidan-Dagli, M.L.; Omori, Y. [International Agency for Research on Cancer, Lyon (France). Unit of Multistage Carcinogenesis

    1999-03-01

    Gap junctional intercellular communication (GJIC) is considered to play a key role in the maintenance of tissue independence and homeostasis in multicellular organisms by controlling the growth of GJIC-connected cells. Gap junction channels are composed of connexin molecules and, so far, more than a dozen different connexin genes have been shown to be expressed in mammals. Reflecting the importance of GJIC in various physiological functions, deletion of different connexin genes from mice results in various disorders, including cancers, heart malformation or conduction abnormality, cataract, etc. The possible involvement of aberrant GJIC in abnormal cell growth and carcinogenesis has long been postulated and recent studies in our own and other laboratories have confirmed that expression and function of connexin genes play an important role in cell growth control. Thus, almost all malignant cells show altered homologous and/or heterologous GJIC and are often associated with aberrant expression or localization of connexins. Aberrant localization of connexins in some tumour cells is associated with lack of function of cell adhesion molecules, suggesting the importance of cell-cell recognition for GJIC. Transfection of connexin genes into tumorigenic cells restores normal cell growth, supporting the idea that connexins form a family of tumour-suppressor genes. Some studies also show that specific connexins may be necessary to control growth of specific cell types. We have produced various dominant-negative mutants of Cx26, Cx32 and Cx43 and showed that some of them prevent the growth control exerted by the corresponding wild-type genes. However, we have found that connexins 32, 37 and 43 genes are rarely mutated in tumours. In some of these studies, we noted that connexin expression per se, rather than GJIC level, is more closely related to growth control, suggesting that connexins may have a GJIC-independent function. We have recently created a transgenic mouse strain

  15. Upregulation of Early and Downregulation of Terminal Pathway Complement Genes in Subcutaneous Adipose Tissue and Adipocytes in Acquired Obesity

    Directory of Open Access Journals (Sweden)

    Sanna Kaye

    2017-05-01

    Full Text Available Inflammation is an important mediator of obesity-related complications such as the metabolic syndrome but its causes and mechanisms are unknown. As the complement system is a key mediator of inflammation, we studied whether it is activated in acquired obesity in subcutaneous adipose tissue (AT and isolated adipocytes. We used a special study design of genetically matched controls of lean and heavy groups, rare monozygotic twin pairs discordant for body mass index (BMI [n = 26, within-pair difference (Δ in body mass index, BMI >3 kg/m2] with as much as 18 kg mean Δweight. Additionally, 14 BMI-concordant (BMI <3 kg/m2 served as a reference group. The detailed measurements included body composition (DEXA, fat distribution (MRI, glucose, insulin, adipokines, C3a and SC5b-9 levels, and the expression of complement and insulin signaling pathway-related genes in AT and adipocytes. In both AT and isolated adipocytes, the classical and alternative pathway genes were upregulated, and the terminal pathway genes downregulated in the heavier co-twins of the BMI-discordant pairs. The upregulated genes included C1q, C1s, C2, ficolin-1, factor H, receptors for C3a and C5a (C5aR1, and the iC3b receptor (CR3. While the terminal pathway components C5 and C6 were downregulated, its inhibitor clusterin was upregulated. Complement gene upregulation in AT and adipocytes correlated positively with adiposity and hyperinsulinemia and negatively with the expression of insulin signaling-related genes. Plasma C3a, but not SC5b-9, levels were elevated in the heavier co-twins. There were no differences between the co-twins in BMI-concordant pairs. Obesity is associated with increased expression of the early, but not late, complement pathway components and of key receptors. The twins with acquired obesity have therefore an inflated inflammatory activity in the AT. The results suggest that complement is likely involved in orchestrating clearance of apoptotic debris

  16. Ureteral relaxation through calcitonin gene-related peptide release from sensory nerve terminals by hypotonic solution.

    Science.gov (United States)

    Materazzi, Serena; Minocci, Daiana; De Siena, Gaetano; Benemei, Silvia; Nassini, Romina

    2015-09-01

    To evaluate the influence of hypotonic solutions on ureteral relaxation mediated by the release of calcitonin gene-related peptide from intramural sensory nerve endings. Urine osmolarity of Sprague-Dawley rats drinking water low in salt content (Fiuggi water) or a reference water for 7 days was measured. Release of calcitonin gene-related peptide-like immunoreactivity from slices of rat ureter and urinary bladder by hypotonic solutions was assessed by an immunometric assay. The mechanism through which hypotonic solutions inhibit neurokinin A-induced phasic contractions of isolated rat ureters was evaluated by organ bath studies. A 7-day consumption of Fiuggi water in rats reduced urine osmolarity by ~40%. Exposure to hypotonic solutions released calcitonin gene-related peptide-like immunoreactivity from slices of rat ureter. This response was abated in a calcium-free medium, after capsaicin desensitization, and in the presence of the unselective transient receptor potential channel antagonist, ruthenium red. Exposure of isolated rat ureteral preparations to a hypotonic solution inhibited neurokinin A-evoked phasic contraction. This response was attenuated by capsaicin desensitization and in the presence of the calcitonin gene-related peptide receptor antagonist, calcitonin gene-related peptide8-37 . Transient receptor potential vanilloid 1 or transient receptor potential vanilloid 4 antagonists did not affect the neurogenic and calcitonin gene-related peptide-dependent relaxation. Present data show that hypotonic solution evokes calcitonin gene-related peptide release from capsaicin-sensitive intramural sensory nerves, thus inhibiting ureteral contractility, through a transient receptor potential-dependent mechanism. However, this mechanism does not involve transient receptor potential vanilloid 1 or transient receptor potential vanilloid 4. Future studies with appropriate in vivo models should investigate the hypothesis that hypostenuric urine diffusing into the

  17. The EBNA-2 N-Terminal Transactivation Domain Folds into a Dimeric Structure Required for Target Gene Activation.

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    Anders Friberg

    2015-05-01

    Full Text Available Epstein-Barr virus (EBV is a γ-herpesvirus that may cause infectious mononucleosis in young adults. In addition, epidemiological and molecular evidence links EBV to the pathogenesis of lymphoid and epithelial malignancies. EBV has the unique ability to transform resting B cells into permanently proliferating, latently infected lymphoblastoid cell lines. Epstein-Barr virus nuclear antigen 2 (EBNA-2 is a key regulator of viral and cellular gene expression for this transformation process. The N-terminal region of EBNA-2 comprising residues 1-58 appears to mediate multiple molecular functions including self-association and transactivation. However, it remains to be determined if the N-terminus of EBNA-2 directly provides these functions or if these activities merely depend on the dimerization involving the N-terminal domain. To address this issue, we determined the three-dimensional structure of the EBNA-2 N-terminal dimerization (END domain by heteronuclear NMR-spectroscopy. The END domain monomer comprises a small fold of four β-strands and an α-helix which form a parallel dimer by interaction of two β-strands from each protomer. A structure-guided mutational analysis showed that hydrophobic residues in the dimer interface are required for self-association in vitro. Importantly, these interface mutants also displayed severely impaired self-association and transactivation in vivo. Moreover, mutations of solvent-exposed residues or deletion of the α-helix do not impair dimerization but strongly affect the functional activity, suggesting that the EBNA-2 dimer presents a surface that mediates functionally important intra- and/or intermolecular interactions. Our study shows that the END domain is a novel dimerization fold that is essential for functional activity. Since this specific fold is a unique feature of EBNA-2 it might provide a novel target for anti-viral therapeutics.

  18. The Use of Transcription Terminators to Generate Transgenic Lines of Chinese Hamster Ovary Cells (CHO) with Stable and High Level of Reporter Gene Expression.

    Science.gov (United States)

    Gasanov, N B; Toshchakov, S V; Georgiev, P G; Maksimenko, O G

    2015-01-01

    Mammalian cell lines are widely used to produce recombinant proteins. Stable transgenic cell lines usually contain many insertions of the expression vector in one genomic region. Transcription through transgene can be one of the reasons for target gene repression after prolonged cultivation of cell lines. In the present work, we used the known transcription terminators from the SV40 virus, as well as the human β- and γ-globin genes, to prevent transcription through transgene. The transcription terminators were shown to increase and stabilize the expression of the EGFP reporter gene in transgenic lines of Chinese hamster ovary (CHO) cells. Hence, transcription terminators can be used to create stable mammalian cells with a high and stable level of recombinant protein production.

  19. Microarray based analysis of an inherited terminal 3p26.3 deletion, containing only the CHL1 gene, from a normal father to his two affected children

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    Lerone Margherita

    2011-04-01

    Full Text Available Abstract Background terminal deletions of the distal portion of the short arm of chromosome 3 cause a rare contiguous gene disorder characterized by growth retardation, developmental delay, mental retardation, dysmorphisms, microcephaly and ptosis. The phenotype of individuals with deletions varies from normal to severe. It was suggested that a 1,5 Mb minimal terminal deletion including the two genes CRBN and CNTN4 is sufficient to cause the syndrome. In addition the CHL1 gene, mapping at 3p26.3 distally to CRBN and CNTN4, was proposed as candidate gene for a non specific mental retardation because of its high level of expression in the brain. Methods and Results we describe two affected siblings in which array-CGH analysis disclosed an identical discontinuous terminal 3p26.3 deletion spanning less than 1 Mb. The deletion was transmitted from their normal father and included only the CHL1 gene. The two brothers present microcephaly, light mental retardation, learning and language difficulties but not the typical phenotype manifestations described in 3p- syndrome. Conclusion a terminal 3p26.3 deletion including only the CHL1 gene is a very rare finding previously reported only in one family. The phenotype of the affected individuals in the two families is very similar and the deletion has been inherited from an apparently normal parent. As already described for others recurrent syndromes with variable phenotype, these findings are challenging in genetic counselling because of an evident variable penetrance.

  20. A new assay based on terminal restriction fragment length polymorphism of homocitrate synthase gene fragments for Candida species identification.

    Science.gov (United States)

    Szemiako, Kasjan; Śledzińska, Anna; Krawczyk, Beata

    2017-08-01

    Candida sp. have been responsible for an increasing number of infections, especially in patients with immunodeficiency. Species-specific differentiation of Candida sp. is difficult in routine diagnosis. This identification can have a highly significant association in therapy and prophylaxis. This work has shown a new application of the terminal restriction fragment length polymorphism (t-RFLP) method in the molecular identification of six species of Candida, which are the most common causes of fungal infections. Specific for fungi homocitrate synthase gene was chosen as a molecular target for amplification. The use of three restriction enzymes, DraI, RsaI, and BglII, for amplicon digestion can generate species-specific fluorescence labeled DNA fragment profiles, which can be used to determine the diagnostic algorithm. The designed method can be a cost-efficient high-throughput molecular technique for the identification of six clinically important Candida species.

  1. A large number of nuclear genes in the human parasite blastocystis require mRNA polyadenylation to create functional termination codons.

    Science.gov (United States)

    Klimeš, Vladimír; Gentekaki, Eleni; Roger, Andrew J; Eliáš, Marek

    2014-07-10

    Termination codons in mRNA molecules are typically specified directly by the sequence of the corresponding gene. However, in mitochondria of a few eukaryotic groups, some mRNAs contain the termination codon UAA deriving one or both adenosines from transcript polyadenylation. Here, we show that a similar phenomenon occurs for a substantial number of nuclear genes in Blastocystis spp., divergent unicellular eukaryote gut parasites. Our analyses of published genomic data from Blastocystis sp. subtype 7 revealed that polyadenylation-mediated creation of termination codons occurs in approximately 15% of all nuclear genes. As this phenomenon has not been noticed before, the procedure previously employed to annotate the Blastocystis nuclear genome sequence failed to correctly define the structure of the 3'-ends of hundreds of genes. From sequence data we have obtained from the distantly related Blastocystis sp. subtype 1 strain, we show that this phenomenon is widespread within the Blastocystis genus. Polyadenylation in Blastocystis appears to be directed by a conserved GU-rich element located four nucleotides downstream of the polyadenylation site. Thus, the highly precise positioning of the polyadenylation in Blastocystis has allowed reduction of the 3'-untranslated regions to the point that, in many genes, only one or two nucleotides of the termination codon are left. © The Author(s) 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  2. Amino-terminal domains of c-myc and N-myc proteins mediate binding to the retinoblastoma gene product

    Science.gov (United States)

    Rustgi, Anil K.; Dyson, Nicholas; Bernards, Rene

    1991-08-01

    THE proteins encoded by the myc gene family are involved in the control of cell proliferation and differentiation, and aberrant expression of myc proteins has been implicated in the genesis of a variety of neoplasms1. In the carboxyl terminus, myc proteins have two domains that encode a basic domain/helix-loop-helix and a leucine zipper motif, respectively. These motifs are involved both in DNA binding and in protein dimerization2-5. In addition, myc protein family members share several regions of highly conserved amino acids in their amino termini that are essential for transformation6,7. We report here that an N-terminal domain present in both the c-myc and N-myc proteins mediates binding to the retinoblastoma gene product, pRb. We show that the human papilloma virus E7 protein competes with c-myc for binding to pRb, indicating that these proteins share overlapping binding sites on pRb. Furthermore, a mutant Rb protein from a human tumour cell line that carried a 35-amino-acid deletion in its C terminus failed to bind to c-myc. Our results suggest that c-myc and pRb cooperate through direct binding to control cell proliferation.

  3. Mutational analysis of the GAP-related domain of the neurofibromatosis type 1 gene in Brazilian NF1 patients

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    Alessandra B. Trovó

    2004-01-01

    Full Text Available Neurofibromatosis type 1 (NF1 is a common autosomal dominant disorder caused by mutations in the NF1 gene. In the present study, a total of 55 unrelated NF1 patients were screened for mutations in the GAP-related domain/GRD (exons 20-27a by single-strand conformation polymorphism (SSCP. Four different mutations were identified and, taken together, they comprise one nonsense substitution (Q1189X, one deletion (3525-3526delAA, one missense substitution (E1356G and one mutation in the splice acceptor site (c.4111-1G>A. One novel polymorphism (c.4514+11C>G and other three putative polymorphisms were also found (c.3315-27G>A, V1146I and V1317A. Genotype-phenotype correlations were investigated, but no particular association was detected.

  4. A mouse homologue of the Drosophila tumor suppressor l(2)tid gene defines a novel Ras GTPase-activating protein (RasGAP)-binding protein.

    Science.gov (United States)

    Trentin, G A; Yin, X; Tahir, S; Lhotak, S; Farhang-Fallah, J; Li, Y; Rozakis-Adcock, M

    2001-04-20

    p120 GTPase-activating protein (GAP) down-regulates Ras by stimulating GTP hydrolysis of active Ras. In addition to its association with Ras, GAP has been shown to bind to several tyrosine-phosphorylated proteins in cells stimulated by growth factors or expressing transforming tyrosine kinase variants. Here we report the cloning and characterization of a novel GAP-binding protein, mTid-1, a DnaJ chaperone protein that represents the murine homolog of the Drosophila tumor suppressor l(2)tid gene. Three alternatively spliced variants of mTid-1 were isolated, two of which correspond to the recently identified hTid-1(L) and hTid-1(S) forms of the human TID1 gene that exhibit opposing effects on apoptosis. We demonstrate that both cytoplasmic precursor and mitochondrial mature forms of mTid-1 associate with GAP in vivo. Interestingly, although mTid-1 is found tyrosine-phosphorylated in v-src-transformed fibroblast cells, GAP selectively binds to the unphosphorylated form of mTid-1. In immunofluorescence experiments, GAP and Tid-1 were shown to colocalize at perinuclear mitochondrial membranes in response to epidermal growth factor stimulation. These findings raise the possibility that Tid chaperone proteins may play a role in governing the conformation, activity, and/or subcellular distribution of GAP, thereby influencing its biochemical and biological activity within cells.

  5. Interleukin-1 (IL-1 system gene expression in granulosa cells: kinetics during terminal preovulatory follicle maturation in the mare

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    Gérard Nadine

    2003-05-01

    Full Text Available Abstract Background A growing body of evidences suggests that the ovary is a site of inflammatory reactions, and thus, ovarian cells could represent sources and targets of the interleukin-1 (IL-1 system. The purpose of this study was to examine the IL-1 system gene expressions in equine granulosa cells, and to study the IL-1β content in follicular fluid during the follicle maturation. For this purpose, granulosa cells and follicular fluids were collected from the largest follicle at the early dominance stage (diameter 24 ± 3 mm or during the preovulatory maturation phase, at T0 h, T6 h, T12 h, T24 h and T34 h after induction of ovulation. Cells were analysed by RT-PCR and follicular fluids were studied by gel electrophoresis and immunoblotting. Results We demonstrated that interleukin-1β (IL-1β, interleukin-1 receptor 2 (IL-1R2 and interleukin-1 receptor antagonist (IL-1RA genes are expressed in equine granulosa cells. We observed that the IL-1β and IL-1RA mRNA content changed in granulosa cells during the terminal follicular maturation whereas IL-1R2 mRNA did not vary. In follicular fluid, IL-1β content fluctuated few hours after induction of ovulation. Conclusions The expression of IL-1β gene in granulosa cells and the follicular fluid IL-1β content seem to be regulated by gonadotropins suggesting that IL-1β could be an intermediate paracrine factor involved in ovulation.

  6. Characterization of microbial communities found in the human vagina by analysis of terminal restriction fragment length polymorphisms of 16S rRNA genes

    NARCIS (Netherlands)

    Coolen, MJL; Post, E; Davis, CC; Forney, LJ

    2005-01-01

    To define and monitor the structure of microbial communities found in the human vagina, a cultivation-independent approach based on analyses of terminal restriction fragment length polymorphisms (T-RFLP) of 16S rRNA genes was developed and validated. Sixteen bacterial strains commonly found in the

  7. Transcription of glycolytic genes and operons in Bacillus subtilis: evidence for the presence of multiple levels of control of the gapA operon.

    Science.gov (United States)

    Ludwig, H; Homuth, G; Schmalisch, M; Dyka, F M; Hecker, M; Stülke, J

    2001-07-01

    Glycolysis is one of the main pathways of carbon catabolism in Bacillus subtilis. Although the biochemical activity of glycolytic enzymes has been studied in detail, no information about the expression of glycolytic genes has so far been available in this organism. Therefore, transcriptional analysis of all glycolytic genes was performed. The genes cggR, gapA, pgk, tpi, pgm and eno, encoding the enzymes required for the interconversion of triose phosphates, are transcribed as a hexacistronic operon as demonstrated by Northern analysis. This gapA operon is repressed by the regulator CggR. The presence of sugars and amino acids synergistically results in the induction of the gapA operon. The transcriptional start site upstream of cggR was mapped by primer extension. Transcripts originating upstream of cggR are processed near the 3' end of cggR. This endonucleolytic cleavage leads to differential stability of the resulting processing products: the monocistronic cggR message is very rapidly degraded, whereas the mRNA species encoding glycolytic enzymes exhibit much higher stability. An additional internal constitutive promoter was identified upstream of pgk. Thus, gapA is the most strongly regulated gene of this operon. The pfk pyk operon encoding phosphofructokinase and pyruvate kinase is weakly induced by glucose. In contrast, the genes pgi and fbaA, coding for phosphoglucoisomerase and fructose-1,6-bisphosphate aldolase, are constitutively expressed.

  8. Bridging the Rice Yield Gaps under Drought: QTLs, Genes, and their Use in Breeding Programs

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    Nitika Sandhu

    2017-04-01

    Full Text Available Rice is the staple food for more than half of the world’s population. Although rice production has doubled in the last 30 years as a result of the development of high-yield, widely adaptable, resource-responsive, semi-dwarf varieties, the threat of a food crisis remains as severe as it was 60 years ago due to the ever-increasing population, water scarcity, labor scarcity, shifting climatic conditions, pest/diseases, loss of productive land to housing, industries, rising sea levels, increasing incidences of drought, flood, urbanization, soil erosion, reduction in soil nutrient status, and environmental issues associated with high-input agriculture. Among these, drought is predicted to be the most severe stress that reduces rice yield. Systematic research on drought over the last 10 years has been conducted across institutes on physiology, breeding, molecular genetics, biotechnology, and cellular and molecular biology. This has provided a better understanding of plant drought mechanisms and has helped scientists to devise better strategies to reduce rice yield losses under drought stress. These include the identification of quantitative trait loci (QTLs for grain yield under drought as well as many agronomically important traits related to drought tolerance, marker-assisted pyramiding of genetic regions that increase yield under drought, development of efficient techniques for genetic transformation, complete sequencing and annotation of rice genomes, and synteny studies of rice and other cereal genomes. Conventional and marker-assisted breeding rice lines containing useful introgressed genes or loci have been field tested and released as varieties. Still, there is a long way to go towards developing drought-tolerant rice varieties by exploiting existing genetic diversity, identifying superior alleles for drought tolerance, understanding interactions among alleles for drought tolerance and their interaction with genetic backgrounds, and

  9. GAP Analysis Program (GAP)

    Data.gov (United States)

    Kansas Data Access and Support Center — The Kansas GAP Analysis Land Cover database depicts 43 land cover classes for the state of Kansas. The database was generated using a two-stage hybrid classification...

  10. Stimulated serotonin release from hyperinnervated terminals subsequent to neonatal dopamine depletion regulates striatal tachykinin, but not enkephalin gene expression.

    Science.gov (United States)

    Basura, G J; Walker, P D

    2000-09-30

    Dopamine (DA) depletion in neonatal rodents results in depressed tachykinin and elevated enkephalin gene expression in the adult striatum (STR). Concurrently, serotonin (5-HT) fibers sprout to hyperinnervate the DA-depleted anterior striatum (A-STR). The present study was designed to determine if increased 5-HT release from sprouted terminals influences dysregulated preprotachykinin (PPT) and preproenkephalin (PPE) mRNA expression in the DA-depleted STR. Three-day-old Sprague-Dawley rat pups received bilateral intracerebroventricular injections of vehicle or the DA neurotoxin 6-hydroxydopamine (6-OHDA, 100 microg). Two months later, rats received a single intraperitoneal injection of vehicle or the acute 5-HT releasing agent p-chloroamphetamine (PCA; 10 mg/kg). Rats were killed 4 h later and striata processed for monoamine content by HPLC-ED and mRNA expression by in situ hybridization within specific subregions of the A-STR and posterior striatum (P-STR). 6-OHDA treatment severely (>98%) reduced striatal DA levels, while 5-HT content in the A-STR was significantly elevated (doubled), indicative of 5-HT hyperinnervation. Following 6-OHDA, PPT mRNA levels were depressed 60-66% across three subregions of the A-STR and 52-59% across two subregions of the P-STR, while PPE mRNA expression was elevated in both the A-STR (50-62%) and P-STR (55-82%). PCA normalized PPT mRNA levels in all regions of the DA-depleted A-STR and P-STR, yet did not alter PPE levels in either dorsal central or medial regions from 6-OHDA alone, but reduced PPE to control levels in the dorsal lateral A-STR. These data indicate that increased 5-HT neurotransmission, following neonatal 6-OHDA treatment, primarily influences PPT-containing neurons of the direct striatal output pathway.

  11. Chemoprevention gene therapy (CGT) of pancreatic cancer using perillyl alcohol and a novel chimeric serotype cancer terminator virus.

    Science.gov (United States)

    Sarkar, S; Azab, B; Quinn, B A; Shen, X; Dent, P; Klibanov, A L; Emdad, L; Das, S K; Sarkar, D; Fisher, P B

    2014-01-01

    Conditionally replication competent adenoviruses (Ads) that selectively replicate in cancer cells and simultaneously express a therapeutic cytokine, such as melanoma differentiation associated gene- 7/Interleukin-24 (mda-7/IL-24), a Cancer Terminator Virus (CTV-M7), hold potential for treating human cancers. To enhance the efficacy of the CTV-M7, we generated a chimeric Ad.5 and Ad.3 modified fiber bipartite CTV (Ad.5/3-CTV-M7) that can infect tumor cells in a Coxsackie Adenovirus receptor (CAR) independent manner, while retaining high infectivity in cancer cells containing high CAR. Although mda-7/IL-24 displays broad-spectrum anticancer properties, pancreatic ductal adenocarcinoma (PDAC) cells display an intrinsic resistance to mda-7/IL-24-mediated killing due to an mda-7/IL-24 mRNA translational block. However, using a chemoprevention gene therapy (CGT) approach with perillyl alcohol (POH) and a replication incompetent Ad to deliver mda-7/IL-24 (Ad.mda-7) there is enhanced conversion of mda-7/IL-24 mRNA into protein resulting in pancreatic cancer cell death in vitro and in vivo in nude mice containing human PDAC xenografts. This combination synergistically induces mda-7/IL-24-mediated cancer-specific apoptosis by inhibiting anti-apoptotic Bcl-xL and Bcl-2 protein expression and inducing an endoplasmic reticulum (ER) stress response through induction of BiP/GRP-78, which is most evident in chimeric-modified non-replicating Ad.5/3- mda-7- and CTV-M7-infected PDAC cells. Moreover, Ad.5/3-CTV-M7 in combination with POH sensitizes therapy-resistant MIA PaCa-2 cell lines over-expressing either Bcl-2 or Bcl-xL to mda-7/IL-24-mediated apoptosis. Ad.5/3-CTV-M7 plus POH also exerts a significant antitumor 'bystander' effect in vivo suppressing both primary and distant site tumor growth, confirming therapeutic utility of Ad.5/3-CTV-M7 plus POH in PDAC treatment, where all other current treatment strategies in clinical settings show minimal efficacy.

  12. Expression of Shigella flexneri gluQ-rs gene is linked to dksA and controlled by a transcriptional terminator

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    Caballero Valeria C

    2012-10-01

    Full Text Available Abstract Background Glutamyl queuosine-tRNAAsp synthetase (GluQ-RS is a paralog of the catalytic domain of glutamyl-tRNA synthetase and catalyzes the formation of glutamyl-queuosine on the wobble position of tRNAAsp. Here we analyze the transcription of its gene in Shigella flexneri, where it is found downstream of dksA, which encodes a transcriptional regulator involved in stress responses. Results The genomic organization, dksA-gluQ-rs, is conserved in more than 40 bacterial species. RT-PCR assays show co-transcription of both genes without a significant change in transcript levels during growth of S. flexneri. However, mRNA levels of the intergenic region changed during growth, increasing at stationary phase, indicating an additional level of control over the expression of gluQ-rs gene. Transcriptional fusions with lacZ as a reporter gene only produced β-galactosidase activity when the constructs included the dksA promoter, indicating that gluQ-rs do not have a separate promoter. Using bioinformatics, we identified a putative transcriptional terminator between dksA and gluQ-rs. Deletion or alteration of the predicted terminator resulted in increased expression of the lacZ reporter compared with cells containing the wild type terminator sequence. Analysis of the phenotype of a gluQ-rs mutant suggested that it may play a role in some stress responses, since growth of the mutant was impaired in the presence of osmolytes. Conclusions The results presented here, show that the expression of gluQ-rs depends on the dksA promoter, and strongly suggest the presence and the functionality of a transcriptional terminator regulating its expression. Also, the results indicate a link between glutamyl-queuosine synthesis and stress response in Shigella flexneri.

  13. Active Center Control of Termination by RNA Polymerase III and tRNA Gene Transcription Levels In Vivo.

    Science.gov (United States)

    Rijal, Keshab; Maraia, Richard J

    2016-08-01

    The ability of RNA polymerase (RNAP) III to efficiently recycle from termination to reinitiation is critical for abundant tRNA production during cellular proliferation, development and cancer. Yet understanding of the unique termination mechanisms used by RNAP III is incomplete, as is its link to high transcription output. We used two tRNA-mediated suppression systems to screen for Rpc1 mutants with gain- and loss- of termination phenotypes in S. pombe. 122 point mutation mutants were mapped to a recently solved 3.9 Å structure of yeast RNAP III elongation complex (EC); they cluster in the active center bridge helix and trigger loop, as well as the pore and funnel, the latter of which indicate involvement of the RNA cleavage domain of the C11 subunit in termination. Purified RNAP III from a readthrough (RT) mutant exhibits increased elongation rate. The data strongly support a kinetic coupling model in which elongation rate is inversely related to termination efficiency. The mutants exhibit good correlations of terminator RT in vitro and in vivo, and surprisingly, amounts of transcription in vivo. Because assessing in vivo transcription can be confounded by various parameters, we used a tRNA reporter with a processing defect and a strong terminator. By ruling out differences in RNA decay rates, the data indicate that mutants with the RT phenotype synthesize more RNA than wild type cells, and than can be accounted for by their increased elongation rate. Finally, increased activity by the mutants appears unrelated to the RNAP III repressor, Maf1. The results show that the mobile elements of the RNAP III active center, including C11, are key determinants of termination, and that some of the mutations activate RNAP III for overall transcription. Similar mutations in spontaneous cancer suggest this as an unforeseen mechanism of RNAP III activation in disease.

  14. Active Center Control of Termination by RNA Polymerase III and tRNA Gene Transcription Levels In Vivo.

    Directory of Open Access Journals (Sweden)

    Keshab Rijal

    2016-08-01

    Full Text Available The ability of RNA polymerase (RNAP III to efficiently recycle from termination to reinitiation is critical for abundant tRNA production during cellular proliferation, development and cancer. Yet understanding of the unique termination mechanisms used by RNAP III is incomplete, as is its link to high transcription output. We used two tRNA-mediated suppression systems to screen for Rpc1 mutants with gain- and loss- of termination phenotypes in S. pombe. 122 point mutation mutants were mapped to a recently solved 3.9 Å structure of yeast RNAP III elongation complex (EC; they cluster in the active center bridge helix and trigger loop, as well as the pore and funnel, the latter of which indicate involvement of the RNA cleavage domain of the C11 subunit in termination. Purified RNAP III from a readthrough (RT mutant exhibits increased elongation rate. The data strongly support a kinetic coupling model in which elongation rate is inversely related to termination efficiency. The mutants exhibit good correlations of terminator RT in vitro and in vivo, and surprisingly, amounts of transcription in vivo. Because assessing in vivo transcription can be confounded by various parameters, we used a tRNA reporter with a processing defect and a strong terminator. By ruling out differences in RNA decay rates, the data indicate that mutants with the RT phenotype synthesize more RNA than wild type cells, and than can be accounted for by their increased elongation rate. Finally, increased activity by the mutants appears unrelated to the RNAP III repressor, Maf1. The results show that the mobile elements of the RNAP III active center, including C11, are key determinants of termination, and that some of the mutations activate RNAP III for overall transcription. Similar mutations in spontaneous cancer suggest this as an unforeseen mechanism of RNAP III activation in disease.

  15. l-Lysine production independent of the oxidative pentose phosphate pathway by Corynebacterium glutamicum with the Streptococcus mutans gapN gene.

    Science.gov (United States)

    Takeno, Seiki; Hori, Kazumasa; Ohtani, Sachiko; Mimura, Akinori; Mitsuhashi, Satoshi; Ikeda, Masato

    2016-09-01

    We have recently developed a Corynebacterium glutamicum strain that generates NADPH via the glycolytic pathway by replacing endogenous NAD-dependent glyceraldehyde 3-phosphate dehydrogenase (GapA) with a nonphosphorylating NADP-dependent glyceraldehyde 3-phosphate dehydrogenase (GapN) from Streptococcus mutans. Strain RE2, a suppressor mutant spontaneously isolated for its improved growth on glucose from the engineered strain, was proven to be a high-potential host for l-lysine production (Takeno et al., 2010). In this study, the suppressor mutation was identified to be a point mutation in rho encoding the transcription termination factor Rho. Strain RE2 still showed retarded growth despite the mutation rho696. Our strategy for reconciling improved growth with a high level of l-lysine production was to use GapA together with GapN only in the early growth phase, and subsequently shift this combination-type glycolysis to one that depends only on GapN in the rest of the growth phase. To achieve this, we expressed gapA under the myo-inositol-inducible promoter of iolT1 encoding a myo-inositol transporter in strain RE2. The resulting strain RE2A(iol) was engineered into an l-lysine producer by introduction of a plasmid carrying the desensitized lysC, followed by examination for culture conditions with myo-inositol supplementation. We found that as a higher concentration of myo-inositol was added to the seed culture, the following fermentation period became shorter while maintaining a high level of l-lysine production. This finally reached a fermentation period comparable to that of the control GapA strain, and yielded a 1.5-fold higher production rate compared with strain RE2. The transcript level of gapA, as well as the GapA activity, in the early growth phase increased in proportion to the myo-inositol concentration and then fell to low levels in the subsequent growth phase, indicating that improved growth was a result of increased GapA activity, especially in the

  16. X-chromosome terminal deletion in a female with premature ovarian failure: Haploinsufficiency of X-linked genes as a possible explanation

    Directory of Open Access Journals (Sweden)

    Melo Joana B

    2010-07-01

    Full Text Available Abstract Background Premature ovarian failure (POF has repeatedly been associated to X-chromosome deletions. FMR1 gene premutation allele's carrier women have an increased risk for POF. We intent to determine the cause of POF in a 29 year old female, evaluating both of these situations. Methods Concomitant analysis of FMR1 gene CGG repeat number and karyotype revealed an X-chromosome terminal deletion. Fluorescence in situ further characterized the breakpoint. A methylation assay for FMR1 gene allowed to determine its methylation status, and hence, the methylation status of the normal X-chromosome. Results We report a POF patient with a 46,X,del(X(q26 karyotype and with skewed X-chromosome inactivation of the structural abnormal X-chromosome. Conclusions Despite the hemizygosity of FMR1 gene, the patient does not present Fragile X syndrome features, since the normal X-chromosome is not subject to methylation. The described deletion supports the hypothesis that haploinsufficiency of X-linked genes can be on the basis of POF, and special attention should be paid to X-linked genes in region Xq28 since they escape inactivation and might have a role in this disorder. A full clinical and cytogenetic characterization of all POF cases is important to highlight a pattern and help to understand which genes are crucial for normal ovarian development.

  17. X-chromosome terminal deletion in a female with premature ovarian failure: Haploinsufficiency of X-linked genes as a possible explanation.

    Science.gov (United States)

    Ferreira, Susana I; Matoso, Eunice; Pinto, Marta; Almeida, Joana; Liehr, Thomas; Melo, Joana B; Carreira, Isabel M

    2010-07-20

    Premature ovarian failure (POF) has repeatedly been associated to X-chromosome deletions. FMR1 gene premutation allele's carrier women have an increased risk for POF. We intent to determine the cause of POF in a 29 year old female, evaluating both of these situations. Concomitant analysis of FMR1 gene CGG repeat number and karyotype revealed an X-chromosome terminal deletion. Fluorescence in situ further characterized the breakpoint. A methylation assay for FMR1 gene allowed to determine its methylation status, and hence, the methylation status of the normal X-chromosome. We report a POF patient with a 46,X,del(X)(q26) karyotype and with skewed X-chromosome inactivation of the structural abnormal X-chromosome. Despite the hemizygosity of FMR1 gene, the patient does not present Fragile X syndrome features, since the normal X-chromosome is not subject to methylation. The described deletion supports the hypothesis that haploinsufficiency of X-linked genes can be on the basis of POF, and special attention should be paid to X-linked genes in region Xq28 since they escape inactivation and might have a role in this disorder. A full clinical and cytogenetic characterization of all POF cases is important to highlight a pattern and help to understand which genes are crucial for normal ovarian development.

  18. Tanshinone IIA increases the bystander effect of herpes simplex virus thymidine kinase/ganciclovir gene therapy via enhanced gap junctional intercellular communication.

    Directory of Open Access Journals (Sweden)

    Jianyong Xiao

    Full Text Available The bystander effect is an intriguing phenomenon by which adjacent cells become sensitized to drug treatment during gene therapy with herpes simplex virus thymidine kinase/ganciclovir (HSV-tk/GCV. This effect is reported to be mediated by gap junctional intercellular communication (GJIC, and therefore, we postulated that upregulation of genes that facilitate GJIC may enhance the HSV-tk/GCV bystander effect. Previous findings have shown Tanshinone IIA (Tan IIA, a chemical substance derived from a Chinese medicine herb, promotes the upregulation of the connexins Cx26 and Cx43 in B16 cells. Because gap junctions are formed by connexins, we hypothesized that Tan IIA might increase GJIC. Our results show that Tan IIA increased GJIC in B16 melanoma cells, leading to more efficient GCV-induced bystander killing in cells stably expressing HSV-tk. Additionally, in vivo experiments demonstrated that tumors in mice with 10% HSV-tk positive B16 cells and 90% wild-type B16 cells became smaller following treatment with the combination of GCV and Tan IIA as compared to GCV or Tan IIA alone. These data demonstrate that Tan IIA can augment the bystander effect of HSV-tk/GCV system through increased gap junction coupling, which adds strength to the promising strategy that develops connexins inducer to potentiate the effects of suicide gene therapy.

  19. Tanshinone IIA increases the bystander effect of herpes simplex virus thymidine kinase/ganciclovir gene therapy via enhanced gap junctional intercellular communication.

    Science.gov (United States)

    Xiao, Jianyong; Zhang, Guangxian; Qiu, Pengxiang; Liu, Xijuan; Wu, Yingya; Du, Biaoyan; Li, Jiefen; Zhou, Jing; Li, Jingjing; Tan, Yuhui

    2013-01-01

    The bystander effect is an intriguing phenomenon by which adjacent cells become sensitized to drug treatment during gene therapy with herpes simplex virus thymidine kinase/ganciclovir (HSV-tk/GCV). This effect is reported to be mediated by gap junctional intercellular communication (GJIC), and therefore, we postulated that upregulation of genes that facilitate GJIC may enhance the HSV-tk/GCV bystander effect. Previous findings have shown Tanshinone IIA (Tan IIA), a chemical substance derived from a Chinese medicine herb, promotes the upregulation of the connexins Cx26 and Cx43 in B16 cells. Because gap junctions are formed by connexins, we hypothesized that Tan IIA might increase GJIC. Our results show that Tan IIA increased GJIC in B16 melanoma cells, leading to more efficient GCV-induced bystander killing in cells stably expressing HSV-tk. Additionally, in vivo experiments demonstrated that tumors in mice with 10% HSV-tk positive B16 cells and 90% wild-type B16 cells became smaller following treatment with the combination of GCV and Tan IIA as compared to GCV or Tan IIA alone. These data demonstrate that Tan IIA can augment the bystander effect of HSV-tk/GCV system through increased gap junction coupling, which adds strength to the promising strategy that develops connexins inducer to potentiate the effects of suicide gene therapy.

  20. 75 FR 72771 - Gap in Termination Provisions

    Science.gov (United States)

    2010-11-26

    ...: Background The Copyright Act gives authors (and some heirs, beneficiaries and representatives who are..., e.g., Comment of Randall D. Wixen, Wixen Music Publishing, Inc., at 1. Several commenters also cited...

  1. De novo transcriptome sequencing and analysis of Coccinella septempunctata L. in non-diapause, diapause and diapause-terminated states to identify diapause-associated genes.

    Science.gov (United States)

    Qi, Xiaoyang; Zhang, Lisheng; Han, Yanhua; Ren, Xiaoyun; Huang, Jian; Chen, Hongyin

    2015-12-21

    The most common ladybird beetle, Coccinella septempunctata L., is an excellent predator of crop pests such as aphids and white flies, and it shows a wide range of adaptability, a large appetite and a high reproductive ability. Diapause research plays an important role in the artificial propagation and shelf-life extension of insect products. Although this lady beetle's regulatory, physiological and biochemical characteristics in the diapause period are well understood, the molecular mechanism of diapause remains unknown. Therefore, we collected female adults in three different states, i.e., non-diapause, diapause and diapause termination, for transcriptome sequencing. After transcriptome sequencing using the Illumina HiSeq 2500 platform with pretreatment, a total of 417.6 million clean reads from nine samples were filtered using the program FASTX (version 0.0). Additionally, 106,262 contigs were assembled into 82,820 unigenes with an average length of 921 bp and an N50 of 1,241 bp. All of the unigenes were annotated through BLASTX alignment against the Nr or UniProt database, and 37,872 unigenes were matched. We performed further analysis of these unigenes using the Clusters of Orthologous Groups of proteins (COG), Gene Ontology (GO), and the Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Through pairwise comparisons of the non-diapause (ND), diapause (D), and diapause-terminated (DT) groups, 3,501 and 1,427 differentially expressed genes (DEGs) were identified between D and ND and between DT and D, respectively. Moreover, 443 of the DEGs were specifically expressed during the diapause period (i.e., DEGs that were expressed at the highest or lowest levels during diapause compared with the other stages). GO function and KEGG pathway enrichment were performed on all DEGs and showed that RNA-directed DNA polymerase activity and fatty acid metabolism were significantly affected. Furthermore, eight specific expressed genes were selected for validation using q

  2. Global gene expression analysis of fission yeast mutants impaired in Ser-2 phosphorylation of the RNA pol II carboxy terminal domain.

    Directory of Open Access Journals (Sweden)

    Reza Saberianfar

    Full Text Available In Schizosaccharomyces pombe the nuclear-localized Lsk1p-Lsc1p cyclin dependent kinase complex promotes Ser-2 phosphorylation of the heptad repeats found within the RNA pol II carboxy terminal domain (CTD. Here, we first provide evidence supporting the existence of a third previously uncharacterized Ser-2 CTD kinase subunit, Lsg1p. As expected for a component of the complex, Lsg1p localizes to the nucleus, promotes Ser-2 phosphorylation of the CTD, and physically interacts with both Lsk1p and Lsc1p in vivo. Interestingly, we also demonstrate that lsg1Δ mutants--just like lsk1Δ and lsc1Δ strains--are compromised in their ability to faithfully and reliably complete cytokinesis. Next, to address whether kinase mediated alterations in CTD phosphorylation might selectively alter the expression of genes with roles in cytokinesis and/or the cytoskeleton, global gene expression profiles were analyzed. Mutants impaired in Ser-2 phosphorylation display little change with respect to the level of transcription of most genes. However, genes affecting cytokinesis--including the actin interacting protein gene, aip1--as well as genes with roles in meiosis, are included in a small subset that are differentially regulated. Significantly, genetic analysis of lsk1Δ aip1Δ double mutants is consistent with Lsk1p and Aip1p acting in a linear pathway with respect to the regulation of cytokinesis.

  3. A ¤Terminal Flower-1¤-like gene from perennial ryegrass involved in floral transition and axillary meristem identity

    DEFF Research Database (Denmark)

    Jensen, C.S.; Salchert, K.; Nielsen, K.K.

    2001-01-01

    . To investigate the regulation of meristem identity and the control of floral transition in perennial ryegrass (Lolium perenne) we isolated a ryegrass TERMINAL FLOWER1-like gene, LpTFL1, and characterized it for its function in ryegrass flower development. Perennial ryegrass requires a cold treatment of at least...... 12 weeks to induce flowering. During this period a decrease in LpTFL1 message was detected in the ryegrass apex. However, upon subsequent induction with elevated temperatures and long-day photoperiods, LpTFL1 message levels increased and reached a maximum M:hen the ryegrass apex has formed visible...... and a controller of axillary meristem identity in ryegrass....

  4. A new family of retroviral long terminal repeat elements in the human genome identified by their homologies to an element 5{prime} to the spider monkey haptoglobin gene

    Energy Technology Data Exchange (ETDEWEB)

    Erickson, L.M.; Maeda, N. [Univ. of North Carolina, Chapel Hill, NC (United States)

    1995-06-10

    A new family of retroviral long terminal repeats that we name Spm-LTR has been identified as a result of DNA sequence comparisons between the entire Gen-Bank databank and an element, SPHP, located 5{prime} to the haptoglobin gene of spider monkeys. The 18 human Spm-LTR sequences so identified fall into three subtypes. There is no sequence similarity between Spm-LTR elements and any endogenous retroviral LTR sequences previously reported except for general features that define LTRs. However, a previously described repeated sequence (MER-4) forms a portion of the Spm-LTR sequence. 13 refs., 1 fig., 1 tab.

  5. Nucleotide polymorphism and evolution in the glyceraldehyde-3-phosphate dehydrogenase gene (gapA) in natural populations of Salmonella and Escherichia coli.

    Science.gov (United States)

    Nelson, K; Whittam, T S; Selander, R K

    1991-08-01

    Nucleotide sequences of the gapA gene, encoding the glycolytic enzyme glyceraldehyde-3-phosphate dehydrogenase, were determined for 16 strains of Salmonella and 13 strains of Escherichia coli recovered from natural populations. Pairs of sequences from strains representing the eight serovar groups of Salmonella differed, on average, at 3.8% of nucleotide sites and 1.1% of inferred amino acids, and comparable values for E. coli were an order of magnitude smaller (0.2% and 0.1%, respectively). The rate of substitution at synonymous sites was significantly higher for codons specifying the catalytic domain of the enzyme than for those encoding the NAD(+)-binding domain, but the nonsynonymous substitution rate showed the opposite relationship. For Salmonella, statistical tests for nonrandom clustering of polymorphic sites failed to provide evidence that intragenic recombination or gene conversion has contributed to the generation of allelic diversity. The topology of a tree constructed from the gapA sequences was generally similar to that of phylogenetic trees of the strains based on multilocus enzyme electrophoresis, but the level of divergence of gapA in Salmonella group V from other Salmonella and E. coli strains is much greater than that indicated by DNA hybridization for the genome as a whole.

  6. New modules for the repeated internal and N-terminal epitope tagging of genes in Saccharomyces cerevisiae.

    Science.gov (United States)

    Gauss, Robert; Trautwein, Mark; Sommer, Thomas; Spang, Anne

    2005-01-15

    Epitope tagging is a powerful method for the rapid analysis of protein function. In Saccharomyces cerevisiae epitope tags are introduced easily into chromosomal loci by homologous recombination using a simple PCR-based strategy. Although quite a number of tools exist for C-terminal tagging as well as N-terminal tagging of proteins expressed by heterologous promoters, there are only very limited possibilities to tag proteins at the N-terminus and retain the endogenous expression level. Furthermore, no PCR-templates for internal tagging have been reported. Here we describe new modules that are suitable for both the repeated N-terminal and internal tagging of proteins, leaving their endogenous promoters intact. The tags include 6xHA, 9xMyc, yEGFP, TEV-GST-6xHIS, ProtA, TEV-ProtA and TEV-ProtA-7xHIS in conjunction with different heterologous selection markers. Copyright 2004 John Wiley & Sons, Ltd.

  7. Effects of pulse addition of carbon sources on continuous cultivation of Escherichia coli containing a recombinant E. coli gapA gene.

    Science.gov (United States)

    Gschaedler, A; Robas, N; Boudrant, J; Branlant, C

    1999-06-20

    At high glucose concentrations, Escherichia coli produces acetate (Crabtree effect). To look for the influence of glucose and/or acetate in the medium on the expression of a recombinant gene in E. coli, the effect of a pulse addition of glucose, on transcription of a cloned E. coli gapA gene and the resulting glyceraldehyde-3P-dehydrogenase activity (GAPDH), was tested during continuous cultivation of E. coli HB101 transformed with the plasmid pBR::EcogapA. Stable continuous cultures were established in a semi-synthetic medium supplemented with 5 g/L of glucose. After the addition of 7 g of glucose within a few seconds, gapA gene expression was strongly and very rapidly induced. As shown by primer-extension analysis, promoter P1, one of the four transcriptional promoters of the gapA gene, was strongly activated, and GAPDH activity increased. However, after rapid glucose consumption, acetate was produced and acetate concentrations above 2 g/L induced stress conditions. This is shown by a strong activation of promoter P2, that is recognized by the stress specific Esigma32 RNA polymerase. During this period, the total cellular RNA content was strongly diminished. Later, when acetate was partially consumed a high level of total RNA was restored, translation was efficient and a regular increase of the GAPDH-specific activity was observed. The transitions between glucose metabolism, acetate production and the end of acetate consumption, were marked by large increases in RNase and protease activities. For comparison, pulse-addition experiments were also performed with serine and alanine. A transient increase of GAPDH production associated with an increase in biomass was also found for serine that can be utilized as an energy source, whereas the addition of alanine, which is only incorporated into newly synthesized proteins, did not increase GAPDH production. The implication of these data for overproduction of recombinant proteins in E. coli is discussed. Copyright 1999

  8. Diverse pattern of gap junction beta-2 and gap junction beta-4 genes mutations and lack of contribution of DFNB21, DFNB24, DFNB29, and DFNB42 loci in autosomal recessive nonsyndromic hearing loss patients in Hormozgan, Iran

    Directory of Open Access Journals (Sweden)

    Masoud Akbarzadeh Laleh

    2017-01-01

    Full Text Available Background: We aimed to determine the contribution of four DFNB loci and mutation analysis of gap junction beta-2 (GJB2 and GJB4 genes in autosomal recessive nonsyndromic hearing loss (ARNSHL in South of Iran. Materials and Methods: A total of 36 large ARNSHL pedigrees with at least two affected subjects were enrolled in the current study. The GJB2 and GJB4 genes mutations were screened using direct sequencing method. The GJB2 and GJB4 negative families were analyzed for the linkage to DFNB21, DFNB24, DFNB29, and DFNB42 loci by genotyping the corresponding STR markers using polymerase chain reaction-PAGE method. Results: We found a homozygous nonsense mutation W77X and a homozygous missense mutation C169W in 5.55% of studied families in GJB2 and GJB4 genes, respectively. Five heterozygous mutations including V63G, A78T, and R127H in GJB2 gene, and R103C and R227W in GJB4 gene were detected. We identified two novel variations V63G in GJB2 and R227W in GJB4. In silico analysis predicted that both novel variations are deleterious mutations. We did not unveil any linkage between DFNB21, DFNB24, DFNB29, and DFNB42 loci and ARNSHL among studied families. Conclusion: This is the first report of GJB2 and GJB4 mutations from Hormozgan population. According to the previous publications regarding GJB2 and GJB4 mutations, the distribution of the mutations is different from other parts of Iran that should be considered in primary health-care programs. Further investigations are needed to evaluate the contribution of other loci in ARNSHL subjects in South of Iran.

  9. Cloning and expression of retinoblastoma-binding protein 4 gene in embryo diapause termination and in response to salinity stress from brine shrimp Artemia sinica.

    Science.gov (United States)

    Wang, Xiaolu; Yao, Feng; Liang, Xiaoyu; Zhu, Xiaolin; Zheng, Ren; Jia, Baolin; Hou, Lin; Zou, Xiangyang

    2016-10-15

    Retinoblastoma binding protein 4 (RBBP4) is a nuclear protein with four WD-repeat sequences and thus belongs to a highly conserved subfamily of proteins with such domains. This retinoblastoma-binding protein plays an important role in nucleosome assembly and histone modification, which influences gene transcription and regulates cell cycle and proliferation. Artemia sinica (brine shrimp) undergoes an unusual diapause process under stress conditions of high salinity and low temperature. However, the role of RBBP4 in diapause termination of embryo development in A. sinica remains unknown. Here, the full-length cDNA of the As-rbbp4 gene was obtained from A. sinica and found to contain 1411 nucleotides, including a 1281 bp open reading frame (ORF), 63 bp 5'-untranslated region (UTR) and a 67-bp 3'-UTR, which encodes a 427 amino acid (48 kDa) protein. Bioinformatic analysis indicated As-RBBP4 to be mainly located in the nucleus, with a theoretical isoelectric point of 4.79. Protein sequence domain analysis showed that As-RBBP4 is a conserved protein, especially in the WD40 domain. No specificity in expression of this gene was observed in tissues or organs by in situ hybridization. Real-time quantitative PCR and Western blot analyses of As-RBBP4 gene and protein expression, respectively, showed notably high levels at 10 h and a subsequent downward trend. Obvious trends in upregulation of As-RBBP4 were observed under conditions of low temperature and high salinity stress. As-E2F1 and As-CyclinE also presented similar trends as that of As-RBBP4 in Western blots. Analysis of the RBBP4 expression in early embryonic development of A. sinica indicated that this protein plays an important role in diapause termination and cell cycle regulation. Copyright © 2016 Elsevier B.V. All rights reserved.

  10. Gene encoding the 5. 7-kilodalton chlorosome protein of Chloroflexus aurantiacus: Regulated message levels and a predicted carboxy-terminal protein extension

    Energy Technology Data Exchange (ETDEWEB)

    Theroux, S.J.; Redlinger, T.E.; Fuller, R.C.; Robinson, S.J. (Univ. of Massachusetts, Amherst (USA))

    1990-08-01

    The major light-harvesting pigment of the green filamentous bacterium Chloroflexus aurantiacus is bacteriochlorophyll (Bchl) c, localized in chlorosomes attached to the inner surface of the cytoplasmic membrane. Chlorosomes consist of four polypeptides and associated pigments and lipids. Previous studies of the inducible assembly of the photosynthetic apparatus had indicated that the major chlorosomal polypeptides are present as high-molecular-weight aggregates before the appearance of mature chlorosomes, and a mechanism for posttranslational processing of a polyprotein had been proposed. The authors have isolated the gene (csmA) encoding the 5.7-kilodalton chlorosomal polypeptide from C. aurantiacus in order to determine whether this protein is synthesized as part of a polyprotein. Analysis of the nucleotide sequence of csmA indicates that the gene is not large enough to encode more than one known chlorosome polypeptide. Transcriptional analysis indicates that csmA is transcribed as a small message whose abundance is regulated in response to oxygen, so that no csmA message is detectable in cells grown aerobically in the dark. Comparison of the sequence predicted by csmA with the peptide sequence of the Bchl c binding protein purified for chlorosomes indicates that this protein is synthesized with a carboxy-terminal extension of 27 amino acids. They discuss possible roles for this carboxy-terminal extension in the assembly of chlorosomes.

  11. Involvement of the LuxR-Type Transcriptional Regulator RamA in Regulation of Expression of the gapA Gene, Encoding Glyceraldehyde-3-Phosphate Dehydrogenase of Corynebacterium glutamicum▿ †

    Science.gov (United States)

    Toyoda, Koichi; Teramoto, Haruhiko; Inui, Masayuki; Yukawa, Hideaki

    2009-01-01

    SugR, RamA, GlxR, GntR1, and a MarR-type transcriptional regulator bind to the promoter region of the gapA gene encoding glyceraldehyde-3-phosphate dehydrogenase (GAPDH), essential for glycolysis in Corynebacterium glutamicum. We previously showed that SugR, a transcriptional repressor of phosphotransferase system genes for the sugar transport system, is involved in the downregulation of gapA expression in the absence of sugar. In this study, the role of RamA in the expression of the gapA gene was examined. Comparing the gapA expression and GAPDH activity of a ramA mutant with those of the wild type revealed that RamA is involved in upregulation of gapA expression in glucose-grown cells. DNase I footprint analyses and electrophoretic mobility shift assays revealed that RamA binds with different affinities to three sites in the gapA promoter. lacZ reporter assays with mutated RamA binding sites in the gapA promoter showed that the middle binding site is the most important for RamA to activate gapA expression and that binding of RamA to the gapA promoter activates the gene expression not only in glucose-grown cells but also in acetate-grown cells. Furthermore, RamA also directly activates sugR expression, indicating that two global regulators, RamA and SugR, are coordinately involved in the complex regulation of gapA expression in C. glutamicum. PMID:19047347

  12. Involvement of the LuxR-type transcriptional regulator RamA in regulation of expression of the gapA gene, encoding glyceraldehyde-3-phosphate dehydrogenase of Corynebacterium glutamicum.

    Science.gov (United States)

    Toyoda, Koichi; Teramoto, Haruhiko; Inui, Masayuki; Yukawa, Hideaki

    2009-02-01

    SugR, RamA, GlxR, GntR1, and a MarR-type transcriptional regulator bind to the promoter region of the gapA gene encoding glyceraldehyde-3-phosphate dehydrogenase (GAPDH), essential for glycolysis in Corynebacterium glutamicum. We previously showed that SugR, a transcriptional repressor of phosphotransferase system genes for the sugar transport system, is involved in the downregulation of gapA expression in the absence of sugar. In this study, the role of RamA in the expression of the gapA gene was examined. Comparing the gapA expression and GAPDH activity of a ramA mutant with those of the wild type revealed that RamA is involved in upregulation of gapA expression in glucose-grown cells. DNase I footprint analyses and electrophoretic mobility shift assays revealed that RamA binds with different affinities to three sites in the gapA promoter. lacZ reporter assays with mutated RamA binding sites in the gapA promoter showed that the middle binding site is the most important for RamA to activate gapA expression and that binding of RamA to the gapA promoter activates the gene expression not only in glucose-grown cells but also in acetate-grown cells. Furthermore, RamA also directly activates sugR expression, indicating that two global regulators, RamA and SugR, are coordinately involved in the complex regulation of gapA expression in C. glutamicum.

  13. The GTPase activating Rap/RanGAP domain-like 1 gene is associated with chicken reproductive traits.

    Directory of Open Access Journals (Sweden)

    Xu Shen

    Full Text Available BACKGROUND: Abundant evidence indicates that chicken reproduction is strictly regulated by the hypothalamic-pituitary-gonad (HPG axis, and the genes included in the HPG axis have been studied extensively. However, the question remains as to whether any other genes outside of the HPG system are involved in regulating chicken reproduction. The present study was aimed to identify, on a genome-wide level, novel genes associated with chicken reproductive traits. METHODOLOGY/PRINCIPAL FINDING: Suppressive subtractive hybridization (SSH, genome-wide association study (GWAS, and gene-centric GWAS were used to identify novel genes underlying chicken reproduction. Single marker-trait association analysis with a large population and allelic frequency spectrum analysis were used to confirm the effects of candidate genes. Using two full-sib Ningdu Sanhuang (NDH chickens, GARNL1 was identified as a candidate gene involved in chicken broodiness by SSH analysis. Its expression levels in the hypothalamus and pituitary were significantly higher in brooding chickens than in non-brooding chickens. GWAS analysis with a NDH two tail sample showed that 2802 SNPs were significantly associated with egg number at 300 d of age (EN300. Among the 2802 SNPs, 2 SNPs composed a block overlapping the GARNL1 gene. The gene-centric GWAS analysis with another two tail sample of NDH showed that GARNL1 was strongly associated with EN300 and age at first egg (AFE. Single marker-trait association analysis in 1301 female NDH chickens confirmed that variation in this gene was related to EN300 and AFE. The allelic frequency spectrum of the SNP rs15700989 among 5 different populations supported the above associations. Western blotting, RT-PCR, and qPCR were used to analyze alternative splicing of the GARNL1 gene. RT-PCR detected 5 transcripts and revealed that the transcript, which has a 141 bp insertion, was expressed in a tissue-specific manner. CONCLUSIONS/SIGNIFICANCE: Our findings

  14. Treacher Collins syndrome may result from insertions, deletions or splicing mutations, which introduce a termination codon into the gene

    NARCIS (Netherlands)

    Gladwin, A. J.; Dixon, J.; Loftus, S. K.; Edwards, S.; Wasmuth, J. J.; Hennekam, R. C.; Dixon, M. J.

    1996-01-01

    Treacher Collins syndrome is an autosomal dominant disorder of craniofacial development the features of which include conductive hearing loss and cleft palate. Recently, the Treacher Collins syndrome gene (TCOF1) has been positionally cloned and a series of five mutations within the coding sequence

  15. Amino-terminal domains of c-myc and N-myc proteins mediate binding to the retinoblastoma gene product

    NARCIS (Netherlands)

    Rustgi, A.K.; Dyson, N.; Bernards, R.A.

    1991-01-01

    The proteins encoded by the myc gene family are involved is the control of cell proliferation and differentiation, and aberrant expression of myc proteins has been implicated in the genesis of a variety of neoplasms. In the carboxyl terminus, myc proteins have two domains that encode a basic

  16. An N-terminal glycine to cysteine mutation in the collagen COL1A1 gene produces moderately severe osteogenesis imperfecta

    Energy Technology Data Exchange (ETDEWEB)

    Wilcox, W.; Scott, L.; Cohn, D. [Cedars-Sinai Medical Center, Los Angeles, CA (United States)

    1994-09-01

    Osteogenesis imperfecta (OI) is usually due to mutations in the type I procollagen genes COL1A1 and COL1A2. Point mutations close to the N-terminus are generally milder than those near the C-terminus of the molecule (the gradient hypothesis of collagen mutations). We describe a patient with moderately severe OI due to a mutation in the N-terminal portion of the triple helical domain of the {alpha}1(I) chain. Electrophoretic analysis of collagen isolated from fibroblast cultures suggested the abnormal presence of a cysteine in the N-terminal portion of the {alpha}1(I) chain. Five overlapping DNA fragments amplified from fibroblast RNA were screened for mutations using single strand conformational polymorphism (SSCP) and heteroduplex analyses. Direct DNA sequence analysis of the single positive fragment demonstrated a G to T transversion, corresponding to a glycine to cysteine substitution at position 226 of the triple helical domain of the {alpha}1(I) chain. The mutation was confirmed by restriction enzyme analysis of amplified genomic DNA. The mutation was not present in fibroblasts from either phenotypically normal parent. Combining this mutation with other reported mutations, glycine to cysteine substitutions at positions 205, 211, 223, and 226 produce a moderately severe phenotype whereas flanking mutations at positions 175 and 382 produce a mild phenotype. This data supports a regional rather than a gradient model of the relationship between the nature and location of type I collagen mutations and OI phenotype.

  17. Melanoma antigen gene protein-A11 (MAGE-11) F-box links the androgen receptor NH2-terminal transactivation domain to p160 coactivators.

    Science.gov (United States)

    Askew, Emily B; Bai, Suxia; Hnat, Andrew T; Minges, John T; Wilson, Elizabeth M

    2009-12-11

    Androgen-dependent transcriptional activity by the androgen receptor (AR) and its coregulators is required for male reproductive development and function. In humans and other primates, melanoma antigen gene protein-A11 (MAGE-11) is an AR selective coregulator that increases AR transcriptional activity. Here we show that the interaction between AR and MAGE-11 is mediated by AR NH(2)-terminal FXXLF motif binding to a highly conserved MAGE-11 F-box in the MAGE homology domain, and is modulated by serum stimulation of mitogen-activated protein kinase phosphorylation of MAGE-11 Ser-174. The MAGE-11-dependent increase in AR transcriptional activity is mediated by a direct interaction between MAGE-11 and transcriptional intermediary factor 2 (TIF2) through the NH(2)-terminal region of TIF2, and by a MAGE-11 FXXIF motif interaction with an F-box-like region in activation domain 1 of TIF2. The results suggest that MAGE-11 functions as a bridging factor to recruit AR coactivators through a novel FXX(L/I)F motif-F-box interaction paradigm.

  18. Melanoma Antigen Gene Protein-A11 (MAGE-11) F-box Links the Androgen Receptor NH2-terminal Transactivation Domain to p160 Coactivators*

    Science.gov (United States)

    Askew, Emily B.; Bai, Suxia; Hnat, Andrew T.; Minges, John T.; Wilson, Elizabeth M.

    2009-01-01

    Androgen-dependent transcriptional activity by the androgen receptor (AR) and its coregulators is required for male reproductive development and function. In humans and other primates, melanoma antigen gene protein-A11 (MAGE-11) is an AR selective coregulator that increases AR transcriptional activity. Here we show that the interaction between AR and MAGE-11 is mediated by AR NH2-terminal FXXLF motif binding to a highly conserved MAGE-11 F-box in the MAGE homology domain, and is modulated by serum stimulation of mitogen-activated protein kinase phosphorylation of MAGE-11 Ser-174. The MAGE-11-dependent increase in AR transcriptional activity is mediated by a direct interaction between MAGE-11 and transcriptional intermediary factor 2 (TIF2) through the NH2-terminal region of TIF2, and by a MAGE-11 FXXIF motif interaction with an F-box-like region in activation domain 1 of TIF2. The results suggest that MAGE-11 functions as a bridging factor to recruit AR coactivators through a novel FXX(L/I)F motif-F-box interaction paradigm. PMID:19828458

  19. xol-1, the master sex-switch gene in C. elegans, is a transcriptional target of the terminal sex-determining factor TRA-1.

    Science.gov (United States)

    Hargitai, Balázs; Kutnyánszky, Vera; Blauwkamp, Timothy A; Steták, Attila; Csankovszki, Györgyi; Takács-Vellai, Krisztina; Vellai, Tibor

    2009-12-01

    In the nematode Caenorhabditis elegans, sex is determined by the ratio of X chromosomes to sets of autosomes: XX animals (2X:2A=1.0) develop as hermaphrodites and XO animals (1X:2A=0.5) develop as males. TRA-1, the worm ortholog of Drosophila Cubitus interruptus and mammalian Gli (Glioma-associated homolog) proteins, is the terminal transcription factor of the C. elegans sex-determination pathway, which specifies hermaphrodite fate by repressing male-specific genes. Here we identify a consensus TRA-1 binding site in the regulatory region of xol-1, the master switch gene controlling sex determination and dosage compensation. xol-1 is normally expressed in males, where it promotes male development and prevents dosage compensation. We show that TRA-1 binds to the consensus site in the xol-1 promoter in vitro and inhibits the expression of xol-1 in XX animals in vivo. Furthermore, inactivation of tra-1 enhances, whereas hyperactivation of tra-1 suppresses, lethality in animals with elevated xol-1 activity. These data imply the existence of a regulatory feedback loop within the C. elegans sex-determination and dosage-compensation cascade that ensures the accurate dose of X-linked genes in cells destined to adopt hermaphrodite fate.

  20. Terminating supervision.

    Science.gov (United States)

    Levendosky, Alytia A; Hopwood, Christopher J

    2017-03-01

    The focus of this paper is on the termination of clinical supervision. Although clinical supervision is considered the backbone of most mental health training programs, it gets relatively little theoretical or empirical attention. The termination of supervision has received even less attention. In this paper, we describe an approach to terminating supervision in our treatment team, which integrates intensive assessment with a relational perspective in a clinical science training program (Levendosky & Hopwood, 2016). We describe our established conceptual framework, review empirical evidence, and provide verbatim examples from final supervision meetings on our team to elaborate the importance of conceptualizing individual differences across trainees and parallels between supervision and psychotherapy dynamics. We conclude by emphasizing the need for research on supervision in general and supervision termination in particular. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

  1. Identification of marker genes for pars tuberalis morphogenesis in chick embryo: expression of Cytokine-like 1 and Gap junction protein alpha 5 in pars tuberalis.

    Science.gov (United States)

    Aizawa, Sayaka; Higaki, Yuriko; Dudaui, Amrita; Nagasaka, Mai; Takahashi, Sumio; Sakata, Ichiro; Sakai, Takafumi

    2016-12-01

    The adenohypophysis is formed from the oral ectoderm and consists of the pars distalis (PD), pars intermedia, and pars tuberalis (PT). The mechanisms of PD development have been extensively studied, and the cellular differentiation of the PD is well understood. However, the morphogenesis and differentiation of the PT are still unclear, and the genes expressed during PT development remain largely unknown. We have explored genes specifically expressed in the PT during embryonic development and analyzed their spatiotemporal expression patterns. Microarray analysis of laser-captured PT and PD tissues obtained from chick embryos on embryonic day 10 (E10.0) has shown high expression of Cytokine-like 1 (CYTL1) and Gap junction protein alpha 5 (GJA5) genes in the PT. Detailed analysis of these spatiotemporal expression patterns during chick embryo development by in situ hybridization has revealed that CYTL1 mRNA first appears in the lateral head ectoderm and ventral head ectoderm at E1.5. The expression of CYTL1 moves into Rathke's pouch at E2.5 and is then localized in the PT primordium where it is continuously expressed until E12.0. GJA5 mRNA is transiently detected in the PT primordium from E6.0 to E12.0, whereas its expression is not detected in the PD during development. Thus, these genes might be involved in the regulation mechanisms of PT development and could be useful markers for PT development.

  2. A Gene Expression-Based Comparison of Cell Adhesion to Extracellular Matrix and RGD-Terminated Monolayers

    Science.gov (United States)

    Sobers, Courtney J.; Wood, Sarah E.; Mrksich, Milan

    2015-01-01

    This work uses global gene expression analysis to compare the extent to which model substrates presenting peptide adhesion motifs mimic the use of conventional extracellular matrix protein coated substrates for cell culture. We compared the transcriptional activities of genes in cells that were cultured on matrix-coated substrates with those cultured on self-assembled monolayers presenting either a linear or cyclic RGD peptide. Cells adherent to cyclic RGD were most similar to those cultured on native ECM, while cells cultured on monolayers presenting the linear RGD peptide had transcriptional activities that were more similar to cells cultured on the uncoated substrates. This study suggests that biomaterials presenting the cyclic RGD peptide are substantially better mimics of extracellular matrix than are uncoated materials or materials presenting the common linear RGD peptide. PMID:25818445

  3. Knowledge Gaps

    DEFF Research Database (Denmark)

    Lyles, Marjorie; Pedersen, Torben; Petersen, Bent

    2003-01-01

    , assimilating, and utilizing knowledge - are crucial determinants ofknowledge gap elimination. In contrast, the two factors deemed essential in traditionalinternationalization process theory - elapsed time of operations and experientiallearning - are found to have no or limited effect.Key words......: Internationalization, knowledge gap, absorptive capacity, learning box....

  4. Gap Resolution

    Energy Technology Data Exchange (ETDEWEB)

    2017-04-25

    Gap Resolution is a software package that was developed to improve Newbler genome assemblies by automating the closure of sequence gaps caused by repetitive regions in the DNA. This is done by performing the follow steps:1) Identify and distribute the data for each gap in sub-projects. 2) Assemble the data associated with each sub-project using a secondary assembler, such as Newbler or PGA. 3) Determine if any gaps are closed after reassembly, and either design fakes (consensus of closed gap) for those that closed or lab experiments for those that require additional data. The software requires as input a genome assembly produce by the Newbler assembler provided by Roche and 454 data containing paired-end reads.

  5. Identification of two pentatricopeptide repeat genes required for RNA editing and zinc binding by C-terminal cytidine deaminase-like domains.

    Science.gov (United States)

    Hayes, Michael L; Giang, Karolyn; Berhane, Beniam; Mulligan, R Michael

    2013-12-20

    Many transcripts expressed from plant organelle genomes are modified by C-to-U RNA editing. Nuclear encoded pentatricopeptide repeat (PPR) proteins are required as RNA binding specificity determinants in the RNA editing mechanism. Bioinformatic analysis has shown that most of the Arabidopsis PPR proteins necessary for RNA editing events include a C-terminal portion that shares structural characteristics with a superfamily of deaminases. The DYW deaminase domain includes a highly conserved zinc binding motif that shares characteristics with cytidine deaminases. The Arabidopsis PPR genes, ELI1 and DOT4, both have DYW deaminase domains and are required for single RNA editing events in chloroplasts. The ELI1 DYW deaminase domain was expressed as a recombinant protein in Escherichia coli and was shown to bind two zinc atoms per polypeptide. Thus, the DYW deaminase domain binds a zinc metal ion, as expected for a cytidine deaminase, and is potentially the catalytic component of an editing complex. Genetic complementation experiments demonstrate that large portions of the DYW deaminase domain of ELI1 may be eliminated, but the truncated genes retain the ability to restore editing site conversion in a mutant plant. These results suggest that the catalytic activity can be supplied in trans by uncharacterized protein(s) of the editosome.

  6. Toward Bridging the Mechanistic Gap Between Genes and Traits by Emphasizing the Role of Proteins in a Computational Environment

    Science.gov (United States)

    Haskel-Ittah, Michal; Yarden, Anat

    2017-12-01

    Previous studies have shown that students often ignore molecular mechanisms when describing genetic phenomena. Specifically, students tend to directly link genes to their encoded traits, ignoring the role of proteins as mediators in this process. We tested the ability of 10th grade students to connect genes to traits through proteins, using concept maps and reasoning questions. The context of this study was a computational learning environment developed specifically to foster this ability. This environment presents proteins as the mechanism-mediating genetic phenomena. We found that students' ability to connect genes, proteins, and traits, or to reason using this connection, was initially poor. However, significant improvement was obtained when using the learning environment. Our results suggest that visual representations of proteins' functions in the context of a specific trait contributed to this improvement. One significant aspect of these results is the indication that 10th graders are capable of accurately describing genetic phenomena and their underlying mechanisms, a task that has been shown to raise difficulties, even in higher grades of high school.

  7. Toward Bridging the Mechanistic Gap Between Genes and Traits by Emphasizing the Role of Proteins in a Computational Environment

    Science.gov (United States)

    Haskel-Ittah, Michal; Yarden, Anat

    2017-10-01

    Previous studies have shown that students often ignore molecular mechanisms when describing genetic phenomena. Specifically, students tend to directly link genes to their encoded traits, ignoring the role of proteins as mediators in this process. We tested the ability of 10th grade students to connect genes to traits through proteins, using concept maps and reasoning questions. The context of this study was a computational learning environment developed specifically to foster this ability. This environment presents proteins as the mechanism-mediating genetic phenomena. We found that students' ability to connect genes, proteins, and traits, or to reason using this connection, was initially poor. However, significant improvement was obtained when using the learning environment. Our results suggest that visual representations of proteins' functions in the context of a specific trait contributed to this improvement. One significant aspect of these results is the indication that 10th graders are capable of accurately describing genetic phenomena and their underlying mechanisms, a task that has been shown to raise difficulties, even in higher grades of high school.

  8. Repression of TERMINAL FLOWER1 primarily mediates floral induction in pear (Pyrus pyrifolia Nakai) concomitant with change in gene expression of plant hormone-related genes and transcription factors.

    Science.gov (United States)

    Bai, Songling; Tuan, Pham Anh; Saito, Takanori; Ito, Akiko; Ubi, Benjamin Ewa; Ban, Yusuke; Moriguchi, Takaya; Wilson, Zoe

    2017-10-13

    Floral induction is an important event in the annual growth cycle of perennial fruit trees. For pear, this event directly affects fruit production in the following year. The flower buds in many species are induced by FLOWERING LOCUS T (FT), whose effect is repressed by the meristem-expressed gene TERMINAL FLOWER1 (TFL1). In this study, we investigated the functions of pear FT and TFL1 genes during floral development. Expression of pear FTs (PpFT1a and PpFT2a) in reproductive meristems was not obviously induced prior to floral initiation, while expression of TFL1s (PpTFL1-1a and PpTFL1-2a) rapidly decreased. The induction of the productive meristem identity MADS-box gene AP1 after repression of PpTFL1s suggested a primary role for PpTFL1 in floral induction. RNA-seq analysis suggested that plant hormone-related genes and several transcription factors that were coexpressed with PpTFL1 were potentially involved in the PpTFL1-mediated floral induction. Our data indicate the essential function of TFL1 in pear floral induction and add another species in the family Rosaceae in addition to strawberry and rose that shows a role for TFL1 in floral induction. © The Author 2017. Published by Oxford University Press on behalf of the Society for Experimental Biology.

  9. Characterization of Microbial Communities Found in the Human Vagina by Analysis of Terminal Restriction Fragment Length Polymorphisms of 16S rRNA Genes

    Science.gov (United States)

    Coolen, Marco J. L.; Post, Eduard; Davis, Catherine C.; Forney, Larry J.

    2005-01-01

    To define and monitor the structure of microbial communities found in the human vagina, a cultivation-independent approach based on analyses of terminal restriction fragment length polymorphisms (T-RFLP) of 16S rRNA genes was developed and validated. Sixteen bacterial strains commonly found in the human vagina were used to construct model communities that were subsequently used to develop efficient means for the isolation of genomic DNA and an optimal strategy for T-RFLP analyses. The various genera in the model community could best be resolved by digesting amplicons made using bacterial primers 8f and 926r with HaeIII; fewer strains could be resolved using other primer-enzyme combinations, and no combination successfully distinguished certain species of the same genus. To demonstrate the utility of the approach, samples from five women that had been collected over a 2-month period were analyzed. Differences and similarities among the vaginal microbial communities of the women were readily apparent. The T-RFLP data suggest that the communities of three women were dominated by a single phylotype, most likely species of Lactobacillus. In contrast, the communities of two other women included numerically abundant populations that differed from Lactobacillus strains whose 16S rRNA genes had been previously determined. The T-RFLP profiles of samples from all the women were largely invariant over time, indicating that the kinds and abundances of the numerically dominant populations were relatively stable throughout two menstrual cycles. These findings show that T-RFLP of 16S rRNA genes can be used to compare vaginal microbial communities and gain information about the numerically dominant populations that are present. PMID:16332868

  10. Identification of potential hot spots in the carboxy-terminal part of the Epstein-Barr virus (EBV) BNLF-1 gene in both malignant and benign EBV-associated diseases

    DEFF Research Database (Denmark)

    Sandvej, K; Peh, S C; Andresen, B S

    1994-01-01

    In this study, we have sequenced the C-terminal part of the Epstein-Barr virus (EBV)-BNLF-1 gene encoding for the latent membrane protein-1 from tissues of EBV-positive Danish Hodgkin's disease (HD) and of Danish and Malaysian peripheral T-cell lymphomas (PTLs) and from tonsils of Danish infectious...

  11. Mythic gaps

    Directory of Open Access Journals (Sweden)

    William Hansen

    2014-11-01

    Full Text Available Different kinds of omissions sometimes occur, or are perceived to occur, in traditional narratives and in tradition-inspired literature. A familiar instance is when a narrator realizes that he or she does not fully remember the story that he or she has begun to tell, and so leaves out part of it, which for listeners may possibly result in an unintelligible narrative. But many instances of narrative gap are not so obvious. From straightforward, objective gaps one can distinguish less-obvious subjective gaps: in many cases narrators do not leave out anything crucial or truly relevant from their exposition, and yet readers perceive gaps and take steps to fill them. The present paper considers four examples of subjective gaps drawn from ancient Greek literature (the Pandora myth, ancient Roman literature (the Pygmalion legend, ancient Hebrew literature (the Joseph legend, and early Christian literature (the Jesus legend. I consider the quite varied ways in which interpreters expand the inherited texts of these stories, such as by devising names, manufacturing motives, creating backstories, and in general filling in biographical ellipses. Finally, I suggest an explanation for the phenomenon of subjective gaps, arguing that, despite their variety, they have a single cause.

  12. GAP Analysis Program (GAP) Raster

    Data.gov (United States)

    Kansas Data Access and Support Center — The Kansas GAP Land Cover database depicts 43 land cover classes for the state of Kansas. The database was generated using a two-stage hybrid classification of...

  13. Terminal Ballistics

    CERN Document Server

    Rosenberg, Zvi

    2012-01-01

    This book covers the important issues of terminal ballistics in a comprehensive way combining experimental data, numerical simulations and analytical modeling. The first chapter reviews the experimental equipment which are used for ballistic tests and the diagnostics for material characterization under impulsive loading conditions. The second chapter covers essential features of the codes which are used for terminal ballistics such as the Euler vs. Lagrange schemes and meshing techniques, as well as the most popular material models. The third chapter, devoted to the penetration mechanics of rigid penetrators, brings the update of modeling in this field. The fourth chapter deals with plate perforation and the fifth chapter deals with the penetration mechanics of shaped charge jets and eroding long rods. The last two chapters discuss several techniques for the disruption and defeating of the main threats in armor design. Throughout the book the authors demonstrate the advantages of numerical simulations in unde...

  14. tBRD-1 selectively controls gene activity in the Drosophila testis and interacts with two new members of the bromodomain and extra-terminal (BET family.

    Directory of Open Access Journals (Sweden)

    Ina Theofel

    Full Text Available Multicellular organisms have evolved specialized mechanisms to control transcription in a spatial and temporal manner. Gene activation is tightly linked to histone acetylation on lysine residues that can be recognized by bromodomains. Previously, the testis-specifically expressed bromodomain protein tBRD-1 was identified in Drosophila. Expression of tBRD-1 is restricted to highly transcriptionally active primary spermatocytes. tBRD-1 is essential for male fertility and proposed to act as a co-factor of testis-specific TATA box binding protein-associated factors (tTAFs for testis-specific transcription. Here, we performed microarray analyses to compare the transcriptomes of tbrd-1 mutant testes and wild-type testes. Our data confirmed that tBRD-1 controls gene activity in male germ cells. Additionally, comparing the transcriptomes of tbrd-1 and tTAF mutant testes revealed a subset of common target genes. We also characterized two new members of the bromodomain and extra-terminal (BET family, tBRD-2 and tBRD-3. In contrast to other members of the BET family in animals, both possess only a single bromodomain, a characteristic feature of plant BET family members. Immunohistology techniques not only revealed that tBRD-2 and tBRD-3 partially co-localize with tBRD-1 and tTAFs in primary spermatocytes, but also that their proper subcellular distribution was impaired in tbrd-1 and tTAF mutant testes. Treating cultured male germ cells with inhibitors showed that localization of tBRD-2 and tBRD-3 depends on the acetylation status within primary spermatocytes. Yeast two-hybrid assays and co-immunoprecipitations using fly testes protein extracts demonstrated that tBRD-1 is able to form homodimers as well as heterodimers with tBRD-2, tBRD-3, and tTAFs. These data reveal for the first time the existence of single bromodomain BET proteins in animals, as well as evidence for a complex containing tBRDs and tTAFs that regulates transcription of a subset of genes

  15. [Inducing synthesis of LacA from Trametes sp. AH28-2 and cloning & analysis of 5'-terminal sequence of transcription control of the gene].

    Science.gov (United States)

    Hong, Yu-Zhi; Xiao, Ya-Zhong; Fang, Wei; Zhang, Shu-Xiang; Cha, Xiang-Dong; Li, Jian-Feng; Zhou, Hong-Min

    2005-07-01

    Copper ion was necessary for the transcription of all laccase isozyme genes from Trametes sp. AH28-2, with higher concentrations of Cu2+ (1-2 mmol/L) being more favorable to the synthesis of laccase. In the glucose media containing 0.5 mmol/L Cu2+, the laccase activity of the supernate was rather low (44.3 u/L) and had an increase of 60.3% (71.0 u/L) when 4.0 mmol/L o-toluidine was added. Moreover, the activity reached up to 2584 u/L as the glucose was replaced by cellobiose. And Native-PAGE showed that LacA was the main laccase component if fungus was induced by o-toluidine or copper ions. It had been demonstrated by quantitative RT-PCR that the regulation of lacA expression, induced by o-toluidine, occurred at the transcriptional level, with the accumulation of mRNA transcripts being accompanied by the increase of laccase activity of the culture fluid. In addition, the structural gene of lacA interrupted by 10 introns was 2110 bp in length and the corresponding cDNA sequence was 1560 bp encoding a 520 aa protein, which had high similarities with other laccases from basidiomycetes. Furthermore, a length of 1881 bp of 5'-terminal sequence of transcription control of lacA, amplified by the improved inverse PCR, contained a TATA box, seven CAAT boxes as well as a number of putative cis-acting elements important for its expression, including five MREs, nine CreA-binding sites, four XREs, two STREs and seven nitrogen factor binding sites. The existence of these elements was well in agreement with the data obtained from Trametes sp. AH28-2 shaken-flask cultures.

  16. Characterization of human cyclin-dependent kinase 12 (CDK12) and CDK13 complexes in C-terminal domain phosphorylation, gene transcription, and RNA processing.

    Science.gov (United States)

    Liang, Kaiwei; Gao, Xin; Gilmore, Joshua M; Florens, Laurence; Washburn, Michael P; Smith, Edwin; Shilatifard, Ali

    2015-03-01

    Cyclin-dependent kinase 9 (CDK9) and CDK12 have each been demonstrated to phosphorylate the RNA polymerase II C-terminal domain (CTD) at serine 2 of the heptad repeat, both in vitro and in vivo. CDK9, as part of P-TEFb and the super elongation complex (SEC), is by far the best characterized of CDK9, CDK12, and CDK13. We employed both in vitro and in vivo assays to further investigate the molecular properties of CDK12 and its paralog CDK13. We isolated Flag-tagged CDK12 and CDK13 and found that they associate with numerous RNA processing factors. Although knockdown of CDK12, CDK13, or their cyclin partner CCNK did not affect the bulk CTD phosphorylation levels in HCT116 cells, transcriptome sequencing (RNA-seq) analysis revealed that CDK12 and CDK13 losses in HCT116 cells preferentially affect expression of DNA damage response and snoRNA genes, respectively. CDK12 and CDK13 depletion also leads to a loss of expression of RNA processing factors and to defects in RNA processing. These findings suggest that in addition to implementing CTD phosphorylation, CDK12 and CDK13 may affect RNA processing through direct physical interactions with RNA processing factors and by regulating their expression. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  17. Role of peptidergic nerve terminals in the skin: reversal of thermal sensation by calcitonin gene-related peptide in TRPV1-depleted neuropathy.

    Directory of Open Access Journals (Sweden)

    Yu-Lin Hsieh

    Full Text Available To investigate the contribution of peptidergic intraepidermal nerve fibers (IENFs to nociceptive responses after depletion of the thermal-sensitive receptor, transient receptor potential vanilloid subtype 1 (TRPV1, we took advantage of a resiniferatoxin (RTX-induced neuropathy which specifically affected small-diameter dorsal root ganglion (DRG neurons and their corresponding nerve terminals in the skin. Thermal hypoalgesia (p<0.001 developed from RTX-treatment day 7 (RTXd7 and became normalized from RTXd56 to RTXd84. Substance P (SP(+ and TRPV1(+ neurons were completely depleted (p = 0.0001 and p<0.0001, respectively, but RTX had a relatively minor effect on calcitonin gene-related peptide (CGRP(+ neurons (p = 0.029. Accordingly, SP(+ (p<0.0001 and TRPV1(+ (p = 0.0008 IENFs were permanently depleted, but CGRP(+ IENFs (p = 0.012 were only transiently reduced and had recovered by RTXd84 (p = 0.83. The different effects of RTX on peptidergic neurons were attributed to the higher co-localization ratio of TRPV1/SP than of TRPV1/CGRP (p = 0.029. Thermal hypoalgesia (p = 0.0018 reappeared with an intraplantar injection of botulinum toxin type A (botox, and the temporal course of withdrawal latencies in the hot-plate test paralleled the innervation of CGRP(+ IENFs (p = 0.0003 and CGRP contents in skin (p = 0.01. In summary, this study demonstrated the preferential effects of RTX on depletion of SP(+ IENFs which caused thermal hypoalgesia. In contrast, the skin was reinnervated by CGRP(+ IENFs, which resulted in a normalization of nociceptive functions.

  18. Terminal ballistics

    CERN Document Server

    Rosenberg, Zvi

    2016-01-01

    This book comprehensively discusses essential aspects of terminal ballistics, combining experimental data, numerical simulations and analytical modeling. Employing a unique approach to numerical simulations as a measure of sensitivity for the major physical parameters, the new edition also includes the following features: new figures to better illustrate the problems discussed; improved explanations for the equation of state of a solid and for the cavity expansion process; new data concerning the Kolsky bar test; and a discussion of analytical modeling for the hole diameter in a thin metallic plate impacted by a shaped charge jet. The section on thick concrete targets penetrated by rigid projectiles has now been expanded to include the latest findings, and two new sections have been added: one on a novel approach to the perforation of thin concrete slabs, and one on testing the failure of thin metallic plates using a hydrodynamic ram.

  19. An N-terminal region of a Myb-like protein is involved in its intracellular localization and activation of a gibberellin-inducible proteinase gene in germinated rice seeds.

    Science.gov (United States)

    Sutoh, Keita; Washio, Kenji; Imai, Ryozo; Wada, Masamitsu; Nakai, Tomonori; Yamauchi, Daisuke

    2015-01-01

    The expression of the gene for a proteinase (Rep1) is upregulated by gibberellins. The CAACTC regulatory element (CARE) of the Rep1 promoter is involved in the gibberellin response. We isolated a cDNA for a CARE-binding protein containing a Myb domain in its carboxyl-terminal region and designated the gene Carboxyl-terminal Myb1 (CTMyb1). This gene encodes two polypeptides of two distinctive lengths, CTMyb1L and CTMyb1S, which include or exclude 213 N-terminal amino acid residues, respectively. CTMyb1S transactivated the Rep1 promoter in the presence of OsGAMyb, but not CTMyb1L. We observed an interaction between CTMyb1S and the rice prolamin box-binding factor (RPBF). A bimolecular fluorescence complex analysis detected the CTMyb1S and RPBF complex in the nucleus, but not the CTMyb1L and RPBF complex. The results suggest that the arrangement of the transfactors is involved in gibberellin-inducible expression of Rep1.

  20. The Ma Gene for Complete-Spectrum Resistance to Meloidogyne Species in Prunus Is a TNL with a Huge Repeated C-Terminal Post-LRR Region1[C][W

    Science.gov (United States)

    Claverie, Michel; Dirlewanger, Elisabeth; Bosselut, Nathalie; Van Ghelder, Cyril; Voisin, Roger; Kleinhentz, Marc; Lafargue, Bernard; Abad, Pierre; Rosso, Marie-Noëlle; Chalhoub, Boulos; Esmenjaud, Daniel

    2011-01-01

    Root-knot nematode (RKN) Meloidogyne species are major polyphagous pests of most crops worldwide, and cultivars with durable resistance are urgently needed because of nematicide bans. The Ma gene from the Myrobalan plum (Prunus cerasifera) confers complete-spectrum, heat-stable, and high-level resistance to RKN, which is remarkable in comparison with the Mi-1 gene from tomato (Solanum lycopersicum), the sole RKN resistance gene cloned. We report here the positional cloning and the functional validation of the Ma locus present at the heterozygous state in the P.2175 accession. High-resolution mapping totaling over 3,000 segregants reduced the Ma locus interval to a 32-kb cluster of three Toll/Interleukin1 Receptor-Nucleotide Binding Site-Leucine-Rich Repeat (LRR) genes (TNL1–TNL3), including a pseudogene (TNL2) and a truncated gene (TNL3). The sole complete gene in this interval (TNL1) was validated as Ma, as it conferred the same complete-spectrum and high-level resistance (as in P.2175) using its genomic sequence and native promoter region in Agrobacterium rhizogenes-transformed hairy roots and composite plants. The full-length cDNA (2,048 amino acids) of Ma is the longest of all Resistance genes cloned to date. Its TNL structure is completed by a huge post-LRR (PL) sequence (1,088 amino acids) comprising five repeated carboxyl-terminal PL exons with two conserved motifs. The amino-terminal region (213 amino acids) of the LRR exon is conserved between alleles and contrasts with the high interallelic polymorphisms of its distal region (111 amino acids) and of PL domains. The Ma gene highlights the importance of these uncharacterized PL domains, which may be involved in pathogen recognition through the decoy hypothesis or in nuclear signaling. PMID:21482634

  1. Plasmids with E2 epitope tags: tagging modules for N- and C-terminal PCR-based gene targeting in both budding and fission yeast, and inducible expression vectors for fission yeast.

    Science.gov (United States)

    Tamm, Tiina

    2009-01-01

    A single-step PCR-based epitope tagging enables fast and efficient gene targeting with various epitope tags. This report presents a series of plasmids for the E2 epitope tagging of proteins in Saccharomyces cerevisiae and Schizosaccharomyces pombe. E2Tags are 10-amino acids (epitope E2a: SSTSSDFRDR)- and 12 amino acids (epitope E2b: GVSSTSSDFRDR)-long peptides derived from the E2 protein of bovine papillomavirus type 1. The modules for C-terminal tagging with E2a and E2b epitopes were constructed by the modification of the pYM-series plasmid. The N-terminal E2a and E2b tagging modules were based on pOM-series plasmid. The pOM-series plasmids were selected for this study because of their use of the Cre-loxP recombination system. The latter enables a marker cassette to be removed after integration into the loci of interest and, thereafter, the tagged protein is expressed under its endogenous promoter. Specifically for fission yeast, high copy pREP plasmids containing the E2a epitope tag as an N-terminal or C-terminal tag were constructed. The properties of E2a and E2b epitopes and the sensitivity of two anti-E2 monoclonal antibodies (5E11 and 3F12) were tested using several S. cerevisiae and Sz. pombe E2-tagged strains.

  2. In vitro gene fusions that join an enzymatically active beta-galactosidase segment to amino-terminal fragments of exogenous proteins: Escherichia coli plasmid vectors for the detection and cloning of translational initiation signals.

    Science.gov (United States)

    Casadaban, M J; Chou, J; Cohen, S N

    1980-01-01

    We report the construction and use of a series of plasmid vectors suitable for the detection and cloning of translational control signals and 5' coding sequences of exogenously derived genes. In these plasmids, the first eight codons of the amino-terminal end of the lactose operon beta-galactosidase gene, lacZ, were removed, and unique BamHI, EcoRI, and SmaI (XmaI) endonuclease cleavage sites were incorporated adjacent to the eighth codon of lacZ. Introduction of deoxyribonucleic acid fragments containing appropriate regulatory signals and 5' coding sequences into such lac fusion plasmids led to the production of hybrid proteins consisting of the carboxyl-terminal segment of a beta-galactosidase remnant plus a peptide fragment that contained the amino-terminal amino acids encoded by the exogenous deoxyribonucleic acid sequence. These hybrid peptides retained beta-galactosidase enzymatic activity and yielded a Lac+ phenotype. Such hybrid proteins are useful for purifying peptide sequences encoded by exogenous deoxyribonucleic acid fragments and for studies relating the structure and function of specific peptide segments. Images PMID:6162838

  3. Contribution of intracellular calcium and pH in ischemic uncoupling of cardiac gap junction channels formed of connexins 43, 40, and 45: a critical function of C-terminal domain.

    Directory of Open Access Journals (Sweden)

    Giriraj Sahu

    Full Text Available Ischemia is known to inhibit gap junction (GJ mediated intercellular communication. However the detail mechanisms of this inhibition are largely unknown. In the present study, we determined the vulnerability of different cardiac GJ channels formed of connexins (Cxs 43, 40, and 45 to simulated ischemia, by creating oxygen glucose deprived (OGD condition. 5 minutes of OGD decreased the junctional conductance (Gj of Cx43, Cx40 and Cx45 by 53±3%, 64±1% and 85±2% respectively. Reduction of Gj was prevented completely by restricting the change of both intracellular calcium ([Ca(2+]i and pH (pHi with potassium phosphate buffer. Clamping of either [Ca(2+]i or pHi, through BAPTA (2 mM or HEPES (80 mM respectively, offered partial resistance to ischemic uncoupling. Anti-calmodulin antibody attenuated the uncoupling of Cx43 and Cx45 significantly but not of Cx40. Furthermore, OGD could reduce only 26±2% of Gj in C-terminus (CT truncated Cx43 (Cx43-Δ257. Tethering CT of Cx43 to the CT-truncated Cx40 (Cx40-Δ249, and Cx45 (Cx45-Δ272 helped to resist OGD mediated uncoupling. Moreover, CT domain played a significant role in determining the junction current density and plaque diameter. Our results suggest; OGD mediated uncoupling of GJ channels is primarily due to elevated [Ca(2+]i and acidic pHi, though the latter contributes more. Among Cx43, Cx40 and Cx45, Cx43 is the most resistant to OGD while Cx45 is the most sensitive one. CT of Cx43 has major necessary elements for OGD induced uncoupling and it can complement CT of Cx40 and Cx45.

  4. GAP Activity, but Not Subcellular Targeting, Is Required for Arabidopsis RanGAP Cellular and Developmental Functions.

    Science.gov (United States)

    Boruc, Joanna; Griffis, Anna H N; Rodrigo-Peiris, Thushani; Zhou, Xiao; Tilford, Bailey; Van Damme, Daniël; Meier, Iris

    2015-07-01

    The Ran GTPase activating protein (RanGAP) is important to Ran signaling involved in nucleocytoplasmic transport, spindle organization, and postmitotic nuclear assembly. Unlike vertebrate and yeast RanGAP, plant RanGAP has an N-terminal WPP domain, required for nuclear envelope association and several mitotic locations of Arabidopsis thaliana RanGAP1. A double null mutant of the two Arabidopsis RanGAP homologs is gametophyte lethal. Here, we created a series of mutants with various reductions in RanGAP levels by combining a RanGAP1 null allele with different RanGAP2 alleles. As RanGAP level decreases, the severity of developmental phenotypes increases, but nuclear import is unaffected. To dissect whether the GAP activity and/or the subcellular localization of RanGAP are responsible for the observed phenotypes, this series of rangap mutants were transformed with RanGAP1 variants carrying point mutations abolishing the GAP activity and/or the WPP-dependent subcellular localization. The data show that plant development is differentially affected by RanGAP mutant allele combinations of increasing severity and requires the GAP activity of RanGAP, while the subcellular positioning of RanGAP is dispensable. In addition, our results indicate that nucleocytoplasmic trafficking can tolerate both partial depletion of RanGAP and delocalization of RanGAP from the nuclear envelope. © 2015 American Society of Plant Biologists. All rights reserved.

  5. International Joint Venture Termination: An Empirical Investigation

    DEFF Research Database (Denmark)

    Nielsen, Ulrik B.; Rasmussen, Erik Stavnsager; Siersbæk, Nikolaj

    for the article stems from data from the project portfolio of a Danish Investment Fund for Developing Countries with a total of 773 investments. A number of hypotheses are established from the literature review and tested related to the empirical data. The result indicates that the most important factor...... the difference between intended termination and unintended termination has left a significant gap in the literature. The purpose of this article is to contribute to a better understanding of IJV exit literature by differentiating empirically between intended and unintended IJV termination. The empirical data...

  6. Graded junction termination extensions for electronic devices

    Science.gov (United States)

    Merrett, J. Neil (Inventor); Isaacs-Smith, Tamara (Inventor); Sheridan, David C. (Inventor); Williams, John R. (Inventor)

    2007-01-01

    A graded junction termination extension in a silicon carbide (SiC) semiconductor device and method of its fabrication using ion implementation techniques is provided for high power devices. The properties of silicon carbide (SiC) make this wide band gap semiconductor a promising material for high power devices. This potential is demonstrated in various devices such as p-n diodes, Schottky diodes, bipolar junction transistors, thyristors, etc. These devices require adequate and affordable termination techniques to reduce leakage current and increase breakdown voltage in order to maximize power handling capabilities. The graded junction termination extension disclosed is effective, self-aligned, and simplifies the implementation process.

  7. Different N-terminal isoforms of Oct-1 control expression of distinct sets of genes and their high levels in Namalwa Burkitt's lymphoma cells affect a wide range of cellular processes.

    Science.gov (United States)

    Pankratova, Elizaveta V; Stepchenko, Alexander G; Portseva, Tatiana; Mogila, Vladic A; Georgieva, Sofia G

    2016-11-02

    Oct-1 transcription factor has various functions in gene regulation. Its expression level is increased in several types of cancer and is associated with poor survival prognosis. Here we identified distinct Oct-1 protein isoforms in human cells and compared gene expression patterns and functions for Oct-1A, Oct-1L, and Oct-1X isoforms that differ by their N-terminal sequences. The longest isoform, Oct-1A, is abundantly expressed and is the main Oct-1 isoform in most of human tissues. The Oct-1L and the weakly expressed Oct-1X regulate the majority of Oct-1A targets as well as additional sets of genes. Oct-1X controls genes involved in DNA replication, DNA repair, RNA processing, and cellular response to stress. The high level of Oct-1 isoforms upregulates genes related to cell cycle progression and activates proliferation both in Namalwa Burkitt's lymphoma cells and primary human fibroblasts. It downregulates expression of genes related to antigen processing and presentation, cytokine-cytokine receptor interaction, oxidative metabolism, and cell adhesion, thus facilitating pro-oncogenic processes. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  8. Analysis of cytadherence-deficient, GapA-negative Mycoplasma gallisepticum strain R.

    Science.gov (United States)

    Papazisi, L; Troy, K E; Gorton, T S; Liao, X; Geary, S J

    2000-12-01

    Comparison of the phenotypic expression of Mycoplasma gallisepticum strain R low (passage 15) to that of strain R high (passage 164) revealed that three proteins, i.e., the cytadhesin molecule GapA, a 116-kDa protein (p116), and a 45-kDa protein (p45), are missing in strain R high. Sequence analysis confirmed that the insertion of an adenine 105 bp downstream of the gapA translational start codon resulted in premature termination of translation in R high. A second adenine insertion had also occurred at position 907. Restoration of expression of wild-type gapA in R high (clone designated GT5) allowed us to evaluate the extent to which the diminished cytadherence capacity could be attributed to GapA alone. The results indicated that GT5 attached to the same limited extent as the parental R high, from which it was derived. The cytadherence capability of the parental R high was not restored solely by gapA complementation alone, indicating that either p116 or p45 or both may play a role in the overall cytadherence process. The gene encoding p116 was found to be immediately downstream of gapA in the same operon and was designated crmA. This gene exhibited striking homology to genes encoding molecules with cytadhesin-related functions in both Mycoplasma pneumoniae and Mycoplasma genitalium. Transcriptional analysis revealed that crmA is not transcribed in R high. We are currently constructing a shuttle vector containing both the wild-type gapA and crmA for transformation into R high to assess the role of CrmA in the cytadherence process.

  9. The Gap Within the Gap

    Directory of Open Access Journals (Sweden)

    Katherine Michelmore

    2017-02-01

    Full Text Available Gaps in educational achievement between high- and low-income children are growing. Administrative data sets maintained by states and districts lack information about income but do indicate whether a student is eligible for subsidized school meals. We leverage the longitudinal structure of these data sets to develop a new measure of economic disadvantage. Half of eighth graders in Michigan are eligible for a subsidized meal, but just 14% have been eligible for subsidized meals in every grade since kindergarten. These children score 0.94 standard deviations below those who are never eligible for meal subsidies and 0.23 below those who are occasionally eligible. There is a negative, linear relationship between grades spent in economic disadvantage and eighth-grade test scores. This is not an exposure effect; the relationship is almost identical in third-grade, before children have been exposed to varying years of economic disadvantage. Survey data show that the number of years that a child will spend eligible for subsidized lunch is negatively correlated with her or his current household income. Years eligible for subsidized meals can therefore be used as a reasonable proxy for income. Our proposed measure can be used to estimate heterogeneous effects in program evaluations, to improve value-added calculations, and to better target resources.

  10. Analysis of the Arabidopsis superman allelic series and the interactions with other genes demonstrate developmental robustness and joint specification of male-female boundary, flower meristem termination and carpel compartmentalization.

    Science.gov (United States)

    Breuil-Broyer, Stéphanie; Trehin, Christophe; Morel, Patrice; Boltz, Véronique; Sun, Bo; Chambrier, Pierre; Ito, Toshiro; Negrutiu, Ioan

    2016-04-01

    SUPERMAN is a cadastral gene controlling the sexual boundary in the flower. The gene's functions and role in flower development and evolution have remained elusive. The analysis of a contrasting SUP allelic series (for which the names superman, superwoman and supersex have been coined) makes it possible to distinguish early vs. late regulatory processes at the flower meristem centre to which SUP is an important contributor. Their understanding is essential in further addressing evolutionary questions linking bisexuality and flower meristem homeostasis. Inter-allelic comparisons were carried out and SUP interactions with other boundary factors and flower meristem patterning and homeostasis regulators (such as CLV, WUS, PAN, CUC, KNU, AG, AP3/PI, CRC and SPT) have been evaluated at genetic, molecular, morphological and histological levels. Early SUP functions include mechanisms of male-female (sexual) boundary specification, flower mersitem termination and control of stamen number. A SUP-dependent flower meristem termination pathway is identified and analysed. Late SUP functions play a role in organ morphogenesis by controlling intra-whorl organ separation and carpel medial region formation. By integrating early and late SUP functions, and by analyzing in one single experiment a series of SUP genetic interactions, the concept of meristematic 'transference' (cascade) - a regulatory bridging process redundantly and sequentially co-ordinating the triggering and completion of flower meristem termination, and carpel margin meristem and placenta patterning - is proposed. Taken together, the results strongly support the view that SUP(-type) function(s) have been instrumental in resolving male/female gradients into sharp male and female identities (whorls, organs) and in enforcing flower homeostasis during evolution. This has probably been achieved by incorporating the meristem patterning system of the floral axis into the female/carpel programme. © The Author 2016

  11. NEMO is essential for Kaposi's sarcoma-associated herpesvirus-encoded vFLIP K13-induced gene expression and protection against death receptor-induced cell death, and its N-terminal 251 residues are sufficient for this process.

    Science.gov (United States)

    Tolani, Bhairavi; Matta, Hittu; Gopalakrishnan, Ramakrishnan; Punj, Vasu; Chaudhary, Preet M

    2014-06-01

    Kaposi's sarcoma-associated herpesvirus-encoded viral FLICE inhibitory protein (vFLIP) K13 was originally believed to protect virally infected cells against death receptor-induced apoptosis by interfering with caspase 8/FLICE activation. Subsequent studies revealed that K13 also activates the NF-κB pathway by binding to the NEMO/inhibitor of NF-κB (IκB) kinase gamma (IKKγ) subunit of an IKK complex and uses this pathway to modulate the expression of genes involved in cellular survival, proliferation, and the inflammatory response. However, it is not clear if K13 can also induce gene expression independently of NEMO/IKKγ. The minimum region of NEMO that is sufficient for supporting K13-induced NF-κB has not been delineated. Furthermore, the contribution of NEMO and NF-κB to the protective effect of K13 against death receptor-induced apoptosis remains to be determined. In this study, we used microarray analysis on K13-expressing wild-type and NEMO-deficient cells to demonstrate that NEMO is required for modulation of K13-induced genes. Reconstitution of NEMO-null cells revealed that the N-terminal 251 amino acid residues of NEMO are sufficient for supporting K13-induced NF-κB but fail to support tumor necrosis factor alpha (TNF-α)-induced NF-κB. K13 failed to protect NEMO-null cells against TNF-α-induced cell death but protected those reconstituted with the NEMO mutant truncated to include only the N-terminal 251 amino acid residues [the NEMO(1-251) mutant]. Taken collectively, our results demonstrate that NEMO is required for modulation of K13-induced genes and the N-terminal 251 amino acids of NEMO are sufficient for supporting K13-induced NF-κB. Finally, the ability of K13 to protect against TNF-α-induced cell death is critically dependent on its ability to interact with NEMO and activate NF-κB. Kaposi's sarcoma-associated herpesvirus-encoded vFLIP K13 is believed to protect virally infected cells against death receptor-induced apoptosis and to

  12. The functional importance of the extreme C-terminal tail in the gene 2 organellar Ca(2+)-transport ATPase (SERCA2a/b).

    OpenAIRE

    Verboomen, H; Wuytack, F; van den Bosch, L; Mertens, L.; Casteels, R

    1994-01-01

    Ca(2+)-uptake experiments in microsomal fractions from transfected COS-1 cells have revealed a functional difference between the non-muscle SERCA2b Ca2+ pump and its muscle-specific SERCA2a splice variant. Structurally, the two pumps differ only in their C-terminal tail. The last four amino acids of SERCA2a are replaced in SERCA2b by a 49-residue-long peptide chain containing a very hydrophobic stretch which could be an additional transmembrane segment. The functionally important subdomains i...

  13. Co-ordinated gene expression of photosynthetic glyceraldehyde-3-phosphate dehydrogenase, phosphoribulokinase, and CP12 in Arabidopsis thaliana.

    Science.gov (United States)

    Marri, Lucia; Sparla, Francesca; Pupillo, Paolo; Trost, Paolo

    2005-01-01

    Photosynthetic glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and phosphoribulokinase (PRK) interact in the chloroplast stroma through the action of the small peptide CP12. This supramolecular complex concurs with the light-dependent modulation in vivo of GAPDH and PRK activities. The expression patterns of several genes potentially involved in the formation of the complex have been studied. The genome of Arabidopsis thaliana includes seven genes for phosphorylating GAPDH isozymes, one PRK gene, and three genes for CP12. The expression of four GAPDH genes was analysed, i.e. GapA-1 and GapB for photosynthetic GAPDH of chloroplasts (NAD(P)-dependent), GapC-1 for cytosolic GAPDH, and GapCp-1 for plastid GAPDH (both NAD-dependent). A similar analysis was performed with PRK and two CP12 genes (CP12-1, CP12-2). The expression of GapA-1, GapB, PRK, and CP12-2 was found to be co-ordinately regulated with the same organ specificity, all four genes being mostly expressed in leaves and flower stalks, less expressed in flowers, and little or not expressed in roots and siliques. The expression of all these genes in leaves was terminated during prolonged darkness or following sucrose treatments, and their transcripts decayed with similar kinetics. At variance with CP12-2, gene CP12-1 appeared to be expressed more in flowers, it was totally insensitive to darkness, and less affected by sucrose. The expression of glycolytic GapC was strong and ubiquitous, insensitive to dark treatments, and unaffected by sucrose. GapCp transcripts were also found to be ubiquitous at lower levels, slowly decreasing in the dark and stable in sucrose-treated leaves. The co-ordinated expression of genes GapA-1, GapB, PRK, and CP12-2 is consistent with their specific involvement in the formation of the photosynthetic regulatory complex of chloroplasts.

  14. Intermodal freight terminals : terminal business planning

    NARCIS (Netherlands)

    Nijkamp, Peter; Wiegmans, Bart W.

    2000-01-01

    The main purpose of this paper is to provide a framework for existing- and newly proposedinter-modal freight terminals in their business planning process. This framework is importantfor constructing- and improving the central terminal service portfolio of handling (loading,discharging, and

  15. Covalent association of the traI gene product of plasmid RP4 with the 5'-terminal nucleotide at the relaxation nick site.

    Science.gov (United States)

    Pansegrau, W; Ziegelin, G; Lanka, E

    1990-06-25

    Formation of relaxosomes is the first step in the initiation of transfer DNA replication during bacterial conjugation. This nucleoprotein complex contains all components capable of introducing a site- and strand-specific nick at a cognate transfer origin (oriT) on supercoiled plasmid DNA, thus providing the substrate for generation of the strand to be transferred. Characterization of the terminal nucleotides at the oriT nick site revealed that relaxation occurs by hydrolysis of a single phosphodiester bond between a 2'-deoxyguanosyl and a 2'-deoxycytidyl residue. The relaxation nick site and a 19-base pair invert repeat sequence that is recognized by asymmetric binding of the RP4 TraJ protein are interspaced by 8 base pairs. The nicking reaction results in covalent attachment of the RP4 TraI protein to the 5'-terminal 2'-deoxycytidyl residue of the cleaved strand. The arrangement of the TraJ binding site and the relaxation nick site on the same side of the DNA double helix suggests that protein-protein interactions between TraJ and TraI are a prerequisite for oriT specific nicking. In accordance with the current model of transfer DNA replication, the 3' end remains accessible for primer extension by DNA polymerase I, enabling replacement strand synthesis in the donor cell by a rolling circle-type mechanism.

  16. Heterogeneous nuclear ribonucleoprotein (HnRNP) K genome-wide binding survey reveals its role in regulating 3'-end RNA processing and transcription termination at the early growth response 1 (EGR1) gene through XRN2 exonuclease.

    Science.gov (United States)

    Mikula, Michal; Bomsztyk, Karol; Goryca, Krzysztof; Chojnowski, Krzysztof; Ostrowski, Jerzy

    2013-08-23

    The heterogeneous nuclear ribonucleoprotein K (hnRNPK) is a nucleic acid-binding protein that acts as a docking platform integrating signal transduction pathways to nucleic acid-related processes. Given that hnRNPK could be involved in other steps that compose gene expression the definition of its genome-wide occupancy is important to better understand its role in transcription and co-transcriptional processes. Here, we used chromatin immunoprecipitation followed by deep sequencing (ChIP-Seq) to analyze the genome-wide hnRNPK-DNA interaction in colon cancer cell line HCT116. 9.1/3.6 and 7.0/3.4 million tags were sequenced/mapped, then 1809 and 642 hnRNPK binding sites were detected in quiescent and 30-min serum-stimulated cells, respectively. The inspection of sequencing tracks revealed inducible hnRNPK recruitment along a number of immediate early gene loci, including EGR1 and ZFP36, with the highest densities present at the transcription termination sites. Strikingly, hnRNPK knockdown with siRNA resulted in increased pre-RNA levels transcribed downstream of the EGR1 polyadenylation (A) site suggesting altered 3'-end pre-RNA degradation. Further ChIP survey of hnRNPK knockdown uncovered decreased recruitment of the 5'-3' exonuclease XRN2 along EGR1 and downstream of the poly(A) signal without altering RNA polymerase II density at these sites. Immunoprecipitation of hnRNPK and XRN2 from intact and RNase A-treated nuclear extracts followed by shotgun mass spectrometry revealed the presence of hnRNPK and XRN2 in the same complexes along with other spliceosome-related proteins. Our data suggest that hnRNPK may play a role in recruitment of XRN2 to gene loci thus regulating coupling 3'-end pre-mRNA processing to transcription termination.

  17. CRISPR/Cas9-mediated endogenous C-terminal Tagging of Trypanosoma cruzi Genes Reveals the Acidocalcisome Localization of the Inositol 1,4,5-Trisphosphate Receptor.

    Science.gov (United States)

    Lander, Noelia; Chiurillo, Miguel A; Storey, Melissa; Vercesi, Anibal E; Docampo, Roberto

    2016-12-02

    Methods for genetic manipulation of Trypanosoma cruzi, the etiologic agent of Chagas disease, have been highly inefficient, and no endogenous tagging of genes has been reported to date. We report here the use of the CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 (CRISPR-associated gene 9) system for endogenously tagging genes in this parasite. The utility of the method was established by tagging genes encoding proteins of known localization such as TcFCaBP (flagellar calcium binding protein) and TcVP1 (vacuolar proton pyrophosphatase), and two proteins of undefined or disputed localization, the TcMCU (mitochondrial calcium uniporter) and TcIP 3 R (inositol 1,4,5-trisphosphate receptor). We confirmed the flagellar and acidocalcisome localization of TcFCaBP and TcVP1 by co-localization with antibodies to the flagellum and acidocalcisomes, respectively. As expected, TcMCU was co-localized with the voltage-dependent anion channel to the mitochondria. However, in contrast to previous reports and our own results using overexpressed TcIP 3 R, endogenously tagged TcIP 3 R showed co-localization with antibodies against VP1 to acidocalcisomes. These results are also in agreement with our previous reports on the localization of this channel to acidocalcisomes of Trypanosoma brucei and suggest that caution should be exercised when overexpression of tagged genes is done to localize proteins in T. cruzi. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  18. pawg Terminal Aerodrome Forecast

    Data.gov (United States)

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  19. Terminated Multifamily Mortgages Database

    Data.gov (United States)

    Department of Housing and Urban Development — Includes all terminated HUD Multifamily insured mortgages. It includes the Holder and Servicer at the time the mortgage was terminated. The data is good as of...

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  6. kjan Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  7. kbce Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  8. ktys Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  9. kcha Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  10. kdug Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  11. Terminated Multifamily Mortgages Database

    Data.gov (United States)

    Department of Housing and Urban Development — This Excel 2010 file includes all terminated HUD Multifamily insured mortgages. It includes the Holder and Servicer at the time the mortgage was terminated. The data...

  12. kpub Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  13. ksrq Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  14. kaeg Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  15. pata Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  16. klgu Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  17. pamc Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  18. kmsl Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  19. kbrl Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  20. ksfb Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  1. kpsc Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  2. kely Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  3. ksyr Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  4. katw Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  5. kama Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  6. kpae Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  7. kmli Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  8. kokc Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  9. kjst Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  10. kgup Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  11. padl Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  12. klit Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  13. kalb Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  14. kact Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  15. kink Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  16. kshv Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  17. pajn Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  18. kpna Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  19. ktph Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  20. ksux Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  1. kcon Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  2. khio Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  3. konp Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  4. kpnc Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  5. kmlu Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  6. kgsp Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  7. kgpt Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  8. kflo Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  9. keri Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  10. kcid Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  11. ksaf Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  12. kcvg Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  13. ptya Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  14. katl Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  15. kmth Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  16. Fail-safe transcription termination: Because one is never enough.

    Science.gov (United States)

    Lemay, Jean-François; Bachand, François

    2015-01-01

    Termination of RNA polymerase II (RNAPII) transcription is a fundamental step of gene expression that involves the release of the nascent transcript and dissociation of RNAPII from the DNA template. As transcription termination is intimately linked to RNA 3' end processing, termination pathways have a key decisive influence on the fate of the transcribed RNA. Quite remarkably, when reaching the 3' end of genes, a substantial fraction of RNAPII fail to terminate transcription, requiring the contribution of alternative or "fail-safe" mechanisms of termination to release the polymerase. This point of view covers redundant mechanisms of transcription termination and how they relate to conventional termination models. In particular, we expand on recent findings that propose a reverse torpedo model of termination, in which the 3'5' exonucleolytic activity of the RNA exosome targets transcription events associated with paused and backtracked RNAPII.

  17. 75 FR 15390 - Gap in Termination Provisions; Inquiry

    Science.gov (United States)

    2010-03-29

    ... . SUPPLEMENTARY INFORMATION: Background The Copyright Act gives authors (and some heirs, beneficiaries and... composer signed an agreement with a music publisher in 1977 transferring the copyrights to future musical...

  18. The terminal oxidases of Paracoccus denitrificans

    NARCIS (Netherlands)

    de Gier, J.-W.; Lübben, M; Reijnders, W N; Tipker, C A; Slotboom, D.J.; van Spanning, R J; Stouthamer, A.H.; van der Oost, J.

    Three distinct types of terminal oxidases participate in the aerobic respiratory pathways of Paracoccus denitrificans. Two alternative genes encoding subunit I of the aa3-type cytochrome c oxidase have been isolated before, namely ctaDI and ctaDII. Each of these genes can be expressed separately to

  19. The terminal oxidases of Paracoccus denitrificans

    NARCIS (Netherlands)

    Gier, Jan-Willem L. de; Lübben, Mathias; Reijnders, Willem N.M.; Tipker, Corinne A.; Slotboom, Dirk-Jan; Spanning, Rob J.M. van; Stouthamer, Adriaan H.; Oost, John van der

    1994-01-01

    Three distinct types of terminal oxidases participate in the aerobic respiratory pathways of Paracoccus denitrificans. Two alternative genes encoding subunit I of the aa3-type cytochrome c oxidase have been isolated before, namely ctaDI and ctaDII. Each of these genes can be expressed separately to

  20. Analysis of the Arabidopsis superman allelic series and the interactions with other genes demonstrate developmental robustness and joint specification of male–female boundary, flower meristem termination and carpel compartmentalization

    Science.gov (United States)

    Breuil-Broyer, Stéphanie; Trehin, Christophe; Morel, Patrice; Boltz, Véronique; Sun, Bo; Chambrier, Pierre; Ito, Toshiro; Negrutiu, Ioan

    2016-01-01

    Background and Aims SUPERMAN is a cadastral gene controlling the sexual boundary in the flower. The gene’s functions and role in flower development and evolution have remained elusive. The analysis of a contrasting SUP allelic series (for which the names superman, superwoman and supersex have been coined) makes it possible to distinguish early vs. late regulatory processes at the flower meristem centre to which SUP is an important contributor. Their understanding is essential in further addressing evolutionary questions linking bisexuality and flower meristem homeostasis. Methods Inter-allelic comparisons were carried out and SUP interactions with other boundary factors and flower meristem patterning and homeostasis regulators (such as CLV, WUS, PAN, CUC, KNU, AG, AP3/PI, CRC and SPT) have been evaluated at genetic, molecular, morphological and histological levels. Key Results Early SUP functions include mechanisms of male–female (sexual) boundary specification, flower mersitem termination and control of stamen number. A SUP-dependent flower meristem termination pathway is identified and analysed. Late SUP functions play a role in organ morphogenesis by controlling intra-whorl organ separation and carpel medial region formation. By integrating early and late SUP functions, and by analyzing in one single experiment a series of SUP genetic interactions, the concept of meristematic ‘transference’ (cascade) – a regulatory bridging process redundantly and sequentially co-ordinating the triggering and completion of flower meristem termination, and carpel margin meristem and placenta patterning – is proposed. Conclusions Taken together, the results strongly support the view that SUP(-type) function(s) have been instrumental in resolving male/female gradients into sharp male and female identities (whorls, organs) and in enforcing flower homeostasis during evolution. This has probably been achieved by incorporating the meristem patterning system of the floral

  1. A novel mutation of the C-terminal amino acid of FUS (Y526C) strengthens FUS gene as the most frequent genetic factor in aggressive juvenile ALS.

    Science.gov (United States)

    Corcia, Philippe; Danel, Veronique; Lacour, Arnaud; Beltran, Stephane; Andres, Christian; Couratier, Philippe; Blasco, Helene; Vourc'h, Patrick

    2017-05-01

    Although amyotrophic lateral sclerosis (ALS) typically occurs around 60 years, numerous publications report an onset of ALS before the age of 25 years that define juvenile ALS (jALS). Over the last decade, growing literature mentioned jALS with an aggressive evolution which are mainly linked to the FUS gene. We report here the case of a 25-year-old woman with a bulbar onset ALS that progressed in less than 12 months to invasive ventilation due to respiratory failure; Genetic screening identified a new mutation in the FUS gene that lies within the last codon. After reading the literature, it might be legitimate to consider that jALS linked to FUS mutations represent a specific entity different from both classical jALS and adult ALS linked to FUS gene. This should encourage clinician to firstly screen the FUS gene in the presence of a sporadic ALS that occurs before the age of 25 and with an aggressive profile of evolution.

  2. Intermodal freight terminals : terminal business planning

    OpenAIRE

    Nijkamp, Peter; Bart W Wiegmans

    2000-01-01

    The main purpose of this paper is to provide a framework for existing- and newly proposedinter-modal freight terminals in their business planning process. This framework is importantfor constructing- and improving the central terminal service portfolio of handling (loading,discharging, and transhipping) and storage of containerised cargo. Supportive activities (e.g. administration, customs) are taken into account as well.In particular, its aim is to investigate whether business planning offer...

  3. 29 CFR 4043.24 - Termination or partial termination.

    Science.gov (United States)

    2010-07-01

    ... 29 Labor 9 2010-07-01 2010-07-01 false Termination or partial termination. 4043.24 Section 4043.24....24 Termination or partial termination. (a) Reportable event. A reportable event occurs when the Secretary of the Treasury determines that there has been a termination or partial termination of a plan...

  4. Filling the Gaps in the Kirromycin Biosynthesis: Deciphering the Role of Genes Involved in Ethylmalonyl-CoA Supply and Tailoring Reactions

    DEFF Research Database (Denmark)

    Robertsen, Helene L.; Musiol-Kroll, Ewa M.; Ding, Ling

    2018-01-01

    /NRPS). This was the first example of an assembly line integrating the three biosynthetic principles in one pathway. However, information about other enzymes involved in kirromycin biosynthesis remained scarce. In this study, genes encoding tailoring enzymes KirM, KirHVI, KirOI, and KirOII, and the putative crotonyl...

  5. Three Medicago MtFUL genes have distinct and overlapping expression patterns during vegetative and reproductive development and 35S:MtFULb accelerates flowering and causes a terminal flower phenotype in Arabidopsis

    Science.gov (United States)

    Jaudal, Mauren; Zhang, Lulu; Che, Chong; Putterill, Joanna

    2015-01-01

    The timing of the transition to flowering is carefully controlled by plants in order to optimize sexual reproduction and the ensuing production of seeds, grains, and fruits. The genetic networks that regulate floral induction are best characterized in the temperate eudicot Arabidopsis in which the florigen gene FT plays a major role in promoting the transition to flowering. Legumes are an important plant group, but less is known about the regulation of their flowering time. In the model legume Medicago truncatula (Medicago), a temperate annual plant like Arabidopsis, flowering is induced by prolonged cold (vernalization) followed by long day lengths (LD). Recent molecular-genetic experiments have revealed that a FT-like gene, MtFTa1, is a central regulator of flowering time in Medicago. Here, we characterize the three Medicago FRUITFULL (FUL) MADS transcription factors, MtFULa, MtFULb, and MtFULc using phylogenetic analyses, gene expression profiling through developmental time courses, and functional analyses in transgenic plants. MtFULa and MtFULb have similarity in sequence and expression profiles under inductive environmental conditions during both vegetative and reproductive development while MtFULc is only up regulated in the apex after flowering in LD conditions. Sustained up regulation of MtFULs requires functional MtFTa1 but their transcript levels are not affected during cold treatment. Overexpression of MtFULa and MtFULb promotes flowering in transgenic Arabidopsis plants with an additional terminal flower phenotype on some 35S:MtFULb plants. An increase in transcript levels of the MtFULs was also observed in Medicago plants overexpressing MtFTa1. Our results suggest that the MtFULs are targets of MtFTa1. Overall, this work highlights the conserved functions of FUL-like genes in promoting flowering and other roles in plant development and thus contributes to our understanding of the genetic control of the flowering process in Medicago. PMID:25745430

  6. Variable expression of cerebral cavernous malformations in carriers of a premature termination codon in exon 17 of the Krit1 gene

    Directory of Open Access Journals (Sweden)

    Gamero Miguel A

    2003-07-01

    Full Text Available Abstract Background Cerebral cavernous malformations (CCM present as either sporadic or autosomal dominant conditions with incomplete penetrance of symptoms. Differences in genetic and environmental factors might be minimized among first-degree relatives. We therefore studied clinical expression in a family with several affected members. Methods We studied a three-generation family with the onset of CCM as a cerebral haemorrhage in the younger (four-year-old sibling. Identification and enumeration of CCMs were performed in T2-weighted or gradient-echo MRIs of the whole brains. Genetic analysis comprised SCCP, sequencing and restriction polymorphism of the Krit1 gene in the proband and at risk relatives. Results The phenotypes of cerebral cavernous malformations (CCMs in carriers of Krit1 mutations were very variable. We identified a novel frameshift mutation caused by a 1902A insertion in exon 17 of the Krit1 gene, which leads to a premature TAA triplet and predicts the truncating phenotype Y634X. A very striking finding was the absence of both clinical symptoms and CCMs in the eldest sibling harbouring the 1902insA. Conclusions Patients in this family, harbouring the same mutation, illustrate the very variable clinical and radiological expression of a Krit1 mutation. The early and critical onset in the proband contrasts with minor clinical findings in affected relatives. This consideration is important in genetic counselling.

  7. Regulation of Cx43 gap junctions: the gatekeeper and the password.

    Science.gov (United States)

    Hossain, M Z; Boynton, A L

    2000-10-17

    Gap junctions are regulatable pores that connect the cytoplasms of neighboring cells. Hossain and Boynton focus on connexin 43 gap junctions and their regulation by changing the phosphorylation status of the COOH-terminal domain of connexin 43 or by altering protein-protein interactions in this region. The COOH-terminal domain of connexin 43 appears to be a key player in regulating gap junctional communication (GJC) because many divergent signals in many different cell types modify this domain to inhibit GJC.

  8. CONTAINER TERMINALS IN EUROPE

    Directory of Open Access Journals (Sweden)

    Bart W. WIEGMANS

    2001-01-01

    Full Text Available This paper aims to address the linkage between logistics (in particular, the management of marketing channel flows and transport markets, while also the interaction between these two markets and intermodal container terminals is analysed. The marketing channel theory is used to describe all relevant actors and flows that run through marketing channels, starting with customer needs and ending with customer satisfaction. Porter's theory of competitive advantages is used to review competitive forces in both markets. Finally, a competitor analysis is performed for the logistics and transport market. These theories are applied so as to be able to determine the competitive position of intermodal container terminals with a view to the management of marketing channel flows and the physical transport of freight flows. Hence, the central question of this paper is: Which markets are served by intermodal container terminals and with whom are they competing? At present, neither the maritime container terminals nor the continental container terminals appear to have a significant influence in the logistics service market; they concentrate mainly on the physical movement of containers (transshipment. Furthermore, maritime container terminals and continental container terminals are not dominant players in the transport service market. Our conclusion is that continental terminals are predominantly competing with unimodal road transport, with neighbouring continental terminals and with barge transport companies.

  9. Organizational Relationship Termination Competence

    DEFF Research Database (Denmark)

    Ritter, Thomas; Geersbro, Jens

    2011-01-01

    that a firm's percentage of unwanted customers decreases significantly as acceptance of termination increases, if the firm's definition of unwanted customers is well understood, and if a firm has clear termination routines. In addition, general focus on profitability and external constraints on relationship...

  10. Applying a 4D multiscale in vivo tumor growth model to the exploration of radiotherapy scheduling: The effects of weekend treatment gaps and p53 gene status on the response of fast growing solid tumors

    Directory of Open Access Journals (Sweden)

    Dimitra D. Dionysiou

    2006-01-01

    Full Text Available The present paper aims at demonstrating clinically oriented applications of the multiscale four dimensional in vivo tumor growth simulation model previously developed by our research group. To this end the effect of weekend radiotherapy treatment gaps and p53 gene status on two virtual glioblastoma tumors differing only in p53 gene status is investigated in silico. Tumor response predictions concerning two rather extreme dose fractionation schedules (daily dose of 4.5 Gy administered in 3 equal fractions namely HART (Hyperfractionated Accelerated Radiotherapy weekend less 54 Gy and CHART (Continuous HART 54 Gy are presented and compared. The model predictions suggest that, for the same p53 status, HART 54 Gy and CHART 54 Gy have almost the same long term effects on locoregional tumor control. However, no data have been located in the literature concerning a comparison of HART and CHART radiotherapy schedules for glioblastoma. As non small cell lung carcinoma (NSCLC may also be a fast growing and radiosensitive tumor, a comparison of the model predictions with the outcome of clinical studies concerning the response of NSCLC to HART 54 Gy and CHART 54 Gy is made. The model predictions are in accordance with corresponding clinical observations, thus strengthening the potential of the model.

  11. Comsat's TDMA traffic terminal

    Science.gov (United States)

    Benjamin, M. C.; Bogaert, W. M.

    1985-06-01

    Comsat has installed two traffic terminals in the Etam earth-station and is currently installing a third in the new Roaring Creek earth-station to access the Intelsat TDMA network. This paper describes the Comsat TDMA traffic terminal equipment from the supergroup interface to the antenna. Comsat's 1: N redundancy approach for terrestrial interface equipment and DSI unit back-up is described as well as electrical path length, amplitude and group delay equalization techniques, special on-line RF monitoring and failure reporting facilities and the operation and maintenance center which can operate and perform diagnostic testing on up to four traffic terminals from a central location.

  12. C-terminal region of EBNA-2 determines the superior transforming ability of type 1 Epstein-Barr virus by enhanced gene regulation of LMP-1 and CXCR7.

    Directory of Open Access Journals (Sweden)

    Laila Cancian

    2011-07-01

    Full Text Available Type 1 Epstein-Barr virus (EBV strains immortalize B lymphocytes in vitro much more efficiently than type 2 EBV, a difference previously mapped to the EBNA-2 locus. Here we demonstrate that the greater transforming activity of type 1 EBV correlates with a stronger and more rapid induction of the viral oncogene LMP-1 and the cell gene CXCR7 (which are both required for proliferation of EBV-LCLs during infection of primary B cells with recombinant viruses. Surprisingly, although the major sequence differences between type 1 and type 2 EBNA-2 lie in N-terminal parts of the protein, the superior ability of type 1 EBNA-2 to induce proliferation of EBV-infected lymphoblasts is mostly determined by the C-terminus of EBNA-2. Substitution of the C-terminus of type 1 EBNA-2 into the type 2 protein is sufficient to confer a type 1 growth phenotype and type 1 expression levels of LMP-1 and CXCR7 in an EREB2.5 cell growth assay. Within this region, the RG, CR7 and TAD domains are the minimum type 1 sequences required. Sequencing the C-terminus of EBNA-2 from additional EBV isolates showed high sequence identity within type 1 isolates or within type 2 isolates, indicating that the functional differences mapped are typical of EBV type sequences. The results indicate that the C-terminus of EBNA-2 accounts for the greater ability of type 1 EBV to promote B cell proliferation, through mechanisms that include higher induction of genes (LMP-1 and CXCR7 required for proliferation and survival of EBV-LCLs.

  13. C-terminal region of EBNA-2 determines the superior transforming ability of type 1 Epstein-Barr virus by enhanced gene regulation of LMP-1 and CXCR7.

    Science.gov (United States)

    Cancian, Laila; Bosshard, Rachel; Lucchesi, Walter; Karstegl, Claudio Elgueta; Farrell, Paul J

    2011-07-01

    Type 1 Epstein-Barr virus (EBV) strains immortalize B lymphocytes in vitro much more efficiently than type 2 EBV, a difference previously mapped to the EBNA-2 locus. Here we demonstrate that the greater transforming activity of type 1 EBV correlates with a stronger and more rapid induction of the viral oncogene LMP-1 and the cell gene CXCR7 (which are both required for proliferation of EBV-LCLs) during infection of primary B cells with recombinant viruses. Surprisingly, although the major sequence differences between type 1 and type 2 EBNA-2 lie in N-terminal parts of the protein, the superior ability of type 1 EBNA-2 to induce proliferation of EBV-infected lymphoblasts is mostly determined by the C-terminus of EBNA-2. Substitution of the C-terminus of type 1 EBNA-2 into the type 2 protein is sufficient to confer a type 1 growth phenotype and type 1 expression levels of LMP-1 and CXCR7 in an EREB2.5 cell growth assay. Within this region, the RG, CR7 and TAD domains are the minimum type 1 sequences required. Sequencing the C-terminus of EBNA-2 from additional EBV isolates showed high sequence identity within type 1 isolates or within type 2 isolates, indicating that the functional differences mapped are typical of EBV type sequences. The results indicate that the C-terminus of EBNA-2 accounts for the greater ability of type 1 EBV to promote B cell proliferation, through mechanisms that include higher induction of genes (LMP-1 and CXCR7) required for proliferation and survival of EBV-LCLs.

  14. Docosahexaenoic acid downregulates phenobarbital-induced cytochrome P450 2B1 gene expression in rat primary hepatocytes via the c-Jun NH2-terminal kinase mitogen-activated protein kinase pathway.

    Science.gov (United States)

    Lu, Chia-Yang; Li, Chien-Chun; Liu, Kai-Li; Lii, Chong-Kuei; Chen, Haw-Wen

    2009-03-01

    Mitogen-activated protein kinase (MAPK) pathways play central roles in the transduction of extracellular stimuli into cells and the regulation of expression of numerous genes. Docosahexaenoic acid (DHA) was shown to be involved in the regulation of expression of drug metabolizing enzymes (DMEs) in rat primary hepatocytes in response to xenobiotics. Cytochrome P450 2B1 (CYP 2B1) is a DME that is dramatically induced by phenobarbital-type inducers. The constitutive androstane receptor (CAR) plays a critical role in regulating the expression of DMEs, and the phosphorylation/dephosphorylation of CAR is an important event in CYP 2B1 expression. In the present study, we determined the effect of DHA on MAPK transactivation and its role in CYP 2B1 expression induced by phenobarbital. c-Jun NH2-terminal kinase (JNK) JNK1/2 and ERK1/2 were activated by phenobarbital in a dose-dependent manner. DHA (100 muM) inhibited JNK1/2 and ERK2 activation induced by phenobarbital in a time-dependent manner. Both SP600125 (a JNK inhibitor) and SB203580 (a p38 MAPK inhibitor) inhibited CYP 2B1 protein and mRNA expression induced by phenobarbital. SB203580 significantly increased the intracellular 3'-5'-cyclic adenosine monophosphate (cAMP) concentration compared with a control group (p expression induced by phenobarbital.

  15. Gene

    Data.gov (United States)

    U.S. Department of Health & Human Services — Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes,...

  16. Terminated Multifamily Mortgages Database

    Data.gov (United States)

    Department of Housing and Urban Development — This dataset includes all terminated HUD Multifamily mortgages except those from the Hospital Mortgage Insurance Program. It includes the Holder and Servicer at the...

  17. Gap and density theorems

    CERN Document Server

    Levinson, N

    1940-01-01

    A typical gap theorem of the type discussed in the book deals with a set of exponential functions { \\{e^{{{i\\lambda}_n} x}\\} } on an interval of the real line and explores the conditions under which this set generates the entire L_2 space on this interval. A typical gap theorem deals with functions f on the real line such that many Fourier coefficients of f vanish. The main goal of this book is to investigate relations between density and gap theorems and to study various cases where these theorems hold. The author also shows that density- and gap-type theorems are related to various propertie

  18. Bridging the Gap

    DEFF Research Database (Denmark)

    Kramer Overgaard, Majken; Broeng, Jes; Jensen, Monika Luniewska

    Bridging the Gap (BtG) is a 2-year project funded by The Danish Industry Foundation. The goal of Bridging the Gap has been to create a new innovation model which will increase the rate at which Danish universities can spinout new technology ventures.......Bridging the Gap (BtG) is a 2-year project funded by The Danish Industry Foundation. The goal of Bridging the Gap has been to create a new innovation model which will increase the rate at which Danish universities can spinout new technology ventures....

  19. Antecedents of Customer Relationship Termination

    DEFF Research Database (Denmark)

    Geersbro, Jens; Ritter, Thomas

    relationships as a managerial task. This paper contributes by (1) developing a conceptualization of relationship termination competence and (2) analyzing its antecedents. The empirical results identify termination acceptance, definition non-customers, organizational relationship termination routines...

  20. Bridge the Gap

    DEFF Research Database (Denmark)

    Marselis, Randi Lorenz

    2017-01-01

    This article focuses on photo projects organised for teenage refugees by the Society for Humanistic Photography (Berlin, Germany). These projects, named Bridge the Gap I (2015), and Bridge the Gap II (2016), were carried out in Berlin and brought together teenagers with refugee and German...

  1. Coal terminal guide 1999

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1999-08-01

    IBJ`s third edition of its annual guide to the world`s multi-user coal terminals includes comprehensive details of terminals in 44 countries. The guide sets out information for rapid and easy reference comprising contact, full address and communication details as well as berth dimensions and constraints, loading equipment and daily loading rate, annual loading capacity, daily discharge rate, annual discharge capacity, annual throughput capacity, storage facilities, stockyard capacity and equipment, processing facilities and so on. All information has been compiled from specific questionnaires and is presented alphabetically in country order.

  2. Windows Terminal Servers Orchestration

    Science.gov (United States)

    Bukowiec, Sebastian; Gaspar, Ricardo; Smith, Tim

    2017-10-01

    Windows Terminal Servers provide application gateways for various parts of the CERN accelerator complex, used by hundreds of CERN users every day. The combination of new tools such as Puppet, HAProxy and Microsoft System Center suite enable automation of provisioning workflows to provide a terminal server infrastructure that can scale up and down in an automated manner. The orchestration does not only reduce the time and effort necessary to deploy new instances, but also facilitates operations such as patching, analysis and recreation of compromised nodes as well as catering for workload peaks.

  3. EXTREME AND TERMINAL STATES

    Directory of Open Access Journals (Sweden)

    P.F. Litvitsky

    2010-01-01

    Full Text Available Author brings modern conception of extreme and terminal states, their types, likenesses and differences, etiology, key common chains of pathogenesis, principles and methods of their treatment. Pathophysiological data on one of extreme states — collapse — is described in details. Next publications will present the data on shock and coma.Key words: extreme and terminal states, vicious circle of pathogenesis, extreme regulation, principles of treatment.(Voprosy sovremennoi pediatrii — Current Pediatrics. – 2010;9(3:74-80

  4. Electrical termination techniques

    Science.gov (United States)

    Oakey, W. E.; Schleicher, R. R.

    1976-01-01

    A technical review of high reliability electrical terminations for electronic equipment was made. Seven techniques were selected from this review for further investigation, experimental work, and preliminary testing. From the preliminary test results, four techniques were selected for final testing and evaluation. These four were: (1) induction soldering, (2) wire wrap, (3) percussive arc welding, and (4) resistance welding. Of these four, induction soldering was selected as the best technique in terms of minimizing operator errors, controlling temperature and time, minimizing joint contamination, and ultimately producing a reliable, uniform, and reusable electrical termination.

  5. Terminal oxidases of cyanobacteria.

    Science.gov (United States)

    Hart, S E; Schlarb-Ridley, B G; Bendall, D S; Howe, C J

    2005-08-01

    The respiratory chain of cyanobacteria appears to be branched rather than linear; furthermore, respiratory and photosynthetic electron-transfer chains co-exist in the thylakoid membrane and even share components. This review will focus on the three types of terminal respiratory oxidases identified so far on a genetic level in cyanobacteria: aa3-type cytochrome c oxidase, cytochrome bd-quinol oxidase and the alternative respiratory terminal oxidase. We summarize here their genetic, biochemical and biophysical characterization to date and discuss their interactions with electron donors as well as their physiological roles.

  6. The genetic regulation of the terminating phase of liver regeneration

    DEFF Research Database (Denmark)

    Nygård, Ingvild E.; Mortensen, Kim E.; Hedegaard, Jakob

    2012-01-01

    Background After partial hepatectomy (PHx), the liver regeneration process terminates when the normal liver-mass/body-weight ratio of 2.5% has been re-established. To investigate the genetic regulation of the terminating phase of liver regeneration, we performed a 60% PHx in a porcine model. Liver...... biopsies were taken at the time of resection, after three weeks and upon termination the sixth week. Gene expression profiles were obtained using porcine oligonucleotide microarrays. Our study reveals the interactions between genes regulating the cell cycle, apoptosis and angiogenesis, and the role...

  7. Wide-Gap Chalcopyrites

    CERN Document Server

    Siebentritt, Susanne

    2006-01-01

    Chalcopyrites, in particular those with a wide band gap, are fascinating materials in terms of their technological potential in the next generation of thin-film solar cells and in terms of their basic material properties. They exhibit uniquely low defect formation energies, leading to unusual doping and phase behavior and to extremely benign grain boundaries. This book collects articles on a number of those basic material properties of wide-gap chalcopyrites, comparing them to their low-gap cousins. They explore the doping of the materials, the electronic structure and the transport through interfaces and grain boundaries, the formation of the electric field in a solar cell, the mechanisms and suppression of recombination, the role of inhomogeneities, and the technological role of wide-gap chalcopyrites.

  8. Coordinated control of terminal differentiation and restriction of cellular plasticity

    Science.gov (United States)

    Patel, Tulsi; Hobert, Oliver

    2017-01-01

    The acquisition of a specific cellular identity is usually paralleled by a restriction of cellular plasticity. Whether and how these two processes are coordinated is poorly understood. Transcription factors called terminal selectors activate identity-specific effector genes during neuronal differentiation to define the structural and functional properties of a neuron. To study restriction of plasticity, we ectopically expressed C. elegans CHE-1, a terminal selector of ASE sensory neuron identity. In undifferentiated cells, ectopic expression of CHE-1 results in activation of ASE neuron type-specific effector genes. Once cells differentiate, their plasticity is restricted and ectopic expression of CHE-1 no longer results in activation of ASE effector genes. In striking contrast, removal of the respective terminal selectors of other sensory, inter-, or motor neuron types now enables ectopically expressed CHE-1 to activate its ASE-specific effector genes, indicating that terminal selectors not only activate effector gene batteries but also control the restriction of cellular plasticity. Terminal selectors mediate this restriction at least partially by organizing chromatin. The chromatin structure of a CHE-1 target locus is less compact in neurons that lack their resident terminal selector and genetic epistasis studies with H3K9 methyltransferases suggest that this chromatin modification acts downstream of a terminal selector to restrict plasticity. Taken together, terminal selectors activate identity-specific genes and make non-identity-defining genes less accessible, thereby serving as a checkpoint to coordinate identity specification with restriction of cellular plasticity. DOI: http://dx.doi.org/10.7554/eLife.24100.001 PMID:28422646

  9. The Gender Pay Gap

    OpenAIRE

    Alan Manning

    2006-01-01

    Empirical research on gender pay gaps has traditionally focused on the role of gender-specific factors, particularly gender differences in qualifications and differences in the treatment of otherwise equally qualified male and female workers (i.e., labor market discrimination). This paper explores the determinants of the gender pay gap and argues for the importance of an additional factor, wage structure, the array of prices set for labor market skills and the rewards received for employment ...

  10. Settings for Terminal Care.

    Science.gov (United States)

    Corless, Inge B.

    1988-01-01

    Examines topics related to delivery of terminal care services: ability of various hospice programs to survive financially, contributions of various models of hospice care, impact of Medicare legislation on hospice movement, demonstration of unique hospice intervention, integration of spiritual care into hospice, and role of hospice in care of…

  11. Termination of protein synthesis.

    Science.gov (United States)

    Tuite, M F; Stansfield, I

    1994-05-01

    One of three mRNA codons--UAA, UAG and UGA--is used to signal to the elongating ribosome that translation should be terminated at this point. Upon the arrival of the stop codon at the ribosomal acceptor(A)-site, a protein release factor (RF) binds to the ribosome resulting in the peptidyl transferase centre of the ribosome switching to a hydrolytic function to remove the completed polypeptide chain from the peptidyl-tRNA bound at the adjacent ribosomal peptidyl(P)-site. In this review recent advances in our understanding of the mechanism of termination in the bacterium Escherichia coli will be summarised, paying particular attention to the roles of 16S ribosomal RNA and the release factors RF-1, RF-2 and RF-3 in stop codon recognition. Our understanding of the translation termination process in eukaryotes is much more rudimentary with the identity of the single eukaryotic release factor (eRF) still remaining elusive. Finally, several examples of how the termination mechanism can be subverted either to expand the genetic code (e.g. selenocysteine insertion at UGA codons) or to regulate the expression of mammalian retroviral or plant viral genomes will be discussed.

  12. Making Wireless Terminals Simpler

    DEFF Research Database (Denmark)

    Christensen, Søren Skovgaard; Popovski, Petar; De Carvalho, Elisabeth

    2005-01-01

    The exponential growth of user demands and the limitations of 3G systems have brought researchers and industry to propose solutions for the next generation. Among the requirements are higher bit rates and cheaper deployment. In this paper we focus on a terminal complexity problem related to channel...

  13. The composite N1 component to gaps in noise.

    Science.gov (United States)

    Pratt, Hillel; Bleich, Naomi; Mittelman, Nomi

    2005-11-01

    To indicate whether the double peaked N(1) to gaps in continuous white noise is a composite of onset and offset responses to transients or whether it reflects higher processing such as change or mismatch detection and to assess the role of attention in this process. Evoked potentials were recorded to two binaural stimulus types: (1) gaps of different durations randomly distributed in continuous white noise; and (2) click pairs at intervals identical to those between gap onsets and offsets in the continuous noise stimulus. Potentials to these stimuli were recorded while subjects read a text and while detecting gaps in noise or click pairs. Potentials were detected to all click pairs and to gaps of 5 ms or longer, corresponding to the subjects' psychoacoustic gap detection threshold. With long gap durations of 200-800 ms, distinct potentials to gap onset and gap offset were observed. The waveforms to all click pairs and to offsets of long gaps were similar and single-peaked, while potentials to gaps of 10 ms and longer, and potentials to onsets of long gaps were double-peaked, consisting of two N(1) negativities, 60 ms apart, irrespective of gap duration. The first (N(1a)), was more frontal in its distribution and similar to that of clicks. The second (N(1b)) peak's distribution was more central/temporal and its source locations and time course of activity were distinct. No effects of attention on any of the varieties and constituents of N(1) were observed. Comparing potentials to gap onsets, to click pairs and to gap offsets, suggests that potentials to gap onsets involve not only sound onset/offset responses (N(1), N(1a)) but also the subsequent pre-attentive perception of the cessation of an ongoing sound (N(1b)). We propose that N(1b) is distinct from change or mismatch detection and is associated with termination of an ongoing continuous stimulus. We propose to call it the N(egation)-process. A constituent of the N(1) complex is shown to be associated with the

  14. Ice age terminations.

    Science.gov (United States)

    Cheng, Hai; Edwards, R Lawrence; Broecker, Wallace S; Denton, George H; Kong, Xinggong; Wang, Yongjin; Zhang, Rong; Wang, Xianfeng

    2009-10-09

    230Th-dated oxygen isotope records of stalagmites from Sanbao Cave, China, characterize Asian Monsoon (AM) precipitation through the ends of the third- and fourthmost recent ice ages. As a result, AM records for the past four glacial terminations can now be precisely correlated with those from ice cores and marine sediments, establishing the timing and sequence of major events. In all four cases, observations are consistent with a classic Northern Hemisphere summer insolation intensity trigger for an initial retreat of northern ice sheets. Meltwater and icebergs entering the North Atlantic alter oceanic and atmospheric circulation and associated fluxes of heat and carbon, causing increases in atmospheric CO2 and Antarctic temperatures that drive the termination in the Southern Hemisphere. Increasing CO2 and summer insolation drive recession of northern ice sheets, with probable positive feedbacks between sea level and CO2.

  15. Equilibrium and Termination

    Directory of Open Access Journals (Sweden)

    Nicolas Oury

    2010-06-01

    Full Text Available We present a reduction of the termination problem for a Turing machine (in the simplified form of the Post correspondence problem to the problem of determining whether a continuous-time Markov chain presented as a set of Kappa graph-rewriting rules has an equilibrium. It follows that the problem of whether a computable CTMC is dissipative (ie does not have an equilibrium is undecidable.

  16. Coal terminal project report

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2004-03-01

    Malaysia is building the necessary infrastructure to cope with an increasing demand for electricity. Its restructured energy policy has led to construction of the 2,100 MW Manjung coal-fired power plant in the state of Perak, for which coal has to be imported via the new Lekiv Bulk Terminal (LBT) adjacent to the plant. Contracts for the LBC and the TNBJ coal stockyard were awarded to the Koch Consortium. The article describes equipment for handling and storing coal. 4 photos.

  17. Terminal Satisfiability in GSTE

    OpenAIRE

    Yongsheng Xu; Guowu Yang; Zhengwei Chang; Desheng Zheng; Wensheng Guo

    2014-01-01

    Generalized symbolic trajectory evaluation (GSTE) is an extension of symbolic trajectory evaluation (STE) and a method of model checking. GSTE specifications are given as assertion graphs. There are four efficient methods to verify whether a circuit model obeys an assertion graph in GSTE, Model Checking Strong Satisfiability (SMC), Model Checking Normal Satisfiability (NMC), Model Checking Fair Satisfiability (FMC), and Model Checking Terminal Satisfiability (TMC). SMC, NMC, and FMC have been...

  18. Mass gap without confinement

    Science.gov (United States)

    Faedo, Antón F.; Mateos, David; Pravos, David; Subils, Javier G.

    2017-06-01

    We revisit a one-parameter family of three-dimensional gauge theories with known supergravity duals. We show that three infrared behaviors are possible. For generic values of the parameter, the theories exhibit a mass gap but no confinement, meaning no linear quark-antiquark potential; for one limiting value of the parameter the theory flows to an infrared fixed point; and for another limiting value it exhibits both a mass gap and confinement. Theories close to these limiting values exhibit quasi-conformal and quasi-confining dynamics, respectively. Eleven-dimensional supergravity provides a simple, geometric explanation of these features.

  19. The longevity gender gap

    DEFF Research Database (Denmark)

    Aviv, Abraham; Shay, Jerry; Christensen, Kaare

    2005-01-01

    resistant to the ravages of time. We discuss the interplay of these factors with telomere biology and oxidative stress and suggest that an explanation for the longevity gender gap may arise from a better understanding of the differences in telomere dynamics between men and women.......In this Perspective, we focus on the greater longevity of women as compared with men. We propose that, like aging itself, the longevity gender gap is exceedingly complex and argue that it may arise from sex-related hormonal differences and from somatic cell selection that favors cells more...

  20. Bridging the Emissions Gap

    OpenAIRE

    Blok, K.

    2012-01-01

    The analyses in Chapters 2 and 3 of this report concluded that the emissions gap in 2020 will likely be between 8 and 13 GtCO2e. The chapters also estimated the difference between BaU emissions in 2020 and the emissions level consistent with a “likely” chance of staying within the 2°C target to be 14 GtCO2e. This chapter explores the potential for bridging this gap using a sector policy approach. Firstly, the chapter provides a summary and update of the estimated emission reduction potential ...

  1. Molecular and biochemical analysis of a 105 kDa Mycoplasma gallisepticum cytadhesin (GapA).

    Science.gov (United States)

    Goh, M S; Gorton, T S; Forsyth, M H; Troy, K E; Geary, S J

    1998-11-01

    The identification of a gene (gapA) from Mycoplasma gallisepticum with homology to the P1 cytadherence gene of Mycoplasma pneumoniae is reported. The gapA gene is a 2895 bp ORF encoding a protein with a molecular mass of 105 kDa. Nucleotide sequence analysis of the gapA gene revealed 45% homology to the M. pneumoniae P1 gene, 46% homology to the Mycoplasma genitalium MgPa gene and 47% homology to the Mycoplasma pirum P1-like protein gene. It has a 64 mol % A+T content compared to 46, 60 and 72 mol % respectively for the P1, MgPa and the P1-like protein genes. As with the P1 and MgPa genes, gapA is a central gene in a multi-gene operon, but unlike the P1 and MgPa genes, there is only a single copy of gapA in the genome. GapA is a trypsin-sensitive surface-exposed protein. Chicken tracheal-ring inhibition-of-attachment assays, using anti-GapA Fab fragments, resulted in 64% inhibition of attachment. These results indicated that GapA plays a role in cytadherence of M. gallisepticum to host cells.

  2. The Ethics of Terminal Care

    Science.gov (United States)

    Agich, George J.

    1978-01-01

    Need for a critical and analytical approach to ethics of terminal care is suggested by considering a series of unexamined questions regarding justification of terminal care. If terminal care is a moral and ethical enterprise, such considerations must be given a more prominent place in discussions of the hospice movement. (Author)

  3. Promiscuous and specific phospholipid binding by domains in ZAC, a membrane-associated Arabidopsis protein with an ARF GAP zinc finger and a C2 domain

    DEFF Research Database (Denmark)

    Jensen, R B; Lykke-Andersen, K; Frandsen, G I

    2000-01-01

    Arabidopsis proteins were predicted which share an 80 residue zinc finger domain known from ADP-ribosylation factor GTPase-activating proteins (ARF GAPs). One of these is a 37 kDa protein, designated ZAC, which has a novel domain structure in which the N-terminal ARF GAP domain and a C-terminal C...

  4. cDNA cloning and chromosomal mapping of a novel human GAP (GAP1M), GTPase-activating protein of Ras

    Energy Technology Data Exchange (ETDEWEB)

    Li, Shaowei; Nakamura, Shun; Hattori, Seisuke [National Center of Neurology and Psychiatry, Kodaira, Tokyo (Japan)] [and others

    1996-08-01

    We have previously isolated a novel Ras GTPase-activating protein (Ras GAP), Gapl{sup m}, from rat brain. Gap1{sup m} is considered to be a negative regulator of the Ras signaling pathways, like other Ras GAPs, neurofibromin, which is a gene product of the neurofibromatosis type I gene, and p120GAP. In this study we have isolated a human cDNA of this Gap and mapped the gene. The gene encodes a protein of 853 amino acids that shows 89% sequence identity to rat Gapl{sup m}. The human gene was mapped to chromosome 3 by PCR analysis on a panel of human-mouse hybrid cells. FISH analysis refined the location of the gene further to 3q22-q23. 11 refs., 2 figs.

  5. Bridge the Gap.

    Science.gov (United States)

    Klein, Mel; Cufaude, Jeffrey B.

    1989-01-01

    This document consists of two paired articles: the first, "Preparing Faculty Out of Class Experiences," by Mel Klein, and the second, "Help Advisers Be More Than Ghost Signatures," by Jeffrey B. Calfaude. Each article shares insights on how faculty advisers "bridge the gap" between students and faculty. When faculty members are asked to advise…

  6. Bridging the gap

    Science.gov (United States)

    2012-08-01

    Astronomy is flourishing in China, with impressive achievements in instrument design and construction matched by a higher international research profile. Yet there remains a mismatch between the facilities available and those needed to progress. Sue Bowler wonders how the country will bridge the gap.

  7. Semantic Gaps Are Dangerous

    DEFF Research Database (Denmark)

    Ejstrup, Michael; le Fevre Jakobsen, Bjarne

    2014-01-01

    Semantic gaps are dangerous Language adapts to the environment where it serves as a tool to communication. Language is a social agreement, and we all have to stick to both grammaticalized and non-grammaticalized rules in order to pass information about the world around us. As such language develops...

  8. Bridging the Emissions Gap

    NARCIS (Netherlands)

    Blok, K.

    2012-01-01

    The analyses in Chapters 2 and 3 of this report concluded that the emissions gap in 2020 will likely be between 8 and 13 GtCO2e. The chapters also estimated the difference between BaU emissions in 2020 and the emissions level consistent with a “likely” chance of staying within the 2°C target to

  9. Estimating Gender Wage Gaps

    Science.gov (United States)

    McDonald, Judith A.; Thornton, Robert J.

    2011-01-01

    Course research projects that use easy-to-access real-world data and that generate findings with which undergraduate students can readily identify are hard to find. The authors describe a project that requires students to estimate the current female-male earnings gap for new college graduates. The project also enables students to see to what…

  10. Sequence and expression analysis of gaps in human chromosome 20

    DEFF Research Database (Denmark)

    Minocherhomji, Sheroy; Seemann, Stefan; Mang, Yuan

    2012-01-01

    /or overlap disease-associated loci, including the DLGAP4 locus. In this study, we sequenced ~99% of all three unfinished gaps on human chr 20, determined their complete genomic sizes and assessed epigenetic profiles using a combination of Sanger sequencing, mate pair paired-end high-throughput sequencing......The finished human genome-assemblies comprise several hundred un-sequenced euchromatic gaps, which may be rich in long polypurine/polypyrimidine stretches. Human chromosome 20 (chr 20) currently has three unfinished gaps remaining on its q-arm. All three gaps are within gene-dense regions and...

  11. Loss and terminal illness.

    Science.gov (United States)

    Benoliel, J Q

    1985-06-01

    The experience of terminal illness can best be viewed as a situation of multiple losses involving the dying person, family members and friends, and the health care providers engaged in offering services to them. It is a major transition during which the central participants must cope with the personal meanings of the forthcoming death as well as other losses brought about by the disease process, medical treatments, and the need to provide care for the dying person. How families adapt to the stresses and changes imposed by the experience of living with dying depends on their previous experiences with death, their established patterns of communication about serious matters, and their decision-making practices. Some individuals and families are at greater risk than others for developing maladaptive responses and behaviors during and after the experience of terminal illness. Risk factors to be considered in making hypotheses about the potential for maladaptive reactions include the strength of the attachment to the dying person, uncontrollable and distressing symptoms, and coping limitations associated with age and other factors contributing to increased vulnerability to the demands of continuous change. Working effectively with different kinds of families during the transition of terminal illness can best be accomplished within a conceptual framework built upon knowledge about people undergoing change. The concept of safe conduct can serve as an overall guide for the creation of nursing services designed to offer personalized care and accessibility of professional help at times of maximum need by the family. Assisting dying patients and their families toward the achievement of their personal goals is fundamental to the idea of safe conduct. The delivery of nursing care in terminal illness requires an orientation to assessment as an ongoing process that makes use of knowledge about disease processes, medical treatments, individual and group adaptations to loss, risk

  12. Acetylene terminated matrix resins

    Science.gov (United States)

    Goldfarb, I. J.; Lee, Y. C.; Arnold, F. E.; Helminiak, T. E.

    1985-01-01

    The synthesis of resins with terminal acetylene groups has provided a promising technology to yield high performance structural materials. Because these resins cure through an addition reaction, no volatile by-products are produced during the processing. The cured products have high thermal stability and good properties retention after exposure to humidity. Resins with a wide variety of different chemical structures between the terminal acetylene groups are synthesized and their mechanical properties studied. The ability of the acetylene cured polymers to give good mechanical properties is demonstrated by the resins with quinoxaline structures. Processibility of these resins can be manipulated by varying the chain length between the acetylene groups or by blending in different amounts of reactive deluents. Processing conditions similar to the state-of-the-art epoxy can be attained by using backbone structures like ether-sulfone or bis-phenol-A. The wide range of mechanical properties and processing conditions attainable by this class of resins should allow them to be used in a wide variety of applications.

  13. Termination: A Case Study.

    Science.gov (United States)

    Friedberg, Ahron L

    2015-12-01

    In this article I posit and examine certain criteria and qualities for ending an analysis. The case study describes the end phase of a four-year psychoanalysis in which the patient's decision to move to another area forced the end of his analysis. We continued to explore and work through his core neurotic conflicts that included issues of competitive rivalry, dominance and submission, control, and anxiety about birth and death. A shift in the transference from me as a negative father to me as a supportive but competitive older brother was also examined in the context of ending treatment as well as other aspects of the transference. In addition, we analyzed the meaning of his ending treatment based on an extra-analytic circumstance. In discussing this phase of treatment, the definition and history of the term "termination" and its connotations are reviewed. Various criteria for completing an analysis are examined, and technical observations about this phase of treatment are investigated. It was found that while a significant shift in the transference occurred in this phase of the patient's analysis, conflicts related to the transference were not "resolved" in the classical sense. Terminating treatment was considered as a practical matter in which the patient's autonomy and sense of choice were respected and analyzed.

  14. Bridge the Gap

    DEFF Research Database (Denmark)

    Marselis, Randi Lorenz

    2017-01-01

    This article focuses on photo projects organised for teenage refugees by the Society for Humanistic Photography (Berlin, Germany). These projects, named Bridge the Gap I (2015), and Bridge the Gap II (2016), were carried out in Berlin and brought together teenagers with refugee and German-majorit...... was produced – and sometimes not produced - within the projects. The importance of memory work in the context of refugee resettlement is often overlooked, but is particularly relevant when cultural encounters are organised in museums and exhibition galleries.......-majority backgrounds to experiment with digital photography and create joint exhibitions. Drawing on concepts from memory studies, such as travelling memory and multidirectional memory, the author examines the projects as interventions in German and Berlin memory cultures, and examines how multidirectional memory...

  15. Closing the Gap

    DEFF Research Database (Denmark)

    Tamke, Martin; Kobiella, Olaf

    2007-01-01

    The e4d design series is looking for an innovative use of digital technology in architectural education to overcome the gap between design development and the acquisition of digital skills. Digital design approaches include multimedia technology, the crossover of analogue and digital techniques, ...... architectural projects can be discussed; in addition, a competent monitoring of the process and outcome of innovative and efficient design strategies in architectural and pedagogical aspect is included.......The e4d design series is looking for an innovative use of digital technology in architectural education to overcome the gap between design development and the acquisition of digital skills. Digital design approaches include multimedia technology, the crossover of analogue and digital techniques......, rapid-prototyping, visualization, and the presentation in artistic movies. Over the past two years a problem- based design approach was developed, which enabled students to learn digital and architectural skills simultaneously and efficiently. The educational concept consisted generally of four steps...

  16. Minding the Gap

    Energy Technology Data Exchange (ETDEWEB)

    Firestone, Millicent Anne [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2015-02-23

    Neutron & X-ray scattering provides nano- to meso-scale details of complex fluid structure; 1D electronic density maps dervied from SAXS yield molecular level insights; Neutron reflectivity provides substructure details of substrate supported complex fluids; Complex fluids composition can be optimized to support a wide variety of both soluble and membrane proteins; The water gap dimensions can be finely tuned through polymer component.

  17. 'Mind the Gap!'

    DEFF Research Database (Denmark)

    Persson, Karl Gunnar

    This paper challenges the widely held view that sharply falling real transport costs closed the transatlantic gap in grain prices in the second half of the 19th century. Several new results emerge from an analysis of a new data set of weekly wheat prices and freight costs from New York to UK mark...... convergence (or divergence) can appear if quality differences associated with allegedly homogeneous commodities like wheat are not controlled for....

  18. Mind the Gap

    OpenAIRE

    Dorsett, R.; Rienzo, C.; Rolfe, H.; Burns, H.; Robertson, B-A.; Thorpe, B.; Wall, K.

    2014-01-01

    Mind the Gap sought to improve the metacognition and academic attainment of pupils in Year 4. There were two aspects to the intervention. The first involved training teachers in how to embed metacognitive approaches in their work, and how to continue to effectively and strategically involve parents. This training took place over a day and was provided by a consultant. The second component focused on parental engagement and offered families the opportunity to participate in a series of facilit...

  19. SUBORDINATE GAPS IN MANDARIN CHINESE

    Directory of Open Access Journals (Sweden)

    Ting-Chi Wei

    2011-06-01

    Full Text Available The existence of subordinate gaps in Mandarin Chinese casts doubt on analyses built on canonical coordinate gapping. We observe that the minimality of contrastive focus and the type of subordinate clause determine the acceptability of a missing gap in subordinate structure. Along this vein, we propose that a semantic-based deletion account can be used to interpret gapping in Mandarin. Such account relies on two violable constraints, AvoidF and Focus condition on gapping (Schwarzchild 1999, Merchant 2001 to compute the acceptability of a gap.

  20. Gender gaps and gains.

    Science.gov (United States)

    Conly, S

    1998-01-01

    Findings from studies conducted worldwide indicate that educating girls allows them to gain more control over their lives, which, in turn, means that they have fewer, healthier children. In patriarchal societies, however, this education must last 6 or 7 years to be fully beneficial. Education of girls is also among the best economic investments a country can make because it leads to increased productivity and economic growth. However, women still suffer from a gender gap that has resulted in lower literacy among women and lower school attendance and duration of schooling among girls. However, gains have been made, and the gender gap in enrollment is narrowing in some regions, such as Latin America and East Asia. The gender gap continues its stranglehold, however, in the most populous and impoverished countries of sub-Saharan Africa. Enrollment rates in secondary schools have risen faster than for primary schools worldwide, with striking gains in East Asia. In some regions, such as Latin America, the secondary school enrollment rates are actually higher for girls than for boys. Strategies to improve girls' educational participation include 1) building more schools, 2) providing "girl-friendly" facilities, 3) increasing the number of women teachers, 4) improving the quality and relevance of the curriculum, 5) promoting education among parents, 6) providing sexual health education and services to reduce pregnancy-related drop-outs, and 7) making school hours flexible to accommodate girls' schedules.

  1. [Treatment of glottal gap].

    Science.gov (United States)

    Voigt-Zimmermann, S; Arens, C

    2013-02-01

    Glottal gaps can be either physiological or pathological. The latter are multifactorial, predominantly organic in origin and occasionally functional. Organic causes include vocal fold paralysis or scarring, as well as a deficiency or excess of tissue. In addition to loss of the mucosal wave, the degree of hoarseness is primarily determined by the circumferential area of the glottal gap. It is thus important to quantify the extent of glottal insufficiency. Although a patient's symptoms form the basis for treatment decisions, these may be subjective and inadequately reflected by the results of auditory-perceptual evaluation, voice analysis and voice performance tests. The therapeutic approach should always combine phonosurgery with conventional voice therapy methods. Voice therapy utilises all the resources made available by the sphincter model of the aerodigestive tract and knowledge on the mechanism of voice production. The aim of phonosurgery is medialization, reconstruction or reinnervation by injection laryngoplasty or larynx framework surgery. These different methods can be combined and often applied directly after vocal fold surgery (primary reconstruction). In conclusion, the techniques described here can be effectively employed to compensate for glottal gaps.

  2. 77 FR 38817 - Credit Watch Termination Initiative; Termination of Direct Endorsement (DE) Approval

    Science.gov (United States)

    2012-06-29

    ... URBAN DEVELOPMENT Credit Watch Termination Initiative; Termination of Direct Endorsement (DE) Approval.... SUMMARY: This notice advises of the cause and effect of termination of Direct Endorsement (DE) Approval... procedures for terminating Underwriting Authority of Direct Endorsement mortgagees. Termination of Direct...

  3. Resolution and termination

    Directory of Open Access Journals (Sweden)

    Adina FOLTIŞ

    2012-01-01

    Full Text Available The resolution, the termination and the reduction of labour conscription are regulated by articles 1549-1554 in the new Civil Code, which represents the common law in this matter. We appreciate that the new regulation does not conclusively clarify the issue related to whether the existence of liability in order to call upon the resolution is necessary or not, because the existence of this condition has been inferred under the previous regulation from the fact that the absence of liability shifts the inexecution issue on the domain of fortuitous impossibility of execution, situation in which the resolution of the contract is not in question, but that of the risk it implies.

  4. GapBlaster-A Graphical Gap Filler for Prokaryote Genomes.

    Directory of Open Access Journals (Sweden)

    Pablo H C G de Sá

    Full Text Available The advent of NGS (Next Generation Sequencing technologies has resulted in an exponential increase in the number of complete genomes available in biological databases. This advance has allowed the development of several computational tools enabling analyses of large amounts of data in each of the various steps, from processing and quality filtering to gap filling and manual curation. The tools developed for gap closure are very useful as they result in more complete genomes, which will influence downstream analyses of genomic plasticity and comparative genomics. However, the gap filling step remains a challenge for genome assembly, often requiring manual intervention. Here, we present GapBlaster, a graphical application to evaluate and close gaps. GapBlaster was developed via Java programming language. The software uses contigs obtained in the assembly of the genome to perform an alignment against a draft of the genome/scaffold, using BLAST or Mummer to close gaps. Then, all identified alignments of contigs that extend through the gaps in the draft sequence are presented to the user for further evaluation via the GapBlaster graphical interface. GapBlaster presents significant results compared to other similar software and has the advantage of offering a graphical interface for manual curation of the gaps. GapBlaster program, the user guide and the test datasets are freely available at https://sourceforge.net/projects/gapblaster2015/. It requires Sun JDK 8 and Blast or Mummer.

  5. Mobile termination and mobile penetration

    OpenAIRE

    Hurkens, Sjaak; Jeon, Doh-Shin

    2009-01-01

    In this paper, we study how access pricing affects network competition when subscription demand is elastic and each network uses non-linear prices and can apply termination-based price discrimination. In the case of a fixed per minute termination charge, we find that a reduction of the termination charge below cost has two oppos- ing effects: it softens competition but helps to internalize network externalities. The former reduces mobile penetration while the latter boosts it. We find that fi...

  6. Cloning and sequence analysis of cDNAs encoding the cytosolic precursors of subunits GapA and GapB of chloroplast glyceraldehyde-3-phosphate dehydrogenase from pea and spinach.

    Science.gov (United States)

    Brinkmann, H; Cerff, R; Salomon, M; Soll, J

    1989-07-01

    Chloroplast glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is composed of two different subunits, GapA and GapB. cDNA clones containing the entire coding sequences of the cytosolic precursors for GapA from pea and for GapB from pea and spinach have been identified, sequenced and the derived amino acid sequences have been compared to the corresponding sequences from tobacco, maize and mustard. These comparisons show that GapB differs from GapA in about 20% of its amino acid residues and by the presence of a flexible and negatively charged C-terminal extension, possibly responsible for the observed association of the enzyme with chloroplast envelopes in vitro. This C-terminal extension (29 or 30 residues) may be susceptible to proteolytic cleavage thereby leading to a conversion of chloroplast GAPDH isoenzyme I into isoenzyme II. Evolutionary rate comparisons at the amino acid sequence level show that chloroplast GapA and GapB evolve roughly two-fold slower than their cytosolic counterpart GapC. GapA and GapB transit peptides evolve about 10 times faster than the corresponding mature subunits. They are relatively long (68 and 83 residues for pea GapA and spinach GapB respectively) and share a similar amino acid framework with other chloroplast transit peptides.

  7. Service Quality Evaluation and Ranking of Container Terminal Operators

    Directory of Open Access Journals (Sweden)

    Jafar Sayareh

    2016-12-01

    Full Text Available In the service industry, the regular assessment of service quality is considered as a means of promoting the quality of services. Container market is no exception, and the quality of providing service in a container terminal is of prime importance in attracting new customers and maintaining the existing ones. The main aim of present research is to evaluate the quality of service being offered at Shahid Rajaee Container Terminal (SRCT in Bandar Abbas port. The evaluation process uses SERVQUAL model which is an appropriate tool for measuring the service quality, identifying and analyzing available gaps between service expectations and perceptions. Target population in this research includes customers of SRCT. The standard and customized questionnaires were distributed among 165 samples, out of which 127 (77% were returned. For the purpose of data analyses, initially the reliability of SERVQUAL model was checked, and then paired sample t-test was performed to reveal any possible gap between expectations and perceptions of respondents. Finally, TOPSIS was used to rank the 9 main container service companies in the SRCT. The results indicated that there are significant gaps between customers’ expectations and perceptions in SRCT, in all five dimensions of services quality. Additionally, from weighing point of view, ‘Tangibles’ was the most important dimension, followed by ‘Reliability’, ‘Assurance’, ‘Responsiveness’ and ‘Empathy’. In addition, ‘Tangibles’ dimension had maximum gap and ‘Empathy’ dimension had minimum gap between customers’ expectations and perceptions. Finally, after ranking companies, BandarAbbas Aria Container Terminal (BACT Company was ranked first among nine companies in satisfying customers’ expectations.

  8. Closing the stop gap

    Energy Technology Data Exchange (ETDEWEB)

    Czakon, Michal [RWTH Aachen Univ. (Germany). Inst. fuer Theoretische Teilchnphysik und Kosmologie; Mitov, Alexander [Univ. of Cambridge (United Kingdom). Cavendish Lab.; Papucci, Michele [Lawrence Berkeley National Laboratory, CA (United States). Theoretical Physics Group; California Univ., Berkeley, CA (United States). Dept. of Physics; Ruderman, Joshua T. [Lawrence Berkeley National Laboratory, CA (United States). Theoretical Physics Group; California Univ., Berkeley, CA (United States). Dept. of Physics; New York Univ., NY (United States). Center for Cosmology and Particle Physics; Weiler, Andreas [Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany); CERN - European Organization for Nuclear Research, Geneva (Switzerland). Theory Div.

    2014-07-15

    Light stops are a hallmark of the most natural realizations of weak-scale supersymmetry. While stops have been extensively searched for, there remain open gaps around and below the top mass, due to similarities of stop and top signals with current statistics. We propose a new fast-track avenue to improve light stop searches for R-parity conserving supersymmetry, by comparing top cross section measurements to the theoretical prediction. Stop masses below ∝180 GeV can now be ruled out for a light neutralino. The possibility of a stop signal contaminating the top mass measurement is also briefly addressed.

  9. Addressing the innovation gap.

    Science.gov (United States)

    Jeffrey, Phillip; Warne, Peter; Williams, Robert

    2007-05-01

    The 10 years since the mid-1990s have witnessed an unprecedented investment in Drug Discovery driven by both the unraveling of the human genome and the parallel introduction of various high-throughput technologies. During the same period, industry metrics describe a decline in the numbers of new molecular entities launched upon the global pharmaceutical markets. The Society for Medicines Research (SMR) meeting entitled "Addressing the Innovation Gap" brought together a program of expert speakers to comment upon the challenges currently facing the pharmaceutical industry and some of the measures being undertaken to enable future success.

  10. Is Lake Tahoe Terminal?

    Science.gov (United States)

    Coats, R. N.; Reuter, J.; Heyvaert, A.; Lewis, J.; Sahoo, G. B.; Schladow, G.; Thorne, J. H.

    2014-12-01

    ) the climatic water deficit will increase, especially at high elevations that will be most affected by the loss of snow, with likely consequences for existing vegetation and fire frequency. Hydrologically, Lake Tahoe is intermittently terminal; in a medical sense it is not yet terminal, but its condition—especially its valued clarity and deep blue color--is serious.

  11. Gap Task Force

    CERN Multimedia

    Lissuaer, D

    One of the more congested areas in the ATLAS detector is the GAP region (the area between the Barrel Calorimeter and the End Cap calorimeter) where Inner Detector services, LAr Services and some Tile services all must co-habitat in a very limited area. It has been clear for some time that the space in the GAP region is not sufficient to accommodate all that is needed. In the last few month additional problems of routing all the services to Z=0 have been encountered due to the very limited space between the Tile Calorimeter and the first layer of Muon chambers. The Technical Management Board (TMB) and the Executive Board (EB) decided in the middle of March to establish a Task Force to look at this problem and come up with a solution within well-specified guidelines. The task force consisted of experts from the ID, Muon, Liquid Argon and Tile systems in addition to experts from the Technical Coordination team and the Physics coordinator. The task force held many meetings and in general there were some very l...

  12. GAP-REACH

    Science.gov (United States)

    Lewis-Fernández, Roberto; Raggio, Greer A.; Gorritz, Magdaliz; Duan, Naihua; Marcus, Sue; Cabassa, Leopoldo J.; Humensky, Jennifer; Becker, Anne E.; Alarcón, Renato D.; Oquendo, María A.; Hansen, Helena; Like, Robert C.; Weiss, Mitchell; Desai, Prakash N.; Jacobsen, Frederick M.; Foulks, Edward F.; Primm, Annelle; Lu, Francis; Kopelowicz, Alex; Hinton, Ladson; Hinton, Devon E.

    2015-01-01

    Growing awareness of health and health care disparities highlights the importance of including information about race, ethnicity, and culture (REC) in health research. Reporting of REC factors in research publications, however, is notoriously imprecise and unsystematic. This article describes the development of a checklist to assess the comprehensiveness and the applicability of REC factor reporting in psychiatric research publications. The 16-itemGAP-REACH© checklist was developed through a rigorous process of expert consensus, empirical content analysis in a sample of publications (N = 1205), and interrater reliability (IRR) assessment (N = 30). The items assess each section in the conventional structure of a health research article. Data from the assessment may be considered on an item-by-item basis or as a total score ranging from 0% to 100%. The final checklist has excellent IRR (κ = 0.91). The GAP-REACH may be used by multiple research stakeholders to assess the scope of REC reporting in a research article. PMID:24080673

  13. Terminal Satisfiability in GSTE

    Directory of Open Access Journals (Sweden)

    Yongsheng Xu

    2014-01-01

    Full Text Available Generalized symbolic trajectory evaluation (GSTE is an extension of symbolic trajectory evaluation (STE and a method of model checking. GSTE specifications are given as assertion graphs. There are four efficient methods to verify whether a circuit model obeys an assertion graph in GSTE, Model Checking Strong Satisfiability (SMC, Model Checking Normal Satisfiability (NMC, Model Checking Fair Satisfiability (FMC, and Model Checking Terminal Satisfiability (TMC. SMC, NMC, and FMC have been proved and applied in industry, but TMC has not. This paper gives a six-tuple definition and presents a new algorithm for TMC. Based on these, we prove that our algorithm is sound and complete. It solves the SMC’s limitation (resulting in false negative without extending from finite specification to infinite specification. At last, a case of using TMC to verify a realistic hardware circuit round-robin arbiter is achieved. Avoiding verifying the undesired paths which are not related to the specifications, TMC makes it possible to reduce the computational complexity, and the experimental results suggest that the time cost by SMC is 3.14× with TMC in the case.

  14. Acetylene-Terminated Polyimide Siloxanes

    Science.gov (United States)

    St. Clair, Terry L.; Maudgal, Shubba

    1987-01-01

    Siloxane-containing addition polyimides yield toughened high-temperature adhesives and matrix resins. Addition polyimide made by reaction of aromatic tetracarboxylic acid dianhydride with aromatic diamine in presence of ethynyl-substituted aromatic monoamine. Acetylene-terminated siloxane imide cured by heating to yield acetylene-terminated polyimide siloxane.

  15. Selection of Air Terminal Device

    DEFF Research Database (Denmark)

    Nielsen, Peter V.

    This paper discusses the selection of the air terminal device for the experiments and numerical prediction in the International Energy Agency Annex 20 work: Air Flow Pattern within Buildings,......This paper discusses the selection of the air terminal device for the experiments and numerical prediction in the International Energy Agency Annex 20 work: Air Flow Pattern within Buildings,...

  16. The Politics of Achievement Gaps

    DEFF Research Database (Denmark)

    Valant, J.; Newark, D. A.

    2016-01-01

    on achievement gaps have received little attention from researchers, despite playing an important role in shaping policymakers’ behaviors. Drawing on randomized experiments with a nationally representative sample of adults, we explore the public’s beliefs about test score gaps and its support for gap......For decades, researchers have documented large differences in average test scores between minority and White students and between poor and wealthy students. These gaps are a focal point of reformers’ and policymakers’ efforts to address educational inequities. However, the U.S. public’s views......-closing initiatives. We find that Americans are more concerned about—and more supportive of proposals to close—wealth-based achievement gaps than Black-White or Hispanic-White gaps. Americans also explain the causes of wealth-based gaps more readily. © 2016 AERA....

  17. Minding the gap

    Directory of Open Access Journals (Sweden)

    Mia Carlberg

    2013-12-01

    Full Text Available The plan for the Round table session was to focus on organizational and social/cultural differences between librarians and faculty with the aim to increase our awareness of the differences when we try to find ways to cooperate within the academy or school. This may help us to sort things out, experience acceptance and take adequate actions, saving energy and perhaps be less frustrated.  The questions that the workshop addressed were: What is in the gap between librarians and faculty when dealing with information literacy? How can we fill the gap? Participants discussed this in detail with the aim of together finding ways to understand it better and make it possible to find ways to fill this gap. By defining it and thereby making it easier to work out a strategy for future action to improve the teaching of information literacy, including listing possible, impossible or nearly impossible ways. The springboard to the discussion was extracted from some projects that the workshop leader has been engaged in since 2009. The first example is a research circle where Uppsala University Library used action research to observe and understand the process when we had the opportunity to implement information literacy classes with progression in an undergraduate program. What worked well? What did not? Why? This work was described together with other examples from Uppsala University to an international panel working with quality issues. What did they think of our work? May this change the ways we are working? How? Another example is an ongoing joint project where librarians and faculty members are trying to define ways to increase the cooperation between the library and faculty and make this cooperation sustainable. Recent experience from this was brought to the discussion.   There are an overwhelming number of papers written in this field. A few papers have inspired these ideas. One article in particular: Christiansen, L., Stombler, M. & Thaxton, L. (2004. A

  18. Small Multiples with Gaps.

    Science.gov (United States)

    Meulemans, Wouter; Dykes, Jason; Slingsby, Aidan; Turkay, Cagatay; Wood, Jo

    2017-01-01

    Small multiples enable comparison by providing different views of a single data set in a dense and aligned manner. A common frame defines each view, which varies based upon values of a conditioning variable. An increasingly popular use of this technique is to project two-dimensional locations into a gridded space (e.g. grid maps), using the underlying distribution both as the conditioning variable and to determine the grid layout. Using whitespace in this layout has the potential to carry information, especially in a geographic context. Yet, the effects of doing so on the spatial properties of the original units are not understood. We explore the design space offered by such small multiples with gaps. We do so by constructing a comprehensive suite of metrics that capture properties of the layout used to arrange the small multiples for comparison (e.g. compactness and alignment) and the preservation of the original data (e.g. distance, topology and shape). We study these metrics in geographic data sets with varying properties and numbers of gaps. We use simulated annealing to optimize for each metric and measure the effects on the others. To explore these effects systematically, we take a new approach, developing a system to visualize this design space using a set of interactive matrices. We find that adding small amounts of whitespace to small multiple arrays improves some of the characteristics of 2D layouts, such as shape, distance and direction. This comes at the cost of other metrics, such as the retention of topology. Effects vary according to the input maps, with degree of variation in size of input regions found to be a factor. Optima exist for particular metrics in many cases, but at different amounts of whitespace for different maps. We suggest multiple metrics be used in optimized layouts, finding topology to be a primary factor in existing manually-crafted solutions, followed by a trade-off between shape and displacement. But the rich range of possible

  19. Bridging the gaps

    Directory of Open Access Journals (Sweden)

    Victoria Francis

    2004-10-01

    Full Text Available By the year 2020, the international eye care community hopes to have eliminated avoidable blindness as a public health problem. The global partnership, VISION 2020: The Right to Sight, has provided a focus for all concerned (from international policy makers to village level health workers, identified five priority eye conditions, and clarified the key components to achieve this purpose.1,2 However, as Daniel Etya’ale, co-ordinator for VISION 2020 in Africa points out, there is still a big gap between what needs to be done and what is being done and he estimates that currently hardly 20 per cent of the current needs in Africa are being met. On a more optimistic note, there has been a move towards closer and more functional partnerships between professional groups, governments, NGOs and industry.

  20. Unveiling the Gap

    DEFF Research Database (Denmark)

    Jensson, Pall; Rokkjær, Ole; Nørgaard, Bente

    needs, how universities decide what to teach, and how to bridge the gap. Do the university programs simply reflect the expertise of the faculty members? Is there need for increasing emphasis on continuing education? Is life-long education the answer, and has this been addressed by the CDIO community?......This paper describes a project in Europe called Industrial Engineering Standards in Europe (IESE). The project was collaboration between universities and organizations that offer Industrial Engineering (IE) education and/or continuing education in 6 European countries. The project was funded...... by the EU Leonardo da Vinci Partnership program. The project had two objectives. The first objective was to use the European Qualification Framework (EQF) as a benchmark against the National Qualification Framework (NQF) of the partner countries and the IE educations offered by the partner institutions...

  1. Bridging the Evaluation Gap

    Directory of Open Access Journals (Sweden)

    Paul Wouters

    2017-02-01

    Full Text Available Paul Wouters’ essay is concerned with bridging the gap between what we value in our academic work and how we are assessed in formal evaluation exercises. He reflects on the recent evaluation of his own center, and reminds us that it is productive to see evaluations not as the (obviously impossible attempt to produce a true representation of past work, but rather as the exploration and performance of “who one wants to be.” Reflecting on why STS should do more than just play along to survive in the indicator game, he suggests that our field should contribute to changing its very rules. In this endeavor, the attitude and sensibilities developed in our field may be more important than any specific theoretical concepts or methodologies.

  2. Glyceraldehyde-3-phosphate dehydrogenase gene diversity in eubacteria and eukaryotes: evidence for intra- and inter-kingdom gene transfer.

    Science.gov (United States)

    Figge, R M; Schubert, M; Brinkmann, H; Cerff, R

    1999-04-01

    Cyanobacteria contain up to three highly divergent glyceraldehyde-3-phosphate dehydrogenase (GAPDH) genes: gap1, gap2, and gap3. Genes gap1 and gap2 are closely related at the sequence level to the nuclear genes encoding cytosolic and chloroplast GAPDH of higher plants and have recently been shown to play distinct key roles in catabolic and anabolic carbon flow, respectively, of the unicellular cyanobacterium Synechocystis sp. PCC6803. In the present study, sequences of 10 GAPDH genes distributed across the cyanobacteria Prochloron didemni, Gloeobacter violaceus PCC7421, and Synechococcus PCC7942 and the alpha-proteobacterium Paracoccus denitrificans and the beta-proteobacterium Ralstonia solanacearum were determined. Prochloron didemni possesses homologs to the gap2 and gap3 genes from Anabaena, Gloeobacter harbors gap1 and gap2 homologs, and Synechococcus possesses gap1, gap2, and gap3. Paracoccus harbors two highly divergent gap genes that are related to gap3, and Ralstonia possesses a homolog of the gap1 gene. Phylogenetic analyses of these sequences in the context of other eubacterial and eukaryotic GAPDH genes reveal that divergence across eubacterial gap1, and gap2, and gap3 genes is greater than that between eubacterial gap1 and eukaroytic glycolytic GapC or between eubacterial gap2 and eukaryotic Calvin cycle GapAB. These data strongly support previous analyses which suggested that eukaryotes acquired their nuclear genes for GapC and GapAB via endosymbiotic gene transfer from the antecedents of mitochondria and chloroplasts, and extend the known range of sequence diversity of the antecedent eubacterial genes. Analyses of available GAPDH sequences from other eubacterial sources indicate that the glycosomal gap gene from trypanosomes (cytosolic in Euglena) and the gap gene from the spirochete Treponema pallidum are each other's closest relatives. This specific relationship can therefore not reflect organismal evolution but must be the result of an

  3. Quantitative modeling of a gene's expression from its intergenic sequence.

    Science.gov (United States)

    Samee, Md Abul Hassan; Sinha, Saurabh

    2014-03-01

    Modeling a gene's expression from its intergenic locus and trans-regulatory context is a fundamental goal in computational biology. Owing to the distributed nature of cis-regulatory information and the poorly understood mechanisms that integrate such information, gene locus modeling is a more challenging task than modeling individual enhancers. Here we report the first quantitative model of a gene's expression pattern as a function of its locus. We model the expression readout of a locus in two tiers: 1) combinatorial regulation by transcription factors bound to each enhancer is predicted by a thermodynamics-based model and 2) independent contributions from multiple enhancers are linearly combined to fit the gene expression pattern. The model does not require any prior knowledge about enhancers contributing toward a gene's expression. We demonstrate that the model captures the complex multi-domain expression patterns of anterior-posterior patterning genes in the early Drosophila embryo. Altogether, we model the expression patterns of 27 genes; these include several gap genes, pair-rule genes, and anterior, posterior, trunk, and terminal genes. We find that the model-selected enhancers for each gene overlap strongly with its experimentally characterized enhancers. Our findings also suggest the presence of sequence-segments in the locus that would contribute ectopic expression patterns and hence were "shut down" by the model. We applied our model to identify the transcription factors responsible for forming the stripe boundaries of the studied genes. The resulting network of regulatory interactions exhibits a high level of agreement with known regulatory influences on the target genes. Finally, we analyzed whether and why our assumption of enhancer independence was necessary for the genes we studied. We found a deterioration of expression when binding sites in one enhancer were allowed to influence the readout of another enhancer. Thus, interference between enhancer

  4. Ports and Terminals : Planning and Functional Design

    NARCIS (Netherlands)

    Groenveld, R.; Velsink, H.

    1993-01-01

    1. Maritime transport, means and commodities 3. Principles of integrated port planning 4. Planning and design of a port's water areas 5. Port terminals - introduction 6. Conventional general cargo terminals 7. Container terminals 8. Oil & liquid gas terminals 9. Dry bulk cargo terminals 10. Fishery

  5. Terminal Antennas in ACE2

    Directory of Open Access Journals (Sweden)

    M. Martinez-Vazquez

    2008-06-01

    Full Text Available The ACE Network of Excellence was a European Commission funded Network of Excellence, which lasted from 2004 to 2007. One of the activities performed by this Network was in the frame of terminal antennas. In this activity, three aspects were covered in three projects: Small antenna technologies, small terminal antenna technologies and benchmarking of small terminal antennas measurement facilities. The overall aim was to identify the newest trends in antenna design and measurement for personal communications devices, and suggest novel solutions and design methodologies for various applications. The results of this work are presented in this paper.

  6. The Adaptation Finance Gap Report

    DEFF Research Database (Denmark)

    UNEP’s Adaptation Gap Report series focuses on Finance, Technology and Knowledge gaps in climate change adaptation. It compliments the Emissions Gap Report series, and explores the implications of failing to close the emissions gap. The report builds on a 2014 assessment by the United Nations...... Environment Programme (UNEP), which laid out the concept of ‘adaptation gaps’ and outlined three such gaps: technology, finance and knowledge. The 2016 Adaptation Gap Report assesses the difference between the financial costs of adapting to climate change in developing countries and the amount of money...... actually available to meet these costs – a difference known as the “adaptation finance gap”. Like the 2014 report, the 2016 report focuses on developing countries, where adaptation capacity is often the lowest and needs the highest, and concentrates on the period up to 2050. The report identifies trends...

  7. Supersize me: Cronobacter sakazakii phage GAP32

    Energy Technology Data Exchange (ETDEWEB)

    Abbasifar, Reza; Griffiths, Mansel W. [Canadian Research Institute for Food Safety, University of Guelph, Guelph, ON, Canada N1G 2W1 (Canada); Sabour, Parviz M. [Agriculture and Agri-Food Canada, Guelph Food Research Centre, Guelph, ON, Canada N1G 5C9 (Canada); Ackermann, Hans-Wolfgang [Department of Microbiology-Infectiology and Immunology, Faculty of Medicine, Université Laval, Quebec, QC (Canada); Vandersteegen, Katrien; Lavigne, Rob [Laboratory of Gene Technology, Katholieke Universiteit Leuven, Leuven (Belgium); Noben, Jean-Paul [Biomedical Research Institute and Transnational University Limburg, School of Life Sciences, Hasselt University, Diepenbeek (Belgium); Alanis Villa, Argentina; Abbasifar, Arash [Canadian Research Institute for Food Safety, University of Guelph, Guelph, ON, Canada N1G 2W1 (Canada); Nash, John H.E. [Public Health Agency of Canada, Laboratory for Foodborne Zoonoses, Guelph, ON, Canada N1G 3W4 (Canada); Kropinski, Andrew M., E-mail: akropins@uoguelph.ca [Public Health Agency of Canada, Laboratory for Foodborne Zoonoses, Guelph, ON, Canada N1G 3W4 (Canada); Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada N1G 2W1 (Canada)

    2014-07-15

    Cronobacter sakazakii is a Gram-negative pathogen found in milk-based formulae that causes infant meningitis. Bacteriophages have been proposed to control bacterial pathogens; however, comprehensive knowledge about a phage is required to ensure its safety before clinical application. We have characterized C. sakazakii phage vB{sub C}saM{sub G}AP32 (GAP32), which possesses the second largest sequenced phage genome (358,663 bp). A total of 571 genes including 545 protein coding sequences and 26 tRNAs were identified, thus more genes than in the smallest bacterium, Mycoplasma genitalium G37. BLASTP and HHpred searches, together with proteomic analyses reveal that only 23.9% of the putative proteins have defined functions. Some of the unique features of this phage include: a chromosome condensation protein, two copies of the large subunit terminase, a predicted signal-arrest-release lysin; and an RpoD-like protein, which is possibly involved in the switch from immediate early to delayed early transcription. Its closest relatives are all extremely large myoviruses, namely coliphage PBECO4 and Klebsiella phage vB{sub K}leM-RaK2, with whom it shares approximately 44% homologous proteins. Since the homologs are not evenly distributed, we propose that these three phages belong to a new subfamily. - Highlights: • Cronobacter sakazakii phage vB{sub C}saM{sub G}AP32 has a genome of 358,663 bp. • It encodes 545 proteins which is more than Mycoplasma genitalium G37. • It is a member of the Myoviridae. • It is peripherally related to coliphage PBECO4 and Klebsiella phage vB{sub K}leM-RaK2. • GAP32 encodes a chromosome condensation protein.

  8. Regulation of expression of terminal oxidases in Paracoccus denitrificans.

    NARCIS (Netherlands)

    Otten, M.F.; Stork, D.M.; Reijnders, W.N.M.; Westerhoff, H.V.; van Spanning, R.J.M.

    2001-01-01

    In order to study the induction of terminal oxidases in Paracoccus denitrificans, their promoters were fused to the lacZ reporter gene and analysed in the wild-type strain, in an FnrP-negative mutant, in a cytochrome bc

  9. Understanding the Tax Gap1

    OpenAIRE

    Mazur, Mark J.; Plumley, Alan H.

    2007-01-01

    The Tax Gap is defined as the difference between the amount of tax imposed by the Tax Code and the amount that is reported and paid with timely filed returns. For the federal government, the gross tax gap is estimated at $345 billion for Tax Year 2001 (after the collection of late and enforced payments, the net tax gap is estimated at $290 billion for Tax Year 2001). This paper explains the concept of the tax gap, discusses how it is estimated, and points out some limitations with the estimates.

  10. Erythropoietin prevents the effect of chronic restraint stress on the number of hippocampal CA3c dendritic terminals-relation to expression of genes involved in synaptic plasticity, angiogenesis, inflammation, and oxidative stress in male rats

    DEFF Research Database (Denmark)

    Aalling, Nadia; Hageman, Ida; Miskowiak, Kamilla

    2018-01-01

    Stress-induced allostatic load affects a variety of biological processes including synaptic plasticity, angiogenesis, oxidative stress, and inflammation in the brain, especially in the hippocampus. Erythropoietin (EPO) is a pleiotropic cytokine that has shown promising neuroprotective effects....... Recombinant human EPO is currently highlighted as a new candidate treatment for cognitive impairment in neuropsychiatric disorders. Because EPO enhances synaptic plasticity, attenuates oxidative stress, and inhibits generation of proinflammatory cytokines, EPO may be able to modulate the effects of stress...... in synaptic plasticity, angiogenesis, oxidative stress, and inflammation; and (iii) remodeling of the dendritic structure of the CA3c area of the hippocampus in male rats. As expected, chronic restraint stress lowered the number of CA3c apical dendritic terminals, and EPO treatment reversed this effect...

  11. Automated inspection of gaps on the free-form shape parts by laser scanning technologies

    Science.gov (United States)

    Zhou, Sen; Xu, Jian; Tao, Lei; An, Lu; Yu, Yan

    2018-01-01

    In industrial manufacturing processes, the dimensional inspection of the gaps on the free-form shape parts is critical and challenging, and is directly associated with subsequent assembly and terminal product quality. In this paper, a fast measuring method for automated gap inspection based on laser scanning technologies is presented. The proposed measuring method consists of three steps: firstly, the relative position is determined according to the geometric feature of measuring gap, which considers constraints existing in a laser scanning operation. Secondly, in order to acquire a complete gap profile, a fast and effective scanning path is designed. Finally, the range dimension of the gaps on the free-form shape parts including width, depth and flush, correspondingly, is described in a virtual environment. In the future, an appliance machine based on the proposed method will be developed for the on-line dimensional inspection of gaps on the automobile or aerospace production line.

  12. 75 FR 61165 - Credit Watch Termination Initiative Termination of Direct Endorsement (DE) Approval

    Science.gov (United States)

    2010-10-04

    ... URBAN DEVELOPMENT Credit Watch Termination Initiative Termination of Direct Endorsement (DE) Approval.... SUMMARY: This notice advises of the cause and effect of termination of Direct Endorsement (DE) Approval... advised the extended procedures for ] terminating Underwriting Authority of Direct Endorsement mortgagees...

  13. 76 FR 38407 - Credit Watch Termination Initiative; Termination of Direct Endorsement (DE) Approval

    Science.gov (United States)

    2011-06-30

    ... URBAN DEVELOPMENT Credit Watch Termination Initiative; Termination of Direct Endorsement (DE) Approval.... SUMMARY: This notice advises of the cause and effect of termination of Direct Endorsement (DE) Approval... advised the extended procedures for ] terminating Underwriting Authority of Direct Endorsement mortgagees...

  14. 77 FR 5262 - Credit Watch Termination Initiative Termination of Direct Endorsement (DE) Approval

    Science.gov (United States)

    2012-02-02

    ... URBAN DEVELOPMENT Credit Watch Termination Initiative Termination of Direct Endorsement (DE) Approval.... SUMMARY: This notice advises of the cause and effect of termination of Direct Endorsement (DE) Approval... the extended procedures for terminating Underwriting Authority of Direct Endorsement (DE) mortgagees...

  15. 76 FR 53148 - Credit Watch Termination Initiative; Termination of Direct Endorsement (DE) Approval

    Science.gov (United States)

    2011-08-25

    ... URBAN DEVELOPMENT Credit Watch Termination Initiative; Termination of Direct Endorsement (DE) Approval.... SUMMARY: This notice advises of the cause and effect of termination of Direct Endorsement (DE) Approval... advised the extended procedures for terminating Underwriting Authority of Direct Endorsement mortgagees...

  16. Mechanisms of DNA replication termination.

    Science.gov (United States)

    Dewar, James M; Walter, Johannes C

    2017-08-01

    Genome duplication is carried out by pairs of replication forks that assemble at origins of replication and then move in opposite directions. DNA replication ends when converging replication forks meet. During this process, which is known as replication termination, DNA synthesis is completed, the replication machinery is disassembled and daughter molecules are resolved. In this Review, we outline the steps that are likely to be common to replication termination in most organisms, namely, fork convergence, synthesis completion, replisome disassembly and decatenation. We briefly review the mechanism of termination in the bacterium Escherichia coli and in simian virus 40 (SV40) and also focus on recent advances in eukaryotic replication termination. In particular, we discuss the recently discovered E3 ubiquitin ligases that control replisome disassembly in yeast and higher eukaryotes, and how their activity is regulated to avoid genome instability.

  17. Measuring the Gap

    Directory of Open Access Journals (Sweden)

    Xinshu She MD, MPH

    2016-02-01

    Full Text Available China is a large country where rapid development is accompanied by growing inequalities. How economic inequalities translate to health inequalities is unknown. Baseline health assessment is lacking among rural Chinese children. We aimed at assessing baseline student health of rural Chinese children and comparing them with those of urban children of similar ages. A cross-sectional study was conducted using the 2003 Global School-Based Student Health Survey among 100 students Grade 4 to 6 from rural Guizhou, China. Results were summarized and compared with public data from urban Beijing using multivariate logistic regression models. Rural children are more likely to not wash their hands before a meal (odds ratio [OR] = 5.71, P .05. Rural parents are more likely to not know their children’s whereabouts (OR = 1.81, P < .05. Rural children are more than 4 times likely to have serious injuries (OR = 4.64, P < .01 and to be bullied (OR = 4.01, P < .01. In conclusion, school-age rural Chinese children exhibit more health risk behaviors and fewer protective factors at baseline compared to their urban counterparts. Any intervention aimed at improving child health should take this distributive gap into consideration.

  18. Flight Termination Systems Commonality Standard

    Science.gov (United States)

    2014-09-01

    EFI exploding foil initiator EFTR enhanced flight termination receiver EFTS enhanced flight termination system ELS equivalent level of safety EMC ...account shielding effectiveness of the vehicle. 3.3.13 Other Environments An FTS component shall satisfy all of its performance requirements and not...solid-state power transfer switches, and arm-and-enable circuits. 3.9.6 Circuit Isolation, Shielding , and Grounding The circuitry of an FTS

  19. Innovation gap, performance gap and policy gap in the service economies

    OpenAIRE

    Faridah Djellal; Faïz Gallouj

    2009-01-01

    International audience; This work is devoted to an analysis of the innovation-performance relationship in contemporary developed economies. It reveals a double « gap » relating to innovation and performance. The « innovation gap » reflects the difference between the reality of innovation produced in an economy and what traditional innovation indicators (R&D, patents) capture. As for the « performance gap », this measures the difference between the reality of performance in an economy and the ...

  20. Four Terminal Gallium Nitride MOSFETs

    Science.gov (United States)

    Veety, Matthew Thomas

    All reported gallium nitride (GaN) transistors to date have been three-terminal devices with source, drain, and gate electrodes. In the case of GaN MOSFETs, this leaves the bulk of the device at a floating potential which can impact device threshold voltage. In more traditional silicon-based MOSFET fabrication a bulk contact can be made on the back side of the silicon wafer. For GaN grown on sapphire substrates, however, this is not possible and an alternate, front-side bulk contact must be investigated. GaN is a III-V, wide band gap semiconductor that as promising material parameters for use in high frequency and high power applications. Possible applications are in the 1 to 10 GHz frequency band and power inverters for next generation grid solid state transformers and inverters. GaN has seen significant academic and commercial research for use in Heterojunction Field Effect Transistors (HFETs). These devices however are depletion-mode, meaning the device is considered "on" at zero gate bias. A MOSFET structure allows for enhancement mode operation, which is normally off. This mode is preferrable in high power applications as the device has lower off-state power consumption and is easier to implement in circuits. Proper surface passivation of seminconductor surface interface states is an important processing step for any device. Preliminary research on surface treatments using GaN wet etches and depletion-mode GaN devices utilizing this process are discussed. Devices pretreated with potassium pursulfate prior to gate dielectric deposition show significant device improvements. This process can be applied to any current GaN FET. Enhancement-mode GaN MOSFETs were fabricated on magnesium doped p-type Wurtzite gallium nitride grown by Metal Organic Chemical Vapor Deposition (MOCVD) on c-plane sapphire substrates. Devices utilized ion implant source and drain which was activated under NH3 overpressure in MOCVD. Also, devices were fabricated with a SiO2 gate dielectric

  1. Growth arrest- and DNA-damage-inducible 45beta gene inhibits c-Jun N-terminal kinase and extracellular signal-regulated kinase and decreases IL-1beta-induced apoptosis in insulin-producing INS-1E cells

    DEFF Research Database (Denmark)

    Larsen, Claus Morten; Døssing, M G; Papa, S

    2006-01-01

    -activated protein kinase (MAPK) family. Inhibition of JNK prevents IL-1beta-mediated beta cell destruction. In mouse embryo fibroblasts and 3DO T cells, overexpression of the gene encoding growth arrest and DNA-damage-inducible 45beta (Gadd45b) downregulates pro-apoptotic JNK signalling. The aim of this study...

  2. PhoneGap for enterprise

    CERN Document Server

    Shotts, Kerri

    2014-01-01

    This book is intended for developers who wish to use PhoneGap to develop useful, rich, secure mobile applications for their enterprise environment. The book assumes you have working knowledge of PhoneGap, HTML5, CSS3, and JavaScript, and a reasonable understanding of networking and n-tier architectures.

  3. Microstrip microwave band gap structures

    Indian Academy of Sciences (India)

    Microwave band gap structures exhibit certain stop band characteristics based on the periodicity, impedance contrast and effective refractive index contrast. These structures though formed in one-, two- and three-dimensional periodicity, are huge in size. In this paper, microstrip-based microwave band gap structures are ...

  4. Components of the Belief Gap

    Directory of Open Access Journals (Sweden)

    Cecilie Gaziano

    2014-01-01

    Full Text Available Knowledge gap research focuses on education as an indicator of socioeconomic status (SES. Belief gap research centers on ideology as potentially more powerful than education in comparing sociopolitical groups with scientifically established knowledge and groups with opposing beliefs accepted on faith. This study examined the relationship between education and ideology to understand belief gaps better. The study used 2008 American National Election Study (ANES data to compare conservatives, moderates, and liberals by education on religiosity, child rearing values, opinionation, need for cognition, orientation toward politics, and mass media access and use. Although liberals tended to be more educated than conservatives overall, better-educated conservatives had the highest household incomes and were a much larger group. No known knowledge gap studies have reported results on one group characterized by high education and an opposing group distinguished by a different indicator of SES. Reformulations of the belief gap hypothesis are offered.

  5. c-Jun N-terminal kinase 2 prevents luminal cell commitment in normal mammary glands and tumors by inhibiting p53/Notch1 and breast cancer gene 1 expression

    Science.gov (United States)

    Pfefferle, Adam D.; Perou, Charles M.; Van Den Berg, Carla Lynn

    2015-01-01

    Breast cancer is a heterogeneous disease with several subtypes carrying unique prognoses. Patients with differentiated luminal tumors experience better outcomes, while effective treatments are unavailable for poorly differentiated tumors, including the basal-like subtype. Mechanisms governing mammary tumor subtype generation could prove critical to developing better treatments. C-Jun N-terminal kinase 2 (JNK2) is important in mammary tumorigenesis and tumor progression. Using a variety of mouse models, human breast cancer cell lines and tumor expression data, studies herein support that JNK2 inhibits cell differentiation in normal and cancer-derived mammary cells. JNK2 prevents precocious pubertal mammary development and inhibits Notch-dependent expansion of luminal cell populations. Likewise, JNK2 suppresses luminal populations in a p53-competent Polyoma Middle T-antigen tumor model where jnk2 knockout causes p53-dependent upregulation of Notch1 transcription. In a p53 knockout model, JNK2 restricts luminal populations independently of Notch1, by suppressing Brca1 expression and promoting epithelial to mesenchymal transition. JNK2 also inhibits estrogen receptor (ER) expression and confers resistance to fulvestrant, an ER inhibitor, while stimulating tumor progression. These data suggest that therapies inhibiting JNK2 in breast cancer may promote tumor differentiation, improve endocrine therapy response, and inhibit metastasis. PMID:25970777

  6. Comparative analysis of the pteridophyte Adiantum MFT ortholog reveals the specificity of combined FT/MFT C and N terminal interaction with FD for the regulation of the downstream gene AP1.

    Science.gov (United States)

    Hou, Cheng-Jing; Yang, Chang-Hsien

    2016-07-01

    To study the evolution of phosphatidylethanolamine-binding protein (PEBP) gene families in non-flowering plants, we performed a functional analysis of the PEBP gene AcMFT of the MFT clade in the pteridophyte Adiantum capillus-veneris. The expression of AcMFT was regulated by photoperiod similar to that for FT under both long day and short day conditions. Ectopic expression of AcMFT in Arabidopsis promotes the floral transition and partially complements the late flowering defect in transgenic Arabidopsis ft-1 mutants, suggesting that AcMFT functions similarly to FT in flowering plants. Interestingly, a similar partial compensation of the ft-1 late flowering phenotype was observed in Arabidopsis ectopically expressing only exon 4 of the C terminus of AcMFT and FT. This result indicated that the fourth exon of AcMFT and FT plays a similar and important role in promoting flowering. Further analysis indicated that exons 1-3 in the N terminus specifically enhanced the function of FT exon 4 in controlling flowering in Arabidopsis. Protein pull-down assays indicated that Arabidopsis FD proteins interact with full-length FT and AcMFT, as well as peptides encoded by 1-3 exon fragments or the 4th exon alone. Furthermore, similar FRET efficiencies for FT-FD and AcMFT-FD heterodimer in nucleus were observed. These results indicated that FD could form the similar complex with FT and AcMFT. Further analysis indicated that the expression of AP1, a gene downstream of FT, was up-regulated more strongly by FT than AcMFT in transgenic Arabidopsis. Our results revealed that AcMFT from a non-flowering plant could interact with FD to regulate the floral transition and that this function was reduced due to the weakened ability of AcMFT-FD to activate the downstream gene AP1.

  7. Evolution of the terminal regions of the Streptomyces linear chromosome.

    Science.gov (United States)

    Choulet, Frédéric; Aigle, Bertrand; Gallois, Alexandre; Mangenot, Sophie; Gerbaud, Claude; Truong, Chantal; Francou, François-Xavier; Fourrier, Céline; Guérineau, Michel; Decaris, Bernard; Barbe, Valérie; Pernodet, Jean-Luc; Leblond, Pierre

    2006-12-01

    Comparative analysis of the Streptomyces chromosome sequences, between Streptomyces coelicolor, Streptomyces avermitilis, and Streptomyces ambofaciens ATCC23877 (whose partial sequence is released in this study), revealed a highly compartmentalized genetic organization of their genome. Indeed, despite the presence of specific genomic islands, the central part of the chromosome appears highly syntenic. In contrast, the chromosome of each species exhibits large species-specific terminal regions (from 753 to 1,393 kb), even when considering closely related species (S. ambofaciens and S. coelicolor). Interestingly, the size of the central conserved region between species decreases as the phylogenetic distance between them increases, whereas the specific terminal fraction reciprocally increases in size. Between highly syntenic central regions and species-specific chromosomal parts, there is a notable degeneration of synteny due to frequent insertions/deletions. This reveals a massive and constant genomic flux (from lateral gene transfer and DNA rearrangements) affecting the terminal contingency regions. We speculate that a gradient of recombination rate (i.e., insertion/deletion events) toward the extremities is the force driving the exclusion of essential genes from the terminal regions (i.e., chromosome compartmentalization) and generating a fast gene turnover for strong adaptation capabilities.

  8. A novel tandem reporter quantifies RNA polymerase II termination in mammalian cells.

    Directory of Open Access Journals (Sweden)

    Ayan Banerjee

    2009-07-01

    Full Text Available Making the correct choice between transcription elongation and transcription termination is essential to the function of RNA polymerase II, and fundamental to gene expression. This choice can be influenced by factors modifying the transcription complex, factors modifying chromatin, or signals mediated by the template or transcript. To aid in the study of transcription elongation and termination we have developed a transcription elongation reporter system that consists of tandem luciferase reporters flanking a test sequence of interest. The ratio of expression from the reporters provides a measure of the relative rates of successful elongation through the intervening sequence.Size matched fragments containing the polyadenylation signal of the human beta-actin gene (ACTB and the human beta-globin gene (HBB were evaluated for transcription termination using this new ratiometric tandem reporter assay. Constructs bearing just 200 base pairs on either side of the consensus poly(A addition site terminated 98% and 86% of transcription for ACTB and HBB sequences, respectively. The nearly 10-fold difference in read-through transcription between the two short poly(A regions was eclipsed when additional downstream poly(A sequence was included for each gene. Both poly(A regions proved very effective at termination when 1100 base pairs were included, stopping 99.6% of transcription. To determine if part of the increased termination was simply due to the increased template length, we inserted several kilobases of heterologous coding sequence downstream of each poly(A region test fragment. Unexpectedly, the additional length reduced the effectiveness of termination of HBB sequences 2-fold and of ACTB sequences 3- to 5-fold.The tandem construct provides a sensitive measure of transcription termination in human cells. Decreased Xrn2 or Senataxin levels produced only a modest release from termination. Our data support overlap in allosteric and torpedo mechanisms

  9. Impact of combined hospice care on terminal cancer patients.

    Science.gov (United States)

    Loke, Song-Seng; Rau, Kung-Ming; Huang, Chih-Fang

    2011-06-01

    Many patients with advanced cancer will develop physical and psychological symptoms related to their disease. These symptoms are infrequently treated by conventional care. Palliative care programs have been developed to fill this gap in care. However, there are limited beds in hospice units. To allow more terminal cancer patients to receive care from a hospice team, a combined hospice care system was recently developed in Taiwan. This study is a report of our experiences with this system. From January to December 2009, terminal cancer patients who accepted consultation from a hospice team for combined hospice care were enrolled in the study. Demographic data, clinical symptoms, referring department, type of cancer, and outcome were analyzed. A total of 354 terminal cancer patients in acute wards were referred to a hospice consulting team. The mean patient age was 61 years, and the proportion of males was 63.28%. After combined hospice care, there was a significant improvement in the sign rate of do-not-resuscitate (DNR) orders from 41.53% to 71.47% (p care also enabled 64.21% of terminal cancer patients who were not transferred to hospice ward to receive combined care by a hospice consulting team while in acute wards, thus increasing the hospice utilization of terminal cancer patients. The major symptoms presented by the patients were pain (58%), dyspnea (52%), constipation (45%), and fatigue (23%). Through the hospice consulting system, hospice combined care has a positive effect on the utilization of hospice care, rate of DNR signing and quality of end-of-life care for terminal cancer patients.

  10. The EIIGlc protein is involved in glucose-mediated activation of Escherichia coli gapA and gapB-pgk transcription.

    Science.gov (United States)

    Charpentier, B; Bardey, V; Robas, N; Branlant, C

    1998-12-01

    The Escherichia coli gapB gene codes for a protein that is very similar to bacterial glyceraldehyde-3-phosphate dehydrogenases (GAPDH). In most bacteria, the gene for GAPDH is located upstream of the pgk gene encoding 3-phosphoglycerate kinase (PGK). This is the case for gapB. However, this gene is poorly expressed and encodes a protein with an erythrose 4-phosphate dehydrogenase activity (E4PDH). The active GAPDH is encoded by the gapA gene. Since we found that the nucleotide region upstream of the gapB open reading frame is responsible for part of the PGK production, we analyzed gapB promoter activity in vivo by direct measurement of the mRNA levels by reverse transcription. We showed the presence of a unique transcription promoter, gapB P0, with a cyclic AMP (cAMP) receptor protein (CRP)-cAMP binding site centered 70.5 bp upstream of the start site. Interestingly, the gapB P0 promoter activity was strongly enhanced when glucose was used as the carbon source. In these conditions, deletion of the CRP-cAMP binding site had little effect on promoter gapB P0 activity. In contrast, abolition of CRP production or of cAMP biosynthesis (crp or cya mutant strains) strongly reduced promoter gapB P0 activity. This suggests that in the presence of glucose, the CRP-cAMP complex has an indirect effect on promoter gapB P0 activity. We also showed that glucose stimulation of gapB P0 promoter activity depends on the expression of enzyme IIGlc (EIIGlc), encoded by the ptsG gene, and that the gapA P1 promoter is also activated by glucose via the EIIGlc protein. A similar glucose-mediated activation, dependent on the EIIGlc protein, was described by others for the pts operon. Altogether, this shows that when glucose is present in the growth medium expression of the E. coli genes required for its uptake (pts) and its metabolism (gapA and gapB-pgk) are coordinately activated by a mechanism dependent upon the EIIGlc protein.

  11. Electronic structures of the F-terminated AlN nanoribbons

    Indian Academy of Sciences (India)

    Using the first-principles calculations, electronic properties for the F-terminated AlN nanoribbons with both zigzag and armchair edges are studied. The results show that both the zigzag and armchair AlN nanoribbons are semiconducting and nonmagnetic, and the indirect band gap of the zigzag AlN nanoribbons and the ...

  12. Chromatin condensation during terminal erythropoiesis.

    Science.gov (United States)

    Zhao, Baobing; Yang, Jing; Ji, Peng

    2016-09-02

    Mammalian terminal erythropoiesis involves gradual but dramatic chromatin condensation steps that are essential for cell differentiation. Chromatin and nuclear condensation is followed by a unique enucleation process, which is believed to liberate more spaces for hemoglobin enrichment and enable the generation of a physically flexible mature red blood cell. Although these processes have been known for decades, the mechanisms are still unclear. Our recent study reveals an unexpected nuclear opening formation during mouse terminal erythropoiesis that requires caspase-3 activity. Major histones, except H2AZ, are partially released from the opening, which is important for chromatin condensation. Block of the nuclear opening through caspase inhibitor or knockdown of caspase-3 inhibits chromatin condensation and enucleation. We also demonstrate that nuclear opening and histone release are cell cycle regulated. These studies reveal a novel mechanism for chromatin condensation in mammalia terminal erythropoiesis.

  13. SIRKULASI TERMINAL PENUMPANG KAPAL LAUT

    Directory of Open Access Journals (Sweden)

    Etsa Purnama Sari

    2014-01-01

    Full Text Available Wilayah Indonesia yang terdiri dari pulau dan perairan menjadikan angkutan laut menjadi salah satu sarana transportasi yang cukup efektif di negara ini. Daya angkut yang besar dan beragam serta biaya yang lebih murah dengan jarak jangkauan yang luas, membuat sarana ini banyak diminati oleh masyarakat sekaligus juga merupakan pendukung utama perkembangan kehidupan sosial budaya dan roda perekonomian. Untuk mendukung proses transportasi laut ini perlu sarana berupa pelabuhan. Pelabuhan dalam melakukan pelayanan terhadap kapal memiliki beberapa fasilitas pokok dan penunjang yang wajib dimiliki. Salah satunya adalah terminal penumpang kapal laut dengan berbagai kegiatan di dalamnya untuk kedatangan maupun keberangkatan. Masalah ketidaknyamanan dalam berkegiatan, jauhnya akses sirkulasi antara satu kegiatan dengan kegiatan kegiatan embarkasi dan debarkasi yang tidak teratur, pembagian jalur sirkulasi penumpang dan pengantar penumpang yang tidak jelas seringkali muncul akibat sirkulasi yang tidak direncanakan dengan baik pada terminal penumpang kapal laut. Bahkan tidak jarang dapat menimbulkan adanya calo tiket hingga adanya penumpang tanpa tiket yang dapat masuk ke dalam kapal hingga kapal berlayar. Perencanaan sebuah sirkulasi yang tepat pada terminal penumpang kapal laut memerlukan kajian terhadap unsur-unsur sirkulasi seperti pencapaian, pola sirkulasi, jalur sirkulasi, serta bentuk ruang sirkulasi. Kajian unsur-unsur ini selanjutnya diselidiki melalui penelusuran masalah dengan analisis deskriptif melalui penggambaran objek penelitian yang terdapat pada Terminal Penumpang Pelabuhan International Yokohama, Terminal Penumpang Pelabuhan Kobe dan Terminal Penumpang Pelabuhan Osanbashi Hall   As one of the largest archipelago country, sea transportation acts as one of the most effective means of transportation in Indonesia. Large and diverse carrying capacity, lower cost with wide range of distances, are factors which making sea

  14. Terminal Disease: A Biolaw Management

    Directory of Open Access Journals (Sweden)

    Francisco Rivas García

    2017-10-01

    Full Text Available There are numerous and varied pathologies that can lead to a state of terminal illness, provoking numerous bioethical dilemmas that are inherent and specific to each circumstance. The objective of the present work has been to provide a current and useful analysis that can help to understand the main bioethical problems, from the perspective of biolaw that must be solved in the inevitable path towards the end of life that any terminal illness implies. The methodology used included a study of bibliographic documentation in the main databases of interest in bioethics. It can be concluded that the biolaw is a very useful tool that helps health care professionals and relatives when it comes to the analysis and decision making regarding a terminal illness. Independently of medical practice based on protocols and scientific knowledge, it is necessary to ensure that not everything that can legally be carried out is accepted in the field of biolaw.

  15. Electronic structure of oxygen-terminated zigzag graphene nanoribbons: A hybrid density functional theory study

    Science.gov (United States)

    Ramasubramaniam, Ashwin

    2010-06-01

    The size-dependent electronic structure of oxygen-terminated zigzag graphene nanoribbons is investigated using standard density functional theory (DFT) with an exchange-correlation functional of the generalized gradient approximation form as well as hybrid DFT calculations with two different exchange-correlation functionals. Hybrid DFT calculations, which typically provide more accurate band gaps than standard DFT, are found to predict semiconducting behavior in oxygen-terminated zigzag graphene nanoribbons; this is in distinct contrast to standard DFT with (semi)local exchange-correlation functionals, which have been widely employed in previous studies and shown to predict metallic behavior. (Semi)local exchange-correlation functionals employed in standard DFT calculations cause unphysical delocalization of lone pairs from the oxygen atoms due to self-interaction errors and lead to metallic behavior. Hybrid DFT calculations do not suffer from this spurious effect and produce a clear size-dependent band gap. Appreciable fundamental band gaps (˜1eV) are found for the smallest ribbons (two zigzag rows); the band gap decreases rapidly with increasing ribbon width, resulting eventually in a zero band-gap semiconductor at about 4-5 zigzag rows. This finding could have useful implications for molecular electronics, in particular, since oxygen-terminated zigzag graphene nanoribbons are thermodynamically stable unlike their hydrogenated counterparts. More generally, through a concrete example, this study suggests caution when employing (semi)local functionals in DFT studies of functionalized graphene/graphene derivatives when the functional groups contain electron lone pairs.

  16. Gap Surface Plasmon Waveguide Analysis

    DEFF Research Database (Denmark)

    Nielsen, Michael Grøndahl; Bozhevolnyi, Sergey I.

    2014-01-01

    Plasmonic waveguides supporting gap surface plasmons (GSPs) localized in a dielectric spacer between metal films are investigated numerically and the waveguiding properties at telecommunication wavelengths are presented. Especially, we emphasize that the mode confinement can advantageously be con...

  17. Closing the Cybersecurity Skills Gap

    Directory of Open Access Journals (Sweden)

    Rebecca Vogel

    2016-05-01

    Full Text Available The current consensus is that there is a worldwide gap in skills needed for a competent cybersecurity workforce. This skills gap has implications for the national security sector, both public and private. Although the view is that this will take a concerted effort to rectify, it presents an opportunity for IT professionals, university students, and aspirants to take-up jobs in national security national intelligence as well military and law enforcement intelligence. This paper examines context of the issue, the nature of the cybersecurity skills gap, and some key responses by governments to address the problem. The paper also examines the emerging employment trends, some of the employment challenges, and what these might mean for practice. The paper argues that the imperative is to close the cyber skills gap by taking advantage of the window of opportunity, allowing individuals interested in moving into the cybersecurity field to do so via education and training.

  18. Sistem Pengelolaan Terminal Mangkang Kota Semarang

    OpenAIRE

    Sushernawan, Prasetya; Sulistyowati; Fitriyah

    2014-01-01

    This study, entitled "SYSTEM MANAGEMENT TERMINAL CITY MangkangSemarang". Terminal Mangkang a master terminal type A that is in the province of CentralJava is managed by Dishubkominfo. Terminal is a facility for public service units, as publicfacilities, the terminal should be able to provide services to the community as well as possible.So that they can be expected to contribute the maximum to PAD (the original income) withoutcompromising service to the community.Formulation of the problem in...

  19. Examining the gender wealth gap

    OpenAIRE

    Sierminska, Eva M.; Frick, Joachim R.; Markus M. Grabka

    2010-01-01

    Economic research on the determinants of gender differences in economic outcomes particularly in income and consumption is well established. Extending these investigations to other outcomes such as wealth up till now has been limited due to lack of individual-level data. Using the German Socio-Economic Panel (SOEP) we find a significant ‘raw’ gender wealth gap of 50,000€ for married partners. Decomposition analyses reveal that the gap is largely driven by differences in characteristics betwee...

  20. Protected P-Element Termini Suggest a Role for Inverted-Repeat-Binding Protein in Transposase-Induced Gap Repair in Drosophila Melanogaster

    Science.gov (United States)

    Staveley, B. E.; Heslip, T. R.; Hodgetts, R. B.; Bell, J. B.

    1995-01-01

    P-element transposition is thought to occur by a cut-and-paste mechanism that generates a double-strand break at the donor site, the repair of which can lead to internally deleted elements. We have generated a series of both phenotypically stronger and weaker allelic derivatives of vg(21), a vestigial mutant caused by a P-element insertion in the 5' region of the gene. Virtually all of the new alleles arose by internal deletion of the parental element in vg(21), and we have characterized a number of these internally deleted P elements. Depending upon the selection scheme used, we see a very different spectrum of amount and source of P-element sequences in the resultant derivatives. Strikingly, most of the breakpoints occur within the inverted-repeats such that the last 15-17 bp of the termini are retained. This sequence is known to bind the inverted-repeat-binding protein (IRBP). We propose that the IRBP may act to preserve the P-element ends when transposition produces a double-strand gap. This allows the terminus to serve as a template upon which DNA synthesis can act to repair the gap. Filler sequences found at the breakpoints of the internally deleted P elements resemble short stretches, often in tandem arrays, of these terminal sequences. The structure of the filler sequences suggests replication slippage may occur during the process of gap repair. PMID:7768441

  1. Getting a Suitable Terminal Cost and Maximizing the Terminal Region for MPC

    Directory of Open Access Journals (Sweden)

    Wang Ya-feng

    2010-01-01

    Full Text Available The model predictive control (MPC subject to control and state constraint is studied. Given a terminal cost, a terminal region is obtained through iterative estimation by using support vector machine (SVM. It is proved that the obtained terminal region is the largest terminal region when the terminal cost is given. The relationships between terminal cost and terminal region and between terminal cost and total cost are discussed, respectively. Based on these relationships, a simple method to get a suitable terminal cost is proposed and it can be adjusted according to our need. Finally, some experiment results are presented.

  2. New offshore terminal for Ecuador

    Energy Technology Data Exchange (ETDEWEB)

    1979-04-15

    W. Halcrow and Partners will design and supervise construction of the second phase of Corporacion Estatal Petrolera Ecuatoriana's offshore tanker terminal for the export of refined products from its 65,000 bbl/day Esmeraldas refinery, which will be expanded to 130,000 bbl/day. Ewbank and Partners Ltd. will handle mechanical and electrical engineering of the terminal. Halcrow also designed and built the first stage of the terminal, which comprised a four-hose seabed manifold 4 km offshore in water depths of 16 m and which became operational in Nov. 1977 with capacity to handle tankers up to 20,000 dwt and with pipeline connection to the Esmeradas refinery. The seabed manifold will be replaced by a two-berth sea island terminal to handle tankers up to 50,000 dwt; a contract for this has been signed. Future plans call for a two-berth central loading platform, separate berthing and mooring dolphins, an accommodation platform, and auxiliary services. The main structure will be a steel-piled jacket design interconnected by steel access bridges. The additional works should be completed by the end of 1981.

  3. The impact of 'terminator' technology

    NARCIS (Netherlands)

    Visser, B.; Meer, van der I.J.M.; Louwaars, N.; Beekwilder, J.; Eaton, D.

    2001-01-01

    Genetic use-restriction technologies enable the developers of transgenic plants or animals to protect their variety or breed from unauthorized use in a biological way. The use of 'terminator technology' can have different impacts on farmers and breeders. If the technology is effective, it impacts on

  4. What Determines Joint Venture Termination?

    DEFF Research Database (Denmark)

    Nielsen, Bo Bernhard

    2012-01-01

    Joint venture (JV) research continues to flourish as researchers seek to advance our understanding of why so many JVs fail. Cui and Kumar (this issue) take a contingency approach to explain how and why business relatedness may provide new insights as to what determines JV termination...

  5. Combining norms to prove termination

    DEFF Research Database (Denmark)

    Genaim, S.; Codish, M.; Gallagher, John Patrick

    2002-01-01

    Automatic termination analysers typically measure the size of terms applying norms which are mappings from terms to the natural numbers. This paper illustrates howt o enable the use of size functions defined as tuples of these simpler norm functions. This approach enables us to simplify the problem...

  6. 26 CFR 1.411(d)-2 - Termination or partial termination; discontinuance of contributions.

    Science.gov (United States)

    2010-04-01

    ... 26 Internal Revenue 5 2010-04-01 2010-04-01 false Termination or partial termination... Bonus Plans, Etc. § 1.411(d)-2 Termination or partial termination; discontinuance of contributions. (a... such plan is not a qualified trust) unless the plan provides that— (i) Upon the termination or partial...

  7. Terminal decline in motor function.

    Science.gov (United States)

    Wilson, Robert S; Segawa, Eisuke; Buchman, Aron S; Boyle, Patricia A; Hizel, Loren P; Bennett, David A

    2012-12-01

    The study aim was to test the hypothesis that motor function undergoes accelerated decline proximate to death. As part of a longitudinal clinical-pathologic study, 124 older Roman Catholic nuns, priests, and monks completed at least 7 annual clinical evaluations, died, and underwent brain autopsy and uniform neuropathologic examination. Each evaluation included administration of 11 motor tests and 19 cognitive tests from which global measures of motor and cognitive function were derived. The global motor measure (baseline M = 0.82, SD = 0.21) declined a mean 0.024 unit per year (95% confidence interval [CI]: -0.032, -0.016) until a mean of 2.46 years (95% CI: -2.870, -2.108) before death when rate of decline increased nearly fivefold to -0.117 unit per year (95% CI: -0.140, -0.097). The global cognitive measure (baseline M = 0.07, SD = 0.45) declined a mean of 0.027-unit per year (95% CI: -0.041, -0.014) until a mean of 2.76 years (95% CI: -3.157, -2.372) before death when rate of decline increased more than 13-fold to -0.371 unit per year (95% CI: -0.443, -0.306). Onset of terminal motor decline was highly correlated with onset of terminal cognitive decline (r = .94, 95% CI: 0.81, 0.99), but rates of motor and cognitive change were not strongly correlated (preterminal r = .20, 95% CI: -0.05, 0.38; terminal r = .34, 95% CI: 0.03, 0.62). Higher level of plaques and tangles was associated with earlier onset of terminal decline in motor function, but no pathologic measures were associated with rate of preterminal or terminal motor decline. The results demonstrate that motor and cognitive functions both undergo a period of accelerated decline in the last few years of life. 2013 APA, all rights reserved

  8. Carboxy terminal tail of polycystin-1 regulates localization of TSC2 to repress mTOR.

    Directory of Open Access Journals (Sweden)

    Ruhee Dere

    2010-02-01

    Full Text Available Autosomal dominant polycystic kidney disease (ADPKD is a commonly inherited renal disorder caused by defects in the PKD1 or PKD2 genes. ADPKD is associated with significant morbidity, and is a major underlying cause of end-stage renal failure (ESRF. Commonly, treatment options are limited to the management of hypertension, cardiovascular risk factors, dialysis, and transplantation when ESRF develops, although several new pharmacotherapies, including rapamycin, have shown early promise in animal and human studies. Evidence implicates polycystin-1 (PC-1, the gene product of the PKD1 gene, in regulation of the mTOR pathway. Here we demonstrate a mechanism by which the intracellular, carboxy-terminal tail of polycystin-1 (CP1 regulates mTOR signaling by altering the subcellular localization of the tuberous sclerosis complex 2 (TSC2 tumor suppressor, a gatekeeper for mTOR activity. Phosphorylation of TSC2 at S939 by AKT causes partitioning of TSC2 away from the membrane, its GAP target Rheb, and its activating partner TSC1 to the cytosol via 14-3-3 protein binding. We found that TSC2 and a C-terminal polycystin-1 peptide (CP1 directly interact and that a membrane-tethered CP1 protects TSC2 from AKT phosphorylation at S939, retaining TSC2 at the membrane to inhibit the mTOR pathway. CP1 decreased binding of 14-3-3 proteins to TSC2 and increased the interaction between TSC2 and its activating partner TSC1. Interestingly, while membrane tethering of CP1 was required to activate TSC2 and repress mTOR, the ability of CP1 to inhibit mTOR signaling did not require primary cilia and was independent of AMPK activation. These data identify a unique mechanism for modulation of TSC2 repression of mTOR signaling via membrane retention of this tumor suppressor, and identify PC-1 as a regulator of this downstream component of the PI3K signaling cascade.

  9. Global analysis of translation termination in E. coli.

    Science.gov (United States)

    Baggett, Natalie E; Zhang, Yan; Gross, Carol A

    2017-03-01

    Terminating protein translation accurately and efficiently is critical for both protein fidelity and ribosome recycling for continued translation. The three bacterial release factors (RFs) play key roles: RF1 and 2 recognize stop codons and terminate translation; and RF3 promotes disassociation of bound release factors. Probing release factors mutations with reporter constructs containing programmed frameshifting sequences or premature stop codons had revealed a propensity for readthrough or frameshifting at these specific sites, but their effects on translation genome-wide have not been examined. We performed ribosome profiling on a set of isogenic strains with well-characterized release factor mutations to determine how they alter translation globally. Consistent with their known defects, strains with increasingly severe release factor defects exhibit increasingly severe accumulation of ribosomes over stop codons, indicative of an increased duration of the termination/release phase of translation. Release factor mutant strains also exhibit increased occupancy in the region following the stop codon at a significant number of genes. Our global analysis revealed that, as expected, translation termination is generally efficient and accurate, but that at a significant number of genes (≥ 50) the ribosome signature after the stop codon is suggestive of translation past the stop codon. Even native E. coli K-12 exhibits the ribosome signature suggestive of protein extension, especially at UGA codons, which rely exclusively on the reduced function RF2 variant of the K-12 strain for termination. Deletion of RF3 increases the severity of the defect. We unambiguously demonstrate readthrough and frameshifting protein extensions and their further accumulation in mutant strains for a few select cases. In addition to enhancing recoding, ribosome accumulation over stop codons disrupts attenuation control of biosynthetic operons, and may alter expression of some overlapping genes

  10. Development of Low Energy Gap and Fully Regioregular Polythienylenevinylene Derivative

    Directory of Open Access Journals (Sweden)

    Tanya M. S. David

    2014-01-01

    Full Text Available Low energy gap and fully regioregular conjugated polymers find its wide use in solar energy conversion applications. This paper will first briefly review this type of polymers and also report synthesis and characterization of a specific example new polymer, a low energy gap, fully regioregular, terminal functionalized, and processable conjugated polymer poly-(3-dodecyloxy-2,5-thienylene vinylene or PDDTV. The polymer exhibited an optical energy gap of 1.46 eV based on the UV-vis-NIR absorption spectrum. The electrochemically measured highest occupied molecular orbital (HOMO level is −4.79 eV, resulting in the lowest unoccupied molecular orbital (LUMO level of −3.33 eV based on optical energy gap. The polymer was synthesized via Horner-Emmons condensation and is fairly soluble in common organic solvents such as tetrahydrofuran and chloroform with gentle heating. DSC showed two endothermic peaks at 67°C and 227°C that can be attributed to transitions between crystalline and liquid states. The polymer is thermally stable up to about 300°C. This polymer appears very promising for cost-effective solar cell applications.

  11. Explaining the gender wealth gap.

    Science.gov (United States)

    Ruel, Erin; Hauser, Robert M

    2013-08-01

    To assess and explain the United States' gender wealth gap, we use the Wisconsin Longitudinal Study to examine wealth accumulated by a single cohort over 50 years by gender, by marital status, and limited to the respondents who are their family's best financial reporters. We find large gender wealth gaps between currently married men and women, and between never-married men and women. The never-married accumulate less wealth than the currently married, and there is a marital disruption cost to wealth accumulation. The status-attainment model shows the most power in explaining gender wealth gaps between these groups explaining about one-third to one-half of the gap, followed by the human-capital explanation. In other words, a lifetime of lower earnings for women translates into greatly reduced wealth accumulation. After controlling for the full model, we find that a gender wealth gap remains between married men and women that we speculate may be related to gender differences in investment strategies and selection effects.

  12. Comparison of the Regulation, Metabolic Functions, and Roles in Virulence of the Glyceraldehyde-3-Phosphate Dehydrogenase Homologues gapA and gapB in Staphylococcus aureus▿

    Science.gov (United States)

    Purves, Joanne; Cockayne, Alan; Moody, Peter C. E.; Morrissey, Julie A.

    2010-01-01

    The Gram-positive bacterium Staphylococcus aureus contains two glyceraldehyde-3-phosphate dehydrogenase (GAPDH) homologues known as GapA and GapB. GapA has been characterized as a functional GAPDH protein, but currently there is no biological evidence for the role of GapB in metabolism in S. aureus. In this study we show through a number of complementary methods that S. aureus GapA is essential for glycolysis while GapB is essential in gluconeogenesis. These proteins are reciprocally regulated in response to glucose concentrations, and both are influenced by the glycolysis regulator protein GapR, which is the first demonstration of the role of this regulator in S. aureus and the first indication that GapR homologues control genes other than those within the glycolytic operon. Furthermore, we show that both GapA and GapB are important in the pathogenesis of S. aureus in a Galleria mellonella model of infection, showing for the first time in any bacteria that both glycolysis and gluconeogenesis have important roles in virulence. PMID:20876289

  13. Comparison of the regulation, metabolic functions, and roles in virulence of the glyceraldehyde-3-phosphate dehydrogenase homologues gapA and gapB in Staphylococcus aureus.

    Science.gov (United States)

    Purves, Joanne; Cockayne, Alan; Moody, Peter C E; Morrissey, Julie A

    2010-12-01

    The Gram-positive bacterium Staphylococcus aureus contains two glyceraldehyde-3-phosphate dehydrogenase (GAPDH) homologues known as GapA and GapB. GapA has been characterized as a functional GAPDH protein, but currently there is no biological evidence for the role of GapB in metabolism in S. aureus. In this study we show through a number of complementary methods that S. aureus GapA is essential for glycolysis while GapB is essential in gluconeogenesis. These proteins are reciprocally regulated in response to glucose concentrations, and both are influenced by the glycolysis regulator protein GapR, which is the first demonstration of the role of this regulator in S. aureus and the first indication that GapR homologues control genes other than those within the glycolytic operon. Furthermore, we show that both GapA and GapB are important in the pathogenesis of S. aureus in a Galleria mellonella model of infection, showing for the first time in any bacteria that both glycolysis and gluconeogenesis have important roles in virulence.

  14. Calcium electrotransfer for termination of transgene expression in muscle

    DEFF Research Database (Denmark)

    Hojman, Pernille; Spanggaard, Iben; Olsen, Caroline Holkman

    2011-01-01

    Gene electrotransfer is expanding in clinical use, thus we have searched for an emergency procedure to stop transgene expression in case of serious adverse events. Calcium is cytotoxic at high intracellular levels, so we tested effects of calcium electrotransfer on transgene expression in muscle....... showed muscle damage and subsequent regeneration. Electrotransfer of isotonic CaCl(2) terminates transgenic protein expression in muscles and may be used for contingency elimination of transgene expression....

  15. Clothes Dryer Automatic Termination Evaluation

    Energy Technology Data Exchange (ETDEWEB)

    TeGrotenhuis, Ward E.

    2014-10-01

    Volume 2: Improved Sensor and Control Designs Many residential clothes dryers on the market today provide automatic cycles that are intended to stop when the clothes are dry, as determined by the final remaining moisture content (RMC). However, testing of automatic termination cycles has shown that many dryers are susceptible to over-drying of loads, leading to excess energy consumption. In particular, tests performed using the DOE Test Procedure in Appendix D2 of 10 CFR 430 subpart B have shown that as much as 62% of the energy used in a cycle may be from over-drying. Volume 1 of this report shows an average of 20% excess energy from over-drying when running automatic cycles with various load compositions and dryer settings. Consequently, improving automatic termination sensors and algorithms has the potential for substantial energy savings in the U.S.

  16. Virtual gap dielectric wall accelerator

    Science.gov (United States)

    Caporaso, George James; Chen, Yu-Jiuan; Nelson, Scott; Sullivan, Jim; Hawkins, Steven A

    2013-11-05

    A virtual, moving accelerating gap is formed along an insulating tube in a dielectric wall accelerator (DWA) by locally controlling the conductivity of the tube. Localized voltage concentration is thus achieved by sequential activation of a variable resistive tube or stalk down the axis of an inductive voltage adder, producing a "virtual" traveling wave along the tube. The tube conductivity can be controlled at a desired location, which can be moved at a desired rate, by light illumination, or by photoconductive switches, or by other means. As a result, an impressed voltage along the tube appears predominantly over a local region, the virtual gap. By making the length of the tube large in comparison to the virtual gap length, the effective gain of the accelerator can be made very large.

  17. Complexity of Terminating Preference Elicitation

    OpenAIRE

    Walsh, Toby

    2009-01-01

    Complexity theory is a useful tool to study computational issues surrounding the elicitation of preferences, as well as the strategic manipulation of elections aggregating together preferences of multiple agents. We study here the complexity of determining when we can terminate eliciting preferences, and prove that the complexity depends on the elicitation strategy. We show, for instance, that it may be better from a computational perspective to elicit all preferences from one agent at a time...

  18. Pairing gaps in nucleonic superfluids

    Energy Technology Data Exchange (ETDEWEB)

    Chen, J.M.C. (McDonnell Center for the Space Sciences and Dept. of Physics, Washington Univ., St. Louis, MO (United States)); Clark, J.W. (McDonnell Center for the Space Sciences and Dept. of Physics, Washington Univ., St. Louis, MO (United States)); Dave, R.D. (McDonnell Center for the Space Sciences and Dept. of Physics, Washington Univ., St. Louis, MO (United States)); Khodel, V.V. (McDonnell Center for the Space Sciences and Dept. of Physics, Washington Univ., St. Louis, MO (United States))

    1993-04-05

    Singlet S-wave nucleonic superfluids are studied within a microscopic many-body theory that incorporates explicit spatial correlations due to strong short-range repulsive forces as well as the momentum-space pairing correlations of BCS theory. The theory is formulated within the method of correlated basis functions (CBF). Within this scheme, there results a nonlinear problem for the superfluid energy gap that is identical in form to the gap problem of conventional BCS theory. However, the input single-particle energies and pairing matrix elements are dressed by the short-range spatial correlations and accordingly incorporate an important class of medium corrections. The effective pairing force of the theory is finite even if the bare two-nucleon potential contains an infinitely hard core; both the pairing matrix elements and single-particle energies are to be constructed from normal-state CBF matrix elements and may be evaluated by cluster-expansion techniques. The theory is explicated and applied at a variational level that is equivalent to the leading order of a CBF superstate perturbation theory. New results are presented for the [sup 1]S[sub 0] pairing gap [Delta][sub kF] in pure neutron matter at densities relevant to the inner crust of a neutron star, based on a simplified version of the Reid soft-core interaction and spin-dependent spatial correlations optimized in the correlated normal state. Careful considering is given to the treatment of the gap equation at large intermediate-state momenta. The variational gap function evaluated at the Fermi surface, [Delta][sub F], is found to be larger than predicted in earlier work. Estimates of the suppression of the gap due to polarization processes (and other particle-particle and hole-irreducible medium effects of higher order within CBF superstate perturbation theory) yield values of [Delta][sub kF].

  19. High Octane Fuel: Terminal Backgrounder

    Energy Technology Data Exchange (ETDEWEB)

    Moriarty, Kristi [National Renewable Energy Lab. (NREL), Golden, CO (United States)

    2016-02-11

    The Bioenergy Technologies Office of the U.S. Department of Energy Office of Energy Efficiency and Renewable Energy sponsored a scoping study to assess the potential of ethanol-based high octane fuel (HOF) to reduce energy consumption and greenhouse gas emissions. When the HOF blend is made with 25%-40% ethanol by volume, this energy efficiency improvement is potentially sufficient to offset the reduced vehicle range often associated with the decreased volumetric energy density of ethanol. The purpose of this study is to assess the ability of the fuel supply chain to accommodate more ethanol at fuel terminals. Fuel terminals are midstream in the transportation fuel supply chain and serve to store and distribute fuels to end users. While there are no technical issues to storing more ethanol at fuel terminals, there are several factors that could impact the ability to deploy more ethanol. The most significant of these issues include the availability of land to add more infrastructure and accommodate more truck traffic for ethanol deliveries as well as a lengthy permitting process to erect more tanks.

  20. GAP Analysis. Bulletin Number 11

    Science.gov (United States)

    2002-01-01

    AL Y SI S ~’ GAPA DISTRIBUTION STATEMENTA B U L L E T I N Approved for Public Release No. 1.11 Distribution Unlimited A Geographic Approach to...Analysis Program Bulletin No. 11, December 2002 5 GAPA L Y SI S Lidicker, W.Z., Jr. 1962. Emigration as a possible mechanism O’Connor, R.J. 2002. The...cover type was considered in spatial agreement be- Gap Analysis Program Bulletin No, 11, December 2002 19 GAPA L Y SI S tween the GAP and SRS models if

  1. The Emissions Gap Report 2014

    DEFF Research Database (Denmark)

    Farrell, Timothy Clifford

    This fifth Emissions Gap report has a different focus from previous years. While it updates the 2020 emissions gap analysis, it gives particular attention to the implications of the global carbon dioxide emissions budget for staying within the 2 °C limit beyond 2020. It does so because countries ...... are giving increasing attention to where they need to be in 2025, 2030 and beyond. Furthermore, this year’s update of the report benefits from the findings on the emissions budget from the latest series of Intergovernmental Panel on Climate Change (IPCC) reports...

  2. Explaining the Gender Wealth Gap

    OpenAIRE

    Ruel, Erin; Hauser, Robert M.

    2013-01-01

    To assess and explain the United States’ gender wealth gap, we use the Wisconsin Longitudinal Study to examine wealth accumulated by a single cohort over 50 years by gender, by marital status, and limited to the respondents who are their family’s best financial reporters. We find large gender wealth gaps between currently married men and women, and never-married men and women. The never-married accumulate less wealth than the currently married, and there is a marital disruption cost to wealth...

  3. A Systems Approach Identifies Essential FOXO3 Functions at Key Steps of Terminal Erythropoiesis.

    Directory of Open Access Journals (Sweden)

    Raymond Liang

    2015-10-01

    Full Text Available Circulating red blood cells (RBCs are essential for tissue oxygenation and homeostasis. Defective terminal erythropoiesis contributes to decreased generation of RBCs in many disorders. Specifically, ineffective nuclear expulsion (enucleation during terminal maturation is an obstacle to therapeutic RBC production in vitro. To obtain mechanistic insights into terminal erythropoiesis we focused on FOXO3, a transcription factor implicated in erythroid disorders. Using an integrated computational and experimental systems biology approach, we show that FOXO3 is essential for the correct temporal gene expression during terminal erythropoiesis. We demonstrate that the FOXO3-dependent genetic network has critical physiological functions at key steps of terminal erythropoiesis including enucleation and mitochondrial clearance processes. FOXO3 loss deregulated transcription of genes implicated in cell polarity, nucleosome assembly and DNA packaging-related processes and compromised erythroid enucleation. Using high-resolution confocal microscopy and imaging flow cytometry we show that cell polarization is impaired leading to multilobulated Foxo3-/- erythroblasts defective in nuclear expulsion. Ectopic FOXO3 expression rescued Foxo3-/- erythroblast enucleation-related gene transcription, enucleation defects and terminal maturation. Remarkably, FOXO3 ectopic expression increased wild type erythroblast maturation and enucleation suggesting that enhancing FOXO3 activity may improve RBCs production. Altogether these studies uncover FOXO3 as a novel regulator of erythroblast enucleation and terminal maturation suggesting FOXO3 modulation might be therapeutic in disorders with defective erythroid maturation.

  4. k36u Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  5. THE FORMALIZATION PROCESS OF CARGO TERMINAL OPERATION

    Directory of Open Access Journals (Sweden)

    N. Yu. Shramenko

    2011-01-01

    Full Text Available The mathematical formalization of operation process for a terminal complex is proposed and a model taking into account characteristics of a freight terminal and all the possible states of a system is developed.

  6. Gap junctions between AII amacrine cells and calbindin-positive bipolar cells in the rabbit retina.

    Science.gov (United States)

    Massey, S C; Mills, S L

    1999-01-01

    Electrical synapses or gap junctions occur between many retinal neurons. However, in most cases, the gap junctions have not been visualized directly. Instead, their presence has been inferred from tracer spread throughout the network of cells. Thus, tracer coupling is taken as a marker for the presence of gap junctions between coupled cells. AII amacrine cells are critical interneurons in the rod pathway of the mammalian retina. Rod bipolar cell output passes to AII amacrine cells, which in turn make conventional synapses with OFF cone bipolar cells and gap junctions with ON cone bipolar cells. Injections of biotinylated tracers into AII amacrine cells reveals coupling between the AII amacrine cell network and heterologous coupling with a variety of ON cone bipolar cells, including the calbindin-positive cone bipolar cell. To directly visualize gap junctions in this network, we prepared material for electron microscopy that was double labeled with antibodies to calretinin and calbindin to label AII amacrine cells and calbindin-positive cone bipolar cells, respectively. AII amacrine cells were postsynaptic to large vesicle-laden rod bipolar terminals, as previously reported. Gap junctions were identified between AII amacrine cells and calbindin-positive cone bipolar cell terminals identified by the presence of immunostaining and ribbon synapses. This represents direct confirmation of gap junctions between two different yet positively identified cells, which are tracer coupled, and provides additional evidence that tracer coupling with Neurobiotin indicates the presence of gap junctions. These results also definitively establish the presence of gap junctions between AII amacrine cells and calbindin bipolar cells which can therefore carry rod signals to the ON alpha ganglion cell.

  7. The quasiparticle spectrum termination in a quantum spin liquid

    Science.gov (United States)

    Zaliznyak, Igor

    2005-03-01

    The crossover from a single quasi-particle to a spin-continuum response was recently observed in the spin dynamics of the Haldane-chain antiferromagnet CsNiCl3 [1,2]. It can be understood as a manifestation, in the particular case of the quantum spin liquid, of the peculiar property of the quantum Bose liquids, the quasiparticle spectrum termination point. The spectrum termination was first predicted for the superfluid helium-4 [3], where it was extensively studied both theoretically and experimentally. The quantum-spin-liquid (QSL) state of the two-dimensional (2D) S=1/2 Heisenberg antiferromagnet (HAFM) is of particular interest, as it may be relevant to the type of high-temperature superconductivity found in the cuprates. An organo-metallic material piperazinium hexachlorodicuprate (PHCC) is among the best known examples of the 2D QSL [4]. The spin excitations in this material have spectral gap of about 1 meV above which they follow a nearly 2D- isotropic dispersion with a bandwidth slightly larger than the gap. Recent experiments indicate that a quasiparticle spectrum termination point also exists in the excitation spectrum of the 2D quantum spin liquid existing in PHCC [5]. It signals the failure of the Bose-quasiparticle description in an extended region of the system's phase space. REFERENCES [1] I. A. Zaliznyak, S.-H. Lee, in Y. Zhu (Ed.), Modern Techniques for Characterizing Magnetic Materials, Kluwer Academic, New York (2005). [2] I. A. Zaliznyak, S.-H. Lee and S. V. Petrov, Phys. Rev. Lett. 87, 017202 (2001); Phys. Rev. Lett. 91, 039902 (2003). [3] Landau & Lifshitz, Course of Theoretical Physics (Statistical Physics, Part 2, by Lifshitz, E. M. & Pitaevskii, L. P.) Vol. 9, 125-139 (Pergamon Press, Oxford, 1981). [4] Stone, M. B., Zaliznyak, I., Reich, D. H., and Broholm, C., Phys. Rev. B 64, 144405 (2001). [5] M. Stone, I. A. Zaliznyak, et. al., in preparation (2004).

  8. The C-terminal domain of Nrf1 negatively regulates the full-length CNC-bZIP factor and its shorter isoform LCR-F1/Nrf1β; both are also inhibited by the small dominant-negative Nrf1γ/δ isoforms that down-regulate ARE-battery gene expression.

    Science.gov (United States)

    Zhang, Yiguo; Qiu, Lu; Li, Shaojun; Xiang, Yuancai; Chen, Jiayu; Ren, Yonggang

    2014-01-01

    The C-terminal domain (CTD, aa 686-741) of nuclear factor-erythroid 2 p45-related factor 1 (Nrf1) shares 53% amino acid sequence identity with the equivalent Neh3 domain of Nrf2, a homologous transcription factor. The Neh3 positively regulates Nrf2, but whether the Neh3-like (Neh3L) CTD of Nrf1 has a similar role in regulating Nrf1-target gene expression is unknown. Herein, we report that CTD negatively regulates the full-length Nrf1 (i.e. 120-kDa glycoprotein and 95-kDa deglycoprotein) and its shorter isoform LCR-F1/Nrf1β (55-kDa). Attachment of its CTD-adjoining 112-aa to the C-terminus of Nrf2 yields the chimaeric Nrf2-C112Nrf1 factor with a markedly decreased activity. Live-cell imaging of GFP-CTD reveals that the extra-nuclear portion of the fusion protein is allowed to associate with the endoplasmic reticulum (ER) membrane through the amphipathic Neh3L region of Nrf1 and its basic c-tail. Thus removal of either the entire CTD or the essential Neh3L portion within CTD from Nrf1, LCR-F1/Nrf1β and Nrf2-C112Nrf1, results in an increase in their transcriptional ability to regulate antioxidant response element (ARE)-driven reporter genes. Further examinations unravel that two smaller isoforms, 36-kDa Nrf1γ and 25-kDa Nrf1δ, act as dominant-negative inhibitors to compete against Nrf1, LCR-F1/Nrf1β and Nrf2. Relative to Nrf1, LCR-F1/Nrf1β is a weak activator, that is positively regulated by its Asn/Ser/Thr-rich (NST) domain and acidic domain 2 (AD2). Like AD1 of Nrf1, both AD2 and NST domain of LCR-F1/Nrf1β fused within two different chimaeric contexts to yield Gal4D:Nrf1β607 and Nrf1β:C270Nrf2, positively regulate their transactivation activity of cognate Gal4- and Nrf2-target reporter genes. More importantly, differential expression of endogenous ARE-battery genes is attributable to up-regulation by Nrf1 and LCR-F1/Nrf1β and down-regulation by Nrf1γ and Nrf1δ.

  9. Convergent use of RhoGAP toxins by eukaryotic parasites and bacterial pathogens.

    Directory of Open Access Journals (Sweden)

    Dominique Colinet

    2007-12-01

    Full Text Available Inactivation of host Rho GTPases is a widespread strategy employed by bacterial pathogens to manipulate mammalian cellular functions and avoid immune defenses. Some bacterial toxins mimic eukaryotic Rho GTPase-activating proteins (GAPs to inactivate mammalian GTPases, probably as a result of evolutionary convergence. An intriguing question remains whether eukaryotic pathogens or parasites may use endogenous GAPs as immune-suppressive toxins to target the same key genes as bacterial pathogens. Interestingly, a RhoGAP domain-containing protein, LbGAP, was recently characterized from the parasitoid wasp Leptopilina boulardi, and shown to protect parasitoid eggs from the immune response of Drosophila host larvae. We demonstrate here that LbGAP has structural characteristics of eukaryotic RhoGAPs but that it acts similarly to bacterial RhoGAP toxins in mammals. First, we show by immunocytochemistry that LbGAP enters Drosophila immune cells, plasmatocytes and lamellocytes, and that morphological changes in lamellocytes are correlated with the quantity of LbGAP they contain. Demonstration that LbGAP displays a GAP activity and specifically interacts with the active, GTP-bound form of the two Drosophila Rho GTPases Rac1 and Rac2, both required for successful encapsulation of Leptopilina eggs, was then achieved using biochemical tests, yeast two-hybrid analysis, and GST pull-down assays. In addition, we show that the overall structure of LbGAP is similar to that of eukaryotic RhoGAP domains, and we identify distinct residues involved in its interaction with Rac GTPases. Altogether, these results show that eukaryotic parasites can use endogenous RhoGAPs as virulence factors and that despite their differences in sequence and structure, eukaryotic and bacterial RhoGAP toxins are similarly used to target the same immune pathways in insects and mammals.

  10. 29 CFR 402.5 - Terminal reports.

    Science.gov (United States)

    2010-07-01

    ... organization at the time of its termination or loss of reporting identity and, together with a copy thereof... such termination or loss of reporting identity, as the case may be. (b) Labor organizations which... other form of termination of its existence as a labor organization, or which loses its identity as a...

  11. Kajian Kinerja Terminal Batu Ampar Kota Balikpapan

    Directory of Open Access Journals (Sweden)

    Randha Alief Chikita

    2018-01-01

    Full Text Available Batu Ampar Terminal Balikpapan is the only type A passenger terminal in Balikpapan City. The purpose of this study is to determine the operational performance of the terminal at this time and also to determine the level of service in the terminal. The results of this study indicate that for FIFO queue discipline analysis on AKDP and AKAP bus lines, it is known that ρ <1 means that there is currently no queue in the terminal. For the analysis of terminal facilities it is known that there are still some terminal facilities that are not yet available from the main facilities and supporting facilities, therefore the need for additional facilities in order to meet the standard of passenger terminal type A. In the next 15 years analysis for traffic intensity value is approaching 1 which means in the future will cause the queue in the terminal, so it is necessary for the improvement of terminal performance. For the service performance with IPA method there are 35 variables that there are 7 variables that enter in quadrant I. In the next step to do analysis to know the priority of handling by using QFD method. Keywords: Batu Ampar Terminal Balikpapan, IPA, terminal performance, QFD

  12. 42 CFR 460.54 - Termination procedures.

    Science.gov (United States)

    2010-10-01

    ... 42 Public Health 4 2010-10-01 2010-10-01 false Termination procedures. 460.54 Section 460.54 Public Health CENTERS FOR MEDICARE & MEDICAID SERVICES, DEPARTMENT OF HEALTH AND HUMAN SERVICES... ELDERLY (PACE) Sanctions, Enforcement Actions, and Termination § 460.54 Termination procedures. (a) Except...

  13. Globalization and the Gender Gap

    NARCIS (Netherlands)

    Oostendorp, R.H.

    2004-01-01

    There are several theoretical reasons why globalization will have a narrowing as well as a widening effect on the gender wage gap, but little is known about the actual impact, except for some country studies. This study contributes to the literature in three respects. First, it is a large

  14. Multiple input electrode gap controller

    Science.gov (United States)

    Hysinger, C.L.; Beaman, J.J.; Melgaard, D.K.; Williamson, R.L.

    1999-07-27

    A method and apparatus for controlling vacuum arc remelting (VAR) furnaces by estimation of electrode gap based on a plurality of secondary estimates derived from furnace outputs. The estimation is preferably performed by Kalman filter. Adaptive gain techniques may be employed, as well as detection of process anomalies such as glows. 17 figs.

  15. Brain Responses to Filled Gaps

    Science.gov (United States)

    Hestvik, Arild; Maxfield, Nathan; Schwartz, Richard G.; Shafer, Valerie

    2007-01-01

    An unresolved issue in the study of sentence comprehension is whether the process of gap-filling is mediated by the construction of empty categories (traces), or whether the parser relates fillers directly to the associated verb's argument structure. We conducted an event-related potentials (ERP) study that used the violation paradigm to examine…

  16. Versatile epitope tagging vector for gene expression in mammalian cells.

    Science.gov (United States)

    Hosfield, T; Lu, Q

    1998-08-01

    We have constructed an epitope-tagging vector, pCMV-Tag1, for gene expression in mammalian cells. This vector, which allows for N-terminal, C-terminal and internal tagging of the gene product of interest with the FLAG and/or c-myc epitopes, enables researchers to rapidly and efficiently characterize gene products in vivo.

  17. Bi-modal regulation of a formin by srGAP2.

    Science.gov (United States)

    Mason, Frank M; Heimsath, Ernest G; Higgs, Henry N; Soderling, Scott H

    2011-02-25

    The maintenance of rapid and efficient actin dynamics in vivo requires coordination of filament assembly and disassembly. This regulation requires temporal and spatial integration of signaling pathways by protein complexes. However, it remains unclear how these complexes form and then regulate the actin cytoskeleton. Here, we identify a srGAP2 and formin-like 1 (FMNL1, also known as FRL1 or FRLα) complex whose assembly is regulated by Rac signaling. Our data suggest srGAP2 regulates FMNL1 in two ways; 1) Rac-mediated activation of FMNL1 leads to the recruitment of srGAP2, which contains a Rac-specific GAP domain; 2) the SH3 domain of srGAP2 binds the formin homology 1 domain of FMNL1 to inhibit FMNL1-mediated actin severing. Thus, srGAP2 can efficiently terminate the upstream activating Rac signal while also opposing an important functional output of FMNL1, namely actin severing. We also show that FMNL1 and srGAP2 localize to the actin-rich phagocytic cup of macrophage-derived cells, suggesting the complex may regulate this Rac- and actin-driven process in vivo. We propose that after Rac-dependent activation of FMNL1, srGAP2 mediates a potent mechanism to limit the duration of Rac action and inhibit formin activity during rapid actin dynamics.

  18. 76 FR 22119 - Credit Watch Termination Initiative; Termination of Direct Endorsement (DE) Approval

    Science.gov (United States)

    2011-04-20

    ... URBAN DEVELOPMENT Credit Watch Termination Initiative; Termination of Direct Endorsement (DE) Approval.... SUMMARY: This notice advises of the cause and effect of termination of Direct Endorsement (DE) Approval... Endorsement mortgagees. Termination of Direct Endorsement Approval: Approval of a DE mortgagee by HUD/FHA...

  19. Distinct roles of the RasGAP family proteins in C. elegans associative learning and memory.

    Science.gov (United States)

    Gyurkó, M Dávid; Csermely, Péter; Sőti, Csaba; Steták, Attila

    2015-10-15

    The Ras GTPase activating proteins (RasGAPs) are regulators of the conserved Ras/MAPK pathway. Various roles of some of the RasGAPs in learning and memory have been reported in different model systems, yet, there is no comprehensive study to characterize all gap genes in any organism. Here, using reverse genetics and neurobehavioural tests, we studied the role of all known genes of the rasgap family in C. elegans in associative learning and memory. We demonstrated that their proteins are implicated in different parts of the learning and memory processes. We show that gap-1 contribute redundantly with gap-3 to the chemosensation of volatile compounds, gap-1 plays a major role in associative learning, while gap-2 and gap-3 are predominantly required for short- and long-term associative memory. Our results also suggest that the C. elegans Ras orthologue let-60 is involved in multiple processes during learning and memory. Thus, we show that the different classes of RasGAP proteins are all involved in cognitive function and their complex interplay ensures the proper formation and storage of novel information in C. elegans.

  20. Multigene expression in vivo: supremacy of large versus small terminators for T7 RNA polymerase.

    Science.gov (United States)

    Du, Liping; Villarreal, Seth; Forster, Anthony C

    2012-04-01

    Designing and building multigene constructs is commonplace in synthetic biology. Yet functional successes at first attempts are rare because the genetic parts are not fully modular. In order to improve the modularity of transcription, we previously showed that transcription termination in vitro by bacteriophage T7 RNA polymerase could be made more efficient by substituting the standard, single, TΦ large (class I) terminator with adjacent copies of the vesicular stomatitis virus (VSV) small (class II) terminator. However, in vitro termination at the downstream VSV terminator was less efficient than at the upstream VSV terminator, and multigene overexpression in vivo was complicated by unexpectedly inefficient VSV termination within Escherichia coli cells. Here, we address hypotheses raised in that study by showing that VSV or preproparathyroid hormone (PTH) small terminators spaced further apart can work independently (i.e., more efficiently) in vitro, and that VSV and PTH terminations are severely inhibited in vivo. Surprisingly, the difference between class II terminator function in vivo versus in vitro is not due to differences in plasmid supercoiling, as supercoiling had a minimal effect on termination in vitro. We therefore turned to TΦ terminators for "BioBrick" synthesis of a pentameric gene construct suitable for overexpression in vivo. This indeed enabled coordinated overexpression and copurification of five His-tagged proteins using the first construct attempted, indicating that this strategy is more modular than other strategies. An application of this multigene overexpression and protein copurification method is demonstrated by supplying five of the six E. coli translation factors required for reconstitution of translation from a single cell line via copurification, greatly simplifying the reconstitution. Copyright © 2011 Wiley Periodicals, Inc.

  1. submitter Triggering of a pressurized spark gap by a laser beam

    CERN Document Server

    Deutsch, F

    1968-01-01

    A delay line was discharged into a terminating resistor by a spark gap of coaxial design. The spark gap was triggered by a focused laser beam, introduced along the axis; a Q-switched ruby laser giving pulses of 20 ns duration and up to 50 MW power was used. The range of operation of the gap, formative time of the breakdown and jitter were investigated for different gases at pressures above atmospheric, gap widths of 4-10 mm and voltages of up to 120 kv. Mixtures of argon and nitrogen were found to have certain advantages, such as a low threshold for ionization by the laser beam, sufficient dielectric strength, low values of the formative-time jitter and chemical inertness. Formative times of down to about 1 ns and jitters below 1 ns were found. The laser power can be relatively low (0centerdot5-5 MW). An explanation for the breakdown mechanism is proposed.

  2. Untangling spider silk evolution with spidroin terminal domains

    Directory of Open Access Journals (Sweden)

    Garb Jessica E

    2010-08-01

    Full Text Available Abstract Background Spidroins are a unique family of large, structural proteins that make up the bulk of spider silk fibers. Due to the highly variable nature of their repetitive sequences, spidroin evolutionary relationships have principally been determined from their non-repetitive carboxy (C-terminal domains, though they offer limited character data. The few known spidroin amino (N-terminal domains have been difficult to obtain, but potentially contain critical phylogenetic information for reconstructing the diversification of spider silks. Here we used silk gland expression data (ESTs from highly divergent species to evaluate the functional significance and phylogenetic utility of spidroin N-terminal domains. Results We report 11 additional spidroin N-termini found by sequencing ~1,900 silk gland cDNAs from nine spider species that shared a common ancestor > 240 million years ago. In contrast to their hyper-variable repetitive regions, spidroin N-terminal domains have retained striking similarities in sequence identity, predicted secondary structure, and hydrophobicity. Through separate and combined phylogenetic analyses of N-terminal domains and their corresponding C-termini, we find that combined analysis produces the most resolved trees and that N-termini contribute more support and less conflict than the C-termini. These analyses show that paralogs largely group by silk gland type, except for the major ampullate spidroins. Moreover, spidroin structural motifs associated with superior tensile strength arose early in the history of this gene family, whereas a motif conferring greater extensibility convergently evolved in two distantly related paralogs. Conclusions A non-repetitive N-terminal domain appears to be a universal attribute of spidroin proteins, likely retained from the origin of spider silk production. Since this time, spidroin N-termini have maintained several features, consistent with this domain playing a key role in silk

  3. Termination of Transcription of Short Noncoding RNAs by RNA Polymerase II.

    Science.gov (United States)

    Arndt, Karen M; Reines, Daniel

    2015-01-01

    The RNA polymerase II transcription cycle is often divided into three major stages: initiation, elongation, and termination. Research over the last decade has blurred these divisions and emphasized the tightly regulated transitions that occur as RNA polymerase II synthesizes a transcript from start to finish. Transcription termination, the process that marks the end of transcription elongation, is regulated by proteins that interact with the polymerase, nascent transcript, and/or chromatin template. The failure to terminate transcription can cause accumulation of aberrant transcripts and interfere with transcription at downstream genes. Here, we review the mechanism, regulation, and physiological impact of a termination pathway that targets small noncoding transcripts produced by RNA polymerase II. We emphasize the Nrd1-Nab3-Sen1 pathway in yeast, in which the process has been extensively studied. The importance of understanding small RNA termination pathways is underscored by the need to control noncoding transcription in eukaryotic genomes.

  4. Widespread disruption of host transcription termination in HSV-1 infection

    Science.gov (United States)

    Rutkowski, Andrzej J.; Erhard, Florian; L'Hernault, Anne; Bonfert, Thomas; Schilhabel, Markus; Crump, Colin; Rosenstiel, Philip; Efstathiou, Stacey; Zimmer, Ralf; Friedel, Caroline C.; Dölken, Lars

    2015-01-01

    Herpes simplex virus 1 (HSV-1) is an important human pathogen and a paradigm for virus-induced host shut-off. Here we show that global changes in transcription and RNA processing and their impact on translation can be analysed in a single experimental setting by applying 4sU-tagging of newly transcribed RNA and ribosome profiling to lytic HSV-1 infection. Unexpectedly, we find that HSV-1 triggers the disruption of transcription termination of cellular, but not viral, genes. This results in extensive transcription for tens of thousands of nucleotides beyond poly(A) sites and into downstream genes, leading to novel intergenic splicing between exons of neighbouring cellular genes. As a consequence, hundreds of cellular genes seem to be transcriptionally induced but are not translated. In contrast to previous reports, we show that HSV-1 does not inhibit co-transcriptional splicing. Our approach thus substantially advances our understanding of HSV-1 biology and establishes HSV-1 as a model system for studying transcription termination. PMID:25989971

  5. Homolumo Gap and Matrix Model

    CERN Document Server

    Andric, I; Jurman, D; Nielsen, H B

    2007-01-01

    We discuss a dynamical matrix model by which probability distribution is associated with Gaussian ensembles from random matrix theory. We interpret the matrix M as a Hamiltonian representing interaction of a bosonic system with a single fermion. We show that a system of second-quantized fermions influences the ground state of the whole system by producing a gap between the highest occupied eigenvalue and the lowest unoccupied eigenvalue.

  6. Investigations of Pulsed Vacuum Gap.

    Science.gov (United States)

    1981-02-10

    re-az4,irc t:ata -.as taken .0thcut t1he cury-ent vino r’esistor. Initial data, with no current viewing resistor, were taken for a 35 mmn gap using an...Eastman, and J. Kivlin, "The Appearance of Micro- particles in Accelerator Tubes," Proc. of 8th Symp., Paper F6-1, Albuquerque, . . Mexico , (1978). 71391

  7. Multiple roles of genome-attached bacteriophage terminal proteins

    Energy Technology Data Exchange (ETDEWEB)

    Redrejo-Rodríguez, Modesto; Salas, Margarita, E-mail: msalas@cbm.csic.es

    2014-11-15

    Protein-primed replication constitutes a generalized mechanism to initiate DNA or RNA synthesis in linear genomes, including viruses, gram-positive bacteria, linear plasmids and mobile elements. By this mechanism a specific amino acid primes replication and becomes covalently linked to the genome ends. Despite the fact that TPs lack sequence homology, they share a similar structural arrangement, with the priming residue in the C-terminal half of the protein and an accumulation of positively charged residues at the N-terminal end. In addition, various bacteriophage TPs have been shown to have DNA-binding capacity that targets TPs and their attached genomes to the host nucleoid. Furthermore, a number of bacteriophage TPs from different viral families and with diverse hosts also contain putative nuclear localization signals and localize in the eukaryotic nucleus, which could lead to the transport of the attached DNA. This suggests a possible role of bacteriophage TPs in prokaryote-to-eukaryote horizontal gene transfer. - Highlights: • Protein-primed genome replication constitutes a strategy to initiate DNA or RNA synthesis in linear genomes. • Bacteriophage terminal proteins (TPs) are covalently attached to viral genomes by their primary function priming DNA replication. • TPs are also DNA-binding proteins and target phage genomes to the host nucleoid. • TPs can also localize in the eukaryotic nucleus and may have a role in phage-mediated interkingdom gene transfer.

  8. Hyper-active gap filling.

    Science.gov (United States)

    Omaki, Akira; Lau, Ellen F; Davidson White, Imogen; Dakan, Myles L; Apple, Aaron; Phillips, Colin

    2015-01-01

    Much work has demonstrated that speakers of verb-final languages are able to construct rich syntactic representations in advance of verb information. This may reflect general architectural properties of the language processor, or it may only reflect a language-specific adaptation to the demands of verb-finality. The present study addresses this issue by examining whether speakers of a verb-medial language (English) wait to consult verb transitivity information before constructing filler-gap dependencies, where internal arguments are fronted and hence precede the verb. This configuration makes it possible to investigate whether the parser actively makes representational commitments on the gap position before verb transitivity information becomes available. A key prediction of the view that rich pre-verbal structure building is a general architectural property is that speakers of verb-medial languages should predictively construct dependencies in advance of verb transitivity information, and therefore that disruption should be observed when the verb has intransitive subcategorization frames that are incompatible with the predicted structure. In three reading experiments (self-paced and eye-tracking) that manipulated verb transitivity, we found evidence for reading disruption when the verb was intransitive, although no such reading difficulty was observed when the critical verb was embedded inside a syntactic island structure, which blocks filler-gap dependency completion. These results are consistent with the hypothesis that in English, as in verb-final languages, information from preverbal noun phrases is sufficient to trigger active dependency completion without having access to verb transitivity information.

  9. Lowering Band Gap of an Electroactive Metal-Organic Framework via Complementary Guest Intercalation.

    Science.gov (United States)

    Guo, Zhiyong; Panda, Dillip K; Gordillo, Monica A; Khatun, Amina; Wu, Hui; Zhou, Wei; Saha, Sourav

    2017-09-27

    A new honeycomb-shaped electroactive metal-organic framework (MOF) has been constructed from an electron deficient naphthalenediimide (NDI) ligand equipped with two terminal salicylic acid groups. π-Intercalation of electron-rich planar tetrathiafulvalene (TTF) guests between the NDI ligands stacked along the walls lowers the electronic band gap of the material by ca. 1 eV. An improved electron delocalization through the guest-mediated π-donor/acceptor stacks is attributed to the diminished band gap of the doped material, which forecasts an improved electrical conductivity.

  10. Gambling with video lottery terminals.

    Science.gov (United States)

    Doiron, J P; Mazer, D B

    2001-09-01

    Semistructured interviews were conducted with 7 persons who had significant involvements with video lottery terminal (VLT) gambling, and themes associated with different phases of the gambling experience were identified. The preinvolvement phase was characterized by lack of meaningful relationships, problematic relationships, and feelings of loss. Early involvement reflected attempts to "fill the void" and the casual innocence of initial VLT playing. The deepening involvement phase indicated themes of the language of relationship, for example, focused engagement, emotional highs and lows, and the escape and competition offered by gambling. Ending involvement themes included the emotional difficulty of quitting and strategies used to break the habit. Implications of these results for models of addiction and for the treatment of gambling problems are explored.

  11. Gene number determination and genetic polymorphism of the gamma delta T cell co-receptor WC1 genes

    Directory of Open Access Journals (Sweden)

    Chen Chuang

    2012-10-01

    Full Text Available Abstract Background WC1 co-receptors belong to the scavenger receptor cysteine-rich (SRCR superfamily and are encoded by a multi-gene family. Expression of particular WC1 genes defines functional subpopulations of WC1+ γδ T cells. We have previously identified partial or complete genomic sequences for thirteen different WC1 genes through annotation of the bovine genome Btau_3.1 build. We also identified two WC1 cDNA sequences from other cattle that did not correspond to sequences in the Btau_3.1 build. Their absence in the Btau_3.1 build may have reflected gaps in the genome assembly or polymorphisms among animals. Since the response of γδ T cells to bacterial challenge is determined by WC1 gene expression, it was critical to understand whether individual cattle or breeds differ in the number of WC1 genes or display polymorphisms. Results Real-time quantitative PCR using DNA from the animal whose genome was sequenced (“Dominette” and sixteen other animals representing ten breeds of cattle, showed that the number of genes coding for WC1 co-receptors is thirteen. The complete coding sequences of those thirteen WC1 genes is presented, including the correction of an error in the WC1-2 gene due to mis-assembly in the Btau_3.1 build. All other cDNA sequences were found to agree with the previous annotation of complete or partial WC1 genes. PCR amplification and sequencing of the most variable N-terminal SRCR domain (domain 1 which has the SRCR “a” pattern of each of the thirteen WC1 genes showed that the sequences are highly conserved among individuals and breeds. Of 160 sequences of domain 1 from three breeds of cattle, no additional sequences beyond the thirteen described WC1 genes were found. Analysis of the complete WC1 cDNA sequences indicated that the thirteen WC1 genes code for three distinct WC1 molecular forms. Conclusion The bovine WC1 multi-gene family is composed of thirteen genes coding for three structural forms whose

  12. Cpeb4-mediated translational regulatory circuitry controls terminal erythroid differentiation.

    Science.gov (United States)

    Hu, Wenqian; Yuan, Bingbing; Lodish, Harvey F

    2014-09-29

    While we have considerable understanding of the transcriptional networks controlling mammalian cell differentiation, our knowledge of posttranscriptional regulatory events is very limited. Using differentiation of primary erythroid cells as a model, we show that the sequence-specific mRNA-binding protein Cpeb4 is strongly induced by the erythroid-important transcription factors Gata1 and Tal1 and is essential for terminal erythropoiesis. By interacting with the translation initiation factor eIF3, Cpeb4 represses the translation of a large set of mRNAs, including its own mRNA. Thus, transcriptional induction and translational repression combine to form a negative feedback loop to control Cpeb4 protein levels within a specific range that is required for terminal erythropoiesis. Our study provides an example of how translational control is integrated with transcriptional regulation to precisely control gene expression during mammalian cell differentiation. Copyright © 2014 Elsevier Inc. All rights reserved.

  13. Wide band gap semiconductor templates

    Energy Technology Data Exchange (ETDEWEB)

    Arendt, Paul N. (Los Alamos, NM); Stan, Liliana (Los Alamos, NM); Jia, Quanxi (Los Alamos, NM); DePaula, Raymond F. (Santa Fe, NM); Usov, Igor O. (Los Alamos, NM)

    2010-12-14

    The present invention relates to a thin film structure based on an epitaxial (111)-oriented rare earth-Group IVB oxide on the cubic (001) MgO terminated surface and the ion-beam-assisted deposition ("IBAD") techniques that are amendable to be over coated by semiconductors with hexagonal crystal structures. The IBAD magnesium oxide ("MgO") technology, in conjunction with certain template materials, is used to fabricate the desired thin film array. Similarly, IBAD MgO with appropriate template layers can be used for semiconductors with cubic type crystal structures.

  14. A SEMIOLOGIC APPROACH TO AUDIT EXPECTATIONS GAP

    Directory of Open Access Journals (Sweden)

    Ciolpan Daniela

    2009-05-01

    Full Text Available Audit expectations gap (AEG is one of the most debated phenomena animating the international scientific research scene. The volume of papers focused on defining the AEG concept, examining its determinants, implications, and mechanisms to minimize the gap

  15. The human SUMF1 gene, required for posttranslational sulfatase modification, defines a new gene family which is conserved from pro- to eukaryotes.

    Science.gov (United States)

    Landgrebe, Jobst; Dierks, Thomas; Schmidt, Bernhard; von Figura, Kurt

    2003-10-16

    Recently, the human C(alpha)-formylglycine (FGly)-generating enzyme (FGE), whose deficiency causes the autosomal-recessively transmitted lysosomal storage disease multiple sulfatase deficiency (MSD), has been identified. In sulfatases, FGE posttranslationally converts a cysteine residue to FGly, which is part of the catalytic site and is essential for sulfatase activity. FGE is encoded by the sulfatase modifying factor 1 (SUMF1) gene, which defines a new gene family comprising orthologs from prokaryotes to higher eukaryotes. The genomes of E. coli, S. cerevisiae and C. elegans lack SUMF1, indicating a phylogenetic gap and the existence of an alternative FGly-generating system. The genomes of vertebrates including mouse, man and pufferfish contain a sulfatase modifying factor 2 (SUMF2) gene encoding an FGE paralog of unknown function. SUMF2 evolved from a single exon SUMF1 gene as found in diptera prior to divergent intron acquisition. In several prokaryotic genomes, the SUMF1 gene is cotranscribed with genes encoding sulfatases which require FGly modification. The FGE protein contains a single domain that is made up of three highly conserved subdomains spaced by nonconserved sequences of variable lengths. The similarity among the eukaryotic FGE orthologs varies between 72% and 100% for the three subdomains and is highest for the C-terminal subdomain, which is a hotspot for mutations in MSD patients.

  16. "Explaining the Gender Wage Gap in Georgia"

    OpenAIRE

    Khitarishvili, Tamar

    2009-01-01

    This paper evaluates gender wage differentials in Georgia between 2000 and 2004. Using ordinary least squares, we find that the gender wage gap in Georgia is substantially higher than in other transition countries. Correcting for sample selection bias using the Heckman approach further increases the gender wage gap. The Blinder Oaxaca decomposition results suggest that most of the wage gap remains unexplained. The explained portion of the gap is almost entirely attributed to industrial variab...

  17. Gap Year: Time off, with a Plan

    Science.gov (United States)

    Torpey, Elka Maria

    2009-01-01

    A gap year allows people to step off the usual educational or career path and reassess their future. According to people who have taken a gap year, the time away can be well worth it. This article can help a person decide whether to take a gap year and how to make the most of his time off. It describes what a gap year is, including its pros and…

  18. A large-scale biomass bulk terminal

    OpenAIRE

    Wu, M.R.

    2012-01-01

    This research explores the possibility of a large-scale bulk terminal in West Europe dedicated to handle solid and liquid biomass materials. Various issues regarding the conceptual design of such a terminal have been investigated and demonstrated in this research: the potential biomass materials that will be the major international trade flows in the future, the characteristics of these potential biomass materials, the interaction between the material properties and terminal equipment, the pe...

  19. Dynamic optimization problems with bounded terminal conditions

    Science.gov (United States)

    Lee, A. Y.

    1987-01-01

    Bounded terminal conditions of nonlinear optimization problems are converted to equality terminal conditions via Valentine's device. In so doing, additional unknown parameters are introduced into the problem. The transformed problems can still be easily solved using the sequential gradient-restoration algorithm (SGRA) via a simple augmentation of the unknown parameter vector pi. Three example problems with bounded terminal conditions are solved to verify this technique.

  20. Performance Evaluation and Modelling of Container Terminals

    Science.gov (United States)

    Venkatasubbaiah, K.; Rao, K. Narayana; Rao, M. Malleswara; Challa, Suresh

    2017-11-01

    The present paper evaluates and analyzes the performance of 28 container terminals of south East Asia through data envelopment analysis (DEA), principal component analysis (PCA) and hybrid method of DEA-PCA. DEA technique is utilized to identify efficient decision making unit (DMU)s and to rank DMUs in a peer appraisal mode. PCA is a multivariate statistical method to evaluate the performance of container terminals. In hybrid method, DEA is integrated with PCA to arrive the ranking of container terminals. Based on the composite ranking, performance modelling and optimization of container terminals is carried out through response surface methodology (RSM).

  1. Hyper-active gap filling

    Directory of Open Access Journals (Sweden)

    Akira eOmaki

    2015-04-01

    Full Text Available Much work has demonstrated that speakers of verb-final languages are able to construct rich syntactic representations in advance of verb information. This may reflect general architectural properties of the language processor, or it may only reflect a language-specific adaptation to the demands of verb-finality. The present study addresses this issue by examining whether speakers of a verb-medial language (English wait to consult verb transitivity information before constructing filler-gap dependencies, where internal arguments are fronted and hence precede the verb. This configuration makes it possible to investigate whether the parser actively makes representational commitments on the gap position before verb transitivity information becomes available. A key prediction of the view that rich pre-verbal structure-building is a general architectural property is that speakers of verb-medial languages should predictively construct dependencies in advance of verb transitivity information, and therefore that disruption should be observed when the verb has intransitive subcategorization frames that are incompatible with the predicted structure. In three reading experiments (self-paced and eye-tracking that manipulated verb transitivity, we found evidence for reading disruption when the verb was intransitive, although no such reading difficulty was observed when the critical verb was embedded inside a syntactic island structure, which blocks filler-gap dependency completion. These results are consistent with the hypothesis that in English, as in verb-final languages, information from preverbal NPs is sufficient to trigger active dependency completion without having access to verb transitivity information.

  2. Terminal Control Area Aircraft Scheduling and Trajectory Optimization Approaches

    Directory of Open Access Journals (Sweden)

    Samà Marcella

    2017-01-01

    Full Text Available Aviation authorities are seeking optimization methods to better use the available infrastructure and better manage aircraft movements. This paper deals with the realtime scheduling of take-off and landing aircraft at a busy terminal control area and with the optimization of aircraft trajectories during the landing procedures. The first problem aims to reduce the propagation of delays, while the second problem aims to either minimize the travel time or reduce the fuel consumption. Both problems are particularly complex, since the first one is NP-hard while the second one is nonlinear and a combined solution needs to be computed in a short-time during operations. This paper proposes a framework for the lexicographic optimization of the two problems. Computational experiments are performed for the Milano Malpensa airport and show the existing gaps between the performance indicators of the two problems when different lexicographic optimization approaches are considered.

  3. Genes and Gene Therapy

    Science.gov (United States)

    ... correctly, a child can have a genetic disorder. Gene therapy is an experimental technique that uses genes to ... or prevent disease. The most common form of gene therapy involves inserting a normal gene to replace an ...

  4. The Emissions Gap Report 2015

    DEFF Research Database (Denmark)

    Following the historic signing of the 2030 Agenda for Sustainable Development, this sixth edition of the UNEP Emissions Gap Report comes as world leaders start gathering in Paris to establish a new agreement on climate change. The report offers an independent assessment of the mitigation...... contributions from the Intended Nationally Determined Contributions (INDC) committed to by 1 October 2015, by the 146 countries that account for around 90 per cent of global emissions. It compares the 2030 emission levels that would result from these commitments with what science tells us would keep average...

  5. Filling in biodiversity threat gaps

    DEFF Research Database (Denmark)

    Joppa, L. N.; O'Connor, Brian; Visconti, Piero

    2016-01-01

    he diversity of life on Earth—which provides vital services to humanity (1)—stems from the difference between rates of evolutionary diversification and extinction. Human activities have shifted the balance (2): Species extinction rates are an estimated 1000 times the “background” rate (3) and cou...... into the United Nations' 2030 Agenda for Sustainable Development and its 17 Sustainable Development Goals (SDGs). We identify major gaps in data available for assessing global biodiversity threats and suggest mechanisms for closing them....

  6. A PHOTONIC BAND GAP FIBRE

    DEFF Research Database (Denmark)

    1999-01-01

    An optical fibre having a periodicidal cladding structure provididing a photonic band gap structure with superior qualities. The periodical structure being one wherein high index areas are defined and wherein these are separated using a number of methods. One such method is the introduction...... of additional low index elements, another method is providing elongated elements deformed in relation to a circular cross section. Also described is a cladding structure comprising elongated elements of a material having an index of refraction higher than that of the material adjacent thereto. Using...

  7. Bridging the Vector Calculus Gap

    Science.gov (United States)

    Dray, Tevian; Manogue, Corinne

    2003-05-01

    As with Britain and America, mathematicians and physicists are separated from each other by a common language. In a nutshell, mathematics is about functions, but physics is about things. For the last several years, we have led an NSF-supported effort to "bridge the vector calculus gap" between mathematics and physics. The unifying theme we have discovered is to emphasize geometric reasoning, not (just) algebraic computation. In this talk, we will illustrate the language differences between mathematicians and physicists, and how we are trying reconcile them in the classroom. For further information about the project go to: http://www.physics.orst.edu/bridge

  8. What Proportion of Terminally Ill and Dying People Require Specialist Palliative Care Services?

    Directory of Open Access Journals (Sweden)

    Donna M. Wilson

    2014-01-01

    Full Text Available Currently, around 55 million people die each year worldwide. That number is expected to increase rapidly with accelerating population aging. Despite growth in the number of palliative care specialists and specialist services in most countries, the prospect of an increasing number of terminally ill and dying persons is daunting. This paper attempts to answer the question: what proportion of terminally ill and dying persons require specialist palliative care services? To address this question and highlight which persons require specialist palliative care, the current state of access to specialist palliative care services and specialists in Canada and other countries is highlighted, along with available evidence-based information on specialist services utilization and the care needs of terminally ill and dying persons. Current evidence and information gaps reveal that this question cannot be answered now, but it should be answered in advance of a crisis of unmet end-of-life care needs with the rising death toll.

  9. Engineering multigene expression in vitro and in vivo with small terminators for T7 RNA polymerase.

    Science.gov (United States)

    Du, Liping; Gao, Rong; Forster, Anthony C

    2009-12-15

    Engineering protein expression in vitro or in vivo is usually straightforward for single genes, but remains challenging for multiple genes because of the requirement of coordinated control. RNA and protein overexpression strategies often exploit T7 RNA polymerase and its natural TPhi Class I terminator. However, this terminator's inefficiency and large size (100 bp) are problematic for multigene construction and expression. Here, we measure the effects of tandem copies of a small (18 bp) Class II T7 terminator from vesicular stomatitis virus on transcription in vitro and on translation in vitro and in vivo. We first test monomeric and dimeric gene constructs, then attempt extension to pentameric gene constructs. "BioBrick" versions of a pET vector and translation factor genes were constructed to facilitate cloning, and His-tags were incorporated to allow copurification of all protein products for relatively unbiased analysis and easy purification. Several results were surprising, including imbalanced expression of the pentameric constructs in vivo, illustrating the value of synthetic biology for investigating gene expression. However, these problems were solved rationally by changing the orders of the genes and by adding extra promoters to the upstream gene or by moving to a more predictable in vitro translation system. These successes were significant, given our initial unexpected results and that we are unaware of another example of coordinated overexpression of five proteins. Our modular, flexible, rational method should further empower synthetic biologists wishing to overexpress multiple proteins simultaneously. 2009 Wiley Periodicals, Inc.

  10. Does a global DNA barcoding gap exist in Annelida?

    Science.gov (United States)

    Kvist, Sebastian

    2016-05-01

    Accurate identification of unknown specimens by means of DNA barcoding is contingent on the presence of a DNA barcoding gap, among other factors, as its absence may result in dubious specimen identifications - false negatives or positives. Whereas the utility of DNA barcoding would be greatly reduced in the absence of a distinct and sufficiently sized barcoding gap, the limits of intraspecific and interspecific distances are seldom thoroughly inspected across comprehensive sampling. The present study aims to illuminate this aspect of barcoding in a comprehensive manner for the animal phylum Annelida. All cytochrome c oxidase subunit I sequences (cox1 gene; the chosen region for zoological DNA barcoding) present in GenBank for Annelida, as well as for "Polychaeta", "Oligochaeta", and Hirudinea separately, were downloaded and curated for length, coverage and potential contaminations. The final datasets consisted of 9782 (Annelida), 5545 ("Polychaeta"), 3639 ("Oligochaeta"), and 598 (Hirudinea) cox1 sequences and these were either (i) used as is in an automated global barcoding gap detection analysis or (ii) further analyzed for genetic distances, separated into bins containing intraspecific and interspecific comparisons and plotted in a graph to visualize any potential global barcoding gap. Over 70 million pairwise genetic comparisons were made and results suggest that although there is a tendency towards separation, no distinct or sufficiently sized global barcoding gap exists in either of the datasets rendering future barcoding efforts at risk of erroneous specimen identifications (but local barcoding gaps may still exist allowing for the identification of specimens at lower taxonomic ranks). This seems to be especially true for earthworm taxa, which account for fully 35% of the total number of interspecific comparisons that show 0% divergence.

  11. The role of Ctk1 kinase in termination of small non-coding RNAs.

    Science.gov (United States)

    Lenstra, Tineke L; Tudek, Agnieszka; Clauder, Sandra; Xu, Zhenyu; Pachis, Spyridon T; van Leenen, Dik; Kemmeren, Patrick; Steinmetz, Lars M; Libri, Domenico; Holstege, Frank C P

    2013-01-01

    Transcription termination in Saccharomyces cerevisiae can be performed by at least two distinct pathways and is influenced by the phosphorylation status of the carboxy-terminal domain (CTD) of RNA polymerase II (Pol II). Late termination of mRNAs is performed by the CPF/CF complex, the recruitment of which is dependent on CTD-Ser2 phosphorylation (Ser2P). Early termination of shorter cryptic unstable transcripts (CUTs) and small nucleolar/nuclear RNAs (sno/snRNAs) is performed by the Nrd1-Nab3-Sen1 (NNS) complex that binds phosphorylated CTD-Ser5 (Ser5P) via the CTD-interacting domain (CID) of Nrd1p. In this study, mutants of the different termination pathways were compared by genome-wide expression analysis. Surprisingly, the expression changes observed upon loss of the CTD-Ser2 kinase Ctk1p are more similar to those derived from alterations in the Ser5P-dependent NNS pathway, than from loss of CTD-Ser2P binding factors. Tiling array analysis of ctk1Δ cells reveals readthrough at snoRNAs, at many cryptic unstable transcripts (CUTs) and stable uncharacterized transcripts (SUTs), but only at some mRNAs. Despite the suggested predominant role in termination of mRNAs, we observed that a CTK1 deletion or a Pol II CTD mutant lacking all Ser2 positions does not result in a global mRNA termination defect. Rather, termination defects in these strains are widely observed at NNS-dependent genes. These results indicate that Ctk1p and Ser2 CTD phosphorylation have a wide impact in termination of small non-coding RNAs but only affect a subset of mRNA coding genes.

  12. The role of Ctk1 kinase in termination of small non-coding RNAs.

    Directory of Open Access Journals (Sweden)

    Tineke L Lenstra

    Full Text Available Transcription termination in Saccharomyces cerevisiae can be performed by at least two distinct pathways and is influenced by the phosphorylation status of the carboxy-terminal domain (CTD of RNA polymerase II (Pol II. Late termination of mRNAs is performed by the CPF/CF complex, the recruitment of which is dependent on CTD-Ser2 phosphorylation (Ser2P. Early termination of shorter cryptic unstable transcripts (CUTs and small nucleolar/nuclear RNAs (sno/snRNAs is performed by the Nrd1-Nab3-Sen1 (NNS complex that binds phosphorylated CTD-Ser5 (Ser5P via the CTD-interacting domain (CID of Nrd1p. In this study, mutants of the different termination pathways were compared by genome-wide expression analysis. Surprisingly, the expression changes observed upon loss of the CTD-Ser2 kinase Ctk1p are more similar to those derived from alterations in the Ser5P-dependent NNS pathway, than from loss of CTD-Ser2P binding factors. Tiling array analysis of ctk1Δ cells reveals readthrough at snoRNAs, at many cryptic unstable transcripts (CUTs and stable uncharacterized transcripts (SUTs, but only at some mRNAs. Despite the suggested predominant role in termination of mRNAs, we observed that a CTK1 deletion or a Pol II CTD mutant lacking all Ser2 positions does not result in a global mRNA termination defect. Rather, termination defects in these strains are widely observed at NNS-dependent genes. These results indicate that Ctk1p and Ser2 CTD phosphorylation have a wide impact in termination of small non-coding RNAs but only affect a subset of mRNA coding genes.

  13. When gaps really are gaps: statistical phylogeography of hydrothermal vent invertebrates.

    Science.gov (United States)

    Audzijonyte, Asta; Vrijenhoek, Robert C

    2010-08-01

    The invertebrate animals endemic to deep-sea hydrothermal vents are distributed intermittently along relatively linear oceanic ridge axes. A one-dimensional stepping-stone model, therefore, provides a reasonable starting hypothesis of population structure for these species. Nevertheless, population genetic studies of many species from eastern Pacific vents did not detect the expected signatures of isolation-by-distance (IBD). Instead, distinct patterns of geographical subdivision have been attributed to the unique dispersal modes of individual species, topographical discontinuities of the ridge axes, nonequilibrium metapopulation scenarios and cryptic species. Here, we reexamined these inferences in light of expectations generated by computer simulations of a one-dimensional stepping-stone model. We evaluated whether the previously inferred subdivisions are statistically robust to an alternative explanation that continuous stepping-stone migration has occurred along the ridge axes but discontinuities in the sampling design (gaps) have generated the apparent disjunctions. We found that previous inferences about barriers to gene flow (vicariance) were supported in many cases, but that failures to detect evidence for IBD could be explained by low statistical power associated with the sampling effort. The simulation approaches presented here might be useful for testing the significance of inferred phylogeographic gaps in other species.

  14. Closing the mycetoma knowledge gap.

    Science.gov (United States)

    van de Sande, Wendy; Fahal, Ahmed; Ahmed, Sarah Abdalla; Serrano, Julian Alberto; Bonifaz, Alexandro; Zijlstra, Ed

    2017-09-09

    On 28th May 2016, mycetoma was recognized as a neglected tropical disease by the World Health Organization. This was the result of a 4-year journey starting in February 2013 with a meeting of global mycetoma experts. Knowledge gaps were identified and included the incidence, prevalence, and mapping of mycetoma; the mode of transmission; the development of methods for early diagnosis; and better treatment. In this review, we review the road to recognition, the ISHAM working group meeting in Argentina, and we address the progress made in closing the knowledge gaps since 2013. Progress included adding another 9000 patients to the literature, which allowed us to update the prevalence map on mycetoma. Furthermore, based on molecular phylogeny, species names were corrected and four novel mycetoma causative agents were identified. By mapping mycetoma causative agents an association with Acacia trees was found. For early diagnosis, three different isothermal amplification techniques were developed, and novel antigens were discovered. To develop better treatment strategies for mycetoma patients, in vitro susceptibility tests for the coelomycete agents of black grain mycetoma were developed, and the first randomized clinical trial for eumycetoma started early 2017. © The Author 2017. Published by Oxford University Press on behalf of The International Society for Human and Animal Mycology. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  15. St. James marine terminal facility description

    Energy Technology Data Exchange (ETDEWEB)

    1993-10-01

    The US Department of Energy (DOE) currently owns and operates a marine terminal on the west bank of the Mississippi River at St. James, Louisiana. The St. James facility was constructed by the Department to provide marine services associated with the fill and drawdown of the Strategic Petroleum Reserve (SPR) crude oil storage facilities located at Bayou Choctaw and Weeks Island, Louisiana. Although strategic to the mission of the SPR in the event of a national emergency, the St. James terminal is situated such that it has a high potential to also serve the commercial industry`s needs for crude oil terminalling and storage. The St. James terminal is located approximately 45 miles west of New Orleans and 30 miles southeast of Baton Rouge, and approximately 160 miles upstream from the mouth of the Mississippi River. Construction of the St. James terminal was initiated in 1978 and was completed in 1980. Since then, the terminal has received and transferred over 125 million barrels of crude oil to the SPR sites for storage. For crude oil distribution, the St. James terminal was connected to the neighboring LOCAP terminal by a 0.1 mile 36-inch pipeline in 1981 and to the Capline terminal by a 0.5 mile 30-inch pipeline in 1988. The terminal also has a 30-inch pipeline connection to the Koch oil terminal which was used for initial fill purposes; however, this pipeline has been disconnected and is currently inactive. A complete description of the St. James terminal facilities, operational capabilities, operational certifications, and future Government requirements are presented in Sections 2, 3, 4, and 5 respectively.

  16. Innovation gaps in Scandinavian rural tourism

    DEFF Research Database (Denmark)

    Hjalager, Anne Mette; Kwiatkowski, Grzegorz; Østervig Larsen, Martin

    2018-01-01

    that rural tourism has its basis in a dichotomy between authenticity and modernization. New and prospective customer groups, particularly from Germany, demand more diversified and higher quality rural tourism products than current groups, for example, in relation to outdoor opportunities, leisure festivals......© 2017 Informa UK Limited, trading as Taylor & Francis Group Drawing on primary data from a consumer survey (N = 2000), this study demonstrates a clear growth potential in rural tourism in Denmark, Norway, and Sweden, which is, however, hampered by innovation gaps. At the conceptual level......, the study offers a model that identifies the following five innovation gaps in Scandinavian rural tourism: (1) the portfolio gap, (2) the policy departmentalization gap, (3) the knowledge gap, (4) the change motivation gap, and (5) the resource interpretation gap. At the empirical level, the study shows...

  17. Electronic properties of doped gapped graphene

    Energy Technology Data Exchange (ETDEWEB)

    Mousavi, Hamze, E-mail: hamze.mousavi@gmail.com [Department of Physics, Razi University, Kermanshah (Iran, Islamic Republic of); Nano Science and Nano Technology Research Center, Razi University, Kermanshah (Iran, Islamic Republic of)

    2013-04-01

    One of the carbon atoms in each Bravais lattice unit cell of pristine graphene plane is substituted by a foreign atom leading to a band gap in the density of states of the system. Then, the gapped graphene is randomly doped by another impurity. The density of states, electronic heat capacity and electrical conductivity of the gapped and doped gapped graphene are investigated within random tight-binding Hamiltonian model and Green's function formalism. The results show that by presence of impurities in the gapped graphene the band gap moves towards lower (higher) values of energy when dopants act as acceptors (donors). The heat capacity decreases (increases) before (after) the Schottky anomaly as well. It is also found that the electrical conductivity of the doped gapped graphene reduces on all ranges of temperature.

  18. 78 FR 5717 - Safety Zone; Military Ocean Terminal Concord Safety Zone, Suisun Bay, Military Ocean Terminal...

    Science.gov (United States)

    2013-01-28

    ... SECURITY Coast Guard 33 CFR Part 165 RIN 1625-AA00 Safety Zone; Military Ocean Terminal Concord Safety Zone, Suisun Bay, Military Ocean Terminal Concord, CA AGENCY: Coast Guard, DHS. ACTION: Interim rule and... Suisun Bay near Military Ocean Terminal Concord, CA in support of military onload and offload operations...

  19. Challenges encountered by women seeking termination of ...

    African Journals Online (AJOL)

    The purpose of the study was to identify possible challenges that prevented women from utilising termination of pregnancy services in the North West Province of South Africa. Fifty structured interviews were conducted with conveniently selected women who requested termination of pregnancy services but who could not ...

  20. A large-scale biomass bulk terminal

    NARCIS (Netherlands)

    Wu, M.R.

    2012-01-01

    This research explores the possibility of a large-scale bulk terminal in West Europe dedicated to handle solid and liquid biomass materials. Various issues regarding the conceptual design of such a terminal have been investigated and demonstrated in this research: the potential biomass materials

  1. [Terminal phase hydration, pain and delirium

    DEFF Research Database (Denmark)

    Heick, A.

    2009-01-01

    Hydration of the terminal patient may relieve confusion and complaints of "dry mouth". But it may worsen oedema of the brain, lungs, and extremities, worsen terminal rattling and cause a need for frequent changing of diapers. The decision of whether and how to treat a dying patient with fluids sh...

  2. 29 CFR 406.4 - Terminal report.

    Science.gov (United States)

    2010-07-01

    ... immediately prior to the time of the person's loss of reporting identity (or by the person himself if he is an individual), together with a statement of the effective date of termination or loss of reporting identity... year ending on the effective date of the termination or loss of identity. ...

  3. Functionalization of hydroxyl terminated polybutadiene with ...

    Indian Academy of Sciences (India)

    ... hydroxyl value and microstructure of the parent HTPB. The formation of hydrogen bonding between the terminal hydroxyl groups and the nitrogen atoms of triazine moiety is the driving force for the terminal attachment chemistry. The functionalized HTPB (HTPB–CBDT) shows a strong fluorescence emission at 385 nm.

  4. 30 CFR 755.15 - Termination.

    Science.gov (United States)

    2010-07-01

    ... Resources OFFICE OF SURFACE MINING RECLAMATION AND ENFORCEMENT, DEPARTMENT OF THE INTERIOR INDIAN LANDS... by either party upon written notice to the other specifying the date upon which the agreement will be terminated. The date of termination shall be no less than 30 days from the date of the notice. ...

  5. Multidisciplinary care of the terminally ill patient.

    Science.gov (United States)

    O'Mahony, S; Coyle, N; Payne, R

    2000-04-01

    This article discusses sedation, the assessment and management of physical symptoms, and symptom-assessment scales for the terminally ill patient. The evaluation of the ability of the family or community to care for a terminally ill patient in pain also is discussed.

  6. Bargaining in Mergers and Termination Fees

    NARCIS (Netherlands)

    Weitzel, U.; Rosenkranz, S.

    We model takeovers as a bargaining process and explain termination fees for, both, the target and the acquirer, subject to parties’ bargaining power and outside options. In equilibrium, termination fees are offered by firms with outside options in exchange for a greater share of merger synergies.

  7. 9 CFR 3.65 - Terminal facilities.

    Science.gov (United States)

    2010-01-01

    ... 9 Animals and Animal Products 1 2010-01-01 2010-01-01 false Terminal facilities. 3.65 Section 3.65... WELFARE STANDARDS Specifications for the Humane Handling, Care, Treatment and Transportation of Rabbits Transportation Standards § 3.65 Terminal facilities. No person subject to the Animal Welfare regulations shall...

  8. 9 CFR 3.141 - Terminal facilities.

    Science.gov (United States)

    2010-01-01

    ... 9 Animals and Animal Products 1 2010-01-01 2010-01-01 false Terminal facilities. 3.141 Section 3... ANIMAL WELFARE STANDARDS Specifications for the Humane Handling, Care, Treatment, and Transportation of... Mammals Transportation Standards § 3.141 Terminal facilities. Carriers and intermediate handlers shall not...

  9. 9 CFR 3.40 - Terminal facilities.

    Science.gov (United States)

    2010-01-01

    ... 9 Animals and Animal Products 1 2010-01-01 2010-01-01 false Terminal facilities. 3.40 Section 3.40... WELFARE STANDARDS Specifications for the Humane Handling, Care, Treatment, and Transportation of Guinea Pigs and Hamsters Transportation Standards § 3.40 Terminal facilities. No person subject to the Animal...

  10. In situ controlled heteroepitaxy of single-domain GaP on As-modified Si(100)

    Energy Technology Data Exchange (ETDEWEB)

    Supplie, Oliver, E-mail: oliver.supplie@tu-ilmenau.de; May, Matthias M. [Institut für Physik, Technische Universität Ilmenau, Gustav-Kirchhoff-Str. 5, 98693 Ilmenau (Germany); Institute for Solar Fuels, Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Hahn-Meitner-Platz 1, 14109 Berlin (Germany); Institut für Physik, Humboldt-Universität zu Berlin, Newtonstr. 15, 12489 Berlin (Germany); Kleinschmidt, Peter; Nägelein, Andreas; Paszuk, Agnieszka [Institut für Physik, Technische Universität Ilmenau, Gustav-Kirchhoff-Str. 5, 98693 Ilmenau (Germany); Brückner, Sebastian; Hannappel, Thomas, E-mail: thomas.hannappel@tu-ilmenau.de [Institut für Physik, Technische Universität Ilmenau, Gustav-Kirchhoff-Str. 5, 98693 Ilmenau (Germany); Institute for Solar Fuels, Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Hahn-Meitner-Platz 1, 14109 Berlin (Germany)

    2015-12-01

    Metalorganic vapor phase epitaxy of III-V compounds commonly involves arsenic. We study the formation of atomically well-ordered, As-modified Si(100) surfaces and subsequent growth of GaP/Si(100) quasisubstrates in situ with reflection anisotropy spectroscopy. Surface symmetry and chemical composition are measured by low energy electron diffraction and X-ray photoelectron spectroscopy, respectively. A two-step annealing procedure of initially monohydride-terminated, (1 × 2) reconstructed Si(100) in As leads to a predominantly (1 × 2) reconstructed surface. GaP nucleation succeeds analogously to As-free systems and epilayers free of antiphase disorder may be grown subsequently. The GaP sublattice orientation, however, is inverted with respect to GaP growth on monohydride-terminated Si(100)

  11. Controlling the polarity of metalorganic vapor phase epitaxy-grown GaP on Si(111) for subsequent III-V nanowire growth

    Energy Technology Data Exchange (ETDEWEB)

    Paszuk, A.; Steidl, M.; Zhao, W.; Dobrich, A.; Kleinschmidt, P. [Technische Universität Ilmenau, Institut für Physik, 98693 Ilmenau (Germany); Brückner, S.; Supplie, O.; Hannappel, T. [Technische Universität Ilmenau, Institut für Physik, 98693 Ilmenau (Germany); Helmholtz-Zentrum Berlin, Institute for Solar Fuels, 14109 Berlin (Germany); Prost, W. [Center for Semiconductor Technology and Optoelectronics (ZHO), University of Duisburg-Essen, 47057 Duisburg (Germany)

    2015-06-08

    Nanowire growth on heteroepitaxial GaP/Si(111) by metalorganic vapor phase epitaxy requires the [-1-1-1] face, i.e., GaP(111) material with B-type polarity. Low-energy electron diffraction (LEED) allows us to identify the polarity of GaP grown on Si(111), since (2×2) and (1×1) surface reconstructions are associated with GaP(111)A and GaP(111)B, respectively. In dependence on the pre-growth treatment of the Si(111) substrates, we were able to control the polarity of the GaP buffers. GaP films grown on the H-terminated Si(111) surface exhibited A-type polarity, while GaP grown on Si surfaces terminated with arsenic exhibited a (1×1) LEED pattern, indicating B-type polarity. We obtained vertical GaAs nanowire growth on heteroepitaxial GaP with (1×1) surface reconstruction only, in agreement with growth experiments on homoepitaxially grown GaP(111)

  12. Weather data gap problem resolved

    Science.gov (United States)

    Bush, Susan

    It looks as though the United States will avoid the crisis situation of a gap in weather data resulting from the aging GOES-7 satellite and technical problems with the next generation of weather satellites (GOESNEXT). Officials at the National Oceanic and Atmospheric Administration, which oversees the National Weather Service, recently announced their decision to borrow at least one and possibly several European satellites until the GOES-NEXT program gets off the ground.The GOES (Geostationary Operational Environmental Satellites) series is currently 3 years behind schedule and $500 million over budget. Problems with its complex design, program management by both NOAA and the National Aeronautics and Space Administration and poor performance by the contractor led Department of Commerce Secretary Robert Mosbacher to slow down the GOES-NEXT series to ensure that it is built right.

  13. Two-terminal video coding.

    Science.gov (United States)

    Yang, Yang; Stanković, Vladimir; Xiong, Zixiang; Zhao, Wei

    2009-03-01

    Following recent works on the rate region of the quadratic Gaussian two-terminal source coding problem and limit-approaching code designs, this paper examines multiterminal source coding of two correlated, i.e., stereo, video sequences to save the sum rate over independent coding of both sequences. Two multiterminal video coding schemes are proposed. In the first scheme, the left sequence of the stereo pair is coded by H.264/AVC and used at the joint decoder to facilitate Wyner-Ziv coding of the right video sequence. The first I-frame of the right sequence is successively coded by H.264/AVC Intracoding and Wyner-Ziv coding. An efficient stereo matching algorithm based on loopy belief propagation is then adopted at the decoder to produce pixel-level disparity maps between the corresponding frames of the two decoded video sequences on the fly. Based on the disparity maps, side information for both motion vectors and motion-compensated residual frames of the right sequence are generated at the decoder before Wyner-Ziv encoding. In the second scheme, source splitting is employed on top of classic and Wyner-Ziv coding for compression of both I-frames to allow flexible rate allocation between the two sequences. Experiments with both schemes on stereo video sequences using H.264/AVC, LDPC codes for Slepian-Wolf coding of the motion vectors, and scalar quantization in conjunction with LDPC codes for Wyner-Ziv coding of the residual coefficients give a slightly lower sum rate than separate H.264/AVC coding of both sequences at the same video quality.

  14. Genome scanning for identification of resistance gene analogs ...

    African Journals Online (AJOL)

    Disease resistance in plants is a desirable economic trait. Many disease resistance genes from various plants have been cloned so far. The gene products of some of these can be distinguished by the presence of an N terminal nucleotide binding site and a C-terminal stretch of leucine-rich repeats. Oligonucleotides already ...

  15. Muscleblind-like 1 (Mbnl1) regulates pre-mRNA alternative splicing during terminal erythropoiesis.

    Science.gov (United States)

    Cheng, Albert W; Shi, Jiahai; Wong, Piu; Luo, Katherine L; Trepman, Paula; Wang, Eric T; Choi, Heejo; Burge, Christopher B; Lodish, Harvey F

    2014-07-24

    The scope and roles of regulated isoform gene expression during erythroid terminal development are poorly understood. We identified hundreds of differentiation-associated isoform changes during terminal erythropoiesis. Sequences surrounding cassette exons of skipped exon events are enriched for motifs bound by the Muscleblind-like (MBNL) family of splicing factors. Knockdown of Mbnl1 in cultured murine fetal liver erythroid progenitors resulted in a strong block in erythroid differentiation and disrupted the developmentally regulated exon skipping of Ndel1 mRNA, which is bound by MBNL1 and critical for erythroid terminal proliferation. These findings reveal an unanticipated scope of the alternative splicing program and the importance of Mbnl1 during erythroid terminal differentiation. © 2014 by The American Society of Hematology.

  16. Participation of Private Investors in Container Terminal Operation: Influence of Global Terminal Operators

    Directory of Open Access Journals (Sweden)

    Heejung YEO

    2015-09-01

    Full Text Available Private container terminal operators have begun to participate in the port business in Asia since the late 1980s. Terminal operators decide whether to invest in terminal infrastructures, and the enhancement of the quality of service level. The paper analyses the influence of global terminal operators and the port ownership structure on the container terminal's efficiency. Two hundred and sixty container terminal data for China, Korea, and Japan were collected. The paper applies a negative binomial regression analysis. The paper finds that the port restructuring has contributed to productivity gains. It is found that the influence of GTO on the efficiency is evident and positively related to the port efficiency. The paper also finds that the country effect prevails over a terminal operator group effect.

  17. Concept Layout Model of Transportation Terminals

    Directory of Open Access Journals (Sweden)

    Li-ya Yao

    2012-01-01

    Full Text Available Transportation terminal is the key node in transport systems. Efficient terminals can improve operation of passenger transportation networks, adjust the layout of public transportation networks, provide a passenger guidance system, and regulate the development of commercial forms, as well as optimize the assembly and distribution of modern logistic modes, among others. This study aims to clarify the relationship between the function and the structure of transportation terminals and establish the function layout design. The mapping mechanism of demand, function, and structure was analyzed, and a quantitative relationship between function and structure was obtained from a design perspective. Passenger demand and terminal structure were decomposed into several demand units and structural elements following the principle of reverse engineering. The relationship maps between these two kinds of elements were then analyzed. Function-oriented concept layout model of transportation terminals was established using the previous method. Thus, a technique in planning and design of transportation structures was proposed. Meaningful results were obtained from the optimization of transportation terminal facilities, which guide the design of the functional layout of transportation terminals and improve the development of urban passenger transportation systems.

  18. Disengaging polymerase: Terminating RNA polymerase II transcription in budding yeast☆

    Science.gov (United States)

    Mischo, Hannah E.; Proudfoot, Nick J.

    2013-01-01

    Termination of transcription by RNA polymerase II requires two distinct processes: The formation of a defined 3′ end of the transcribed RNA, as well as the disengagement of RNA polymerase from its DNA template. Both processes are intimately connected and equally pivotal in the process of functional messenger RNA production. However, research in recent years has elaborated how both processes can additionally be employed to control gene expression in qualitative and quantitative ways. This review embraces these new findings and attempts to paint a broader picture of how this final step in the transcription cycle is of critical importance to many aspects of gene regulation. This article is part of a Special Issue entitled: RNA polymerase II Transcript Elongation. PMID:23085255

  19. National GAP Conference 2007-Discussion Groups Report

    Science.gov (United States)

    Ratz, Joan M.; Lamb, Berton Lee

    2010-01-01

    We led two discussion groups during the 2007 National GAP Conference. These discussion groups provided information to help develop a survey of National Gap Analysis Program (GAP) data users. One group discussed technical issues, and the second group discussed the use of GAP data for decisionmaking. Themes emerging from the technical issues group included concerns about data quality, need for information on how to use data, and passive data distribution. The decisionmaking discussion included a wide range of topics including the need to understand presentation of information, the need to connect with and understand users of data, the revision of GAP's mission, and the adaptability of products and data. The decisionmaking group also raised concerns regarding technical issues. One conclusion is that a deep commitment to ongoing information transfer and support is a key component of success for the GAP program.

  20. Relating the defect band gap and the density functional band gap

    Science.gov (United States)

    Schultz, Peter; Edwards, Arthur

    2014-03-01

    Density functional theory (DFT) is an important tool to probe the physics of materials. The Kohn-Sham (KS) gap in DFT is typically (much) smaller than the observed band gap for materials in nature, the infamous ``band gap problem.'' Accurate prediction of defect energy levels is often claimed to be a casualty--the band gap defines the energy scale for defect levels. By applying rigorous control of boundary conditions in size-converged supercell calculations, however, we compute defect levels in Si and GaAs with accuracies of ~0.1 eV, across the full gap, unhampered by a band gap problem. Using GaAs as a theoretical laboratory, we show that the defect band gap--the span of computed defect levels--is insensitive to variations in the KS gap (with functional and pseudopotential), these KS gaps ranging from 0.1 to 1.1 eV. The defect gap matches the experimental 1.52 eV gap. The computed defect gaps for several other III-V, II-VI, I-VII, and other compounds also agree with the experimental gap, and show no correlation with the KS gap. Where, then, is the band gap problem? This talk presents these results, discusses why the defect gap and the KS gap are distinct, implying that current understanding of what the ``band gap problem'' means--and how to ``fix'' it--need to be rethought. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Company, for the U.S. Department of Energy's NNSA under contract DE-AC04-94AL85000.

  1. A PCR-based strategy to generate yeast strains expressing endogenous levels of amino-terminal epitope-tagged proteins.

    Science.gov (United States)

    Booher, Keith R; Kaiser, Peter

    2008-04-01

    An epitope tag introduced to a gene of interest (GOI) greatly increases the ease of studying cellular proteins. Rapid PCR-based strategies for epitope tagging a protein's C-terminus at its native gene locus are widely used in yeast. C-terminal epitope tagging is not suitable for all proteins, however. Epitope tags fused to the C-terminus can interfere with function of some proteins or can even be removed by C-terminal protein processing. To overcome such problems, proteins can be tagged with epitopes at their amino-termini, but generating yeast strains expressing N-terminal epitope tagged genes under control of the endogenous promoter at the native locus is comparatively more difficult. Strategies to introduce N-terminal epitope tags have been reported previously but often introduce additional sequences other than the epitope tag into the genome. Furthermore, N-terminal tagging of essential genes by current methods requires formation of diploid strains followed by tetrad dissection or expression of an additional copy of the GOI from a plasmid. The strategies described here provide a quick, facile means of epitope tagging the N-terminus of both essential and nonessential genes in a two-step PCR-based procedure. The procedure has the significant advantage of leaving tagged genes under the control of their endogenous promoters, and no additional sequences other than the epitope tag encoding nucleotides are inserted into the genome.

  2. PBX 9502 air-gap tests

    Energy Technology Data Exchange (ETDEWEB)

    Dickson, Peter [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Novak, Alan M. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Foley, Timothy J. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Campbell, Christopher Charles [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2017-06-29

    A small number of simple air-gap tests were performed on 1-inch diameter PBX 9502 cylinders to determine an approximate threshold for detonation failure. The primary diagnostics were streak imaging and dent measurements in a steel witness plate. Relight was found to occur, with negligible excess transit time, for air gaps up to 1 mm. Relight did not occur with a 3-mm air gap.

  3. The Early Career Gender Wage Gap

    OpenAIRE

    Sami Napari

    2006-01-01

    In Finland the gender wage gap increases significantly during the first 10 years after labor market entry accounting most of the life-time increase in the gender wage gap. This paper focuses on the early career gender wage differences among university graduates and considers several explanations for the gender wage gap based on the human capital theory, job mobility and labor market segregation. Gender differences in the accumulation of experience and in the type of education explain about 16...

  4. The Gender Wealth Gap Across European Countries

    OpenAIRE

    Schneebaum, Alyssa; Rehm, Miriam; Mader, Katharina; Hollan, Katarina

    2017-01-01

    This paper studies the gap in wealth between male and female single households using 2010 Household Finance and Consumption Survey data for eight European countries. In the raw data, a large gap emerges at the upper end of the unconditional distribution. While OLS estimates show no difference in average net wealth levels, quantile regressions at the 95th percentile yield mixed evidence for the gender wealth gap in different specifications. Labour market characteristics and participation in as...

  5. Bridging the gap: from massive stars to supernovae

    Science.gov (United States)

    Maund, Justyn R.; Crowther, Paul A.; Janka, Hans-Thomas; Langer, Norbert

    2017-09-01

    Almost since the beginning, massive stars and their resultant supernovae have played a crucial role in the Universe. These objects produce tremendous amounts of energy and new, heavy elements that enrich galaxies, encourage new stars to form and sculpt the shapes of galaxies that we see today. The end of millions of years of massive star evolution and the beginning of hundreds or thousands of years of supernova evolution are separated by a matter of a few seconds, in which some of the most extreme physics found in the Universe causes the explosive and terminal disruption of the star. Key questions remain unanswered in both the studies of how massive stars evolve and the behaviour of supernovae, and it appears the solutions may not lie on just one side of the explosion or the other or in just the domain of the stellar evolution or the supernova astrophysics communities. The need to view massive star evolution and supernovae as continuous phases in a single narrative motivated the Theo Murphy international scientific meeting `Bridging the gap: from massive stars to supernovae' at Chicheley Hall, UK, in June 2016, with the specific purpose of simultaneously addressing the scientific connections between theoretical and observational studies of massive stars and their supernovae, through engaging astronomers from both communities. This article is part of the themed issue 'Bridging the gap: from massive stars to supernovae'.

  6. Bridging the gap: from massive stars to supernovae.

    Science.gov (United States)

    Maund, Justyn R; Crowther, Paul A; Janka, Hans-Thomas; Langer, Norbert

    2017-10-28

    Almost since the beginning, massive stars and their resultant supernovae have played a crucial role in the Universe. These objects produce tremendous amounts of energy and new, heavy elements that enrich galaxies, encourage new stars to form and sculpt the shapes of galaxies that we see today. The end of millions of years of massive star evolution and the beginning of hundreds or thousands of years of supernova evolution are separated by a matter of a few seconds, in which some of the most extreme physics found in the Universe causes the explosive and terminal disruption of the star. Key questions remain unanswered in both the studies of how massive stars evolve and the behaviour of supernovae, and it appears the solutions may not lie on just one side of the explosion or the other or in just the domain of the stellar evolution or the supernova astrophysics communities. The need to view massive star evolution and supernovae as continuous phases in a single narrative motivated the Theo Murphy international scientific meeting 'Bridging the gap: from massive stars to supernovae' at Chicheley Hall, UK, in June 2016, with the specific purpose of simultaneously addressing the scientific connections between theoretical and observational studies of massive stars and their supernovae, through engaging astronomers from both communities.This article is part of the themed issue 'Bridging the gap: from massive stars to supernovae'. © 2017 The Author(s).

  7. Acetylene terminated aspartimides and resins therefrom

    Science.gov (United States)

    Hergenrother, Paul M. (Inventor); Connell, John W. (Inventor); Havens, Stephen J. (Inventor)

    1989-01-01

    Acetylene terminated aspartimides are prepared using two methods. In the first, an amino-substituted aromatic acetylene is reacted with an aromatic bismaleimide in a solvent of glacial acetic acid and/or m-cresol. In the second method, an aromatic diamine is reacted with an ethynyl containing maleimide, such an N-(3-ethynyl phenyl) maleimide, in a solvent of glacial acetic acid and/or m-cresol. In addition, acetylene terminated aspartimides are blended with various acetylene terminated oligomers and polymers to yield composite materials exhibiting improved mechanical properties.

  8. Operational Optimization in Port Container Terminals

    DEFF Research Database (Denmark)

    As a result of the significant increase in worldwide containerized transportation the development of efficient handling systems in marine terminals has become very important for port competitiveness. In order to optimize the productivity the total handling time for containers in the terminal must...... be minimized. An overview of the different operational problems in port container terminals is presented and an aggregated model and solution approach is shown. Next, there will be focused on the yard storage problem and a mathematical formulation and solution proposals will be presented....

  9. Duplication of the ureter with extravesical termination

    Energy Technology Data Exchange (ETDEWEB)

    Steidle, B.; Wolf, K.J.

    1984-02-01

    The renal segment supplying an ectopic ureter is nearly always dysplastic. Usually the ureters cross and the ectopic ureter terminates caudally in relation to the ureter from the normal portion of the kidney. Extravesical termination in women leads to urinary incontinence, since it frequently ends in the vagina or the labia. In men, the effects are much less noticeable. The ureters usually terminate in the urethra, the seminal vesicles, the ductus deferens or the epididymis. Duplication of a ureter or mega-ureter with dysplasia of the appropriate part of the kidney can be readily explained embryologically.

  10. Tyrolean termination tool: Techniques and features

    OpenAIRE

    Hirokawa, Nao; Middeldorp, Aart

    2007-01-01

    The Tyrolean Termination Tool (T_T for short) is a powerful tool for automatically proving termination of rewrite systems. It incorporates several new refinements of the dependency pair method that are easy to implement, increase the power of the method, result in simpler termination proofs, and make the method more efficient. T_T employs polynomial interpretations with negative coefficients, like x − 1 for a unary function symbol or x − y for a binary function symbol, which are useful for ex...

  11. Redefining yield gaps at various spatial scales

    Science.gov (United States)

    Meng, K.; Fishman, R.; Norstrom, A. V.; Diekert, F. K.; Engstrom, G.; Gars, J.; McCarney, G. R.; Sjostedt, M.

    2013-12-01

    Recent research has highlighted the prevalence of 'yield gaps' around the world and the importance of closing them for global food security. However, the traditional concept of yield gap -defined as the difference between observed and optimal yield under biophysical conditions - omit relevant socio-economic and ecological constraints and thus offer limited guidance on potential policy interventions. This paper proposes alternative definitions of yield gaps by incorporating rich, high resolution, national and sub-national agricultural datasets. We examine feasible efforts to 'close yield gaps' at various spatial scales and across different socio-economic and ecological domains.

  12. Edge-Termination and Core-Modification Effects of Hexagonal Nanosheet Graphene

    Directory of Open Access Journals (Sweden)

    Jin-Pei Deng

    2014-02-01

    Full Text Available Optimized geometries and electronic structures of two different hexagonal grapheme nanosheets (HGNSs, with armchair (n-A-HGNS, n = 3–11 and zigzag (n-Z-HGNS, n = 1–8 edges have been calculated by using the GGA/PBE method implemented in the SIESTA package, with the DZP basis set, where n represents the number of peripheral rings. The computed HOMO-LUMO energy gap (Eg = ELUMO − EHOMO decreases for fully H-terminated A- and Z-HGNSs with increasing n, i.e., with increasing nanosheet size and pπ-orbitals being widely delocalized over the sheet surface. The full terminations, calculated with various functional groups, including the electron-withdrawing (F-, Cl-, and CN- and -donating (OH-, and SH- substitutions, were addressed. Significant lowering of EHOMO and ELUMO was obtained for CN-terminated HGNS as compared to those for H-terminated ones due to the mesomeric effect. The calculated Eg value decreases with increasing n for all terminations, whereby for the SH-termination in HGNS, the termination effect becomes less significant with increasing n. Further, the calculation results for stabilities of HGNS oxides support the tendency toward the oxidative reactivity at the edge site of the sheet, which shows most pronounced C-C bond length alternation, by chemical modification. Physical properties of HGNSs with various numbers of the core-defects, which can be obtained by strong oxidation, were also investigated. Their structures can change drastically from planar to saddle-like shapes. These conformations could be used as stationary phases with controlled interaction in the separation methods such as HPLC and the other chemical analysis techniques.

  13. Heat-shock induction of the human immunodeficiency virus long terminal repeat

    NARCIS (Netherlands)

    Geelen, J. L.; Minnaar, R. P.; Boom, R.; van der Noordaa, J.; Goudsmit, J.

    1988-01-01

    Rat cell lines were established in which the bacterial chloramphenicol acetyltransferase (CAT) gene under control of the human immunodeficiency virus (HIV) long terminal repeat (LTR) was stably integrated. The cell lines showed a repressed phenotype for CAT expression, but could be induced for it by

  14. Intraspecific variability of the terminal inverted repeats of the linear chromosome of Streptomyces ambofaciens.

    Science.gov (United States)

    Choulet, Frédéric; Gallois, Alexandre; Aigle, Bertrand; Mangenot, Sophie; Gerbaud, Claude; Truong, Chantal; Francou, François-Xavier; Borges, Frédéric; Fourrier, Céline; Guérineau, Michel; Decaris, Bernard; Barbe, Valérie; Pernodet, Jean-Luc; Leblond, Pierre

    2006-09-01

    The sequences of the terminal inverted repeats (TIRs) ending the linear chromosomal DNA of two Streptomyces ambofaciens strains, ATCC23877 and DSM40697 (198 kb and 213 kb, respectively), were determined from two sets of recombinant cosmids. Among the 215 coding DNA sequences (CDSs) predicted in the TIRs of strain DSM40697, 65 are absent in the TIRs of strain ATCC23877. Reciprocally, 45 of the 194 predicted CDSs are specific to the ATCC23877 strain. The strain-specific CDSs are located mainly at the terminal end of the TIRs. Indeed, although TIRs appear almost identical over 150 kb (99% nucleotide identity), large regions of DNA of 60 kb (DSM40697) and 48 kb (ATCC23877), mostly spanning the ends of the chromosome, are strain specific. These regions are rich in plasmid-associated genes, including genes encoding putative conjugal transfer functions. The strain-specific regions also share a G+C content (68%) lower than that of the rest of the genome (from 71% to 73%), a percentage that is more typical of Streptomyces plasmids and mobile elements. These data suggest that exchanges of replicon extremities have occurred, thereby contributing to the terminal variability observed at the intraspecific level. In addition, the terminal regions include many mobile genetic element-related genes, pseudogenes, and genes related to adaptation. The results give insight into the mechanisms of evolution of the TIRs: integration of new information and/or loss of DNA fragments and subsequent homogenization of the two chromosomal extremities.

  15. High-yield production of Streptavidin with native C-terminal in ...

    African Journals Online (AJOL)

    To increase the production yield of functional recombinant streptavidin in Escherichia coli, the effects of host strains and culture conditions on expression of streptavidin with native C terminal (CNSA, amino acid residues 13 to 159) were investigated. Results show that the CNSA, encoded by the CNSA gene, was produced ...

  16. Minding the gap: access to palliative care and the homeless.

    Science.gov (United States)

    Huynh, Lise; Henry, Blair; Dosani, Naheed

    2015-11-18

    With an ever increasing number of individuals living with chronic and terminal illnesses, palliative care as an emerging field is poised for unprecedented expansion. Today's rising recognition of its key role in patients' illnesses has led to increased interest in access to palliative care. It is known that homelessness as a social determinant of health has been associated with decreased access to health resources in spite of poorer health outcomes and some would argue, higher need. This article aims to discuss the current state of affairs with regards to accessing palliative care for the homeless in Canada. Recent review of the literature reveals differential access to palliative care services and outcomes with differing socio-economic status (SES). Notably, individuals of lower SES and in particular, those who are homeless have poorer health outcomes in addition to poor access to quality palliative care. Current palliative care services are ill equipped to care for this vulnerable population and most programs are built upon an infrastructure that is prohibitive for the homeless to access its services. A preliminary review of existing Canadian programs in place to address this gap in access identified a paucity of sporadic palliative care programs across the country with a focus on homeless and vulnerably-housed individuals. It is apparent that there is no unified national strategy to address this gap in access. The changing landscape of the Canadian population calls for an expansion of palliative care as a field and as many have put it, as a right. The right to access quality palliative and end of life care should not be confined to particular population groups. This article calls for the development of a unified national strategy to address this glaring gap in our healthcare provision and advocates for attention to and adoption of policy and processes that would support the homeless populations' right to quality palliative care.

  17. Presence and expression of hydrogenase specific C-terminal endopeptidases in cyanobacteria

    Directory of Open Access Journals (Sweden)

    Lindblad Peter

    2003-05-01

    Full Text Available Abstract Background Hydrogenases catalyze the simplest of all chemical reactions: the reduction of protons to molecular hydrogen or vice versa. Cyanobacteria can express an uptake, a bidirectional or both NiFe-hydrogenases. Maturation of those depends on accessory proteins encoded by hyp-genes. The last maturation step involves the cleavage of a ca. 30 amino acid long peptide from the large subunit by a C-terminal endopeptidase. Until know, nothing is known about the maturation of cyanobacterial NiFe-hydrogenases. The availability of three complete cyanobacterial genome sequences from strains with either only the uptake (Nostoc punctiforme ATCC 29133/PCC 73102, only the bidirectional (Synechocystis PCC 6803 or both NiFe-hydrogenases (Anabaena PCC 7120 prompted us to mine these genomes for hydrogenase maturation related genes. In this communication we focus on the presence and the expression of the NiFe-hydrogenases and the corresponding C-terminal endopeptidases, in the three strains mentioned above. Results We identified genes encoding putative cyanobacterial hydrogenase specific C-terminal endopeptidases in all analyzed cyanobacterial genomes. The genes are not part of any known hydrogenase related gene cluster. The derived amino acid sequences show only low similarity (28–41% to the well-analyzed hydrogenase specific C-terminal endopeptidase HybD from Escherichia coli, the crystal structure of which is known. However, computational secondary and tertiary structure modeling revealed the presence of conserved structural patterns around the highly conserved active site. Gene expression analysis shows that the endopeptidase encoding genes are expressed under both nitrogen-fixing and non-nitrogen-fixing conditions. Conclusion Anabaena PCC 7120 possesses two NiFe-hydrogenases and two hydrogenase specific C-terminal endopeptidases but only one set of hyp-genes. Thus, in contrast to the Hyp-proteins, the C-terminal endopeptidases are the only known

  18. Oligomers Terminated By Maleimide And Acetylene

    Science.gov (United States)

    St. Clair, Terry L.; Pater, Ruth H.; Gerber, Margaret K.

    1994-01-01

    Oligomeric molecules terminated with maleimide and acetylene groups synthesized and thermally treated to form cross-linked polymers exhibiting high or undetectable glass-transition temperatures and high thermo-oxidative stabilities. Compounds used to make thermally stable, glassy polymers.

  19. 38 CFR 36.4322 - Loan termination.

    Science.gov (United States)

    2010-07-01

    ... require prior approval from VA. VA will maintain the loan termination time allowable timeframes on a Web... writing a shorter validity period, not less than 90 calendar days, for a liquidation appraisal or...

  20. Keerukas terminal valiti aasta betoonehitiseks / Aivo Vahemets

    Index Scriptorium Estoniae

    Vahemets, Aivo

    2002-01-01

    Aasta Betoonehitise nimetuse võitis Muuga kuivpuisteainete terminal, projekteerija Randväli&Karema AS. Eriauhind arhitektuurse osa eest - Birgitta klooster Pirital. Eriauhind tellijale - büroohoone Tallinnas Toompuiestee 33. Eriauhind ehitajale - konteinerterminal Muugal, projekteerija AS Merin