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Sample records for repeat domain ctd

  1. Structure and carboxyl-terminal domain (CTD) binding of the Set2 SRI domain that couples histone H3 Lys36 methylation to transcription.

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    Vojnic, Erika; Simon, Bernd; Strahl, Brian D; Sattler, Michael; Cramer, Patrick

    2006-01-06

    During mRNA elongation, the SRI domain of the histone H3 methyltransferase Set2 binds to the phosphorylated carboxyl-terminal domain (CTD) of RNA polymerase II. The solution structure of the yeast Set2 SRI domain reveals a novel CTD-binding fold consisting of a left-handed three-helix bundle. NMR titration shows that the SRI domain binds an Ser2/Ser5-phosphorylated CTD peptide comprising two heptapeptide repeats and three flanking NH2-terminal residues, whereas a single CTD repeat is insufficient for binding. Residues that show strong chemical shift perturbations upon CTD binding cluster in two regions. Both CTD tyrosine side chains contact the SRI domain. One of the tyrosines binds in the region with the strongest chemical shift perturbations, formed by the two NH2-terminal helices. Unexpectedly, the SRI domain fold resembles the structure of an RNA polymerase-interacting domain in bacterial sigma factors (domain sigma2 in sigma70).

  2. The phosphoCTD-interacting domain of Topoisomerase I

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    Wu, Jianhong; Phatnani, Hemali P.; Hsieh, Tao-Shih [Department of Biochemistry, Duke University Medical Center, Durham, NC 27710 (United States); Greenleaf, Arno L., E-mail: arno.greenleaf@duke.edu [Department of Biochemistry, Duke University Medical Center, Durham, NC 27710 (United States)

    2010-06-18

    The N-terminal domain (NTD) of Drosophila melanogaster (Dm) Topoisomerase I has been shown to bind to RNA polymerase II, but the domain of RNAPII with which it interacts is not known. Using bacterially-expressed fusion proteins carrying all or half of the NTDs of Dm and human (Homo sapiens, Hs) Topo I, we demonstrate that the N-terminal half of each NTD binds directly to the hyperphosphorylated C-terminal repeat domain (phosphoCTD) of the largest RNAPII subunit, Rpb1. Thus, the amino terminal segment of metazoan Topo I (1-157 for Dm and 1-114 for Hs) contains a novel phosphoCTD-interacting domain that we designate the Topo I-Rpb1 interacting (TRI) domain. The long-known in vivo association of Topo I with active genes presumably can be attributed, wholly or in part, to the TRI domain-mediated binding of Topo I to the phosphoCTD of transcribing RNAPII.

  3. Site-specific methylation and acetylation of lysine residues in the C-terminal domain (CTD) of RNA polymerase II

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    Voss, Kirsten; Forné, Ignasi; Descostes, Nicolas; Hintermair, Corinna; Schüller, Roland; Maqbool, Muhammad Ahmad; Heidemann, Martin; Flatley, Andrew; Imhof, Axel; Gut, Marta; Gut, Ivo; Kremmer, Elisabeth; Andrau, Jean-Christophe; Eick, Dirk

    2015-01-01

    Dynamic modification of heptad-repeats with the consensus sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7 of RNA polymerase II (RNAPII) C-terminal domain (CTD) regulates transcription-coupled processes. Mass spectrometry analysis revealed that K7-residues in non-consensus repeats of human RNAPII are modified by acetylation, or mono-, di-, and tri-methylation. K7ac, K7me2, and K7me3 were found exclusively associated with phosphorylated CTD peptides, while K7me1 occurred also in non-phosphorylated CTD. The monoclonal antibody 1F5 recognizes K7me1/2 residues in CTD and reacts with RNAPIIA. Treatment of cellular extracts with phosphatase or of cells with the kinase inhibitor flavopiridol unmasked the K7me1/2 epitope in RNAPII0, consistent with the association of K7me1/2 marks with phosphorylated CTD peptides. Genome-wide profiling revealed high levels of K7me1/2 marks at the transcriptional start site of genes for sense and antisense transcribing RNAPII. The new K7 modifications further expand the mammalian CTD code to allow regulation of differential gene expression. PMID:26566685

  4. Site-specific methylation and acetylation of lysine residues in the C-terminal domain (CTD) of RNA polymerase II.

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    Voss, Kirsten; Forné, Ignasi; Descostes, Nicolas; Hintermair, Corinna; Schüller, Roland; Maqbool, Muhammad Ahmad; Heidemann, Martin; Flatley, Andrew; Imhof, Axel; Gut, Marta; Gut, Ivo; Kremmer, Elisabeth; Andrau, Jean-Christophe; Eick, Dirk

    2015-01-01

    Dynamic modification of heptad-repeats with the consensus sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7 of RNA polymerase II (RNAPII) C-terminal domain (CTD) regulates transcription-coupled processes. Mass spectrometry analysis revealed that K7-residues in non-consensus repeats of human RNAPII are modified by acetylation, or mono-, di-, and tri-methylation. K7ac, K7me2, and K7me3 were found exclusively associated with phosphorylated CTD peptides, while K7me1 occurred also in non-phosphorylated CTD. The monoclonal antibody 1F5 recognizes K7me1/2 residues in CTD and reacts with RNAPIIA. Treatment of cellular extracts with phosphatase or of cells with the kinase inhibitor flavopiridol unmasked the K7me1/2 epitope in RNAPII0, consistent with the association of K7me1/2 marks with phosphorylated CTD peptides. Genome-wide profiling revealed high levels of K7me1/2 marks at the transcriptional start site of genes for sense and antisense transcribing RNAPII. The new K7 modifications further expand the mammalian CTD code to allow regulation of differential gene expression.

  5. Expansion of protein domain repeats.

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    Asa K Björklund

    2006-08-01

    Full Text Available Many proteins, especially in eukaryotes, contain tandem repeats of several domains from the same family. These repeats have a variety of binding properties and are involved in protein-protein interactions as well as binding to other ligands such as DNA and RNA. The rapid expansion of protein domain repeats is assumed to have evolved through internal tandem duplications. However, the exact mechanisms behind these tandem duplications are not well-understood. Here, we have studied the evolution, function, protein structure, gene structure, and phylogenetic distribution of domain repeats. For this purpose we have assigned Pfam-A domain families to 24 proteomes with more sensitive domain assignments in the repeat regions. These assignments confirmed previous findings that eukaryotes, and in particular vertebrates, contain a much higher fraction of proteins with repeats compared with prokaryotes. The internal sequence similarity in each protein revealed that the domain repeats are often expanded through duplications of several domains at a time, while the duplication of one domain is less common. Many of the repeats appear to have been duplicated in the middle of the repeat region. This is in strong contrast to the evolution of other proteins that mainly works through additions of single domains at either terminus. Further, we found that some domain families show distinct duplication patterns, e.g., nebulin domains have mainly been expanded with a unit of seven domains at a time, while duplications of other domain families involve varying numbers of domains. Finally, no common mechanism for the expansion of all repeats could be detected. We found that the duplication patterns show no dependence on the size of the domains. Further, repeat expansion in some families can possibly be explained by shuffling of exons. However, exon shuffling could not have created all repeats.

  6. Structure of Ctk3, a subunit of the RNA polymerase II CTD kinase complex, reveals a noncanonical CTD-interacting domain fold.

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    Mühlbacher, Wolfgang; Mayer, Andreas; Sun, Mai; Remmert, Michael; Cheung, Alan C M; Niesser, Jürgen; Soeding, Johannes; Cramer, Patrick

    2015-10-01

    CTDK-I is a yeast kinase complex that phosphorylates the C-terminal repeat domain (CTD) of RNA polymerase II (Pol II) to promote transcription elongation. CTDK-I contains the cyclin-dependent kinase Ctk1 (homologous to human CDK9/CDK12), the cyclin Ctk2 (human cyclin K), and the yeast-specific subunit Ctk3, which is required for CTDK-I stability and activity. Here we predict that Ctk3 consists of a N-terminal CTD-interacting domain (CID) and a C-terminal three-helix bundle domain. We determine the X-ray crystal structure of the N-terminal domain of the Ctk3 homologue Lsg1 from the fission yeast Schizosaccharomyces pombe at 2.0 Å resolution. The structure reveals eight helices arranged into a right-handed superhelical fold that resembles the CID domain present in transcription termination factors Pcf11, Nrd1, and Rtt103. Ctk3 however shows different surface properties and no binding to CTD peptides. Together with the known structure of Ctk1 and Ctk2 homologues, our results lead to a molecular framework for analyzing the structure and function of the CTDK-I complex.

  7. Fcp1 directly recognizes the C-terminal domain (CTD) and interacts with a site on RNA polymerase II distinct from the CTD

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    Suh, Man-Hee; Ye, Ping; Zhang, Mincheng; Hausmann, Stéphane; Shuman, Stewart; Gnatt, Averell L.; Fu, Jianhua

    2005-01-01

    Fcp1 is an essential protein phosphatase that hydrolyzes phosphoserines within the C-terminal domain (CTD) of the largest subunit of RNA polymerase II (Pol II). Fcp1 plays a major role in the regulation of CTD phosphorylation and, hence, critically influences the function of Pol II throughout the transcription cycle. The basic understanding of Fcp1–CTD interaction has remained ambiguous because two different modes have been proposed: the “dockingsite” model versus the “distributive” mechanism. Here we demonstrate biochemically that Fcp1 recognizes and dephosphorylates the CTD directly, independent of the globular non-CTD part of the Pol II structure. We point out that the recognition of CTD by the phosphatase is based on random access and is not driven by Pol II conformation. Results from three different types of experiments reveal that the overall interaction between Fcp1 and Pol II is not stable but dynamic. In addition, we show that Fcp1 also interacts with a region on the polymerase distinct from the CTD. We emphasize that this non-CTD site is functionally distinct from the docking site invoked previously as essential for the CTD phosphatase activity of Fcp1. We speculate that Fcp1 interaction with the non-CTD site may mediate its stimulatory effect on transcription elongation reported previously. PMID:16301539

  8. NMR studies on domain diffusion and alignment in modular GB1 repeats.

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    Walsh, Joseph D; Meier, Katlyn; Ishima, Rieko; Gronenborn, Angela M

    2010-10-20

    Modular proteins contain individual domains that are often connected by flexible, unstructured linkers. Using a model system based on the GB1 domain, we constructed tandem repeat proteins and investigated the rotational diffusion and long-range angular ordering behavior of individual domains by measuring NMR relaxation parameters and residual dipolar couplings. Although they display almost identical protein-solvent interfaces, each domain exhibits distinct rotational diffusion and alignment properties. The diffusion tensor anisotropy of the N-terminal domain (NTD) is D(‖)/D(⊥) = 1.5-1.6, similar to that of single-GB1 domains (D(‖)/D(⊥) = 1.6-1.7), whereas the value for the C-terminal domain (CTD) is D(‖)/D(⊥) = 2.0-2.2. In addition, the two domains have different rotational correlation times. These effects are observed for linkers of three to 24 residues, irrespective of linker length. The NTD and CTD also differ in their degree of magnetic alignment, even with a flexible linker of 18 residues, exhibiting D(a) values of 7.7 Hz and 9.7 Hz, respectively. Our results suggest that diffusion differences and long-range influences may persist in modular protein systems, even for systems that have highly flexible linkers and exhibit no domain-domain or domain-linker interactions.

  9. Global Patterns of Turbulence and Diapycnal Mixing from CTD-Chipods on the Global Repeat Hydrography Program

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    Pickering, A.; Nash, J. D.; Moum, J. N.; MacKinnon, J. A.

    2016-02-01

    With an aim to quantify global patterns of ocean mixing, we have developed the CTD-chipod, an instrument that measures the turbulent dissipation rate of temperature variance from standard shipboard CTD. First, turbulent diffusivities and turbulent dissipation rate inferred from the CTD-chipod are compared to that from traditional turbulence profilers with shear probes, suggesting the method does not suffer from significant bias. CTD-chipods have now been deployed on several of the global repeat hydrography program cruises, including the complete P16 line from 60S to 55N in the Pacific. Here we discuss broad patterns of mixing from these observations, as well as focusing on some specific interesting features. In particular, a section of higher resolution sampling across the equator from 5S to 5N in the Pacific suggests elevated abyssal mixing in that region. This and other patterns will be examined in relation to large-scale patterns of stratification, velocity, and shear. The observations will also be compared to other common parameterizations of mixing from shear and strain. These chipod measurements are a step towards constraining the spatial and temporal patterns of turbulent mixing across the world's oceans, in order to better understand dissipative mechanisms and their role in ocean dynamics.

  10. TAL effectors target the C-terminal domain of RNA polymerase II (CTD by inhibiting the prolyl-isomerase activity of a CTD-associated cyclophilin.

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    Mariane Noronha Domingues

    Full Text Available Transcriptional activator-like (TAL effectors of plant pathogenic bacteria function as transcription factors in plant cells. However, how TAL effectors control transcription in the host is presently unknown. Previously, we showed that TAL effectors of the citrus canker pathogen Xanthomonas citri, named PthAs, targeted the citrus protein complex comprising the thioredoxin CsTdx, ubiquitin-conjugating enzymes CsUev/Ubc13 and cyclophilin CsCyp. Here we show that CsCyp complements the function of Cpr1 and Ess1, two yeast cyclophilins that regulate transcription by the isomerization of proline residues of the regulatory C-terminal domain (CTD of RNA polymerase II. We also demonstrate that CsCyp, CsTdx, CsUev and four PthA variants interact with the citrus CTD and that CsCyp co-immunoprecipitate with the CTD in citrus cell extracts and with PthA2 transiently expressed in sweet orange epicotyls. The interactions of CsCyp with the CTD and PthA2 were inhibited by cyclosporin A (CsA, a cyclophilin inhibitor. Moreover, we present evidence that PthA2 inhibits the peptidyl-prolyl cis-trans isomerase (PPIase activity of CsCyp in a similar fashion as CsA, and that silencing of CsCyp, as well as treatments with CsA, enhance canker lesions in X. citri-infected leaves. Given that CsCyp appears to function as a negative regulator of cell growth and that Ess1 negatively regulates transcription elongation in yeast, we propose that PthAs activate host transcription by inhibiting the PPIase activity of CsCyp on the CTD.

  11. Dynamic phosphorylation patterns of RNA polymerase II CTD during transcription.

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    Heidemann, Martin; Hintermair, Corinna; Voß, Kirsten; Eick, Dirk

    2013-01-01

    The eukaryotic RNA polymerase II (RNAPII) catalyzes the transcription of all protein encoding genes and is also responsible for the generation of small regulatory RNAs. RNAPII has evolved a unique domain composed of heptapeptide repeats with the consensus sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7 at the C-terminus (CTD) of its largest subunit (Rpb1). Dynamic phosphorylation patterns of serine residues in CTD during gene transcription coordinate the recruitment of factors to the elongating RNAPII and to the nascent transcript. Recent studies identified threonine 4 and tyrosine 1 as new CTD modifications and thereby expanded the "CTD code". In this review, we focus on CTD phosphorylation and its function in the RNAPII transcription cycle. We also discuss in detail the limitations of the phosphospecific CTD antibodies, which are used in all studies. This article is part of a Special Issue entitled: RNA Polymerase II Transcript Elongation.

  12. Molecular evolution of the RNA polymerase II CTD.

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    Chapman, Rob D; Heidemann, Martin; Hintermair, Corinna; Eick, Dirk

    2008-06-01

    In higher eukaryotes, an unusual C-terminal domain (CTD) is crucial to the function of RNA polymerase II in transcription. The CTD consists of multiple heptapeptide repeats; differences in the number of repeats between organisms and their degree of conservation have intrigued researchers for two decades. Here, we review the evolution of the CTD at the molecular level. Several primitive motifs have been integrated into compound heptads that can be readily amplified. The selection of phosphorylatable residues in the heptad repeat provided the opportunity for advanced gene regulation in eukaryotes. Current findings suggest that the CTD should be considered as a collection of continuous overlapping motifs as opposed to a specific functional unit defined by a heptad.

  13. The evolution of filamin – A protein domain repeat perspective

    OpenAIRE

    Light, Sara; Sagit, Rauan; Ithychanda, Sujay S.; Qin, Jun; Elofsson, Arne

    2012-01-01

    Particularly in higher eukaryotes, some protein domains are found in tandem repeats, performing broad functions often related to cellular organization. For instance, the eukaryotic protein filamin interacts with many proteins and is crucial for the cytoskeleton. The functional properties of long repeat domains are governed by the specific properties of each individual domain as well as by the repeat copy number. To provide better understanding of the evolutionary and functional history of rep...

  14. The evolution of filamin – A protein domain repeat perspective

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    Light, Sara; Sagit, Rauan; Ithychanda, Sujay S.; Qin, Jun; Elofsson, Arne

    2013-01-01

    Particularly in higher eukaryotes, some protein domains are found in tandem repeats, performing broad functions often related to cellular organization. For instance, the eukaryotic protein filamin interacts with many proteins and is crucial for the cytoskeleton. The functional properties of long repeat domains are governed by the specific properties of each individual domain as well as by the repeat copy number. To provide better understanding of the evolutionary and functional history of repeating domains, we investigated the mode of evolution of the filamin domain in some detail. Among the domains that are common in long repeat proteins, sushi and spectrin domains evolve primarily through cassette tandem duplications while scavenger and immunoglobulin repeats appear to evolve through clustered tandem duplications. Additionally, immunoglobulin and filamin repeats exhibit a unique pattern where every other domain shows high sequence similarity. This pattern may be the result of tandem duplications, serve to avert aggregation between adjacent domains or it is the result of functional constraints. In filamin, our studies confirm the presence of interspersed integrin binding domains in vertebrates, while invertebrates exhibit more varied patterns, including more clustered integrin binding domains. The most notable case is leech filamin, which contains a 20 repeat expansion and exhibits unique dimerization topology. Clearly, invertebrate filamins are varied and contain examples of similar adjacent integrin-binding domains. Given that invertebrate integrin shows more similarity to the weaker filamin binder, integrin β3, it is possible that the distance between integrin-binding domains is not as crucial for invertebrate filamins as for vertebrates. PMID:22414427

  15. The evolution of filamin-a protein domain repeat perspective.

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    Light, Sara; Sagit, Rauan; Ithychanda, Sujay S; Qin, Jun; Elofsson, Arne

    2012-09-01

    Particularly in higher eukaryotes, some protein domains are found in tandem repeats, performing broad functions often related to cellular organization. For instance, the eukaryotic protein filamin interacts with many proteins and is crucial for the cytoskeleton. The functional properties of long repeat domains are governed by the specific properties of each individual domain as well as by the repeat copy number. To provide better understanding of the evolutionary and functional history of repeating domains, we investigated the mode of evolution of the filamin domain in some detail. Among the domains that are common in long repeat proteins, sushi and spectrin domains evolve primarily through cassette tandem duplications while scavenger and immunoglobulin repeats appear to evolve through clustered tandem duplications. Additionally, immunoglobulin and filamin repeats exhibit a unique pattern where every other domain shows high sequence similarity. This pattern may be the result of tandem duplications, serve to avert aggregation between adjacent domains or it is the result of functional constraints. In filamin, our studies confirm the presence of interspersed integrin binding domains in vertebrates, while invertebrates exhibit more varied patterns, including more clustered integrin binding domains. The most notable case is leech filamin, which contains a 20 repeat expansion and exhibits unique dimerization topology. Clearly, invertebrate filamins are varied and contain examples of similar adjacent integrin-binding domains. Given that invertebrate integrin shows more similarity to the weaker filamin binder, integrin β3, it is possible that the distance between integrin-binding domains is not as crucial for invertebrate filamins as for vertebrates. Copyright © 2012 Elsevier Inc. All rights reserved.

  16. The diversity and evolution of Wolbachia ankyrin repeat domain genes.

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    Stefanos Siozios

    Full Text Available Ankyrin repeat domain-encoding genes are common in the eukaryotic and viral domains of life, but they are rare in bacteria, the exception being a few obligate or facultative intracellular Proteobacteria species. Despite having a reduced genome, the arthropod strains of the alphaproteobacterium Wolbachia contain an unusually high number of ankyrin repeat domain-encoding genes ranging from 23 in wMel to 60 in wPip strain. This group of genes has attracted considerable attention for their astonishing large number as well as for the fact that ankyrin proteins are known to participate in protein-protein interactions, suggesting that they play a critical role in the molecular mechanism that determines host-Wolbachia symbiotic interactions. We present a comparative evolutionary analysis of the wMel-related ankyrin repeat domain-encoding genes present in different Drosophila-Wolbachia associations. Our results show that the ankyrin repeat domain-encoding genes change in size by expansion and contraction mediated by short directly repeated sequences. We provide examples of intra-genic recombination events and show that these genes are likely to be horizontally transferred between strains with the aid of bacteriophages. These results confirm previous findings that the Wolbachia genomes are evolutionary mosaics and illustrate the potential that these bacteria have to generate diversity in proteins potentially involved in the symbiotic interactions.

  17. Pol II CTD Code Light.

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    Corden, Jeffry L

    2016-01-21

    In this issue of Molecular Cell, Schüller et al. (2016) and Suh et al. (2016) describe genetic and mass spectrometry methodologies for mapping phosphorylation sites on the tandem repeats of the RNA polymerase II CTD. The results suggest that the CTD Code may be simpler than expected.

  18. The C-terminal Domain (CTD) of Human DNA Glycosylase NEIL1 Is Required for Forming BERosome Repair Complex with DNA Replication Proteins at the Replicating Genome: DOMINANT NEGATIVE FUNCTION OF THE CTD.

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    Hegde, Pavana M; Dutta, Arijit; Sengupta, Shiladitya; Mitra, Joy; Adhikari, Sanjay; Tomkinson, Alan E; Li, Guo-Min; Boldogh, Istvan; Hazra, Tapas K; Mitra, Sankar; Hegde, Muralidhar L

    2015-08-21

    The human DNA glycosylase NEIL1 was recently demonstrated to initiate prereplicative base excision repair (BER) of oxidized bases in the replicating genome, thus preventing mutagenic replication. A significant fraction of NEIL1 in cells is present in large cellular complexes containing DNA replication and other repair proteins, as shown by gel filtration. However, how the interaction of NEIL1 affects its recruitment to the replication site for prereplicative repair was not investigated. Here, we show that NEIL1 binarily interacts with the proliferating cell nuclear antigen clamp loader replication factor C, DNA polymerase δ, and DNA ligase I in the absence of DNA via its non-conserved C-terminal domain (CTD); replication factor C interaction results in ∼8-fold stimulation of NEIL1 activity. Disruption of NEIL1 interactions within the BERosome complex, as observed for a NEIL1 deletion mutant (N311) lacking the CTD, not only inhibits complete BER in vitro but also prevents its chromatin association and reduced recruitment at replication foci in S phase cells. This suggests that the interaction of NEIL1 with replication and other BER proteins is required for efficient repair of the replicating genome. Consistently, the CTD polypeptide acts as a dominant negative inhibitor during in vitro repair, and its ectopic expression sensitizes human cells to reactive oxygen species. We conclude that multiple interactions among BER proteins lead to large complexes, which are critical for efficient BER in mammalian cells, and the CTD interaction could be targeted for enhancing drug/radiation sensitivity of tumor cells.

  19. Transcribing RNA polymerase II is phosphorylated at CTD residue serine-7.

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    Chapman, Rob D; Heidemann, Martin; Albert, Thomas K; Mailhammer, Reinhard; Flatley, Andrew; Meisterernst, Michael; Kremmer, Elisabeth; Eick, Dirk

    2007-12-14

    RNA polymerase II is distinguished by its large carboxyl-terminal repeat domain (CTD), composed of repeats of the consensus heptapeptide Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. Differential phosphorylation of serine-2 and serine-5 at the 5' and 3' regions of genes appears to coordinate the localization of transcription and RNA processing factors to the elongating polymerase complex. Using monoclonal antibodies, we reveal serine-7 phosphorylation on transcribed genes. This position does not appear to be phosphorylated in CTDs of less than 20 consensus repeats. The position of repeats where serine-7 is substituted influenced the appearance of distinct phosphorylated forms, suggesting functional differences between CTD regions. Our results indicate that restriction of serine-7 epitopes to the Linker-proximal region limits CTD phosphorylation patterns and is a requirement for optimal gene expression.

  20. Tyrosine-1 and threonine-4 phosphorylation marks complete the RNA polymerase II CTD phospho-code.

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    Heidemann, Martin; Eick, Dirk

    2012-09-01

    Eukaryotic RNA polymerase II (RNAP II) has evolved an array of heptad repeats with the consensus sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7 at the carboxy-terminal domain (CTD) of its largest subunit (Rpb1). Dynamic phosphorylation of Ser2, Ser5 and Ser7 residues orchestrates the binding of transcription and RNA processing factors to the transcription machinery. Recent studies show that the two remaining potential phosphorylation sites, tyrosine-1 and threonine-4, are phosphorylated as well and contribute to the previously proposed "CTD code". With the impairment of binding of CTD interacting factors, these novel phosphorylation marks add an accessory layer of regulation to the RNAP II transcription cycle.

  1. The identification of putative RNA polymerase II C-terminal domain associated proteins in red and green algae.

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    Yang, Chunlin; Hager, Paul W; Stiller, John W

    2014-01-01

    A tandemly repeated C-terminal domain (CTD) of the largest subunit of RNA polymerase II is functionally essential and strongly conserved in many organisms, including animal, yeast and plant models. Although present in simple, ancestral red algae, CTD tandem repeats have undergone extensive modifications and degeneration during the evolutionary transition to developmentally complex rhodophytes. In contrast, CTD repeats are conserved in both green algae and their more complex land plant relatives. Understanding the mechanistic differences that underlie these variant patterns of CTD evolution requires knowledge of CTD-associated proteins in these 2 lineages. To provide an initial baseline comparison, we bound potential phospho-CTD associated proteins (PCAPs) to artificially synthesized and phosphorylated CTD repeats from the unicellular red alga Cyanidioschyzon merolae and green alga Chlamydomonas reinhardtii. Our results indicate that red and green algae share a number of PCAPs, including kinases and proteins involved in mRNA export. There also are important taxon-specific differences, including mRNA splicing-related PCAPs recovered from Chlamydomonas but not Cyanidioschyzon, consistent with the relative intron densities in green and red algae. Our results also offer the first experimental indication that different proteins bind 2 distinct types of repeats in Cyanidioschyzon, suggesting a division of function between the proximal and distal CTD, similar to patterns identified in more developmentally complex model organisms.

  2. Repeatability of Perimacular Ganglion Cell Complex Analysis with Spectral-Domain Optical Coherence Tomography

    OpenAIRE

    Ng, Dorothy S. K.; Preeti Gupta; Yih Chung Tham; Chye Fong Peck; Tien Yin Wong; Mohammad Kamran Ikram; Cheung, Carol Y.

    2015-01-01

    Purpose. To assess the repeatability of spectral-domain optical coherence tomography to measure macular and perimacular ganglion cell complex thicknesses and compare retinal ganglion cell parameters between algorithms. Methods. Ninety-two nonglaucomatous eyes from 92 participants underwent macular and perimacular ganglion cell complex thickness measurement using OCT-HS100 Glaucoma 3D algorithm and these measurements were repeated for 34 subjects. All subjects also had macular ganglion cell-in...

  3. Role of Ser7 phosphorylation of the CTD during transcription of snRNA genes

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    Egloff, Sylvain

    2012-01-01

    The largest subunit of RNA polymerase (pol) II, Rpb1, contains an unusual carboxyl-terminal domain (CTD) composed of consecutive repeats of the sequence Tyr-Ser-Pro-Thr-Ser-Pro-Ser (Y1S2P3T4S5P6S7). During transcription, Ser2, Ser5 and Ser7 are subjected to dynamic phosphorylation and dephosphorylation by CTD kinases and phosphatases, creating a characteristic CTD phosphorylation pattern along genes. This CTD “code” allows the coupling of transcription with co-transcriptional RNA processing, through the timely recruitment of the appropriate factors at the right point of the transcription cycle. In mammals, phosphorylation of Ser7 (Ser7P) is detected on all pol II-transcribed genes, but is only essential for expression of a sub-class of genes encoding small nuclear (sn)RNAs. The molecular mechanisms by which Ser7P influences expression of these particular genes are becoming clearer. Here, I discuss our recent findings clarifying how Ser7P facilitates transcription of these genes and 3′end processing of the transcripts, through recruitment of the RPAP2 phosphatase and the snRNA gene-specific Integrator complex. PMID:22858677

  4. Specific threonine-4 phosphorylation and function of RNA polymerase II CTD during M phase progression.

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    Hintermair, Corinna; Voß, Kirsten; Forné, Ignasi; Heidemann, Martin; Flatley, Andrew; Kremmer, Elisabeth; Imhof, Axel; Eick, Dirk

    2016-06-06

    Dynamic phosphorylation of Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7 heptad-repeats in the C-terminal domain (CTD) of the large subunit coordinates progression of RNA polymerase (Pol) II through the transcription cycle. Here, we describe an M phase-specific form of Pol II phosphorylated at Thr4, but not at Tyr1, Ser2, Ser5, and Ser7 residues. Thr4 phosphorylated Pol II binds to centrosomes and midbody and interacts with the Thr4-specific Polo-like kinase 1. Binding of Pol II to centrosomes does not require the CTD but may involve subunits of the non-canonical R2TP-Prefoldin-like complex, which bind to and co-localize with Pol II at centrosomes. CTD Thr4 mutants, but not Ser2 and Ser5 mutants, display severe mitosis and cytokinesis defects characterized by multipolar spindles and polyploid cells. We conclude that proper M phase progression of cells requires binding of Pol II to centrosomes to facilitate regulation of mitosis and cytokinesis in a CTD Thr4-P dependent manner.

  5. Alternative conformations of the Tau repeat domain in complex with an engineered binding protein.

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    Grüning, Clara S R; Mirecka, Ewa A; Klein, Antonia N; Mandelkow, Eckhard; Willbold, Dieter; Marino, Stephen F; Stoldt, Matthias; Hoyer, Wolfgang

    2014-08-15

    The aggregation of Tau into paired helical filaments is involved in the pathogenesis of several neurodegenerative diseases, including Alzheimer disease. The aggregation reaction is characterized by conformational conversion of the repeat domain, which partially adopts a cross-β-structure in the resulting amyloid-like fibrils. Here, we report the selection and characterization of an engineered binding protein, β-wrapin TP4, targeting the Tau repeat domain. TP4 was obtained by phage display using the four-repeat Tau construct K18ΔK280 as a target. TP4 binds K18ΔK280 as well as the longest isoform of human Tau, hTau40, with nanomolar affinity. NMR spectroscopy identified two alternative TP4-binding sites in the four-repeat domain, with each including two hexapeptide motifs with high β-sheet propensity. Both binding sites contain the aggregation-determining PHF6 hexapeptide within repeat 3. In addition, one binding site includes the PHF6* hexapeptide within repeat 2, whereas the other includes the corresponding hexapeptide Tau(337-342) within repeat 4, denoted PHF6**. Comparison of TP4-binding with Tau aggregation reveals that the same regions of Tau are involved in both processes. TP4 inhibits Tau aggregation at substoichiometric concentration, demonstrating that it interferes with aggregation nucleation. This study provides residue-level insight into the interaction of Tau with an aggregation inhibitor and highlights the structural flexibility of Tau. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

  6. Mechanism of intermediate filament recognition by plakin repeat domains revealed by envoplakin targeting of vimentin

    Science.gov (United States)

    Fogl, Claudia; Mohammed, Fiyaz; Al-Jassar, Caezar; Jeeves, Mark; Knowles, Timothy J.; Rodriguez-Zamora, Penelope; White, Scott A.; Odintsova, Elena; Overduin, Michael; Chidgey, Martyn

    2016-03-01

    Plakin proteins form critical connections between cell junctions and the cytoskeleton; their disruption within epithelial and cardiac muscle cells cause skin-blistering diseases and cardiomyopathies. Envoplakin has a single plakin repeat domain (PRD) which recognizes intermediate filaments through an unresolved mechanism. Herein we report the crystal structure of envoplakin's complete PRD fold, revealing binding determinants within its electropositive binding groove. Four of its five internal repeats recognize negatively charged patches within vimentin via five basic determinants that are identified by nuclear magnetic resonance spectroscopy. Mutations of the Lys1901 or Arg1914 binding determinants delocalize heterodimeric envoplakin from intracellular vimentin and keratin filaments in cultured cells. Recognition of vimentin is abolished when its residues Asp112 or Asp119 are mutated. The latter slot intermediate filament rods into basic PRD domain grooves through electrosteric complementarity in a widely applicable mechanism. Together this reveals how plakin family members form dynamic linkages with cytoskeletal frameworks.

  7. Structural Analyses of the Ankyrin Repeat Domain of TRPV6 and Related TRPV Ion Channels

    Energy Technology Data Exchange (ETDEWEB)

    Phelps, C.B.; Huang, R.J.; Lishko, P.V.; Wang, R.R.; Gaudet, R. (Harvard)

    2008-06-03

    Transient receptor potential (TRP) proteins are cation channels composed of a transmembrane domain flanked by large N- and C-terminal cytoplasmic domains. All members of the vanilloid family of TRP channels (TRPV) possess an N-terminal ankyrin repeat domain (ARD). The ARD of mammalian TRPV6, an important regulator of calcium uptake and homeostasis, is essential for channel assembly and regulation. The 1.7 A crystal structure of the TRPV6-ARD reveals conserved structural elements unique to the ARDs of TRPV proteins. First, a large twist between the fourth and fifth repeats is induced by residues conserved in all TRPV ARDs. Second, the third finger loop is the most variable region in sequence, length and conformation. In TRPV6, a number of putative regulatory phosphorylation sites map to the base of this third finger. Size exclusion chromatography and crystal packing indicate that the TRPV6-ARD does not assemble as a tetramer and is monomeric in solution. Adenosine triphosphate-agarose and calmodulin-agarose pull-down assays show that the TRPV6-ARD does not interact with either ligand, indicating a different functional role for the TRPV6-ARD than in the paralogous thermosensitive TRPV1 channel. Similar biochemical findings are also presented for the highly homologous mammalian TRPV5-ARD. The implications of the structural and biochemical data on the role of the ankyrin repeats in different TRPV channels are discussed.

  8. The Bordetella Adenylate Cyclase Repeat-in-Toxin (RTX) Domain Is Immunodominant and Elicits Neutralizing Antibodies*

    Science.gov (United States)

    Wang, Xianzhe; Maynard, Jennifer A.

    2015-01-01

    The adenylate cyclase toxin (ACT) is a multifunctional virulence factor secreted by Bordetella species. Upon interaction of its C-terminal hemolysin moiety with the cell surface receptor αMβ2 integrin, the N-terminal cyclase domain translocates into the host cell cytosol where it rapidly generates supraphysiological cAMP concentrations, which inhibit host cell anti-bacterial activities. Although ACT has been shown to induce protective immunity in mice, it is not included in any current acellular pertussis vaccines due to protein stability issues and a poor understanding of its role as a protective antigen. Here, we aimed to determine whether any single domain could recapitulate the antibody responses induced by the holo-toxin and to characterize the dominant neutralizing antibody response. We first immunized mice with ACT and screened antibody phage display libraries for binding to purified ACT. The vast majority of unique antibodies identified bound the C-terminal repeat-in-toxin (RTX) domain. Representative antibodies binding two nonoverlapping, neutralizing epitopes in the RTX domain prevented ACT association with J774A.1 macrophages and soluble αMβ2 integrin, suggesting that these antibodies inhibit the ACT-receptor interaction. Sera from mice immunized with the RTX domain showed similar neutralizing activity as ACT-immunized mice, indicating that this domain induced an antibody response similar to that induced by ACT. These data demonstrate that RTX can elicit neutralizing antibodies and suggest it may present an alternative to ACT. PMID:25505186

  9. MSH2 ATPase domain mutation affects CTG*CAG repeat instability in transgenic mice.

    Directory of Open Access Journals (Sweden)

    Stéphanie Tomé

    2009-05-01

    Full Text Available Myotonic dystrophy type 1 (DM1 is associated with one of the most highly unstable CTG*CAG repeat expansions. The formation of further repeat expansions in transgenic mice carrying expanded CTG*CAG tracts requires the mismatch repair (MMR proteins MSH2 and MSH3, forming the MutSbeta complex. It has been proposed that binding of MutSbeta to CAG hairpins blocks its ATPase activity compromising hairpin repair, thereby causing expansions. This would suggest that binding, but not ATP hydrolysis, by MutSbeta is critical for trinucleotide expansions. However, it is unknown if the MSH2 ATPase activity is dispensible for instability. To get insight into the mechanism by which MSH2 generates trinucleotide expansions, we crossed DM1 transgenic mice carrying a highly unstable >(CTG(300 repeat tract with mice carrying the G674A mutation in the MSH2 ATPase domain. This mutation impairs MSH2 ATPase activity and ablates base-base MMR, but does not affect the ability of MSH2 (associated with MSH6 to bind DNA mismatches. We found that the ATPase domain mutation of MSH2 strongly affects the formation of CTG expansions and leads instead to transmitted contractions, similar to a Msh2-null or Msh3-null deficiency. While a decrease in MSH2 protein level was observed in tissues from Msh2(G674 mice, the dramatic reduction of expansions suggests that the expansion-biased trinucleotide repeat instability requires a functional MSH2 ATPase domain and probably a functional MMR system.

  10. A KH-Domain RNA-Binding Protein Interacts with FIERY2/CTD Phosphatase-Like 1 and Splicing Factors and Is Important for Pre-mRNA Splicing in Arabidopsis

    KAUST Repository

    Chen, Tao

    2013-10-17

    Eukaryotic genomes encode hundreds of RNA-binding proteins, yet the functions of most of these proteins are unknown. In a genetic study of stress signal transduction in Arabidopsis, we identified a K homology (KH)-domain RNA-binding protein, HOS5 (High Osmotic Stress Gene Expression 5), as required for stress gene regulation and stress tolerance. HOS5 was found to interact with FIERY2/RNA polymerase II (RNAP II) carboxyl terminal domain (CTD) phosphatase-like 1 (FRY2/CPL1) both in vitro and in vivo. This interaction is mediated by the first double-stranded RNA-binding domain of FRY2/CPL1 and the KH domains of HOS5. Interestingly, both HOS5 and FRY2/CPL1 also interact with two novel serine-arginine (SR)-rich splicing factors, RS40 and RS41, in nuclear speckles. Importantly, FRY2/CPL1 is required for the recruitment of HOS5. In fry2 mutants, HOS5 failed to be localized in nuclear speckles but was found mainly in the nucleoplasm. hos5 mutants were impaired in mRNA export and accumulated a significant amount of mRNA in the nuclei, particularly under salt stress conditions. Arabidopsis mutants of all these genes exhibit similar stress-sensitive phenotypes. RNA-seq analyses of these mutants detected significant intron retention in many stress-related genes under salt stress but not under normal conditions. Our study not only identified several novel regulators of pre-mRNA processing as important for plant stress response but also suggested that, in addition to RNAP II CTD that is a well-recognized platform for the recruitment of mRNA processing factors, FRY2/CPL1 may also recruit specific factors to regulate the co-transcriptional processing of certain transcripts to deal with environmental challenges. © 2013 Chen et al.

  11. Stages and conformations of the Tau repeat domain during aggregation and its effect on neuronal toxicity.

    Science.gov (United States)

    Kumar, Satish; Tepper, Katharina; Kaniyappan, Senthilvelrajan; Biernat, Jacek; Wegmann, Susanne; Mandelkow, Eva-Maria; Müller, Daniel J; Mandelkow, Eckhard

    2014-07-18

    Several neurodegenerative diseases are characterized by the aggregation and posttranslational modifications of Tau protein. Its "repeat domain" (TauRD) is mainly responsible for the aggregation properties, and oligomeric forms are thought to dominate the toxic effects of Tau. Here we investigated the conformational transitions of this domain during oligomerization and aggregation in different states of β-propensity and pseudo-phosphorylation, using several complementary imaging and spectroscopic methods. Although the repeat domain generally aggregates more readily than full-length Tau, its aggregation was greatly slowed down by phosphorylation or pseudo-phosphorylation at the KXGS motifs, concomitant with an extended phase of oligomerization. Analogous effects were observed with pro-aggregant variants of TauRD. Oligomers became most evident in the case of the pro-aggregant mutant TauRDΔK280, as monitored by atomic force microscopy, and the fluorescence lifetime of Alexa-labeled Tau (time-correlated single photon counting (TCSPC)), consistent with its pronounced toxicity in mouse models. In cell models or primary neurons, neither oligomers nor fibrils of TauRD or TauRDΔK280 had a toxic effect, as seen by assays with lactate dehydrogenase and 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide, respectively. However, oligomers of pro-aggregant TauRDΔK280 specifically caused a loss of spine density in differentiated neurons, indicating a locally restricted impairment of function. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

  12. LRR conservation mapping to predict functional sites within protein leucine-rich repeat domains.

    Directory of Open Access Journals (Sweden)

    Laura Helft

    Full Text Available Computational prediction of protein functional sites can be a critical first step for analysis of large or complex proteins. Contemporary methods often require several homologous sequences and/or a known protein structure, but these resources are not available for many proteins. Leucine-rich repeats (LRRs are ligand interaction domains found in numerous proteins across all taxonomic kingdoms, including immune system receptors in plants and animals. We devised Repeat Conservation Mapping (RCM, a computational method that predicts functional sites of LRR domains. RCM utilizes two or more homologous sequences and a generic representation of the LRR structure to identify conserved or diversified patches of amino acids on the predicted surface of the LRR. RCM was validated using solved LRR+ligand structures from multiple taxa, identifying ligand interaction sites. RCM was then used for de novo dissection of two plant microbe-associated molecular pattern (MAMP receptors, EF-TU RECEPTOR (EFR and FLAGELLIN-SENSING 2 (FLS2. In vivo testing of Arabidopsis thaliana EFR and FLS2 receptors mutagenized at sites identified by RCM demonstrated previously unknown functional sites. The RCM predictions for EFR, FLS2 and a third plant LRR protein, PGIP, compared favorably to predictions from ODA (optimal docking area, Consurf, and PAML (positive selection analyses, but RCM also made valid functional site predictions not available from these other bioinformatic approaches. RCM analyses can be conducted with any LRR-containing proteins at www.plantpath.wisc.edu/RCM, and the approach should be modifiable for use with other types of repeat protein domains.

  13. Tetratricopeptide repeat domain 9A is an interacting protein for tropomyosin Tm5NM-1

    Directory of Open Access Journals (Sweden)

    Ho Gay

    2008-08-01

    Full Text Available Abstract Background Tetratricopeptide repeat domain 9A (TTC9A protein is a recently identified protein which contains three tetratricopeptide repeats (TPRs on its C-terminus. In our previous studies, we have shown that TTC9A was a hormonally-regulated gene in breast cancer cells. In this study, we found that TTC9A was over-expressed in breast cancer tissues compared with the adjacent controls (P Methods Breast samples from 25 patients including the malignant breast tissues and the adjacent normal tissues were processed for Southern blot analysis. Yeast-two-hybrid assay, GST pull-down assay and co-immunoprecipitation were used to identify and verify the interaction between TTC9A and other proteins. Results Tropomyosin Tm5NM-1 was identified as one of the TTC9A partner proteins. The interaction between TTC9A and Tm5NM-1 was further confirmed by GST pull-down assay and co-immunoprecipitation in mammalian cells. TTC9A domains required for the interaction were also characterized in this study. The results suggested that the first TPR domain and the linker fragment between the first two TPR domains of TTC9A were important for the interaction with Tm5NM-1 and the second and the third TPR might play an inhibitory role. Conclusion Since the primary function of tropomyosin is to stabilize actin filament, its interaction with TTC9A may play a role in cell shape and motility. In our previous results, we have found that progesterone-induced TTC9A expression was associated with increased cell motility and cell spreading. We speculate that TTC9A acts as a chaperone protein to facilitate the function of tropomyosins in stabilizing microfilament and it may play a role in cancer cell invasion and metastasis.

  14. Stages and Conformations of the Tau Repeat Domain during Aggregation and Its Effect on Neuronal Toxicity*

    Science.gov (United States)

    Kumar, Satish; Tepper, Katharina; Kaniyappan, Senthilvelrajan; Biernat, Jacek; Wegmann, Susanne; Mandelkow, Eva-Maria; Müller, Daniel J.; Mandelkow, Eckhard

    2014-01-01

    Several neurodegenerative diseases are characterized by the aggregation and posttranslational modifications of Tau protein. Its “repeat domain” (TauRD) is mainly responsible for the aggregation properties, and oligomeric forms are thought to dominate the toxic effects of Tau. Here we investigated the conformational transitions of this domain during oligomerization and aggregation in different states of β-propensity and pseudo-phosphorylation, using several complementary imaging and spectroscopic methods. Although the repeat domain generally aggregates more readily than full-length Tau, its aggregation was greatly slowed down by phosphorylation or pseudo-phosphorylation at the KXGS motifs, concomitant with an extended phase of oligomerization. Analogous effects were observed with pro-aggregant variants of TauRD. Oligomers became most evident in the case of the pro-aggregant mutant TauRDΔK280, as monitored by atomic force microscopy, and the fluorescence lifetime of Alexa-labeled Tau (time-correlated single photon counting (TCSPC)), consistent with its pronounced toxicity in mouse models. In cell models or primary neurons, neither oligomers nor fibrils of TauRD or TauRDΔK280 had a toxic effect, as seen by assays with lactate dehydrogenase and 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide, respectively. However, oligomers of pro-aggregant TauRDΔK280 specifically caused a loss of spine density in differentiated neurons, indicating a locally restricted impairment of function. PMID:24825901

  15. Repeatability of Perimacular Ganglion Cell Complex Analysis with Spectral-Domain Optical Coherence Tomography.

    Science.gov (United States)

    Ng, Dorothy S K; Gupta, Preeti; Tham, Yih Chung; Peck, Chye Fong; Wong, Tien Yin; Ikram, Mohammad Kamran; Cheung, Carol Y

    2015-01-01

    Purpose. To assess the repeatability of spectral-domain optical coherence tomography to measure macular and perimacular ganglion cell complex thicknesses and compare retinal ganglion cell parameters between algorithms. Methods. Ninety-two nonglaucomatous eyes from 92 participants underwent macular and perimacular ganglion cell complex thickness measurement using OCT-HS100 Glaucoma 3D algorithm and these measurements were repeated for 34 subjects. All subjects also had macular ganglion cell-inner plexiform layer thickness measured by Cirrus HD-OCT Ganglion Cell Analysis algorithm. Intraclass correlation coefficient and Pearson's correlation analyses were performed. Results. Subfields of both macular and perimacular ganglion cell complex thicknesses had high intraclass correlation coefficient values between 0.979 (95% confidence interval [CI]: 0.958-0.989) and 0.981 (95% CI: 0.963, 0.991) and between 0.70 (95% CI: 0.481-0.838) and 0.987 (95% CI: 0.956-0.989), respectively. The overall average ganglion cell complex and macular average ganglion cell-inner plexiform layer thicknesses were strongly correlated (r = 0.83,  P HS100 Glaucoma 3D algorithm is highly repeatable, and strongly correlates to retinal ganglion cell parameters assessed by Ganglion Cell Analysis algorithm. A comprehensive evaluation of retinal ganglion cells may be possible with OCT-HS100.

  16. Repeatability of Perimacular Ganglion Cell Complex Analysis with Spectral-Domain Optical Coherence Tomography

    Directory of Open Access Journals (Sweden)

    Dorothy S. K. Ng

    2015-01-01

    Full Text Available Purpose. To assess the repeatability of spectral-domain optical coherence tomography to measure macular and perimacular ganglion cell complex thicknesses and compare retinal ganglion cell parameters between algorithms. Methods. Ninety-two nonglaucomatous eyes from 92 participants underwent macular and perimacular ganglion cell complex thickness measurement using OCT-HS100 Glaucoma 3D algorithm and these measurements were repeated for 34 subjects. All subjects also had macular ganglion cell-inner plexiform layer thickness measured by Cirrus HD-OCT Ganglion Cell Analysis algorithm. Intraclass correlation coefficient and Pearson’s correlation analyses were performed. Results. Subfields of both macular and perimacular ganglion cell complex thicknesses had high intraclass correlation coefficient values between 0.979 (95% confidence interval [CI]: 0.958–0.989 and 0.981 (95% CI: 0.963, 0.991 and between 0.70 (95% CI: 0.481–0.838 and 0.987 (95% CI: 0.956–0.989, respectively. The overall average ganglion cell complex and macular average ganglion cell-inner plexiform layer thicknesses were strongly correlated (r=0.83, P<0.001.  Conclusions. The assessment of macular and perimacular retinal ganglion cell parameters by OCT-HS100 Glaucoma 3D algorithm is highly repeatable, and strongly correlates to retinal ganglion cell parameters assessed by Ganglion Cell Analysis algorithm. A comprehensive evaluation of retinal ganglion cells may be possible with OCT-HS100.

  17. Positive selection in the leucine-rich repeat domain of Gro1 genes in Solanum species

    Indian Academy of Sciences (India)

    Valentino Ruggieri; Angelina Nunziata; Amalia Barone

    2014-12-01

    In pathogen resistant plants, solvent-exposed residues in the leucine-rich repeat (LRR) proteins are thought to mediate resistance by recognizing plant pathogen elicitors. In potato, the gene Gro1-4 confers resistance to Globodera rostochiensis. The investigation of variablity in different copies of this gene represents a good model for the verification of positive selection mechanisms. Two datasets of Gro1 LRR sequences were constructed, one derived from the Gro1-4 gene, belonging to different cultivated and wild Solanum species, and the other belonging to paralogues of a resistant genotype. Analysis of non-synonymous to synonymous substitution rates $(K_{a}/K_{s})$ highlighted 14 and six amino acids with $K_{a}/K_{s} \\gt 1$ in orthologue and paralogue datasets, respectively. Selection analysis revealed that the leucine-rich regions accumulate variability in a very specific way, and we found that some combinations of amino acids in these sites might be involved in pathogen recognition. The results confirm previous studies on positive selection in the LRR domain of R protein in Arabidopsis and other model plants and extend these to wild Solanum species. Moreover, positively selected sites in the Gro1 LRR domain show that coevolution mainly occurred in two regions on the internal surface of the three-dimensional horseshoe structure of the domain, albeit with different evolutionary forces between paralogues and orthologues.

  18. The crystal structure of a partial mouse Notch-1 ankyrin domain: Repeats 4 through 7 preserve an ankyrin fold

    Energy Technology Data Exchange (ETDEWEB)

    Lubman, Olga Y.; Kopan, Raphael; Waksman, Gabriel; Korolev, Sergey (Birbeck); (St. Louis-MED); (WU-MED)

    2010-07-20

    Folding and stability of proteins containing ankyrin repeats (ARs) is of great interest because they mediate numerous protein-protein interactions involved in a wide range of regulatory cellular processes. Notch, an ankyrin domain containing protein, signals by converting a transcriptional repression complex into an activation complex. The Notch ANK domain is essential for Notch function and contains seven ARs. Here, we present the 2.2 {angstrom} crystal structure of ARs 4-7 from mouse Notch 1 (m1ANK). These C-terminal repeats were resistant to degradation during crystallization, and their secondary and tertiary structures are maintained in the absence of repeats 1-3. The crystallized fragment adopts a typical ankyrin fold including the poorly conserved seventh AR, as seen in the Drosophila Notch ANK domain (dANK). The structural preservation and stability of the C-terminal repeats shed a new light onto the mechanism of hetero-oligomeric assembly during Notch-mediated transcriptional activation.

  19. Comprehensive RNA Polymerase II Interactomes Reveal Distinct and Varied Roles for Each Phospho-CTD Residue

    Directory of Open Access Journals (Sweden)

    Kevin M. Harlen

    2016-06-01

    Full Text Available Transcription controls splicing and other gene regulatory processes, yet mechanisms remain obscure due to our fragmented knowledge of the molecular connections between the dynamically phosphorylated RNA polymerase II (Pol II C-terminal domain (CTD and regulatory factors. By systematically isolating phosphorylation states of the CTD heptapeptide repeat (Y1S2P3T4S5P6S7, we identify hundreds of protein factors that are differentially enriched, revealing unappreciated connections between the Pol II CTD and co-transcriptional processes. These data uncover a role for threonine-4 in 3′ end processing through control of the transition between cleavage and termination. Furthermore, serine-5 phosphorylation seeds spliceosomal assembly immediately downstream of 3′ splice sites through a direct interaction with spliceosomal subcomplex U1. Strikingly, threonine-4 phosphorylation also impacts splicing by serving as a mark of co-transcriptional spliceosome release and ensuring efficient post-transcriptional splicing genome-wide. Thus, comprehensive Pol II interactomes identify the complex and functional connections between transcription machinery and other gene regulatory complexes.

  20. Quantification of interaction strengths between chaperones and tetratricopeptide repeat domain-containing membrane proteins.

    Science.gov (United States)

    Schweiger, Regina; Soll, Jürgen; Jung, Kirsten; Heermann, Ralf; Schwenkert, Serena

    2013-10-18

    The three tetratricopeptide repeat domain-containing docking proteins Toc64, OM64, and AtTPR7 reside in the chloroplast, mitochondrion, and endoplasmic reticulum of Arabidopsis thaliana, respectively. They are suggested to act during post-translational protein import by association with chaperone-bound preprotein complexes. Here, we performed a detailed biochemical, biophysical, and computational analysis of the interaction between Toc64, OM64, and AtTPR7 and the five cytosolic chaperones HSP70.1, HSP90.1, HSP90.2, HSP90.3, and HSP90.4. We used surface plasmon resonance spectroscopy in combination with Interaction Map® analysis to distinguish between chaperone oligomerization and docking protein-chaperone interactions and to calculate binding affinities for all tested interactions. Complementary to this, we applied pulldown assays as well as microscale thermophoresis as surface immobilization independent techniques. The data revealed that OM64 prefers HSP70 over HSP90, whereas Toc64 binds all chaperones with comparable affinities. We could further show that AtTPR7 is able to bind HSP90 in addition to HSP70. Moreover, differences between the HSP90 isoforms were detected and revealed a weaker binding for HSP90.1 to AtTPR7 and OM64, showing that slight differences in the amino acid composition or structure of the chaperones influence binding to the tetratricopeptide repeat domain. The combinatory approach of several methods provided a powerful toolkit to determine binding affinities of similar interaction partners in a highly quantitative manner.

  1. Differential antibiosis against Helicoverpa armigera exerted by distinct inhibitory repeat domains of Capsicum annuum proteinase inhibitors.

    Science.gov (United States)

    Joshi, Rakesh S; Gupta, Vidya S; Giri, Ashok P

    2014-05-01

    Plant defensive serine proteinase inhibitors (PIs) are known to have negative impact on digestive physiology of herbivore insects and thus have a crucial role in plant protection. Here, we have assessed the efficacy and specificity of three previously characterized inhibitory repeat domain (IRD) variants from Capsicum annuum PIs viz., IRD-7, -9 and -12 against gut proteinases from Helicoverpa armigera. Comparative study of in silico binding energy revealed that IRD-9 possesses higher affinity towards H. armigera serine proteinases as compared to IRD-7 and -12. H. armigera fed on artificial diet containing 5 TIU/g of recombinant IRD proteins exhibited differential effects on larval growth, survival rate and other nutritional parameters. Major digestive gut trypsin and chymotrypsin genes were down regulated in the IRD fed larvae, while few of them were up-regulated, this indicate alterations in insect digestive physiology. The results corroborated with proteinase activity assays and zymography. These findings suggest that the sequence variations among PIs reflect in their efficacy against proteinases in vitro and in vivo, which also could be used for developing tailor-made multi-domain inhibitor gene(s).

  2. Rat1p maintains RNA polymerase II CTD phosphorylation balance

    DEFF Research Database (Denmark)

    Jimeno-González, Silvia; Schmid, Manfred; Malagon, Francisco

    2014-01-01

    In S. cerevisiae, the 5'-3' exonuclease Rat1p partakes in transcription termination. Although Rat1p-mediated RNA degradation has been suggested to play a role for this activity, the exact mechanisms by which Rat1p helps release RNA polymerase II (RNAPII) from the DNA template are poorly understood....... Here we describe a function of Rat1p in regulating phosphorylation levels of the C-terminal domain (CTD) of the largest RNAPII subunit, Rpb1p, during transcription elongation. The rat1-1 mutant exhibits highly elevated levels of CTD phosphorylation as well as RNAPII distribution and transcription...... termination defects. These phenotypes are all rescued by overexpression of the CTD phosphatase Fcp1p, suggesting a functional relationship between the absence of Rat1p activity, elevated CTD phosphorylation, and transcription defects. We also demonstrate that rat1-1 cells display increased RNAPII...

  3. Emerging roles for RNA polymerase II CTD in Arabidopsis.

    Science.gov (United States)

    Hajheidari, Mohsen; Koncz, Csaba; Eick, Dirk

    2013-11-01

    Post-translational modifications of the carboxy-terminal domain of the largest subunit of RNA polymerase II (RNAPII CTD) provide recognition marks to coordinate recruitment of numerous nuclear factors controlling transcription, cotranscriptional RNA processing, chromatin remodeling, and RNA export. Compared with the progress in yeast and mammals, deciphering the regulatory roles of position-specific combinatorial CTD modifications, the so-called CTD code, is still at an early stage in plants. In this review, we discuss some of the recent advances in understanding of the molecular mechanisms controlling the deposition and recognition of RNAPII CTD marks in plants during the transcriptional cycle and highlight some intriguing differences between regulatory components characterized in yeast, mammals, and plants.

  4. Novel Mutations of the Tetratricopeptide Repeat Domain 7A Gene and Phenotype/Genotype Comparison

    Directory of Open Access Journals (Sweden)

    Reyin Lien

    2017-09-01

    Full Text Available The gastrointestinal tract contains the largest lymphoid organ to react with pathogenic microorganisms and suppress excess inflammation. Patients with primary immunodeficiency diseases (PIDs can suffer from refractory diarrhea. In this study, we present two siblings who began to suffer from refractory diarrhea with a poor response to aggressive antibiotic and immunosuppressive treatment after surgical release of neonatal intestinal obstruction. Their lymphocyte proliferation was low, but superoxide production and IL-10 signaling were normal. Candidate genetic approach targeted to genes involved in PIDs with inflammatory bowel disease (IBD-like manifestation was unrevealing. Whole-genome sequencing revealed novel heterozygous mutations Glu75Lys and nucleotide 520–521 CT deletion in the tetratricopeptide repeat domain 7A (TTC7A gene. A Medline search identified 49 patients with TTC7A mutations, of whom 20 survived. Their phenotypes included both multiple intestinal atresia (MIA and combined T and/or B immunodeficiency (CID in 16, both IBD and CID in 14, isolated MIA in 8, MIA, IBD, and CID complex in 8, and isolated IBD in 3. Of these 98 mutant alleles over-through the coding region clustering on exon 2 (40 alleles, exon 7 (12 alleles, and exon 20 (10 alleles, 2 common hotspot mutations were c.211 G>A (p.E71K in exon 2 in 26 alleles and AAGT deletion in exon 7 (+3 in 10 alleles. Kaplan–Meier analysis showed that those with biallelic missense mutations (p = 0.0168, unaffected tetratricopeptide repeat domains (p = 0.0311, and developing autoimmune disorders (p = 0.001 had a relatively better prognosis. Hematopoietic stem cell transplantation (HSCT restored immunity and seemed to decrease the frequency of infections; however, refractory diarrhea persisted. Clinical improvement was reported upon intestinal and liver transplantation in a child with CID and MIA of unknown genetic etiology. In conclusion, patients with TTC7A mutations

  5. Structural analysis of the KRIT1 ankyrin repeat and FERM domains reveals a conformationally stable ARD-FERM interface

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Rong [Yale Univ., New Haven, CT (United States); Li, Xiaofeng [Yale Univ., New Haven, CT (United States); Boggon, Titus J. [Yale Univ., New Haven, CT (United States)

    2015-10-14

    Cerebral cavernous malformations (CCM) are vascular dysplasias that usually occur in the brain and are associated with mutations in the KRIT1/CCM1, CCM2/MGC4607/OSM/Malcavernin, and PDCD10/CCM3/ TFAR15 genes. Here we report the 2.9 Å crystal structure of the ankyrin repeat domain (ARD) and FERM domain of the protein product of KRIT1 (KRIT1; Krev interaction trapped 1). The crystal structure reveals that the KRIT1 ARD contains 4 ankyrin repeats. There is also an unusual conformation in the ANK4 repeat that is stabilized by Trp-404, and the structure reveals a solvent exposed ankyrin groove. Domain orientations of the three copies within the asymmetric unit suggest a stable interaction between KRIT1 ARD and FERM domains, indicating a globular ARD–FERM module. It resembles the additional F0 domain found N-terminal to the FERM domain of talin. Structural analysis of KRIT1 ARD–FERM highlights surface regions of high evolutionary conservation, and suggests potential sites that could mediate interaction with binding partners. The structure therefore provides a better understanding of KRIT1 at the molecular level.

  6. Structural analysis of the KRIT1 ankyrin repeat and FERM domains reveals a conformationally stable ARD-FERM interface.

    Science.gov (United States)

    Zhang, Rong; Li, Xiaofeng; Boggon, Titus J

    2015-12-01

    Cerebral cavernous malformations (CCM) are vascular dysplasias that usually occur in the brain and are associated with mutations in the KRIT1/CCM1, CCM2/MGC4607/OSM/Malcavernin, and PDCD10/CCM3/TFAR15 genes. Here we report the 2.9 Å crystal structure of the ankyrin repeat domain (ARD) and FERM domain of the protein product of KRIT1 (KRIT1; Krev interaction trapped 1). The crystal structure reveals that the KRIT1 ARD contains 4 ankyrin repeats. There is an unusual conformation in the ANK4 repeat that is stabilized by Trp-404, and the structure reveals a solvent exposed ankyrin groove. Domain orientations of the three copies within the asymmetric unit suggest a stable interaction between KRIT1 ARD and FERM domains, indicating a globular ARD-FERM module. This resembles the additional F0 domain found N-terminal to the FERM domain of talin. Structural analysis of KRIT1 ARD-FERM highlights surface regions of high evolutionary conservation, and suggests potential sites that could mediate interaction with binding partners. The structure therefore provides a better understanding of KRIT1 at the molecular level.

  7. Plasmodium alveolins possess distinct but structurally and functionally related multi-repeat domains.

    Science.gov (United States)

    Al-Khattaf, Fatimah S; Tremp, Annie Z; Dessens, Johannes T

    2015-02-01

    The invasive and motile life stages of malaria parasites (merozoite, ookinete and sporozoite) possess a distinctive cortical structure termed the pellicle. The pellicle is characterised by a double-layered 'inner membrane complex' (IMC) located underneath the plasma membrane, which is supported by a cytoskeletal structure termed the subpellicular network (SPN). The SPN consists of intermediate filaments, whose major constituents include a family of proteins called alveolins. Here, we re-appraise the alveolins in the genus Plasmodium with respect to their repertoire, structure and interrelatedness. Amongst 13 family members identified, we distinguish two domain types that, albeit distinct at the primary structure level, are structurally related and contain tandem repeats with a consensus 12-amino acid periodicity. Analysis in Plasmodium berghei of the most divergent alveolin, PbIMC1d, reveals a zoite-specific expression in ookinetes and a subcellular localisation in the pellicle, consistent with its predicted role as a SPN component. Knockout of PbIMC1d gives rise to a wild-type phenotype with respect to ookinete morphogenesis, tensile strength, gliding motility and infectivity, presenting the first example of apparent functional redundancy amongst alveolin family members.

  8. Increased leucine-rich repeats and immunoglobulin- like domains 1 expression enhances chemosensitivity in glioma

    Institute of Scientific and Technical Information of China (English)

    Baohui Liu; Shenqi Zhang; Dong Ruan; Xiaonan Zhu; Zhentao Guo; Huimin Dong; Mingmin Yan; Qianxue Chen; Daofeng Tian; Liquan Wu; Junmin Wang; Qiang Cai; Heng Shen; Baowei Ji; Long Wang

    2011-01-01

    Leucine-rich repeats and immunoglobulin-like domains 1 (LRIG1) is an anti-oncogene.LRIG1 is correlated with Bcl-2 in ependymomas.Decreased Bcl-2 and manganese superoxide dismutase expression can improve the chemosensitivity of glioma.In the present study, a tissue microarray of human brain astrocytomas was constructed.To investigate the relationship of LRIG1 with Bcl-2 and manganese superoxide dismutase, LRIG1, Bcl-2 and manganese superoxide dismutase expression in our tissue microarray was determined using immunohistochemistry.In addition, we constructed the LRIG1-U251 cell line, and its responses to doxorubicin and temozolomide were detected using the MTT assay.Results showed that LRIG1 expression was significantly negatively correlated with Bcl-2 and manganese superoxide dismutase expression in glioma.Also, proliferation of LRIG1-U251 cells exposed to doxorubicin or temozolomide was significantly inhibited, i.e.in the LRIG1-U251 cell line, the chemosensitivity to doxorubicin and temozolomide was increased.This indicates that increased LRIG1 expression produces a chemosensitivity in glioma.

  9. Hybrid Sterility in Rice (Oryza sativa L.) Involves the Tetratricopeptide Repeat Domain Containing Protein.

    Science.gov (United States)

    Yu, Yang; Zhao, Zhigang; Shi, Yanrong; Tian, Hua; Liu, Linglong; Bian, Xiaofeng; Xu, Yang; Zheng, Xiaoming; Gan, Lu; Shen, Yumin; Wang, Chaolong; Yu, Xiaowen; Wang, Chunming; Zhang, Xin; Guo, Xiuping; Wang, Jiulin; Ikehashi, Hiroshi; Jiang, Ling; Wan, Jianmin

    2016-07-01

    Intersubspecific hybrid sterility is a common form of reproductive isolation in rice (Oryza sativa L.), which significantly hampers the utilization of heterosis between indica and japonica varieties. Here, we elucidated the mechanism of S7, which specially causes Aus-japonica/indica hybrid female sterility, through cytological and genetic analysis, map-based cloning, and transformation experiments. Abnormal positioning of polar nuclei and smaller embryo sac were observed in F1 compared with male and female parents. Female gametes carrying S7(cp) and S7(i) were aborted in S7(ai)/S7(cp) and S7(ai)/S7(i), respectively, whereas they were normal in both N22 and Dular possessing a neutral allele, S7(n) S7 was fine mapped to a 139-kb region in the centromere region on chromosome 7, where the recombination was remarkably suppressed due to aggregation of retrotransposons. Among 16 putative open reading frames (ORFs) localized in the mapping region, ORF3 encoding a tetratricopeptide repeat domain containing protein was highly expressed in the pistil. Transformation experiments demonstrated that ORF3 is the candidate gene: downregulated expression of ORF3 restored spikelet fertility and eliminated absolutely preferential transmission of S7(ai) in heterozygote S7(ai)/S7(cp); sterility occurred in the transformants Cpslo17-S7(ai) Our results may provide implications for overcoming hybrid embryo sac sterility in intersubspecific hybrid rice and utilization of hybrid heterosis for cultivated rice improvement.

  10. CTD writing and editing standards

    Science.gov (United States)

    Caruthers, C. M.

    1991-03-01

    The Computer and Telecommunication Division (CTD) recognizes that the communication of clear, accurate, reasonably complete information is essential to the success of its Laboratory mission. CTD therefore encourages all Division personnel to adhere to the principles of good writing and to the standards for grammar, usage, style, formats, and publication procedures that are described in CTD Writing and Editing Standards. We encourage CTD personnel to read CTD Writing and Editing Standards and to use it continually as a desktop reference. It will help CTD writers to produce better documents consistent with CTD standards in less time. Applying the principles specified in this document on how to write and organize technical information will speed up the editing, review, and revision processes. CTD Writing and Editing Standards complements the Argonne National Laboratory Technical Publications Guide, which serves as the basic Argonne documentation reference on issues concerning DOE orders and guidelines, NRC directives, and other sponsor requirements. However, this Laboratory-wide document does not address matters of grammar or style. Documents recommended in CTD Writing and Editing Standards are usually available for purchase at the Document Distribution Counter (Building 221, Room A-134) or through the mail (by calling extension 2-5405 and ordering copies).

  11. FF domains of CA150 bind transcription and splicing factors through multiple weak interactions.

    Science.gov (United States)

    Smith, Matthew J; Kulkarni, Sarang; Pawson, Tony

    2004-11-01

    The human transcription factor CA150 modulates human immunodeficiency virus type 1 gene transcription and contains numerous signaling elements, including six FF domains. Repeated FF domains are present in several transcription and splicing factors and can recognize phosphoserine motifs in the C-terminal domain (CTD) of RNA polymerase II (RNAPII). Using mass spectrometry, we identify a number of nuclear binding partners for the CA150 FF domains and demonstrate a direct interaction between CA150 and Tat-SF1, a protein involved in the coupling of splicing and transcription. CA150 FF domains recognize multiple sites within the Tat-SF1 protein conforming to the consensus motif (D/E)(2/5)-F/W/Y-(D/E)(2/5). Individual FF domains are capable of interacting with Tat-SF1 peptide ligands in an equivalent and noncooperative manner, with affinities ranging from 150 to 500 microM. Repeated FF domains therefore appear to bind their targets through multiple weak interactions with motifs comprised of negatively charged residues flanking aromatic amino acids. The RNAPII CTD represents a consensus FF domain-binding site, contingent on generation of the requisite negative charges by phosphorylation of serines 2 and 5. We propose that CA150, through the dual recognition of acidic motifs in proteins such as Tat-SF1 and the phosphorylated CTD, could mediate the recruitment of transcription and splicing factors to actively transcribing RNAPII.

  12. Programmable DNA-binding proteins from Burkholderia provide a fresh perspective on the TALE-like repeat domain.

    Science.gov (United States)

    de Lange, Orlando; Wolf, Christina; Dietze, Jörn; Elsaesser, Janett; Morbitzer, Robert; Lahaye, Thomas

    2014-06-01

    The tandem repeats of transcription activator like effectors (TALEs) mediate sequence-specific DNA binding using a simple code. Naturally, TALEs are injected by Xanthomonas bacteria into plant cells to manipulate the host transcriptome. In the laboratory TALE DNA binding domains are reprogrammed and used to target a fused functional domain to a genomic locus of choice. Research into the natural diversity of TALE-like proteins may provide resources for the further improvement of current TALE technology. Here we describe TALE-like proteins from the endosymbiotic bacterium Burkholderia rhizoxinica, termed Bat proteins. Bat repeat domains mediate sequence-specific DNA binding with the same code as TALEs, despite less than 40% sequence identity. We show that Bat proteins can be adapted for use as transcription factors and nucleases and that sequence preferences can be reprogrammed. Unlike TALEs, the core repeats of each Bat protein are highly polymorphic. This feature allowed us to explore alternative strategies for the design of custom Bat repeat arrays, providing novel insights into the functional relevance of non-RVD residues. The Bat proteins offer fertile grounds for research into the creation of improved programmable DNA-binding proteins and comparative insights into TALE-like evolution.

  13. Terminal-repeat retrotransposons with GAG domain in plant genomes: a new testimony on the complex world of transposable elements.

    Science.gov (United States)

    Chaparro, Cristian; Gayraud, Thomas; de Souza, Rogerio Fernandes; Domingues, Douglas Silva; Akaffou, Sélastique; Laforga Vanzela, Andre Luis; Kochko, Alexandre de; Rigoreau, Michel; Crouzillat, Dominique; Hamon, Serge; Hamon, Perla; Guyot, Romain

    2015-01-07

    A novel structure of nonautonomous long terminal repeat (LTR) retrotransposons called terminal repeat with GAG domain (TR-GAG) has been described in plants, both in monocotyledonous, dicotyledonous and basal angiosperm genomes. TR-GAGs are relatively short elements in length (element into the virus-like particle. GAG precursors show similarities with both Copia and Gypsy GAG proteins, suggesting evolutionary relationships of TR-GAG elements with both families. Despite the lack of the enzymatic machinery required for their mobility, strong evidences suggest that TR-GAGs are still active. TR-GAGs represent ubiquitous nonautonomous structures that could be involved in the molecular diversities of plant genomes.

  14. The structure of Prp40 FF1 domain and its interaction with the crn-TPR1 motif of Clf1 gives a new insight into the binding mode of FF domains.

    Science.gov (United States)

    Gasch, Alexander; Wiesner, Silke; Martin-Malpartida, Pau; Ramirez-Espain, Ximena; Ruiz, Lidia; Macias, Maria J

    2006-01-06

    The yeast splicing factor Prp40 (pre-mRNA processing protein 40) consists of a pair of WW domains followed by several FF domains. The region comprising the FF domains has been shown to associate with the 5' end of U1 small nuclear RNA and to interact directly with two proteins, the Clf1 (Crooked neck-like factor 1) and the phosphorylated repeats of the C-terminal domain of RNA polymerase II (CTD-RNAPII). In this work we reported the solution structure of the first FF domain of Prp40 and the identification of a novel ligand-binding site in FF domains. By using chemical shift assays, we found a binding site for the N-terminal crooked neck tetratricopeptide repeat of Clf1 that is distinct and structurally separate from the previously identified CTD-RNAPII binding pocket of the FBP11 (formin-binding protein 11) FF1 domain. No interaction, however, was observed between the Prp40 FF1 domain and three different peptides derived from the CTD-RNAPII protein. Indeed, the equivalent CTD-RNAPII-binding site in the Prp40 FF1 domain is predominantly negatively charged and thus unfavorable for an interaction with phosphorylated peptide sequences. Sequence alignments and phylogenetic tree reconstructions using the FF domains of three functionally related proteins, Prp40, FBP11, and CA150, revealed that Prp40 and FBP11 are not orthologous proteins and supported the different ligand specificities shown by their respective FF1 domains. Our results also revealed that not all FF domains in Prp40 are functionally equivalent. We proposed that at least two different interaction surfaces exist in FF domains that have evolved to recognize distinct binding motifs.

  15. A conserved gene family encodes transmembrane proteins with fibronectin, immunoglobulin and leucine-rich repeat domains (FIGLER

    Directory of Open Access Journals (Sweden)

    Haga Christopher L

    2007-09-01

    Full Text Available Abstract Background In mouse the cytokine interleukin-7 (IL-7 is required for generation of B lymphocytes, but human IL-7 does not appear to have this function. A bioinformatics approach was therefore used to identify IL-7 receptor related genes in the hope of identifying the elusive human cytokine. Results Our database search identified a family of nine gene candidates, which we have provisionally named fibronectin immunoglobulin leucine-rich repeat (FIGLER. The FIGLER 1–9 genes are predicted to encode type I transmembrane glycoproteins with 6–12 leucine-rich repeats (LRR, a C2 type Ig domain, a fibronectin type III domain, a hydrophobic transmembrane domain, and a cytoplasmic domain containing one to four tyrosine residues. Members of this multichromosomal gene family possess 20–47% overall amino acid identity and are differentially expressed in cell lines and primary hematopoietic lineage cells. Genes for FIGLER homologs were identified in macaque, orangutan, chimpanzee, mouse, rat, dog, chicken, toad, and puffer fish databases. The non-human FIGLER homologs share 38–99% overall amino acid identity with their human counterpart. Conclusion The extracellular domain structure and absence of recognizable cytoplasmic signaling motifs in members of the highly conserved FIGLER gene family suggest a trophic or cell adhesion function for these molecules.

  16. Crystal structures of the human G3BP1 NTF2-like domain visualize FxFG Nup Repeat Specificity

    DEFF Research Database (Denmark)

    Vognsen, Tina Reinholdt; Möller, Ingvar Rúnar; Kristensen, Ole

    2013-01-01

    Ras GTPase Activating Protein SH3 Domain Binding Protein (G3BP) is a potential anti-cancer drug target implicated in several cellular functions. We have used protein crystallography to solve crystal structures of the human G3BP1 NTF2-like domain both alone and in complex with an FxFG Nup repeat...... crystal form might indicate a novel ligand binding site that, however, remains to be validated. The crystal structures give insight into the nuclear transportation mechanisms of G3BP and provide a basis for future structure based drug design....

  17. Repeat organization and epigenetic regulation of the DH-Cmu domain of the immunoglobulin heavy-chain gene locus.

    Science.gov (United States)

    Chakraborty, Tirtha; Chowdhury, Dipanjan; Keyes, Amanda; Jani, Anant; Subrahmanyam, Ramesh; Ivanova, Irina; Sen, Ranjan

    2007-09-07

    The first steps of murine immunoglobulin heavy-chain (IgH) gene recombination take place within a chromosomal domain that contains diversity (D(H)) and joining (J(H)) gene segments, but not variable (V(H)) gene segments. Here we show that the chromatin state of this domain is markedly heterogeneous. Specifically, only 5'- and 3'-most D(H) gene segments carry active chromatin modifications, whereas intervening D(H)s are associated with heterochromatic marks that are maintained by ongoing histone deacetylation. The intervening D(H)s form part of a tandemly repeated sequence that expresses tissue-specific, antisense oriented transcripts. We propose that the intervening D(H) genes are actively suppressed by repeat-induced epigenetic silencing, which is reflected in their infrequent representation in DJ(H) junctions compared to the flanking D(H) genes.

  18. PRR repeats in the intracellular domain of KISS1R are important for its export to cell membrane.

    Science.gov (United States)

    Chevrier, Lucie; de Brevern, Alexandre; Hernandez, Eva; Leprince, Jérome; Vaudry, Hubert; Guedj, Anne Marie; de Roux, Nicolas

    2013-06-01

    Inactivating mutations of KISS-1 receptor (KISS1R) have been recently described as a rare cause of isolated hypogonadotropic hypogonadism transmitted as a recessive trait. Few mutations have been described, and the structure-function relationship of KISS1R remains poorly understood. Here, we have taken advantage of the discovery of a novel mutation of KISS1R to characterize the structure and function of an uncommon protein motif composed of 3 proline-arginine-arginine (PRR) repeats located within the intracellular domain. A heterozygous insertion of 1 PRR repeat in-frame with 3 PRR repeats leading to synthesis of a receptor bearing 4 PRR repeats (PRR-KISS1R) was found in the index case. Functional analysis of PRR-KISS1R showed a decrease of the maximal response to kisspeptin stimulation, associated to a lower cell surface expression without modification of total expression. PRR-KISS1R exerts a dominant negative effect on the synthesis of the wild-type (WT)-KISS1R. This effect was due to the nature of inserted residues but also to the difference of the length of the intracellular domain between PRR-KISS1R and WT-KISS1R. A molecular dynamic analysis showed that the additional PRR constrained this arginine-rich region into a polyproline type II helix. Altogether, this study shows that a heterozygous insertion in KISS1R may lead to hypogonadotropic hypogonadism by a dominant negative effect on the WT receptor. An additional PRR repeat into a proline-arginine-rich motif can dramatically changed the conformation of the intracellular domain of KISS1R and its probable interaction with partner proteins.

  19. Comparative genome analysis of cortactin and HS1: the significance of the F-actin binding repeat domain

    Directory of Open Access Journals (Sweden)

    Seggelen Vera

    2005-02-01

    Full Text Available Abstract Background In human carcinomas, overexpression of cortactin correlates with poor prognosis. Cortactin is an F-actin-binding protein involved in cytoskeletal rearrangements and cell migration by promoting actin-related protein (Arp2/3 mediated actin polymerization. It shares a high amino acid sequence and structural similarity to hematopoietic lineage cell-specific protein 1 (HS1 although their functions differ considerable. In this manuscript we describe the genomic organization of these two genes in a variety of species by a combination of cloning and database searches. Based on our analysis, we predict the genesis of the actin-binding repeat domain during evolution. Results Cortactin homologues exist in sponges, worms, shrimps, insects, urochordates, fishes, amphibians, birds and mammalians, whereas HS1 exists in vertebrates only, suggesting that both genes have been derived from an ancestor cortactin gene by duplication. In agreement with this, comparative genome analysis revealed very similar exon-intron structures and sequence homologies, especially over the regions that encode the characteristic highly conserved F-actin-binding repeat domain. Cortactin splice variants affecting this F-actin-binding domain were identified not only in mammalians, but also in amphibians, fishes and birds. In mammalians, cortactin is ubiquitously expressed except in hematopoietic cells, whereas HS1 is mainly expressed in hematopoietic cells. In accordance with their distinct tissue specificity, the putative promoter region of cortactin is different from HS1. Conclusions Comparative analysis of the genomic organization and amino acid sequences of cortactin and HS1 provides inside into their origin and evolution. Our analysis shows that both genes originated from a gene duplication event and subsequently HS1 lost two repeats, whereas cortactin gained one repeat. Our analysis genetically underscores the significance of the F-actin binding domain in

  20. A nested leucine rich repeat (LRR domain: The precursor of LRRs is a ten or eleven residue motif

    Directory of Open Access Journals (Sweden)

    Matsushima Norio

    2010-09-01

    Full Text Available Abstract Background Leucine rich repeats (LRRs are present in over 60,000 proteins that have been identified in viruses, bacteria, archae, and eukaryotes. All known structures of repeated LRRs adopt an arc shape. Most LRRs are 20-30 residues long. All LRRs contain LxxLxLxxNxL, in which "L" is Leu, Ile, Val, or Phe and "N" is Asn, Thr, Ser, or Cys and "x" is any amino acid. Seven classes of LRRs have been identified. However, other LRR classes remains to be characterized. The evolution of LRRs is not well understood. Results Here we describe a novel LRR domain, or nested repeat observed in 134 proteins from 54 bacterial species. This novel LRR domain has 21 residues with the consensus sequence of LxxLxLxxNxLxxLDLxx(N/L/Q/xxx or LxxLxCxxNxLxxLDLxx(N/L/xxx. This LRR domain is characterized by a nested periodicity; it consists of alternating 10- and 11- residues units of LxxLxLxxNx(x/-. We call it "IRREKO" LRR, since the Japanese word for "nested" is "IRREKO". The first unit of the "IRREKO" LRR domain is frequently occupied by an "SDS22-like" LRR with the consensus of LxxLxLxxNxLxxLxxLxxLxx or a "Bacterial" LRR with the consensus of LxxLxLxxNxLxxLPxLPxx. In some proteins an "SDS22-like" LRR intervenes between "IRREKO" LRRs. Conclusion Proteins having "IRREKO" LRR domain are almost exclusively found in bacteria. It is suggested that IRREKO@LRR evolved from a common ancestor with "SDS22-like" and "Bacterial" classes and that the ancestor of IRREKO@LRR is 10 or 11 residues of LxxLxLxxNx(x/-. The "IRREKO" LRR is predicted to adopt an arc shape with smaller curvature in which β-strands are formed on both concave and convex surfaces.

  1. Long-range effects and functional consequences of stabilizing mutations in the ankyrin repeat domain of IκBα.

    Science.gov (United States)

    Cervantes, Carla F; Handley, Lindsey D; Sue, Shih-Che; Dyson, H Jane; Komives, Elizabeth A

    2013-03-11

    Protein domains containing three or more ankyrin repeats (ARs) are ubiquitous in all phyla. Sequence alignments previously identified certain conserved positions, which have been shown to stabilize AR domains and promote their folding. Consensus mutations [Y254L/T257A (YLTA) and C186P/A220P (CPAP)] stabilize the naturally occuring AR domain of human IκBα to denaturation; however, only the YLTA mutations stabilize the protein to proteasomal degradation. We present results from NMR experiments designed to probe the roles of these consensus mutations in IκBα. According to residual dipolar coupling analysis, the gross structures of the AR domains of both mutants appear to be similar to the wild type (WT). Comparison of chemical shifts of mutant and WT proteins reveals that the YLTA and CPAP consensus mutations cause unexpected long-range effects throughout the AR domains. Backbone dynamics experiments reveal that the YLTA mutations in the sixth AR order the C-terminal PEST sequence on the picosecond-to-nanosecond timescale, compared to either the WT or the CPAP mutant IκBαs. This property is likely the mechanism by which the half-life of YLTA IκBα is extended in vivo.

  2. Short consensus repeat domains extend the E-selectin structure in order to grab cells out of flow

    KAUST Repository

    Aleisa, Fajr

    2017-01-08

    Selectins are key adhesion molecules responsible for initiating a multistep process that leads a cell out of the blood circulation and into a tissue or organ. They are composed of an N-terminal extracellular C-type lectin like domain, followed by an Endothelial Growth Factor like domain (EGF), a defined number of short consensus repeats SCR (also called “sushi” domains), a transmembrane domain and a C-terminal cytoplasmic tail. The adhesion of cells (expressing ligands) to the endothelium (expressing the selection i.e., E-selectin) occurs through the interaction between the lectin domain of selectins and sLeX presenting ligands. Structural/function studies to date have mainly focused on investigating the influence of the lectin domain of E-selectin on its ability to bind its ligands while other domains received less atention. We prepared a number of different recombinant E-selectin proteins with changes in the SCR units. Specifically we generated wild-type E-selectin proteins as monomeric or dimeric structures, mutant proteins with varied numbers of SCRs as well as proteins where strategic residues were mutated to change the conformation of the selectin. Using a novel real time immunoprecipitation surface plasmon resonance (SPR)-based in vitro binding study developed in our lab, the interaction of recombinant E-selectin proteins with immunoprecipitated endogenous ligands (i.e. CD44) captured on a CM-5 chip was assessed. These studies provided quantitative binding kinetics with on and off rates of selectin-ligand interactions and suggested that robust binding is dependent on the presence of the SCRs and oligomerization. These results provide significant implications on the functional mechanism of E-selectin binding to its ligands.

  3. Cdc15 Phosphorylates the C-terminal Domain of RNA Polymerase II for Transcription during Mitosis.

    Science.gov (United States)

    Singh, Amit Kumar; Rastogi, Shivangi; Shukla, Harish; Asalam, Mohd; Rath, Srikanta Kumar; Akhtar, Md Sohail

    2017-03-31

    In eukaryotes, the basal transcription in interphase is orchestrated through the regulation by kinases (Kin28, Bur1, and Ctk1) and phosphatases (Ssu72, Rtr1, and Fcp1), which act through the post-translational modification of the C-terminal domain (CTD) of the largest subunit of RNA polymerase II. The CTD comprises the repeated Tyr-Ser-Pro-Thr-Ser-Pro-Ser motif with potential epigenetic modification sites. Despite the observation of transcription and periodic expression of genes during mitosis with entailing CTD phosphorylation and dephosphorylation, the associated CTD specific kinase(s) and its role in transcription remains unknown. Here we have identified Cdc15 as a potential kinase phosphorylating Ser-2 and Ser-5 of CTD for transcription during mitosis in the budding yeast. The phosphorylation of CTD by Cdc15 is independent of any prior Ser phosphorylation(s). The inactivation of Cdc15 causes reduction of global CTD phosphorylation during mitosis and affects the expression of genes whose transcript levels peak during mitosis. Cdc15 also influences the complete transcription of clb2 gene and phosphorylates Ser-5 at the promoter and Ser-2 toward the 3' end of the gene. The observation that Cdc15 could phosphorylate Ser-5, as well as Ser-2, during transcription in mitosis is in contrast to the phosphorylation marks put by the kinases in interphase (G1, S, and G2), where Cdck7/Kin28 phosphorylates Ser-5 at promoter and Bur1/Ctk1 phosphorylates Ser-2 at the 3' end of the genes. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  4. Terminal-Repeat Retrotransposons with GAG Domain in Plant Genomes: A New Testimony on the Complex World of Transposable Elements

    Science.gov (United States)

    Chaparro, Cristian; Gayraud, Thomas; de Souza, Rogerio Fernandes; Domingues, Douglas Silva; Akaffou, Sélastique; Laforga Vanzela, Andre Luis; de Kochko, Alexandre; Rigoreau, Michel; Crouzillat, Dominique; Hamon, Serge; Hamon, Perla; Guyot, Romain

    2015-01-01

    A novel structure of nonautonomous long terminal repeat (LTR) retrotransposons called terminal repeat with GAG domain (TR-GAG) has been described in plants, both in monocotyledonous, dicotyledonous and basal angiosperm genomes. TR-GAGs are relatively short elements in length (<4 kb) showing the typical features of LTR-retrotransposons. However, they carry only one open reading frame coding for the GAG precursor protein involved for instance in transposition, the assembly, and the packaging of the element into the virus-like particle. GAG precursors show similarities with both Copia and Gypsy GAG proteins, suggesting evolutionary relationships of TR-GAG elements with both families. Despite the lack of the enzymatic machinery required for their mobility, strong evidences suggest that TR-GAGs are still active. TR-GAGs represent ubiquitous nonautonomous structures that could be involved in the molecular diversities of plant genomes. PMID:25573958

  5. Single-molecule FRET reveals the native-state dynamics of the IκBα ankyrin repeat domain.

    Science.gov (United States)

    Lamboy, Jorge A; Kim, Hajin; Dembinski, Holly; Ha, Taekjip; Komives, Elizabeth A

    2013-07-24

    Previous single-molecule fluorescence resonance energy transfer (smFRET) studies in which the second and sixth ankyrin repeats (ARs) of IκBα were labeled with FRET pairs showed slow fluctuations as if the IκBα AR domain was unfolding in its native state. To systematically probe where these slow dynamic fluctuations occur, we now present data from smFRET studies wherein FRET labels were placed at ARs 1 and 4 (mutant named AR 1-4), at ARs 2 and 5 (AR 2-5), and at ARs 3 and 6 (AR 3-6). The results presented here reveal that AR 6 most readily detaches/unfolds from the AR domain, undergoing substantial fluctuations at room temperature. AR 6 has fewer stabilizing consensus residues than the other IκBα ARs, probably contributing to the ease with which AR 6 "loses grip". AR 5 shows almost no fluctuations at room temperature, but a significant fraction of molecules shows fluctuations at 37 °C. Introduction of stabilizing mutations that are known to fold AR 6 dampen the fluctuations of AR 5, indicating that the AR 5 fluctuations are likely due to weakened inter-repeat stabilization from AR 6. AR 1 also fluctuates somewhat at room temperature, suggesting that fluctuations are a general behavior of ARs at ends of AR domains. Remarkably, AR 1 still fluctuates in the bound state, but mainly between 0.6 and 0.9 FRET efficiency, whereas in the free IκBα, the fluctuations extend to <0.5 FRET efficiency. Overall, our results provide a more complete picture of the energy landscape of the native state dynamics of an AR domain.

  6. The Non-canonical Tetratricopeptide Repeat (TPR) Domain of Fluorescent (FLU) Mediates Complex Formation with Glutamyl-tRNA Reductase.

    Science.gov (United States)

    Zhang, Min; Zhang, Feilong; Fang, Ying; Chen, Xuemin; Chen, Yuhong; Zhang, Wenxia; Dai, Huai-En; Lin, Rongcheng; Liu, Lin

    2015-07-10

    The tetratricopeptide repeat (TPR)-containing protein FLU is a negative regulator of chlorophyll biosynthesis in plants. It directly interacts through its TPR domain with glutamyl-tRNA reductase (GluTR), the rate-limiting enzyme in the formation of δ-aminolevulinic acid (ALA). Delineation of how FLU binds to GluTR is important for understanding the molecular basis for FLU-mediated repression of synthesis of ALA, the universal tetrapyrrole precursor. Here, we characterize the FLU-GluTR interaction by solving the crystal structures of the uncomplexed TPR domain of FLU (FLU(TPR)) at 1.45-Å resolution and the complex of the dimeric domain of GluTR bound to FLU(TPR) at 2.4-Å resolution. Three non-canonical TPR motifs of each FLU(TPR) form a concave surface and clamp the helix bundle in the C-terminal dimeric domain of GluTR. We demonstrate that a 2:2 FLU(TPR)-GluTR complex is the functional unit for FLU-mediated GluTR regulation and suggest that the formation of the FLU-GluTR complex prevents glutamyl-tRNA, the GluTR substrate, from binding with this enzyme. These results also provide insights into the spatial regulation of ALA synthesis by the membrane-located FLU protein.

  7. Crystal structures of ryanodine receptor SPRY1 and tandem-repeat domains reveal a critical FKBP12 binding determinant.

    Science.gov (United States)

    Yuchi, Zhiguang; Yuen, Siobhan M Wong King; Lau, Kelvin; Underhill, Ainsley Q; Cornea, Razvan L; Fessenden, James D; Van Petegem, Filip

    2015-08-06

    Ryanodine receptors (RyRs) form calcium release channels located in the membranes of the sarcoplasmic and endoplasmic reticulum. RyRs play a major role in excitation-contraction coupling and other Ca(2+)-dependent signalling events, and consist of several globular domains that together form a large assembly. Here we describe the crystal structures of the SPRY1 and tandem-repeat domains at 1.2-1.5 Å resolution, which reveal several structural elements not detected in recent cryo-EM reconstructions of RyRs. The cryo-EM studies disagree on the position of SPRY domains, which had been proposed based on homology modelling. Computational docking of the crystal structures, combined with FRET studies, show that the SPRY1 domain is located next to FK506-binding protein (FKBP). Molecular dynamics flexible fitting and mutagenesis experiments suggest a hydrophobic cluster within SPRY1 that is crucial for FKBP binding. A RyR1 disease mutation, N760D, appears to directly impact FKBP binding through interfering with SPRY1 folding.

  8. Identification of multiple binding sites for the THAP domain of the Galileo transposase in the long terminal inverted-repeats.

    Science.gov (United States)

    Marzo, Mar; Liu, Danxu; Ruiz, Alfredo; Chalmers, Ronald

    2013-08-01

    Galileo is a DNA transposon responsible for the generation of several chromosomal inversions in Drosophila. In contrast to other members of the P-element superfamily, it has unusually long terminal inverted-repeats (TIRs) that resemble those of Foldback elements. To investigate the function of the long TIRs we derived consensus and ancestral sequences for the Galileo transposase in three species of Drosophilids. Following gene synthesis, we expressed and purified their constituent THAP domains and tested their binding activity towards the respective Galileo TIRs. DNase I footprinting located the most proximal DNA binding site about 70 bp from the transposon end. Using this sequence we identified further binding sites in the tandem repeats that are found within the long TIRs. This suggests that the synaptic complex between Galileo ends may be a complicated structure containing higher-order multimers of the transposase. We also attempted to reconstitute Galileo transposition in Drosophila embryos but no events were detected. Thus, although the limited numbers of Galileo copies in each genome were sufficient to provide functional consensus sequences for the THAP domains, they do not specify a fully active transposase. Since the THAP recognition sequence is short, and will occur many times in a large genome, it seems likely that the multiple binding sites within the long, internally repetitive, TIRs of Galileo and other Foldback-like elements may provide the transposase with its binding specificity.

  9. Crystal structures of histone and p53 methyltransferase SmyD2 reveal a conformational flexibility of the autoinhibitory C-terminal domain.

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    Yuanyuan Jiang

    Full Text Available SmyD2 belongs to a new class of chromatin regulators that control gene expression in heart development and tumorigenesis. Besides methylation of histone H3 K4, SmyD2 can methylate non-histone targets including p53 and the retinoblastoma tumor suppressor. The methyltransferase activity of SmyD proteins has been proposed to be regulated by autoinhibition via the intra- and interdomain bending of the conserved C-terminal domain (CTD. However, there has been no direct evidence of a conformational change in the CTD. Here, we report two crystal structures of SmyD2 bound either to the cofactor product S-adenosylhomocysteine or to the inhibitor sinefungin. SmyD2 has a two-lobed structure with the active site located at the bottom of a deep crevice formed between the CTD and the catalytic domain. By extensive engagement with the methyltransferase domain, the CTD stabilizes the autoinhibited conformation of SmyD2 and restricts access to the catalytic site. Unexpectedly, despite that the two SmyD2 structures are highly superimposable, significant differences are observed in the first two helices of the CTDs: the two helices bend outwards and move away from the catalytic domain to generate a less closed conformation in the sinefungin-bound structure. Although the overall fold of the individual domains is structurally conserved among SmyD proteins, SmyD2 appear to be a conformational "intermediate" between a close form of SmyD3 and an open form of SmyD1. In addition, the structures reveal that the CTD is structurally similar to tetratricopeptide repeats (TPR, a motif through which many cochaperones bind to the heat shock protein Hsp90. Our results thus provide the first evidence for the intradomain flexibility of the TPR-like CTD, which may be important for the activation of SmyD proteins by Hsp90.

  10. Taxonomic distribution, repeats, and functions of the S1 domain-containing proteins as members of the OB-fold family.

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    Deryusheva, Evgeniia I; Machulin, Andrey V; Selivanova, Olga M; Galzitskaya, Oxana V

    2017-04-01

    Proteins of the nucleic acid-binding proteins superfamily perform such functions as processing, transport, storage, stretching, translation, and degradation of RNA. It is one of the 16 superfamilies containing the OB-fold in protein structures. Here, we have analyzed the superfamily of nucleic acid-binding proteins (the number of sequences exceeds 200,000) and obtained that this superfamily prevalently consists of proteins containing the cold shock DNA-binding domain (ca. 131,000 protein sequences). Proteins containing the S1 domain compose 57% from the cold shock DNA-binding domain family. Furthermore, we have found that the S1 domain was identified mainly in the bacterial proteins (ca. 83%) compared to the eukaryotic and archaeal proteins, which are available in the UniProt database. We have found that the number of multiple repeats of S1 domain in the S1 domain-containing proteins depends on the taxonomic affiliation. All archaeal proteins contain one copy of the S1 domain, while the number of repeats in the eukaryotic proteins varies between 1 and 15 and correlates with the protein size. In the bacterial proteins, the number of repeats is no more than 6, regardless of the protein size. The large variation of the repeat number of S1 domain as one of the structural variants of the OB-fold is a distinctive feature of S1 domain-containing proteins. Proteins from the other families and superfamilies have either one OB-fold or change slightly the repeat numbers. On the whole, it can be supposed that the repeat number is a vital for multifunctional activity of the S1 domain-containing proteins. Proteins 2017; 85:602-613. © 2016 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  11. The repeat domain of the type III effector protein PthA shows a TPR-like structure and undergoes conformational changes upon DNA interaction.

    Science.gov (United States)

    Murakami, Mário Tyago; Sforça, Mauricio Luis; Neves, Jorge Luiz; Paiva, Joice Helena; Domingues, Mariane Noronha; Pereira, André Luiz Araujo; Zeri, Ana Carolina de Mattos; Benedetti, Celso Eduardo

    2010-12-01

    Many plant pathogenic bacteria rely on effector proteins to suppress defense and manipulate host cell mechanisms to cause disease. The effector protein PthA modulates the host transcriptome to promote citrus canker. PthA possesses unusual protein architecture with an internal region encompassing variable numbers of near-identical tandem repeats of 34 amino acids termed the repeat domain. This domain mediates protein-protein and protein-DNA interactions, and two polymorphic residues in each repeat unit determine DNA specificity. To gain insights into how the repeat domain promotes protein-protein and protein-DNA contacts, we have solved the structure of a peptide corresponding to 1.5 units of the PthA repeat domain by nuclear magnetic resonance (NMR) and carried out small-angle X-ray scattering (SAXS) and spectroscopic studies on the entire 15.5-repeat domain of PthA2 (RD2). Consistent with secondary structure predictions and circular dichroism data, the NMR structure of the 1.5-repeat peptide reveals three α-helices connected by two turns that fold into a tetratricopeptide repeat (TPR)-like domain. The NMR structure corroborates the theoretical TPR superhelix predicted for RD2, which is also in agreement with the elongated shape of RD2 determined by SAXS. Furthermore, RD2 undergoes conformational changes in a pH-dependent manner and upon DNA interaction, and shows sequence similarities to pentatricopeptide repeat (PPR), a nucleic acid-binding motif structurally related to TPR. The results point to a model in which the RD2 structure changes its compactness as it embraces the DNA with the polymorphic diresidues facing the interior of the superhelix oriented toward the nucleotide bases.

  12. Nuclear Magnetic Resonance Structure of a Novel Globular Domain in RBM10 Containing OCRE, the Octamer Repeat Sequence Motif.

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    Martin, Bryan T; Serrano, Pedro; Geralt, Michael; Wüthrich, Kurt

    2016-01-01

    The OCtamer REpeat (OCRE) has been annotated as a 42-residue sequence motif with 12 tyrosine residues in the spliceosome trans-regulatory elements RBM5 and RBM10 (RBM [RNA-binding motif]), which are known to regulate alternative splicing of Fas and Bcl-x pre-mRNA transcripts. Nuclear magnetic resonance structure determination showed that the RBM10 OCRE sequence motif is part of a 55-residue globular domain containing 16 aromatic amino acids, which consists of an anti-parallel arrangement of six β strands, with the first five strands containing complete or incomplete Tyr triplets. This OCRE globular domain is a distinctive component of RBM10 and is more widely conserved in RBM10s across the animal kingdom than the ubiquitous RNA recognition components. It is also found in the functionally related RBM5. Thus, it appears that the three-dimensional structure of the globular OCRE domain, rather than the 42-residue OCRE sequence motif alone, confers specificity on RBM10 intermolecular interactions in the spliceosome.

  13. Rat1p maintains RNA polymerase II CTD phosphorylation balance

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    Jimeno-González, Silvia; Schmid, Manfred; Malagon, Francisco; Haaning, Line Lindegaard; Jensen, Torben Heick

    2014-01-01

    In S. cerevisiae, the 5′-3′ exonuclease Rat1p partakes in transcription termination. Although Rat1p-mediated RNA degradation has been suggested to play a role for this activity, the exact mechanisms by which Rat1p helps release RNA polymerase II (RNAPII) from the DNA template are poorly understood. Here we describe a function of Rat1p in regulating phosphorylation levels of the C-terminal domain (CTD) of the largest RNAPII subunit, Rpb1p, during transcription elongation. The rat1-1 mutant exhibits highly elevated levels of CTD phosphorylation as well as RNAPII distribution and transcription termination defects. These phenotypes are all rescued by overexpression of the CTD phosphatase Fcp1p, suggesting a functional relationship between the absence of Rat1p activity, elevated CTD phosphorylation, and transcription defects. We also demonstrate that rat1-1 cells display increased RNAPII transcription kinetics, a feature that may contribute to the cellular phenotypes of the mutant. Consistently, the rat1-1 allele is synthetic lethal with the rpb1-E1103G mutation, causing increased RNAPII speed, and is suppressed by the rpb2-10 mutation, causing slowed transcription. Thus, Rat1p plays more complex roles in controlling transcription than previously thought. PMID:24501251

  14. The relationship between the L1 and L2 domains of the insulin and epidermal growth factor receptors and leucine-rich repeat modules

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    Ward Colin W

    2001-07-01

    Full Text Available Abstract Background Leucine-rich repeats are one of the more common modules found in proteins. The leucine-rich repeat consensus motif is LxxLxLxxNxLxxLxxLxxLxx- where the first 11–12 residues are highly conserved and the remainder of the repeat can vary in size Leucine-rich repeat proteins have been subdivided into seven subfamilies, none of which include members of the epidermal growth factor receptor or insulin receptor families despite the similarity between the 3D structure of the L domains of the type I insulin-like growth factor receptor and some leucine-rich repeat proteins. Results Here we have used profile searches and multiple sequence alignments to identify the repeat motif Ixx-LxIxx-Nx-Lxx-Lxx-Lxx-Lxx- in the L1 and L2 domains of the insulin receptor and epidermal growth factor receptors. These analyses were aided by reference to the known three dimensional structures of the insulin-like growth factor type I receptor L domains and two members of the leucine rich repeat family, porcine ribonuclease inhibitor and internalin 1B. Pectate lyase, another beta helix protein, can also be seen to contain the sequence motif and much of the structural features characteristic of leucine-rich repeat proteins, despite the existence of major insertions in some of its repeats. Conclusion Multiple sequence alignments and comparisons of the 3D structures has shown that right-handed beta helix proteins such as pectate lyase and the L domains of members of the insulin receptor and epidermal growth factor receptor families, are members of the leucine-rich repeat superfamily.

  15. The nebulette repeat domain is necessary for proper maintenance of tropomyosin with the cardiac sarcomere.

    Science.gov (United States)

    Bonzo, Jeremy R; Norris, Andrea A; Esham, Michael; Moncman, Carole L

    2008-11-15

    Nebulette is a cardiac-specific isoform of the giant actin-binding protein nebulin. Nebulette, having a mass of approximately 100 kDa, is only predicted to extend 150 nm from the edge of the Z-lines. Overexpression of the nebulette C-terminal linker and/or SH3 domains in chicken cardiomyocytes results in a loss of endogenous nebulette with a concomitant loss of tropomyosin (TPM) and troponin, as well as a shortening of the thin filaments. These data suggest that nebulette's position in the sarcomere is important for the maintenance of TPM, troponin and thin filament length. To evaluate this hypothesis, N-terminal nested truncations tagged with GFP were expressed in chicken cardiomyocytes and the cells were analyzed for the distribution of myofilament proteins. Minimal effects on the myofilaments were observed with N-terminal deletions of up to 10 modules; however, deletion of 15 modules replicated the phenotype observed with expression of the C-terminal fragments. Expression of internal deletions of nebulette verifies that a site between module 10 and 15 is important for TPM maintenance within the sarcomeric lattice. We have additionally isolated TPM cDNAs from a yeast two hybrid (Y2H) analysis. These data indicate the importance of the nebulette-TPM interactions in the maintenance and stability of the thin filaments.

  16. The repeat domain of the melanosome fibril protein Pmel17 forms the amyloid core promoting melanin synthesis.

    Science.gov (United States)

    McGlinchey, Ryan P; Shewmaker, Frank; McPhie, Peter; Monterroso, Begoña; Thurber, Kent; Wickner, Reed B

    2009-08-18

    Pmel17 is a melanocyte protein necessary for eumelanin deposition 1 in mammals and found in melanosomes in a filamentous form. The luminal part of human Pmel17 includes a region (RPT) with 10 copies of a partial repeat sequence, pt.e.gttp.qv., known to be essential in vivo for filament formation. We show that this RPT region readily forms amyloid in vitro, but only under the mildly acidic conditions typical of the lysosome-like melanosome lumen, and the filaments quickly become soluble at neutral pH. Under the same mildly acidic conditions, the Pmel filaments promote eumelanin formation. Electron diffraction, circular dichroism, and solid-state NMR studies of Pmel17 filaments show that the structure is rich in beta sheet. We suggest that RPT is the amyloid core domain of the Pmel17 filaments so critical for melanin formation.

  17. Toxic PR poly-dipeptides encoded by the C9orf72 repeat expansion target LC domain polymers

    Science.gov (United States)

    Lin, Yi; Mori, Eiichiro; Kato, Masato; Xiang, Siheng; Wu, Leeju; Kwon, Ilmin; McKnight, Steven L.

    2016-01-01

    Summary Two complementary approaches were used in search of the intracellular targets of the toxic PR poly-dipeptide encoded by the repeat sequences expanded in the C9orf72 form of amyotrophic lateral sclerosis. The top categories of PRn-bound proteins include constituents of non-membrane invested cellular organelles and intermediate filaments. PRn targets are enriched for the inclusion of low complexity (LC) sequences. Evidence is presented indicating that LC sequences represent the direct target of PRn binding, and that interaction between the PRn poly-dipeptide and LC domains is polymer-dependent. These studies indicate that PRn-mediated toxicity may result from broad impediments to the dynamics of cell structure and information flow from gene to message to protein. PMID:27768897

  18. Toxic PR Poly-Dipeptides Encoded by the C9orf72 Repeat Expansion Target LC Domain Polymers.

    Science.gov (United States)

    Lin, Yi; Mori, Eiichiro; Kato, Masato; Xiang, Siheng; Wu, Leeju; Kwon, Ilmin; McKnight, Steven L

    2016-10-20

    Two complementary approaches were used in search of the intracellular targets of the toxic PR poly-dipeptide encoded by the repeat sequences expanded in the C9orf72 form of amyotrophic lateral sclerosis. The top categories of PRn-bound proteins include constituents of non-membrane invested cellular organelles and intermediate filaments. PRn targets are enriched for the inclusion of low complexity (LC) sequences. Evidence is presented indicating that LC sequences represent the direct target of PRn binding and that interaction between the PRn poly-dipeptide and LC domains is polymer-dependent. These studies indicate that PRn-mediated toxicity may result from broad impediments to the dynamics of cell structure and information flow from gene to message to protein.

  19. Structural and Biochemical Consequences of Disease-Causing Mutations in the Ankyrin Repeat Domain of the Human TRPV4 Channel

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    Inada, Hitoshi; Procko, Erik; Sotomayor, Marcos; Gaudet, Rachelle (Harvard-Med); (Harvard)

    2012-10-23

    The TRPV4 calcium-permeable cation channel plays important physiological roles in osmosensation, mechanosensation, cell barrier formation, and bone homeostasis. Recent studies reported that mutations in TRPV4, including some in its ankyrin repeat domain (ARD), are associated with human inherited diseases, including neuropathies and skeletal dysplasias, probably because of the increased constitutive activity of the channel. TRPV4 activity is regulated by the binding of calmodulin and small molecules such as ATP to the ARD at its cytoplasmic N-terminus. We determined structures of ATP-free and -bound forms of human TRPV4-ARD and compared them with available TRPV-ARD structures. The third inter-repeat loop region (Finger 3 loop) is flexible and may act as a switch to regulate channel activity. Comparisons of TRPV-ARD structures also suggest an evolutionary link between ARD structure and ATP binding ability. Thermal stability analyses and molecular dynamics simulations suggest that ATP increases stability in TRPV-ARDs that can bind ATP. Biochemical analyses of a large panel of TRPV4-ARD mutations associated with human inherited diseases showed that some impaired thermal stability while others weakened ATP binding ability, suggesting molecular mechanisms for the diseases.

  20. The molecular chaperone Hsp70 activates protein phosphatase 5 (PP5) by binding the tetratricopeptide repeat (TPR) domain.

    Science.gov (United States)

    Connarn, Jamie N; Assimon, Victoria A; Reed, Rebecca A; Tse, Eric; Southworth, Daniel R; Zuiderweg, Erik R P; Gestwicki, Jason E; Sun, Duxin

    2014-01-31

    Protein phosphatase 5 (PP5) is auto-inhibited by intramolecular interactions with its tetratricopeptide repeat (TPR) domain. Hsp90 has been shown to bind PP5 to activate its phosphatase activity. However, the functional implications of binding Hsp70 to PP5 are not yet clear. In this study, we find that both Hsp90 and Hsp70 bind to PP5 using a luciferase fragment complementation assay. A fluorescence polarization assay shows that Hsp90 (MEEVD motif) binds to the TPR domain of PP5 almost 3-fold higher affinity than Hsp70 (IEEVD motif). However, Hsp70 binding to PP5 stimulates higher phosphatase activity of PP5 than the binding of Hsp90. We find that PP5 forms a stable 1:1 complex with Hsp70, but the interaction appears asymmetric with Hsp90, with one PP5 binding the dimer. Solution NMR studies reveal that Hsc70 and PP5 proteins are dynamically independent in complex, tethered by a disordered region that connects the Hsc70 core and the IEEVD-TPR contact area. This tethered binding is expected to allow PP5 to carry out multi-site dephosphorylation of Hsp70-bound clients with a range of sizes and shapes. Together, these results demonstrate that Hsp70 recruits PP5 and activates its phosphatase activity which suggests dual roles for PP5 that might link chaperone systems with signaling pathways in cancer and development.

  1. Tyrosine phosphorylation of RNA polymerase II CTD is associated with antisense promoter transcription and active enhancers in mammalian cells

    Science.gov (United States)

    Descostes, Nicolas; Heidemann, Martin; Spinelli, Lionel; Schüller, Roland; Maqbool, Muhammad Ahmad; Fenouil, Romain; Koch, Frederic; Innocenti, Charlène; Gut, Marta; Gut, Ivo; Eick, Dirk; Andrau, Jean-Christophe

    2014-01-01

    In mammals, the carboxy-terminal domain (CTD) of RNA polymerase (Pol) II consists of 52 conserved heptapeptide repeats containing the consensus sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. Post-translational modifications of the CTD coordinate the transcription cycle and various steps of mRNA maturation. Here we describe Tyr1 phosphorylation (Tyr1P) as a hallmark of promoter (5′ associated) Pol II in mammalian cells, in contrast to what was described in yeast. Tyr1P is predominantly found in antisense orientation at promoters but is also specifically enriched at active enhancers. Mutation of Tyr1 to phenylalanine (Y1F) prevents the formation of the hyper-phosphorylated Pol IIO form, induces degradation of Pol II to the truncated Pol IIB form, and results in a lethal phenotype. Our results suggest that Tyr1P has evolved specialized and essential functions in higher eukaryotes associated with antisense promoter and enhancer transcription, and Pol II stability. DOI: http://dx.doi.org/10.7554/eLife.02105.001 PMID:24842994

  2. Effects of pH on aggregation kinetics of the repeat domain of a functional amyloid, Pmel17

    Science.gov (United States)

    Pfefferkorn, Candace M.; McGlinchey, Ryan P.; Lee, Jennifer C.

    2010-01-01

    Pmel17 is a functional amyloidogenic protein whose fibrils act as scaffolds for pigment deposition in human skin and eyes. We have used the repeat domain (RPT, residues 315–444), an essential luminal polypeptide region of Pmel17, as a model system to study conformational changes from soluble unstructured monomers to β-sheet-containing fibrils. Specifically, we report on the effects of solution pH (4 → 7) mimicking pH conditions of melanosomes, acidic organelles where Pmel17 fibrils are formed. Local, secondary, and fibril structure were monitored via intrinsic Trp fluorescence, circular dichroism spectroscopy, and transmission electron microscopy, respectively. We find that W423 is a highly sensitive probe of amyloid assembly with spectral features reflecting local conformational and fibril morphological changes. A critical pH regime (5 ± 0.5) was identified for fibril formation suggesting the involvement of at least three carboxylic acids in the structural rearrangement necessary for aggregation. Moreover, we demonstrate that RPT fibril morphology can be transformed directly by changing solution pH. Based on these results, we propose that intramelanosomal pH regulates Pmel17 amyloid formation and its subsequent dissolution in vivo. PMID:21106765

  3. Ankyrin repeat domain-encoding genes in the wPip strain of Wolbachia from the Culex pipiens group

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    Parkhill Julian

    2007-09-01

    Full Text Available Abstract Background Wolbachia are obligate endosymbiotic bacteria maternally transmitted through the egg cytoplasm that are responsible for several reproductive disorders in their insect hosts, such as cytoplasmic incompatibility (CI in infected mosquitoes. Species in the Culex pipiens complex display an unusually high number of Wolbachia-induced crossing types, and based on present data, only the wPip strain is present. Results The sequencing of the wPip strain of Wolbachia revealed the presence of 60 ankyrin repeat domain (ANK encoding genes and expression studies of these genes were carried out in adult mosquitoes. One of these ANK genes, pk2, is shown to be part of an operon of three prophage-associated genes with sex-specific expression, and is present in two identical copies in the genome. Another homolog of pk2 is also present that is differentially expressed in different Cx. pipiens group strains. A further two ANK genes showed sex-specific regulation in wPip-infected Cx. pipiens group adults. Conclusion The high number, variability and differential expression of ANK genes in wPip suggest an important role in Wolbachia biology, and the gene family provides both markers and promising candidates for the study of reproductive manipulation.

  4. Structure and Membrane Binding Properties of the Endosomal Tetratricopeptide Repeat (TPR) Domain-containing Sorting Nexins SNX20 and SNX21.

    Science.gov (United States)

    Clairfeuille, Thomas; Norwood, Suzanne J; Qi, Xiaying; Teasdale, Rohan D; Collins, Brett M

    2015-06-01

    Sorting nexins (SNX) orchestrate membrane trafficking and signaling events required for the proper distribution of proteins within the endosomal network. Their phox homology (PX) domain acts as a phosphoinositide (PI) recognition module that targets them to specific endocytic membrane domains. The modularity of SNX proteins confers a wide variety of functions from signaling to membrane deformation and cargo binding, and many SNXs are crucial modulators of endosome dynamics and are involved in a myriad of physiological and pathological processes such as neurodegenerative diseases, cancer, and inflammation. Here, we have studied the poorly characterized SNX20 and its paralogue SNX21, which contain an N-terminal PX domain and a C-terminal PX-associated B (PXB) domain of unknown function. The two proteins share similar PI-binding properties and are recruited to early endosomal compartments by their PX domain. The crystal structure of the SNX21 PXB domain reveals a tetratricopeptide repeat (TPR)-fold, a module that typically binds short peptide motifs, with three TPR α-helical repeats. However, the C-terminal capping helix adopts a highly unusual and potentially self-inhibitory topology. SAXS solution structures of SNX20 and SNX21 show that these proteins adopt a compact globular architecture, and membrane interaction analyses indicate the presence of overlapping PI-binding sites that may regulate their intracellular localization. This study provides the first structural analysis of this poorly characterized subfamily of SNX proteins, highlighting a likely role as endosome-associated scaffolds.

  5. Probing the mechanism of amyloidogenesis through a tandem repeat of the PI3-SH3 domain suggests a generic model for protein aggregation and fibril formation.

    Science.gov (United States)

    Bader, Reto; Bamford, Richard; Zurdo, Jesús; Luisi, Ben F; Dobson, Christopher M

    2006-02-10

    Aggregation of the SH3 domain of the PI3 kinase, both as a single domain and as a tandem repeat in which the C terminus of one domain is linked to the N terminus of another by a flexible linker of ten glycine/serine residues, has been studied under a range of conditions in order to investigate the mechanism of protein aggregation and amyloid formation. The tandem repeat was found to form amyloid fibrils much more readily than the single domain under the acidic conditions used here, and the fibrils themselves have higher morphological homogeneity. The folding-unfolding transition of the PI3-SH3 domain shows two-state behaviour and is pH dependent; at pH 3.6, which is near the pH mid-point for folding and only slightly below the isoelectric point of the protein, both the single domain and the tandem repeat spontaneously form broad distributions of soluble oligomers without requirement for nucleation. Under prolonged incubation under these conditions, the oligomers convert into thin, curly fibrils that interact with thioflavin-T, suggesting that they contain an organised beta-sheet structure. Under more acidic conditions (pH 2.0) where the proteins are fully denatured and carry a positive net charge, long, straight fibrils are formed in a process having a pronounced lag phase. The latter was found to be reduced dramatically by the addition of oligomers exceeding a critical size of approximately 20 molecules. The results suggest that the process of aggregation of these SH3 domains can take place by a variety of mechanisms, ranging from downhill formation of relatively amorphous species to nucleated formation of highly organised structures, the relative importance of which varies greatly with solution conditions. Comparison with the behaviour of other amyloidogenic systems suggests that the general mechanistic features outlined here are likely to be common to at least a wide variety of peptides and proteins.

  6. The ankyrin repeats and DHHC S-acyl transferase domain of AKR1 act independently to regulate switching from vegetative to mating states in yeast.

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    Piers A Hemsley

    Full Text Available Signal transduction from G-protein coupled receptors to MAPK cascades through heterotrimeric G-proteins has been described for many eukaryotic systems. One of the best-characterised examples is the yeast pheromone response pathway, which is negatively regulated by AKR1. AKR1-like proteins are present in all eukaryotes and contain a DHHC domain and six ankyrin repeats. Whilst the DHHC domain dependant S-acyl transferase (palmitoyl transferase function of AKR1 is well documented it is not known whether the ankyrin repeats are also required for this activity. Here we show that the ankyrin repeats of AKR1 are required for full suppression of the yeast pheromone response pathway, by sequestration of the Gβγ dimer, and act independently of AKR1 S-acylation function. Importantly, the functions provided by the AKR1 ankyrin repeats and DHHC domain are not required on the same molecule to fully restore WT phenotypes and function. We also show that AKR1 molecules are S-acylated at locations other than the DHHC cysteine, increasing the abundance of AKR1 in the cell. Our results have important consequences for studies of AKR1 function, including recent attempts to characterise S-acylation enzymology and kinetics. Proteins similar to AKR1 are found in all eukaryotes and our results have broad implications for future work on these proteins and the control of switching between Gβγ regulated pathways.

  7. Cross-talk between the epidermal growth factor-like repeats/fibronectin 6-8 repeats domains of Tenascin-R and microglia modulates neural stem/progenitor cell proliferation and differentiation.

    Science.gov (United States)

    Liao, Hong; Huang, Wenhui; Niu, Rui; Sun, Lixin; Zhang, Luyong

    2008-01-01

    Mounting evidence has demonstrated that the microenvironment of stem/progenitor cells plays an important role in their proliferation and commitment to their fate. However, it remains unclear how all elements, such as astrocytes, microglia, extracellular matrix molecules, soluble factors, and their cross-talk interactions in the microenvironments, affect neural stem/progenitor cell fate. This work explored the influences of cross-talk between Tenascin-R (TN-R) and microglia on neural stem/progenitor cell proliferation and differentiation. Our results show that microglia triggered by TN-R distinct domains EGF-like repeats (EGFL) and fibronectin 6-8 repeats (FN6-8) significantly enhanced the proliferation of neural stem/progenitor cells and also obviously induced the differentiation into neurons but not oligodendrocytes. Neurite processes of neurons generated from neural progenitor cells were promoted by both EGFL and FN6-8 domains-activated microglia. Microglia triggered by EGFL and FN6-8 secreted brain-derived neurotrophic factor (BDNF) and transforming growth factor-beta (TGF-beta); interestingly, FN6-8 could activate microglia to secrete nerve growth factor in addition to BDNF and TGF-beta, but EGFL domain could not. All these data implied that the cross-talk between TN-R distinct domains EGFL/FN6-8 and microglia promoted neural stem/progenitor cell proliferation and induced their differentiation into neurons.

  8. Anchoring skeletal muscle development and disease: The role of ankyrin repeat domain containing proteins in muscle physiology

    NARCIS (Netherlands)

    J-M. Tee (Jin-Ming); M.P. Peppelenbosch (Maikel)

    2010-01-01

    textabstractThe ankyrin repeat is a protein module with high affinity for other ankyrin repeats based on strong Van der Waals forces. The resulting dimerization is unusually resistant to both mechanical forces and alkanization, making this module exceedingly useful for meeting the extraordinary dema

  9. One repeat of the cell wall binding domain is sufficient for anchoring the Lactobacillus acidophilus surface layer protein

    NARCIS (Netherlands)

    Smit, E.; Pouwels, P.H.

    2002-01-01

    The N-terminal repeat (SAC1) of the S-protein of Lactobacillus acidophilus bound efficiently and specifically to cell wall fragments (CWFs) when fused to green fluorescent protein, whereas the C-terminal repeat (SAC2) did not. Treatment of CWFs with hydrofluoric acid, but not phenol, prevented bindi

  10. Crystal Structure of the Human Symplekin-Ssu72-CTD Phosphopeptide Complex

    Energy Technology Data Exchange (ETDEWEB)

    K Xiang; T Nigaike; S Xiang; T Kilic; M Beh; J Manley; L Tong

    2011-12-31

    Symplekin (Pta1 in yeast) is a scaffold in the large protein complex that is required for 3'-end cleavage and polyadenylation of eukaryotic messenger RNA precursors (pre-mRNAs); it also participates in transcription initiation and termination by RNA polymerase II (Pol II). Symplekin mediates interactions between many different proteins in this machinery, although the molecular basis for its function is not known. Here we report the crystal structure at 2.4 {angstrom} resolution of the amino-terminal domain (residues 30-340) of human symplekin in a ternary complex with the Pol II carboxy-terminal domain (CTD) Ser5 phosphatase Ssu72 and a CTD Ser5 phosphopeptide. The N-terminal domain of symplekin has the ARM or HEAT fold, with seven pairs of antiparallel {alpha}-helices arranged in the shape of an arc. The structure of Ssu72 has some similarity to that of low-molecular-mass phosphotyrosine protein phosphatase, although Ssu72 has a unique active-site landscape as well as extra structural features at the C terminus that are important for interaction with symplekin. Ssu72 is bound to the concave face of symplekin, and engineered mutations in this interface can abolish interactions between the two proteins. The CTD peptide is bound in the active site of Ssu72, with the pSer5-Pro6 peptide bond in the cis configuration, which contrasts with all other known CTD peptide conformations. Although the active site of Ssu72 is about 25 {angstrom} from the interface with symplekin, we found that the symplekin N-terminal domain stimulates Ssu72 CTD phosphatase activity in vitro. Furthermore, the N-terminal domain of symplekin inhibits polyadenylation in vitro, but only when coupled to transcription. Because catalytically active Ssu72 overcomes this inhibition, our results show a role for mammalian Ssu72 in transcription-coupled pre-mRNA 3'-end processing.

  11. A Two-amino Acid Mutation Encountered in Duchenne Muscular Dystrophy Decreases Stability of the Rod Domain 23 (R23) Spectrin-like Repeat of Dystrophin.

    Science.gov (United States)

    Legardinier, Sébastien; Legrand, Baptiste; Raguénès-Nicol, Céline; Bondon, Arnaud; Hardy, Serge; Tascon, Christophe; Le Rumeur, Elisabeth; Hubert, Jean-François

    2009-03-27

    Lack of functional dystrophin causes severe Duchenne muscular dystrophy. The subsarcolemmal location of dystrophin, as well as its association with both cytoskeleton and membrane, suggests a role in the mechanical regulation of muscular membrane stress. In particular, phenotype rescue in a Duchenne muscular dystrophy mice model has shown that some parts of the central rod domain of dystrophin, constituted by 24 spectrin-like repeats, are essential. In this study, we made use of rare missense pathogenic mutations in the dystrophin gene and analyzed the biochemical properties of the isolated repeat 23 bearing single or double mutations E2910V and N2912D found in muscle dystrophy with severity grading. No dramatic effect on secondary and tertiary structure of the repeat was found in mutants compared with wild type as revealed by circular dichroism and NMR. Thermal and chemical unfolding data from circular dichroism and tryptophan fluorescence show significant decrease of stability for the mutants, and stopped-flow spectroscopy shows decreased refolding rates. The most deleterious single mutation is the N2912D replacement, although we observe additive effects of the two mutations on repeat stability. Based on three-dimensional structures built by homology molecular modeling, we discuss the modifications of the mutation-induced repeat stability. We conclude that the main forces involved in repeat stability are electrostatic inter-helix interactions that are disrupted following mutations. This study represents the first analysis at the protein level of the consequences of missense mutations in the human dystrophin rod domain. Our results suggest that it may participate in mechanical weakening of dystrophin-deficient muscle.

  12. The crystal structure of the signature domain of cartilage oligomeric matrix protein: implications for collagen, glycosaminoglycan and integrin binding.

    Science.gov (United States)

    Tan, Kemin; Duquette, Mark; Joachimiak, Andrzej; Lawler, Jack

    2009-08-01

    Cartilage oligomeric matrix protein (COMP), or thrombospondin-5 (TSP-5), is a secreted glycoprotein that is important for growth plate organization and function. Mutations in COMP cause two skeletal dysplasias, pseudoachondroplasia (PSACH) and multiple epiphyseal dysplasia (EDM1). In this study, we determined the structure of a recombinant protein that contains the last epidermal growth factor repeat, the type 3 repeats and the C-terminal domain (CTD) of COMP to 3.15-A resolution limit by X-ray crystallography. The CTD is a beta-sandwich that is composed of 15 antiparallel beta-strands, and the type 3 repeats are a contiguous series of calcium binding sites that associate with the CTD at multiple points. The crystal packing reveals an exposed potential metal-ion-dependent adhesion site (MIDAS) on one edge of the beta-sandwich that is common to all TSPs and may serve as a binding site for collagens and other ligands. Disease-causing mutations in COMP disrupt calcium binding, disulfide bond formation, intramolecular interactions, or sites for potential ligand binding. The structure presented here and its unique molecular packing in the crystal identify potential interactive sites for glycosaminoglycans, integrins, and collagens, which are key to cartilage structure and function.

  13. Inducible polymerization and two-dimensional assembly of the repeats-in-toxin (RTX) domain from the Pseudomonas aeruginosa alkaline protease.

    Science.gov (United States)

    Zhang, Liang; Franks, Jonathon; Stolz, Donna B; Conway, James F; Thibodeau, Patrick H

    2014-10-21

    Self-assembling proteins represent potential scaffolds for the organization of enzymatic activities. The alkaline protease repeats-in-toxin (RTX) domain from Pseudomonas aeruginosa undergoes multiple structural transitions in the presence and absence of calcium, a native structural cofactor. In the absence of calcium, this domain is capable of spontaneous, ordered polymerization, producing amyloid-like fibrils and large two-dimensional protein sheets. This polymerization occurs under near-physiological conditions, is rapid, and can be controlled by regulating calcium in solution. Fusion of the RTX domain to a soluble protein results in the incorporation of engineered protein function into these macromolecular assemblies. Applications of this protein sequence in bacterial adherence and colonization and the generation of biomaterials are discussed.

  14. Threonine-4 of mammalian RNA polymerase II CTD is targeted by Polo-like kinase 3 and required for transcriptional elongation.

    Science.gov (United States)

    Hintermair, Corinna; Heidemann, Martin; Koch, Frederic; Descostes, Nicolas; Gut, Marta; Gut, Ivo; Fenouil, Romain; Ferrier, Pierre; Flatley, Andrew; Kremmer, Elisabeth; Chapman, Rob D; Andrau, Jean-Christophe; Eick, Dirk

    2012-06-13

    Eukaryotic RNA polymerase II (Pol II) has evolved an array of heptad repeats with the consensus sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7 at the carboxy-terminal domain (CTD) of the large subunit (Rpb1). Differential phosphorylation of Ser2, Ser5, and Ser7 in the 5' and 3' regions of genes coordinates the binding of transcription and RNA processing factors to the initiating and elongating polymerase complexes. Here, we report phosphorylation of Thr4 by Polo-like kinase 3 in mammalian cells. ChIPseq analyses indicate an increase of Thr4-P levels in the 3' region of genes occurring subsequently to an increase of Ser2-P levels. A Thr4/Ala mutant of Pol II displays a lethal phenotype. This mutant reveals a global defect in RNA elongation, while initiation is largely unaffected. Since Thr4 replacement mutants are viable in yeast we conclude that this amino acid has evolved an essential function(s) in the CTD of Pol II for gene transcription in mammalian cells.

  15. The ACR11 encodes a novel type of chloroplastic ACT domain repeat protein that is coordinately expressed with GLN2 in Arabidopsis

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    Hsu Chih-Ping

    2011-08-01

    Full Text Available Abstract Background The ACT domain, named after bacterial aspartate kinase, chorismate mutase and TyrA (prephenate dehydrogenase, is a regulatory domain that serves as an amino acid-binding site in feedback-regulated amino acid metabolic enzymes. We have previously identified a novel type of ACT domain-containing protein family, the ACT domain repeat (ACR protein family, in Arabidopsis. Members of the ACR family, ACR1 to ACR8, contain four copies of the ACT domain that extend throughout the entire polypeptide. Here, we describe the identification of four novel ACT domain-containing proteins, namely ACR9 to ACR12, in Arabidopsis. The ACR9 and ACR10 proteins contain three copies of the ACT domain, whereas the ACR11 and ACR12 proteins have a putative transit peptide followed by two copies of the ACT domain. The functions of these plant ACR proteins are largely unknown. Results The ACR11 and ACR12 proteins are predicted to target to chloroplasts. We used protoplast transient expression assay to demonstrate that the Arabidopsis ACR11- and ACR12-green fluorescent fusion proteins are localized to the chloroplast. Analysis of an ACR11 promoter-β-glucuronidase (GUS fusion in transgenic Arabidopsis revealed that the GUS activity was mainly detected in mature leaves and sepals. Interestingly, coexpression analysis revealed that the GLN2, which encodes a chloroplastic glutamine synthetase, has the highest mutual rank in the coexpressed gene network connected to ACR11. We used RNA gel blot analysis to confirm that the expression pattern of ACR11 is similar to that of GLN2 in various organs from 6-week-old Arabidopsis. Moreover, the expression of ACR11 and GLN2 is highly co-regulated by sucrose and light/dark treatments in 2-week-old Arabidopsis seedlings. Conclusions This study reports the identification of four novel ACT domain repeat proteins, ACR9 to ACR12, in Arabidopsis. The ACR11 and ACR12 proteins are localized to the chloroplast, and the expression

  16. Gulf of Mexico Nutrient, carbon, CTD data

    Data.gov (United States)

    U.S. Environmental Protection Agency — Gulf of Mexico cruise, nearshore and CTD data collected by the USEPA during 2002 - 2008. This dataset is associated with the following publications: Pauer , J., T....

  17. Leucine-rich repeat, immunoglobulin-like and transmembrane domain 3 (LRIT3) is a modulator of FGFR1

    NARCIS (Netherlands)

    Kim, S.D.; Liu, J.L.; Roscioli, T.; Buckley, M.F.; Yagnik, G.; Boyadjiev, S.A.; Kim, J.

    2012-01-01

    Fibroblast growth factor receptors (FGFRs) play critical roles in craniofacial and skeletal development via multiple signaling pathways including MAPK, PI3K/AKT, and PLC-?. FGFR-mediated signaling is modulated by several regulators. Proteins with leucine-rich repeat (LRR) and/or immunoglobulin (IG)

  18. Alternative splicing of the angiogenesis associated extra-domain B of fibronectin regulates the accessibility of the B-C loop of the type III repeat 8.

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    Elisa Ventura

    Full Text Available BACKGROUND: Fibronectin (FN is a multi-domain molecule involved in many cellular processes, including tissue repair, embryogenesis, blood clotting, and cell migration/adhesion. The biological activities of FN are mediated by exposed loops located mainly at the interdomain interfaces that interact with various molecules such as, but not only, integrins. Different FN isoforms arise from the alternative splicing of the pre-mRNA. In malignancies, the splicing pattern of FN pre-mRNA is altered; in particular, the FN isoform containing the extra-domain B (ED-B, a complete FN type III repeat constituted by 91 residues, is undetectable in normal adult tissues, but exhibits a much greater expression in fetal and tumor tissues, and is accumulated around neovasculature during angiogenic processes, thus making ED-B one of the best markers and targets of angiogenesis. The functions of ED-B are still unclear; however, it has been postulated that the insertion of an extra-domain such as ED-B modifies the domain-domain interface and may unmask loops that are otherwise cryptic, thus giving FN new potential activities. METHODOLOGY: We used the mAb C6, which reacts with ED-B containing FN, but not with ED-B-free FN and various recombinant FN fragments containing mutations, to precisely localize the epitopes recognized by the mAb C6. CONCLUSION: We formally demonstrated that the inclusion of the alternatively spliced angiogenesis-associated ED-B leads to the unmasking of the FNIII 8 B-C loop that is cryptic in FN molecules lacking ED-B. Thus, the mAb C6, in addition to providing a new reagent for angiogenesis targeting, represents a new tool for the study of the potential biological functions of the B-C loop of the repeat FNIII 8 that is unmasked during angiogenic processes.

  19. Regulation of Nucleocytoplasmic Shuttling of Bruton's Tyrosine Kinase (Btk) through a Novel SH3-Dependent Interaction with Ankyrin Repeat Domain 54 (ANKRD54)

    Science.gov (United States)

    Hussain, Alamdar; Mohammad, Dara K.; Mohamed, Abdalla J.; Nguyen, Vivian; Metalnikov, Pavel; Colwill, Karen; Pawson, Tony; Nore, Beston F.

    2012-01-01

    Bruton's tyrosine kinase (Btk), belonging to the Tec family of tyrosine kinases (TFKs), is essential for B-lymphocyte development. Abrogation of Btk signaling causes human X-linked agammaglobulinemia (XLA) and murine X-linked immunodeficiency (Xid). We employed affinity purification of Flag-tagged Btk, combined with tandem mass spectrometry, to capture and identify novel interacting proteins. We here characterize the interaction with ankryin repeat domain 54 protein (ANKRD54), also known as Lyn-interacting ankyrin repeat protein (Liar). While Btk is a nucleocytoplasmic protein, the Liar pool was found to shuttle at a higher rate than Btk. Importantly, our results suggest that Liar mediates nuclear export of both Btk and another TFK, Txk/Rlk. Liar-mediated Btk shuttling was enriched for activation loop, nonphosphorylated Btk and entirely dependent on Btk's SH3 domain. Liar also showed reduced binding to an aspartic acid phosphomimetic SH3 mutant. Three other investigated nucleus-located proteins, Abl, estrogen receptor β (ERβ), and transcription factor T-bet, were all unaffected by Liar. We mapped the interaction site to the C terminus of the Btk SH3 domain. A biotinylated, synthetic Btk peptide, ARDKNGQEGYIPSNYVTEAEDS, was sufficient for this interaction. Liar is the first protein identified that specifically influences the nucleocytoplasmic shuttling of Btk and Txk and belongs to a rare group of known proteins carrying out this activity in a Crm1-dependent manner. PMID:22527282

  20. 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.

  1. Interplay between I308 and Y310 residues in the third repeat of microtubule-binding domain is essential for tau filament formation.

    Science.gov (United States)

    Naruto, Keiko; Minoura, Katsuhiko; Okuda, Ryouhei; Taniguchi, Taizo; In, Yasuko; Ishida, Toshimasa; Tomoo, Koji

    2010-10-08

    Investigation of the mechanism of tau polymerization is indispensable for finding inhibitory conditions or identifying compounds preventing the formation of paired helical filament or oligomers. Tau contains a microtubule-binding domain consisting of three or four repeats in its C-terminal half. It has been considered that the key event in tau polymerization is the formation of a β-sheet structure arising from a short hexapeptide (306)VQIVYK(311) in the third repeat of tau. In this paper, we report for the first time that the C-H⋯π interaction between Ile308 and Tyr310 is the elemental structural scaffold essential for forming a dry "steric zipper" structure in tau amyloid fibrils.

  2. Bipartite Topology of Treponema pallidum Repeat Proteins C/D and I: OUTER MEMBRANE INSERTION, TRIMERIZATION, AND PORIN FUNCTION REQUIRE A C-TERMINAL β-BARREL DOMAIN.

    Science.gov (United States)

    Anand, Arvind; LeDoyt, Morgan; Karanian, Carson; Luthra, Amit; Koszelak-Rosenblum, Mary; Malkowski, Michael G; Puthenveetil, Robbins; Vinogradova, Olga; Radolf, Justin D

    2015-05-08

    We previously identified Treponema pallidum repeat proteins TprC/D, TprF, and TprI as candidate outer membrane proteins (OMPs) and subsequently demonstrated that TprC is not only a rare OMP but also forms trimers and has porin activity. We also reported that TprC contains N- and C-terminal domains (TprC(N) and TprC(C)) orthologous to regions in the major outer sheath protein (MOSP(N) and MOSP(C)) of Treponema denticola and that TprC(C) is solely responsible for β-barrel formation, trimerization, and porin function by the full-length protein. Herein, we show that TprI also possesses bipartite architecture, trimeric structure, and porin function and that the MOSP(C)-like domains of native TprC and TprI are surface-exposed in T. pallidum, whereas their MOSP(N)-like domains are tethered within the periplasm. TprF, which does not contain a MOSP(C)-like domain, lacks amphiphilicity and porin activity, adopts an extended inflexible structure, and, in T. pallidum, is tightly bound to the protoplasmic cylinder. By thermal denaturation, the MOSP(N) and MOSP(C)-like domains of TprC and TprI are highly thermostable, endowing the full-length proteins with impressive conformational stability. When expressed in Escherichia coli with PelB signal sequences, TprC and TprI localize to the outer membrane, adopting bipartite topologies, whereas TprF is periplasmic. We propose that the MOSP(N)-like domains enhance the structural integrity of the cell envelope by anchoring the β-barrels within the periplasm. In addition to being bona fide T. pallidum rare outer membrane proteins, TprC/D and TprI represent a new class of dual function, bipartite bacterial OMP.

  3. Hepatitis C virus NS4B carboxy terminal domain is a membrane binding domain

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    Spaan Willy JM

    2009-05-01

    Full Text Available Abstract Background Hepatitis C virus (HCV induces membrane rearrangements during replication. All HCV proteins are associated to membranes, pointing out the importance of membranes for HCV. Non structural protein 4B (NS4B has been reported to induce cellular membrane alterations like the membranous web. Four transmembrane segments in the middle of the protein anchor NS4B to membranes. An amphipatic helix at the amino-terminus attaches to membranes as well. The carboxy-terminal domain (CTD of NS4B is highly conserved in Hepaciviruses, though its function remains unknown. Results A cytosolic localization is predicted for the NS4B-CTD. However, using membrane floatation assays and immunofluorescence, we now show targeting of the NS4B-CTD to membranes. Furthermore, a profile-profile search, with an HCV NS4B-CTD multiple sequence alignment, indicates sequence similarity to the membrane binding domain of prokaryotic D-lactate dehydrogenase (d-LDH. The crystal structure of E. coli d-LDH suggests that the region similar to NS4B-CTD is located in the membrane binding domain (MBD of d-LDH, implying analogy in membrane association. Targeting of d-LDH to membranes occurs via electrostatic interactions of positive residues on the outside of the protein with negative head groups of lipids. To verify that anchorage of d-LDH MBD and NS4B-CTD is analogous, NS4B-CTD mutants were designed to disrupt these electrostatic interactions. Membrane association was confirmed by swopping the membrane contacting helix of d-LDH with the corresponding domain of the 4B-CTD. Furthermore, the functionality of these residues was tested in the HCV replicon system. Conclusion Together these data show that NS4B-CTD is associated to membranes, similar to the prokaryotic d-LDH MBD, and is important for replication.

  4. Hepatitis C virus NS4B carboxy terminal domain is a membrane binding domain.

    Science.gov (United States)

    Liefhebber, Jolanda M P; Brandt, Bernd W; Broer, Rene; Spaan, Willy J M; van Leeuwen, Hans C

    2009-05-25

    Hepatitis C virus (HCV) induces membrane rearrangements during replication. All HCV proteins are associated to membranes, pointing out the importance of membranes for HCV. Non structural protein 4B (NS4B) has been reported to induce cellular membrane alterations like the membranous web. Four transmembrane segments in the middle of the protein anchor NS4B to membranes. An amphipatic helix at the amino-terminus attaches to membranes as well. The carboxy-terminal domain (CTD) of NS4B is highly conserved in Hepaciviruses, though its function remains unknown. A cytosolic localization is predicted for the NS4B-CTD. However, using membrane floatation assays and immunofluorescence, we now show targeting of the NS4B-CTD to membranes. Furthermore, a profile-profile search, with an HCV NS4B-CTD multiple sequence alignment, indicates sequence similarity to the membrane binding domain of prokaryotic D-lactate dehydrogenase (d-LDH). The crystal structure of E. coli d-LDH suggests that the region similar to NS4B-CTD is located in the membrane binding domain (MBD) of d-LDH, implying analogy in membrane association. Targeting of d-LDH to membranes occurs via electrostatic interactions of positive residues on the outside of the protein with negative head groups of lipids. To verify that anchorage of d-LDH MBD and NS4B-CTD is analogous, NS4B-CTD mutants were designed to disrupt these electrostatic interactions. Membrane association was confirmed by swopping the membrane contacting helix of d-LDH with the corresponding domain of the 4B-CTD. Furthermore, the functionality of these residues was tested in the HCV replicon system. Together these data show that NS4B-CTD is associated to membranes, similar to the prokaryotic d-LDH MBD, and is important for replication.

  5. A repeat sequence domain of the ring-exported protein-1 of Plasmodium falciparum controls export machinery architecture and virulence protein trafficking.

    Science.gov (United States)

    McHugh, Emma; Batinovic, Steven; Hanssen, Eric; McMillan, Paul J; Kenny, Shannon; Griffin, Michael D W; Crawford, Simon; Trenholme, Katharine R; Gardiner, Donald L; Dixon, Matthew W A; Tilley, Leann

    2015-12-01

    The malaria parasite Plasmodium falciparum dramatically remodels its host red blood cell to enhance its own survival, using a secretory membrane system that it establishes outside its own cell. Cisternal organelles, called Maurer's clefts, act as a staging point for the forward trafficking of virulence proteins to the red blood cell (RBC) membrane. The Ring-EXported Protein-1 (REX1) is a Maurer's cleft resident protein. We show that inducible knockdown of REX1 causes stacking of Maurer's cleft cisternae without disrupting the organization of the knob-associated histidine-rich protein at the RBC membrane. Genetic dissection of the REX1 sequence shows that loss of a repeat sequence domain results in the formation of giant Maurer's cleft stacks. The stacked Maurer's clefts are decorated with tether-like structures and retain the ability to dock onto the RBC membrane skeleton. The REX1 mutant parasites show deficient export of the major virulence protein, PfEMP1, to the red blood cell surface and markedly reduced binding to the endothelial cell receptor, CD36. REX1 is predicted to form a largely α-helical structure, with a repetitive charge pattern in the repeat sequence domain, providing potential insights into the role of REX1 in Maurer's cleft sculpting.

  6. Inhibitor of apoptosis (IAP)-like protein lacks a baculovirus IAP repeat (BIR) domain and attenuates cell death in plant and animal systems.

    Science.gov (United States)

    Kim, Woe Yeon; Lee, Sun Yong; Jung, Young Jun; Chae, Ho Byoung; Nawkar, Ganesh M; Shin, Mi Rim; Kim, Sun Young; Park, Jin Ho; Kang, Chang Ho; Chi, Yong Hun; Ahn, Il Pyung; Yun, Dae Jin; Lee, Kyun Oh; Kim, Young-Myeong; Kim, Min Gab; Lee, Sang Yeol

    2011-12-09

    A novel Arabidopsis thaliana inhibitor of apoptosis was identified by sequence homology to other known inhibitor of apoptosis (IAP) proteins. Arabidopsis IAP-like protein (AtILP) contained a C-terminal RING finger domain but lacked a baculovirus IAP repeat (BIR) domain, which is essential for anti-apoptotic activity in other IAP family members. The expression of AtILP in HeLa cells conferred resistance against tumor necrosis factor (TNF)-α/ActD-induced apoptosis through the inactivation of caspase activity. In contrast to the C-terminal RING domain of AtILP, which did not inhibit the activity of caspase-3, the N-terminal region, despite displaying no homology to known BIR domains, potently inhibited the activity of caspase-3 in vitro and blocked TNF-α/ActD-induced apoptosis. The anti-apoptotic activity of the AtILP N-terminal domain observed in plants was reproduced in an animal system. Transgenic Arabidopsis lines overexpressing AtILP exhibited anti-apoptotic activity when challenged with the fungal toxin fumonisin B1, an agent that induces apoptosis-like cell death in plants. In AtIPL transgenic plants, suppression of cell death was accompanied by inhibition of caspase activation and DNA fragmentation. Overexpression of AtILP also attenuated effector protein-induced cell death and increased the growth of an avirulent bacterial pathogen. The current results demonstrated the existence of a novel plant IAP-like protein that prevents caspase activation in Arabidopsis and showed that a plant anti-apoptosis gene functions similarly in plant and animal systems.

  7. ALS-causing cleavages of TDP-43 abolish its RRM2 structure and unlock CTD for enhanced aggregation and toxicity.

    Science.gov (United States)

    Wei, Yuanyuan; Lim, Liangzhong; Wang, Lu; Song, Jianxing

    2017-04-15

    Pathological TDP-43 is cleaved into various fragments. Two major groups of ∼35 and ∼25 kDa have enhanced aggregation and cytotoxicity but the underlying mechanisms remain elusive. While the ∼35-kDa fragments contain entire RRM1, RRM2 and C-terminal domain (CTD) with a middle hydrophobic segment flanked by two prion-like regions; the ∼25-kDa one cleaved at Arg208 only consists of the truncated RRM2 and CTD. Remarkably, the 25-kDa fragment was characterized to induce cell death by gain of cytotoxicity and recapitulate pathological features of TDP-43 proteinopathies. Here by NMR spectroscopy we successfully characterized residue-specific conformations and inter-domain interactions of several fragments and the results show that: 1) ALS-causing truncation at Arg208 completely eliminates the intrinsic ability of RRM2 to fold, and consequently the truncated RRM2 becomes highly disordered and prone to aggregation. 2) By disrupting inter-domain interactions upon deleting the N-terminal ubiquitin-like fold in TDP-43 (102-414), the extreme C-terminal prion-like region of CTD is released, while in TDP-43 (208-414), almost the whole CTD is unlocked. As CTD itself is prone to aggregation and highly toxic, our study suggests that at least two mechanisms, namely to abolish RRM2 structure and to release CTD, may account for enhanced aggregation and toxicity of pathologically cleaved TDP-43. Copyright © 2017 Elsevier Inc. All rights reserved.

  8. Structural and biochemical analysis of nuclease domain of clustered regularly interspaced short palindromic repeat (CRISPR)-associated protein 3 (Cas3).

    Science.gov (United States)

    Mulepati, Sabin; Bailey, Scott

    2011-09-09

    RNA transcribed from clustered regularly interspaced short palindromic repeats (CRISPRs) protects many prokaryotes from invasion by foreign DNA such as viruses, conjugative plasmids, and transposable elements. Cas3 (CRISPR-associated protein 3) is essential for this CRISPR protection and is thought to mediate cleavage of the foreign DNA through its N-terminal histidine-aspartate (HD) domain. We report here the 1.8 Å crystal structure of the HD domain of Cas3 from Thermus thermophilus HB8. Structural and biochemical studies predict that this enzyme binds two metal ions at its active site. We also demonstrate that the single-stranded DNA endonuclease activity of this T. thermophilus domain is activated not by magnesium but by transition metal ions such as manganese and nickel. Structure-guided mutagenesis confirms the importance of the metal-binding residues for the nuclease activity and identifies other active site residues. Overall, these results provide a framework for understanding the role of Cas3 in the CRISPR system.

  9. Gibraltar Experiment, CTD Data Report 2

    Science.gov (United States)

    1989-12-01

    268.07 SST: 99.0 Tdrw: 99.0 Twat: 99.0 Wspd: 14.0 CT3 #: 1 E and N of Tarifa: -212.2km 54.6km IX-9 ctd#l reread 24sup88 an Tempurature PR THETA SA SGTH...14.0 CTD #: 3 L/RAO E and N of Tarifa: -38.8km -28.4km K-109 Tempurature PR THETA SA SGTH 2.8 7.0 12.0 17.0 22.0 27.0 18.9 22.711 36.502 25.175 0 20.0

  10. Global analysis of ankyrin repeat domain C3HC4-type RING finger gene family in plants.

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    Xiaowei Yuan

    Full Text Available Ankyrin repeat (ANK C3HC4-type RING finger (RF genes comprise a large family in plants and play important roles in various physiological processes of plant life. In this study, we identified 187 ANK C3HC4-type RF proteins from 29 species with complete genomes and named the ANK C3HC4-type RF proteins the XB3-like proteins because they are structurally related to the rice (Oryza sativa XB3. A phylogenetic relationship analysis suggested that the XB3-like genes originated from ferns, and the encoded proteins fell into 3 major groups. Among these groups, we found that the spacing between the metal ligand position 6 and 7, and the conserved residues, which was in addition to the metal ligand amino acids, in the C3HC4-type RF were different. Using a wide range of protein structural analyses, protein models were established, and all XB3-like proteins were found to contain two to seven ANKs and a C3HC4-type RF. The microarray data for the XB3-like genes of Arabidopsis, Oryza sative, Zea mays and Glycine max revealed that the expression of XB3-like genes was in different tissues and during different life stages. The preferential expression of XB3-like genes in specified tissues and the response to phytohormone and abiotic stress treatments of Arabidopsis and Zea mays not only confirmed the microarray analysis data but also demonstrated that the XB3-like proteins play roles in plant growth and development as well as in stress responses. Our data provide a very useful reference for the identification and functional analysis of members of this gene family and also provide a new method for the genome-wide analysis of gene families.

  11. Intronic mutations outside of Alu-repeat-rich domains of the LDL receptor gene are a cause of familial hypercholesterolemia.

    Science.gov (United States)

    Amsellem, Sabine; Briffaut, Dorothée; Carrié, Alain; Rabès, Jean Pierre; Girardet, Jean Philippe; Fredenrich, Alexandre; Moulin, Philippe; Krempf, Michel; Reznik, Yves; Vialettes, Bernard; de Gennes, Jean Luc; Brukert, Eric; Benlian, Pascale

    2002-12-01

    Familial hypercholesterolemia (FH), a frequent monogenic condition complicated by premature cardiovascular disease, is characterized by high allelic heterogeneity at the low-density lipoprotein receptor ( LDLR) locus. Despite more than a decade of genetic testing, knowledge about intronic disease-causing mutations has remained limited because of lack of available genomic sequences. Based on the finding from bioinformatic analysis that Alu repeats represent 85% of LDLR intronic sequences outside exon-intron junctions, we designed a strategy to improve the exploration of genomic regions in the vicinity of exons in 110 FH subjects from an admixed population. In the first group of 42 patients of negative mutation carriers, as previously established by former screening strategies (denaturing gradient gel electrophoresis, DNA sequencing with former primers overlapping splice-sites, Southern Blotting), about half ( n=22) were found to be carriers of at least one heterozygous mutation. Among a second group of 68 newly recruited patients, 27% of mutation carriers ( n=37) had a splicing regulatory mutation. Overall, out of the 54 mutations identified, 13 were intronic, and 18 were novel, out of which nearly half were intronic. Two novel intronic mutations (IVS8-10G-->A within the polypyrimidine tract and IVS7+10G-->A downstream of donor site) might create potential aberrant splice sites according to neural-network computed estimation, contrary to 31 common single nucleotide variations also identified at exon-intron junctions. This new strategy of detecting the most likely disease-causing LDLR mutations outside of Alu-rich genomic regions reveals that intronic mutations may have a greater impact than previously reported on the molecular basis of FH.

  12. The Role of α-CTD in the Genome-Wide Transcriptional Regulation of the Bacillus subtilis Cells.

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    Satohiko Murayama

    Full Text Available The amino acid sequence of the RNA polymerase (RNAP α-subunit is well conserved throughout the Eubacteria. Its C-terminal domain (α-CTD is important for the transcriptional regulation of specific promoters in both Escherichia coli and Bacillus subtilis, through interactions with transcription factors and/or a DNA element called the "UP element". However, there is only limited information regarding the α-CTD regulated genes in B. subtilis and the importance of this subunit in the transcriptional regulation of B. subtilis. Here, we established strains and the growth conditions in which the α-subunit of RNAP was replaced with a C-terminally truncated version. Transcriptomic and ChAP-chip analyses revealed that α-CTD deficiency reduced the transcription and RNAP binding of genes related to the utilization of secondary carbon sources, transition state responses, and ribosome synthesis. In E. coli, it is known that α-CTD also contributes to the expression of genes related to the utilization of secondary carbon sources and ribosome synthesis. Our results suggest that the biological importance of α-CTD is conserved in B. subtilis and E. coli, but that its specific roles have diversified between these two bacteria.

  13. Expression and sub-cellular localization of leucine-rich repeats and immunoglobulin-like domains are related to antioxidant enzymes in human ependymoma and oligodendroglioma

    Institute of Scientific and Technical Information of China (English)

    Wei Yi; Lin Liu; Okechi Humphrey; Qianxue Chen; Shulan Huang

    2011-01-01

    The current study investigated correlations between the expression of leucine-rich repeats and immunoglobulin-like domain 1 (LRIG1) and antioxidant enzymes and related proteins, including manganese superoxide dismutase, glutamate cysteine ligase catalytic or regulatory subunit, thioredoxin and thioredoxin reductase, in both human ependymoma and oligodendroglioma. Results revealed that the cytoplasmic expression of LRIG1 was associated with expression of glutamate cysteine ligase catalytic subunit in the human ependymoma, while the nuclear expression of LRIG1 was associated with expression of thioredoxin reductase. In human oligodendroglioma, the cytoplasmic expression of LRIG1 was associated with expression of the glutamate cysteine ligase catalytic subunit. Both the nuclear and perinuclear expressions of LRIG1 were associated with expression of glutamate cysteine ligase regulatory subunit. These results indicated that several antioxidant enzymes and related proteins contributed to LRIG1 expression, and that these may participate in the antioxidation of the cells.

  14. A novel bispecific peptide HIV-1 fusion inhibitor targeting the N-terminal heptad repeat and fusion peptide domains in gp41.

    Science.gov (United States)

    Jiang, Xifeng; Jia, Qiyan; Lu, Lu; Yu, Fei; Zheng, Jishen; Shi, Weiguo; Cai, Lifeng; Jiang, Shibo; Liu, Keliang

    2016-12-01

    HIV-1 fusion with the target cell is initiated by the insertion of the gp41 fusion peptide (FP) into the target cell membrane and the interaction between the gp41 N- and C-terminal heptad repeats (NHR and CHR), followed by the formation of the six-helix bundle (6-HB) fusion core. Therefore, both FP and NHR are important targets for HIV-1 fusion inhibitors. Here, we designed and synthesized a dual-target peptidic HIV-1 fusion inhibitor, 4HR-LBD-VIRIP, in which 4HR-LBD is able to bind to the gp41 NHR domain, while VIRIP is able to interact with gp41 FP. We found that 4HR-LBD-VIRIP is about tenfold more potent than 4HR-LBD and VIRIP in inhibiting HIV-1IIIB infection and HIV-1 envelope glycoprotein (Env)-mediated cell-cell fusion, suggesting that this dual-target HIV-1 fusion inhibitor possesses a strong synergistic antiviral effect. A biophysical analysis indicates that 4HR-LBD-VIRIP can interact with N70 peptide that contains the gp41 NHR and FP domains and binds with lipid membrane. This study provides a new approach for designing novel viral fusion inhibitors against HIV and other enveloped viruses with class I membrane fusion proteins.

  15. COMP mutations: domain-dependent relationship between abnormal chondrocyte trafficking and clinical PSACH and MED phenotypes.

    Science.gov (United States)

    Chen, Tung-Ling L; Posey, Karen L; Hecht, Jacqueline T; Vertel, Barbara M

    2008-02-15

    Mutations in cartilage oligomeric matrix protein (COMP) produce clinical phenotypes ranging from the severe end of the spectrum, pseudoachondroplasia (PSACH), which is a dwarfing condition, to a mild condition, multiple epiphyseal dysplasia (MED). Patient chondrocytes have a unique morphology characterized by distended rER cisternae containing lamellar deposits of COMP and other extracellular matrix proteins. It has been difficult to determine why different mutations give rise to variable clinical phenotypes. Using our in vitro cell system, we previously demonstrated that the most common PSACH mutation, D469del, severely impedes trafficking of COMP and type IX collagen in chondrocytic cells, consistent with observations from patient cells. Here, we hypothesize that PSACH and MED mutations variably affect the cellular trafficking behavior of COMP and that the extent of defective trafficking correlates with clinical phenotype. Twelve different recombinant COMP mutations were expressed in rat chondrosarcoma cells and the percent cells with ER-retained COMP was assessed. For mutations in type 3 (T3) repeats, trafficking defects correlated with clinical phenotype; PSACH mutations had more cells retaining mutant COMP, while MED mutations had fewer. In contrast, the cellular trafficking pattern observed for mutations in the C-terminal globular domain (CTD) was not predictive of clinical phenotype. The results demonstrate that different COMP mutations in the T3 repeat domain have variable effects on intracellular transport, which correlate with clinical severity, while CTD mutations do not show such a correlation. These findings suggest that other unidentified factors contribute to the effect of the CTD mutations. J. Cell. Biochem. 103: 778-787, 2008. (c) 2007 Wiley-Liss, Inc. Copyright 2007 Wiley-Liss, Inc.

  16. A small peptide modeled after the NRAGE repeat domain inhibits XIAP-TAB1-TAK1 signaling for NF-κB activation and apoptosis in P19 cells.

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    Jennifer A Rochira

    Full Text Available In normal growth and development, apoptosis is necessary to shape the central nervous system and to eliminate excess neurons which are not required for innervation. In some diseases, however, apoptosis can be either overactive as in some neurodegenerative disorders or severely attenuated as in the spread of certain cancers. Bone morphogenetic proteins (BMPs transmit signals for regulating cell growth, differentiation, and apoptosis. Responding to BMP receptors stimulated from BMP ligands, neurotrophin receptor-mediated MAGE homolog (NRAGE binds and functions with the XIAP-TAK1-TAB1 complex to activate p38(MAPK and induces apoptosis in cortical neural progenitors. NRAGE contains a unique repeat domain that is only found in human, mouse, and rat homologs that we theorize is pivotal in its BMP MAPK role. Previously, we showed that deletion of the repeat domain inhibits apoptosis, p38(MAPK phosphorylation, and caspase-3 cleavage in P19 neural progenitor cells. We also showed that the XIAP-TAB1-TAK1 complex is dependent on NRAGE for IKK-α/β phosphorylation and NF-κB activation. XIAP is a major inhibitor of caspases, the main executioners of apoptosis. Although it has been shown previously that NRAGE binds to the RING domain of XIAP, it has not been determined which NRAGE domain binds to XIAP. Here, we used fluorescence resonance energy transfer (FRET to determine that there is a strong likelihood of a direct interaction between NRAGE and XIAP occurring at NRAGE's unique repeat domain which we also attribute to be the domain responsible for downstream signaling of NF-κB and activating IKK subunits. From these results, we designed a small peptide modeled after the NRAGE repeat domain which we have determined inhibits NF-κB activation and apoptosis in P19 cells. These intriguing results illustrate that the paradigm of the NRAGE repeat domain may hold promising therapeutic strategies in developing pharmaceutical solutions for combating harmful

  17. Creation of a novel telomere-cutting endonuclease based on the EN domain of telomere-specific non-long terminal repeat retrotransposon, TRAS1

    Directory of Open Access Journals (Sweden)

    Yoshitake Kazutoshi

    2010-04-01

    Full Text Available Abstract Background The ends of chromosomes, termed telomeres consist of repetitive DNA. The telomeric sequences shorten with cell division and, when telomeres are critically abbreviated, cells stop proliferating. However, in cancer cells, by the expression of telomerase which elongates telomeres, the cells can continue proliferating. Many approaches for telomere shortening have been pursued in the past, but to our knowledge, cutting telomeres in vivo has not so far been demonstrated. In addition, there is lack of information on the cellular effects of telomere shortening in human cells. Results Here, we created novel chimeric endonucleases to cut telomeres by fusing the endonuclease domain (TRAS1EN of the silkworm's telomere specific non-long terminal repeat retrotransposon TRAS1 to the human telomere-binding protein, TRF1. An in vitro assay demonstrated that the TRAS1EN-TRF1 chimeric endonucleases (T-EN and EN-T cut the human (TTAGGGn repeats specifically. The concentration of TRAS1EN-TRF1 chimeric endonucleases necessary for the cleavage of (TTAGGGn repeats was about 40-fold lower than that of TRAS1EN alone. When TRAS1EN-TRF1 endonucleases were introduced into human U2OS cancer cells using adenovirus vectors, the enzymes localized at telomeres of nuclei, cleaved and shortened the telomeric DNA by double-strand breaks. When human U2OS and HFL-1 fibroblast cells were infected with EN-T recombinant adenovirus, their cellular proliferation was suppressed for about 2 weeks after infection. In contrast, the TRAS1EN mutant (H258A chimeric endonuclease fused with TRF1 (ENmut-T did not show the suppression effect. The EN-T recombinant adenovirus induced telomere shortening in U2OS cells, activated the p53-dependent pathway and caused the senescence associated cellular responses, while the ENmut-T construct did not show such effects. Conclusions A novel TRAS1EN-TRF1 chimeric endonuclease (EN-T cuts the human telomeric repeats (TTAGGGn specifically in

  18. Repeatability and Reproducibility of Retinal Neuronal and Axonal Measures on Spectral-Domain Optical Coherence Tomography in Patients with Cognitive Impairment

    Directory of Open Access Journals (Sweden)

    Edwin Hong-Teck Loh

    2017-08-01

    Full Text Available BackgroundWith increasing interest in determining if measurement of retinal neuronal structure with spectral-domain optical coherence tomography (SD-OCT is useful in accessing neurodegenerative process in cognitive decline and development of dementia, it is important to evaluate whether the SD-OCT measurements are repeatable and reproducible in these patients.MethodsThis is a retrospective cohort study. Patients with Alzheimer’s disease (AD or mild cognitive impairment (MCI with no change in global clinical dementia rating (CDR score at 1-year follow-up were eligible to be included. Ganglion cell-inner plexiform layer (GC-IPL and retinal nerve fiber layer (RNFL parameters were measured with SD-OCT at baseline, 6-month, and 1-year follow-up visits. At baseline, SD-OCT scans were repeated to access intra-visit repeatability of the SD-OCT measurement. SD-OCT measurement over three visits was used to access inter-visit reproducibility. We calculated intraclass correlation coefficients (ICC and coefficients of variation (CoVs.ResultsWe included 32 patients with stable AD and 29 patients with stable MCI in the final analysis. For GC-IPL measures, the average intra-visit ICC was 0.969 (range: 0.948–0.985, and CoV was 1.81% (range: 1.14–2.40; while the average inter-visit ICC was 0.968 (0.941–0.985, and CoV was 1.91% (range: 1.24–2.32. The average ICC and CoV of intra-visit RNFL measured were 0.965 (range: 0.937–0.986 and 2.32% (range: 1.34–2.90%, respectively. The average ICC and CoV of inter-visit RNFL measures were 0.927 (range: 0.845–0.961 and 3.83% (range: 2.71–5.25%, respectively.ConclusionBoth GC-IPL and RNFL measurements had good intra-visit repeatability and inter-visit reproducibility over 1 year in elderly patients with no decline in cognitive function, suggesting that SD-OCT is a reliable tool to assess neurodegenerative process over time.

  19. The C-terminal pentapeptide of Nanog tryptophan repeat domain interacts with Nac1 and regulates stem cell proliferation but not pluripotency.

    Science.gov (United States)

    Ma, Tianhua; Wang, Zhe; Guo, Yunqian; Pei, Duanqing

    2009-06-12

    Overexpression of Nanog in mouse embryonic stem (ES) cells has been shown to abrogate the requirement of leukemia inhibitory factor for self-renewal in culture. Little is known about the molecular mechanism of Nanog function. Here we describe the role of the tryptophan repeat (WR) domain, one of the two transactivators at its C terminus, in regulating stem cell proliferation as well as pluripotency. We first created a supertransactivator, W2W3x10, by duplicating repeats W2W3 10 times and discovered that it can functionally substitute for wild type WR at sustaining pluripotency, albeit with a significantly slower cell cycle, phenocopying Nanog(9W) with the C-terminal pentapeptide (WNAAP) of WR deleted. ES cells carrying both W2W3x10 and Nanog(9W) have a longer G1 phase, a shorter S phase in cell cycle distribution and progression analysis, and a lower level of pAkt(Ser473) compared with wild type Nanog, suggesting that both mutants impact the cell cycle machinery via the phosphatidylinositol 3-kinase/Akt pathway. Both mutants remain competent in dimerizing with Nanog but cannot form a complex with Nac1 efficiently, suggesting that WNAAP may be involved in Nac1 binding. By tagging Gal4DBD with WNAAP, we demonstrated that this pentapeptide is sufficient to confer Nac1 binding. Furthermore, we can rescue W2W3x10 by placing WNAAP at the corresponding locations. Finally, we found that Nanog and Nac1 synergistically up-regulate ERas expression and promote the proliferation of ES cells. These results suggest that Nanog interacts with Nac1 through WNAAP to regulate the cell cycle of ES cells via the ERas/phosphatidylinositol 3-kinase/Akt pathway, but not pluripotency, thus decoupling cell cycle control from pluripotency.

  20. Pleckstrin Homology (PH) Domain Leucine-rich Repeat Protein Phosphatase Controls Cell Polarity by Negatively Regulating the Activity of Atypical Protein Kinase C.

    Science.gov (United States)

    Xiong, Xiaopeng; Li, Xin; Wen, Yang-An; Gao, Tianyan

    2016-11-25

    The proper establishment of epithelial polarity allows cells to sense and respond to signals that arise from the microenvironment in a spatiotemporally controlled manner. Atypical PKCs (aPKCs) are implicated as key regulators of epithelial polarity. However, the molecular mechanism underlying the negative regulation of aPKCs remains largely unknown. In this study, we demonstrated that PH domain leucine-rich repeat protein phosphatase (PHLPP), a novel family of Ser/Thr protein phosphatases, plays an important role in regulating epithelial polarity by controlling the phosphorylation of both aPKC isoforms. Altered expression of PHLPP1 or PHLPP2 disrupted polarization of Caco2 cells grown in 3D cell cultures as indicated by the formation of aberrant multi-lumen structures. Overexpression of PHLPP resulted in a decrease in aPKC phosphorylation at both the activation loop and the turn motif sites; conversely, knockdown of PHLPP increased aPKC phosphorylation. Moreover, in vitro dephosphorylation experiments revealed that both aPKC isoforms were substrates of PHLPP. Interestingly, knockdown of PKCζ, but not PKCι, led to similar disruption of the polarized lumen structure, suggesting that PKCζ likely controls the polarization process of Caco2 cells. Furthermore, knockdown of PHLPP altered the apical membrane localization of aPKCs and reduced the formation of aPKC-Par3 complex. Taken together, our results identify a novel role of PHLPP in regulating aPKC and cell polarity. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  1. Genetic analysis of the leucine-rich repeat and lg domain containing Nogo receptor-interacting protein 1 gene in essential tremor.

    Science.gov (United States)

    Liang, Hui; Song, Zhi; Deng, Xiong; Xu, Hongbo; Zhu, Anding; Zheng, Wen; Zhao, Yongxiang; Deng, Hao

    2013-10-01

    Variants in the leucine-rich repeat and lg domain containing nogo receptor-interacting protein 1 gene (LINGO1) have been identified to be associated with the increased risk of essential tremor (ET), especially among Caucasians. To explore whether the LINGO1 gene plays a role in ET susceptibility, we performed a systematic genetic analysis of the coding region in the LINGO1 gene. Four nucleotide variants have been genotyped, including three known variants (rs2271398, rs2271397, and rs3743481), and a novel G → C transition (ss491228439). Extended analysis showed no significant difference in genotypic and allelic distributions between 151 patients and 301 control subjects for these four variants (all P > 0.05). However, further sex-stratified analysis revealed that the C allele of rs2271397 and ss491228439 contributed the risk of ET in female (P = 0.017, OR = 2.139, 95 % CI 1.135 ~ 4.030 for rs2271397 and P = 0.038, OR = 1.812, 95 % CI 1.027 ~ 3.194 for ss491228439). Haplotype analysis indicated that A465-C474-C714 haplotype was significantly associated with increased risk of ET in female (P = 0.041, OR = 1.800, 95 % CI 1.020 ~ 3.178). Our results indicate that the LINGO1 variants are associated with ET in Chinese Han female patients.

  2. A tetratricopeptide repeat domain-containing protein SSR1 located in mitochondria is involved in root development and auxin polar transport in Arabidopsis.

    Science.gov (United States)

    Zhang, Min; Wang, Cuiping; Lin, Qingfang; Liu, Aihua; Wang, Ting; Feng, Xuanjun; Liu, Jie; Han, Huiling; Ma, Yan; Bonea, Diana; Zhao, Rongmin; Hua, Xuejun

    2015-08-01

    Auxin polar transport mediated by a group of Pin-formed (PIN) transporters plays important roles in plant root development. However, the mechanism underlying the PIN expression and targeting in response to different developmental and environmental stimuli is still not fully understood. Here, we report a previously uncharacterized gene SSR1, which encodes a mitochondrial protein with tetratricopeptide repeat (TPR) domains, and show its function in root development in Arabidopsis thaliana. In ssr1-2, a SSR1 knock-out mutant, the primary root growth was dramatically inhibited due to severely impaired cell proliferation and cell elongation. Significantly lowered level of auxin was found in ssr1-2 roots by auxin measurement and was further supported by reduced expression of DR5-driven reporter gene. As a result, the maintenance of the root stem cell niche is compromised in ssr1-2. It is further revealed that the expression level of several PIN proteins, namely, PIN1, PIN2, PIN3, PIN4 and PIN7, were markedly reduced in ssr1-2 roots. In particular, we showed that the reduced protein level of PIN2 on cell membrane in ssr1-2 is due to impaired retrograde trafficking, possibly resulting from a defect in retromer sorting system, which destines PIN2 for degradation in vacuoles. In conclusion, our results indicated that SSR1 is functioning in root development in Arabidopsis, possibly by affecting PIN protein expression and subcellular targeting.

  3. A Superhelical Spiral in the Escherichia coli DNA Gyrase A C-terminal Domain Imparts Unidirectional Supercoiling Bias

    Energy Technology Data Exchange (ETDEWEB)

    Ruthenburg,A.; Graybosch, D.; Huetsch, J.; Verdine, G.

    2005-01-01

    DNA gyrase is unique among type II topoisomerases in that its DNA supercoiling activity is unidirectional. The C-terminal domain of the gyrase A subunit (GyrA-CTD) is required for this supercoiling bias. We report here the x-ray structure of the Escherichia coli GyrA-CTD (Protein Data Bank code 1ZI0). The E. coli GyrA-CTD adopts a circular-shaped {beta}-pinwheel fold first seen in the Borrelia burgdorferi GyrA-CTD. However, whereas the B. burgdorferi GyrA-CTD is flat, the E. coli GyrA-CTD is spiral. DNA relaxation assays reveal that the E. coli GyrA-CTD wraps DNA inducing substantial (+) superhelicity, while the B. burgdorferi GyrA-CTD introduces a more modest (+) superhelicity. The observation of a superhelical spiral in the present structure and that of the Bacillus stearothermophilus ParC-CTD structure suggests unexpected similarities in substrate selectivity between gyrase and Topo IV enzymes. We propose a model wherein the right-handed ((+) solenoidal) wrapping of DNA around the E. coli GyrA-CTD enforces unidirectional (-) DNA supercoiling.

  4. An antibody against the C-terminal domain of PCSK9 lowers LDL cholesterol levels in vivo.

    Science.gov (United States)

    Schiele, Felix; Park, John; Redemann, Norbert; Luippold, Gerd; Nar, Herbert

    2014-02-20

    Proprotein convertase subtilisin/kexin type 9 (PCSK9) is associated with autosomal dominant hypercholesterolemia, a state of elevated levels of LDL (low-density lipoprotein) cholesterol. Autosomal dominant hypercholesterolemia can result in severe implications such as stroke and coronary heart disease. The inhibition of PCSK9 function by therapeutic antibodies that block interaction of PCSK9 with the epidermal growth factor-like repeat A domain of LDL receptor (LDLR) was shown to successfully lower LDL cholesterol levels in clinical studies. Here we present data on the identification, structural and biophysical characterization and in vitro and in vivo pharmacology of a PCSK9 antibody (mAb1). The X-ray structure shows that mAb1 binds the module 1 of the C-terminal domain (CTD) of PCSK9. It blocks access to an area bearing several naturally occurring gain-of-function and loss-of-function mutations. Although the antibody does not inhibit binding of PCSK9 to epidermal growth factor-like repeat A, it partially reverses PCSK9-induced reduction of the LDLR and LDL cholesterol uptake in a cellular assay. mAb1 is also effective in lowering serum levels of LDL cholesterol in cynomolgus monkeys in vivo. Complete loss of PCSK9 is associated with insufficient liver regeneration and increased risk of hepatitis C infections. Blocking of the CTD is sufficient to partially inhibit PCSK9 function. Antibodies binding the CTD of PCSK9 may thus be advantageous in patients that do not tolerate complete inhibition of PCSK9.

  5. Structural dynamics of native and V260E mutant C-terminal domain of HIV-1 integrase

    Science.gov (United States)

    Sangeetha, Balasubramanian; Muthukumaran, Rajagopalan; Amutha, Ramaswamy

    2015-04-01

    The C-terminal domain (CTD) of HIV-1 integrase is a five stranded β-barrel resembling an SH3 fold. Mutational studies on isolated CTD and full-length IN have reported V260E mutant as either homo-dimerization defective or affecting the stability and folding of CTD. In this study, molecular dynamics simulation techniques were used to unveil the effect of V260E mutation on isolated CTD monomer and dimer. Both monomeric and dimeric forms of wild type and V260E mutant are highly stable during the simulated period. However, the stabilizing π-stacking interaction between Trp243 and Trp243' at the dimer interface is highly disturbed in CTD-V260E (>6 Å apart). The loss in entropy for dimerization is -30 and -25 kcal/mol for CTD-wt and CTD-V260E respectively signifying a weak hydrophobic interaction and its perturbation in CTD-V260E. The mutant Glu260 exhibits strong attraction/repulsion with all the basic/acidic residues of CTD. In addition to this, the dynamics of CTD-wild type and V260E monomers at 498 K was analyzed to elucidate the effect of V260E mutation on CTD folding. Increase in SASA and reduction in the number of contacts in CTD-V260E during simulation highlights the instability caused by the mutation. In general, V260E mutation affects both multimerization and protein folding with a pronounced effect on protein folding rather than multimerization. This study emphasizes the importance of the hydrophobic nature and SH3 fold of CTD in proper functioning of HIV integrase and perturbing this nature would be a rational approach toward designing more selective and potent allosteric anti-HIV inhibitors.

  6. Studying the Origin of Kuroshio with an Array of ADCP-CTD Moorings

    Science.gov (United States)

    2012-09-30

    distinct T-S properties. The T-S properties in the downstream Kuroshio (Fig. 3, right panel; black dots) suggests that the warm and salty upstream...may have mixed with South China Sea (SCS) water and/or western Pacific water . Ten repeated hydrographic cross-sections were generated from the CTD...transects along 18.8°N. The characteristics of North Pacific Tropical Water (NPTW) with a salinity maximum (> 34.8 psu) at 100– 200-m depth and North

  7. Down-regulation of Leucine-rich Repeats and Immunoglobulin-like Domain Proteins (LRIG1-3) in HP75 Pituitary Adenoma Cell Line

    Institute of Scientific and Technical Information of China (English)

    GUO Dongsheng; HAN Lin; SHU Kai; CHEN Jian; LEI Ting

    2007-01-01

    Three human leucine-rich repeats and immunoglobulin-like domains (LRIG) genes and proteins, named LRIG1-3, has been previously characterized and it was proposed that they may act as suppressors of tumor growth. The LRIG1 protein can inhibit the growth of tumors of glial cells and the down-regulation of the LRIG1 gene may be involved in the development and progression of the tumor. Real-time reverse transcription-polymerase chain reaction (RT-PCR) is a recently developed technique for quantitative assessment of specific RNA levels. In the current study, it was demonstrated that LRIG1-3 and EGFR mRNA was detected in human pituitary adenoma cell lines and a normal pituitary sample, with differences in the expression levels. Compared to the normal pituitary samples, the expression of LRIG1-3 in HP75 cell line was lower, but the expression of EGFR in HP75 cell line was higher. The results are consistent with LRIG1-3 being tumour suppressor genes, and LRIG genes decreasing the expression of EGFR. The ratio of EGFR/LRIG1 was increased at least 13-fold in HP75 cells compared with the normal pituitary cells, which was also the case for the ratio of EGFR/LRIG2 (14-fold increase in HP75) and EGFR/LRIG3 (11-fold increase in HP75). Further studies were needed to elucidate the explicit role of LRIG genes as negative regulators of oncogenesis in human pituitary adenoma.

  8. CTD data from CTD casts in the Northeast Pacific Ocean from NOAA Ship DISCOVERER and other platforms from 09 March 1996 to 24 June 1996 (NODC Accession 9600096)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CTD data were collected from CTD casts from NOAA Ship DISCOVERER and other platforms in the Northeast Pacific Ocean from 09 March 1996 to 24 June 1996. Data were...

  9. Current direction and CTD data from moored current meter and CTD casts in the Delaware Bay from 01 January 1984 - 01 December 1984 (NODC Accession 8600001)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Current direction and CTD data were collected using moored current meter and CTD casts in the Delaware Bay from January 1, 1984 to December 1, 1985. Data were...

  10. Current direction and CTD data from moored current meter and CTD casts in the North Pacific Ocean from 05 February 1979 - 01 December 1980 (NODC Accession 8300042)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Current direction and CTD data were collected using moored current meter and CTD casts in the North Pacific Ocean from February 5, 1979 to December 1, 1980. Data...

  11. Current direction and CTD data from moored current meter and CTD casts in the Atlantic Ocean from 04 August 1980 - 14 August 1981 (NODC Accession 8200240)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Current direction and CTD data were collected using moored current meter and CTD casts in the Atlantic Ocean from August 4, 1980 to August 14, 1981. Data were...

  12. New type of starch-binding domain: the direct repeat motif in the C-terminal region of Bacillus sp. no. 195 alpha-amylase contributes to starch binding and raw starch degrading.

    Science.gov (United States)

    Sumitani, J; Tottori, T; Kawaguchi, T; Arai, M

    2000-09-01

    The alpha-amylase from Bacillus sp. no. 195 (BAA) consists of two domains: one is the catalytic domain similar to alpha-amylases from animals and Streptomyces in the N-terminal region; the other is the functionally unknown domain composed of an approx. 90-residue direct repeat in the C-terminal region. The gene coding for BAA was expressed in Streptomyces lividans TK24. Three active forms of the gene products were found. The pH and thermal profiles of BAAs, and their catalytic activities for p-nitrophenyl maltopentaoside and soluble starch, showed almost the same behaviours. The largest, 69 kDa, form (BAA-alpha) was of the same molecular mass as that of the mature protein estimated from the nucleotide sequence, and had raw-starch-binding and -degrading abilities. The second largest, 60 kDa, form (BAA-beta), whose molecular mass was the same as that of the natural enzyme from Bacillus sp. no. 195, was generated by proteolytic processing between the two repeat sequences in the C-terminal region, and had lower activities for raw starch binding and degrading than those of BAA-alpha. The smallest, 50 kDa, form (BAA-gamma) contained only the N-terminal catalytic domain as a result of removal of the C-terminal repeat sequence, which led to loss of binding and degradation of insoluble starches. Thus the starch adsorption capacity and raw-starch-degrading activity of BAAs depends on the existence of the repeat sequence in the C-terminal region. BAA-alpha was specifically adsorbed on starch or dextran (alpha-1,4 or alpha-1,6 glucan), and specifically desorbed with maltose or beta-cyclodextrin. These observations indicated that the repeat sequence of the enzyme was functional in the starch-binding domain (SBD). We propose the designation of the homologues to the SBD of glucoamylase from Aspergillus niger as family I SBDs, the homologues to that of glucoamylase from Rhizopus oryzae as family II, and the homologues of this repeat sequence of BAA as family III.

  13. Bio-molecular architects: a scaffold provided by the C-terminal domain of eukaryotic RNA polymerase II.

    Science.gov (United States)

    Zhang, Mengmeng; Gill, Gordon N; Zhang, Yan

    2010-01-01

    In eukaryotic cells, the transcription of genes is accurately orchestrated both spatially and temporally by the C-terminal domain of RNA polymerase II (CTD). The CTD provides a dynamic platform to recruit different regulators of the transcription apparatus. Different posttranslational modifications are precisely applied to specific sites of the CTD to coordinate transcription process. Regulators of the RNA polymerase II must identify specific sites in the CTD for cellular survival, metabolism, and development. Even though the CTD is disordered in the eukaryotic RNA polymerase II crystal structures due to its intrinsic flexibility, recent advances in the complex structural analysis of the CTD with its binding partners provide essential clues for understanding how selectivity is achieved for individual site recognition. The recent discoveries of the interactions between the CTD and histone modification enzymes disclose an important role of the CTD in epigenetic control of the eukaryotic gene expression. The intersection of the CTD code with the histone code discloses an intriguing yet complicated network for eukaryotic transcriptional regulation.

  14. Lethal mutations in the major homology region and their suppressors act by modulating the dimerization of the rous sarcoma virus capsid protein C-terminal domain.

    Science.gov (United States)

    Dalessio, Paula M; Craven, Rebecca C; Lokhandwala, Parvez M; Ropson, Ira J

    2013-02-01

    An infective retrovirus requires a mature capsid shell around the viral replication complex. This shell is formed by about 1500 capsid protein monomers, organized into hexamer and pentamer rings that are linked to each other by the dimerization of the C-terminal domain (CTD). The major homology region (MHR), the most highly conserved protein sequence across retroviral genomes, is part of the CTD. Several mutations in the MHR appear to block infectivity by preventing capsid formation. Suppressor mutations have been identified that are distant in sequence and structure from the MHR and restore capsid formation. The effects of two lethal and two suppressor mutations on the stability and function of the CTD were examined. No correlation with infectivity was found for the stability of the lethal mutations (D155Y-CTD, F167Y-CTD) and suppressor mutations (R185W-CTD, I190V-CTD). The stabilities of three double mutant proteins (D155Y/R185W-CTD, F167Y/R185W-CTD, and F167Y/I190V-CTD) were additive. However, the dimerization affinity of the mutant proteins correlated strongly with biological function. The CTD proteins with lethal mutations did not dimerize, while those with suppressor mutations had greater dimerization affinity than WT-CTD. The suppressor mutations were able to partially correct the dimerization defect caused by the lethal MHR mutations in double mutant proteins. Despite their dramatic effects on dimerization, none of these residues participate directly in the proposed dimerization interface in a mature capsid. These findings suggest that the conserved sequence of the MHR has critical roles in the conformation(s) of the CTD that are required for dimerization and correct capsid maturation. Copyright © 2012 Wiley Periodicals, Inc.

  15. The N-terminal repeat and the ligand binding domain A of SdrI protein is involved in hydrophobicity of S. saprophyticus.

    Science.gov (United States)

    Kleine, Britta; Ali, Liaqat; Wobser, Dominique; Sakιnç, Türkân

    2015-03-01

    Staphylococcus saprophyticus is an important cause of urinary tract infection, and its cell surface hydrophobicity may contribute to virulence by facilitating adherence of the organism to uroepithelia. S. saprophyticus expresses the surface protein SdrI, a member of the serine-aspartate repeat (SD) protein family, which has multifunctional properties. The SdrI knock out mutant has a reduced hydrophobicity index (HPI) of 25%, and expressed in the non-hydrophobic Staphylococcus carnosus strain TM300 causes hydrophobicity. Using hydrophobic interaction chromatography (HIC), we confined the hydrophobic site of SdrI to the N-terminal repeat region. S. saprophyticus strains carrying different plasmid constructs lacking either the N-terminal repeats, both B or SD-repeats were less hydrophobic than wild type and fully complemented SdrI mutant (HPI: 51%). The surface hydrophobicity and HPI of both wild type and the complemented strain were also influenced by calcium (Ca(2+)) and were reduced from 81.3% and 82.4% to 10.9% and 12.3%, respectively. This study confirms that the SdrI protein of S. saprophyticus is a crucial factor for surface hydrophobicity and also gives a first significant functional description of the N-terminal repeats, which in conjunction with the B-repeats form an optimal hydrophobic conformation.

  16. SWFSC FED Mid Water Trawl Juvenile Rockfish Survey, CTD Data

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — SWFSC FED Mid Water Trawl Juvenile Rockfish Survey: CTD Data. Surveys have been conducted along the central California coast in May/June every year since 1983. In...

  17. Liquid Robotics Wave Glider, Honey Badger (G3), 2015, CTD

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Liquid Robotics Wave Glider, Honey Badger (G3), 2015, CTD. The MAGI mission is to use the Wave Glider to sample the late summer chlorophyll bloom that develops near...

  18. Structural characterization of minor ampullate spidroin domains and their distinct roles in fibroin solubility and fiber formation.

    Directory of Open Access Journals (Sweden)

    Zhenwei Gao

    Full Text Available Spider silk is protein fibers with extraordinary mechanical properties. Up to now, it is still poorly understood how silk proteins are kept in a soluble form before spinning into fibers and how the protein molecules are aligned orderly to form fibers. Minor ampullate spidroin is one of the seven types of silk proteins, which consists of four types of domains: N-terminal domain, C-terminal domain (CTD, repetitive domain (RP and linker domain (LK. Here we report the tertiary structure of CTD and secondary structures of RP and LK in aqueous solution, and their roles in protein stability, solubility and fiber formation. The stability and solubility of individual domains are dramatically different and can be explained by their distinct structures. For the tri-domain miniature fibroin, RP-LK-CTD(Mi, the three domains have no or weak interactions with one another at low protein concentrations (<1 mg/ml. The CTD in RP-LK-CTD(Mi is very stable and soluble, but it cannot stabilize the entire protein against chemical and thermal denaturation while it can keep the entire tri-domain in a highly water-soluble state. In the presence of shear force, protein aggregation is greatly accelerated and the aggregation rate is determined by the stability of folded domains and solubility of the disordered domains. Only the tri-domain RP-LK-CTD(Mi could form silk-like fibers, indicating that all three domains play distinct roles in fiber formation: LK as a nucleation site for assembly of protein molecules, RP for assistance of the assembly and CTD for regulating alignment of the assembled molecules.

  19. Southern Ocean JGOFS Time Series CTD and Current Meters (NODC Accession 9900167)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CTD and current meter data sets were collected in the Southern Oceans from ROGER REVILLE and moored CTD. Data were collected from 30 October 1997 to 16 March 1998 by...

  20. EX1103L1: Exploration and Mapping, Galapagos Spreading Center: Mapping, CTD and Tow-yo

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This project will be a transit from San Diego, CA to the Galapagos Spreading Center, where multibeam mapping, CTD casts, and CTD tow-yo operations will be performed....

  1. Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRi) plasmids | Office of Cancer Genomics

    Science.gov (United States)

    CTD2 researchers at the University of California in San Francisco developed a modified Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) CRISPR/dCas9 system. Catalytically inactive dCas9 enables modular and programmable RNA-guided genome regulation in eukaryotes.

  2. Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRi) plasmids | Office of Cancer Genomics

    Science.gov (United States)

    CTD2 researchers at the University of California in San Francisco developed a modified Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) CRISPR/dCas9 system. Catalytically inactive dCas9 enables modular and programmable RNA-guided genome regulation in eukaryotes.

  3. Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRi) plasmids | Office of Cancer Genomics

    Science.gov (United States)

    CTD2 researchers at the University of California in San Francisco developed a modified Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) CRISPR/dCas9 system. Catalytically inactive dCas9 enables modular and programmable RNA-guided genome regulation in eukaryotes.

  4. The C-Terminal Domain of RNA Polymerase II Is Modified by Site-Specific Methylation

    OpenAIRE

    Sims, Robert J.; Rojas, Luis Alejandro; Beck, David B.; Bonasio, Roberto; Schüller, Roland; Drury, William J.; Eick, Dirk; Reinberg, Danny

    2011-01-01

    The carboxy-terminal domain (CTD) of RNA polymerase II (RNAPII) in mammals undergoes extensive posttranslational modification, which is essential for transcriptional initiation and elongation. Here, we show that the CTD of RNAPII is methylated at a single arginine (R1810) by the coactivator-associated arginine methyltransferase 1 (CARM1). Although methylation at R1810 is present on the hyperphosphorylated form of RNAPII in vivo, Ser2 or Ser5 phosphorylation inhibits CARM1 activity toward this...

  5. Chromatin structure-dependent conformations of the H1 CTD.

    Science.gov (United States)

    Fang, He; Wei, Sijie; Lee, Tae-Hee; Hayes, Jeffrey J

    2016-11-02

    Linker histones are an integral component of chromatin but how these proteins promote assembly of chromatin fibers and higher order structures and regulate gene expression remains an open question. Using Förster resonance energy transfer (FRET) approaches we find that association of a linker histone with oligonucleosomal arrays induces condensation of the intrinsically disordered H1 CTD in a manner consistent with adoption of a defined fold or ensemble of folds in the bound state. However, H1 CTD structure when bound to nucleosomes in arrays is distinct from that induced upon H1 association with mononucleosomes or bare double stranded DNA. Moreover, the H1 CTD becomes more condensed upon condensation of extended nucleosome arrays to the contacting zig-zag form found in moderate salts, but does not detectably change during folding to fully compacted chromatin fibers. We provide evidence that linker DNA conformation is a key determinant of H1 CTD structure and that constraints imposed by neighboring nucleosomes cause linker DNAs to adopt distinct trajectories in oligonucleosomes compared to H1-bound mononucleosomes. Finally, inter-molecular FRET between H1s within fully condensed nucleosome arrays suggests a regular spatial arrangement for the H1 CTD within the 30 nm chromatin fiber. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  6. Sequence-specific double strand breaks trigger P-TEFb-dependent Rpb1-CTD hyperphosphorylation

    Energy Technology Data Exchange (ETDEWEB)

    Napolitano, Giuliana; Amente, Stefano; Lavadera, Miriam Lubrano; Di Palo, Giacomo; Ambrosio, Susanna; Lania, Luigi [Department of Biology, University of Naples ‘Federico II’, Naples (Italy); Dellino, Gaetano Ivan; Pelicci, Pier Giuseppe [Department of Experimental Oncology, European Institute of Oncology, Milan (Italy); Majello, Barbara, E-mail: majello@unina.it [Department of Biology, University of Naples ‘Federico II’, Naples (Italy)

    2013-09-15

    Highlights: • Using an inducible restriction enzyme, hundreds of site-specific DSBs are generated across the genome. • Site-specific DSBs trigger activation of P-TEFb and consequent Rpb1-CTD hyperphosphorylation. • Site-specific DSBs induce activation of p53-transcriptional axis. - Abstract: Double strand DNA breaks (DSBs) are one of the most challenging forms of DNA damage which, if left unrepaired, can trigger cellular death and can contribute to cancer. A number of studies have been focused on DNA-damage response (DDR) mechanisms, and most of them rely on the induction of DSBs triggered by chemical compounds or radiations. However, genotoxic drugs and radiation treatments of cultured cell lines induce random DSBs throughout the genome, thus heterogeneously across the cell population, leading to variability of the cellular response. To overcome this aspect, we used here a recently described cell-based DSBs system whereby, upon induction of an inducible restriction enzyme, hundreds of site-specific DSBs are generated across the genome. We show here that sequence-specific DSBs are sufficient to activate the positive transcription elongation factor b (P-TEFb), to trigger hyperphosphorylation of the largest RNA polymerase II carboxyl-terminal-domain (Rpb1-CTD) and to induce activation of p53-transcriptional axis resulting in cell cycle arrest.

  7. RNA Pol II Dynamics Modulate Co-transcriptional Chromatin Modification, CTD Phosphorylation, and Transcriptional Direction.

    Science.gov (United States)

    Fong, Nova; Saldi, Tassa; Sheridan, Ryan M; Cortazar, Michael A; Bentley, David L

    2017-05-18

    Eukaryotic genes are marked by conserved post-translational modifications on the RNA pol II C-terminal domain (CTD) and the chromatin template. How the 5'-3' profiles of these marks are established is poorly understood. Using pol II mutants in human cells, we found that slow transcription repositioned specific co-transcriptionally deposited chromatin modifications; histone H3 lysine 36 trimethyl (H3K36me3) shifted within genes toward 5' ends, and histone H3 lysine 4 dimethyl (H3K4me2) extended farther upstream of start sites. Slow transcription also evoked a hyperphosphorylation of CTD Ser2 residues at 5' ends of genes that is conserved in yeast. We propose a "dwell time in the target zone" model to explain the effects of transcriptional dynamics on the establishment of co-transcriptionally deposited protein modifications. Promoter-proximal Ser2 phosphorylation is associated with a longer pol II dwell time at start sites and reduced transcriptional polarity because of strongly enhanced divergent antisense transcription at promoters. These results demonstrate that pol II dynamics help govern the decision between sense and divergent antisense transcription. Copyright © 2017 Elsevier Inc. All rights reserved.

  8. The near-infrared spectroscopy-derived deoxygenated haemoglobin breaking-point is a repeatable measure that demarcates exercise intensity domains.

    Science.gov (United States)

    Iannetta, Danilo; Qahtani, Ahmad; Mattioni Maturana, Felipe; Murias, Juan Manuel

    2017-09-01

    A breaking-point in the near-infrared spectroscopy (NIRS)-derived deoxygenated haemoglobin ([HHb]) profile towards the end of a ramp incremental (RI) cycling test has been associated to the respiratory compensation point (RCP). Despite the physiological value of this measure, its repeatability remains unknown. The aim was to examine the repeatability of the [HHb] breaking-point ([HHb]BP) and its association to RCP during a RI cycling test. A repeated measures design was performed on 11 males (30.5±8.4 year; 76.5±8.4kg) and 4 females (30.5±5.9 year; 61.9±4.4 Kg). Gas exchange and NIRS [HHb] data were collected during RI tests performed on two different days separated by 48h. The [HHb]BP and the RCP were determined and compared for each trial. The [HHb]BP and the respiratory compensation point (RCP) occurred at the same VO2 in test 1 and test 2 ([HHb]BP: 3.49±0.52Lmin(-1) test 1; 3.48±0.45Lmin(-1) test 2; RCP: 3.38±0.40Lmin(-1) test 1; 3.38±0.44Lmin(-1) test 2) (P>0.05). The VO2 associated with the [HHb]BP and the VO2 at RCP were not significantly different from each other either in test 1 as well as in test 2 (P>0.05). Neither test 1 nor test 2 showed significant mean average error between the VO2 at the [HHb]BP and RCP using Bland & Altman plots. The [HHb]BP is a repeatable measure that consistently occurs towards the end of a RI test. The association between the [HHb]BP and the RCP reinforces the idea that these parameters may share similar mechanistic basis. Copyright © 2017 Sports Medicine Australia. Published by Elsevier Ltd. All rights reserved.

  9. Identification of Bacillus thuringiensis Cry3Aa toxin domain II loop 1 as the binding site of Tenebrio molitor cadherin repeat CR12.

    Science.gov (United States)

    Zúñiga-Navarrete, Fernando; Gómez, Isabel; Peña, Guadalupe; Amaro, Itzel; Ortíz, Ernesto; Becerril, Baltazar; Ibarra, Jorge E; Bravo, Alejandra; Soberón, Mario

    2015-04-01

    Bacillus thuringiensis Cry toxins exert their toxic effect by specific recognition of larval midgut proteins leading to oligomerization of the toxin, membrane insertion and pore formation. The exposed domain II loop regions of Cry toxins have been shown to be involved in receptor binding. Insect cadherins have shown to be functionally involved in toxin binding facilitating toxin oligomerization. Here, we isolated a VHH (VHHA5) antibody by phage display that binds Cry3Aa loop 1 and competed with the binding of Cry3Aa to Tenebrio molitor brush border membranes. VHHA5 also competed with the binding of Cry3Aa to a cadherin fragment (CR12) that was previously shown to be involved in binding and toxicity of Cry3Aa, indicating that Cry3Aa binds CR12 through domain II loop 1. Moreover, we show that a loop 1 mutant, previously characterized to have increased toxicity to T. molitor, displayed a correlative enhanced binding affinity to T. molitor CR12 and to VHHA5. These results show that Cry3Aa domain II loop 1 is a binding site of CR12 T. molitor cadherin.

  10. C6: A Monoclonal Antibody Specific for a Fibronectin Epitope Situated at the Interface between the Oncofoetal Extra-Domain B and the Repeat III8

    OpenAIRE

    Elisa Ventura; Cinzia Cordazzo; Rodolfo Quarto; Luciano Zardi; Camillo Rosano

    2016-01-01

    Background Fibronectin (FN) is a large multidomain molecule that is involved in many cellular processes. Different FN isoforms arise from alternative splicing of the pre-mRNA including, most notably, the FN isoform that contains the “extra-domain-B” (ED-B). The FN isoform containing ED-B (known as B-FN) is undetectable in healthy adult tissues but is present in large amounts in neoplastic and foetal tissues as well as on the blood vessels during angiogenesis. Thus, antibodies specific for B-F...

  11. The calcium-induced conformation and glycosylation of scavenger-rich cysteine repeat (SRCR) domains of glycoprotein 340 influence the high affinity interaction with antigen I/II homologs.

    Science.gov (United States)

    Purushotham, Sangeetha; Deivanayagam, Champion

    2014-08-01

    Oral streptococci adhere to tooth-immobilized glycoprotein 340 (GP340) via the surface protein antigen I/II (AgI/II) and its homologs as the first step in pathogenesis. Studying this interaction using recombinant proteins, we observed that calcium increases the conformational stability of the scavenger-rich cysteine repeat (SRCRs) domains of GP340. Our results also show that AgI/II adheres specifically with nanomolar affinity to the calcium-induced SRCR conformation in an immobilized state and not in solution. This interaction is significantly dependent on the O-linked carbohydrates present on the SRCRs. This study also establishes that a single SRCR domain of GP340 contains the two surfaces to which the apical and C-terminal regions of AgI/II noncompetitively adhere. Compared with the single SRCR domain, the three tandem SRCR domains displayed a collective/cooperative increase in their bacterial adherence and aggregation. The previously described SRCRP2 peptide that was shown to aggregate several oral streptococci displayed limited aggregation and also nonspecific adherence compared to SRCR domains. Finally, we show distinct species-specific adherence/aggregation between Streptococcus mutans AgI/II and Streptococcus gordonii SspB in their interaction with the SRCRs. This study concludes that identification of the metal ion and carbohydrate adherence motifs on both SRCRs and AgI/II homologs could lead to the development of anti-adhesive inhibitors that could deter the adherence of pathogenic oral streptococci and thereby prevent the onset of infections.

  12. The conserved residue Arg46 in the N-terminal heptad repeat domain of HIV-1 gp41 is critical for viral fusion and entry.

    Directory of Open Access Journals (Sweden)

    Xiaoyi Wang

    Full Text Available During the process of HIV-1 fusion with the target cell, the N-terminal heptad repeat (NHR of gp41 interacts with the C-terminal heptad repeat (CHR to form fusogenic six-helix bundle (6-HB core. We previously identified a crucial residue for 6-HB formation and virus entry--Lys63 (K63 in the C-terminal region of NHR (aa 54-70, which forms a hydrophobic cavity. It can form an important salt bridge with Asp121 (D121 in gp41 CHR. Here, we found another important conserved residue for virus fusion and entry, Arg46 (R46, in the N-terminal region of NHR (aa 35-53, which forms a hydrogen bond with a polar residue, Asn43 (N43, in NHR, as a part of the hydrogen-bond network. R46 can also form a salt bridge with a negatively charged residue, Glu137 (E137, in gp41 CHR. Substitution of R46 with the hydrophobic residue Ala (R46A or the negatively charged residue Glu (R46E resulted in disruption of the hydrogen bond network, breakage of the salt bridge and reduction of 6-HB's stability, leading to impairment of viral fusion and decreased inhibition of N36, an NHR peptide. Similarly, CHR peptide C34 with substitution of E137 for Ala (E137A or Arg (E137R also exhibited reduced inhibitory activity against HIV-1 infection and HIV-1-mediated cell-to-cell fusion. These results suggest that the positively charged residue R46 and its hydrogen bond network, together with the salt bridge between R46 and E137, are important for viral fusion and entry and may therefore serve as a target for designing novel HIV fusion/entry inhibitors.

  13. Revisiting the TALE repeat.

    Science.gov (United States)

    Deng, Dong; Yan, Chuangye; Wu, Jianping; Pan, Xiaojing; Yan, Nieng

    2014-04-01

    Transcription activator-like (TAL) effectors specifically bind to double stranded (ds) DNA through a central domain of tandem repeats. Each TAL effector (TALE) repeat comprises 33-35 amino acids and recognizes one specific DNA base through a highly variable residue at a fixed position in the repeat. Structural studies have revealed the molecular basis of DNA recognition by TALE repeats. Examination of the overall structure reveals that the basic building block of TALE protein, namely a helical hairpin, is one-helix shifted from the previously defined TALE motif. Here we wish to suggest a structure-based re-demarcation of the TALE repeat which starts with the residues that bind to the DNA backbone phosphate and concludes with the base-recognition hyper-variable residue. This new numbering system is consistent with the α-solenoid superfamily to which TALE belongs, and reflects the structural integrity of TAL effectors. In addition, it confers integral number of TALE repeats that matches the number of bound DNA bases. We then present fifteen crystal structures of engineered dHax3 variants in complex with target DNA molecules, which elucidate the structural basis for the recognition of bases adenine (A) and guanine (G) by reported or uncharacterized TALE codes. Finally, we analyzed the sequence-structure correlation of the amino acid residues within a TALE repeat. The structural analyses reported here may advance the mechanistic understanding of TALE proteins and facilitate the design of TALEN with improved affinity and specificity.

  14. Peptides corresponding to the predicted heptad repeat 2 domain of the feline coronavirus spike protein are potent inhibitors of viral infection.

    Directory of Open Access Journals (Sweden)

    I-Jung Liu

    Full Text Available BACKGROUND: Feline infectious peritonitis (FIP is a lethal immune-mediated disease caused by feline coronavirus (FCoV. Currently, no therapy with proven efficacy is available. In searching for agents that may prove clinically effective against FCoV infection, five analogous overlapping peptides were designed and synthesized based on the putative heptad repeat 2 (HR2 sequence of the spike protein of FCoV, and the antiviral efficacy was evaluated. METHODS: Plaque reduction assay and MTT (3-(4,5-dimethylthiazol-2-yl-2,5-diphenyltetrazolium bromide cytotoxicity assay were performed in this study. Peptides were selected using a plaque reduction assay to inhibit Feline coronavirus infection. RESULTS: The results demonstrated that peptide (FP5 at concentrations below 20 μM inhibited viral replication by up to 97%. The peptide (FP5 exhibiting the most effective antiviral effect was further combined with a known anti-viral agent, human interferon-α (IFN-α, and a significant synergistic antiviral effect was observed. CONCLUSION: Our data suggest that the synthetic peptide FP5 could serve as a valuable addition to the current FIP prevention methods.

  15. Cytoplasmic tail domain of glycoprotein B is essential for HHV-6 infection

    Energy Technology Data Exchange (ETDEWEB)

    Mahmoud, Nora F. [Division of Clinical Virology, Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe (Japan); Faculty of Pharmacy, Suez Canal University, Ismailia (Egypt); Jasirwan, Chyntia [Division of Clinical Virology, Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe (Japan); Division of Hepatobiliary, Department of Internal Medicine, Faculty of Medicine, University of Indonesia (Indonesia); Kanemoto, Satoshi; Wakata, Aika; Wang, Bochao; Hata, Yuuki [Division of Clinical Virology, Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe (Japan); Nagamata, Satoshi [Division of Clinical Virology, Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe (Japan); Department of Obstetrics and Gynecology, Kobe University Graduate School of Medicine, Kobe (Japan); Kawabata, Akiko [Division of Clinical Virology, Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe (Japan); Tang, Huamin [Division of Clinical Virology, Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe (Japan); Department of Immunology, Nanjing Medical University, Nanjing (China); Mori, Yasuko, E-mail: ymori@med.kobe-u.ac.jp [Division of Clinical Virology, Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe (Japan)

    2016-03-15

    Human herpesvirus 6 (HHV-6) glycoprotein B (gB) is an abundantly expressed viral glycoprotein required for viral entry and cell fusion, and is highly conserved among herpesviruses. The present study examined the function of HHV-6 gB cytoplasmic tail domain (CTD). A gB CTD deletion mutant was constructed which, in contrast to its revertant, could not be reconstituted. Moreover, deletion of gB cytoplasmic tail impaired the intracellular transport of gB protein to the trans-Golgi network (TGN). Taken together, these results suggest that gB CTD is critical for HHV-6 propagation and important for intracellular transportation. - Highlights: • Glycoprotein B (gB) is highly conserved among herpesviruses. • HHV-6 gB is also abundantly expressed in virions. • In the present study, we showed the function of HHV-6 gB cytoplasmic tail domain (CTD). • We found that deletion of gB CTD impairs the intracellular transport of gB protein to the trans-Golgi network (TGN), and CTD of gB is critical for HHV-6 propagation.

  16. Calibration process for CTD (Conductivity, Temperature and Depth)

    OpenAIRE

    Garcia Benadí, Albert; Molino Minero, Erik; Manuel Lázaro, Antonio; Río Fernandez, Joaquín del

    2011-01-01

    Detailed herein is the procedure to perform the calibration of a marine observation instrument, in this case a CTD, within the parameters of temperature, pressure and conductivity. It includes a calibration demonstration of the temperature and the pressure parameters. Peer Reviewed

  17. Ascertaining depths for samples from hydrographic casts without CTD

    Digital Repository Service at National Institute of Oceanography (India)

    Narvekar, P.V.; Bhushan, R.; Somayajulu, B.L.K.

    A fairly extensive study was conducted in the Arabian Sea in April-May 1195 to ascertain sample depths without CTD. It is shown that depths (degrees 4000 m) derived using (1) only protected thermometer data, and (2) wire angle (degrees 35 degrees...

  18. Cyclin-dependent kinase 2 phosphorylates s/t-p sites in the hepadnavirus core protein C-terminal domain and is incorporated into viral capsids.

    Science.gov (United States)

    Ludgate, Laurie; Ning, Xiaojun; Nguyen, David H; Adams, Christina; Mentzer, Laura; Hu, Jianming

    2012-11-01

    Phosphorylation of the hepadnavirus core protein C-terminal domain (CTD) is important for viral RNA packaging, reverse transcription, and subcellular localization. Hepadnavirus capsids also package a cellular kinase. The identity of the host kinase that phosphorylates the core CTD or gets packaged remains to be resolved. In particular, both the human hepatitis B virus (HBV) and duck hepatitis B virus (DHBV) core CTDs harbor several conserved serine/threonine-proline (S/T-P) sites whose phosphorylation state is known to regulate CTD functions. We report here that the endogenous kinase in the HBV capsids was blocked by chemical inhibitors of the cyclin-dependent kinases (CDKs), in particular, CDK2 inhibitors. The kinase phosphorylated the HBV CTD at the serine-proline (S-P) sites. Furthermore, we were able to detect CDK2 in purified HBV capsids by immunoblotting. Purified CDK2 phosphorylated the S/T-P sites of the HBV and DHBV CTD in vitro. Inhibitors of CDKs, of CDK2 in particular, decreased both HBV and DHBV CTD phosphorylation in vivo. Moreover, CDK2 inhibitors blocked DHBV CTD phosphorylation, specifically at the S/T-P sites, in a mammalian cell lysate. These results indicate that cellular CDK2 phosphorylates the functionally critical S/T-P sites of the hepadnavirus core CTD and is incorporated into viral capsids.

  19. The Pentapeptide Repeat Proteins

    Energy Technology Data Exchange (ETDEWEB)

    Vetting,M.; Hegde, S.; Fajardo, J.; Fiser, A.; Roderick, S.; Takiff, H.; Blanchard, J.

    2006-01-01

    The Pentapeptide Repeat Protein (PRP) family has over 500 members in the prokaryotic and eukaryotic kingdoms. These proteins are composed of, or contain domains composed of, tandemly repeated amino acid sequences with a consensus sequence of [S, T,A, V][D, N][L, F]-[S, T,R][G]. The biochemical function of the vast majority of PRP family members is unknown. The three-dimensional structure of the first member of the PRP family was determined for the fluoroquinolone resistance protein (MfpA) from Mycobacterium tuberculosis. The structure revealed that the pentapeptide repeats encode the folding of a novel right-handed quadrilateral {beta}-helix. MfpA binds to DNA gyrase and inhibits its activity. The rod-shaped, dimeric protein exhibits remarkable size, shape and electrostatic similarity to DNA.

  20. Interaction between the tRNA-binding and C-terminal domains of Yeast Gcn2 regulates kinase activity in vivo.

    Directory of Open Access Journals (Sweden)

    Sebastien Lageix

    2015-02-01

    Full Text Available The stress-activated protein kinase Gcn2 regulates protein synthesis by phosphorylation of translation initiation factor eIF2α. Gcn2 is activated in amino acid-deprived cells by binding of uncharged tRNA to the regulatory domain related to histidyl-tRNA synthetase, but the molecular mechanism of activation is unclear. We used a genetic approach to identify a key regulatory surface in Gcn2 that is proximal to the predicted active site of the HisRS domain and likely remodeled by tRNA binding. Mutations leading to amino acid substitutions on this surface were identified that activate Gcn2 at low levels of tRNA binding (Gcd- phenotype, while other substitutions block kinase activation (Gcn- phenotype, in some cases without altering tRNA binding by Gcn2 in vitro. Remarkably, the Gcn- substitutions increase affinity of the HisRS domain for the C-terminal domain (CTD, previously implicated as a kinase autoinhibitory segment, in a manner dampened by HisRS domain Gcd- substitutions and by amino acid starvation in vivo. Moreover, tRNA specifically antagonizes HisRS/CTD association in vitro. These findings support a model wherein HisRS-CTD interaction facilitates the autoinhibitory function of the CTD in nonstarvation conditions, with tRNA binding eliciting kinase activation by weakening HisRS-CTD association with attendant disruption of the autoinhibitory KD-CTD interaction.

  1. Thermotoga maritima NusG: domain interaction mediates autoinhibition and thermostability

    Science.gov (United States)

    Drögemüller, Johanna; Schneider, Christin; Schweimer, Kristian; Strauß, Martin; Wöhrl, Birgitta M.; Rösch, Paul; Knauer, Stefan H.

    2017-01-01

    NusG, the only universally conserved transcription factor, comprises an N- and a C-terminal domain (NTD, CTD) that are flexibly connected and move independently in Escherichia coli and other organisms. In NusG from the hyperthermophilic bacterium Thermotoga maritima (tmNusG), however, NTD and CTD interact tightly. This closed state stabilizes the CTD, but masks the binding sites for the interaction partners Rho, NusE and RNA polymerase (RNAP), suggesting that tmNusG is autoinhibited. Furthermore, tmNusG and some other bacterial NusGs have an additional domain, DII, of unknown function. Here we demonstrate that tmNusG is indeed autoinhibited and that binding to RNAP may stabilize the open conformation. We identified two interdomain salt bridges as well as Phe336 as major determinants of the domain interaction. By successive weakening of this interaction we show that after domain dissociation tmNusG-CTD can bind to Rho and NusE, similar to the Escherichia coli NusG-CTD, indicating that these interactions are conserved in bacteria. Furthermore, we show that tmNusG-DII interacts with RNAP as well as nucleic acids with a clear preference for double stranded DNA. We suggest that tmNusG-DII supports tmNusG recruitment to the transcription elongation complex and stabilizes the tmNusG:RNAP complex, a necessary adaptation to high temperatures. PMID:27899597

  2. (1)H, (15)N and (13)C resonance assignments for free and IEEVD peptide-bound forms of the tetratricopeptide repeat domain from the human E3 ubiquitin ligase CHIP.

    Science.gov (United States)

    Zhang, Huaqun; McGlone, Cameron; Mannion, Matthew M; Page, Richard C

    2017-04-01

    The ubiquitin ligase CHIP catalyzes covalent attachment of ubiquitin to unfolded proteins chaperoned by the heat shock proteins Hsp70/Hsc70 and Hsp90. CHIP interacts with Hsp70/Hsc70 and Hsp90 by binding of a C-terminal IEEVD motif found in Hsp70/Hsc70 and Hsp90 to the tetratricopeptide repeat (TPR) domain of CHIP. Although recruitment of heat shock proteins to CHIP via interaction with the CHIP-TPR domain is well established, alterations in structure and dynamics of CHIP upon binding are not well understood. In particular, the absence of a structure for CHIP-TPR in the free form presents a significant limitation upon studies seeking to rationally design inhibitors that may disrupt interactions between CHIP and heat shock proteins. Here we report the (1)H, (13)C, and (15)N backbone and side chain chemical shift assignments for CHIP-TPR in the free form, and backbone chemical shift assignments for CHIP-TPR in the IEEVD-bound form. The NMR resonance assignments will enable further studies examining the roles of dynamics and structure in regulating interactions between CHIP and the heat shock proteins Hsp70/Hsc70 and Hsp90.

  3. NMR studies of the R2 repeat and related peptide fragments of the DNA binding domain of c-Myb. New light on the structure and folding of R2.

    Science.gov (United States)

    Ségalas, I.; Desjardins, S.; Oulyadi, H.; Prigent, Y.; Tribouillard, S.; Bernardi, E.; Schoofs, A. R.; Davoust1, D.; Toma, F.

    1999-10-01

    The solution structure of the R2 repeat of the DNA binding domain of the protooncogene c-Myb contains a N-terminal structural motif comprising two antiparallel helices. The motif is stabilized by interactions involving conserved residues. The recognition region in C-terminal position is flexible. This structure differs from that of R2 of another c-Myb protein. La structure en solution de la répétition R2 du domaine de liaison à l'ADN du protooncogène c-Myb possède un motif à deux hélices antiparallèles dans la moitié N-terminale, stabilisé par des interactions entre résidus conservés. La région de reconnaissance à l'ADN en position C-terminale est flexible. Cette structure diffère de celle montrée pour la répétition R2 d'une autre protéine c-Myb.

  4. Deployment Repeatability

    Science.gov (United States)

    2016-04-01

    controlled to great precision, but in a Cubesat , there may be no attitude determination at all. Such a Cubesat might treat sun angle and tumbling rates as...could be sensitive to small differences in motor controller timing. In these cases, the analyst might choose to model the entire deployment path, with...knowledge of the material damage model or motor controller timing precision. On the other hand, if many repeated and environmentally representative

  5. Current direction, wind wave spectra, and CTD data from moored current meter and CTD casts in the North Atlantic Ocean from 15 September 1982 - 15 September 1983 (NODC Accession 8500148)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Current direction, wind wave spectra, and CTD data were collected using moored current meter and CTD casts in the Gulf of Mexico from September 3, 1982 to September...

  6. Antiviral activity of α-helical stapled peptides designed from the HIV-1 capsid dimerization domain

    Directory of Open Access Journals (Sweden)

    Cowburn David

    2011-05-01

    Full Text Available Abstract Background The C-terminal domain (CTD of HIV-1 capsid (CA, like full-length CA, forms dimers in solution and CTD dimerization is a major driving force in Gag assembly and maturation. Mutations of the residues at the CTD dimer interface impair virus assembly and render the virus non-infectious. Therefore, the CTD represents a potential target for designing anti-HIV-1 drugs. Results Due to the pivotal role of the dimer interface, we reasoned that peptides from the α-helical region of the dimer interface might be effective as decoys to prevent CTD dimer formation. However, these small peptides do not have any structure in solution and they do not penetrate cells. Therefore, we used the hydrocarbon stapling technique to stabilize the α-helical structure and confirmed by confocal microscopy that this modification also made these peptides cell-penetrating. We also confirmed by using isothermal titration calorimetry (ITC, sedimentation equilibrium and NMR that these peptides indeed disrupt dimer formation. In in vitro assembly assays, the peptides inhibited mature-like virus particle formation and specifically inhibited HIV-1 production in cell-based assays. These peptides also showed potent antiviral activity against a large panel of laboratory-adapted and primary isolates, including viral strains resistant to inhibitors of reverse transcriptase and protease. Conclusions These preliminary data serve as the foundation for designing small, stable, α-helical peptides and small-molecule inhibitors targeted against the CTD dimer interface. The observation that relatively weak CA binders, such as NYAD-201 and NYAD-202, showed specificity and are able to disrupt the CTD dimer is encouraging for further exploration of a much broader class of antiviral compounds targeting CA. We cannot exclude the possibility that the CA-based peptides described here could elicit additional effects on virus replication not directly linked to their ability to bind

  7. Crystal structure of the DNA cytosine deaminase APOBEC3F: the catalytically active and HIV-1 Vif-binding domain.

    Science.gov (United States)

    Bohn, Markus-Frederik; Shandilya, Shivender M D; Albin, John S; Kouno, Takahide; Anderson, Brett D; McDougle, Rebecca M; Carpenter, Michael A; Rathore, Anurag; Evans, Leah; Davis, Ahkillah N; Zhang, Jingying; Lu, Yongjian; Somasundaran, Mohan; Matsuo, Hiroshi; Harris, Reuben S; Schiffer, Celia A

    2013-06-04

    Human APOBEC3F is an antiretroviral single-strand DNA cytosine deaminase, susceptible to degradation by the HIV-1 protein Vif. In this study the crystal structure of the HIV Vif binding, catalytically active, C-terminal domain of APOBEC3F (A3F-CTD) was determined. The A3F-CTD shares structural motifs with portions of APOBEC3G-CTD, APOBEC3C, and APOBEC2. Residues identified to be critical for Vif-dependent degradation of APOBEC3F all fit within a predominantly negatively charged contiguous region on the surface of A3F-CTD. Specific sequence motifs, previously shown to play a role in Vif susceptibility and virion encapsidation, are conserved across APOBEC3s and between APOBEC3s and HIV-1 Vif. In this structure these motifs pack against each other at intermolecular interfaces, providing potential insights both into APOBEC3 oligomerization and Vif interactions.

  8. A miniature, low cost CTD system for coastal salinity measurements

    Science.gov (United States)

    Broadbent, Heather A.; Ivanov, Stanislav Z.; Fries, David P.

    2007-11-01

    In this work we describe a small, low cost conductivity, temperature and depth (CTD) system for measurements of salinity in coastal waters. The system incorporates three low cost expendable sensors, a novel planar four-electrode conductivity cell, a planar resistive temperature device and a piezoelectric pressure sensor. The conductivity cell and the resistive temperature device were fabricated using novel printed circuit board (PCB) microelectromechanical (MEMS) techniques combined with a new thin-film material, liquid crystal polymer (LCP). Printed circuit board techniques allow for mass production of the sensors, thereby lowering the cost of the system. The three sensors are packaged so that they are independent of one another and can be quickly replaced if bio-fouled or damaged. Deployments in Bayboro Harbor, St Petersburg, FL demonstrate that the novel CTD systems are capable of obtaining highly resolved in situ salinity measurements comparable to measurements obtained using commercially available instruments. The estimated accuracies for the conductivity, temperature and pressure sensors are ±1.47%, ±0.546 °C and ±0.02 bar, respectively. This work indicates that a small, low cost CTD system with expendable/replaceable sensors can be used to provide accurate, precise and highly resolved conductivity, temperature and pressure measurements in a coastal environment.

  9. Hepatitis B Virus Core Protein Phosphorylation Sites Affect Capsid Stability and Transient Exposure of the C-terminal Domain.

    Science.gov (United States)

    Selzer, Lisa; Kant, Ravi; Wang, Joseph C-Y; Bothner, Brian; Zlotnick, Adam

    2015-11-20

    Hepatitis B virus core protein has 183 amino acids divided into an assembly domain and an arginine-rich C-terminal domain (CTD) that regulates essential functions including genome packaging, reverse transcription, and intracellular trafficking. Here, we investigated the CTD in empty hepatitis B virus (HBV) T=4 capsids. We examined wild-type core protein (Cp183-WT) and a mutant core protein (Cp183-EEE), in which three CTD serines are replaced with glutamate to mimic phosphorylated protein. We found that Cp183-WT capsids were less stable than Cp183-EEE capsids. When we tested CTD sensitivity to trypsin, we detected two different populations of CTDs differentiated by their rate of trypsin cleavage. Interestingly, CTDs from Cp183-EEE capsids exhibited a much slower rate of proteolytic cleavage when compared with CTDs of Cp183-WT capsids. Cryo-electron microscopy studies of trypsin-digested capsids show that CTDs at five-fold symmetry vertices are most protected. We hypothesize that electrostatic interactions between glutamates and arginines in Cp183-EEE, particularly at five-fold, increase capsid stability and reduce CTD exposure. Our studies show that quasi-equivalent CTDs exhibit different rates of exposure and thus might perform distinct functions during the hepatitis B virus lifecycle. Our results demonstrate a structural role for CTD phosphorylation and indicate crosstalk between CTDs within a capsid particle. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  10. Developing a low-cost open-source CTD for research and outreach

    Science.gov (United States)

    Thaler, A. D.; Sturdivant, K.

    2013-12-01

    Developing a low-cost open-source CTD for research and outreach Andrew David Thaler and Kersey Sturdivant Conductivity, temperature, and depth (CTD). With these three measurements, marine scientists can unlock ocean patterns hidden beneath the waves. The ocean is not uniform, it its filled with swirling eddies, temperature boundaries, layers of high and low salinity, changing densities, and many other physical characteristics. To reveal these patterns, oceanographers use a tool called the CTD. A CTD is found on almost every major research vessel. Rare is the scientific expedition-whether it be coastal work in shallow estuaries or journeys to the deepest ocean trenches-that doesn't begin with the humble CTD cast. The CTD is not cheap. Commercial CTD's start at more the 5,000 and can climb as high as 25,000 or more. We believe that the prohibitive cost of a CTD is an unacceptable barrier to open science. The price tag excludes individuals and groups who lack research grants or significant private funds from conducting oceanographic research. We want to make this tool-the workhorse of oceanographic research-available to anyone with an interest in the oceans. The OpenCTD is a low-cost, open-source CTD suitable for both educators and scientists. The platform is built using readily available parts and is powered by an Arduino-based microcontroller. Our goal is to create a device that is accurate enough to be used for scientific research and can be constructed for less than $200. Source codes, circuit diagrams, and building plans will be freely available. The final instrument will be effective to 200 meters depth. Why 200 meters? For many coastal regions, 200 meters of water depth covers the majority of the ocean that is accessible by small boat. The OpenCTD is targeted to people working in this niche, where entire research projects can be conducted for less than the cost of a commercial CTD. However, the Open CTD is scalable, and anyone with the inclination can adapt our

  11. SOT1, a pentatricopeptide repeat protein with a small MutS-related domain, is required for correct processing of plastid 23S-4.5S rRNA precursors in Arabidopsis thaliana.

    Science.gov (United States)

    Wu, Wenjuan; Liu, Sheng; Ruwe, Hannes; Zhang, Delin; Melonek, Joanna; Zhu, Yajuan; Hu, Xupeng; Gusewski, Sandra; Yin, Ping; Small, Ian D; Howell, Katharine A; Huang, Jirong

    2016-03-01

    Ribosomal RNA processing is essential for plastid ribosome biogenesis, but is still poorly understood in higher plants. Here, we show that SUPPRESSOR OF THYLAKOID FORMATION1 (SOT1), a plastid-localized pentatricopeptide repeat (PPR) protein with a small MutS-related domain, is required for maturation of the 23S-4.5S rRNA dicistron. Loss of SOT1 function leads to slower chloroplast development, suppression of leaf variegation, and abnormal 23S and 4.5S processing. Predictions based on the PPR motif sequences identified the 5' end of the 23S-4.5S rRNA dicistronic precursor as a putative SOT1 binding site. This was confirmed by electrophoretic mobility shift assay, and by loss of the abundant small RNA 'footprint' associated with this site in sot1 mutants. We found that more than half of the 23S-4.5S rRNA dicistrons in sot1 mutants contain eroded and/or unprocessed 5' and 3' ends, and that the endonucleolytic cleavage product normally released from the 5' end of the precursor is absent in a sot1 null mutant. We postulate that SOT1 binding protects the 5' extremity of the 23S-4.5S rRNA dicistron from exonucleolytic attack, and favours formation of the RNA structure that allows endonucleolytic processing of its 5' and 3' ends. © 2016 The Authors The Plant Journal © 2016 John Wiley & Sons Ltd.

  12. Discovery of a Highly Potent, Cell-Permeable Macrocyclic Peptidomimetic (MM-589) Targeting the WD Repeat Domain 5 Protein (WDR5)–Mixed Lineage Leukemia (MLL) Protein–Protein Interaction

    Energy Technology Data Exchange (ETDEWEB)

    Karatas, Hacer; Li, Yangbing; Liu, Liu; Ji, Jiao; Lee, Shirley; Chen, Yong; Yang, Jiuling; Huang, Liyue; Bernard, Denzil; Xu, Jing; Townsend, Elizabeth C.; Cao, Fang; Ran, Xu; Li, Xiaoqin; Wen, Bo; Sun, Duxin; Stuckey, Jeanne A; Lei, Ming; Dou, Yali; Wang, Shaomeng (Michigan)

    2017-06-06

    We report herein the design, synthesis, and evaluation of macrocyclic peptidomimetics that bind to WD repeat domain 5 (WDR5) and block the WDR5–mixed lineage leukemia (MLL) protein–protein interaction. Compound 18 (MM-589) binds to WDR5 with an IC50 value of 0.90 nM (Ki value <1 nM) and inhibits the MLL H3K4 methyltransferase (HMT) activity with an IC50 value of 12.7 nM. Compound 18 potently and selectively inhibits cell growth in human leukemia cell lines harboring MLL translocations and is >40 times better than the previously reported compound MM-401. Cocrystal structures of 16 and 18 complexed with WDR5 provide structural basis for their high affinity binding to WDR5. Additionally, we have developed and optimized a new AlphaLISA-based MLL HMT functional assay to facilitate the functional evaluation of these designed compounds. Compound 18 represents the most potent inhibitor of the WDR5–MLL interaction reported to date, and further optimization of 18 may yield a new therapy for acute leukemia.

  13. Chaperone-like effect of the linker on the isolated C-terminal domain of rabbit muscle creatine kinase.

    Science.gov (United States)

    Chen, Zhe; Chen, Xiang-Jun; Xia, Mengdie; He, Hua-Wei; Wang, Sha; Liu, Huihui; Gong, Haipeng; Yan, Yong-Bin

    2012-08-01

    Intramolecular chaperones (IMCs), which are specific domains/segments encoded in the primary structure of proteins, exhibit chaperone-like activity against the aggregation of the other domains in the same molecule. In this research, we found that the truncation of the linker greatly promoted the thermal aggregation of the isolated C-terminal domain (CTD) of rabbit muscle creatine kinase (RMCK). Either the existence of the linker covalently linked to CTD or the supply of the synthetic linker peptide additionally could successfully protect the CTD of RMCK against aggregation in a concentration-dependent manner. Truncated fragments of the linker also behaved as a chaperone-like effect with lower efficiency, revealing the importance of its C-terminal half in the IMC function of the linker. The aggregation sites in the CTD of RMCK were identified by molecular dynamics simulations. Mutational analysis of the three key hydrophobic residues resulted in opposing effects on the thermal aggregation between the CTD with intact or partial linker, confirming the role of linker as a lid to protect the hydrophobic residues against exposure to solvent. These observations suggested that the linkers in multidomain proteins could act as IMCs to facilitate the correct folding of the aggregation-prone domains. Furthermore, the intactness of the IMC linker after proteolysis modulates the production of off-pathway aggregates, which may be important to the onset of some diseases caused by the toxic effects of aggregated proteolytic fragments.

  14. Overexpression of YB1 C-terminal domain inhibits proliferation, angiogenesis and tumorigenicity in a SK-BR-3 breast cancer xenograft mouse model.

    Science.gov (United States)

    Shi, Jian-Hong; Cui, Nai-Peng; Wang, Shuo; Zhao, Ming-Zhi; Wang, Bing; Wang, Ya-Nan; Chen, Bao-Ping

    2016-01-01

    Y-box-binding protein 1 (YB1) is a multifunctional transcription factor with vital roles in proliferation, differentiation and apoptosis. In this study, we have examined the role of its C-terminal domain (YB1 CTD) in proliferation, angiogenesis and tumorigenicity in breast cancer. Breast cancer cell line SK-BR-3 was infected with GFP-tagged YB1 CTD adenovirus expression vector. An 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium (MTS) proliferation assay showed that YB1 CTD decreased SK-BR-3 cell proliferation, and down-regulated cyclin B1 and up-regulated p21 levels in SK-BR-3 cells. YB1 CTD overexpression changed the cytoskeletal organization and slightly inhibited the migration of SK-BR-3 cells. YB1 CTD also inhibited secreted VEGF expression in SK-BR-3 cells, which decreased SK-BR-3-induced EA.hy926 endothelial cell angiogenesis in vitro. YB1 CTD overexpression attenuated the ability of SK-BR-3 cells to form tumours in nude mice, and decreased in vivo VEGF levels and angiogenesis in the xenografts in SK-BR-3 tumour-bearing mice. Taken together, our findings demonstrate the vital role of YB1 CTD overexpression in inhibiting proliferation, angiogenesis and tumorigenicity of breast cancer cell line SK-BR-3.

  15. CTD data collected using CTD casts from NOAA Ship RESEARCHER in the Gulf of Mexico from 1977-07-13 to 1977-07-23 (NCEI Accession 7800876)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Temperature profile and other data were collected using CTD casts from NOAA Ship RESEARCHER in the Gulf of Mexico. Data were collected from 13 July 1977 to 23 July...

  16. Origin and fate of repeats in bacteria.

    Science.gov (United States)

    Achaz, G; Rocha, E P C; Netter, P; Coissac, E

    2002-07-01

    We investigated 53 complete bacterial chromosomes for intrachromosomal repeats. In previous studies on eukaryote chromosomes, we proposed a model for the dynamics of repeats based on the continuous genesis of tandem repeats, followed by an active process of high deletion rate, counteracted by rearrangement events that may prevent the repeats from being deleted. The present study of long repeats in the genomes of Bacteria and Archaea suggests that our model of interspersed repeats dynamics may apply to them. Thus the duplication process might be a consequence of very ancient mechanisms shared by all three domains. Moreover, we show that there is a strong negative correlation between nucleotide composition bias and the repeat density of genomes. We hypothesise that in highly biased genomes, non-duplicated small repeats arise more frequently by random effects and are used as primers for duplication mechanisms, leading to a higher density of large repeats.

  17. Seedling Lethal1, a Pentatricopeptide Repeat Protein Lacking an E/E+ or DYW Domain in Arabidopsis, Is Involved in Plastid Gene Expression and Early Chloroplast Development1[C][W

    Science.gov (United States)

    Pyo, Young Jae; Kwon, Kwang-Chul; Kim, Anna; Cho, Myeon Haeng

    2013-01-01

    Chloroplasts are the site of photosynthesis and the biosynthesis of essential metabolites, including amino acids, fatty acids, and secondary metabolites. It is known that many seedling-lethal mutants are impaired in chloroplast function or development, indicating the development of functional chloroplast is essential for plant growth and development. Here, we isolated a novel transfer DNA insertion mutant, dubbed sel1 (for seedling lethal1), that exhibited a pigment-defective and seedling-lethal phenotype with a disrupted pentatricopeptide repeat (PPR) gene. Sequence analysis revealed that SEL1 is a member of the PLS subgroup, which is lacking known E/E+ or DYW domains at the C terminus, in the PLS subfamily of the PPR protein family containing a putative N-terminal transit peptide and 14 putative PPR or PPR-like motifs. Confocal microscopic analysis showed that the SEL1-green fluorescent protein fusion protein is localized in chloroplasts. Transmission electron microscopic analysis revealed that the sel1 mutant is impaired in the etioplast, as well as in chloroplast development. In sel1 mutants, plastid-encoded proteins involved in photosynthesis were rarely detected due to the lack of the corresponding transcripts. Furthermore, transcript profiles of plastid genes revealed that, in sel1 mutants, the transcript levels of plastid-encoded RNA polymerase-dependent genes were greatly reduced, but those of nuclear-encoded RNA polymerase-dependent genes were increased or not changed. Additionally, the RNA editing of two editing sites of the acetyl-CoA carboxylase beta subunit gene transcripts in the sel1 mutant was compromised, though it is not directly connected with the sel1 mutant phenotype. Our results demonstrate that SEL1 is involved in the regulation of plastid gene expression required for normal chloroplast development. PMID:24144791

  18. Synchrotron radiation circular dichroism spectroscopy-defined structure of the C-terminal domain of NaChBac and its role in channel assembly

    Science.gov (United States)

    Powl, Andrew M.; O’Reilly, Andrias O.; Miles, Andrew J.; Wallace, B. A.

    2010-01-01

    Extramembranous domains play important roles in the structure and function of membrane proteins, contributing to protein stability, forming association domains, and binding ancillary subunits and ligands. However, these domains are generally flexible, making them difficult or unsuitable targets for obtaining high-resolution X-ray and NMR structural information. In this study we show that the highly sensitive method of synchrotron radiation circular dichroism (SRCD) spectroscopy can be used as a powerful tool to investigate the structure of the extramembranous C-terminal domain (CTD) of the prokaryotic voltage-gated sodium channel (NaV) from Bacillus halodurans, NaChBac. Sequence analyses predict its CTD will consist of an unordered region followed by an α-helix, which has a propensity to form a multimeric coiled-coil motif, and which could form an association domain in the homotetrameric NaChBac channel. By creating a number of shortened constructs we have shown experimentally that the CTD does indeed contain a stretch of ∼20 α-helical residues preceded by a nonhelical region adjacent to the final transmembrane segment and that the efficiency of assembly of channels in the membrane progressively decreases as the CTD residues are removed. Analyses of the CTDs of 32 putative prokaryotic NaV sequences suggest that a CTD helical bundle is a structural feature conserved throughout the bacterial sodium channel family. PMID:20663949

  19. Roc, a Ras/GTPase domain in complex proteins

    NARCIS (Netherlands)

    Bosgraaf, Leonard; Haastert, Peter J.M. van

    2003-01-01

    We identified a novel group of the Ras/GTPase superfamily, termed Roc, that is present as domain in complex proteins together with other domains, including leucine-rich repeats (LRRs), ankyrin repeats, WD40 repeats, kinase domains, RasGEF and RhoGAP domains. Roc is always succeeded by a novel 300–40

  20. Structures of the nucleoid occlusion protein SlmA bound to DNA and the C-terminal domain of the cytoskeletal protein FtsZ.

    Science.gov (United States)

    Schumacher, Maria A; Zeng, Wenjie

    2016-05-03

    Cell division in most prokaryotes is mediated by FtsZ, which polymerizes to create the cytokinetic Z ring. Multiple FtsZ-binding proteins regulate FtsZ polymerization to ensure the proper spatiotemporal formation of the Z ring at the division site. The DNA-binding protein SlmA binds to FtsZ and prevents Z-ring formation through the nucleoid in a process called "nucleoid occlusion" (NO). As do most FtsZ-accessory proteins, SlmA interacts with the conserved C-terminal domain (CTD) that is connected to the FtsZ core by a long, flexible linker. However, SlmA is distinct from other regulatory factors in that it must be DNA-bound to interact with the FtsZ CTD. Few structures of FtsZ regulator-CTD complexes are available, but all reveal the CTD bound as a helix. To deduce the molecular basis for the unique SlmA-DNA-FtsZ CTD regulatory interaction and provide insight into FtsZ-regulator protein complex formation, we determined structures of Escherichia coli, Vibrio cholera, and Klebsiella pneumonia SlmA-DNA-FtsZ CTD ternary complexes. Strikingly, the FtsZ CTD does not interact with SlmA as a helix but binds as an extended conformation in a narrow, surface-exposed pocket formed only in the DNA-bound state of SlmA and located at the junction between the DNA-binding and C-terminal dimer domains. Binding studies are consistent with the structure and underscore key interactions in complex formation. Combined, these data reveal the molecular basis for the SlmA-DNA-FtsZ interaction with implications for SlmA's NO function and underscore the ability of the FtsZ CTD to adopt a wide range of conformations, explaining its ability to bind diverse regulatory proteins.

  1. The outer-membrane export signal of Porphyromonas gingivalis type IX secretion system (T9SS) is a conserved C-terminal β-sandwich domain.

    Science.gov (United States)

    de Diego, Iñaki; Ksiazek, Miroslaw; Mizgalska, Danuta; Koneru, Lahari; Golik, Przemyslaw; Szmigielski, Borys; Nowak, Magdalena; Nowakowska, Zuzanna; Potempa, Barbara; Houston, John A; Enghild, Jan J; Thøgersen, Ida B; Gao, Jinlong; Kwan, Ann H; Trewhella, Jill; Dubin, Grzegorz; Gomis-Rüth, F Xavier; Nguyen, Ky-Anh; Potempa, Jan

    2016-03-23

    In the recently characterized Type IX Secretion System (T9SS), the conserved C-terminal domain (CTD) in secreted proteins functions as an outer membrane translocation signal for export of virulence factors to the cell surface in the Gram-negative Bacteroidetes phylum. In the periodontal pathogen Porphyromonas gingivalis, the CTD is cleaved off by PorU sortase in a sequence-independent manner, and anionic lipopolysaccharide (A-LPS) is attached to many translocated proteins, thus anchoring them to the bacterial surface. Here, we solved the atomic structure of the CTD of gingipain B (RgpB) from P. gingivalis, alone and together with a preceding immunoglobulin-superfamily domain (IgSF). The CTD was found to possess a typical Ig-like fold encompassing seven antiparallel β-strands organized in two β-sheets, packed into a β-sandwich structure that can spontaneously dimerise through C-terminal strand swapping. Small angle X-ray scattering (SAXS) revealed no fixed orientation of the CTD with respect to the IgSF. By introducing insertion or substitution of residues within the inter-domain linker in the native protein, we were able to show that despite the region being unstructured, it nevertheless is resistant to general proteolysis. These data suggest structural motifs located in the two adjacent Ig-like domains dictate the processing of CTDs by the T9SS secretion pathway.

  2. Versatility of the carboxy-terminal domain of the alpha subunit of RNA polymerase in transcriptional activation: use of the DNA contact site as a protein contact site for MarA.

    Science.gov (United States)

    Dangi, Bindi; Gronenborn, Angela M; Rosner, Judah L; Martin, Robert G

    2004-10-01

    The transcriptional activator, MarA, interacts with RNA polymerase (RNAP) to activate promoters of the mar regulon. Here, we identify the interacting surfaces of MarA and of the carboxy-terminal domain of the alpha subunit of RNAP (alpha-CTD) by NMR-based chemical shift mapping. Spectral changes were monitored for a MarA-DNA complex upon titration with alpha-CTD, and for alpha-CTD upon titration with MarA-DNA. The mapping results were confirmed by mutational studies and retention chromatography. A model of the ternary complex shows that alpha-CTD uses a '265-like determinant' to contact MarA at a surface distant from the DNA. This is unlike the interaction of alpha-CTD with the CRP or Fis activators where the '265 determinant' contacts DNA while another surface of the same alpha-CTD molecule contacts the activator. These results reveal a new versatility for alpha-CTD in transcriptional activation.

  3. The Myc Transactivation Domain Promotes Global Phosphorylation of the RNA Polymerase II Carboxy-Terminal Domain Independently of Direct DNA Binding▿ †

    Science.gov (United States)

    Cowling, Victoria H.; Cole, Michael D.

    2007-01-01

    Myc is a transcription factor which is dependent on its DNA binding domain for transcriptional regulation of target genes. Here, we report the surprising finding that Myc mutants devoid of direct DNA binding activity and Myc target gene regulation can rescue a substantial fraction of the growth defect in myc−/− fibroblasts. Expression of the Myc transactivation domain alone induces a transcription-independent elevation of the RNA polymerase II (Pol II) C-terminal domain (CTD) kinases cyclin-dependent kinase 7 (CDK7) and CDK9 and a global increase in CTD phosphorylation. The Myc transactivation domain binds to the transcription initiation sites of these promoters and stimulates TFIIH binding in an MBII-dependent manner. Expression of the Myc transactivation domain increases CDK mRNA cap methylation, polysome loading, and the rate of translation. We find that some traditional Myc transcriptional target genes are also regulated by this Myc-driven translation mechanism. We propose that Myc transactivation domain-driven RNA Pol II CTD phosphorylation has broad effects on both transcription and mRNA metabolism. PMID:17242204

  4. Development of a CTD biotag: Challenges and pitfalls

    Science.gov (United States)

    Broadbent, Heather A.; Ketterl, Thomas P.; Silverman, Alex M.; Torres, Joseph J.

    2013-04-01

    This paper describes the design and development of a small CTD biotag that measures a suite of oceanographic data. Though presently configured to measure conductivity, temperature, and depth along with geo-location, it is expandable to acquire behaviorally related data, including acceleration, ambient light, and compass heading. The size of the instrument (100 mm x 40 mm x 20 mm) has been optimized for deployments on medium-sized marine predators such as penguins, tuna, and sharks. Several first generation prototypes have been constructed and initial laboratory and field tests have been performed and are reported. In addition, this paper highlights the challenges and difficulties encountered during the developmental process of a new biologging instrument.

  5. Domains and domain loss

    DEFF Research Database (Denmark)

    Haberland, Hartmut

    2005-01-01

    The domain concept, originally suggested by Schmidt-Rohr in the 1930’s (as credited in Fishman’s writings in the 1970s), was an attempt to sort out different areas of language use in multilingual societies, which are relevant for language choice. In Fishman’s version, domains were considered...... not described in terms of domains, and recent research e.g. about the multilingual communities in the Danish-German border area seems to confirm this....

  6. cis-Proline-mediated Ser(P)[superscript 5] Dephosphorylation by the RNA Polymerase II C-terminal Domain Phosphatase Ssu72

    Energy Technology Data Exchange (ETDEWEB)

    Werner-Allen, Jon W.; Lee, Chul-Jin; Liu, Pengda; Nicely, Nathan I.; Wang, Su; Greenleaf, Arno L.; Zhou, Pei (Duke)

    2012-05-16

    RNA polymerase II coordinates co-transcriptional events by recruiting distinct sets of nuclear factors to specific stages of transcription via changes of phosphorylation patterns along its C-terminal domain (CTD). Although it has become increasingly clear that proline isomerization also helps regulate CTD-associated processes, the molecular basis of its role is unknown. Here, we report the structure of the Ser(P){sup 5} CTD phosphatase Ssu72 in complex with substrate, revealing a remarkable CTD conformation with the Ser(P){sup 5}-Pro{sup 6} motif in the cis configuration. We show that the cis-Ser(P){sup 5}-Pro{sup 6} isomer is the minor population in solution and that Ess1-catalyzed cis-trans-proline isomerization facilitates rapid dephosphorylation by Ssu72, providing an explanation for recently discovered in vivo connections between these enzymes and a revised model for CTD-mediated small nuclear RNA termination. This work presents the first structural evidence of a cis-proline-specific enzyme and an unexpected mechanism of isomer-based regulation of phosphorylation, with broad implications for CTD biology

  7. Chromatin condensing functions of the linker histone C-terminal domain are mediated by specific amino acid composition and intrinsic protein disorder.

    Science.gov (United States)

    Lu, Xu; Hamkalo, Barbara; Parseghian, Missag H; Hansen, Jeffrey C

    2009-01-13

    Linker histones bind to the nucleosomes and linker DNA of chromatin fibers, causing changes in linker DNA structure and stabilization of higher order folded and oligomeric chromatin structures. Linker histones affect chromatin structure acting primarily through their approximately 100-residue C-terminal domain (CTD). We have previously shown that the ability of the linker histone H1 degrees to alter chromatin structure was localized to two discontinuous 24-/25-residue CTD regions (Lu, X., and Hansen, J. C. (2004) J. Biol. Chem. 279, 8701-8707). To determine the biochemical basis for these results, we have characterized chromatin model systems assembled with endogenous mouse somatic H1 isoforms or recombinant H1 degrees CTD mutants in which the primary sequence has been scrambled, the amino acid composition mutated, or the location of various CTD regions swapped. Our results indicate that specific amino acid composition plays a fundamental role in molecular recognition and function by the H1 CTD. Additionally, these experiments support a new molecular model for CTD function and provide a biochemical basis for the redundancy observed in H1 isoform knockout experiments in vivo.

  8. Physical, nutrients, and other data from CTD and bottle casts from the SW Pacific Ocean from 24 February 1990 to 12 April 1990 (NODC Accession 0000184)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CTD and bottle data were collected from the SW Pacific Ocean 24 February 1990 to 12 April 1990. CTD parameters include temperature profiles, salinity profiles, and...

  9. Temperature, salinity, and other data from CTD and XCTD casts in the Arctic Ocean from 26 March 1995 to 08 May 1995 (NODC Accession 0000474)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CTD, XCTD, and other data were collected in the Arctic Ocean from 26 March 1995 to 08 May 1995. Surface data were collected by CTD. XCTD data were corrected for...

  10. Current meter, CTD, and other data from the Mid-Atlantic Bight from 13 April 2003 to 17 April 2003 (NODC Accession 0002443)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Current meter, CTD, and other data were collected using CTD, current meter, fluorometer, and tow in the Mid-Atlantic Bight from April 14, 2003 to April 17, 2003....

  11. CTD cast data collected in Dabob Bay, Hood Canal, Puget Sound, Washington during eight cruises aboard the CLIFFORD A. BARNES, May 2006 - April 2008 (NODC Accession 0041970)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This dataset contains raw and processed CTD cast data collected during eight cruises to Dabob Bay, Washington in 2006 - 2008. Data were collected on one CTD cast per...

  12. Temperature, salinity, and nutrients data from CTD and bottle casts in the North Atlantic Ocean from 01 April 1969 to 31 August 1995 (NODC Accession 0000426)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CTD, bottle, and other data were collected from the CHARLES DARWIN and other vessels in the Atlantic Ocean from 01 April 1969 to 31 August 199. CTD data include...

  13. Repeat-until-success quantum repeaters

    Science.gov (United States)

    Bruschi, David Edward; Barlow, Thomas M.; Razavi, Mohsen; Beige, Almut

    2014-09-01

    We propose a repeat-until-success protocol to improve the performance of probabilistic quantum repeaters. Conventionally, these rely on passive static linear-optics elements and photodetectors to perform Bell-state measurements (BSMs) with a maximum success rate of 50%. This is a strong impediment for entanglement swapping between distant quantum memories. Every time a BSM fails, entanglement needs to be redistributed between the corresponding memories in the repeater link. The key ingredients of our scheme are repeatable BSMs. Under ideal conditions, these turn probabilistic quantum repeaters into deterministic ones. Under realistic conditions, our protocol too might fail. However, using additional threshold detectors now allows us to improve the entanglement generation rate by almost orders of magnitude, at a nominal distance of 1000 km, compared to schemes that rely on conventional BSMs. This improvement is sufficient to make the performance of our scheme comparable to the expected performance of some deterministic quantum repeaters.

  14. The Cytoplasmic Tail Domain of Epstein-Barr Virus gH Regulates Membrane Fusion Activity through Altering gH Binding to gp42 and Epithelial Cell Attachment.

    Science.gov (United States)

    Chen, Jia; Jardetzky, Theodore S; Longnecker, Richard

    2016-11-15

    Epstein-Barr virus (EBV) is associated with infectious mononucleosis and a variety of cancers as well as lymphoproliferative disorders in immunocompromised patients. EBV mediates viral entry into epithelial and B cells using fusion machinery composed of four glycoproteins: gB, the gH/gL complex, and gp42. gB and gH/gL are required for both epithelial and B cell fusion. The specific role of gH/gL in fusion has been the most elusive among the required herpesvirus entry glycoproteins. Previous mutational studies have focused on the ectodomain of EBV gH and not on the gH cytoplasmic tail domain (CTD). In this study, we chose to examine the function of the gH CTD by making serial gH truncation mutants as well as amino acid substitution mutants to determine the importance of the gH CTD in epithelial and B cell fusion. Truncation of 8 amino acids (aa 698 to 706) of the gH CTD resulted in diminished fusion activity using a virus-free syncytium formation assay and fusion assay. The importance of the amino acid composition of the gH CTD was also investigated by amino acid substitutions that altered the hydrophobicity or hydrophilicity of the CTD. These mutations also resulted in diminished fusion activity. Interestingly, some of the gH CTD truncation mutants and hydrophilic tail substitution mutants lost the ability to bind to gp42 and epithelial cells. In summary, our studies indicate that the gH CTD is an important functional domain.

  15. The Cytoplasmic Tail Domain of Epstein-Barr Virus gH Regulates Membrane Fusion Activity through Altering gH Binding to gp42 and Epithelial Cell Attachment

    Directory of Open Access Journals (Sweden)

    Jia Chen

    2016-11-01

    Full Text Available Epstein-Barr virus (EBV is associated with infectious mononucleosis and a variety of cancers as well as lymphoproliferative disorders in immunocompromised patients. EBV mediates viral entry into epithelial and B cells using fusion machinery composed of four glycoproteins: gB, the gH/gL complex, and gp42. gB and gH/gL are required for both epithelial and B cell fusion. The specific role of gH/gL in fusion has been the most elusive among the required herpesvirus entry glycoproteins. Previous mutational studies have focused on the ectodomain of EBV gH and not on the gH cytoplasmic tail domain (CTD. In this study, we chose to examine the function of the gH CTD by making serial gH truncation mutants as well as amino acid substitution mutants to determine the importance of the gH CTD in epithelial and B cell fusion. Truncation of 8 amino acids (aa 698 to 706 of the gH CTD resulted in diminished fusion activity using a virus-free syncytium formation assay and fusion assay. The importance of the amino acid composition of the gH CTD was also investigated by amino acid substitutions that altered the hydrophobicity or hydrophilicity of the CTD. These mutations also resulted in diminished fusion activity. Interestingly, some of the gH CTD truncation mutants and hydrophilic tail substitution mutants lost the ability to bind to gp42 and epithelial cells. In summary, our studies indicate that the gH CTD is an important functional domain.

  16. Mutational analysis of the C-terminal domain of the Rhodobacter sphaeroides response regulator PrrA

    OpenAIRE

    Jones, Denise F.; Stenzel, Rachelle A.; Donohue, Timothy J.

    2005-01-01

    The Rhodobacter sphaeroides response regulator PrrA directly activates transcription of genes necessary for energy conservation at low O2 tensions and under anaerobic conditions. It is proposed that PrrA homologues contain a C-terminal DNA-binding domain (PrrA-CTD) that lacks significant amino acid sequence similarity to those found in other response regulators. To test this hypothesis, single amino acid substitutions were created at 12 residues in the PrrA-CTD. These mutant PrrA proteins wer...

  17. Sirt1 carboxyl-domain is an ATP-repressible domain that is transferrable to other proteins

    Science.gov (United States)

    Kang, Hyeog; Oka, Shinichi; Lee, Duck-Yeon; Park, Junhong; Aponte, Angel M.; Jung, Young-Sang; Bitterman, Jacob; Zhai, Peiyong; He, Yi; Kooshapur, Hamed; Ghirlando, Rodolfo; Tjandra, Nico; Lee, Sean B.; Kim, Myung K.; Sadoshima, Junichi; Chung, Jay H.

    2017-01-01

    Sirt1 is an NAD+-dependent protein deacetylase that regulates many physiological functions, including stress resistance, adipogenesis, cell senescence and energy production. Sirt1 can be activated by energy deprivation, but the mechanism is poorly understood. Here, we report that Sirt1 is negatively regulated by ATP, which binds to the C-terminal domain (CTD) of Sirt1. ATP suppresses Sirt1 activity by impairing the CTD's ability to bind to the deacetylase domain as well as its ability to function as the substrate recruitment site. ATP, but not NAD+, causes a conformational shift to a less compact structure. Mutations that prevent ATP binding increase Sirt1's ability to promote stress resistance and inhibit adipogenesis under high-ATP conditions. Interestingly, the CTD can be attached to other proteins, thereby converting them into energy-regulated proteins. These discoveries provide insight into how extreme energy deprivation can impact Sirt1 activity and underscore the complex nature of Sirt1 structure and regulation. PMID:28504272

  18. Characterization of TonB interactions with the FepA cork domain and FecA N-terminal signaling domain.

    Science.gov (United States)

    Peacock, R Sean; Andrushchenko, Valery V; Demcoe, A Ross; Gehmlich, Matt; Lu, Lily Sia; Herrero, Alicia Garcia; Vogel, Hans J

    2006-04-01

    The mechanism of TonB dependent siderophore uptake through outer membrane transporters in Gram-negative bacteria is poorly understood. In an effort to expand our knowledge of the interaction between TonB and the outer membrane transporters, we have cloned and expressed the FepA cork domain (11-154) from Salmonella typhimurium and characterized its interaction with the periplasmic C-terminal domain of TonB (103-239) by isotope assisted FTIR and NMR spectroscopy. For comparison we also performed similar experiments using the FecA N-terminal domain (1-96) from Escherichia coli which includes the conserved TonB box. The FepA cork domain was completely unfolded in solution, as observed for the E. coli cork domain previously [Usher et al. (2001) Proc Natl Acad Sci USA 98, 10676-10681]. The FepA cork domain was found to bind to TonB, eliciting essentially the same chemical shift changes in TonB C-terminal domain as was observed in the presence of TonB box peptides. The FecA construct did not cause this same structural change in TonB. The binding of the FepA cork domain to TonB-CTD was found to decrease the amount of ordered secondary structure in TonB-CTD. It is likely that the FecA N-terminal domain interferes with TonB-CTD binding to the TonB box. Binding of the FepA cork domain induces a loss of secondary structure in TonB, possibly exposing TonB surface area for additional intermolecular interactions such as potential homodimerization or additional interactions with the barrel of the outer membrane transporter.

  19. Membrane binding properties of EBV gp110 C-terminal domain; evidences for structural transition in the membrane environment.

    Science.gov (United States)

    Park, Sung Jean; Seo, Min-Duk; Lee, Suk Kyeong; Lee, Bong Jin

    2008-09-30

    Gp110 of Epstein-Barr virus (EBV) mainly localizes on nuclear/ER membranes and plays a role in the assembly of EBV nucleocapsid. The C-terminal tail domain (gp110 CTD) is essential for the function of gp110 and the nuclear/ER membranes localization of gp110 is ruled by its C-terminal unique nuclear localization signal (NLS), consecutive four arginines. In the present study, the structural properties of gp110 CTD in membrane mimics were investigated using CD, size-exclusion chromatography, and NMR, to elucidate the effect of membrane environment on the structural transition and to compare the structural feature of the protein in the solution state with that of the membrane-bound form. CD and NMR analysis showed that gp110 CTD in a buffer solution appears to adopt a stable folding intermediate which lacks compactness, and a highly helical structure is formed only in membrane environments. The helical content of gp110 CTD was significantly affected by the negative charge as well as the size of membrane mimics. Based on the elution profiles of the size-exclusion chromatography, we found that gp110 CTD intrinsically forms a trimer, revealing that a trimerization region may exist in the C-terminal domain of gp110 like the ectodomain of gp110. The mutation of NLS (RRRR) to RTTR does not affect the overall structure of gp110 CTD in membrane mimics, while the helical propensity in a buffer solution was slightly different between the wild-type and the mutant proteins. This result suggests that not only the helicity induced in membrane environment but also the local structure around NLS may be related to trafficking to the nuclear membrane. More detailed structural difference between the wild-type and the mutant in membrane environment was examined using synthetic two peptides including the wild-type NLS and the mutant NLS.

  20. CTD, marine invertebrate pathology, benthic organisms, and marine toxic substances and pollutants data collected using CTD casts and other instruments from SEA TRANSPORTER and other platforms in Gulf of Mexico from 20 May 1978 to 15 January 1979 (NODC Accession 8000022)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CTD, marine invertebrate pathology, benthic organisms, and marine toxic substances and pollutants data were collected using CTD, net casts, and other instruments...

  1. The impact of the human DNA topoisomerase II C-terminal domain on activity.

    Directory of Open Access Journals (Sweden)

    Emma L Meczes

    Full Text Available BACKGROUND: Type II DNA topoisomerases (topos are essential enzymes needed for the resolution of topological problems that occur during DNA metabolic processes. Topos carry out an ATP-dependent strand passage reaction whereby one double helix is passed through a transient break in another. Humans have two topoII isoforms, alpha and beta, which while enzymatically similar are differentially expressed and regulated, and are thought to have different cellular roles. The C-terminal domain (CTD of the enzyme has the most diversity, and has been implicated in regulation. We sought to investigate the impact of the CTD domain on activity. METHODOLOGY/PRINCIPLE FINDINGS: We have investigated the role of the human topoII C-terminal domain by creating constructs encoding C-terminally truncated recombinant topoIIalpha and beta and topoIIalpha+beta-tail and topoIIbeta+alpha-tail chimeric proteins. We then investigated function in vivo in a yeast system, and in vitro in activity assays. We find that the C-terminal domain of human topoII isoforms is needed for in vivo function of the enzyme, but not needed for cleavage activity. C-terminally truncated enzymes had similar strand passage activity to full length enzymes, but the presence of the opposite C-terminal domain had a large effect, with the topoIIalpha-CTD increasing activity, and the topoIIbeta-CTD decreasing activity. CONCLUSIONS/SIGNIFICANCE: In vivo complementation data show that the topoIIalpha C-terminal domain is needed for growth, but the topoIIbeta isoform is able to support low levels of growth without a C-terminal domain. This may indicate that topoIIbeta has an additional localisation signal. In vitro data suggest that, while the lack of any C-terminal domain has little effect on activity, the presence of either the topoIIalpha or beta C-terminal domain can affect strand passage activity. Data indicates that the topoIIbeta-CTD may be a negative regulator. This is the first report of in vitro

  2. Overexpression of YB1 C‐terminal domain inhibits proliferation, angiogenesis and tumorigenicity in a SK‐BR‐3 breast cancer xenograft mouse model

    OpenAIRE

    Shi, Jian‐hong; Cui, Nai‐peng; Wang, Shuo; Zhao, Ming‐zhi; Wang, Bing; Wang, Ya‐nan; Chen, Bao‐ping

    2016-01-01

    Y‐box‐binding protein 1 (YB1) is a multifunctional transcription factor with vital roles in proliferation, differentiation and apoptosis. In this study, we have examined the role of its C‐terminal domain (YB1 CTD) in proliferation, angiogenesis and tumorigenicity in breast cancer. Breast cancer cell line SK‐BR‐3 was infected with GFP‐tagged YB1 CTD adenovirus expression vector. An 3‐(4,5‐dimethylthiazol‐2‐yl)‐5‐(3‐carboxymethoxyphenyl)‐2‐(4‐sulfophenyl)‐2H‐tetrazolium (MTS) proliferation assa...

  3. Quantum repeated games revisited

    CERN Document Server

    Frackiewicz, Piotr

    2011-01-01

    We present a scheme for playing quantum repeated 2x2 games based on the Marinatto and Weber's approach to quantum games. As a potential application, we study twice repeated Prisoner's Dilemma game. We show that results not available in classical game can be obtained when the game is played in the quantum way. Before we present our idea, we comment on the previous scheme of playing quantum repeated games.

  4. Domain analysis

    DEFF Research Database (Denmark)

    Hjørland, Birger

    2017-01-01

    The domain-analytic approach to knowledge organization (KO) (and to the broader field of library and information science, LIS) is outlined. The article reviews the discussions and proposals on the definition of domains, and provides an example of a domain-analytic study in the field of art studie....... Varieties of domain analysis as well as criticism and controversies are presented and discussed....

  5. CRED Shallow CTD Profiles; Maui, Main Hawaiian Islands; Cruise: OES0810, Data Date Range: 20081017-20081103 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  6. CRED Shallow CTD Profiles; Molokai, Main Hawaiian Islands; Cruise: HA1008, Data Date Range: 20101023-20101104 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  7. CRED Shallow CTD Profiles; Tutuila, American Samoa; Cruise: HI0802, Data Date Range: 20080218-20080223 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  8. CRED Shallow CTD Profiles; Swains Island, American Samoa; Cruise: HI0802, Data Date Range: 20080317-20080318 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  9. CRED Shallow CTD Profiles; Niihau, Main Hawaiian Islands; Cruise: OES0810, Data Date Range: 20081109-20081111 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  10. CRED Shallow CTD Profiles; Oahu, Main Hawaiian Islands; Cruise: HI0610, Data Date Range: 20060727-20060728 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  11. CRED Shallow CTD Profiles; Guam; Cruise: HI0902, Data Date Range: 20090404-20090408 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  12. CRED Shallow CTD Profiles; Maui, Main Hawaiian Islands; Cruise: HA1008, Data Date Range: 20101015-20101020 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  13. Gibraltar Experiment CTD data report, USNS Lynch, 1986-03-26 to 1986-04-19 (NODC Accession 8800167)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Temperature profile, ocean circulation, and chemical data were collected using CTD casts from the USNS LYNCH in the Gulf of Cadiz, Alboran Sea, and Strait of...

  14. CRED Shallow CTD Profiles; Rose Atoll, American Samoa; Cruise: OES0402, Data Date Range: 20040209-20040211 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  15. CRED Shallow CTD Profiles; Molokai, Main Hawaiian Islands; Cruise: HI0505, Data Date Range: 20050801-20050802 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  16. CRED Shallow CTD Profiles; Guam; Cruise: OES0307, Data Date Range: 20030922-20030925 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  17. CRED Shallow CTD Profiles; Swains Island, American Samoa; Cruise: HI0602, Data Date Range: 20060212-20060213 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  18. CRED Shallow CTD Profiles; Guam; Cruise: HI0702, Data Date Range: 20070511-20070515 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  19. CRED Shallow CTD Profiles; Guam; Cruise: OES0512, Data Date Range: 20051003-20051008 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  20. CRED Shallow CTD Profiles; Rose Atoll, American Samoa; Cruise: HI0602, Data Date Range: 20060305-20060309 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  1. CRED Shallow CTD Profiles; Molokai, Main Hawaiian Islands; Cruise: HI0610, Data Date Range: 20060730-20060815 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  2. CRED Shallow CTD Profiles; Niihau, Main Hawaiian Islands; Cruise: HI0610, Data Date Range: 20060809-20060811 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  3. CRED Shallow CTD Profiles; Tutuila, American Samoa; Cruise: OES0402, Data Date Range: 20040219-20040225 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  4. CRED Shallow CTD Profiles; Tutuila, American Samoa; Cruise: HA1201_LEGI, Data Date Range: 20120325-20120326 (NODC Accession 0107470)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  5. Delayed CTD data submitted by INIDEP ranging from 11/26/1984 - 10/16/1989 (NODC Accession 0039468)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CTD data were collected in the South Atlantic aboard the Oca Balda from 26 November 1984 to 16 October 1989. These data were submitted to NODC by the INSTITUTO...

  6. Conductivity-Temperature-Depth (CTD) profile data in the National Park of American Samoa, Tutuila, American Samoa, 2015

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — Spatial surveys of water column physical properties were acquired with a conductivity-temperature-depth (CTD) profiler for four days in February 2015 and one day in...

  7. CRED Shallow CTD Profiles; Maui, Main Hawaiian Islands; Cruise: HI0505, Data Date Range: 20050804-20050805 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  8. CRED Shallow CTD Profiles; Guam; Cruise: HA1101_LEGIII, Data Date Range: 20110504-20110507. (NODC Accession 0107470)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  9. CRED Shallow CTD Profiles; Niihau, Main Hawaiian Islands; Cruise: HI0505, Data Date Range: 20050717-20050720 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  10. CRED Shallow CTD Profiles; Maui, Main Hawaiian Islands; Cruise: OES0502, Data Date Range: 20050225-20050225 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  11. CRED Shallow CTD Profiles; Tutuila, American Samoa; Cruise: HI0602, Data Date Range: 20060218-20060226 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  12. CRED Shallow CTD Profiles; Oahu, Main Hawaiian Islands; Cruise: OES0810, Data Date Range: 20081112-20081113 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  13. CRED Shallow CTD Profiles; Swains Island, American Samoa; Cruise: OES0402, Data Date Range: 20040215-20040218 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  14. CRED Shallow CTD Profiles; Oahu, Main Hawaiian Islands; Cruise: HA1008, Data Date Range: 20101024-20101102 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  15. CRED Shallow CTD Profiles; Tutuila, American Samoa; Cruise: TC0201_LEGII, Data Date Range: 20020210-20020304 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  16. CRED Shallow CTD Profiles; Rose Atoll, American Samoa; Cruise: HI0802, Data Date Range: 20080313-20080314 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  17. CRED Shallow CTD Profiles; Oahu, Main Hawaiian Islands; Cruise: HI0505, Data Date Range: 20050715-20050724 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  18. CRED Shallow CTD Profiles; Tutuila, American Samoa; Cruise: HI1001_LEGII, Data Date Range: 20100217-20100227 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  19. CRED Shallow CTD Profiles; Niihau, Main Hawaiian Islands; Cruise: HA1008, Data Date Range: 20101029-20101101 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  20. CRED Shallow CTD Profiles; Molokai, Main Hawaiian Islands; Cruise: OES0810, Data Date Range: 20081021-20081025 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  1. Reconfigurable multiport EPON repeater

    Science.gov (United States)

    Oishi, Masayuki; Inohara, Ryo; Agata, Akira; Horiuchi, Yukio

    2009-11-01

    An extended reach EPON repeater is one of the solutions to effectively expand FTTH service areas. In this paper, we propose a reconfigurable multi-port EPON repeater for effective accommodation of multiple ODNs with a single OLT line card. The proposed repeater, which has multi-ports in both OLT and ODN sides, consists of TRs, BTRs with the CDR function and a reconfigurable electrical matrix switch, can accommodate multiple ODNs to a single OLT line card by controlling the connection of the matrix switch. Although conventional EPON repeaters require full OLT line cards to accommodate subscribers from the initial installation stage, the proposed repeater can dramatically reduce the number of required line cards especially when the number of subscribers is less than a half of the maximum registerable users per OLT. Numerical calculation results show that the extended reach EPON system with the proposed EPON repeater can save 17.5% of the initial installation cost compared with a conventional repeater, and can be less expensive than conventional systems up to the maximum subscribers especially when the percentage of ODNs in lightly-populated areas is higher.

  2. Structural studies of FF domains of the transcription factor CA150 provide insights into the organization of FF domain tandem arrays.

    Science.gov (United States)

    Murphy, James M; Hansen, D Flemming; Wiesner, Silke; Muhandiram, D Ranjith; Borg, Mikael; Smith, Matthew J; Sicheri, Frank; Kay, Lewis E; Forman-Kay, Julie D; Pawson, Tony

    2009-10-23

    FF domains are poorly understood protein interaction modules that are present within eukaryotic transcription factors, such as CA150 (TCERG-1). The CA150 FF domains have been shown to mediate interactions with the phosphorylated C-terminal domain of RNA polymerase II (phosphoCTD) and a multitude of transcription factors and RNA processing proteins, and may therefore have a central role in organizing transcription. FF domains occur in tandem arrays of up to six domains, although it is not known whether they adopt higher-order structures. We have used the CA150 FF1+FF2 domains as a model system to examine whether tandem FF domains form higher-order structures in solution using NMR spectroscopy. In the solution structure of FF1 fused to the linker that joins FF1 to FF2, we observed that the highly conserved linker peptide is ordered and forms a helical extension of helix alpha3, suggesting that the interdomain linker might have a role in orientating FF1 relative to FF2. However, examination of the FF1+FF2 domains using relaxation NMR experiments revealed that although these domains are not rigidly orientated relative to one another, they do not tumble independently. Thus, the FF1+FF2 structure conforms to a dumbbell-shape in solution, where the helical interdomain linker maintains distance between the two dynamic FF domains without cementing their relative orientations. This model for FF domain organization within tandem arrays suggests a general mechanism by which individual FF domains can manoeuvre to achieve optimal recognition of flexible binding partners, such as the intrinsically-disordered phosphoCTD.

  3. Recursive quantum repeater networks

    CERN Document Server

    Van Meter, Rodney; Horsman, Clare

    2011-01-01

    Internet-scale quantum repeater networks will be heterogeneous in physical technology, repeater functionality, and management. The classical control necessary to use the network will therefore face similar issues as Internet data transmission. Many scalability and management problems that arose during the development of the Internet might have been solved in a more uniform fashion, improving flexibility and reducing redundant engineering effort. Quantum repeater network development is currently at the stage where we risk similar duplication when separate systems are combined. We propose a unifying framework that can be used with all existing repeater designs. We introduce the notion of a Quantum Recursive Network Architecture, developed from the emerging classical concept of 'recursive networks', extending recursive mechanisms from a focus on data forwarding to a more general distributed computing request framework. Recursion abstracts independent transit networks as single relay nodes, unifies software layer...

  4. Histone deacetylases and phosphorylated polymerase II C-terminal domain recruit Spt6 for cotranscriptional histone reassembly.

    Science.gov (United States)

    Burugula, Bala Bharathi; Jeronimo, Célia; Pathak, Rakesh; Jones, Jeffery W; Robert, François; Govind, Chhabi K

    2014-11-15

    Spt6 is a multifunctional histone chaperone involved in the maintenance of chromatin structure during elongation by RNA polymerase II (Pol II). Spt6 has a tandem SH2 (tSH2) domain within its C terminus that recognizes Pol II C-terminal domain (CTD) peptides phosphorylated on Ser2, Ser5, or Try1 in vitro. Deleting the tSH2 domain, however, only has a partial effect on Spt6 occupancy in vivo, suggesting that more complex mechanisms are involved in the Spt6 recruitment. Our results show that the Ser2 kinases Bur1 and Ctk1, but not the Ser5 kinase Kin28, cooperate in recruiting Spt6, genome-wide. Interestingly, the Ser2 kinases promote the association of Spt6 in early transcribed regions and not toward the 3' ends of genes, where phosphorylated Ser2 reaches its maximum level. In addition, our results uncover an unexpected role for histone deacetylases (Rpd3 and Hos2) in promoting Spt6 interaction with elongating Pol II. Finally, our data suggest that phosphorylation of the Pol II CTD on Tyr1 promotes the association of Spt6 with the 3' ends of transcribed genes, independently of Ser2 phosphorylation. Collectively, our results show that a complex network of interactions, involving the Spt6 tSH2 domain, CTD phosphorylation, and histone deacetylases, coordinate the recruitment of Spt6 to transcribed genes in vivo. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

  5. Quality Control of Temperature and Salinity from CTD based on Anomaly Detection

    CERN Document Server

    Castelão, Guilherme P

    2015-01-01

    The CTD is a set of sensors used by oceanographers to measure fundamental hydrographic properties of the oceans. It is characterized by a high precision product, only achieved if a quality control procedure identifies and removes the bad samples. Such procedure has been traditionally done by a sequence of independent tests that minimize false negatives. It is here proposed a novel approach to identify the bad samples as anomalies in respect to the typical behavior of good data. Several tests are combined into a single multidimensional evaluation to provide a more flexible classification criterion. The traditional approach is reproduced with an error of 0.04%, otherwise, the Anomaly Detection technique surpasses the reference if calibrated by visual inspection. CoTeDe is a Python package developed to apply the traditional and the Anomaly Detection quality control of temperature and salinity data from CTD, and can be extended to XBT, ARGO and other sensors.

  6. CTD and fluorometer data were collected in the Gulf of Alaska as part of the GLobal Ocean Ecosystem dynamiCs (GLOBEC) project from 05 March 2002 to 11 December 2002 (NODC Accession 0001062)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CTD and fluorometer data were collected using CTD and fluorometer from the R/V ALPHA HELIX in the Gulf of Alaska and Prince Williams Sound from March 5, to December...

  7. Physical and chemical profile data collected from CTD aboard the R/V Endeavor during the cruise EN492 in the North Atlantic Ocean from 26 April 2011 to 20 May 2011 (NODC Accession 0100255)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The dataset consists of 115 CTD casts in the region north of Flemish Cap. Some casts cover the full water column, while others only cover the upper 1000 db. The CTD...

  8. Oceanographic profile temperature and salinity data using underway CTD, collected by the Graduate School of Oceanography, University of Rhode Island, cruise KN200-2, North Atlantic Ocean, 2011-03 (NODC Accession 0115494)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The dataset consists of 81 Underway CTD (UCTD) casts in the region north of Flemish Cap. The UCTD is an un-pumped profiling CTD, manufactured by the Oceanscience...

  9. Physical, nutrient, meteorological, and other data from CTD and bottle casts from AEGIR and other platforms from the North Atlantic Ocean from 01 January 2000 to 31 December 2000 (NODC Accession 0000127)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CTD and bottle data were collected from AEGIR and other platforms in the North Atlantic Ocean from 01 January 2000 to 31 December 2000. CTD parameters include...

  10. Oceanographic profile temperature and salinity data using underway CTD, collected by the Graduate School of Oceanography, University of Rhode Island, cruise EN492, North Atlantic Ocean, 2011-04 to 2011-05 (NODC Accession 0116845)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The dataset consists of 79 Underway CTD (UCTD) casts in the region north of Flemish Cap. The UCTD is an un-pumped profiling CTD, manufactured by the Oceanscience...

  11. Conductivity, Temperature, Depth (CTD) collected aboard the R/V GARUPPA from August 02, 2010 through August 03, 2010. Data include vertical profiles of temperature, salinity, and dissolved oxygen.

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CTD data were collected using a Sea-Bird 19 CTD during the summer SADCP survey of Vieques Sound and Virgin Passage in the US Caribbean.

  12. Physical and chemical profile data collected from CTD in the R/V Knorr cruise KN200-2 during March 2011 in the North Atlantic Ocean (NODC Accession 0100287)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The dataset consists of 100 CTD casts in the region north of Flemish Cap. Some casts cover the full water column, while others only cover the upper 1000 db. The CTD...

  13. Forecast of drifter trajectories using a Rapid Environmental Assessment based on CTD observations

    Science.gov (United States)

    Sorgente, R.; Tedesco, C.; Pessini, F.; De Dominicis, M.; Gerin, R.; Olita, A.; Fazioli, L.; Di Maio, A.; Ribotti, A.

    2016-11-01

    A high resolution submesoscale resolving ocean model was implemented in a limited area north of Island of Elba where a maritime exercise, named Serious Game 1 (SG1), took place on May 2014 in the framework of the project MEDESS-4MS (Mediterranean Decision Support System for Marine Safety). During the exercise, CTD data have been collected responding to the necessity of a Rapid Environmental Assessment, i.e. to a rapid evaluation of the marine conditions able to provide sensible information for initialisation of modelling tools, in the scenario of possible maritime accidents. The aim of this paper is to evaluate the impact of such mesoscale-resolving CTD observations on short-term forecasts of the surface currents, within the framework of possible oil-spill related emergencies. For this reason, modelling outputs were compared with Lagrangian observations at sea: the high resolution modelled currents, together with the ones of the coarser sub-regional model WMED, are used to force the MEDSLIK-II oil-spill model to simulate drifter trajectories. Both ocean models have been assessed by comparing the prognostic scalar and vector fields as an independent CTD data set and with real drifter trajectories acquired during SG1. The diagnosed and prognosed circulation reveals that the area was characterised by water masses of Atlantic origin influenced by small mesoscale cyclonic and anti-cyclonic eddies, which govern the spatial and temporal evolution of the drifter trajectories and of the water masses distribution. The assimilation of CTD data into the initial conditions of the high resolution model highly improves the accuracy of the short-term forecast in terms of location and structure of the thermocline and positively influence the ability of the model in reproducing the observed paths of the surface drifters.

  14. Studying the Origin of the Kuroshio with an Array of ADCP-CTD Moorings

    Science.gov (United States)

    2014-09-30

    ADCP-CTD Moorings Ren-Chieh Lien Applied Physics Laboratory University of Washington 1013 NE 40th Street Seattle, Washington 98105 Phone: (206...APPROACH An array of six subsurface moorings was deployed in June 2012 northeast of the Philippines, where the strong Kuroshio enters Luzon Strait...All moorings were recovered in June 2013. Each mooring had an Acoustic Doppler Current Profiler (ADCP) to measure the velocity field in the upper

  15. The Kinematic and Spectral Ages of the Compact Radio Source CTD 93

    CERN Document Server

    Nagai, H; Asada, K; Kameno, S; Doi, A; Nagai, Hiroshi; Inoue, Makoto; Asada, Keiichi; Kameno, Seiji; Doi, Akihiro

    2006-01-01

    We present a study of the kinematic and spectral ages of the Gigahertz-Peaked Spectrum (GPS) source CTD~93. Measurements of the hot spot separation over 8.5 yr show evidence of an increase. The separation rate along the source axis is 0.34$\\pm0.11c$ (H$_{0}$=72 km s$^{-1}$ Mpc$^{-1}$), which results in a kinematic age of 2200$\\pm$700 yr. Assuming that two hot spots are moving apart at equal speeds, we derive an advance speed of 0.17$\\pm0.06c$. The radio lobe spectra show a high frequency steepening, as expected if energetic electrons lose energy by synchrotron radiation. The spectral break decreases with the distance from the hot spot in the northern component of CTD~93. This tendency is expected from the basic scenario of radio lobe evolution involving particle acceleration at the hot spots, with the radio lobes populated by high energy electrons which have leaked from the hot spots. Although a core-jet morphology for CTD~93 has previously been proposed, these results indicate that the morphology is similar ...

  16. Structural basis for the recognition of RNA polymerase II C-terminal domain by CREPT and p15RS.

    Science.gov (United States)

    Mei, Kunrong; Jin, Zhe; Ren, Fangli; Wang, Yinying; Chang, Zhijie; Wang, Xinquan

    2014-01-01

    CREPT and p15RS are two recently identified homologous proteins that regulate cell proliferation in an opposite way and are closely related to human cancer development. Both CREPT and p15RS consist of an N-terminal RPR domain and a C-terminal domain with high sequence homology. The transcription enhancement by CREPT is attributed to its interaction with RNA polymerase II (Pol II). Here we provide biochemical and structural evidence to support and extend this molecular mechanism. Through fluorescence polarization analysis, we show that the RPR domains of CREPT and p15RS (CREPT-RPR and p15RS-RPR) bind to different Pol II C-terminal domain (CTD) phosphoisoforms with similar affinity and specificity. We also determined the crystal structure of p15RS-RPR. Sequence and structural comparisons with RPR domain of Rtt103, a homolog of CREPT and p15RS in yeast, reveal structural basis for the similar binding profile of CREPT-RPR and p15RS-RPR with Pol II CTD. We also determined the crystal structure of the C-terminal domain of CREPT (CREPT-CTD), which is a long rod-like dimer and each monomer adopts a coiled-coil structure. We propose that dimerization through the C-terminal domain enhances the binding strength between CREPT or p15RS with Pol II by increasing binding avidity. Our results collectively reveal the respective roles of N-terminal RPR domain and C-terminal domain of CREPT and p15RS in recognizing RNA Pol II.

  17. The C-Terminal Domain of Eukaryotic Initiation Factor 5 Promotes Start Codon Recognition by Its Dynamic Interplay with eIF1 and eIF2β

    Directory of Open Access Journals (Sweden)

    Rafael E. Luna

    2012-06-01

    Full Text Available Recognition of the proper start codon on mRNAs is essential for protein synthesis, which requires scanning and involves eukaryotic initiation factors (eIFs eIF1, eIF1A, eIF2, and eIF5. The carboxyl terminal domain (CTD of eIF5 stimulates 43S preinitiation complex (PIC assembly; however, its precise role in scanning and start codon selection has remained unknown. Using nuclear magnetic resonance (NMR spectroscopy, we identified the binding sites of eIF1 and eIF2β on eIF5-CTD and found that they partially overlapped. Mutating select eIF5 residues in the common interface specifically disrupts interaction with both factors. Genetic and biochemical evidence indicates that these eIF5-CTD mutations impair start codon recognition and impede eIF1 release from the PIC by abrogating eIF5-CTD binding to eIF2β. This study provides mechanistic insight into the role of eIF5-CTD's dynamic interplay with eIF1 and eIF2β in switching PICs from an open to a closed state at start codons.

  18. Repeating the Past

    Science.gov (United States)

    Moore, John W.

    1998-05-01

    As part of the celebration of the Journal 's 75th year, we are scanning each Journal issue from 25, 50, and 74 years ago. Many of the ideas and practices described are so similar to present-day "innovations" that George Santayana's adage (1) "Those who cannot remember the past are condemned to repeat it" comes to mind. But perhaps "condemned" is too strong - sometimes it may be valuable to repeat something that was done long ago. One example comes from the earliest days of the Division of Chemical Education and of the Journal.

  19. 锚蛋白重复和激酶域1基因多态性与精神分裂症的关联研究%Association study of schizophrenia and ankyrin repeat and kinase domain containing 1 gene polymorphism

    Institute of Scientific and Technical Information of China (English)

    郭娟; 陈元堂; 何长江; 张丽; 吴瑜; 行养玲; 敖磊

    2010-01-01

    目的 探讨锚蛋白重复和激酶域1(ANKK1)基因多态性与精神分裂症的相关性.方法 收集符合美国DSM-Ⅳ精神分裂症诊断标准的112个先证者及其父母组成的核心家系,运用聚合酶链反应扩增及单核苷酸多态性的分子生物学技术,对ANK K1基因的rs4938015、rs7118900、rs2734849、rs1800497多态性分型,进行精神分裂症与锚蛋白重复和激酶域1基因多态性的关联分析和单体型相对风险率分析.结果 rs2734849等位基因与精神分裂症相关联(P=0.026),其中等位基因T是保护因素(Z=-2.19),A为危险因素(Z=2.19);rs4938015、rs7118900、rs1800497与精神分裂症无关联.三种单体型rs7118900-rs2734849的G/A、rs 2734849-rs1800497的A/C、rs7118900-rs2734849-rs1800497中的G/A/C与精神分裂症有关联(P值分别为0.032,0.041,0.046,基因型频率分别为0.36,0.29,0.17).结论 ANKK1基因与精神分裂症相关联.%Objective To detect the genetic association between schizophrenia and polymorphism of Ankyrin repeat and kinase domain containing 1 ( ANKK1 ) gene. Methods Observed in a sample of 112 parent/offspring trios where the proband net the American Classification and diagnostic Criteria for Mental Disorders The Forth Revised Edition, criteria for schizophrenia using correlation analysis and haplotype relative risk analysis. The polymorphism of Ankyrin repeat and kinase domain containing 1 gene was detected with PCR methods and SNP typing in all nucleus families. Results The rs2734849 allele was connected with schizophrenia(P= 0. 026). Allele T was protective factor( Z= -2.19) and allele A was the hazard factor( Z=2. 19). The rs4938015,rs7118900 and rs1800497 allele were independence with schizophrenia. Three kinds haplotypes of G/A in the rs7118900 -rs2734849, A/C in the rs2734849 -rs1800497, G/A/C in the rs7118900 -rs2734849 -rs1800497 were associated with schizophrenia ( The P values were 0.032,0. 041,0.046, the genotype frequencies were 0. 36,0.29,0. 17

  20. Disease-Homologous Mutation in the Cation Diffusion Facilitator Protein MamM Causes Single-Domain Structural Loss and Signifies Its Importance.

    Science.gov (United States)

    Barber-Zucker, Shiran; Uebe, René; Davidov, Geula; Navon, Yotam; Sherf, Dror; Chill, Jordan H; Kass, Itamar; Bitton, Ronit; Schüler, Dirk; Zarivach, Raz

    2016-08-23

    Cation diffusion facilitators (CDF) are highly conserved, metal ion efflux transporters that maintain divalent transition metal cation homeostasis. Most CDF proteins contain two domains, the cation transporting transmembrane domain and the regulatory cytoplasmic C-terminal domain (CTD). MamM is a magnetosome-associated CDF protein essential for the biomineralization of magnetic iron-oxide particles in magnetotactic bacteria. To investigate the structure-function relationship of CDF cytoplasmic domains, we characterized a MamM M250P mutation that is synonymous with the disease-related mutation L349P of the human CDF protein ZnT-10. Our results show that the M250P exchange in MamM causes severe structural changes in its CTD resulting in abnormal reduced function. Our in vivo, in vitro and in silico studies indicate that the CTD fold is critical for CDF proteins' proper function and support the previously suggested role of the CDF cytoplasmic domain as a CDF regulatory element. Based on our results, we also suggest a mechanism for the effects of the ZnT-10 L349P mutation in human.

  1. Role of Autoantibodies in the Diagnosis of Connective-Tissue Disease ILD (CTD-ILD and Interstitial Pneumonia with Autoimmune Features (IPAF

    Directory of Open Access Journals (Sweden)

    Adelle S. Jee

    2017-05-01

    Full Text Available The diagnosis of interstitial lung disease (ILD requires meticulous evaluation for an underlying connective tissue disease (CTD, with major implications for prognosis and management. CTD associated ILD (CTD-ILD occurs most commonly in the context of an established CTD, but can be the first and/or only manifestation of an occult CTD or occur in patients who have features suggestive of an autoimmune process, but not meeting diagnostic criteria for a defined CTD—recently defined as “interstitial pneumonia with autoimmune features” (IPAF. The detection of specific autoantibodies serves a critical role in the diagnosis of CTD-ILD, but there remains a lack of data to guide clinical practice including which autoantibodies should be tested on initial assessment and when or in whom serial testing should be performed. The implications of detecting autoantibodies in patients with IPAF on disease behaviour and management remain unknown. The evaluation of CTD-ILD is challenging due to the heterogeneity of presentations and types of CTD and ILD that may be encountered, and thus it is imperative that immunologic tests are interpreted in conjunction with a detailed rheumatologic history and examination and multidisciplinary collaboration between respiratory physicians, rheumatologists, immunologists, radiologists and pathologists.

  2. A Novel Domain in Translational GTPase BipA Mediates Interaction with the 70S Ribosome and Influences GTP Hydrolysis

    Energy Technology Data Exchange (ETDEWEB)

    deLivron, M.; Makanji, H; Lane, M; Robinson, V

    2009-01-01

    BipA is a universally conserved prokaryotic GTPase that exhibits differential ribosome association in response to stress-related events. It is a member of the translation factor family of GTPases along with EF-G and LepA. BipA has five domains. The N-terminal region of the protein, consisting of GTPase and {beta}-barrel domains, is common to all translational GTPases. BipA domains III and V have structural counterparts in EF-G and LepA. However, the C-terminal domain (CTD) of the protein is unique to the BipA family. To investigate how the individual domains of BipA contribute to the biological properties of the protein, deletion constructs were designed and their GTP hydrolysis and ribosome binding properties assessed. Data presented show that removal of the CTD abolishes the ability of BipA to bind to the ribosome and that ribosome complex formation requires the surface provided by domains III and V and the CTD. Additional mutational analysis was used to outline the BipA-70S interaction surface extending across these domains. Steady state kinetic analyses revealed that successive truncation of domains from the C-terminus resulted in a significant increase in the intrinsic GTP hydrolysis rate and a loss of ribosome-stimulated GTPase activity. These results indicate that, similar to other translational GTPases, the ribosome binding and GTPase activities of BipA are tightly coupled. Such intermolecular regulation likely plays a role in the differential ribosome binding by the protein.

  3. A novel domain in translational GTPase BipA mediates interaction with the 70S ribosome and influences GTP hydrolysis.

    Science.gov (United States)

    deLivron, Megan A; Makanji, Heeren S; Lane, Maura C; Robinson, Victoria L

    2009-11-10

    BipA is a universally conserved prokaryotic GTPase that exhibits differential ribosome association in response to stress-related events. It is a member of the translation factor family of GTPases along with EF-G and LepA. BipA has five domains. The N-terminal region of the protein, consisting of GTPase and beta-barrel domains, is common to all translational GTPases. BipA domains III and V have structural counterparts in EF-G and LepA. However, the C-terminal domain (CTD) of the protein is unique to the BipA family. To investigate how the individual domains of BipA contribute to the biological properties of the protein, deletion constructs were designed and their GTP hydrolysis and ribosome binding properties assessed. Data presented show that removal of the CTD abolishes the ability of BipA to bind to the ribosome and that ribosome complex formation requires the surface provided by domains III and V and the CTD. Additional mutational analysis was used to outline the BipA-70S interaction surface extending across these domains. Steady state kinetic analyses revealed that successive truncation of domains from the C-terminus resulted in a significant increase in the intrinsic GTP hydrolysis rate and a loss of ribosome-stimulated GTPase activity. These results indicate that, similar to other translational GTPases, the ribosome binding and GTPase activities of BipA are tightly coupled. Such intermolecular regulation likely plays a role in the differential ribosome binding by the protein.

  4. All-optical repeater.

    Science.gov (United States)

    Silberberg, Y

    1986-06-01

    An all-optical device containing saturable gain, saturable loss, and unsaturable loss is shown to transform weak, distorted optical pulses into uniform standard-shape pulses. The proposed device performs thresholding, amplification, and pulse shaping as required from an optical repeater. It is shown that such a device could be realized by existing semiconductor technology.

  5. Bidirectional Manchester repeater

    Science.gov (United States)

    Ferguson, J.

    1980-01-01

    Bidirectional Manchester repeater is inserted at periodic intervals along single bidirectional twisted pair transmission line to detect, amplify, and transmit bidirectional Manchester 11 code signals. Requiring only 18 TTL 7400 series IC's, some line receivers and drivers, and handful of passive components, circuit is simple and relatively inexpensive to build.

  6. Cell-Free Hepatitis B Virus Capsid Assembly Dependent on the Core Protein C-Terminal Domain and Regulated by Phosphorylation

    Science.gov (United States)

    Ludgate, Laurie; Liu, Kuancheng; Luckenbaugh, Laurie; Streck, Nicholas; Eng, Stacey; Voitenleitner, Christian; Delaney, William E.

    2016-01-01

    ABSTRACT Multiple subunits of the hepatitis B virus (HBV) core protein (HBc) assemble into an icosahedral capsid that packages the viral pregenomic RNA (pgRNA). The N-terminal domain (NTD) of HBc is sufficient for capsid assembly, in the absence of pgRNA or any other viral or host factors, under conditions of high HBc and/or salt concentrations. The C-terminal domain (CTD) is deemed dispensable for capsid assembly although it is essential for pgRNA packaging. We report here that HBc expressed in a mammalian cell lysate, rabbit reticulocyte lysate (RRL), was able to assemble into capsids when (low-nanomolar) HBc concentrations mimicked those achieved under conditions of viral replication in vivo and were far below those used previously for capsid assembly in vitro. Furthermore, at physiologically low HBc concentrations in RRL, the NTD was insufficient for capsid assembly and the CTD was also required. The CTD likely facilitated assembly under these conditions via RNA binding and protein-protein interactions. Moreover, the CTD underwent phosphorylation and dephosphorylation events in RRL similar to those seen in vivo which regulated capsid assembly. Importantly, the NTD alone also failed to accumulate in mammalian cells, likely resulting from its failure to assemble efficiently. Coexpression of the full-length HBc rescued NTD assembly in RRL as well as NTD expression and assembly in mammalian cells, resulting in the formation of mosaic capsids containing both full-length HBc and the NTD. These results have important implications for HBV assembly during replication and provide a facile cell-free system to study capsid assembly under physiologically relevant conditions, including its modulation by host factors. IMPORTANCE Hepatitis B virus (HBV) is an important global human pathogen and the main cause of liver cancer worldwide. An essential component of HBV is the spherical capsid composed of multiple copies of a single protein, the core protein (HBc). We have

  7. RepeatsDB 2.0: improved annotation, classification, search and visualization of repeat protein structures

    Science.gov (United States)

    Paladin, Lisanna; Hirsh, Layla; Piovesan, Damiano; Andrade-Navarro, Miguel A.; Kajava, Andrey V.; Tosatto, Silvio C.E.

    2017-01-01

    RepeatsDB 2.0 (URL: http://repeatsdb.bio.unipd.it/) is an update of the database of annotated tandem repeat protein structures. Repeat proteins are a widespread class of non-globular proteins carrying heterogeneous functions involved in several diseases. Here we provide a new version of RepeatsDB with an improved classification schema including high quality annotations for ∼5400 protein structures. RepeatsDB 2.0 features information on start and end positions for the repeat regions and units for all entries. The extensive growth of repeat unit characterization was possible by applying the novel ReUPred annotation method over the entire Protein Data Bank, with data quality is guaranteed by an extensive manual validation for >60% of the entries. The updated web interface includes a new search engine for complex queries and a fully re-designed entry page for a better overview of structural data. It is now possible to compare unit positions, together with secondary structure, fold information and Pfam domains. Moreover, a new classification level has been introduced on top of the existing scheme as an independent layer for sequence similarity relationships at 40%, 60% and 90% identity. PMID:27899671

  8. Multi-domain proteins in the three kingdoms of life: orphan domains and other unassigned regions.

    Science.gov (United States)

    Ekman, Diana; Björklund, Asa K; Frey-Skött, Johannes; Elofsson, Arne

    2005-04-22

    Comparative studies of the proteomes from different organisms have provided valuable information about protein domain distribution in the kingdoms of life. Earlier studies have been limited by the fact that only about 50% of the proteomes could be matched to a domain. Here, we have extended these studies by including less well-defined domain definitions, Pfam-B and clustered domains, MAS, in addition to Pfam-A and SCOP domains. It was found that a significant fraction of these domain families are homologous to Pfam-A or SCOP domains. Further, we show that all regions that do not match a Pfam-A or SCOP domain contain a significantly higher fraction of disordered structure. These unstructured regions may be contained within orphan domains or function as linkers between structured domains. Using several different definitions we have re-estimated the number of multi-domain proteins in different organisms and found that several methods all predict that eukaryotes have approximately 65% multi-domain proteins, while the prokaryotes consist of approximately 40% multi-domain proteins. However, these numbers are strongly dependent on the exact choice of cut-off for domains in unassigned regions. In conclusion, all eukaryotes have similar fractions of multi-domain proteins and disorder, whereas a high fraction of repeating domain is distinguished only in multicellular eukaryotes. This implies a role for repeats in cell-cell contacts while the other two features are important for intracellular functions.

  9. Transcription of lncRNA prt, clustered prt RNA sites for Mmi1 binding, and RNA polymerase II CTD phospho-sites govern the repression of pho1 gene expression under phosphate-replete conditions in fission yeast.

    Science.gov (United States)

    Chatterjee, Debashree; Sanchez, Ana M; Goldgur, Yehuda; Shuman, Stewart; Schwer, Beate

    2016-07-01

    Expression of fission yeast Pho1 acid phosphatase is repressed during growth in phosphate-rich medium. Repression is mediated by transcription of the prt locus upstream of pho1 to produce a long noncoding (lnc) prt RNA. Repression is also governed by RNA polymerase II CTD phosphorylation status, whereby inability to place a Ser7-PO4 mark (as in S7A) derepresses Pho1 expression, and inability to place a Thr4-PO4 mark (as in T4A) hyper-represses Pho1 in phosphate replete cells. Here we find that basal pho1 expression from the prt-pho1 locus is inversely correlated with the activity of the prt promoter, which resides in a 110-nucleotide DNA segment preceding the prt transcription start site. CTD mutations S7A and T4A had no effect on the activity of the prt promoter or the pho1 promoter, suggesting that S7A and T4A affect post-initiation events in prt lncRNA synthesis that make it less and more repressive of pho1, respectively. prt lncRNA contains clusters of DSR (determinant of selective removal) sequences recognized by the YTH-domain-containing protein Mmi1. Altering the nucleobase sequence of two DSR clusters in the prt lncRNA caused hyper-repression of pho1 in phosphate replete cells, concomitant with increased levels of the prt transcript. The isolated Mmi1 YTH domain binds to RNAs with single or tandem DSR elements, to the latter in a noncooperative fashion. We report the 1.75 Å crystal structure of the Mmi1 YTH domain and provide evidence that Mmi1 recognizes DSR RNA via a binding mode distinct from that of structurally homologous YTH proteins that recognize m(6)A-modified RNA.

  10. Duct Leakage Repeatability Testing

    Energy Technology Data Exchange (ETDEWEB)

    Walker, Iain [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Sherman, Max [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

    2014-01-01

    Duct leakage often needs to be measured to demonstrate compliance with requirements or to determine energy or Indoor Air Quality (IAQ) impacts. Testing is often done using standards such as ASTM E1554 (ASTM 2013) or California Title 24 (California Energy Commission 2013 & 2013b), but there are several choices of methods available within the accepted standards. Determining which method to use or not use requires an evaluation of those methods in the context of the particular needs. Three factors that are important considerations are the cost of the measurement, the accuracy of the measurement and the repeatability of the measurement. The purpose of this report is to evaluate the repeatability of the three most significant measurement techniques using data from the literature and recently obtained field data. We will also briefly discuss the first two factors. The main question to be answered by this study is to determine if differences in the repeatability of these tests methods is sufficient to indicate that any of these methods is so poor that it should be excluded from consideration as an allowed procedure in codes and standards.

  11. Technical Note: Animal-borne CTD-Satellite Relay Data Loggers for real-time oceanographic data collection

    Directory of Open Access Journals (Sweden)

    L. Boehme

    2009-06-01

    Full Text Available The increasing need for continuous monitoring of the world oceans has stimulated the development of a range of autonomous sampling platforms. One novel addition to these approaches is a small, relatively inexpensive data-relaying device that can be deployed on marine mammals to provide vertical oceanographic profiles throughout the upper 2000 m of the water column. When an animal dives, the CTD-Satellite Relay Data Logger (CTD-SRDL records vertical profiles of temperature, conductivity and pressure. Data are compressed once the animal returns to the surface where it is located by, and relays data to, the Argos satellite system. The technical challenges met in the design of the CTD-SRDL are the maximising of energy efficiency by minimising size, whilst simultaneously maintaining the reliability of an instrument that cannot be recovered and is required to survive its lifetime attached to a marine mammal. The CTD-SRDLs record temperature and salinity with an accuracy of better than 0.005°C and 0.02 respectively. However, due to the limited availability of reference data for post-processing, data are often associated with slightly higher errors. The potential to collect large numbers of profiles cost-effectively makes data collection using CTD-SRDL technology particularly beneficial in regions where traditional oceanographic measurements are scarce. Depending on the CTD-SRDL configuration, it is possible to sample and transmit hydrographic profiles on a daily basis, providing valuable and often unique information for a real-time ocean observing system.

  12. A triclinic crystal structure of the carboxy-terminal domain of HIV-1 capsid protein with four molecules in the asymmetric unit reveals a novel packing interface

    Science.gov (United States)

    Lampel, Ayala; Yaniv, Oren; Berger, Or; Bacharach, Eran; Gazit, Ehud; Frolow, Felix

    2013-01-01

    The Gag precursor is the major structural protein of the virion of human immunodeficiency virus-1 (HIV-1). Capsid protein (CA), a cleavage product of Gag, plays an essential role in virus assembly both in Gag-precursor multimerization and in capsid core formation. The carboxy-terminal domain (CTD) of CA contains 20 residues that are highly conserved across retroviruses and constitute the major homology region (MHR). Genetic evidence implies a role for the MHR in interactions between Gag precursors during the assembly of the virus, but the structural basis for this role remains elusive. This paper describes a novel triclinic structure of the HIV-1 CA CTD at 1.6 Å resolution with two canonical dimers of CA CTD in the asymmetric unit. The canonical dimers form a newly identified packing interface where interactions of four conserved MHR residues take place. This is the first structural indication that these MHR residues participate in the putative CTD–CTD interactions. These findings suggest that the molecules forming this novel interface resemble an intermediate structure that participates in the early steps of HIV-1 assembly. This interface may therefore provide a novel target for antiviral drugs. PMID:23722834

  13. Implementing Marine XML for Observed CTD Data in a Marine Data Exchange Platform

    Institute of Scientific and Technical Information of China (English)

    JIANG Yongguo; FENG Yuan; CHE Zhaodong; ZHU Tieyi

    2008-01-01

    In order to archive,quality control and disseminate a large variety of marine data in a marine data exchange platform,a marine XML has been developed to encapsulate marine data,which provides an efficient means to store,transfer and display marine data.This paper first presents the details of the main marine XML elements and then gives an example showing how to transform CTD-observed data into Marine XML format,which illustrates the XML encapsulation process of marine observed data.

  14. Zinc-finger directed double-strand breaks within CAG repeat tracts promote repeat instability in human cells.

    Science.gov (United States)

    Mittelman, David; Moye, Christopher; Morton, Jason; Sykoudis, Kristen; Lin, Yunfu; Carroll, Dana; Wilson, John H

    2009-06-16

    Expanded triplet repeats have been identified as the genetic basis for a growing number of neurological and skeletal disorders. To examine the contribution of double-strand break repair to CAG x CTG repeat instability in mammalian systems, we developed zinc finger nucleases (ZFNs) that recognize and cleave CAG repeat sequences. Engineered ZFNs use a tandem array of zinc fingers, fused to the FokI DNA cleavage domain, to direct double-strand breaks (DSBs) in a site-specific manner. We first determined that the ZFNs cleave CAG repeats in vitro. Then, using our previously described tissue culture assay for identifying modifiers of CAG repeat instability, we found that transfection of ZFN-expression vectors induced up to a 15-fold increase in changes to the CAG repeat in human and rodent cell lines, and that longer repeats were much more sensitive to cleavage than shorter ones. Analysis of individual colonies arising after treatment revealed a spectrum of events consistent with ZFN-induced DSBs and dominated by repeat contractions. We also found that expressing a dominant-negative form of RAD51 in combination with a ZFN, dramatically reduced the effect of the nuclease, suggesting that DSB-induced repeat instability is mediated, in part, through homology directed repair. These studies identify a ZFN as a useful reagent for characterizing the effects of DSBs on CAG repeats in cells.

  15. Repeatability of Cryogenic Multilayer Insulation

    Science.gov (United States)

    Johnson, W. L.; Vanderlaan, M.; Wood, J. J.; Rhys, N. O.; Guo, W.; Van Sciver, S.; Chato, D. J.

    2017-01-01

    Due to the variety of requirements across aerospace platforms, and one off projects, the repeatability of cryogenic multilayer insulation has never been fully established. The objective of this test program is to provide a more basic understanding of the thermal performance repeatability of MLI systems that are applicable to large scale tanks. There are several different types of repeatability that can be accounted for: these include repeatability between multiple identical blankets, repeatability of installation of the same blanket, and repeatability of a test apparatus. The focus of the work in this report is on the first two types of repeatability. Statistically, repeatability can mean many different things. In simplest form, it refers to the range of performance that a population exhibits and the average of the population. However, as more and more identical components are made (i.e. the population of concern grows), the simple range morphs into a standard deviation from an average performance. Initial repeatability testing on MLI blankets has been completed at Florida State University. Repeatability of five GRC provided coupons with 25 layers was shown to be +/- 8.4 whereas repeatability of repeatedly installing a single coupon was shown to be +/- 8.0. A second group of 10 coupons have been fabricated by Yetispace and tested by Florida State University, through the first 4 tests, the repeatability has been shown to be +/- 16. Based on detailed statistical analysis, the data has been shown to be statistically significant.

  16. 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.

  17. A multi-wavelength study of nuclear activity and environment of a low power radio galaxy CTD 86

    CERN Document Server

    Pandge, M B; Singh, K P; Patil, M K

    2012-01-01

    We present multiwavelength X-ray, optical and radio study of the Fanaroff & Riley class I radio galaxy CTD 86 based on \\xmm{}, \\rosat{}, Sloan Digital Sky Survey (SDSS), Vainu Bappu Telescope (VBT) observations and the Faint Images of the Radio Sky at Twenty centimeters (FIRST) survey. X-ray emission from CTD 86 originates from two components - diffuse thermal emission from hot gas ($kT\\sim 0.9\\kev$, $n_e\\sim 10^{-3}{\\rm cm^{-3}}$, $L_X \\sim 5\\times10^{42}{\\rm ergs s^{-1}}$ and size $\\sim 186{\\rm kpc}$), and a central point source representing the active nucleus. The hot gaseous environment of CTD 86 is similar to those found in galaxy groups or bright early-type galaxies. We found no clear signature of radio-lobes interacting with the diffuse hot gas. X-ray emission from the active nucleus is well described by an intrinsically absorbed ($N_H \\sim 5.9\\times10^{22}{\\rm cm^{-2}}$) power law ($\\Gamma \\sim 1.5$) with a $2-10\\kev$ luminosity $L_X \\sim 2.1\\times10^{42}{\\rm ergs s^{-1}}$. CTD 86 has a weak optic...

  18. Investigation of Arctic and Antarctic spatial and depth patterns of sea water in CTD profiles using chemometric data analysis

    DEFF Research Database (Denmark)

    Kotwa, Ewelina Katarzyna; Lacorte, Silvia; Duarte, Carlos

    2014-01-01

    In this paper we examine 2- and 3-way chemometric methods for analysis of Arctic and Antarctic water samples. Standard CTD (conductivity–temperature–depth) sensor devices were used during two oceanographic expeditions (July 2007 in the Arctic; February 2009 in the Antarctic) covering a total of 1...

  19. Using the Technology of Critical Thinking Development (CTD) as a Means of Forming Competencies of Students Majoring in "Life Safety"

    Science.gov (United States)

    Kayumova, Leysan R.; Morozova, Marina A.

    2016-01-01

    The relevance of the research problem is caused by the need to use various teaching methods and techniques in training students majoring in pedagogical specialties while implementing the competency approach in education. Information about the technology of critical thinking development (CTD) in future teachers training is limited, and the…

  20. Trusted Domain

    DEFF Research Database (Denmark)

    Hjorth, Theis Solberg; Torbensen, Rune

    2012-01-01

    that enables secure end-to-end communication with home automation devices, and it supports device revocations as well as a structure of intersecting sets of nodes for scalability. Devices in the Trusted Domain are registered in a list that is distributed using a robust epidemic protocol optimized...

  1. Domain crossing

    DEFF Research Database (Denmark)

    Schraefel, M. C.; Rouncefield, Mark; Kellogg, Wendy

    2012-01-01

    In CSCW, how much do we need to know about another domain/culture before we observe, intersect and intervene with designs. What optimally would that other culture need to know about us? Is this a “how long is a piece of string” question, or an inquiry where we can consider a variety of contexts a...

  2. 3.3 Å structure of Niemann–Pick C1 protein reveals insights into the function of the C-terminal luminal domain in cholesterol transport

    Energy Technology Data Exchange (ETDEWEB)

    Li, Xiaochun; Lu, Feiran; Trinh, Michael N.; Schmiege, Philip; Seemann, Joachim; Wang, Jiawei; Blobel, Günter

    2017-08-07

    Niemann–Pick C1 (NPC1) and NPC2 proteins are indispensable for the export of LDL-derived cholesterol from late endosomes. Mutations in these proteins result in Niemann–Pick type C disease, a lysosomal storage disease. Despite recent reports of the NPC1 structure depicting its overall architecture, the function of its C-terminal luminal domain (CTD) remains poorly understood even though 45% of NPC disease-causing mutations are in this domain. Here, we report a crystal structure at 3.3 Å resolution of NPC1* (residues 314–1,278), which—in contrast to previous lower resolution structures—features the entire CTD well resolved. Notably, all eight cysteines of the CTD form four disulfide bonds, one of which (C909–C914) enforces a specific loop that in turn mediates an interaction with a loop of the N-terminal domain (NTD). Importantly, this loop and its interaction with the NTD were not observed in any previous structures due to the lower resolution. Our mutagenesis experiments highlight the physiological relevance of the CTD–NTD interaction, which might function to keep the NTD in the proper orientation for receiving cholesterol from NPC2. Additionally, this structure allows us to more precisely map all of the disease-causing mutations, allowing future molecular insights into the pathogenesis of NPC disease.

  3. Text mining and manual curation of chemical-gene-disease networks for the comparative toxicogenomics database (CTD).

    Science.gov (United States)

    Wiegers, Thomas C; Davis, Allan Peter; Cohen, K Bretonnel; Hirschman, Lynette; Mattingly, Carolyn J

    2009-10-08

    The Comparative Toxicogenomics Database (CTD) is a publicly available resource that promotes understanding about the etiology of environmental diseases. It provides manually curated chemical-gene/protein interactions and chemical- and gene-disease relationships from the peer-reviewed, published literature. The goals of the research reported here were to establish a baseline analysis of current CTD curation, develop a text-mining prototype from readily available open source components, and evaluate its potential value in augmenting curation efficiency and increasing data coverage. Prototype text-mining applications were developed and evaluated using a CTD data set consisting of manually curated molecular interactions and relationships from 1,600 documents. Preliminary results indicated that the prototype found 80% of the gene, chemical, and disease terms appearing in curated interactions. These terms were used to re-rank documents for curation, resulting in increases in mean average precision (63% for the baseline vs. 73% for a rule-based re-ranking), and in the correlation coefficient of rank vs. number of curatable interactions per document (baseline 0.14 vs. 0.38 for the rule-based re-ranking). This text-mining project is unique in its integration of existing tools into a single workflow with direct application to CTD. We performed a baseline assessment of the inter-curator consistency and coverage in CTD, which allowed us to measure the potential of these integrated tools to improve prioritization of journal articles for manual curation. Our study presents a feasible and cost-effective approach for developing a text mining solution to enhance manual curation throughput and efficiency.

  4. The solution structure of the C-terminal domain of TonB and interaction studies with TonB box peptides.

    Science.gov (United States)

    Sean Peacock, R; Weljie, Aalim M; Peter Howard, S; Price, Feodor D; Vogel, Hans J

    2005-02-04

    The TonB protein transduces energy from the proton gradient across the cytoplasmic membrane of Gram-negative bacteria to TonB-dependent outer membrane receptors. It is a critically important protein in iron uptake, and deletion of this protein is known to decrease virulence of bacteria in animal models. This system has been used for Trojan horse antibiotic delivery. Here, we describe the high-resolution solution structure of Escherichia coli TonB residues 103-239 (TonB-CTD). TonB-CTD is monomeric with an unstructured N terminus (103-151) and a well structured C terminus (152-239). The structure contains a four-stranded antiparallel beta-sheet packed against two alpha-helices and an extended strand in a configuration homologous to the C-terminal domain of the TolA protein. Chemical shift perturbations to the TonB-CTD (1)H-(15)N HSCQ spectrum titrated with TonB box peptides modeled from the E.coli FhuA, FepA and BtuB proteins were all equivalent, indicating that all three peptides bind to the same region of TonB. Isothermal titration calorimetry measurements demonstrate that TonB-CTD interacts with the FhuA-derived peptide with a K(D)=36(+/-7) microM. On the basis of chemical shift data, the position of Gln160, and comparison to the TolA gp3 N1 complex crystal structure, we propose that the TonB box binds to TonB-CTD along the beta3-strand.

  5. CRED Shallow CTD Profiles; Ta'u, American Samoa; Cruise: HA1201_LEGII&III, Data Date Range: 20120422-20120423 (NODC Accession 0107470)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data...

  6. CRED Shallow CTD Profiles; Ta'u, American Samoa; Cruise: HI0802, Data Date Range: 20080301-20080303 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  7. CRED Shallow CTD Profiles; Ta'u, American Samoa; Cruise: TC0201_LEGII, Data Date Range: 20020211-20020213 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  8. Temperature profile, pressure, and chemical data from XBT, bottle, CTD casts in the Arctic Ocean from 06 May 2003 to 06 May 2004 (NODC Accession 0002203)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Temperature profile, pressure, and chemical data were collected using XBT, bottle, and CTD casts in the Arctic Ocean from May 6, 2003 to May 5, 2004. Data were...

  9. CRED Shallow CTD Profiles; Johnston Atoll, Pacific Remote Island Areas; Cruise: HI0601, Data Date Range: 20060122-20060123 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  10. NODC Standard Product: Texas-Louisiana Shelf Circulation and Transport Processes Study: Current Meter, Meteorological Buoy, XBT/XSV/XCP/CTD/IES (NODC Accession 9700319)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This package contains current direction/velocity, water temperature, air temperature, salinity, and other data which were collected using current meter, CTD casts,...

  11. CRED Shallow CTD Profiles; Rota, Commonwealth of the Northern Mariana Islands; Cruise: OES0307, Data Date Range: 20030918-20030920 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  12. CRED Shallow CTD Profiles; Howland Island, Pacific Remote Island Areas; Cruise: HI0801, Data Date Range: 20080206-20080207 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  13. CRED Shallow CTD Profiles; Maui - Molokini, Main Hawaiian Islands; Cruise: HI0505, Data Date Range: 20050806-20050806 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  14. CRED Shallow CTD Profiles; French Frigate Shoals, Northwestern Hawaiian Islands (Papahanaumokuakea Marine National Monument); Cruise: TC0207, Data Date Range: 20020913-20020914 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  15. CRED Shallow CTD Profiles; Saipan, Commonwealth of the Northern Mariana Islands; Cruise: OES0307, Data Date Range: 20030821-20030822 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  16. CRED Shallow CTD Profiles; Anatahan, Commonwealth of the Northern Mariana Islands; Cruise: HI0703, Data Date Range: 20070527-20070527 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  17. CRED Shallow CTD Profiles; Rose Atoll, American Samoa; Cruise: HI1001_LEGII, Data Date Range: 20100302-20100306 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  18. CRED Shallow CTD Profiles; Jarvis Island, Pacific Remote Island Areas; Cruise: OES0404, Data Date Range: 20040327-20040328 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  19. CRED Shallow CTD Profiles; Asuncion Island, Commonwealth of the Northern Mariana Islands; Cruise: HI0703, Data Date Range: 20070603-20070604 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  20. CRED Shallow CTD Profiles; Ta'u, American Samoa; Cruise: OES0402, Data Date Range: 20040204-20040205 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  1. CRED Shallow CTD Profiles; Kingman Reef, Pacific Remote Island Areas; Cruise: HI0604, Data Date Range: 20060330-20060403 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  2. CRED Shallow CTD Profiles; Pearl and Hermes Atoll, Northwestern Hawaiian Islands (Papahanaumokuakea Marine National Monument); Cruise: HI0611, Data Date Range: 20060913-20060923 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  3. CRED Shallow CTD Profiles; Farallon de Pajaros, Commonwealth of the Northern Mariana Islands; Cruise: OES0307, Data Date Range: 20030830-20030830 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  4. CRED Shallow CTD Profiles; Guguan, Commonwealth of the Northern Mariana Islands; Cruise: OES0511, Data Date Range: 20050905-20050905 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  5. CRED Shallow CTD Profiles; Agrihan, Commonwealth of the Northern Mariana Islands; Cruise: HI0903, Data Date Range: 20090501-20090502 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  6. CRED Shallow CTD Profiles; Tinian, Commonwealth of the Northern Mariana Islands; Cruise: OES0511, Data Date Range: 20050925-20050927 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  7. CRED Shallow CTD Profiles; Anatahan, Commonwealth of the Northern Mariana Islands; Cruise: OES0511, Data Date Range: 20050922-20050923 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  8. CRED Shallow CTD Profiles; Saipan, Commonwealth of the Northern Mariana Islands; Cruise: OES0511, Data Date Range: 20050903-20050922 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  9. CRED Shallow CTD Profiles; Sarigan, Commonwealth of the Northern Mariana Islands; Cruise: OES0511, Data Date Range: 20050917-20050918 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  10. CRED Shallow CTD Profiles; Pagan, Commonwealth of the Northern Mariana Islands; Cruise: HA1101_LEGII, Data Date Range: 20110411-20110413. (NODC Accession 0107470)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  11. CRED Shallow CTD Profiles; Swains Island, American Samoa; Cruise: TC0201_LEGII, Data Date Range: 20020220-20020220 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  12. CRED Shallow CTD Profiles; Farallon de Pajaros, Commonwealth of the Northern Mariana Islands; Cruise: HI0703, Data Date Range: 20070602-20070603 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  13. CRED Shallow CTD Profiles; Laysan Island, Northwestern Hawaiian Islands (Papahanaumokuakea Marine National Monument); Cruise: HI0401, Data Date Range: 20040924-20040924 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  14. Temperature profile data from CTD casts from the NOAA WHITING in the Northwest Atlantic Ocean from 1998-07-05 to 1998-11-13 (NODC Accession 9800198)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Temperature profile data were collected using CTD casts from the NOAA WHITING in the Northwest Atlantic Ocean from July 5, 1998 to November 13, 1998. Data were...

  15. Temperature and salinity profiles from CTD casts from ALPHA HELIX from NE Pacific (limit-180) from 09 February 1991 to 25 February 1991 (NODC Accession 9100097)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CTD data was collected from the R/V ALPHA HELIX from the NE Pacific (limit-180). Data were collected by the University of Alaska - Fairbanks; Institute of Marine...

  16. Physical, chemical and optical data collected from CTD casts and other instruments in southwestern Lake Michigan, 1/30/1998 - 10/24/2002 (NODC Accession 0002064)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Physical, chemical and optical data were collected with CTD casts in southwestern Lake Michigan from January 30, 1998 to October 24, 2002. Dr. Russel L. Cuhel of the...

  17. Salinity, sound velocity, and other data from CTD, XBT, XSV, AXBT, and XCTD casts from 20 May 1978 to 01 September 2000 (NODC Accession 0000383)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Salinity, sound velocity, depth, and temperature data were collected using CTD, XBT, XSV, AXBT, and XCTD casts from May 20, 1978 to September 1, 2000. Data were...

  18. CTD observations off Oregon and California : R/V Wecoma, W8201B, 28 January to 6 February 1982 (NODC Accession 8300065)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Temperature profile were collected using CTD casts from the R.V. WECOMA and other platforms in the coastal waters of Oregon and California from 28 January 1982 to 04...

  19. CRED Shallow CTD Profiles; Midway Atoll, Northwestern Hawaiian Islands (Papahanaumokuakea Marine National Monument); Cruise: OES0306, Data Date Range: 20030729-20030808 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  20. CRED Shallow CTD Profiles; Saipan, Commonwealth of the Northern Mariana Islands; Cruise: HI0903, Data Date Range: 20090414-20090420 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  1. CRED Shallow CTD Profiles; Asuncion Island, Commonwealth of the Northern Mariana Islands; Cruise: HI0903, Data Date Range: 20090424-20090426 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  2. CRED Shallow CTD Profiles; Lisianski Island, Northwestern Hawaiian Islands (Papahanaumokuakea Marine National Monument); Cruise: HI0809, Data Date Range: 20081005-20081006 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  3. CRED Shallow CTD Profiles; Ofu and Olosega Islands, American Samoa; Cruise: HI1001_LEGII, Data Date Range: 20100310-20100320 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  4. CRED Shallow CTD Profiles; Ofu and Olosega Islands, American Samoa; Cruise: OES0402, Data Date Range: 20040206-20040213 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  5. CRED Shallow CTD Profiles; Maro Reef, Northwestern Hawaiian Islands (Papahanaumokuakea Marine National Monument); Cruise: HI0401, Data Date Range: 20040921-20040923 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  6. CRED Shallow CTD Profiles; Laysan Island, Northwestern Hawaiian Islands (Papahanaumokuakea Marine National Monument); Cruise: OES0306, Data Date Range: 20030723-20030724 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  7. CRED Shallow CTD Profiles; Guguan, Commonwealth of the Northern Mariana Islands; Cruise: HI0703, Data Date Range: 20070607-20070608 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  8. CRED Shallow CTD Profiles; Pagan, Commonwealth of the Northern Mariana Islands; Cruise: OES0307, Data Date Range: 20030825-20030908 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  9. CRED Shallow CTD Profiles; Ofu and Olosega Islands, American Samoa; Cruise: HI0802, Data Date Range: 20080229-20080229 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  10. CRED Shallow CTD Profiles; Kaua'i, Main Hawaiian Islands; Cruise: OES0810, Data Date Range: 20081105-20081108 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  11. CRED Shallow CTD Profiles; Maug, Commonwealth of the Northern Mariana Islands; Cruise: OES0511, Data Date Range: 20050911-20050912 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  12. Physical, nutrients, and other data from CTD, MBT, XBT, and bottle casts from the Indian Ocean from 01 January 1976 to 31 December 1996 (NODC Accession 0000462)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Physical, nutrients, and other data were collected from CTD, MBT, XBT, and bottle casts from the Indian Ocean. Data were collected from 01 January 1976 to 31...

  13. Temperature profile data collected using CTD casts from the JAMES CLARK ROSS in the South Atlantic Ocean from 15 November 1996 to 20 November 1996 (NODC Accession 0000874)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Temperature profile data were collected using CTD casts in the South Atlantic Ocean from JAMES CLARK ROSS. Data were collected from 15 November 1996 to 20 November...

  14. Temperature profile data collected using CTD casts from the JAMES CLARK ROSS in the South Atlantic Ocean from 15 November 1994 to 21 November 1994 (NODC Accession 0000873)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Temperature profile data were collected using CTD casts in the South Atlantic Ocean from JAMES CLARK ROSS. Data were collected from 15 November 1994 to 21 November...

  15. CRED Shallow CTD Profiles; Swains Island, American Samoa; Cruise: TC0201_LEGII, Data Date Range: 20020219-20020219 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  16. Physical, nutrients, biological, meteorological, and other data from bottle casts, CTD casts, and divers, from FIXED PLATFORMS from 06 February 1989 to 12 March 1998 (NODC Accession 9800185)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Physical, chemical, biological, meteorological, and other data were collected from bottle casts, CTD casts, and divers from FIXED PLATFORMS. Data were collected by...

  17. Profile temperature, salinity, and hydrostatic pressure from CTD casts in McMurdo Sound from 2011-11-26 to 2011-12-03 (NCEI Accession 0131073)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Full-depth CTD profiles taken on along-sound and cross-sound transects of McMurdo Sound. Eleven stations with six independent sites were visited.

  18. Temperature, salinity, oxygen, beam attenuation coefficient, and pressure measurements collected using CTD in the global ocean from 1990 to 1998 (NODC Accession 0002369)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CTD and Transmissometer data from JGOFS Programs: Equatorial Pacific (EqPac), Antarctic Polar Front Zone (APFZ), North Atlantic Bloom Experiment (NABE), Arabian Sea...

  19. Chemical data collected from THOMAS G. THOMPSON using CTD and bottle casts in Arabian Sea from 08 January 1995 to 26 November 1995 (NODC Accession 9800161)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Chemical data were collected using CTD and bottle casts in the Arabian Sea from THOMAS G. THOMPSON. Data were collected from 08 January 1995 to 26 November 1995 by...

  20. CRED Shallow CTD Profiles; Kingman Reef, Pacific Remote Island Areas; Cruise: TC0001, Data Date Range: 20000404-20000405 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  1. CRED Shallow CTD Profiles; Howland Island, Pacific Remote Island Areas; Cruise: TC0201_LEGI, Data Date Range: 20020131-20020201 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  2. CRED Shallow CTD Profiles; Jarvis Island, Pacific Remote Island Areas; Cruise: TC0001, Data Date Range: 20000326-20000326 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  3. Temperature profile, fluorescence, and other data collected using CTD casts in the Gulf of Alaska from 10 October 1997 to 17 July 1998 (NODC Accession 0000224)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Depth, fluorescence, temperature and other data were collected using CTD casts from the R/V ALPHA HELIX in the Gulf of Alaska from October 10, 1997 to July 17, 1998....

  4. Temperature profile and other data collected using CTD casts in the Southeast Atlantic Ocean from the KNORR from 13 November 1983 to 10 December 1983 (NODC Accession 8600266)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Temperature profile, salinity, pressure, and oxygen data were collected using CTD casts from the KNORR in the Southeast Atlantic Ocean. Data were collected from 13...

  5. CRED Shallow CTD Profiles; Baker Island, Pacific Remote Island Areas; Cruise: TC0001, Data Date Range: 20000319-20000320 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  6. Oceanographic temperature, salinity, oxygen, transmissivity, and PAR measurements collected using CTD from NOAA Ship McArthur II during 2007 (NCEI Accession 0034511)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Oceanographic temperature, salinity, oxygen, transmissivity, and PAR measurements collected using CTD from NOAA Ship McArthur II during 2007 as part of PACOOS.

  7. Chemical and temperature profile data from CTD casts in the East China Sea, Sea of Japan, and North Pacific Ocean (NODC Accession 9700022)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Chemical and temperature profile data were collected from CTD casts in the East China Sea, Sea of Japan, and North Pacific Ocean. Data were submitted by the Japan...

  8. CRED Shallow CTD Profiles; Lisianski Island, Northwestern Hawaiian Islands (Papahanaumokuakea Marine National Monument); Cruise: HI0401, Data Date Range: 20041009-20041011 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data...

  9. CRED Shallow CTD Profiles; Anatahan, Commonwealth of the Northern Mariana Islands; Cruise: OES0307, Data Date Range: 20030909-20030910 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data...

  10. CRED Shallow CTD Profiles; Pearl and Hermes Atoll, Northwestern Hawaiian Islands (Papahanaumokuakea Marine National Monument); Cruise: OES0306, Data Date Range: 20030730-20030802 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data...

  11. CRED Shallow CTD Profiles; Anatahan, Commonwealth of the Northern Mariana Islands; Cruise: HI0903, Data Date Range: 20090506-20090506 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data...

  12. CRED Shallow CTD Profiles; Sarigan, Commonwealth of the Northern Mariana Islands; Cruise: HI0703, Data Date Range: 20070525-20070526 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data...

  13. CRED Shallow CTD Profiles; Farallon de Pajaros, Commonwealth of the Northern Mariana Islands; Cruise: OES0511, Data Date Range: 20050909-20050910 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  14. CRED Shallow CTD Profiles; Niihau - Kaula Rock, Main Hawaiian Islands; Cruise: HI0610, Data Date Range: 20060810-20060811 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  15. CRED Shallow CTD Profiles; Palmyra Atoll, Pacific Remote Island Areas; Cruise: HI0803, Data Date Range: 20080330-20080404 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  16. CRED Shallow CTD Profiles; Baker Island, Pacific Remote Island Areas; Cruise: TC0201_LEGI, Data Date Range: 20020129-20020131 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  17. CRED Shallow CTD Profiles; Stingray Shoals, Commonwealth of the Northern Mariana Islands; Cruise: OES0307, Data Date Range: 20030829-20030829 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  18. CRED Shallow CTD Profiles; Guguan, Commonwealth of the Northern Mariana Islands; Cruise: OES0307, Data Date Range: 20030910-20030911 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  19. CRED Shallow CTD Profiles; Rose Atoll, American Samoa; Cruise: TC0201_LEGII, Data Date Range: 20020226-20020226 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  20. CRED Shallow CTD Profiles; Hawai'i (Big Island), Main Hawaiian Islands; Cruise: HA1008, Data Date Range: 20101008-20101014 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  1. CRED Shallow CTD Profiles; Midway Atoll, Northwestern Hawaiian Islands (Papahanaumokuakea Marine National Monument); Cruise: HI0401, Data Date Range: 20041001-20041004 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  2. CRED Shallow CTD Profiles; Lana'i, Main Hawaiian Islands; Cruise: HI0610, Data Date Range: 20060804-20060806 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  3. CRED Shallow CTD Profiles; Jarvis Island, Pacific Remote Island Areas; Cruise: HI0604, Data Date Range: 20060321-20060323 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  4. CRED Shallow CTD Profiles; Ta'u, American Samoa; Cruise: HI0602, Data Date Range: 20060302-20060304 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  5. CRED Shallow CTD Profiles; Necker Island, Northwestern Hawaiian Islands (Papahanaumokuakea Marine National Monument); Cruise: HI0501, Data Date Range: 20050410-20050410 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  6. CRED Shallow CTD Profiles; Maro Reef, Northwestern Hawaiian Islands (Papahanaumokuakea Marine National Monument); Cruise: OES0306, Data Date Range: 20030720-20030723 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  7. CRED Shallow CTD Profiles; Lisianski Island, Northwestern Hawaiian Islands (Papahanaumokuakea Marine National Monument); Cruise: HA1007, Data Date Range: 20100923-20100924 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  8. CRED Shallow CTD Profiles; Agrihan, Commonwealth of the Northern Mariana Islands; Cruise: OES0511, Data Date Range: 20050914-20050915 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  9. CRED Shallow CTD Profiles; Niihau - Kaula Rock, Main Hawaiian Islands; Cruise: OES0810, Data Date Range: 20081111-20081111 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  10. CRED Shallow CTD Profiles; Tinian, Commonwealth of the Northern Mariana Islands; Cruise: HI0702, Data Date Range: 20070518-20070519 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  11. CRED Shallow CTD Profiles; Ofu and Olosega Islands, American Samoa; Cruise: TC0201_LEGII, Data Date Range: 20020213-20020215 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  12. CRED Shallow CTD Profiles; French Frigate Shoals, Northwestern Hawaiian Islands (Papahanaumokuakea Marine National Monument); Cruise: HI0401, Data Date Range: 20040917-20040919 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  13. CRED Shallow CTD Profiles; Alamagan, Commonwealth of the Northern Mariana Islands; Cruise: OES0511, Data Date Range: 20050915-20050916 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  14. CRED Shallow CTD Profiles; Maug, Commonwealth of the Northern Mariana Islands; Cruise: HA1101_LEGII, Data Date Range: 20110418-20110420. (NODC Accession 0107470)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  15. CRED Shallow CTD Profiles; French Frigate Shoals, Northwestern Hawaiian Islands (Papahanaumokuakea Marine National Monument); Cruise: OES0306, Data Date Range: 20030716-20030719 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  16. CRED Shallow CTD Profiles; Maro Reef, Northwestern Hawaiian Islands (Papahanaumokuakea Marine National Monument); Cruise: HI0611, Data Date Range: 20060907-20060909 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  17. CRED Shallow CTD Profiles; Tinian, Commonwealth of the Northern Mariana Islands; Cruise: OES0307, Data Date Range: 20030822-20030823 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  18. Temperature, salinity, biological and nutrient profiles collected by CTD in the North Atlantic Ocean from 1/28/1905 - 4/12/1994 (NODC Accession 0000125)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Temperature profile, nutrients, and other data were collected using CTD from the HELGA and other platforms in the North Atlantic Ocean. Data were collected from 28...

  19. CRED Shallow CTD Profiles; Pagan, Commonwealth of the Northern Mariana Islands; Cruise: OES0307, Data Date Range: 20030912-20030912 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  20. CRED Shallow CTD Profiles; Alamagan, Commonwealth of the Northern Mariana Islands; Cruise: HI0903, Data Date Range: 20090503-20090504 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  1. CRED Shallow CTD Profiles; Kure Atoll, Northwestern Hawaiian Islands (Papahanaumokuakea Marine National Monument); Cruise: OES0306, Data Date Range: 20030804-20030805 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  2. CRED Shallow CTD Profiles; Saipan, Commonwealth of the Northern Mariana Islands; Cruise: HI0702, Data Date Range: 20070519-20070521 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  3. CRED Shallow CTD Profiles; Aguijan (Goat Is.), Commonwealth of the Northern Mariana Islands; Cruise: HI0902, Data Date Range: 20090410-20090410 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  4. CRED Shallow CTD Profiles; Kure Atoll, Northwestern Hawaiian Islands (Papahanaumokuakea Marine National Monument); Cruise: TC0207, Data Date Range: 20020922-20020924 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  5. CRED Shallow CTD Profiles; Aguijan (Goat Is.), Commonwealth of the Northern Mariana Islands; Cruise: OES0307, Data Date Range: 20030917-20030917 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  6. CRED Shallow CTD Profiles; Asuncion Island, Commonwealth of the Northern Mariana Islands; Cruise: OES0307, Data Date Range: 20030904-20030905 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  7. CRED Shallow CTD Profiles; Hawai'i (Big Island), Main Hawaiian Islands; Cruise: HI0610, Data Date Range: 20060802-20060818 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  8. CRED Shallow CTD Profiles; Hawai'i (Big Island), Main Hawaiian Islands; Cruise: OES0502, Data Date Range: 20050227-20050305 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  9. CRED Shallow CTD Profiles; Howland Island, Pacific Remote Island Areas; Cruise: OES0401, Data Date Range: 20040122-20040122 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  10. CRED Shallow CTD Profiles; Wake Atoll, Pacific Remote Island Areas; Cruise: HA1101_LEGI, Data Date Range: 20110322-20110325. (NODC Accession 0107470)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  11. CRED Shallow CTD Profiles; Johnston Atoll, Pacific Remote Island Areas; Cruise: OES0401, Data Date Range: 20040112-20040115 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  12. CRED Shallow CTD Profiles; Gardner Pinnacle, Northwestern Hawaiian Islands (Papahanaumokuakea Marine National Monument); Cruise: HI0401, Data Date Range: 20040920-20040920 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  13. CRED Shallow CTD Profiles; Laysan Island, Northwestern Hawaiian Islands (Papahanaumokuakea Marine National Monument); Cruise: HI0611, Data Date Range: 20060911-20060911 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  14. CRED Shallow CTD Profiles; Aguijan (Goat Is.), Commonwealth of the Northern Mariana Islands; Cruise: HI0702, Data Date Range: 20070517-20070518 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  15. CRED Shallow CTD Profiles; Guguan, Commonwealth of the Northern Mariana Islands; Cruise: HI0903, Data Date Range: 20090504-20090505 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  16. CRED Shallow CTD Profiles; Lana'i, Main Hawaiian Islands; Cruise: HI0505, Data Date Range: 20050802-20050804 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  17. CRED Shallow CTD Profiles; Tinian, Commonwealth of the Northern Mariana Islands; Cruise: HA1101_LEGIII, Data Date Range: 20110502-20110503. (NODC Accession 0107470)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  18. CRED Shallow CTD Profiles; Pagan, Commonwealth of the Northern Mariana Islands; Cruise: OES0511, Data Date Range: 20050906-20050908 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  19. CRED Shallow CTD Profiles; Kingman Reef, Pacific Remote Island Areas; Cruise: OES0404, Data Date Range: 20040403-20040404 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  20. CRED Shallow CTD Profiles; Agrihan, Commonwealth of the Northern Mariana Islands; Cruise: OES0307, Data Date Range: 20030826-20030906 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  1. CRED Shallow CTD Profiles; Maug, Commonwealth of the Northern Mariana Islands; Cruise: HI0703, Data Date Range: 20070529-20070531 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  2. CRED Shallow CTD Profiles; Midway Atoll, Northwestern Hawaiian Islands (Papahanaumokuakea Marine National Monument); Cruise: HI0611, Data Date Range: 20060921-20060922 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  3. CRED Shallow CTD Profiles; Hawai'i (Big Island), Main Hawaiian Islands; Cruise: OES0810, Data Date Range: 20081026-20081102 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  4. CRED Shallow CTD Profiles; Johnston Atoll, Pacific Remote Island Areas; Cruise: HI0801, Data Date Range: 20080128-20080202 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  5. CRED Shallow CTD Profiles; Midway Atoll, Northwestern Hawaiian Islands (Papahanaumokuakea Marine National Monument); Cruise: TC0207, Data Date Range: 20020925-20020926 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  6. CRED Shallow CTD Profiles; Wake Atoll, Pacific Remote Island Areas; Cruise: OES0513, Data Date Range: 20051017-20051020 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  7. CRED Shallow CTD Profiles; Rota, Commonwealth of the Northern Mariana Islands; Cruise: HI0702, Data Date Range: 20070515-20070517 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  8. CRED Shallow CTD Profiles; Palmyra Atoll, Pacific Remote Island Areas; Cruise: HI0604, Data Date Range: 20060323-20060328 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  9. CRED Shallow CTD Profiles; Johnston Atoll, Pacific Remote Island Areas; Cruise: HA1201_LEGI, Data Date Range: 20120302-20120304 (NODC Accession 0107470)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  10. CRED Shallow CTD Profiles; Kure Atoll, Northwestern Hawaiian Islands (Papahanaumokuakea Marine National Monument); Cruise: HI0401, Data Date Range: 20041006-20041007 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  11. Temperature and salinity profile data from CTD casts from the icebreaker ODEN during the Lomonosov Ridge off Greenland (LOMROG) expedition in 2007 (NODC Accession 0093533)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The CTD data were taken during the expedition "Lomonosov Ridge off Greenland" (LOMROG) in summer 2007 with the Swedish icebreaker Oden. The LOMROG expedition...

  12. Oceanographic temperature and salinity measurements collected using CTD and XBT from URANIA in the Mediterranean Sea from 2001 to 2002 (NODC Accession 0043698)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Temperature, tritium and other measurements found in datasets XBT and CTD taken from the URANIA (Call sign IQSU) in the Mediteranean from 2001 to 2002 (NODC...

  13. Zooplankton and other data collected in Northwest Atlantic Ocean from CTD, bottle casts, and other instruments from 10 September 1963 to 24 August 1964 (NODC Accession 7101509)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Zooplankton and other data were collected using CTD, bottle casts, and other instruments in the Northwest Atlantic Ocean. Data were collected from 10 September 1963...

  14. CRED Shallow CTD Profiles; Asuncion Island, Commonwealth of the Northern Mariana Islands; Cruise: HA1101_LEGII, Data Date Range: 20110414-20110414. (NODC Accession 0107470)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  15. CRED Shallow CTD Profiles; Jarvis Island, Pacific Remote Island Areas; Cruise: TC0101, Data Date Range: 20010217-20010218 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  16. CRED Shallow CTD Profiles; Johnston Atoll, Pacific Remote Island Areas; Cruise: HI0601, Data Date Range: 20060119-20060121 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  17. CRED Shallow CTD Profiles; Baker Island, Pacific Remote Island Areas; Cruise: TC0101, Data Date Range: 20010210-20010211 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  18. CRED Shallow CTD Profiles; Rota, Commonwealth of the Northern Mariana Islands; Cruise: OES0511, Data Date Range: 20050929-20050930 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  19. CRED Shallow CTD Profiles; Palmyra Atoll, Pacific Remote Island Areas; Cruise: TC0201_LEGIII, Data Date Range: 20020313-20020317 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  20. CRED Shallow CTD Profiles; Kingman Reef, Pacific Remote Island Areas; Cruise: HI0803, Data Date Range: 20080406-20080407 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  1. CRED Shallow CTD Profiles; Swains Island, American Samoa; Cruise: HA1201_LEGI, Data Date Range: 20120321-20120323 (NODC Accession 0107470)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  2. CRED Shallow CTD Profiles; Maug, Commonwealth of the Northern Mariana Islands; Cruise: OES0307, Data Date Range: 20030901-20030904 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  3. CRED Shallow CTD Profiles; Pagan, Commonwealth of the Northern Mariana Islands; Cruise: HI0903, Data Date Range: 20090422-20090424 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  4. CRED Shallow CTD Profiles; Pearl and Hermes Atoll, Northwestern Hawaiian Islands (Papahanaumokuakea Marine National Monument); Cruise: HI0809, Data Date Range: 20080922-20081004 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  5. CRED Shallow CTD Profiles; Kingman Reef, Pacific Remote Island Areas; Cruise: HA1201_LEGIV, Data Date Range: 20120509-20120512 (NODC Accession 0107470)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  6. CRED Shallow CTD Profiles; Baker Island, Pacific Remote Island Areas; Cruise: HI0801, Data Date Range: 20080209-20080209 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  7. CRED Shallow CTD Profiles; Laysan Island, Northwestern Hawaiian Islands (Papahanaumokuakea Marine National Monument); Cruise: TC0207, Data Date Range: 20020916-20020916 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  8. CRED Shallow CTD Profiles; Saipan, Commonwealth of the Northern Mariana Islands; Cruise: HA1101_LEGIII, Data Date Range: 20110430-20110430. (NODC Accession 0107470)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  9. CRED Shallow CTD Profiles; Gardner Pinnacle, Northwestern Hawaiian Islands (Papahanaumokuakea Marine National Monument); Cruise: OES0306, Data Date Range: 20030719-20030720 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  10. CRED Shallow CTD Profiles; Midway Atoll, Northwestern Hawaiian Islands (Papahanaumokuakea Marine National Monument); Cruise: HI0809, Data Date Range: 20080928-20080929 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  11. CRED Shallow CTD Profiles; Wake Atoll, Pacific Remote Island Areas; Cruise: HI0701, Data Date Range: 20070429-20070501 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  12. CRED Shallow CTD Profiles; Jarvis Island, Pacific Remote Island Areas; Cruise: HI0803, Data Date Range: 20080328-20080329 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  13. CRED Shallow CTD Profiles; Tinian, Commonwealth of the Northern Mariana Islands; Cruise: HI0902, Data Date Range: 20090411-20090413 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  14. CRED Shallow CTD Profiles; Lana'i, Main Hawaiian Islands; Cruise: HA1008, Data Date Range: 20101021-20101023 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  15. CRED Shallow CTD Profiles; French Frigate Shoals, Northwestern Hawaiian Islands (Papahanaumokuakea Marine National Monument); Cruise: HA1007, Data Date Range: 20100908-20100910 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  16. CRED Shallow CTD Profiles; Ofu and Olosega Islands, American Samoa; Cruise: HA1201_LEGII&III, Data Date Range: 20120424-20120426 (NODC Accession 0107470)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  17. Physical and other data from CTD casts, current meters, and other instruments from 01 January 1989 to 31 December 1989 (NODC Accession 9100163)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Physical and other data were collected from CTD casts, current meters, and other instruments. Data were collected by the Japanese Hydrographic Office from 01 January...

  18. Physical and other data from CTD casts, current meters, and other instruments from 01 January 1990 to 31 December 1990 (NODC Accession 9300092)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — hysical and other data were collected from CTD casts, current meters, and other instruments. Data were collected by the Japanese Hydrographic Office from 01 January...

  19. Oceanographic profile temperature and salinity measurements collected using CTD from R/V Hecla in the North Atlantic during 1996 (NODC Accession 0046839)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Oceanographic profile temperature and salinity measurements collected using CTD from R/V Hecla in the North Atlantic during 1996. Data submitted by Garry Dawson...

  20. CRED Shallow CTD Profiles; Laysan Island, Northwestern Hawaiian Islands (Papahanaumokuakea Marine National Monument); Cruise: HI0809, Data Date Range: 20080920-20080920 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  1. CRED Shallow CTD Profiles; Maro Reef, Northwestern Hawaiian Islands (Papahanaumokuakea Marine National Monument); Cruise: TC0207, Data Date Range: 20021002-20021003 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  2. CRED Shallow CTD Profiles; Pearl and Hermes Atoll, Northwestern Hawaiian Islands (Papahanaumokuakea Marine National Monument); Cruise: HI0401, Data Date Range: 20040926-20040930 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  3. Temperature profile and wave data from CTD casts in the East/South China Sea from 10 January 1977 to 12 December 1986 (NODC Accession 9400045)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Temperature profile and wave data were collected using CTD casts and other instruments in the East / South China Sea. Data were collected from 10 January 1977 to 12...

  4. CRED Shallow CTD Profiles; Palmyra Atoll, Pacific Remote Island Areas; Cruise: TC0101, Data Date Range: 20010220-20010221 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  5. Temperature and salinity profile data from CTD casts from NOAA Ship WHITING from 2001-04 to 2001-11 (NODC Accession 0000636)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CTD data were collected from NOAA Ship WHITING in the NW Atlantic (limit-40) from 05 April 2001 to 15 November 2001. Data include temperature and salinity profiles....

  6. CRED Shallow CTD Profiles; Aguijan (Goat Is.), Commonwealth of the Northern Mariana Islands; Cruise: OES0511, Data Date Range: 20050927-20050928 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  7. Temperature and salinity profile data from CTD casts by the National Ocean Service's Navigation Response Team No. 2, January - May 2001 (NODC Accession 0000646)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CTD and other data were collected by the National Ocean Service's Response Team No. 2 in the Gulf of Mexico from 25 January 2001 to 05 May 2001. Data include...

  8. Physical, nutrients, and other data from CTD and bottle casts from the North Pacific Ocean from 19 February 1991 to 31 December 2000 (NODC Accession 0000472)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Physical, nutrients, and other data were collected from CTD and bottle casts from the North Pacific Ocean from 19 February 1991 to 31 December 2000. Parameters...

  9. Oceanographic profile temperature, salinity and other measurements collected using bottle and high resolution CTD from the POLARSTERN in the Antarctic and South Atlantic in 1992 (NODC Accession 0000463)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Temperature profile, nutrients, and other data were collected using plankton net, bottle, and CTD casts from the POLARSTERN in the Southern Oceans. Data were...

  10. CRED Shallow CTD Profiles; Sarigan, Commonwealth of the Northern Mariana Islands; Cruise: HI0903, Data Date Range: 20090420-20090421 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  11. CRED Shallow CTD Profiles; Baker Island, Pacific Remote Island Areas; Cruise: HI0601, Data Date Range: 20060131-20060201 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  12. CRED Shallow CTD Profiles; Pearl and Hermes Atoll, Northwestern Hawaiian Islands (Papahanaumokuakea Marine National Monument); Cruise: TC0207, Data Date Range: 20020917-20020920 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  13. CRED Shallow CTD Profiles; Baker Island, Pacific Remote Island Areas; Cruise: OES0401, Data Date Range: 20040124-20040125 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  14. CRED Shallow CTD Profiles; Palmyra Atoll, Pacific Remote Island Areas; Cruise: HA1201_LEGIV, Data Date Range: 20120514-20120518 (NODC Accession 0107470)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  15. CRED Shallow CTD Profiles; Sarigan, Commonwealth of the Northern Mariana Islands; Cruise: OES0307, Data Date Range: 20030823-20030824 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  16. CRED Shallow CTD Profiles; Ofu and Olosega Islands, American Samoa; Cruise: HI0602, Data Date Range: 20060226-20060228 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  17. CRED Shallow CTD Profiles; Rose Atoll, American Samoa; Cruise: HA1201_LEGII&III, Data Date Range: 20120419-20120422 (NODC Accession 0107470)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  18. CRED Shallow CTD Profiles; Kaua'i, Main Hawaiian Islands; Cruise: HI0610, Data Date Range: 20060728-20060814 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  19. CRED Shallow CTD Profiles; Johnston Atoll, Pacific Remote Island Areas; Cruise: HI1001_LEGI, Data Date Range: 20100125-20100129 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  20. Salinity and sigma-t data from moored current meter and CTD casts in the North Pacific Ocean from 26 August 1979 - 07 June 1982 (NODC Accession 8200146)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Salinity and sigma-t data were collected using moored current meter and CTD casts in the North Pacific Ocean from August 26, 1979 to June 7, 1982. Data were...

  1. CRED Shallow CTD Profiles; Agrihan, Commonwealth of the Northern Mariana Islands; Cruise: HI0703, Data Date Range: 20070528-20070529 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  2. CRED Shallow CTD Profiles; Baker Island, Pacific Remote Island Areas; Cruise: HI1001_LEGI, Data Date Range: 20100207-20100208 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  3. CRED Shallow CTD Profiles; Kaua'i, Main Hawaiian Islands; Cruise: HI0505, Data Date Range: 20050715-20050722 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  4. CRED Shallow CTD Profiles; Howland Island, Pacific Remote Island Areas; Cruise: HI1001_LEGI, Data Date Range: 20100203-20100205 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  5. CRED Shallow CTD Profiles; Necker Island, Northwestern Hawaiian Islands (Papahanaumokuakea Marine National Monument); Cruise: OES0306, Data Date Range: 20030714-20030714 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  6. CRED Shallow CTD Profiles; Howland Island, Pacific Remote Island Areas; Cruise: TC0101, Data Date Range: 20010207-20010209 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  7. CRED Shallow CTD Profiles; French Frigate Shoals, Northwestern Hawaiian Islands (Papahanaumokuakea Marine National Monument); Cruise: TC0011, Data Date Range: 20000914-20000915 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  8. Temperature and salinity profile data collected by CTD and XBT on multiple cruises from 1991-09-10 to 1993-08-29 (NODC Accession 0000123)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Temperature profile data were collected using CTD and XBT casts from LANCE and other platforms in the Norwegian Sea and Arctic Ocean. Data were collected from 10...

  9. Temperature and other data from tow and CTD casts in the North Atlantic Ocean from 1995-08-31 to 1995-09-15 (NODC Accession 9700182)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Temperature, conductivity, pressure, oxygen, and depth data were collected using tow and CTD casts from the ENDEAVOR in the North Atlantic Ocean from August 31, 1995...

  10. CRED Shallow CTD Profiles; Palmyra Atoll, Pacific Remote Island Areas; Cruise: TC0001, Data Date Range: 20000403-20000404 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  11. CRED Shallow CTD Profiles; Howland Island, Pacific Remote Island Areas; Cruise: HI0601, Data Date Range: 20060128-20060130 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  12. CRED Shallow CTD Profiles; Jarvis Island, Pacific Remote Island Areas; Cruise: TC0201_LEGIII, Data Date Range: 20020310-20020311 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  13. Salinity and sigma-t data from CTD casts in the TOGA Area - Pacific Ocean from 06 January 1994 - 03 August 1995 (NODC Accession 9600024)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Salinity and sigma-t data were collected using current meter, pressure gauge, and CTD casts in the TOGA Area - Pacific Ocean from January 6, 1994 to August 3, 1995....

  14. Temperature profile and oxygen data collected from multiple ships using CTD casts in a world wide distribution from 04 September 1979 to 15 April 1998 (NODC Accession 0002716)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Temperature profile and oxygen data were collected using CTD casts in a world wide distribution from multiple platforms from 04 September 1979 to 15 April 1998. Data...

  15. Biological, chemical, and physical data from CTD/XCTD from five Japanese R/Vs in the North Pacific Ocean from January to December 2002 (NODC Accession 0001334)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Temperature profile, nutrients, and other data were collected using XCTD and CTD casts from KOFU MARU and other platforms in the North Pacific Ocean from 01 January...

  16. CRED Shallow CTD Profiles; Palmyra Atoll, Pacific Remote Island Areas; Cruise: OES0404, Data Date Range: 20040329-20040401 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  17. CRED Shallow CTD Profiles; Lisianski Island, Northwestern Hawaiian Islands (Papahanaumokuakea Marine National Monument); Cruise: OES0306, Data Date Range: 20030726-20030726 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  18. CRED Shallow CTD Profiles; Alamagan, Commonwealth of the Northern Mariana Islands; Cruise: OES0307, Data Date Range: 20030911-20030912 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  19. CRED Shallow CTD Profiles; Kure Atoll, Northwestern Hawaiian Islands (Papahanaumokuakea Marine National Monument); Cruise: HA1007, Data Date Range: 20100919-20100920 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  20. CRED Shallow CTD Profiles; Kingman Reef, Pacific Remote Island Areas; Cruise: TC0201_LEGIII, Data Date Range: 20020318-20020318 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  1. CRED Shallow CTD Profiles; Alamagan, Commonwealth of the Northern Mariana Islands; Cruise: HI0703, Data Date Range: 20070527-20070528 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  2. CRED Shallow CTD Profiles; Jarvis Island, Pacific Remote Island Areas; Cruise: HI1001_LEGIII, Data Date Range: 20100402-20100405 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  3. CRED Shallow CTD Profiles; French Frigate Shoals, Northwestern Hawaiian Islands (Papahanaumokuakea Marine National Monument); Cruise: HI0611, Data Date Range: 20060930-20061001 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  4. CRED Shallow CTD Profiles; Pearl and Hermes Atoll, Northwestern Hawaiian Islands (Papahanaumokuakea Marine National Monument); Cruise: HA1007, Data Date Range: 20100914-20100916 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  5. CRED Shallow CTD Profiles; Swains Island, American Samoa; Cruise: HI1001_LEGII, Data Date Range: 20100316-20100318 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  6. CRED Shallow CTD Profiles; Agrihan, Commonwealth of the Northern Mariana Islands; Cruise: HA1101_LEGII, Data Date Range: 20110420-20110422. (NODC Accession 0107470)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  7. CRED Shallow CTD Profiles; Rota, Commonwealth of the Northern Mariana Islands; Cruise: HI0902, Data Date Range: 20090409-20090410 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  8. CRED Shallow CTD Profiles; Tutuila, American Samoa; Cruise: HA1201_LEGII&III, Data Date Range: 20120401-20120406 (NODC Accession 0107470)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  9. CRED Shallow CTD Profiles; Lana'i, Main Hawaiian Islands; Cruise: OES0810, Data Date Range: 20081019-20081020 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  10. CRED Shallow CTD Profiles; Farallon de Pajaros, Commonwealth of the Northern Mariana Islands; Cruise: HI0903, Data Date Range: 20090427-20090428 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  11. CRED Shallow CTD Profiles; Saipan, Commonwealth of the Northern Mariana Islands; Cruise: HA1101_LEGII, Data Date Range: 20110407-20110426. (NODC Accession 0107470)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  12. CRED Shallow CTD Profiles; Ta'u, American Samoa; Cruise: HI1001_LEGII, Data Date Range: 20100312-20100320 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  13. CRED Shallow CTD Profiles; Baker Island, Pacific Remote Island Areas; Cruise: HA1201_LEGI, Data Date Range: 20120315-20120317 (NODC Accession 0107470)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  14. CRED Shallow CTD Profiles; Kure Atoll, Northwestern Hawaiian Islands (Papahanaumokuakea Marine National Monument); Cruise: HI0809, Data Date Range: 20080930-20081001 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  15. CRED Shallow CTD Profiles; Jarvis Island, Pacific Remote Island Areas; Cruise: HI0803, Data Date Range: 20080328-20080329 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  16. CRED Shallow CTD Profiles; Kaua'i, Main Hawaiian Islands; Cruise: HA1008, Data Date Range: 20101030-20101031 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  17. CRED Shallow CTD Profiles; French Frigate Shoals, Northwestern Hawaiian Islands (Papahanaumokuakea Marine National Monument); Cruise: HI0809, Data Date Range: 20080916-20080917 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  18. CRED Shallow CTD Profiles; Rota, Commonwealth of the Northern Mariana Islands; Cruise: HA1101_LEGIII, Data Date Range: 20110501-20110502. (NODC Accession 0107470)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  19. CRED Shallow CTD Profiles; Palmyra Atoll, Pacific Remote Island Areas; Cruise: HI1001_LEGIII, Data Date Range: 20100407-20100412 (NODC Accession 0039382).

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...

  20. CRED Shallow CTD Profiles; Jarvis Island, Pacific Remote Island Areas; Cruise: HA1201_LEGIV, Data Date Range: 20120503-20120505 (NODC Accession 0107470)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — CRED shallow Conductivity-Temperature-Depth (CTD) casts are vertical profiles (max 30 meter depth, downcast only) of temperature, conductivity and pressure. Data are...