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.

Structural rearrangement of the intracellular domains during AMPA receptor activation

DEFF Research Database (Denmark)

Zachariassen, Linda Grønborg; Katchan, Ljudmila; Jensen, Anna Guldvang

2016-01-01

-clamp fluorometry of the double- and single-insert constructs showed that both the intracellular C-terminal domain (CTD) and the loop region between the M1 and M2 helices move during activation and the CTD is detached from the membrane. Our time-resolved measurements revealed unexpectedly complex fluorescence...

Alternative Conformations of the Tau Repeat Domain in Complex with an Engineered Binding Protein*

Science.gov (United States)

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

2014-01-01

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. PMID:24966331

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

Directory of Open Access Journals (Sweden)

Emma L Meczes

2008-03-01

Full Text Available 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.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.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 data with chimeric human topoIIs.

Yeast screens identify the RNA polymerase II CTD and SPT5 as relevant targets of BRCA1 interaction.

Directory of Open Access Journals (Sweden)

Craig B Bennett

2008-01-01

Full Text Available BRCA1 has been implicated in numerous DNA repair pathways that maintain genome integrity, however the function responsible for its tumor suppressor activity in breast cancer remains obscure. To identify the most highly conserved of the many BRCA1 functions, we screened the evolutionarily distant eukaryote Saccharomyces cerevisiae for mutants that suppressed the G1 checkpoint arrest and lethality induced following heterologous BRCA1 expression. A genome-wide screen in the diploid deletion collection combined with a screen of ionizing radiation sensitive gene deletions identified mutants that permit growth in the presence of BRCA1. These genes delineate a metabolic mRNA pathway that temporally links transcription elongation (SPT4, SPT5, CTK1, DEF1 to nucleopore-mediated mRNA export (ASM4, MLP1, MLP2, NUP2, NUP53, NUP120, NUP133, NUP170, NUP188, POM34 and cytoplasmic mRNA decay at P-bodies (CCR4, DHH1. Strikingly, BRCA1 interacted with the phosphorylated RNA polymerase II (RNAPII carboxy terminal domain (P-CTD, phosphorylated in the pattern specified by the CTDK-I kinase, to induce DEF1-dependent cleavage and accumulation of a RNAPII fragment containing the P-CTD. Significantly, breast cancer associated BRCT domain defects in BRCA1 that suppressed P-CTD cleavage and lethality in yeast also suppressed the physical interaction of BRCA1 with human SPT5 in breast epithelial cells, thus confirming SPT5 as a relevant target of BRCA1 interaction. Furthermore, enhanced P-CTD cleavage was observed in both yeast and human breast cells following UV-irradiation indicating a conserved eukaryotic damage response. Moreover, P-CTD cleavage in breast epithelial cells was BRCA1-dependent since damage-induced P-CTD cleavage was only observed in the mutant BRCA1 cell line HCC1937 following ectopic expression of wild type BRCA1. Finally, BRCA1, SPT5 and hyperphosphorylated RPB1 form a complex that was rapidly degraded following MMS treatment in wild type but not BRCA1

Phosphatase Rtr1 Regulates Global Levels of Serine 5 RNA Polymerase II C-Terminal Domain Phosphorylation and Cotranscriptional Histone Methylation.

Science.gov (United States)

Hunter, Gerald O; Fox, Melanie J; Smith-Kinnaman, Whitney R; Gogol, Madelaine; Fleharty, Brian; Mosley, Amber L

2016-09-01

In eukaryotes, the C-terminal domain (CTD) of Rpb1 contains a heptapeptide repeat sequence of (Y1S2P3T4S5P6S7)n that undergoes reversible phosphorylation through the opposing action of kinases and phosphatases. Rtr1 is a conserved protein that colocalizes with RNA polymerase II (RNAPII) and has been shown to be important for the transition from elongation to termination during transcription by removing RNAPII CTD serine 5 phosphorylation (Ser5-P) at a selection of target genes. In this study, we show that Rtr1 is a global regulator of the CTD code with deletion of RTR1 causing genome-wide changes in Ser5-P CTD phosphorylation and cotranscriptional histone H3 lysine 36 trimethylation (H3K36me3). Using chromatin immunoprecipitation and high-resolution microarrays, we show that RTR1 deletion results in global changes in RNAPII Ser5-P levels on genes with different lengths and transcription rates consistent with its role as a CTD phosphatase. Although Ser5-P levels increase, the overall occupancy of RNAPII either decreases or stays the same in the absence of RTR1 Additionally, the loss of Rtr1 in vivo leads to increases in H3K36me3 levels genome-wide, while total histone H3 levels remain relatively constant within coding regions. Overall, these findings suggest that Rtr1 regulates H3K36me3 levels through changes in the number of binding sites for the histone methyltransferase Set2, thereby influencing both the CTD and histone codes. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Structure of the Escherichia coli RNA polymerase α subunit C-terminal domain

International Nuclear Information System (INIS)

Lara-González, Samuel; Birktoft, Jens J.; Lawson, Catherine L.

2010-01-01

The crystal structure of the dimethyllysine derivative of the E. coli RNA polymerase α subunit C-terminal domain is reported at 2.0 Å resolution. The α subunit C-terminal domain (αCTD) of RNA polymerase (RNAP) is a key element in transcription activation in Escherichia coli, possessing determinants responsible for the interaction of RNAP with DNA and with transcription factors. Here, the crystal structure of E. coli αCTD (α subunit residues 245–329) determined to 2.0 Å resolution is reported. Crystals were obtained after reductive methylation of the recombinantly expressed domain. The crystals belonged to space group P2 1 and possessed both pseudo-translational symmetry and pseudo-merohedral twinning. The refined coordinate model (R factor = 0.193, R free = 0.236) has improved geometry compared with prior lower resolution determinations of the αCTD structure [Jeon et al. (1995 ▶), Science, 270, 1495–1497; Benoff et al. (2002 ▶), Science, 297, 1562–1566]. An extensive dimerization interface formed primarily by N- and C-terminal residues is also observed. The new coordinates will facilitate the improved modeling of αCTD-containing multi-component complexes visualized at lower resolution using X-ray crystallography and electron-microscopy reconstruction

Constructs for the expression of repeating triple-helical protein domains

International Nuclear Information System (INIS)

Peng, Yong Y; Werkmeister, Jerome A; Vaughan, Paul R; Ramshaw, John A M

2009-01-01

The development of novel scaffolds will be an important aspect in future success of tissue engineering. Scaffolds will preferably contain information that directs the cellular content of constructs so that the new tissue that is formed is closely aligned in structure, composition and function to the target natural tissue. One way of approaching this will be the development of novel protein-based constructs that contain one or more repeats of functional elements derived from various proteins. In the present case, we describe a strategy to make synthetic, recombinant triple-helical constructs that contain repeat segments of biologically relevant domains. Copies of a DNA fragment prepared by PCR from human type III collagen have been inserted in a co-linear contiguous fashion into the yeast expression vector YEpFlag-1, using sequential addition between selected restriction sites. Constructs containing 1, 2 and 3 repeats were designed to maintain the (Gly-X-Y) repeat, which is essential for the formation of an extended triple helix. All constructs gave expressed protein, with the best being the 3-repeat construct which was readily secreted. This material had the expected composition and N-terminal sequence. Incubation of the product at low temperature led to triple-helix formation, shown by reaction with a conformation dependent monoclonal antibody.

Constructs for the expression of repeating triple-helical protein domains

Energy Technology Data Exchange (ETDEWEB)

Peng, Yong Y; Werkmeister, Jerome A; Vaughan, Paul R; Ramshaw, John A M, E-mail: jerome.werkmeister@csiro.a [CSIRO Molecular and Health Technologies, Bag 10, Clayton South, VIC 3169 (Australia)

2009-02-15

The development of novel scaffolds will be an important aspect in future success of tissue engineering. Scaffolds will preferably contain information that directs the cellular content of constructs so that the new tissue that is formed is closely aligned in structure, composition and function to the target natural tissue. One way of approaching this will be the development of novel protein-based constructs that contain one or more repeats of functional elements derived from various proteins. In the present case, we describe a strategy to make synthetic, recombinant triple-helical constructs that contain repeat segments of biologically relevant domains. Copies of a DNA fragment prepared by PCR from human type III collagen have been inserted in a co-linear contiguous fashion into the yeast expression vector YEpFlag-1, using sequential addition between selected restriction sites. Constructs containing 1, 2 and 3 repeats were designed to maintain the (Gly-X-Y) repeat, which is essential for the formation of an extended triple helix. All constructs gave expressed protein, with the best being the 3-repeat construct which was readily secreted. This material had the expected composition and N-terminal sequence. Incubation of the product at low temperature led to triple-helix formation, shown by reaction with a conformation dependent monoclonal antibody.

Domain activities of PapC usher reveal the mechanism of action of an Escherichia coli molecular machine.

Science.gov (United States)

Volkan, Ender; Ford, Bradley A; Pinkner, Jerome S; Dodson, Karen W; Henderson, Nadine S; Thanassi, David G; Waksman, Gabriel; Hultgren, Scott J

2012-06-12

P pili are prototypical chaperone-usher pathway-assembled pili used by Gram-negative bacteria to adhere to host tissues. The PapC usher contains five functional domains: a transmembrane β-barrel, a β-sandwich Plug, an N-terminal (periplasmic) domain (NTD), and two C-terminal (periplasmic) domains, CTD1 and CTD2. Here, we delineated usher domain interactions between themselves and with chaperone-subunit complexes and showed that overexpression of individual usher domains inhibits pilus assembly. Prior work revealed that the Plug domain occludes the pore of the transmembrane domain of a solitary usher, but the chaperone-adhesin-bound usher has its Plug displaced from the pore, adjacent to the NTD. We demonstrate an interaction between the NTD and Plug domains that suggests a biophysical basis for usher gating. Furthermore, we found that the NTD exhibits high-affinity binding to the chaperone-adhesin (PapDG) complex and low-affinity binding to the major tip subunit PapE (PapDE). We also demonstrate that CTD2 binds with lower affinity to all tested chaperone-subunit complexes except for the chaperone-terminator subunit (PapDH) and has a catalytic role in dissociating the NTD-PapDG complex, suggesting an interplay between recruitment to the NTD and transfer to CTD2 during pilus initiation. The Plug domain and the NTD-Plug complex bound all of the chaperone-subunit complexes tested including PapDH, suggesting that the Plug actively recruits chaperone-subunit complexes to the usher and is the sole recruiter of PapDH. Overall, our studies reveal the cooperative, active roles played by periplasmic domains of the usher to initiate, grow, and terminate a prototypical chaperone-usher pathway pilus.

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

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.

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. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Requirement for the E1 Helicase C-Terminal Domain in Papillomavirus DNA Replication In Vivo.

Science.gov (United States)

Bergvall, Monika; Gagnon, David; Titolo, Steve; Lehoux, Michaël; D'Abramo, Claudia M; Melendy, Thomas; Archambault, Jacques

2016-01-06

The papillomavirus (PV) E1 helicase contains a conserved C-terminal domain (CTD), located next to its ATP-binding site, whose function in vivo is still poorly understood. The CTD is comprised of an alpha helix followed by an acidic region (AR) and a C-terminal extension termed the C-tail. Recent biochemical studies on bovine papillomavirus 1 (BPV1) E1 showed that the AR and C-tail regulate the oligomerization of the protein into a double hexamer at the origin. In this study, we assessed the importance of the CTD of human papillomavirus 11 (HPV11) E1 in vivo, using a cell-based DNA replication assay. Our results indicate that combined deletion of the AR and C-tail drastically reduces DNA replication, by 85%, and that further truncation into the alpha-helical region compromises the structural integrity of the E1 helicase domain and its interaction with E2. Surprisingly, removal of the C-tail alone or mutation of highly conserved residues within the domain still allows significant levels of DNA replication (55%). This is in contrast to the absolute requirement for the C-tail reported for BPV1 E1 in vitro and confirmed here in vivo. Characterization of chimeric proteins in which the AR and C-tail from HPV11 E1 were replaced by those of BPV1 indicated that while the function of the AR is transferable, that of the C-tail is not. Collectively, these findings define the contribution of the three CTD subdomains to the DNA replication activity of E1 in vivo and suggest that the function of the C-tail has evolved in a PV type-specific manner. While much is known about hexameric DNA helicases from superfamily 3, the papillomavirus E1 helicase contains a unique C-terminal domain (CTD) adjacent to its ATP-binding site. We show here that this CTD is important for the DNA replication activity of HPV11 E1 in vivo and that it can be divided into three functional subdomains that roughly correspond to the three conserved regions of the CTD: an alpha helix, needed for the structural

Requirement for the E1 Helicase C-Terminal Domain in Papillomavirus DNA Replication In Vivo

Science.gov (United States)

Bergvall, Monika; Gagnon, David; Titolo, Steve; Lehoux, Michaël; D'Abramo, Claudia M.

2016-01-01

ABSTRACT The papillomavirus (PV) E1 helicase contains a conserved C-terminal domain (CTD), located next to its ATP-binding site, whose function in vivo is still poorly understood. The CTD is comprised of an alpha helix followed by an acidic region (AR) and a C-terminal extension termed the C-tail. Recent biochemical studies on bovine papillomavirus 1 (BPV1) E1 showed that the AR and C-tail regulate the oligomerization of the protein into a double hexamer at the origin. In this study, we assessed the importance of the CTD of human papillomavirus 11 (HPV11) E1 in vivo, using a cell-based DNA replication assay. Our results indicate that combined deletion of the AR and C-tail drastically reduces DNA replication, by 85%, and that further truncation into the alpha-helical region compromises the structural integrity of the E1 helicase domain and its interaction with E2. Surprisingly, removal of the C-tail alone or mutation of highly conserved residues within the domain still allows significant levels of DNA replication (55%). This is in contrast to the absolute requirement for the C-tail reported for BPV1 E1 in vitro and confirmed here in vivo. Characterization of chimeric proteins in which the AR and C-tail from HPV11 E1 were replaced by those of BPV1 indicated that while the function of the AR is transferable, that of the C-tail is not. Collectively, these findings define the contribution of the three CTD subdomains to the DNA replication activity of E1 in vivo and suggest that the function of the C-tail has evolved in a PV type-specific manner. IMPORTANCE While much is known about hexameric DNA helicases from superfamily 3, the papillomavirus E1 helicase contains a unique C-terminal domain (CTD) adjacent to its ATP-binding site. We show here that this CTD is important for the DNA replication activity of HPV11 E1 in vivo and that it can be divided into three functional subdomains that roughly correspond to the three conserved regions of the CTD: an alpha helix, needed

Molecular Dissection of the Homotrimeric Sliding Clamp of T4 Phage: Two Domains of a Subunit Display Asymmetric Characteristics.

Science.gov (United States)

Singh, Manika Indrajit; Jain, Vikas

2016-01-26

Sliding clamp proteins are circular dimers or trimers that encircle DNA and serve as processivity factors during DNA replication. Their presence in all the three domains of life and in bacteriophages clearly indicates their high level of significance. T4 gp45, besides functioning as the DNA polymerase processivity factor, also moonlights as the late promoter transcription determinant. Here we report a detailed biophysical analysis of gp45. The chemical denaturation of gp45 probed by circular dichroism spectroscopy, tryptophan fluorescence anisotropy, and blue-native polyacrylamide gel electrophoresis suggests that the protein follows a three-state denaturation profile and displays an intermediate molten globule-like state. The three-state transition was found to be the result of the sequential unfolding of the two domains, the N-terminal domain (NTD) and the C-terminal domain (CTD), of gp45. The experiments involving Trp fluorescence quenching by acrylamide demonstrate that the CTD undergoes substantial changes in conformation during formation of the intermediate state. Further biophysical dissection of the individual domain reveals contrasting properties of the two domains. The NTD unfolds at low urea concentrations and is also susceptible to protease cleavage, whereas the CTD resists urea-mediated denaturation and is not amenable to protease digestion even at higher urea concentrations. These experiments allow us to conclude that the two domains of gp45 differ in their dynamics. While the CTD shows stability and rigidity, we find that the NTD is unstable and flexible. We believe that the asymmetric characteristics of the two domains and the interface they form hold significance in gp45 structure and function.

Solution structure and DNA-binding properties of the C-terminal domain of UvrC from E.coli

NARCIS (Netherlands)

Singh, S.; Folkers, G.E.; Bonvin, A.M.J.J.; Boelens, R.; Wechselberger, R.W.; Niztayev, A.; Kaptein, R.

2002-01-01

The C-terminal domain of the UvrC protein (UvrC CTD) is essential for 5' incision in the prokaryotic nucleotide excision repair process. We have determined the three-dimensional structure of the UvrC CTD using heteronuclear NMR techniques. The structure shows two helix±hairpin±helix (HhH) motifs

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.

Expression, purification and preliminary biochemical and structural characterization of the leucine rich repeat namesake domain of leucine rich repeat kinase 2.

Science.gov (United States)

Vancraenenbroeck, Renée; Lobbestael, Evy; Weeks, Stephen D; Strelkov, Sergei V; Baekelandt, Veerle; Taymans, Jean-Marc; De Maeyer, Marc

2012-03-01

Mutations in leucine-rich repeat kinase 2 (LRRK2) are the most common cause of familial Parkinson's disease. Much research effort has been directed towards the catalytic core region of LRRK2 composed of GTPase (ROC, Ras of complex proteins) and kinase domains and a connecting COR (C-terminus of ROC) domain. In contrast, the precise functions of the protein-protein interaction domains, such as the leucine-rich repeat (LRR) domain, are not known. In the present study, we modeled the LRRK2 LRR domain (LRR(LRRK2)) using a template assembly approach, revealing the presence of 14 LRRs. Next, we focused on the expression and purification of LRR(LRRK2) in Escherichia coli. Buffer optimization revealed that the protein requires the presence of a zwitterionic detergent, namely Empigen BB, during solubilization and the subsequent purification and characterization steps. This indicates that the detergent captures the hydrophobic surface patches of LRR(LRRK2) thereby suppressing its aggregation. Circular dichroism (CD) spectroscopy measured 18% α-helices and 21% β-sheets, consistent with predictions from the homology model. Size exclusion chromatography (SEC) and dynamic light scattering measurements showed the presence of a single species, with a Stokes radius corresponding to the model dimensions of a protein monomer. Furthermore, no obvious LRR(LRRK2) multimerization was detected via cross-linking studies. Finally, the LRR(LRRK2) clinical mutations did not influence LRR(LRRK2) secondary, tertiary or quaternary structure as determined via SEC and CD spectroscopy. We therefore conclude that these mutations are likely to affect putative LRR(LRRK2) inter- and intramolecular interactions. Copyright © 2011 Elsevier B.V. All rights reserved.

Molecular determinants of tetramerization in the KcsA cytoplasmic domain.

Science.gov (United States)

Kamnesky, Guy; Hirschhorn, Orel; Shaked, Hadassa; Chen, Jingfei; Yao, Lishan; Chill, Jordan H

2014-10-01

The cytoplasmic C-terminal domain (CTD) of KcsA, a bacterial homotetrameric potassium channel, is an amphiphilic domain that forms a helical bundle with four-fold symmetry mediated by hydrophobic and electrostatic interactions. Previously we have established that a CTD-derived 34-residue peptide associates into a tetramer in a pH-dependent manner (Kamnesky et al., JMB 2012;418:237-247). Here we further investigate the molecular determinants of tetramer formation in the CTD by characterizing the kinetics of monomer-tetramer equilibrium for 10 alanine mutants using NMR, sedimentation equilibrium (SE) and molecular dynamics simulation. NMR and SE concur in finding single-residue contributions to tetramer stability to be in the 0.5 to 3.5 kcal/mol range. Hydrophobic interactions between residues lining the tetramer core generally contributed more to formation of tetramer than electrostatic interactions between residues R147, D149 and E152. In particular, alanine replacement of residue R147, a key contributor to inter-subunit salt bridges, resulted in only a minor effect on tetramer dissociation. Mutations outside of the inter-subunit interface also influenced tetramer stability by affecting the tetramerization on-rate, possibly by changing the inherent helical propensity of the peptide. These findings are interpreted in the context of established paradigms of protein-protein interactions and protein folding, and lay the groundwork for further studies of the CTD in full-length KcsA channels. © 2014 The Protein Society.

Structural analyses of the Ankyrin Repeat Domain of TRPV6 and related TRPV ion channels†‡

OpenAIRE

Phelps, Christopher B.; Huang, Robert J.; Lishko, Polina V.; Wang, Ruiqi R.; Gaudet, Rachelle

2008-01-01

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 Å crystal structure of the TRPV6-ARD reveals conserved structural elements unique to the...

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.

Crystal Structures of the Tetratricopeptide Repeat Domains of Kinesin Light Chains: Insight into Cargo Recognition Mechanisms

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Zhu, Haizhong; Lee, Han Youl; Tong, Yufeng; Hong, Bum-Soo; Kim, Kyung-Phil; Shen, Yang; Lim, Kyung Jik; Mackenzie, Farrell; Tempel, Wolfram; Park, Hee-Won (SGC-Toronto); (PPCS); (Toronto)

2012-10-23

Kinesin-1 transports various cargos along the axon by interacting with the cargos through its light chain subunit. Kinesin light chains (KLC) utilize its tetratricopeptide repeat (TPR) domain to interact with over 10 different cargos. Despite a high sequence identity between their TPR domains (87%), KLC1 and KLC2 isoforms exhibit differential binding properties towards some cargos. We determined the structures of human KLC1 and KLC2 tetratricopeptide repeat (TPR) domains using X-ray crystallography and investigated the different mechanisms by which KLCs interact with their cargos. Using isothermal titration calorimetry, we attributed the specific interaction between KLC1 and JNK-interacting protein 1 (JIP1) cargo to residue N343 in the fourth TRP repeat. Structurally, the N343 residue is adjacent to other asparagines and lysines, creating a positively charged polar patch within the groove of the TPR domain. Whereas, KLC2 with the corresponding residue S328 did not interact with JIP1. Based on these finding, we propose that N343 of KLC1 can form 'a carboxylate clamp' with its neighboring asparagine to interact with JIP1, similar to that of HSP70/HSP90 organizing protein-1's (HOP1) interaction with heat shock proteins. For the binding of cargos shared by KLC1 and KLC2, we propose a different site located within the groove but not involving N343. We further propose a third binding site on KLC1 which involves a stretch of polar residues along the inter-TPR loops that may form a network of hydrogen bonds to JIP3 and JIP4. Together, these results provide structural insights into possible mechanisms of interaction between KLC TPR domains and various cargo proteins.

A β-solenoid model of the Pmel17 repeat domain: insights to the formation of functional amyloid fibrils

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Louros, Nikolaos N.; Baltoumas, Fotis A.; Hamodrakas, Stavros J.; Iconomidou, Vassiliki A.

2016-02-01

Pmel17 is a multidomain protein involved in biosynthesis of melanin. This process is facilitated by the formation of Pmel17 amyloid fibrils that serve as a scaffold, important for pigment deposition in melanosomes. A specific luminal domain of human Pmel17, containing 10 tandem imperfect repeats, designated as repeat domain (RPT), forms amyloid fibrils in a pH-controlled mechanism in vitro and has been proposed to be essential for the formation of the fibrillar matrix. Currently, no three-dimensional structure has been resolved for the RPT domain of Pmel17. Here, we examine the structure of the RPT domain by performing sequence threading. The resulting model was subjected to energy minimization and validated through extensive molecular dynamics simulations. Structural analysis indicated that the RPT model exhibits several distinct properties of β-solenoid structures, which have been proposed to be polymerizing components of amyloid fibrils. The derived model is stabilized by an extensive network of hydrogen bonds generated by stacking of highly conserved polar residues of the RPT domain. Furthermore, the key role of invariant glutamate residues is proposed, supporting a pH-dependent mechanism for RPT domain assembly. Conclusively, our work attempts to provide structural insights into the RPT domain structure and to elucidate its contribution to Pmel17 amyloid fibril formation.

Contribution of the LIM domain and nebulin-repeats to the interaction of Lasp-2 with actin filaments and focal adhesions.

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Hiroyuki Nakagawa

Full Text Available Lasp-2 binds to actin filaments and concentrates in the actin bundles of filopodia and lamellipodia in neural cells and focal adhesions in fibroblastic cells. Lasp-2 has three structural regions: a LIM domain, a nebulin-repeat region, and an SH3 domain; however, the region(s responsible for its interactions with actin filaments and focal adhesions are still unclear. In this study, we revealed that the N-terminal fragment from the LIM domain to the first nebulin-repeat module (LIM-n1 retained actin-binding activity and showed a similar subcellular localization to full-length lasp-2 in neural cells. The LIM domain fragment did not interact with actin filaments or localize to actin filament bundles. In contrast, LIM-n1 showed a clear subcellular localization to filopodial actin bundles. Although truncation of the LIM domain caused the loss of F-actin binding activity and the accumulation of filopodial actin bundles, these truncated fragments localized to focal adhesions. These results suggest that lasp-2 interactions with actin filaments are mediated through the cooperation of the LIM domain and the first nebulin-repeat module in vitro and in vivo. Actin filament binding activity may be a major contributor to the subcellular localization of lasp-2 to filopodia but is not crucial for lasp-2 recruitment to focal adhesions.

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

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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.

Current direction and CTD data from moored current meter and CTD casts in the Delaware Bay from 1984-01-01 to 1984-12-01 (NODC Accession 8600001)

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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...

Current direction and CTD data from moored current meter and CTD casts in the Atlantic Ocean from 1980-08-04 to 1981-08-14 (NODC Accession 8200240)

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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...

ST proteins, a new family of plant tandem repeat proteins with a DUF2775 domain mainly found in Fabaceae and Asteraceae.

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Albornos, Lucía; Martín, Ignacio; Iglesias, Rebeca; Jiménez, Teresa; Labrador, Emilia; Dopico, Berta

2012-11-07

Many proteins with tandem repeats in their sequence have been described and classified according to the length of the repeats: I) Repeats of short oligopeptides (from 2 to 20 amino acids), including structural cell wall proteins and arabinogalactan proteins. II) Repeats that range in length from 20 to 40 residues, including proteins with a well-established three-dimensional structure often involved in mediating protein-protein interactions. (III) Longer repeats in the order of 100 amino acids that constitute structurally and functionally independent units. Here we analyse ShooT specific (ST) proteins, a family of proteins with tandem repeats of unknown function that were first found in Leguminosae, and their possible similarities to other proteins with tandem repeats. ST protein sequences were only found in dicotyledonous plants, limited to several plant families, mainly the Fabaceae and the Asteraceae. ST mRNAs accumulate mainly in the roots and under biotic interactions. Most ST proteins have one or several Domain(s) of Unknown Function 2775 (DUF2775). All deduced ST proteins have a signal peptide, indicating that these proteins enter the secretory pathway, and the mature proteins have tandem repeat oligopeptides that share a hexapeptide (E/D)FEPRP followed by 4 partially conserved amino acids, which could determine a putative N-glycosylation signal, and a fully conserved tyrosine. In a phylogenetic tree, the sequences clade according to taxonomic group. A possible involvement in symbiosis and abiotic stress as well as in plant cell elongation is suggested, although different STs could play different roles in plant development. We describe a new family of proteins called ST whose presence is limited to the plant kingdom, specifically to a few families of dicotyledonous plants. They present 20 to 40 amino acid tandem repeat sequences with different characteristics (signal peptide, DUF2775 domain, conservative repeat regions) from the described group of 20 to 40

Current direction and CTD data from moored current meter and CTD casts in the North Pacific Ocean from 1979-02-05 to 1980-12-01 (NODC Accession 8300042)

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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...

CTD data from CTD casts in the Northeast Pacific Ocean from NOAA Ship DISCOVERER and other platforms from 1996-03-09 to 1996-06-24 (NODC Accession 9600096)

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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...

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

International Nuclear Information System (INIS)

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

2008-01-01

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

CTD data from CTD casts in the Northeast Pacific Ocean from NOAA Ship DISCOVERER and NOAA Ship SURVEYOR from 1985-06-03 to 1988-09-21 (NODC Accession 8900194)

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National Oceanic and Atmospheric Administration, Department of Commerce — CTD data were collected from CTD casts from NOAA Ship DISCOVERER and NOAA Ship SURVEYOR in the Northeast Pacific Ocean from 03 June 1985 to 21 September 1988. Data...

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

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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

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

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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.

Current direction, wind wave spectra, and CTD data from moored current meter and CTD casts in the North Atlantic Ocean from 1982-09-15 to 1983-09-15 (NODC Accession 8500148)

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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...

Gulf of Mexico Nutrient, carbon, CTD data

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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....

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

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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.

Regulation of abiotic stress signalling by Arabidopsis C-terminal domain phosphatase-like 1 requires interaction with a k-homology domain-containing protein.

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In Sil Jeong

Full Text Available Arabidopsis thaliana CARBOXYL-TERMINAL DOMAIN (CTD PHOSPHATASE-LIKE 1 (CPL1 regulates plant transcriptional responses to diverse stress signals. Unlike typical CTD phosphatases, CPL1 contains two double-stranded (ds RNA binding motifs (dsRBMs at its C-terminus. Some dsRBMs can bind to dsRNA and/or other proteins, but the function of the CPL1 dsRBMs has remained obscure. Here, we report identification of REGULATOR OF CBF GENE EXPRESSION 3 (RCF3 as a CPL1-interacting protein. RCF3 co-purified with tandem-affinity-tagged CPL1 from cultured Arabidopsis cells and contains multiple K-homology (KH domains, which were predicted to be important for binding to single-stranded DNA/RNA. Yeast two-hybrid, luciferase complementation imaging, and bimolecular fluorescence complementation analyses established that CPL1 and RCF3 strongly associate in vivo, an interaction mediated by the dsRBM1 of CPL1 and the KH3/KH4 domains of RCF3. Mapping of functional regions of CPL1 indicated that CPL1 in vivo function requires the dsRBM1, catalytic activity, and nuclear targeting of CPL1. Gene expression profiles of rcf3 and cpl1 mutants were similar during iron deficiency, but were distinct during the cold response. These results suggest that tethering CPL1 to RCF3 via dsRBM1 is part of the mechanism that confers specificity to CPL1-mediated transcriptional regulation.

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

International Nuclear Information System (INIS)

Cao, Shenglan; Ho, Gay Hui; Lin, Valerie CL

2008-01-01

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 < 0.00001), suggesting it might be involved in the breast cancer development process. The aim of the current study was to further elucidate the function of TTC9A. 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. 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. 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

The disordered C-terminal domain of human DNA glycosylase NEIL1 contributes to its stability via intramolecular interactions.

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Hegde, Muralidhar L; Tsutakawa, Susan E; Hegde, Pavana M; Holthauzen, Luis Marcelo F; Li, Jing; Oezguen, Numan; Hilser, Vincent J; Tainer, John A; Mitra, Sankar

2013-07-10

NEIL1 [Nei (endonuclease VIII)-like protein 1], one of the five mammalian DNA glycosylases that excise oxidized DNA base lesions in the human genome to initiate base excision repair, contains an intrinsically disordered C-terminal domain (CTD; ~100 residues), not conserved in its Escherichia coli prototype Nei. Although dispensable for NEIL1's lesion excision and AP lyase activities, this segment is required for efficient in vivo enzymatic activity and may provide an interaction interface for many of NEIL1's interactions with other base excision repair proteins. Here, we show that the CTD interacts with the folded domain in native NEIL1 containing 389 residues. The CTD is poised for local folding in an ordered structure that is induced in the purified fragment by osmolytes. Furthermore, deletion of the disordered tail lacking both Tyr and Trp residues causes a red shift in NEIL1's intrinsic Trp-specific fluorescence, indicating a more solvent-exposed environment for the Trp residues in the truncated protein, which also exhibits reduced stability compared to the native enzyme. These observations are consistent with stabilization of the native NEIL1 structure via intramolecular, mostly electrostatic, interactions that were disrupted by mutating a positively charged (Lys-rich) cluster of residues (amino acids 355-360) near the C-terminus. Small-angle X-ray scattering (SAXS) analysis confirms the flexibility and dynamic nature of NEIL1's CTD, a feature that may be critical to providing specificity for NEIL1's multiple, functional interactions. Copyright © 2013 Elsevier Ltd. All rights reserved.

The leucine-rich repeat structure.

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Bella, J; Hindle, K L; McEwan, P A; Lovell, S C

2008-08-01

The leucine-rich repeat is a widespread structural motif of 20-30 amino acids with a characteristic repetitive sequence pattern rich in leucines. Leucine-rich repeat domains are built from tandems of two or more repeats and form curved solenoid structures that are particularly suitable for protein-protein interactions. Thousands of protein sequences containing leucine-rich repeats have been identified by automatic annotation methods. Three-dimensional structures of leucine-rich repeat domains determined to date reveal a degree of structural variability that translates into the considerable functional versatility of this protein superfamily. As the essential structural principles become well established, the leucine-rich repeat architecture is emerging as an attractive framework for structural prediction and protein engineering. This review presents an update of the current understanding of leucine-rich repeat structure at the primary, secondary, tertiary and quaternary levels and discusses specific examples from recently determined three-dimensional structures.

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...... peptide. Despite high structural similarity, the FxFG binding site is located between two alpha helices in the G3BP1 NTF2-like domain and not at the dimer interface as observed for nuclear transport factor 2. ITC studies showed specificity towards the FxFG motif but not FG and GLFG motifs. The unliganded...

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

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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....

Functional role of the cytoplasmic tail domain of the major envelope fusion protein of group II baculoviruses

NARCIS (Netherlands)

Long, G.; Pan, M.; Westenberg, M.; Vlak, J.M.

2006-01-01

F proteins from baculovirus nucleopolyhedrovirus (NPV) group II members are the major budded virus (BV) viral envelope fusion proteins. They undergo furin-like proteolysis processing in order to be functional. F proteins from different baculovirus species have a long cytoplasmic tail domain (CTD),

Surgical results of myelopathy secondary to the cervical disc herniation and the availability of CTD

Energy Technology Data Exchange (ETDEWEB)

Sho, Tomoya; Kataoka, Osamu; Washimi, Masatoshi; Fujita, Masayuki; Bessho, Yasuo (National Kobe Hospital, Hyogo (Japan))

1990-08-01

This study evaluated the contribution of computed tomographic discography (CTD) to the surgical indications and selection of surgical techniques in cervical disc herniation. The study population consisted of 73 patients who were diagnosed as having cervical disc herniation by CTD: Of them, hernia mass was confirmed by surgery in 64 patients (a concordance rate of 88% between CTD and surgical findings). In evaluable 40 patients receiving computed tomographic myelography (CTM), the rate of flattened spinal cord on CTM was significantly correlatd with postoperative prognosis. Flattened spinal cord was favorably improved. Higher preoperative flat rate was associated with severer cervical disc herniation. CTD provided the information concerning the positional relation in the posterior longitudinal ligament of hernia mass. Preoperative severity, preoperative rate of flattened spinal cord, and the site of protrusion of hernia mass were independent of surgical outcome. (N.K.).

Surgical results of myelopathy secondary to the cervical disc herniation and the availability of CTD

International Nuclear Information System (INIS)

Sho, Tomoya; Kataoka, Osamu; Washimi, Masatoshi; Fujita, Masayuki; Bessho, Yasuo

1990-01-01

This study evaluated the contribution of computed tomographic discography (CTD) to the surgical indications and selection of surgical techniques in cervical disc herniation. The study population consisted of 73 patients who were diagnosed as having cervical disc herniation by CTD: Of them, hernia mass was confirmed by surgery in 64 patients (a concordance rate of 88% between CTD and surgical findings). In evaluable 40 patients receiving computed tomographic myelography (CTM), the rate of flattened spinal cord on CTM was significantly correlatd with postoperative prognosis. Flattened spinal cord was favorably improved. Higher preoperative flat rate was associated with severer cervical disc herniation. CTD provided the information concerning the positional relation in the posterior longitudinal ligament of hernia mass. Preoperative severity, preoperative rate of flattened spinal cord, and the site of protrusion of hernia mass were independent of surgical outcome. (N.K.)

Study of domain depinning during repeated polarization reversal in hard PZT ceramics using acoustic emission

International Nuclear Information System (INIS)

Prabakar, K; Rao, S P Mallikarjun

2006-01-01

Acoustic emission (AE) has been studied during repeated polarization reversals (at 50 Hz) in hard PZT-8 ceramics. The AE and hysteresis loop were monitored at regular intervals of electric field (±20 kV cm -1 peak) application till 10 8 cycles. The sample did not fatigue and an increase in saturation polarization (Ps) was observed. AE was observed with zero threshold till 10 5 cycles when the field was increasing in both half cycles of the applied field. The initial increase in AE activity with increasing number of field cycles till 10 5 was explained on the basis of defect dipoles encouraging the 90 deg. domain switches, i.e. domain depinning. The decrease in AE activity, an increase in threshold field for the observed AE and a further increase in Ps after 10 5 cycles were explained based on the changes in the orientation of defect dipoles with respect to Ps due to the applied field cycles. This was found to encourage the 180 0 domain switches but pin the 90 deg. domains. An increase in AE at 10 8 cycles after applying a higher field of ±25 kV cm -1 was found to be mainly due to microcracking

Role of the RNA polymerase α subunits in CII-dependent activation of the bacteriophage λ pE promoter: identification of important residues and positioning of the α C-terminal domains

Science.gov (United States)

Kedzierska, Barbara; Lee, David J.; Węgrzyn, Grzegorz; Busby, Stephen J. W.; Thomas, Mark S.

2004-01-01

The bacteriophage λ CII protein stimulates the activity of three phage promoters, pE, pI and paQ, upon binding to a site overlapping the –35 element at each promoter. Here we used preparations of RNA polymerase carrying a DNA cleavage reagent attached to specific residues in the C-terminal domain of the RNA polymerase α subunit (αCTD) to demonstrate that one αCTD binds near position –41 at pE, whilst the other αCTD binds further upstream. The αCTD bound near position –41 is oriented such that its 261 determinant is in close proximity to σ70. The location of αCTD in CII-dependent complexes at the pE promoter is very similar to that found at many activator-independent promoters, and represents an alternative configuration for αCTD at promoters where activators bind sites overlapping the –35 region. We also used an in vivo alanine scan analysis to show that the DNA-binding determinant of αCTD is involved in stimulation of the pE promoter by CII, and this was confirmed by in vitro transcription assays. We also show that whereas the K271E substitution in αCTD results in a drastic decrease in CII-dependent activation of pE, the pI and paQ promoters are less sensitive to this substitution, suggesting that the role of αCTD at the three lysogenic promoters may be different. PMID:14762211

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

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L. Boehme

2009-12-01

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 and 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, real-time data from remote places 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 or even absent. 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.

Structure of the Z Ring-associated Protein, ZapD, Bound to the C-terminal Domain of the Tubulin-like Protein, FtsZ, Suggests Mechanism of Z Ring Stabilization through FtsZ Cross-linking.

Science.gov (United States)

Schumacher, Maria A; Huang, Kuo-Hsiang; Zeng, Wenjie; Janakiraman, Anuradha

2017-03-03

Cell division in most bacteria is mediated by the tubulin-like FtsZ protein, which polymerizes in a GTP-dependent manner to form the cytokinetic Z ring. A diverse repertoire of FtsZ-binding proteins affects FtsZ localization and polymerization to ensure correct Z ring formation. Many of these proteins bind the C-terminal domain (CTD) of FtsZ, which serves as a hub for FtsZ regulation. FtsZ ring-associated proteins, ZapA-D (Zaps), are important FtsZ regulatory proteins that stabilize FtsZ assembly and enhance Z ring formation by increasing lateral assembly of FtsZ protofilaments, which then form the Z ring. There are no structures of a Zap protein bound to FtsZ; therefore, how these proteins affect FtsZ polymerization has been unclear. Recent data showed ZapD binds specifically to the FtsZ CTD. Thus, to obtain insight into the ZapD-CTD interaction and how it may mediate FtsZ protofilament assembly, we determined the Escherichia coli ZapD-FtsZ CTD structure to 2.67 Å resolution. The structure shows that the CTD docks within a hydrophobic cleft in the ZapD helical domain and adopts an unusual structure composed of two turns of helix separated by a proline kink. FtsZ CTD residue Phe-377 inserts into the ZapD pocket, anchoring the CTD in place and permitting hydrophobic contacts between FtsZ residues Ile-374, Pro-375, and Leu-378 with ZapD residues Leu-74, Trp-77, Leu-91, and Leu-174. The structural findings were supported by mutagenesis coupled with biochemical and in vivo studies. The combined data suggest that ZapD acts as a molecular cross-linking reagent between FtsZ protofilaments to enhance FtsZ assembly. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

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.

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

Science.gov (United States)

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

2014-01-01

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

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 1978-05-20 to 1979-01-15 (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...

Entry into the nuclear pore complex is controlled by a cytoplasmic exclusion zone containing dynamic GLFG-repeat nucleoporin domains.

Science.gov (United States)

Fiserova, Jindriska; Spink, Matthew; Richards, Shane A; Saunter, Christopher; Goldberg, Martin W

2014-01-01

Nuclear pore complexes (NPCs) mediate nucleocytoplasmic movement. The central channel contains proteins with phenylalanine-glycine (FG) repeats, or variations (GLFG, glycine-leucine-phenylalanine-glycine). These are 'intrinsically disordered' and often represent weak interaction sites that become ordered upon interaction. We investigated this possibility during nuclear transport. Using electron microscopy of S. cerevisiae, we show that NPC cytoplasmic filaments form a dome-shaped structure enclosing GLFG domains. GLFG domains extend out of this structure and are part of an 'exclusion zone' that might act as a partial barrier to entry of transport-inert proteins. The anchor domain of a GLFG nucleoporin locates exclusively to the central channel. By contrast, the localisation of the GLFG domains varied between NPCs and could be cytoplasmic, central or nucleoplasmic and could stretch up to 80 nm. These results suggest a dynamic exchange between ordered and disordered states. In contrast to diffusion through the NPC, transport cargoes passed through the exclusion zone and accumulated near the central plane. We also show that movement of cargo through the NPC is accompanied by relocation of GLFG domains, suggesting that binding, restructuring and movement of these domains could be part of the translocation mechanism.

Solution structure of the c-terminal dimerization domain of SARS coronavirus nucleocapsid protein solved by the SAIL-NMR method.

Science.gov (United States)

Takeda, Mitsuhiro; Chang, Chung-ke; Ikeya, Teppei; Güntert, Peter; Chang, Yuan-hsiang; Hsu, Yen-lan; Huang, Tai-huang; Kainosho, Masatsune

2008-07-18

The C-terminal domain (CTD) of the severe acute respiratory syndrome coronavirus (SARS-CoV) nucleocapsid protein (NP) contains a potential RNA-binding region in its N-terminal portion and also serves as a dimerization domain by forming a homodimer with a molecular mass of 28 kDa. So far, the structure determination of the SARS-CoV NP CTD in solution has been impeded by the poor quality of NMR spectra, especially for aromatic resonances. We have recently developed the stereo-array isotope labeling (SAIL) method to overcome the size problem of NMR structure determination by utilizing a protein exclusively composed of stereo- and regio-specifically isotope-labeled amino acids. Here, we employed the SAIL method to determine the high-quality solution structure of the SARS-CoV NP CTD by NMR. The SAIL protein yielded less crowded and better resolved spectra than uniform (13)C and (15)N labeling, and enabled the homodimeric solution structure of this protein to be determined. The NMR structure is almost identical with the previously solved crystal structure, except for a disordered putative RNA-binding domain at the N-terminus. Studies of the chemical shift perturbations caused by the binding of single-stranded DNA and mutational analyses have identified the disordered region at the N-termini as the prime site for nucleic acid binding. In addition, residues in the beta-sheet region also showed significant perturbations. Mapping of the locations of these residues onto the helical model observed in the crystal revealed that these two regions are parts of the interior lining of the positively charged helical groove, supporting the hypothesis that the helical oligomer may form in solution.

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

KAUST Repository

Aleisa, Fajr A

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.

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

KAUST Repository

Aleisa, Fajr A; Sakashita, Kosuke; Lee, Jaeman; Abu Samra, Dina Bashir Kamil; Habuchi, Satoshi; Kusakabe, Takahiro; Merzaban, Jasmeen

2017-01-01

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.

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...

Conservation and divergence of C-terminal domain structure in the retinoblastoma protein family

Energy Technology Data Exchange (ETDEWEB)

Liban, Tyler J.; Medina, Edgar M.; Tripathi, Sarvind; Sengupta, Satyaki; Henry, R. William; Buchler, Nicolas E.; Rubin, Seth M. (UCSC); (Duke); (MSU)

2017-04-24

The retinoblastoma protein (Rb) and the homologous pocket proteins p107 and p130 negatively regulate cell proliferation by binding and inhibiting members of the E2F transcription factor family. The structural features that distinguish Rb from other pocket proteins have been unclear but are critical for understanding their functional diversity and determining why Rb has unique tumor suppressor activities. We describe here important differences in how the Rb and p107 C-terminal domains (CTDs) associate with the coiled-coil and marked-box domains (CMs) of E2Fs. We find that although CTD–CM binding is conserved across protein families, Rb and p107 CTDs show clear preferences for different E2Fs. A crystal structure of the p107 CTD bound to E2F5 and its dimer partner DP1 reveals the molecular basis for pocket protein–E2F binding specificity and how cyclin-dependent kinases differentially regulate pocket proteins through CTD phosphorylation. Our structural and biochemical data together with phylogenetic analyses of Rb and E2F proteins support the conclusion that Rb evolved specific structural motifs that confer its unique capacity to bind with high affinity those E2Fs that are the most potent activators of the cell cycle.

Top-Down Charge Transfer Dissociation (CTD) of Gas-Phase Insulin: Evidence of a One-Step, Two-Electron Oxidation Mechanism

Science.gov (United States)

Li, Pengfei; Kreft, Iris; Jackson, Glen P.

2018-02-01

Top-down analyses of protonated insulin cations of charge states of 4+, 5+, or 6+ were performed by exposing the isolated precursor ions to a beam of helium cations with kinetic energy of more than 6 keV, in a technique termed charge transfer dissociation (CTD). The 100 ms charge transfer reaction resulted in approximately 20% conversion efficiency to other intact charge exchange products (CTnoD), and a range of low abundance fragment ions. To increase backbone and sulfide cleavages, and to provide better structural information than straightforward MS2 CTD, the CTnoD oxidized products were isolated and subjected to collisional activation at the MS3 level. The MS3 CTD/CID reaction effectively broke the disulfide linkages, separated the two chains, and yielded more structurally informative fragment ions within the inter-chain cyclic region. CTD also provided doubly oxidized intact product ions at the MS2 level, and resonance ejection of the singly oxidized product ion revealed that the doubly oxidized product originates directly from the isolated precursor ion and not from consecutive CTD reactions of a singly oxidized intermediate. MS4 experiments were employed to help identify potential radical cations and diradical cations, but the results were negative or inconclusive. Nonetheless, the two-electron oxidation process is a demonstration of the very large potential energy (>20 eV) available through CTD, and is a notable capability for a 3D ion trap platform.

Nonlinear analysis of sequence repeats of multi-domain proteins

Energy Technology Data Exchange (ETDEWEB)

Huang Yanzhao [Biomolecular Physics and Modeling Group, Department of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei (China); Li Mingfeng [Biomolecular Physics and Modeling Group, Department of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei (China); Xiao Yi [Biomolecular Physics and Modeling Group, Department of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei (China)]. E-mail: lmf_bill@sina.com

2007-11-15

Many multi-domain proteins have repetitive three-dimensional structures but nearly-random amino acid sequences. In the present paper, by using a modified recurrence plot proposed by us previously, we show that these amino acid sequences have hidden repetitions in fact. These results indicate that the repetitive domain structures are encoded by the repetitive sequences. This also gives a method to detect the repetitive domain structures directly from amino acid sequences.

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...

Computational study of the human dystrophin repeats: interaction properties and molecular dynamics.

Directory of Open Access Journals (Sweden)

Baptiste Legrand

Full Text Available Dystrophin is a large protein involved in the rare genetic disease Duchenne muscular dystrophy (DMD. It functions as a mechanical linker between the cytoskeleton and the sarcolemma, and is able to resist shear stresses during muscle activity. In all, 75% of the dystrophin molecule consists of a large central rod domain made up of 24 repeat units that share high structural homology with spectrin-like repeats. However, in the absence of any high-resolution structure of these repeats, the molecular basis of dystrophin central domain's functions has not yet been deciphered. In this context, we have performed a computational study of the whole dystrophin central rod domain based on the rational homology modeling of successive and overlapping tandem repeats and the analysis of their surface properties. Each tandem repeat has very specific surface properties that make it unique. However, the repeats share enough electrostatic-surface similarities to be grouped into four separate clusters. Molecular dynamics simulations of four representative tandem repeats reveal specific flexibility or bending properties depending on the repeat sequence. We thus suggest that the dystrophin central rod domain is constituted of seven biologically relevant sub-domains. Our results provide evidence for the role of the dystrophin central rod domain as a scaffold platform with a wide range of surface features and biophysical properties allowing it to interact with its various known partners such as proteins and membrane lipids. This new integrative view is strongly supported by the previous experimental works that investigated the isolated domains and the observed heterogeneity of the severity of dystrophin related pathologies, especially Becker muscular dystrophy.

Lentiviral Gag assembly analyzed through the functional characterization of chimeric simian immunodeficiency viruses expressing different domains of the feline immunodeficiency virus capsid protein.

Directory of Open Access Journals (Sweden)

María J Esteva

Full Text Available To gain insight into the functional relationship between the capsid (CA domains of the Gag polyproteins of simian and feline immunodeficiency viruses (SIV and FIV, respectively, we constructed chimeric SIVs in which the CA-coding region was partially or totally replaced by the equivalent region of the FIV CA. The phenotypic characterization of the chimeras allowed us to group them into three categories: the chimeric viruses that, while being assembly-competent, exhibit a virion-associated unstable FIV CA; a second group represented only by the chimeric SIV carrying the N-terminal domain (NTD of the FIV CA which proved to be assembly-defective; and a third group constituted by the chimeric viruses that produce virions exhibiting a mature and stable FIV CA protein, and which incorporate the envelope glycoprotein and contain wild-type levels of viral genome RNA and reverse transcriptase. Further analysis of the latter group of chimeric SIVs demonstrated that they are non-infectious due to a post-entry impairment, such as uncoating of the viral core, reverse transcription or nuclear import of the preintegration complex. Furthermore, we show here that the carboxyl-terminus domain (CTD of the FIV CA has an intrinsic ability to dimerize in vitro and form high-molecular-weight oligomers, which, together with our finding that the FIV CA-CTD is sufficient to confer assembly competence to the resulting chimeric SIV Gag polyprotein, provides evidence that the CA-CTD exhibits more functional plasticity than the CA-NTD. Taken together, our results provide relevant information on the biological relationship between the CA proteins of primate and nonprimate lentiviruses.

Evolutionary Divergence of the C-terminal Domain of Complexin Accounts for Functional Disparities between Vertebrate and Invertebrate Complexins

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Rachel T. Wragg

2017-05-01

Full Text Available Complexin is a critical presynaptic protein that regulates both spontaneous and calcium-triggered neurotransmitter release in all synapses. Although the SNARE-binding central helix of complexin is highly conserved and required for all known complexin functions, the remainder of the protein has profoundly diverged across the animal kingdom. Striking disparities in complexin inhibitory activity are observed between vertebrate and invertebrate complexins but little is known about the source of these differences or their relevance to the underlying mechanism of complexin regulation. We found that mouse complexin 1 (mCpx1 failed to inhibit neurotransmitter secretion in Caenorhabditis elegans neuromuscular junctions lacking the worm complexin 1 (CPX-1. This lack of inhibition stemmed from differences in the C-terminal domain (CTD of mCpx1. Previous studies revealed that the CTD selectively binds to highly curved membranes and directs complexin to synaptic vesicles. Although mouse and worm complexin have similar lipid binding affinity, their last few amino acids differ in both hydrophobicity and in lipid binding conformation, and these differences strongly impacted CPX-1 inhibitory function. Moreover, function was not maintained if a critical amphipathic helix in the worm CPX-1 CTD was replaced with the corresponding mCpx1 amphipathic helix. Invertebrate complexins generally shared more C-terminal similarity with vertebrate complexin 3 and 4 isoforms, and the amphipathic region of mouse complexin 3 significantly restored inhibitory function to worm CPX-1. We hypothesize that the CTD of complexin is essential in conferring an inhibitory function to complexin, and that this inhibitory activity has been attenuated in the vertebrate complexin 1 and 2 isoforms. Thus, evolutionary changes in the complexin CTD differentially shape its synaptic role across phylogeny.

CTD data collected using CTD casts from NOAA Ship RESEARCHER in the Gulf of Mexico from 1977-07-13 to 1977-07-23 (NODC 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...

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.

Structural determinants at the interface of the ARC2 and leucine-rich repeat domains control the activation of the plant immune receptors Rx1 and Gpa2.

Science.gov (United States)

Slootweg, Erik J; Spiridon, Laurentiu N; Roosien, Jan; Butterbach, Patrick; Pomp, Rikus; Westerhof, Lotte; Wilbers, Ruud; Bakker, Erin; Bakker, Jaap; Petrescu, Andrei-José; Smant, Geert; Goverse, Aska

2013-07-01

Many plant and animal immune receptors have a modular nucleotide-binding-leucine-rich repeat (NB-LRR) architecture in which a nucleotide-binding switch domain, NB-ARC, is tethered to a LRR sensor domain. The cooperation between the switch and sensor domains, which regulates the activation of these proteins, is poorly understood. Here, we report structural determinants governing the interaction between the NB-ARC and LRR in the highly homologous plant immune receptors Gpa2 and Rx1, which recognize the potato cyst nematode Globodera pallida and Potato virus X, respectively. Systematic shuffling of polymorphic sites between Gpa2 and Rx1 showed that a minimal region in the ARC2 and N-terminal repeats of the LRR domain coordinate the activation state of the protein. We identified two closely spaced amino acid residues in this region of the ARC2 (positions 401 and 403) that distinguish between autoactivation and effector-triggered activation. Furthermore, a highly acidic loop region in the ARC2 domain and basic patches in the N-terminal end of the LRR domain were demonstrated to be required for the physical interaction between the ARC2 and LRR. The NB-ARC and LRR domains dissociate upon effector-dependent activation, and the complementary-charged regions are predicted to mediate a fast reassociation, enabling multiple rounds of activation. Finally, we present a mechanistic model showing how the ARC2, NB, and N-terminal half of the LRR form a clamp, which regulates the dissociation and reassociation of the switch and sensor domains in NB-LRR proteins.

Cloning, expression, purification, and characterisation of the HEAT-repeat domain of TOR from the thermophilic eukaryote Chaetomium thermophilum.

Science.gov (United States)

Robinson, Graham C; Vegunta, Yogesh; Gabus, Caroline; Gaubitz, Christl; Thore, Stéphane

2017-05-01

The Target of Rapamycin Complex is a central controller of cell growth and differentiation in eukaryotes. Its global architecture has been described by cryoelectron microscopy, and regions of its central TOR protein have been described by X-ray crystallography. However, the N-terminal region of this protein, which consists of a series of HEAT repeats, remains uncharacterised at high resolution, most likely due to the absence of a suitable purification procedure. Here, we present a robust method for the preparation of the HEAT-repeat domain, utilizing the thermophilic fungus Chaetomium thermophilum as a source organism. We describe construct design and stable expression in insect cells. An efficient two-step purification procedure is presented, and the purified product is characterised by SEC and MALDI-TOF MS. The methods described pave the way for a complete high-resolution characterisation of this elusive region of the TOR protein. Copyright © 2017 Elsevier Inc. All rights reserved.

Forster Resonance Energy Transfer (FRET) Analysis of Dual CFP/YFP Labeled AMPA Receptors Reveals Structural Rearrangement within the C-Terminal Domain during Receptor Activation

DEFF Research Database (Denmark)

Zachariassen, Linda Grønborg; Katchan, Mila; Plested, Andrew

2014-01-01

that retain function and display intrareceptor FRET. This includes a construct (GluA2-6Y-10C) containing YFP in the intracellular loop between the M1 and M2 membrane-embedded segments and CFP inserted in the C-ter- minal domain (CTD). GluA2-6Y-10C displays FRET with an efficiency of 0.11 while retaining wild......-type receptor expression and kinetic properties. We have used GluA2-6Y-10C to study conformational changes in homomeric GluA2 receptors during receptor activation. Our results show that the FRET efficiency is dependent on functional state of GluA2-6Y-10C and hereby indi- cates that the intracellular CTD...

The prediction of the incidence rate of upper limb musculoskeletal disorders, with CTD risk index method on potters of Meybod city

Directory of Open Access Journals (Sweden)

Reza Khani Jazani

2012-02-01

Full Text Available Background: The objective of this study was to predict the incidence of musculoskeletal disorders in potters of Meybod city by performing CTD risk index method.Materials and Method: This is a descriptive cross-sectional study. Target society was all workers in pottery workshops which were located in the Meybod. Information related to musculoskeletal disorders was obtained by the Nordic questionnaire and we used CTD risk index method to predict the incidence of musculoskeletal disorders.Results: We observed in this study that 59.3% of the potters had symptoms of musculoskeletal disorders in at least in one of their upper extremities. Also significant differences between mean CTD risk index on potters with and without symptoms of the upper limb musculoskeletal disorders, respectively (p=0.038.Conclusion: CTD risk index method can be as a suitable method for predicting the incidence of musculoskeletal disorders used in the potters

Nuclear Trafficking of the Rabies Virus Interferon Antagonist P-Protein Is Regulated by an Importin-Binding Nuclear Localization Sequence in the C-Terminal Domain.

Directory of Open Access Journals (Sweden)

Caitlin L Rowe

Full Text Available Rabies virus P-protein is expressed as five isoforms (P1-P5 which undergo nucleocytoplasmic trafficking important to roles in immune evasion. Although nuclear import of P3 is known to be mediated by an importin (IMP-recognised nuclear localization sequence in the N-terminal region (N-NLS, the mechanisms underlying nuclear import of other P isoforms in which the N-NLS is inactive or has been deleted have remained unresolved. Based on the previous observation that mutation of basic residues K214/R260 of the P-protein C-terminal domain (P-CTD can result in nuclear exclusion of P3, we used live cell imaging, protein interaction analysis and in vitro nuclear transport assays to examine in detail the nuclear trafficking properties of this domain. We find that the effect of mutation of K214/R260 on P3 is largely dependent on nuclear export, suggesting that nuclear exclusion of mutated P3 involves the P-CTD-localized nuclear export sequence (C-NES. However, assays using cells in which nuclear export is pharmacologically inhibited indicate that these mutations significantly inhibit P3 nuclear accumulation and, importantly, prevent nuclear accumulation of P1, suggestive of effects on NLS-mediated import activity in these isoforms. Consistent with this, molecular binding and transport assays indicate that the P-CTD mediates IMPα2/IMPβ1-dependent nuclear import by conferring direct binding to the IMPα2/IMPβ1 heterodimer, as well as to a truncated form of IMPα2 lacking the IMPβ-binding autoinhibitory domain (ΔIBB-IMPα2, and IMPβ1 alone. These properties are all dependent on K214 and R260. This provides the first evidence that P-CTD contains a genuine IMP-binding NLS, and establishes the mechanism by which P-protein isoforms other than P3 can be imported to the nucleus. These data underpin a refined model for P-protein trafficking that involves the concerted action of multiple NESs and IMP-binding NLSs, and highlight the intricate regulation of P

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. Copyright © 2013 The Authors. Published by Elsevier B.V. All rights reserved.

Highly sensitive detection of individual HEAT and ARM repeats with HHpred and COACH.

Science.gov (United States)

Kippert, Fred; Gerloff, Dietlind L

2009-09-24

HEAT and ARM repeats occur in a large number of eukaryotic proteins. As these repeats are often highly diverged, the prediction of HEAT or ARM domains can be challenging. Except for the most clear-cut cases, identification at the individual repeat level is indispensable, in particular for determining domain boundaries. However, methods using single sequence queries do not have the sensitivity required to deal with more divergent repeats and, when applied to proteins with known structures, in some cases failed to detect a single repeat. Testing algorithms which use multiple sequence alignments as queries, we found two of them, HHpred and COACH, to detect HEAT and ARM repeats with greatly enhanced sensitivity. Calibration against experimentally determined structures suggests the use of three score classes with increasing confidence in the prediction, and prediction thresholds for each method. When we applied a new protocol using both HHpred and COACH to these structures, it detected 82% of HEAT repeats and 90% of ARM repeats, with the minimum for a given protein of 57% for HEAT repeats and 60% for ARM repeats. Application to bona fide HEAT and ARM proteins or domains indicated that similar numbers can be expected for the full complement of HEAT/ARM proteins. A systematic screen of the Protein Data Bank for false positive hits revealed their number to be low, in particular for ARM repeats. Double false positive hits for a given protein were rare for HEAT and not at all observed for ARM repeats. In combination with fold prediction and consistency checking (multiple sequence alignments, secondary structure prediction, and position analysis), repeat prediction with the new HHpred/COACH protocol dramatically improves prediction in the twilight zone of fold prediction methods, as well as the delineation of HEAT/ARM domain boundaries. A protocol is presented for the identification of individual HEAT or ARM repeats which is straightforward to implement. It provides high

SWFSC FED Mid Water Trawl Juvenile Rockfish Survey, CTD Data, 1987-2015

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...

Structural and dynamics studies of a truncated variant of CI repressor from bacteriophage TP901-1

DEFF Research Database (Denmark)

Rasmussen, Kim Krighaar; Frandsen, Kristian E. H.; Erba, Elisabetta Boeri

2016-01-01

The CI repressor from the temperate bacteriophage TP901-1 consists of two folded domains, an N-terminal helix-turn-helix DNA-binding domain (NTD) and a C-terminal oligomerization domain (CTD), which we here suggest to be further divided into CTD1 and CTD2. Full-length CI is a hexameric protein......, whereas a truncated version, CIΔ58, forms dimers. We identify the dimerization region of CIΔ58 as CTD1 and determine its secondary structure to be helical both within the context of CIΔ58 and in isolation. To our knowledge this is the first time that a helical dimerization domain has been found in a phage...... repressor. We also precisely determine the length of the flexible linker connecting the NTD to the CTD. Using electrophoretic mobility shift assays and native mass spectrometry, we show that CIΔ58 interacts with the O-L operator site as one dimer bound to both half-sites, and with much higher affinity than...

The Pentapeptide Repeat Proteins

OpenAIRE

Vetting, Matthew W.; Hegde, Subray S.; Fajardo, J. Eduardo; Fiser, Andras; Roderick, Steven L.; Takiff, Howard E.; Blanchard, John S.

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 Myc...

Initial combination therapy with ambrisentan and tadalafil in connective tissue disease-associated pulmonary arterial hypertension (CTD-PAH): subgroup analysis from the AMBITION trial.

Science.gov (United States)

Coghlan, John Gerry; Galiè, Nazzareno; Barberà, Joan Albert; Frost, Adaani E; Ghofrani, Hossein-Ardeschir; Hoeper, Marius M; Kuwana, Masataka; McLaughlin, Vallerie V; Peacock, Andrew J; Simonneau, Gérald; Vachiéry, Jean-Luc; Blair, Christiana; Gillies, Hunter; Miller, Karen L; Harris, Julia H N; Langley, Jonathan; Rubin, Lewis J

2017-07-01

Patients with connective tissue disease-associated pulmonary arterial hypertension (CTD-PAH), in particular systemic sclerosis (SSc), had an attenuated response compared with idiopathic PAH in most trials. Thus, there is uncertainty regarding the benefit of PAH-targeted therapy in some forms of CTD-PAH. To explore the safety and efficacy of initial combination therapy with ambrisentan and tadalafil versus ambrisentan or tadalafil monotherapy in patients with CTD-PAH and SSc-PAH enrolled in the AMBITION trial. This was a post hoc analysis of patients with CTD-PAH and SSc-PAH from AMBITION, an event-driven, double-blind trial in patients with WHO functional class II/III PAH. Treatment-naive patients were randomised 2:1:1 to once-daily initial combination therapy with ambrisentan plus tadalafil or monotherapy with ambrisentan or tadalafil, respectively. The primary endpoint was time to the first clinical failure event (first occurrence of death, hospitalisation for worsening PAH, disease progression or unsatisfactory long-term clinical response). In the primary analysis set (N=500), 187 patients had CTD-PAH, of whom 118 had SSc-PAH. Initial combination therapy reduced the risk of clinical failure versus pooled monotherapy in each subgroup: CTD-PAH (HR 0.43 (95% CI 0.24 to 0.77)) and SSc-PAH (0.44 (0.22 to 0.89)). The most common AE was peripheral oedema, which was reported more frequently with initial combination therapy than monotherapy in the two PAH subgroups. The relative frequency of adverse events between those on combination therapy versus monotherapy was similar across subgroups. This post hoc subgroup analysis provides evidence that CTD-PAH and SSc-PAH patients benefit from initial ambrisentan and tadalafil combination therapy. NCT01178073, post results. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

An Amphiphysin-Like Domain in Fus2p Is Required for Rvs161p Interaction and Cortical Localization

Directory of Open Access Journals (Sweden)

Richard A. Stein

2016-02-01

Full Text Available Cell–cell fusion fulfils essential roles in fertilization, development and tissue repair. In the budding yeast, Saccharomyces cerevisiae, fusion between two haploid cells of opposite mating type generates the diploid zygote. Fus2p is a pheromone-induced protein that regulates cell wall removal during mating. Fus2p shuttles from the nucleus to localize at the shmoo tip, bound to Rvs161p, an amphiphysin. However, Rvs161p independently binds a second amphiphysin, Rvs167p, playing an essential role in endocytosis. To understand the basis of the Fus2p–Rvs161p interaction, we analyzed Fus2p structural domains. A previously described N-terminal domain (NTD is necessary and sufficient to regulate nuclear/cytoplasmic trafficking of Fus2p. The Dbl homology domain (DBH binds GTP-bound Cdc42p; binding is required for cell fusion, but not localization. We identified an approximately 200 amino acid region of Fus2p that is both necessary and sufficient for Rvs161p binding. The Rvs161p binding domain (RBD contains three predicted alpha-helices; structural modeling suggests that the RBD adopts an amphiphysin-like structure. The RBD contains a 13-amino-acid region, conserved with Rvs161p and other amphiphysins, which is essential for binding. Mutations in the RBD, predicted to affect membrane binding, abolish cell fusion without affecting Rvs161p binding. We propose that Fus2p/Rvs161p form a novel heterodimeric amphiphysin required for cell fusion. Rvs161p binding is required but not sufficient for Fus2p localization. Mutations in the C-terminal domain (CTD of Fus2p block localization, but not Rvs161p binding, causing a significant defect in cell fusion. We conclude that the Fus2p CTD mediates an additional, Rvs161p-independent interaction at the shmoo tip.

Yeast eIF4B binds to the head of the 40S ribosomal subunit and promotes mRNA recruitment through its N-terminal and internal repeat domains.

Science.gov (United States)

Walker, Sarah E; Zhou, Fujun; Mitchell, Sarah F; Larson, Victoria S; Valasek, Leos; Hinnebusch, Alan G; Lorsch, Jon R

2013-02-01

Eukaryotic translation initiation factor (eIF)4B stimulates recruitment of mRNA to the 43S ribosomal pre-initiation complex (PIC). Yeast eIF4B (yeIF4B), shown previously to bind single-stranded (ss) RNA, consists of an N-terminal domain (NTD), predicted to be unstructured in solution; an RNA-recognition motif (RRM); an unusual domain comprised of seven imperfect repeats of 26 amino acids; and a C-terminal domain. Although the mechanism of yeIF4B action has remained obscure, most models have suggested central roles for its RRM and ssRNA-binding activity. We have dissected the functions of yeIF4B's domains and show that the RRM and its ssRNA-binding activity are dispensable in vitro and in vivo. Instead, our data indicate that the 7-repeats and NTD are the most critical domains, which mediate binding of yeIF4B to the head of the 40S ribosomal subunit via interaction with Rps20. This interaction induces structural changes in the ribosome's mRNA entry channel that could facilitate mRNA loading. We also show that yeIF4B strongly promotes productive interaction of eIF4A with the 43S•mRNA PIC in a manner required for efficient mRNA recruitment.

CTD data from the Madeira and Iberian Abyssal Plains. CHARLES DARWIN cruises 3/85 and 9A/85

International Nuclear Information System (INIS)

Saunders, P.M.

1986-01-01

This report presents lists and graphs of CTD data taken aboard RRS Charles Darwin on cruises 3 (May 1985) and 9A (November 1985). The majority of the lowerings were made in support of two experiments; the deployment of deep SOFAR floats and of deep moored current meters, the latter near 31 0 30'N 25 0 W (GME site). All CTD data is compared with reversing thermometer observations, and with determinations of salinity and dissolved oxygen derived from samples. (author)

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. Copyright © 2010 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Structural Basis for Substrate Recognition by the Ankyrin Repeat Domain of Human DHHC17 Palmitoyltransferase

Energy Technology Data Exchange (ETDEWEB)

Verardi, Raffaello; Kim, Jin-Sik; Ghirlando, Rodolfo; Banerjee, Anirban

2017-09-01

DHHC enzymes catalyze palmitoylation, a major post-translational modification that regulates a number of key cellular processes. There are up to 24 DHHCs in mammals and hundreds of substrate proteins that get palmitoylated. However, how DHHC enzymes engage with their substrates is still poorly understood. There is currently no structural information about the interaction between any DHHC enzyme and protein substrates. In this study we have investigated the structural and thermodynamic bases of interaction between the ankyrin repeat domain of human DHHC17 (ANK17) and Snap25b. We solved a high-resolution crystal structure of the complex between ANK17 and a peptide fragment of Snap25b. Through structure-guided mutagenesis, we discovered key residues in DHHC17 that are critically important for interaction with Snap25b. We further extended our finding by showing that the same residues are also crucial for the interaction of DHHC17 with Huntingtin, one of its most physiologically relevant substrates.

Quantum chemical calculations and molecular docking studies of 5-(4-chlorobenzylidene)thiazolidine-2,4-dione(CTD) and its mannich product 5-(4-chlorobenzylidene)-3-(morpholinomethyl)thiazolidine-2,4-dione (CMTD)

Science.gov (United States)

Fatma, Shaheen; Bishnoi, Abha; Verma, Anil Kumar; Singh, Vineeta; Srivastava, Krishna

2018-04-01

This work presents the synthesis of 5-(4-chlorobenzylidene)thiazolidine-2,4-dione (CTD) by Claisen condensation of thiazolidine-2,4-dione and mannich product of CTD, 5-(4-chlorobenzylidene)-3-(morpholinomethyl)thiazolidine-2,4-dione (CMTD). The static first hyperpolarizability values for thiazolidine-2,4-dione derivatives have been calculated as 10.28 × 10-30 esu for CTD and 19.42 × 10-30 esu for CMTD. The gradual increase in hyperpolarizability values of synthesized thiazolidine-2,4-dione derivatives from CTD to CMTD is due to the blockage of sbnd NH group on CTD by mannich reaction. The structures of these compounds have been derived by spectroscopic(IR, UV, Mass, 1H and 13C NMR) analysis as well as with the help of theoretical studies. The high values of first static hyperpolarizability indicate that the synthesized derivatives are suitable as non-linear optical (NLO) material. CTD with MIC value of 12.5 μg/mL can be developed as an alternative drug for the treatment of enteric fever. Calculated frontier orbital gap values suggest that the CMTD is a soft molecule with high chemical reactivity and is more polarizable as compared to the CTD. Molecular electrostatic potential is calculated for the optimized geometry of the molecules to estimate their chemical reactivity. The inhibitor CTD forms a stable complex with 3-dehydroquinase enzyme of Salmonella typhi. It is evident from the ligand receptor interactions and a binding affinity value of -5.88 kcal/mol and an inhibition constant of 49.22 μM. This is further confirmed by the experimental biological data. The molecular docking studies are supportive of the antibacterial activity of CTD exhibiting high inhibition constant and binding energy.

CTD, nephelometry and currentmeter measurements at the N.E.A. dumpsite during the 1984 Epicea cruise

International Nuclear Information System (INIS)

Vangriesheim, A.

1989-01-01

In May of 1984, an EPICEA cruise to the N.E.A. dumpsite was conducted aboard the french research vessel LE SUROIT. The site work was jointly sponsored by IFREMER and CEA and followed IFREMER studies over Meriadzek Terrace. The main purposes of this joint cruise included first an exploration of a part of the site with the IFREMER unmanned submersible EPAULARD, including bottom photographs. Biological measurements included baited cameras, fish and amphipod traps, radioactive baited traps and one-year mooring of a bottom-mounted autonomous colonisation module (the M.A.C.). Geological measurements were made with a 3.5 Khz echo sounder. Radiochemistry included water samples. Physical oceanography included a CTD equipped with a nephelometer. Five CTD vertical profiles to the bottom were made over the dumpsite, 4 of them in the area previously covered by the SEABEAM and 1 outside of that to the East. At the end of the cruise, a M.A.C. was equipped with a currentmeter at 10 meters above the bottom, and moored for one year. The results of the CTD, nephelometry and current measurements are presented

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...

Trafficking Dynamics of PCSK9-Induced LDLR Degradation: Focus on Human PCSK9 Mutations and C-Terminal Domain.

Directory of Open Access Journals (Sweden)

Steve Poirier

Full Text Available PCSK9 is a secreted ligand and negative post-translational regulator of low-density lipoprotein receptor (LDLR in hepatocytes. Gain-of-function (GOF or loss-of-function (LOF mutations in PCSK9 are directly correlated with high or low plasma LDL-cholesterol levels, respectively. Therefore, PCSK9 is a prevailing lipid-lowering target to prevent coronary heart diseases and stroke. Herein, we fused monomeric fluorescent proteins to PCSK9 and LDLR to visualize their intra- and extracellular trafficking dynamics by live confocal microscopy. Fluorescence recovery after photobleaching (FRAP showed that PCSK9 LOF R46L mutant and GOF mutations S127R and D129G, but not the LDLR high-affinity mutant D374Y, significantly accelerate PCSK9 exit from the endoplasmic reticulum (ER. Quantitative analysis of inverse FRAP revealed that only R46L presented a much slower trafficking from the trans-Golgi network (TGN to the plasma membrane and a lower mobile fraction likely suggesting accumulation or delayed exit at the TGN as an underlying mechanism. While not primarily involved in LDLR binding, PCSK9 C-terminal domain (CTD was found to be essential to induce LDLR degradation both upon its overexpression in cells or via the extracellular pathway. Our data revealed that PCSK9 CTD is required for the localization of PCSK9 at the TGN and increases its LDLR-mediated endocytosis. Interestingly, intracellular lysosomal targeting of PCSK9-ΔCTD was able to rescue its capacity to induce LDLR degradation emphasizing a role of the CTD in the sorting of PCSK9-LDLR complex towards late endocytic compartments. Finally, we validated our dual fluorescence system as a cell based-assay by preventing PCSK9 internalization using a PCSK9-LDLR blocking antibody, which may be expended to identify protein, peptide or small molecule inhibitors of PCSK9.

Recruitment of TREX to the transcription machinery by its direct binding to the phospho-CTD of RNA polymerase II.

Directory of Open Access Journals (Sweden)

Dominik M Meinel

2013-11-01

Full Text Available Messenger RNA (mRNA synthesis and export are tightly linked, but the molecular mechanisms of this coupling are largely unknown. In Saccharomyces cerevisiae, the conserved TREX complex couples transcription to mRNA export and mediates mRNP formation. Here, we show that TREX is recruited to the transcription machinery by direct interaction of its subcomplex THO with the serine 2-serine 5 (S2/S5 diphosphorylated CTD of RNA polymerase II. S2 and/or tyrosine 1 (Y1 phosphorylation of the CTD is required for TREX occupancy in vivo, establishing a second interaction platform necessary for TREX recruitment in addition to RNA. Genome-wide analyses show that the occupancy of THO and the TREX components Sub2 and Yra1 increases from the 5' to the 3' end of the gene in accordance with the CTD S2 phosphorylation pattern. Importantly, in a mutant strain, in which TREX is recruited to genes but does not increase towards the 3' end, the expression of long transcripts is specifically impaired. Thus, we show for the first time that a 5'-3' increase of a protein complex is essential for correct expression of the genome. In summary, we provide insight into how the phospho-code of the CTD directs mRNP formation and export through TREX recruitment.

Recruitment of TREX to the transcription machinery by its direct binding to the phospho-CTD of RNA polymerase II.

Science.gov (United States)

Meinel, Dominik M; Burkert-Kautzsch, Cornelia; Kieser, Anja; O'Duibhir, Eoghan; Siebert, Matthias; Mayer, Andreas; Cramer, Patrick; Söding, Johannes; Holstege, Frank C P; Sträßer, Katja

2013-11-01

Messenger RNA (mRNA) synthesis and export are tightly linked, but the molecular mechanisms of this coupling are largely unknown. In Saccharomyces cerevisiae, the conserved TREX complex couples transcription to mRNA export and mediates mRNP formation. Here, we show that TREX is recruited to the transcription machinery by direct interaction of its subcomplex THO with the serine 2-serine 5 (S2/S5) diphosphorylated CTD of RNA polymerase II. S2 and/or tyrosine 1 (Y1) phosphorylation of the CTD is required for TREX occupancy in vivo, establishing a second interaction platform necessary for TREX recruitment in addition to RNA. Genome-wide analyses show that the occupancy of THO and the TREX components Sub2 and Yra1 increases from the 5' to the 3' end of the gene in accordance with the CTD S2 phosphorylation pattern. Importantly, in a mutant strain, in which TREX is recruited to genes but does not increase towards the 3' end, the expression of long transcripts is specifically impaired. Thus, we show for the first time that a 5'-3' increase of a protein complex is essential for correct expression of the genome. In summary, we provide insight into how the phospho-code of the CTD directs mRNP formation and export through TREX recruitment.

Impact of retinal pigment epithelium pathology on spectral-domain optical coherence tomography-derived macular thickness and volume metrics and their intersession repeatability.

Science.gov (United States)

Hanumunthadu, Daren; Wang, Jin Ping; Chen, Wei; Wong, Evan N; Chen, Yi; Morgan, William H; Patel, Praveen J; Chen, Fred K

2017-04-01

To determine the impact of retinal pigment epithelium (RPE) pathology on intersession repeatability of retinal thickness and volume metrics derived from Spectralis spectral-domain optical coherence tomography (Heidelberg Engineering, Heidelberg, Germany). Prospective cross-sectional single centre study. A total of 56 eyes of 56 subjects were divided into three groups: (i) normal RPE band (25 eyes); (ii) RPE elevation: macular soft drusen (13 eyes); and (iii) RPE attenuation: geographic atrophy or inherited retinal diseases (18 eyes). Each subject underwent three consecutive follow-up macular raster scans (61 B-scans at 119 μm separation) at 1-month intervals. Retinal thicknesses and volumes for each zone of the macular subfields before and after manual correction of segmentation error. Coefficients of repeatability (CR) were calculated. Mean (range) age was 57 (21-88) years. Mean central subfield thickness (CST) and total macular volume were 264 and 258 μm (P = 0.62), and 8.0 and 7.8 mm 3 (P = 0.31), before and after manual correction. Intersession CR (95% confidence interval) for CST and total macular volume were reduced from 40 (38-41) to 8.3 (8.1-8.5) and 0.62 to 0.16 mm 3 after manual correction of segmentation lines. CR for CST were 7.4, 23.5 and 66.7 μm before and 7.0, 10.9 and 7.6 μm after manual correction in groups i, ii and iii. Segmentation error in eyes with RPE disease has a significant impact on intersession repeatability of Spectralis spectral-domain optical coherence tomography macular thickness and volume metrics. Careful examination of each B-scan and manual adjustment can enhance the utility of quantitative measurement. Improved automated segmentation algorithms are needed. © 2016 Royal Australian and New Zealand College of Ophthalmologists.

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

International Nuclear Information System (INIS)

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

2013-01-01

The triclinic structure of the HIV-1 capsid protein contains four molecules in the asymmetric unit that form a novel packing interface that could conceivably resemble an intermediate structure that is involved in the early steps of HIV-1 assembly. 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

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...

Structures of three members of Pfam PF02663 (FmdE) implicated in microbial methanogenesis reveal a conserved α+β core domain and an auxiliary C-terminal treble-clef zinc finger

International Nuclear Information System (INIS)

Axelrod, Herbert L.; Das, Debanu; Abdubek, Polat; Astakhova, Tamara; Bakolitsa, Constantina; Carlton, Dennis; Chen, Connie; Chiu, Hsiu-Ju; Clayton, Thomas; Deller, Marc C.; Duan, Lian; Ellrott, Kyle; Farr, Carol L.; Feuerhelm, Julie; Grant, Joanna C.; Grzechnik, Anna; Han, Gye Won; Jaroszewski, Lukasz; Jin, Kevin K.; Klock, Heath E.; Knuth, Mark W.; Kozbial, Piotr; Krishna, S. Sri; Kumar, Abhinav; Lam, Winnie W.; Marciano, David; McMullan, Daniel; Miller, Mitchell D.; Morse, Andrew T.; Nigoghossian, Edward; Nopakun, Amanda; Okach, Linda; Puckett, Christina; Reyes, Ron; Sefcovic, Natasha; Tien, Henry J.; Trame, Christine B.; Bedem, Henry van den; Weekes, Dana; Wooten, Tiffany; Xu, Qingping; Hodgson, Keith O.; Wooley, John; Elsliger, Marc-André; Deacon, Ashley M.; Godzik, Adam; Lesley, Scott A.; Wilson, Ian A.

2010-01-01

The first structures from the FmdE Pfam family (PF02663) reveal that some members of this family form tightly intertwined dimers consisting of two domains (N-terminal α+β core and C-terminal zinc-finger domains), whereas others contain only the core domain. The presence of the zinc-finger domain suggests that some members of this family may perform functions associated with transcriptional regulation, protein–protein interaction, RNA binding or metal-ion sensing. Examination of the genomic context for members of the FmdE Pfam family (PF02663), such as the protein encoded by the fmdE gene from the methanogenic archaeon Methanobacterium thermoautotrophicum, indicates that 13 of them are co-transcribed with genes encoding subunits of molybdenum formylmethanofuran dehydrogenase (EC 1.2.99.5), an enzyme that is involved in microbial methane production. Here, the first crystal structures from PF02663 are described, representing two bacterial and one archaeal species: B8FYU2-DESHY from the anaerobic dehalogenating bacterium Desulfitobacterium hafniense DCB-2, Q2LQ23-SYNAS from the syntrophic bacterium Syntrophus aciditrophicus SB and Q9HJ63-THEAC from the thermoacidophilic archaeon Thermoplasma acidophilum. Two of these proteins, Q9HJ63-THEAC and Q2LQ23-SYNAS, contain two domains: an N-terminal thioredoxin-like α+β core domain (NTD) consisting of a five-stranded, mixed β-sheet flanked by several α-helices and a C-terminal zinc-finger domain (CTD). B8FYU2-DESHY, on the other hand, is composed solely of the NTD. The CTD of Q9HJ63-THEAC and Q2LQ23-SYNAS is best characterized as a treble-clef zinc finger. Two significant structural differences between Q9HJ63-THEAC and Q2LQ23-SYNAS involve their metal binding. First, zinc is bound to the putative active site on the NTD of Q9HJ63-THEAC, but is absent from the NTD of Q2LQ23-SYNAS. Second, whereas the structure of the CTD of Q2LQ23-SYNAS shows four Cys side chains within coordination distance of the Zn atom, the structure

Alanine repeats influence protein localization in splicing speckles and paraspeckles.

Science.gov (United States)

Chang, Shuo-Hsiu; Chang, Wei-Lun; Lu, Chia-Chen; Tarn, Woan-Yuh

2014-12-16

Mammalian splicing regulatory protein RNA-binding motif protein 4 (RBM4) has an alanine repeat-containing C-terminal domain (CAD) that confers both nuclear- and splicing speckle-targeting activities. Alanine-repeat expansion has pathological potential. Here we show that the alanine-repeat tracts influence the subnuclear targeting properties of the RBM4 CAD in cultured human cells. Notably, truncation of the alanine tracts redistributed a portion of RBM4 to paraspeckles. The alanine-deficient CAD was sufficient for paraspeckle targeting. On the other hand, alanine-repeat expansion reduced the mobility of RBM4 and impaired its splicing activity. We further took advantage of the putative coactivator activator (CoAA)-RBM4 conjoined splicing factor, CoAZ, to investigate the function of the CAD in subnuclear targeting. Transiently expressed CoAZ formed discrete nuclear foci that emerged and subsequently separated-fully or partially-from paraspeckles. Alanine-repeat expansion appeared to prevent CoAZ separation from paraspeckles, resulting in their complete colocalization. CoAZ foci were dynamic but, unlike paraspeckles, were resistant to RNase treatment. Our results indicate that the alanine-rich CAD, in conjunction with its conjoined RNA-binding domain(s), differentially influences the subnuclear localization and biogenesis of RBM4 and CoAZ. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

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...

Expression, purification, crystallization and preliminary X-ray diffraction studies of the human keratin 4-binding domain of serine-rich repeat protein 1 from Streptococcus agalactiae

International Nuclear Information System (INIS)

Sundaresan, Ramya; Samen, Ulrike; Ponnuraj, Karthe

2011-01-01

Expression, purification and crystallization of Srr-1-K4BD, a human keratin 4-binding domain of serine-rich repeat protein 1 from S. agalactiae, was carried out. Native crystals of Srr-1-K4BD diffracted to 3.8 Å resolution using synchrotron radiation. Serine-rich repeat protein 1 (Srr-1) is a surface protein from Streptococcus agalactiae. A 17 kDa region of this protein has been identified to bind to human keratin 4 (K4) and is termed the Srr-1 K4-binding domain (Srr-1-K4BD). Recombinant Srr-1-K4BD was overexpressed in Escherichia coli BL21 (DE3) cells. Native and selenomethionine-substituted proteins were prepared using Luria–Bertani (LB) and M9 minimal media, respectively. A two-step purification protocol was carried out to obtain a final homogenous sample of Srr-1-K4BD. Crystals of native Srr-1-K4BD were obtained using PEG 3350 as a precipitant. The crystals diffracted to 3.8 Å resolution using synchrotron radiation and belonged to space group P2 1 , with unit-cell parameters a = 47.56, b = 59.48, c = 94.71 Å, β = 93.95°

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.

Repeat: a framework to assess empirical reproducibility in biomedical research

Directory of Open Access Journals (Sweden)

Leslie D. McIntosh

2017-09-01

Full Text Available Abstract Background The reproducibility of research is essential to rigorous science, yet significant concerns of the reliability and verifiability of biomedical research have been recently highlighted. Ongoing efforts across several domains of science and policy are working to clarify the fundamental characteristics of reproducibility and to enhance the transparency and accessibility of research. Methods The aim of the proceeding work is to develop an assessment tool operationalizing key concepts of research transparency in the biomedical domain, specifically for secondary biomedical data research using electronic health record data. The tool (RepeAT was developed through a multi-phase process that involved coding and extracting recommendations and practices for improving reproducibility from publications and reports across the biomedical and statistical sciences, field testing the instrument, and refining variables. Results RepeAT includes 119 unique variables grouped into five categories (research design and aim, database and data collection methods, data mining and data cleaning, data analysis, data sharing and documentation. Preliminary results in manually processing 40 scientific manuscripts indicate components of the proposed framework with strong inter-rater reliability, as well as directions for further research and refinement of RepeAT. Conclusions The use of RepeAT may allow the biomedical community to have a better understanding of the current practices of research transparency and accessibility among principal investigators. Common adoption of RepeAT may improve reporting of research practices and the availability of research outputs. Additionally, use of RepeAT will facilitate comparisons of research transparency and accessibility across domains and institutions.

TAIL1: an isthmin-like gene, containing type 1 thrombospondin-repeat and AMOP domain, mapped to ARVD1 critical region.

Science.gov (United States)

Rossi, Valeria; Beffagna, Giorgia; Rampazzo, Alessandra; Bauce, Barbara; Danieli, Gian Antonio

2004-06-23

Isthmins represent a novel family of vertebrate secreted proteins containing one copy of the thrombospondin type 1 repeat (TSR), which in mammals is shared by several proteins with diverse biological functions, including cell adhesion, angiogenesis, and patterning of developing nervous system. We have determined the genomic organization of human TAIL1 (thrombospondin and AMOP containing isthmin-like 1), a novel isthmin-like gene encoding a protein that contains a TSR and a C-terminal AMOP domain (adhesion-associated domain in MUC4 and other proteins), characteristic of extracellular proteins involved in adhesion processes. TAIL1 gene encompasses more than 24.4 kb. Analysis of the DNA sequence surrounding the putative transcriptional start region revealed a TATA-less promoter located in a CpG island. Several consensus binding sites for the transcription factors Sp1 and MZF-1 were identified in this promoter region. In humans, TAIL1 gene is located on chromosome 14q24.3 within ARVD1 (arrhythmogenic right ventricular dysplasia/cardiomyopathy, type 1) critical region; preliminary evidence suggests that it is expressed in several tissues, showing multiple alternative splicing.

Protein domain analysis of genomic sequence data reveals regulation of LRR related domains in plant transpiration in Ficus.

Science.gov (United States)

Lang, Tiange; Yin, Kangquan; Liu, Jinyu; Cao, Kunfang; Cannon, Charles H; Du, Fang K

2014-01-01

Predicting protein domains is essential for understanding a protein's function at the molecular level. However, up till now, there has been no direct and straightforward method for predicting protein domains in species without a reference genome sequence. In this study, we developed a functionality with a set of programs that can predict protein domains directly from genomic sequence data without a reference genome. Using whole genome sequence data, the programming functionality mainly comprised DNA assembly in combination with next-generation sequencing (NGS) assembly methods and traditional methods, peptide prediction and protein domain prediction. The proposed new functionality avoids problems associated with de novo assembly due to micro reads and small single repeats. Furthermore, we applied our functionality for the prediction of leucine rich repeat (LRR) domains in four species of Ficus with no reference genome, based on NGS genomic data. We found that the LRRNT_2 and LRR_8 domains are related to plant transpiration efficiency, as indicated by the stomata index, in the four species of Ficus. The programming functionality established in this study provides new insights for protein domain prediction, which is particularly timely in the current age of NGS data expansion.

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...

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...

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...

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...

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...

A versatile palindromic amphipathic repeat coding sequence horizontally distributed among diverse bacterial and eucaryotic microbes

Directory of Open Access Journals (Sweden)

Glass John I

2010-07-01

Full Text Available Abstract Background Intragenic tandem repeats occur throughout all domains of life and impart functional and structural variability to diverse translation products. Repeat proteins confer distinctive surface phenotypes to many unicellular organisms, including those with minimal genomes such as the wall-less bacterial monoderms, Mollicutes. One such repeat pattern in this clade is distributed in a manner suggesting its exchange by horizontal gene transfer (HGT. Expanding genome sequence databases reveal the pattern in a widening range of bacteria, and recently among eucaryotic microbes. We examined the genomic flux and consequences of the motif by determining its distribution, predicted structural features and association with membrane-targeted proteins. Results Using a refined hidden Markov model, we document a 25-residue protein sequence motif tandemly arrayed in variable-number repeats in ORFs lacking assigned functions. It appears sporadically in unicellular microbes from disparate bacterial and eucaryotic clades, representing diverse lifestyles and ecological niches that include host parasitic, marine and extreme environments. Tracts of the repeats predict a malleable configuration of recurring domains, with conserved hydrophobic residues forming an amphipathic secondary structure in which hydrophilic residues endow extensive sequence variation. Many ORFs with these domains also have membrane-targeting sequences that predict assorted topologies; others may comprise reservoirs of sequence variants. We demonstrate expressed variants among surface lipoproteins that distinguish closely related animal pathogens belonging to a subgroup of the Mollicutes. DNA sequences encoding the tandem domains display dyad symmetry. Moreover, in some taxa the domains occur in ORFs selectively associated with mobile elements. These features, a punctate phylogenetic distribution, and different patterns of dispersal in genomes of related taxa, suggest that the

Repeat-containing protein effectors of plant-associated organisms

Directory of Open Access Journals (Sweden)

Carl H. Mesarich

2015-10-01

Full Text Available Many plant-associated organisms, including microbes, nematodes, and insects, deliver effector proteins into the apoplast, vascular tissue, or cell cytoplasm of their prospective hosts. These effectors function to promote colonization, typically by altering host physiology or by modulating host immune responses. The same effectors however, can also trigger host immunity in the presence of cognate host immune receptor proteins, and thus prevent colonization. To circumvent effector-triggered immunity, or to further enhance host colonization, plant-associated organisms often rely on adaptive effector evolution. In recent years, it has become increasingly apparent that several effectors of plant-associated organisms are repeat-containing proteins (RCPs that carry tandem or non-tandem arrays of an amino acid sequence or structural motif. In this review, we highlight the diverse roles that these repeat domains play in RCP effector function. We also draw attention to the potential role of these repeat domains in adaptive evolution with regards to RCP effector function and the evasion of effector-triggered immunity. The aim of this review is to increase the profile of RCP effectors from plant-associated organisms.

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...

Experiment list: SRX190249 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available datatype description=Chromatin IP Sequencing || antibody antibodydescription=Mous...e monoclonal to RNA polymerase II CTD repeat YSPTSPS antibody (4H8) - ChIP Grade. Antibody Target: POL2 || antibody...ible for synthesizing messenger RNA in eukaryotes || antibody vendorname=abcam || antibody... vendorid=ab5408 || controlid=SL1714 || labexpid=SL1963,SL5611 || softwareversion=MACS || cell sex=F || antibody...=Pol2-4H8 || antibody antibodydescription=Mouse monoclonal to RNA polymerase II CTD repeat YSPTSPS antibody

Experiment list: SRX190275 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available dy antibodydescription=Mouse monoclonal to RNA polymeras...e II CTD repeat YSPTSPS antibody (4H8) - ChIP Grade. Antibody Target: POL2 || antibody targetdescription=Thi...er RNA in eukaryotes || antibody vendorname=abcam || antibody vendorid=ab5408 || ...controlid=SL2339 || labexpid=SL5610,SL2353 || softwareversion=MACS || cell sex=M || antibody=Pol2-4H8 || antibody antibody...description=Mouse monoclonal to RNA polymerase II CTD repeat YSPTSPS antibody (4H8) - ChIP Gra

Experiment list: SRX190280 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available romatin IP Sequencing || antibody antibodydescription=Mouse monoclonal to RNA pol...ymerase II CTD repeat YSPTSPS antibody (4H8) - ChIP Grade. Antibody Target: POL2 || antibody targetdescripti...essenger RNA in eukaryotes || antibody vendorname=abcam || antibody vendorid=ab54...08 || controlid=SL1106 || labexpid=SL1104,SL2387 || softwareversion=MACS || cell sex=U || antibody=Pol2-4H8 || antibody antibody...description=Mouse monoclonal to RNA polymerase II CTD repeat YSPTSPS antibody (4H8) - Ch

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...

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...

APE1 incision activity at abasic sites in tandem repeat sequences.

Science.gov (United States)

Li, Mengxia; Völker, Jens; Breslauer, Kenneth J; Wilson, David M

2014-05-29

Repetitive DNA sequences, such as those present in microsatellites and minisatellites, telomeres, and trinucleotide repeats (linked to fragile X syndrome, Huntington disease, etc.), account for nearly 30% of the human genome. These domains exhibit enhanced susceptibility to oxidative attack to yield base modifications, strand breaks, and abasic sites; have a propensity to adopt non-canonical DNA forms modulated by the positions of the lesions; and, when not properly processed, can contribute to genome instability that underlies aging and disease development. Knowledge on the repair efficiencies of DNA damage within such repetitive sequences is therefore crucial for understanding the impact of such domains on genomic integrity. In the present study, using strategically designed oligonucleotide substrates, we determined the ability of human apurinic/apyrimidinic endonuclease 1 (APE1) to cleave at apurinic/apyrimidinic (AP) sites in a collection of tandem DNA repeat landscapes involving telomeric and CAG/CTG repeat sequences. Our studies reveal the differential influence of domain sequence, conformation, and AP site location/relative positioning on the efficiency of APE1 binding and strand incision. Intriguingly, our data demonstrate that APE1 endonuclease efficiency correlates with the thermodynamic stability of the DNA substrate. We discuss how these results have both predictive and mechanistic consequences for understanding the success and failure of repair protein activity associated with such oxidatively sensitive, conformationally plastic/dynamic repetitive DNA domains. Published by Elsevier Ltd.

Conservation of the human integrin-type beta-propeller domain in bacteria.

Directory of Open Access Journals (Sweden)

Bhanupratap Chouhan

Full Text Available Integrins are heterodimeric cell-surface receptors with key functions in cell-cell and cell-matrix adhesion. Integrin α and β subunits are present throughout the metazoans, but it is unclear whether the subunits predate the origin of multicellular organisms. Several component domains have been detected in bacteria, one of which, a specific 7-bladed β-propeller domain, is a unique feature of the integrin α subunits. Here, we describe a structure-derived motif, which incorporates key features of each blade from the X-ray structures of human αIIbβ3 and αVβ3, includes elements of the FG-GAP/Cage and Ca(2+-binding motifs, and is specific only for the metazoan integrin domains. Separately, we searched for the metazoan integrin type β-propeller domains among all available sequences from bacteria and unicellular eukaryotic organisms, which must incorporate seven repeats, corresponding to the seven blades of the β-propeller domain, and so that the newly found structure-derived motif would exist in every repeat. As the result, among 47 available genomes of unicellular eukaryotes we could not find a single instance of seven repeats with the motif. Several sequences contained three repeats, a predicted transmembrane segment, and a short cytoplasmic motif associated with some integrins, but otherwise differ from the metazoan integrin α subunits. Among the available bacterial sequences, we found five examples containing seven sequential metazoan integrin-specific motifs within the seven repeats. The motifs differ in having one Ca(2+-binding site per repeat, whereas metazoan integrins have three or four sites. The bacterial sequences are more conserved in terms of motif conservation and loop length, suggesting that the structure is more regular and compact than those example structures from human integrins. Although the bacterial examples are not full-length integrins, the full-length metazoan-type 7-bladed β-propeller domains are present, and

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...

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...

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...

Acquisition of an Underway CTD System for the Flow Encountering Abrupt Topography DRI

Science.gov (United States)

2015-09-30

Acquisition of an Underway CTD System for the Flow Encountering Abrupt Topography DRI T. M. Shaun Johnston Scripps Institution of Oceanography...westward flow in the North Equatorial Current (NEC) encounters tall, steep, submarine topography and islands. During the Flow Encountering Abrupt... Topography (FLEAT) DRI, investigators will determine: • Whether appreciable energy/momentum is lost from the large-scale NEC flow to smaller scales and

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...

Ship motion effects in CTD-data from weakly stratified waters of the Puerto Rico trench

NARCIS (Netherlands)

van Haren, H.

2015-01-01

Shipborne SBE 911plus Conductivity Temperature Depth (CTD)-casts have been made to maximum 7220 m in the Puerto Rico Trench (PRT). In PRT-waters from 5500 m and deeper and specifically below the 6500 m transition to the hadal-zone, the vertical density stratification is found very weak, with

Experiment list: SRX190277 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available omatin IP Sequencing || antibody antibodydescription=Mouse monoclonal to RNA poly...merase II CTD repeat YSPTSPS antibody (4H8) - ChIP Grade. Antibody Target: POL2 || antibody targetdescriptio...ssenger RNA in eukaryotes || antibody vendorname=abcam || antibody vendorid=ab540...8 || controlid=SL1781 || labexpid=SL1363,SL5604 || softwareversion=MACS || cell sex=M || antibody=Pol2-4H8 || antibody antibody...description=Mouse monoclonal to RNA polymerase II CTD repeat YSPTSPS antibody (4H8) - ChI

Experiment list: SRX100488 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available romatin IP Sequencing || antibody antibodydescription=Mouse monoclonal to RNA pol...ymerase II CTD repeat YSPTSPS antibody (4H8) - ChIP Grade. Antibody Target: POL2 || antibody targetdescripti...essenger RNA in eukaryotes || antibody vendorname=abcam || antibody vendorid=ab54...08 || controlid=SL2455 || labexpid=SL2940,SL2939 || replicate=1,2 || softwareversion=MACS || antibody=Pol2-4H8 || antibody antibody...description=Mouse monoclonal to RNA polymerase II CTD repeat YSPTSPS antibody (4H8) - ChIP Grade || antibody

Experiment list: SRX100519 [Chip-atlas[Archive

Lifescience Database Archive (English)

Full Text Available omatin IP Sequencing || antibody antibodydescription=Mouse monoclonal to RNA poly...merase II CTD repeat YSPTSPS antibody (4H8) - ChIP Grade. Antibody Target: POL2 || antibody targetdescriptio...ssenger RNA in eukaryotes || antibody vendorname=abcam || antibody vendorid=ab540...8 || controlid=SL3457 || labexpid=SL3830,SL3456 || replicate=1,2 || softwareversion=MACS || antibody=Pol2-4H8 || antibody antibody...description=Mouse monoclonal to RNA polymerase II CTD repeat YSPTSPS antibody (4H8) - ChIP Grade || antibody

O-GlcNAc-specific antibody CTD110.6 cross-reacts with N-GlcNAc2-modified proteins induced under glucose deprivation.

Directory of Open Access Journals (Sweden)

Takahiro Isono

Full Text Available Modification of serine and threonine residues in proteins by O-linked β-N-acetylglucosamine (O-GlcNAc glycosylation is a feature of many cellular responses to the nutritional state and to stress. O-GlcNAc modification is reversibly regulated by O-linked β-N-acetylglucosamine transferase (OGT and β-D-N-acetylglucosaminase (O-GlcNAcase. O-GlcNAc modification of proteins is dependent on the concentration of uridine 5'-diphospho-N-acetylglucosamine (UDP-GlcNAc, which is a substrate of OGT and is synthesized via the hexosamine biosynthetic pathway. Immunoblot analysis using the O-GlcNAc-specific antibody CTD110.6 has indicated that glucose deprivation increases protein O-GlcNAcylation in some cancer cells. The mechanism of this paradoxical phenomenon has remained unclear. Here we show that the increased glycosylation induced by glucose deprivation and detected by CTD110.6 antibodies is actually modification by N-GlcNAc(2, rather than by O-GlcNAc. We found that this induced glycosylation was not regulated by OGT and O-GlcNAcase, unlike typical O-GlcNAcylation, and it was inhibited by treatment with tunicamycin, an N-glycosylation inhibitor. Proteomics analysis showed that proteins modified by this induced glycosylation were N-GlcNAc(2-modified glycoproteins. Furthermore, CTD110.6 antibodies reacted with N-GlcNAc(2-modified glycoproteins produced by a yeast strain with a ts-mutant of ALG1 that could not add a mannose residue to dolichol-PP-GlcNAc(2. Our results demonstrated that N-GlcNAc(2-modified glycoproteins were induced under glucose deprivation and that they cross-reacted with the O-GlcNAc-specific antibody CTD110.6. We therefore propose that the glycosylation status of proteins previously classified as O-GlcNAc-modified proteins according to their reactivity with CTD110.6 antibodies must be re-examined. We also suggest that the repression of mature N-linked glycoproteins due to increased levels of N-GlcNAc(2-modified proteins is a newly

VLBI observations of the quasars CTD20 (0234+285), OJ248 (0827+243), and 4C19.44 (1354+195), and the millimeter-x-ray connection

International Nuclear Information System (INIS)

Marscher, A.P.; Broderick, J.J.

1983-01-01

We have obtained limited VLBI data on the quasars CTD20, OJ248, and 4C19.44 at 2.8 cm. CTD20 was also observed at 6 and 18 cm. All three sources contain multicomponent structure, and rather large fractions of the 2.8-cm flux densities arise in unresolved regions. All of the radio flux density of CTD20 originates in compact components. 4C19.44 is dominated at low frequencies by a steep-spectrum component which exceeds about 7 mas in size. Above 2 GHz the spectrum is flat and variable owing to several compact components. CTD20 and OJ248 belong to a sample of millimeter-excess quasars which were shown by Owen, Helfand, and Spangler to have highly predictable ratios of 90 GHz to 2-keV flux densities. A self-Compton explanation of this relationship is supported by the existence of unresolved radio components. However, the rapid 90-GHz variability of OJ248 and other quasars with strong millimeter emission should destroy the observed tight correlation except under special circumstances. A synchrotron origin of the radio-to-x-ray emission requires that any variations in the radio should be time delayed relative to the x ray

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...

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

Indian Academy of Sciences (India)

history during which the main structure of the domain has been conserved such that ... from the column using 100 μL of distilled water. The LRR fragments from the ... ture of the domain and to obtain the best PDB template for mapping positive ...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

CRED Shallow CTD Profiles; Maui, Main Hawaiian Islands; Cruise: HI0610, Data Date Range: 20060730-20060820 (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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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. © 2016 Chatterjee et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

Distribution and Evolution of Yersinia Leucine-Rich Repeat Proteins

Science.gov (United States)

Hu, Yueming; Huang, He; Hui, Xinjie; Cheng, Xi; White, Aaron P.

2016-01-01

Leucine-rich repeat (LRR) proteins are widely distributed in bacteria, playing important roles in various protein-protein interaction processes. In Yersinia, the well-characterized type III secreted effector YopM also belongs to the LRR protein family and is encoded by virulence plasmids. However, little has been known about other LRR members encoded by Yersinia genomes or their evolution. In this study, the Yersinia LRR proteins were comprehensively screened, categorized, and compared. The LRR proteins encoded by chromosomes (LRR1 proteins) appeared to be more similar to each other and different from those encoded by plasmids (LRR2 proteins) with regard to repeat-unit length, amino acid composition profile, and gene expression regulation circuits. LRR1 proteins were also different from LRR2 proteins in that the LRR1 proteins contained an E3 ligase domain (NEL domain) in the C-terminal region or an NEL domain-encoding nucleotide relic in flanking genomic sequences. The LRR1 protein-encoding genes (LRR1 genes) varied dramatically and were categorized into 4 subgroups (a to d), with the LRR1a to -c genes evolving from the same ancestor and LRR1d genes evolving from another ancestor. The consensus and ancestor repeat-unit sequences were inferred for different LRR1 protein subgroups by use of a maximum parsimony modeling strategy. Structural modeling disclosed very similar repeat-unit structures between LRR1 and LRR2 proteins despite the different unit lengths and amino acid compositions. Structural constraints may serve as the driving force to explain the observed mutations in the LRR regions. This study suggests that there may be functional variation and lays the foundation for future experiments investigating the functions of the chromosomally encoded LRR proteins of Yersinia. PMID:27217422

CTD data from the N. E. Atlantic 31N to 46N, July 1982 Discovery cruise 130

Energy Technology Data Exchange (ETDEWEB)

Saunders, P M

1983-01-01

Lists and graphs of CTD data obtained aboard RRS Discovery during July 1982 are presented. A series of 14 stations were occupied between approximate 31 deg N 24 deg W and 46 deg N 14 deg W in support of sound ranging trials. A further 20 stations were occupied in the vicinity of Discovery Gap, a channel for deep flow between the Madeira and Iberian basins near 37 deg 30 N 15 deg 30 W. All CTD data were reconciled with reversing thermometer measurements, and salinity and oxygen samples. Root mean square differences for pressure, temperature, salinity and oxygen were 7 dB, .012 deg C, .007 PSU and 0.3 ml/l in the depth interval 0 to 2,000 dB and 6 dB, .005 deg C, .003 PSU and .16 ml/l for depths 2,000 to 5,600 dB.

THICKNESS OF THE MACULA, RETINAL NERVE FIBER LAYER, AND GANGLION CELL-INNER PLEXIFORM LAYER IN THE AGE-RELATED MACULAR DEGENERATION: The Repeatability Study of Spectral Domain Optical Coherence Tomography.

Science.gov (United States)

Shin, Il-Hwan; Lee, Woo-Hyuk; Lee, Jong-Joo; Jo, Young-Joon; Kim, Jung-Yeul

2018-02-01

To determine the repeatability of measuring the thickness of the central macula, retinal nerve fiber layer, and ganglion cell-inner plexiform layer (GC-IPL) using spectral domain optical coherence tomography (Cirrus HD-OCT) in eyes with age-related macular degeneration. One hundred and thirty-four eyes were included. The measurement repeatability was assessed by an experienced examiner who performed two consecutive measurements using a 512 × 128 macular cube scan and a 200 × 200 optic disk cube scan. To assess changes in macular morphology in patients with age-related macular degeneration, the patients were divided into the following three groups according to the central macular thickness (CMT): A group, CMT 300 μm. Measurement repeatability was assessed using test-retest variability, a coefficient of variation, and an intraclass correlation coefficient. The mean measurement repeatability for the central macular, retinal nerve fiber layer, and GC-IPL thickness was high in the B group. The mean measurement repeatability for both the central macula and retinal nerve fiber layer thickness was high in the A and C groups, but was lower for the GC-IPL thickness. The measurement repeatability for GC-IPL thickness was high in the B group, but low in the A group and in the C group. The automated measurement repeatability for GC-IPL thickness was significantly lower in patients with age-related macular degeneration with out of normal CMT range. The effect of changes in macular morphology should be considered when analyzing GC-IPL thicknesses in a variety of ocular diseases.

Comparison of the carboxy-terminal DP-repeat region in the co-chaperones Hop and Hip.

Science.gov (United States)

Nelson, Gregory M; Huffman, Holly; Smith, David F

2003-01-01

Functional steroid receptor complexes are assembled and maintained by an ordered pathway of interactions involving multiple components of the cellular chaperone machinery. Two of these components, Hop and Hip, serve as co-chaperones to the major heat shock proteins (Hsps), Hsp70 and Hsp90, and participate in intermediate stages of receptor assembly. In an effort to better understand the functions of Hop and Hip in the assembly process, we focused on a region of similarity located near the C-terminus of each co-chaperone. Contained within this region is a repeated sequence motif we have termed the DP repeat. Earlier mutagenesis studies implicated the DP repeat of either Hop or Hip in Hsp70 binding and in normal assembly of the co-chaperones with progesterone receptor (PR) complexes. We report here that the DP repeat lies within a protease-resistant domain that extends to or is near the C-terminus of both co-chaperones. Point mutations in the DP repeats render the C-terminal regions hypersensitive to proteolysis. In addition, a Hop DP mutant displays altered proteolytic digestion patterns, which suggest that the DP-repeat region influences the folding of other Hop domains. Although the respective DP regions of Hop and Hip share sequence and structural similarities, they are not functionally interchangeable. Moreover, a double-point mutation within the second DP-repeat unit of Hop that converts this to the sequence found in Hip disrupts Hop function; however, the corresponding mutation in Hip does not alter its function. We conclude that the DP repeats are important structural elements within a C-terminal domain, which is important for Hop and Hip function.

National Coral Reef Monitoring Program: Shallow Water Conductivity-Temperature-Depth (CTD) Profiles for selected locations across American Samoa in 2015

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Near-shore shallow water Conductivity-Temperature-Depth (CTD) surveys provided vertical profiles of temperature, salinity, and turbidity providing indications for...

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...

[Knocking-out extra domain A alternative splice fragment of fibronectin using a clustered regularly interspaced short palindromic repeats/associated proteins 9 system].

Science.gov (United States)

Yang, Yue; Wang, Haicheng; Xu, Shuyu; Peng, Jing; Jiang, Jiuhui; Li, Cuiying

2015-08-01

To investigate the effect of the fibronectin extra domain A on the aggressiveness of salivary adenoid cystic carcinoma (SACC) cells, via the clustered regularly interspaced short palindromic repeats (CRISPR)/ associated proteins (Cas) system. One sgRNA was designed to target the upstream of the genome sequences of extra domain A(EDA) exon and the downstream. Then the sgRNA was linked into plasmid PX-330 and transfected into SACC-83 cells. PCR and DNA sequence were used to testify the knockout cells, and the monoclones of EDA absent SACC cells were selected (A+C-2, A+C-6, B+C-10). CCK-8 cell proliferation and invasion was then tested in control group and the experimental group. The sgRNA was successfully linked into PX-330 plasmid. Part of adenoid cystic carcinoma cells' SACC-83 genomic EDA exon was knocked out, and the knockdown efficiency was above 70%, but the total amount of fibronectin did not change significantly. Three monoclones of EDA absent SACC- 83 cells were successfully selected with diminished migration and proliferation. The CRISPR/Cas9 system was a simplified system with relatively high knockout efficiency and EDA knockout could inhibiting SACC cell's mobility and invasiveness.

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. Copyright © 2016 by the Genetics Society of America.

Domain-specific and domain-general constraints on word and sequence learning.

Science.gov (United States)

Archibald, Lisa M D; Joanisse, Marc F

2013-02-01

The relative influences of language-related and memory-related constraints on the learning of novel words and sequences were examined by comparing individual differences in performance of children with and without specific deficits in either language or working memory. Children recalled lists of words in a Hebbian learning protocol in which occasional lists repeated, yielding improved recall over the course of the task on the repeated lists. The task involved presentation of pictures of common nouns followed immediately by equivalent presentations of the spoken names. The same participants also completed a paired-associate learning task involving word-picture and nonword-picture pairs. Hebbian learning was observed for all groups. Domain-general working memory constrained immediate recall, whereas language abilities impacted recall in the auditory modality only. In addition, working memory constrained paired-associate learning generally, whereas language abilities disproportionately impacted novel word learning. Overall, all of the learning tasks were highly correlated with domain-general working memory. The learning of nonwords was additionally related to general intelligence, phonological short-term memory, language abilities, and implicit learning. The results suggest that distinct associations between language- and memory-related mechanisms support learning of familiar and unfamiliar phonological forms and sequences.

Physical (Hydrography), chemical (CTD), and biological (Water Quality) processes of the Texas-Louisiana continental shelf, 2013 (NCEI Accession 0162440)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Two sets of CTD data were taken during the 2013 Shelfwide Hypoxia cruise off the Louisiana continental shelf. Hydrographic data were obtained with the LUMCON SeaBird...

Evaluation of time domain and spectral domain optical coherence tomography in the measurement of diabetic macular edema.

Science.gov (United States)

Forooghian, Farzin; Cukras, Catherine; Meyerle, Catherine B; Chew, Emily Y; Wong, Wai T

2008-10-01

To evaluate macular thickness and volume measurements and their intrasession repeatability in two optical coherence tomography (OCT) systems: the Stratus OCT, a time domain system, and the Cirrus HD-OCT, a spectral domain system (both by Carl Zeiss Meditec, Inc., Dublin, CA), in the context of diabetic macular edema (DME). Thirty-three eyes of 33 diabetic patients with clinically significant macular edema (CSME) were scanned in a single session by a single operator on both OCT systems. Macular thickness measurements of nine standard macular subfields and total macular volume were obtained and analyzed. Bland-Altman plots were constructed to assess agreement in macular measurements. Intraclass correlation coefficients (ICCs), coefficients of repeatability (CR(W)), and coefficients of variation (CV(W)) were used to assess intrasession repeatability. Macular thickness in nine retinal subfields and macular volume were significantly higher in the Cirrus HD-OCT system compared with the Stratus OCT system. Subfield thickness and total volume measurements, respectively, were 30 to 55 microm and 3.2 mm(3) greater for the Cirrus HD-OCT system compared with the Stratus OCT system. Both Stratus OCT and Cirrus HD-OCT systems demonstrated high intrasession repeatability, with overlapping ranges for CR(W), CV(W), and ICC. Repeatability measures (CR(W) and CV(W)) differed significantly between systems in only one of nine subfields (outer temporal subfield). Absolute measures of macular thickness and volume in patients with DME differed significantly in magnitude between the Stratus OCT and Cirrus HD-OCT systems. However, both OCT systems demonstrated high intrasessional repeatability. Although the two systems may not be used interchangeably, they appear equally reliable in generating macular measurements for clinical practice and research.

Predicting detection performance with model observers: Fourier domain or spatial domain?

Science.gov (United States)

Chen, Baiyu; Yu, Lifeng; Leng, Shuai; Kofler, James; Favazza, Christopher; Vrieze, Thomas; McCollough, Cynthia

2016-02-27

The use of Fourier domain model observer is challenged by iterative reconstruction (IR), because IR algorithms are nonlinear and IR images have noise texture different from that of FBP. A modified Fourier domain model observer, which incorporates nonlinear noise and resolution properties, has been proposed for IR and needs to be validated with human detection performance. On the other hand, the spatial domain model observer is theoretically applicable to IR, but more computationally intensive than the Fourier domain method. The purpose of this study is to compare the modified Fourier domain model observer to the spatial domain model observer with both FBP and IR images, using human detection performance as the gold standard. A phantom with inserts of various low contrast levels and sizes was repeatedly scanned 100 times on a third-generation, dual-source CT scanner at 5 dose levels and reconstructed using FBP and IR algorithms. The human detection performance of the inserts was measured via a 2-alternative-forced-choice (2AFC) test. In addition, two model observer performances were calculated, including a Fourier domain non-prewhitening model observer and a spatial domain channelized Hotelling observer. The performance of these two mode observers was compared in terms of how well they correlated with human observer performance. Our results demonstrated that the spatial domain model observer correlated well with human observers across various dose levels, object contrast levels, and object sizes. The Fourier domain observer correlated well with human observers using FBP images, but overestimated the detection performance using IR images.

Structure of filamin A immunoglobulin-like repeat 10 from Homo sapiens

International Nuclear Information System (INIS)

Page, Richard C.; Clark, Jeffrey G.; Misra, Saurav

2011-01-01

The structure of immunoglobulin-like repeat 10 from human filamin A solved at 2.44 Å resolution suggests the potential effects of mutations correlated with otopalatodigital syndrome spectrum disorders. Filamin A (FlnA) plays a critical role in cytoskeletal organization, cell motility and cellular signaling. FlnA utilizes different binding sites on a series of 24 immunoglobulin-like domains (Ig repeats) to interact with diverse cytosolic proteins and with cytoplasmic portions of membrane proteins. Mutations in a specific domain, Ig10 (FlnA-Ig10), are correlated with two severe forms of the otopalatodigital syndrome spectrum disorders Melnick–Needles syndrome and frontometaphyseal dysplasia. The crystal structure of FlnA-Ig10 determined at 2.44 Å resolution provides insight into the perturbations caused by these mutations

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

National Coral Reef Monitoring Program: Shallow Water Conductivity-Temperature-Depth (CTD) Profiles for selected locations across the Mariana Archipelago in 2014

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Near-shore shallow water Conductivity-Temperature-Depth (CTD) surveys provided vertical profiles of temperature, salinity, and turbidity providing indications for...

National Coral Reef Monitoring Program: Shallow Water Conductivity-Temperature-Depth (CTD) Profiles for selected locations across the Hawaiian Archipelago since 2013

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Near-shore shallow water Conductivity-Temperature-Depth (CTD) surveys provided vertical profiles of temperature, salinity, and turbidity providing indications for...

Resolving Hot Spots in the C-Terminal Dimerization Domain that Determine the Stability of the Molecular Chaperone Hsp90

Science.gov (United States)

Reimann, Sven; Smits, Sander H. J.; Schmitt, Lutz; Groth, Georg; Gohlke, Holger

2014-01-01

Human heat shock protein of 90 kDa (hHsp90) is a homodimer that has an essential role in facilitating malignant transformation at the molecular level. Inhibiting hHsp90 function is a validated approach for treating different types of tumors. Inhibiting the dimerization of hHsp90 via its C-terminal domain (CTD) should provide a novel way to therapeutically interfere with hHsp90 function. Here, we predicted hot spot residues that cluster in the CTD dimerization interface by a structural decomposition of the effective energy of binding computed by the MM-GBSA approach and confirmed these predictions using in silico alanine scanning with DrugScorePPI. Mutation of these residues to alanine caused a significant decrease in the melting temperature according to differential scanning fluorimetry experiments, indicating a reduced stability of the mutant hHsp90 complexes. Size exclusion chromatography and multi-angle light scattering studies demonstrate that the reduced stability of the mutant hHsp90 correlates with a lower complex stoichiometry due to the disruption of the dimerization interface. These results suggest that the identified hot spot residues can be used as a pharmacophoric template for identifying and designing small-molecule inhibitors of hHsp90 dimerization. PMID:24760083

Relationship between cognitive and non-cognitive symptoms of delirium.

Science.gov (United States)

Rajlakshmi, Aarya Krishnan; Mattoo, Surendra Kumar; Grover, Sandeep

2013-04-01

To study relationship between the cognitive and the non-cognitive symptoms of delirium. Eighty-four patients referred to psychiatry liaison services and met DSM-IVTR criteria of delirium were assessed using the Delirium Rating Scale Revised-1998 (DRSR-98) and Cognitive Test for Delirium (CTD). The mean DRS-R-98 severity score was 17.19 and DRS-R-98 total score was 23.36. The mean total score on CTD was 11.75. The mean scores on CTD were highest for comprehension (3.47) and lowest for vigilance (1.71). Poor attention was associated with significantly higher motor retardation and higher DRS-R-98 severity scores minus the attention scores. There were no significant differences between those with and without poor attention. Higher attention deficits were associated with higher dysfunction on all other domains of cognition on CTD. There was significant correlation between cognitive functions as assessed on CTD and total DRS-R-98 score, DRS-R-98 severity score and DRS-R-98 severity score without the attention item score. However, few correlations emerged between CTD domains and CTD total scores with cognitive symptom total score of DRS-R-98 (items 9-13) and non-cognitive symptom total score of DRS-R-98 (items 1-8). Our study suggests that in delirium, cognitive deficits are quite prevalent and correlate with overall severity of delirium. Attention deficit is a core symptom of delirium. Copyright © 2012 Elsevier B.V. All rights reserved.

The SPOR Domain, a Widely Conserved Peptidoglycan Binding Domain That Targets Proteins to the Site of Cell Division.

Science.gov (United States)

Yahashiri, Atsushi; Jorgenson, Matthew A; Weiss, David S

2017-07-15

Sporulation-related repeat (SPOR) domains are small peptidoglycan (PG) binding domains found in thousands of bacterial proteins. The name "SPOR domain" stems from the fact that several early examples came from proteins involved in sporulation, but SPOR domain proteins are quite diverse and contribute to a variety of processes that involve remodeling of the PG sacculus, especially with respect to cell division. SPOR domains target proteins to the division site by binding to regions of PG devoid of stem peptides ("denuded" glycans), which in turn are enriched in septal PG by the intense, localized activity of cell wall amidases involved in daughter cell separation. This targeting mechanism sets SPOR domain proteins apart from most other septal ring proteins, which localize via protein-protein interactions. In addition to SPOR domains, bacteria contain several other PG-binding domains that can exploit features of the cell wall to target proteins to specific subcellular sites. Copyright © 2017 American Society for Microbiology.

A large complement of the predicted Arabidopsis ARM repeat proteins are members of the U-box E3 ubiquitin ligase family.

Science.gov (United States)

Mudgil, Yashwanti; Shiu, Shin-Han; Stone, Sophia L; Salt, Jennifer N; Goring, Daphne R

2004-01-01

The Arabidopsis genome was searched to identify predicted proteins containing armadillo (ARM) repeats, a motif known to mediate protein-protein interactions in a number of different animal proteins. Using domain database predictions and models generated in this study, 108 Arabidopsis proteins were identified that contained a minimum of two ARM repeats with the majority of proteins containing four to eight ARM repeats. Clustering analysis showed that the 108 predicted Arabidopsis ARM repeat proteins could be divided into multiple groups with wide differences in their domain compositions and organizations. Interestingly, 41 of the 108 Arabidopsis ARM repeat proteins contained a U-box, a motif present in a family of E3 ligases, and these proteins represented the largest class of Arabidopsis ARM repeat proteins. In 14 of these U-box/ARM repeat proteins, there was also a novel conserved domain identified in the N-terminal region. Based on the phylogenetic tree, representative U-box/ARM repeat proteins were selected for further study. RNA-blot analyses revealed that these U-box/ARM proteins are expressed in a variety of tissues in Arabidopsis. In addition, the selected U-box/ARM proteins were found to be functional E3 ubiquitin ligases. Thus, these U-box/ARM proteins represent a new family of E3 ligases in Arabidopsis.

Physical (Hydrography), chemical (CTD), and biological (Water Quality) processes of the Texas-Louisiana continental shelf, 2012 (NCEI Accession 0162101)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Two sets of CTD data were taken during the 2012 surveys of the Louisiana continental shelf—Transect C off Terrebonne Bay and Transect F off Atchafalaya Bay and the...

Big domains are novel Ca²+-binding modules: evidences from big domains of Leptospira immunoglobulin-like (Lig) proteins.

Science.gov (United States)

Raman, Rajeev; Rajanikanth, V; Palaniappan, Raghavan U M; Lin, Yi-Pin; He, Hongxuan; McDonough, Sean P; Sharma, Yogendra; Chang, Yung-Fu

2010-12-29

Many bacterial surface exposed proteins mediate the host-pathogen interaction more effectively in the presence of Ca²+. Leptospiral immunoglobulin-like (Lig) proteins, LigA and LigB, are surface exposed proteins containing Bacterial immunoglobulin like (Big) domains. The function of proteins which contain Big fold is not known. Based on the possible similarities of immunoglobulin and βγ-crystallin folds, we here explore the important question whether Ca²+ binds to a Big domains, which would provide a novel functional role of the proteins containing Big fold. We selected six individual Big domains for this study (three from the conserved part of LigA and LigB, denoted as Lig A3, Lig A4, and LigBCon5; two from the variable region of LigA, i.e., 9(th) (Lig A9) and 10(th) repeats (Lig A10); and one from the variable region of LigB, i.e., LigBCen2. We have also studied the conserved region covering the three and six repeats (LigBCon1-3 and LigCon). All these proteins bind the calcium-mimic dye Stains-all. All the selected four domains bind Ca²+ with dissociation constants of 2-4 µM. Lig A9 and Lig A10 domains fold well with moderate thermal stability, have β-sheet conformation and form homodimers. Fluorescence spectra of Big domains show a specific doublet (at 317 and 330 nm), probably due to Trp interaction with a Phe residue. Equilibrium unfolding of selected Big domains is similar and follows a two-state model, suggesting the similarity in their fold. We demonstrate that the Lig are Ca²+-binding proteins, with Big domains harbouring the binding motif. We conclude that despite differences in sequence, a Big motif binds Ca²+. This work thus sets up a strong possibility for classifying the proteins containing Big domains as a novel family of Ca²+-binding proteins. Since Big domain is a part of many proteins in bacterial kingdom, we suggest a possible function these proteins via Ca²+ binding.

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

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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...

CRED Shallow CTD Profiles; Baker Island, Pacific Remote Island Areas; Cruise: TC0101, Data Date Range: 20010210-20010211 (NODC Accession 0039382).

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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...

CRED Shallow CTD Profiles; Palmyra Atoll, Pacific Remote Island Areas; Cruise: TC0101, Data Date Range: 20010220-20010221 (NODC Accession 0039382).

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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...

CRED Shallow CTD Profiles; Niihau - Kaula Rock, Main Hawaiian Islands; Cruise: HI0610, Data Date Range: 20060810-20060811 (NODC Accession 0039382).

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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...

CRED Shallow CTD Profiles; Kingman Reef, Pacific Remote Island Areas; Cruise: HI0803, Data Date Range: 20080406-20080406 (NODC Accession 0039382).

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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...

CRED Shallow CTD Profiles; Johnston Atoll, Pacific Remote Island Areas; Cruise: HI0601, Data Date Range: 20060119-20060121 (NODC Accession 0039382).

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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...

CRED Shallow CTD Profiles; Palmyra Atoll, Pacific Remote Island Areas; Cruise: OES0404, Data Date Range: 20040329-20040401 (NODC Accession 0039382).

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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...

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...

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...

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...

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

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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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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 are...

Temperature, salinity, conductivity, pressure, transmissivity measurements collected using CTD from the Alpha Helix in the Chukchi Sea during 1996 (NODC Accession 0061042)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Temperature, salinity, conductivity, pressure, and transmissivity data gathered by CTD from the Alpha Helix (cruise HX194), September 1996

Thermal stability of chicken brain {alpha}-spectrin repeat 17: a spectroscopic study

Energy Technology Data Exchange (ETDEWEB)

Brenner, Annette K. [University of Bergen, Department of Chemistry (Norway); Kieffer, Bruno [Ecole Superieure de Biotechnologie de Strasbourg, IGBMC Biomolecular NMR Group, CNRS UMR 7104 (France); Trave, Gilles [Ecole Superieure de Biotechnologie de Strasbourg, Equipe Oncoproteines, IREBS, UMR 7242 (France); Froystein, Nils Age [University of Bergen, Department of Chemistry (Norway); Raae, Arnt J., E-mail: arnt.raae@mbi.uib.no [University of Bergen, Department of Molecular Biology (Norway)

2012-06-15

Spectrin is a rod-like multi-modular protein that is mainly composed of triple-helical repeats. These repeats show very similar 3D-structures but variable conformational and thermodynamical stabilities, which may be of great importance for the flexibility and dynamic behaviour of spectrin in the cell. For instance, repeat 17 (R17) of the chicken brain spectrin {alpha}-chain is four times less stable than neighbouring repeat 16 (R16) in terms of Increment G. The structure of spectrin repeats has mainly been investigated by X-ray crystallography, but the structures of a few repeats, e.g. R16, have also been determined by NMR spectroscopy. Here, we undertook a detailed characterization of the neighbouring R17 by NMR spectroscopy. We assigned most backbone resonances and observed NOE restraints, relaxation values and coupling constants that all indicated that the fold of R17 is highly similar to that of R16, in agreement with previous X-ray analysis of a tandem repeat of the two domains. However, {sup 15}N heteronuclear NMR spectra measured at different temperatures revealed particular features of the R17 domain that might contribute to its lower stability. Conformational exchange appeared to alter the linker connecting R17 to R16 as well as the BC-loop in close proximity. In addition, heat-induced splitting was observed for backbone resonances of a few spatially related residues including V99 of helix C, which in R16 is replaced by the larger hydrophobic tryptophan residue that is relatively conserved among other spectrin repeats. These data support the view that the substitution of tryptophan by valine at this position may contribute to the lower stability of R17.

Poly-dipeptides encoded by the C9orf72 repeats bind nucleoli, impede RNA biogenesis, and kill cells.

Science.gov (United States)

Kwon, Ilmin; Xiang, Siheng; Kato, Masato; Wu, Leeju; Theodoropoulos, Pano; Wang, Tao; Kim, Jiwoong; Yun, Jonghyun; Xie, Yang; McKnight, Steven L

2014-09-05

Many RNA regulatory proteins controlling pre-messenger RNA splicing contain serine:arginine (SR) repeats. Here, we found that these SR domains bound hydrogel droplets composed of fibrous polymers of the low-complexity domain of heterogeneous ribonucleoprotein A2 (hnRNPA2). Hydrogel binding was reversed upon phosphorylation of the SR domain by CDC2-like kinases 1 and 2 (CLK1/2). Mutated variants of the SR domains changing serine to glycine (SR-to-GR variants) also bound to hnRNPA2 hydrogels but were not affected by CLK1/2. When expressed in mammalian cells, these variants bound nucleoli. The translation products of the sense and antisense transcripts of the expansion repeats associated with the C9orf72 gene altered in neurodegenerative disease encode GRn and PRn repeat polypeptides. Both peptides bound to hnRNPA2 hydrogels independent of CLK1/2 activity. When applied to cultured cells, both peptides entered cells, migrated to the nucleus, bound nucleoli, and poisoned RNA biogenesis, which caused cell death. Copyright © 2014, American Association for the Advancement of Science.

RING finger and WD repeat domain 3 (RFWD3) associates with replication protein A (RPA) and facilitates RPA-mediated DNA damage response.

Science.gov (United States)

Liu, Shangfeng; Chu, Jessica; Yucer, Nur; Leng, Mei; Wang, Shih-Ya; Chen, Benjamin P C; Hittelman, Walter N; Wang, Yi

2011-06-24

DNA damage response is crucial for maintaining genomic integrity and preventing cancer by coordinating the activation of checkpoints and the repair of damaged DNA. Central to DNA damage response are the two checkpoint kinases ATM and ATR that phosphorylate a wide range of substrates. RING finger and WD repeat domain 3 (RFWD3) was initially identified as a substrate of ATM/ATR from a proteomic screen. Subsequent studies showed that RFWD3 is an E3 ubiquitin ligase that ubiquitinates p53 in vitro and positively regulates p53 levels in response to DNA damage. We report here that RFWD3 associates with replication protein A (RPA), a single-stranded DNA-binding protein that plays essential roles in DNA replication, recombination, and repair. Binding of RPA to single-stranded DNA (ssDNA), which is generated by DNA damage and repair, is essential for the recruitment of DNA repair factors to damaged sites and the activation of checkpoint signaling. We show that RFWD3 is physically associated with RPA and rapidly localizes to sites of DNA damage in a RPA-dependent manner. In vitro experiments suggest that the C terminus of RFWD3, which encompass the coiled-coil domain and the WD40 domain, is necessary for binding to RPA. Furthermore, DNA damage-induced phosphorylation of RPA and RFWD3 is dependent upon each other. Consequently, loss of RFWD3 results in the persistent foci of DNA damage marker γH2AX and the repair protein Rad51 in damaged cells. These findings suggest that RFWD3 is recruited to sites of DNA damage and facilitates RPA-mediated DNA damage signaling and repair.

CTD data from R/V Kilo Moana Cruise KM1123 during 2011-08 north of Hawaii (NODC Accession 0125443)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Profiles were taken with a Sea-Bird SBE-911 plus CTD from the R/V Kilo Moana on cruise KM1123 2011-08-11 to 2011-08-25 in the vicinity of Station ALOHA, the Hawaii...

Repeat-associated plasticity in the Helicobacter pylori RD gene family.

Science.gov (United States)

Shak, Joshua R; Dick, Jonathan J; Meinersmann, Richard J; Perez-Perez, Guillermo I; Blaser, Martin J

2009-11-01

The bacterium Helicobacter pylori is remarkable for its ability to persist in the human stomach for decades without provoking sterilizing immunity. Since repetitive DNA can facilitate adaptive genomic flexibility via increased recombination, insertion, and deletion, we searched the genomes of two H. pylori strains for nucleotide repeats. We discovered a family of genes with extensive repetitive DNA that we have termed the H. pylori RD gene family. Each gene of this family is composed of a conserved 3' region, a variable mid-region encoding 7 and 11 amino acid repeats, and a 5' region containing one of two possible alleles. Analysis of five complete genome sequences and PCR genotyping of 42 H. pylori strains revealed extensive variation between strains in the number, location, and arrangement of RD genes. Furthermore, examination of multiple strains isolated from a single subject's stomach revealed intrahost variation in repeat number and composition. Despite prior evidence that the protein products of this gene family are expressed at the bacterial cell surface, enzyme-linked immunosorbent assay and immunoblot studies revealed no consistent seroreactivity to a recombinant RD protein by H. pylori-positive hosts. The pattern of repeats uncovered in the RD gene family appears to reflect slipped-strand mispairing or domain duplication, allowing for redundancy and subsequent diversity in genotype and phenotype. This novel family of hypervariable genes with conserved, repetitive, and allelic domains may represent an important locus for understanding H. pylori persistence in its natural host.

Characterization of a novel gene encoding ankyrin repeat domain from Cotesia vestalis polydnavirus (CvBV)

International Nuclear Information System (INIS)

Shi Min; Chen Yafeng; Huang Fang; Liu Pengcheng; Zhou Xueping; Chen Xuexin

2008-01-01

Cotesia vestalis (Haliday) is an endoparasitoid of Plutella xylostella (L.) larvae and injects a polydnavirus (CvBV) into its host during oviposition. In this report we describe the characterization of a gene (CvBV805) and its products. CvBV805 is located on the segment S8 of CvBV genome; it has a size of 909 bp and encodes a predicted protein of 125 amino acids. This protein contains an ankyrin repeat domain with a high degree of similarity with IκB-like genes. Gene transcripts were detected in extracts of the host as early as 2 h post-parasitization (p.p.) and continued to be detected through 24 h. Tissue-specific expression patterns showed that CvBV805 might be involved in early host immunosuppression. CvBV805 was detected in parasitized hosts at 12 h p.p. and in rBac-eGFP-CvBV805-infected Tn-5B1-4 cells at 72 h.p.i. by using western blots analysis. The size of the protein expressed in the host hemocytes and infected Tn-5B1-4 cells was 17 kDa and 56 kDa (including eGFP), respectively, which nearly corresponded with the predicted molecular weight (14.31 kDa) of CvBV805, suggesting that the protein did not undergo extensive post-translational modification. The protein was confirmed to be present within the nuclear region in hemocytes of the parasitized P. xylostella larvae at 48 h p.p. using confocal laser scanning microscopy

The Jasmonate-ZIM-domain proteins interact with the WD-Repeat/bHLH/MYB complexes to regulate Jasmonate-mediated anthocyanin accumulation and trichome initiation in Arabidopsis thaliana.

Science.gov (United States)

Qi, Tiancong; Song, Susheng; Ren, Qingcuo; Wu, Dewei; Huang, Huang; Chen, Yan; Fan, Meng; Peng, Wen; Ren, Chunmei; Xie, Daoxin

2011-05-01

Jasmonates (JAs) mediate plant responses to insect attack, wounding, pathogen infection, stress, and UV damage and regulate plant fertility, anthocyanin accumulation, trichome formation, and many other plant developmental processes. Arabidopsis thaliana Jasmonate ZIM-domain (JAZ) proteins, substrates of the CORONATINE INSENSITIVE1 (COI1)-based SCF(COI1) complex, negatively regulate these plant responses. Little is known about the molecular mechanism for JA regulation of anthocyanin accumulation and trichome initiation. In this study, we revealed that JAZ proteins interact with bHLH (Transparent Testa8, Glabra3 [GL3], and Enhancer of Glabra3 [EGL3]) and R2R3 MYB transcription factors (MYB75 and Glabra1), essential components of WD-repeat/bHLH/MYB transcriptional complexes, to repress JA-regulated anthocyanin accumulation and trichome initiation. Genetic and physiological evidence showed that JA regulates WD-repeat/bHLH/MYB complex-mediated anthocyanin accumulation and trichome initiation in a COI1-dependent manner. Overexpression of the MYB transcription factor MYB75 and bHLH factors (GL3 and EGL3) restored anthocyanin accumulation and trichome initiation in the coi1 mutant, respectively. We speculate that the JA-induced degradation of JAZ proteins abolishes the interactions of JAZ proteins with bHLH and MYB factors, allowing the transcriptional function of WD-repeat/bHLH/MYB complexes, which subsequently activate respective downstream signal cascades to modulate anthocyanin accumulation and trichome initiation.

An in-situ experiment identifying flow effects on temperature measurements using a pumped CTD in weakly stratified waters

NARCIS (Netherlands)

van Haren, H.; Laan, M

2016-01-01

A simple experiment shows that the tubing leading to and from the pumped duct of temperature T and conductivity C-sensors of a Sea-Bird Electronics 911plus CTD can cause artificial T-effects as a function of the instrument package vertical velocity. This artifact is due to a pressure difference

Quantitative analysis and prediction of curvature in leucine-rich repeat proteins.

Science.gov (United States)

Hindle, K Lauren; Bella, Jordi; Lovell, Simon C

2009-11-01

Leucine-rich repeat (LRR) proteins form a large and diverse family. They have a wide range of functions most of which involve the formation of protein-protein interactions. All known LRR structures form curved solenoids, although there is large variation in their curvature. It is this curvature that determines the shape and dimensions of the inner space available for ligand binding. Unfortunately, large-scale parameters such as the overall curvature of a protein domain are extremely difficult to predict. Here, we present a quantitative analysis of determinants of curvature of this family. Individual repeats typically range in length between 20 and 30 residues and have a variety of secondary structures on their convex side. The observed curvature of the LRR domains correlates poorly with the lengths of their individual repeats. We have, therefore, developed a scoring function based on the secondary structure of the convex side of the protein that allows prediction of the overall curvature with a high degree of accuracy. We also demonstrate the effectiveness of this method in selecting a suitable template for comparative modeling. We have developed an automated, quantitative protocol that can be used to predict accurately the curvature of leucine-rich repeat proteins of unknown structure from sequence alone. This protocol is available as an online resource at http://www.bioinf.manchester.ac.uk/curlrr/.

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

CRED Shallow CTD Profiles; Howland Island, Pacific Remote Island Areas; Cruise: HA1201_LEGI, Data Date Range: 20120311-20120313 (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...

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...

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...

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...

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...

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 are...

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...

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...

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...

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...

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...

CRED Shallow CTD Profiles; Pagan, Commonwealth of the Northern Mariana Islands; Cruise: HI0703, Data Date Range: 20070604-20070606 (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...

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...

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 are...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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 are...

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...

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...

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...

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...

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...

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...

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 174...

Structure and biochemical function of a prototypical Arabidopsis U-box domain

DEFF Research Database (Denmark)

Andersen, Pernille; Kragelund, Birthe B; Olsen, Addie N

2004-01-01

U-box proteins, as well as other proteins involved in regulated protein degradation, are apparently over-represented in Arabidopsis compared with other model eukaryotes. The Arabidopsis protein AtPUB14 contains a typical U-box domain followed by an Armadillo repeat region, a domain organization t...

National Coral Reef Monitoring Program: Shallow Water Conductivity-Temperature-Depth (CTD) Profiles for selected locations across the Pacific Remote Island Areas since 2014

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Near-shore shallow water Conductivity-Temperature-Depth (CTD) surveys provided vertical profiles of temperature, salinity, and turbidity providing indications for...

A Large Complement of the Predicted Arabidopsis ARM Repeat Proteins Are Members of the U-Box E3 Ubiquitin Ligase Family1[w

Science.gov (United States)

Mudgil, Yashwanti; Shiu, Shin-Han; Stone, Sophia L.; Salt, Jennifer N.; Goring, Daphne R.

2004-01-01

The Arabidopsis genome was searched to identify predicted proteins containing armadillo (ARM) repeats, a motif known to mediate protein-protein interactions in a number of different animal proteins. Using domain database predictions and models generated in this study, 108 Arabidopsis proteins were identified that contained a minimum of two ARM repeats with the majority of proteins containing four to eight ARM repeats. Clustering analysis showed that the 108 predicted Arabidopsis ARM repeat proteins could be divided into multiple groups with wide differences in their domain compositions and organizations. Interestingly, 41 of the 108 Arabidopsis ARM repeat proteins contained a U-box, a motif present in a family of E3 ligases, and these proteins represented the largest class of Arabidopsis ARM repeat proteins. In 14 of these U-box/ARM repeat proteins, there was also a novel conserved domain identified in the N-terminal region. Based on the phylogenetic tree, representative U-box/ARM repeat proteins were selected for further study. RNA-blot analyses revealed that these U-box/ARM proteins are expressed in a variety of tissues in Arabidopsis. In addition, the selected U-box/ARM proteins were found to be functional E3 ubiquitin ligases. Thus, these U-box/ARM proteins represent a new family of E3 ligases in Arabidopsis. PMID:14657406

EX1103: Exploration and Mapping, Galapagos Spreading Center: Mapping, CTD, Tow-Yo, and ROV on NOAA Ship Okeanos Explorer (EM302)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — This cruise will be composed of two separate legs. The first leg will be a transit from San Diego, CA to the Galapagos Spreading Center, where multibeam mapping, CTD...

Big domains are novel Ca²+-binding modules: evidences from big domains of Leptospira immunoglobulin-like (Lig proteins.

Directory of Open Access Journals (Sweden)

Rajeev Raman

Full Text Available BACKGROUND: Many bacterial surface exposed proteins mediate the host-pathogen interaction more effectively in the presence of Ca²+. Leptospiral immunoglobulin-like (Lig proteins, LigA and LigB, are surface exposed proteins containing Bacterial immunoglobulin like (Big domains. The function of proteins which contain Big fold is not known. Based on the possible similarities of immunoglobulin and βγ-crystallin folds, we here explore the important question whether Ca²+ binds to a Big domains, which would provide a novel functional role of the proteins containing Big fold. PRINCIPAL FINDINGS: We selected six individual Big domains for this study (three from the conserved part of LigA and LigB, denoted as Lig A3, Lig A4, and LigBCon5; two from the variable region of LigA, i.e., 9(th (Lig A9 and 10(th repeats (Lig A10; and one from the variable region of LigB, i.e., LigBCen2. We have also studied the conserved region covering the three and six repeats (LigBCon1-3 and LigCon. All these proteins bind the calcium-mimic dye Stains-all. All the selected four domains bind Ca²+ with dissociation constants of 2-4 µM. Lig A9 and Lig A10 domains fold well with moderate thermal stability, have β-sheet conformation and form homodimers. Fluorescence spectra of Big domains show a specific doublet (at 317 and 330 nm, probably due to Trp interaction with a Phe residue. Equilibrium unfolding of selected Big domains is similar and follows a two-state model, suggesting the similarity in their fold. CONCLUSIONS: We demonstrate that the Lig are Ca²+-binding proteins, with Big domains harbouring the binding motif. We conclude that despite differences in sequence, a Big motif binds Ca²+. This work thus sets up a strong possibility for classifying the proteins containing Big domains as a novel family of Ca²+-binding proteins. Since Big domain is a part of many proteins in bacterial kingdom, we suggest a possible function these proteins via Ca²+ binding.

Single molecule study of the intrinsically disordered FG-repeat nucleoporin 153.

Science.gov (United States)

Milles, Sigrid; Lemke, Edward A

2011-10-05

Nucleoporins (Nups), which are intrinsically disordered, form a selectivity filter inside the nuclear pore complex, taking a central role in the vital nucleocytoplasmic transport mechanism. These Nups display a complex and nonrandom amino-acid architecture of phenylalanine glycine (FG)-repeat clusters and intra-FG linkers. How such heterogeneous sequence composition relates to function and could give rise to a transport mechanism is still unclear. Here we describe a combined chemical biology and single-molecule fluorescence approach to study the large human Nup153 FG-domain. In order to obtain insights into the properties of this domain beyond the average behavior, we probed the end-to-end distance (R(E)) of several ∼50-residues long FG-repeat clusters in the context of the whole protein domain. Despite the sequence heterogeneity of these FG-clusters, we detected a reoccurring and consistent compaction from a relaxed coil behavior under denaturing conditions (R(E)/R(E,RC) = 0.99 ± 0.15 with R(E,RC) corresponding to ideal relaxed coil behavior) to a collapsed state under native conditions (R(E)/R(E,RC) = 0.79 ± 0.09). We then analyzed the properties of this protein on the supramolecular level, and determined that this human FG-domain was in fact able to form a hydrogel with physiological permeability barrier properties. Copyright © 2011 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Domain movement within a gene: a novel evolutionary mechanism for protein diversification.

Directory of Open Access Journals (Sweden)

Yoshikazu Furuta

Full Text Available A protein function is carried out by a specific domain localized at a specific position. In the present study, we report that, within a gene, a specific amino acid sequence can move between a certain position and another position. This was discovered when the sequences of restriction-modification systems within the bacterial species Helicobacter pylori were compared. In the specificity subunit of Type I restriction-modification systems, DNA sequence recognition is mediated by target recognition domain 1 (TRD1 and TRD2. To our surprise, several sequences are shared by TRD1 and TRD2 of genes (alleles at the same locus (chromosomal location; these domains appear to have moved between the two positions. The gene/protein organization can be represented as x-(TRD1-y-x-(TRD2-y, where x and y represent repeat sequences. Movement probably occurs by recombination at these flanking DNA repeats. In accordance with this hypothesis, recombination at these repeats also appears to decrease two TRDs into one TRD or increase these two TRDs to three TRDs (TRD1-TRD2-TRD2 and to allow TRD movement between genes even at different loci. Similar movement of domains between TRD1 and TRD2 was observed for the specificity subunit of a Type IIG restriction enzyme. Similar movement of domain between TRD1 and TRD2 was observed for Type I restriction-modification enzyme specificity genes in two more eubacterial species, Streptococcus pyogenes and Mycoplasma agalactiae. Lateral domain movements within a protein, which we have designated DOMO (domain movement, represent novel routes for the diversification of proteins.

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,...

CTD, Phytoplankton and Other Data from WEATHERBIRD and Other Platforms from the JGOFS/BATS Project from 19911001 to 19930930 (NODC Accession 9500091)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — The Bottle; Conductivity, Temperature and Depth (CTD); and phytoplankton data were collected in NW Atlantic (limit-40 W) as part of Joint Global Ocean Flux Study,...

Temperature, salinity, and other data from CTD casts in the Indian Ocean and other locations from 19890901 to 19910831 (NODC Accession 9700263)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Temperature, salinity, and other data were collected from CTD casts in the Mediterranean Sea, Indian Ocean, and other locations from 01 September 1989 to 31 August...

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

Directory of Open Access Journals (Sweden)

Tineke L Lenstra

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

Solution properties of the archaeal CRISPR DNA repeat-binding homeodomain protein Cbp2

DEFF Research Database (Denmark)

Kenchappa, Chandra; Heiðarsson, Pétur Orri; Kragelund, Birthe

2013-01-01

Clustered regularly interspaced short palindromic repeats (CRISPR) form the basis of diverse adaptive immune systems directed primarily against invading genetic elements of archaea and bacteria. Cbp1 of the crenarchaeal thermoacidophilic order Sulfolobales, carrying three imperfect repeats, binds...... specifically to CRISPR DNA repeats and has been implicated in facilitating production of long transcripts from CRISPR loci. Here, a second related class of CRISPR DNA repeat-binding protein, denoted Cbp2, is characterized that contains two imperfect repeats and is found amongst members of the crenarchaeal...... in facilitating high affinity DNA binding of Cbp2 by tethering the two domains. Structural studies on mutant proteins provide support for Cys(7) and Cys(28) enhancing high thermal stability of Cbp2(Hb) through disulphide bridge formation. Consistent with their proposed CRISPR transcriptional regulatory role, Cbp2...

CTD: a computer program to solve the three dimensional multi-group diffusion equation in X, Y, Z, and triangular Z geometries

Energy Technology Data Exchange (ETDEWEB)

Fletcher, J K

1973-05-01

CTD is a computer program written in Fortran 4 to solve the multi-group diffusion theory equations in X, Y, Z and triangular Z geometries. A power print- out neutron balance and breeding gain are also produced. 4 references. (auth)

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

Conformational analysis of isolated domains of Helicobacter pylori CagA.

Directory of Open Access Journals (Sweden)

Amanda P Woon

Full Text Available The CagA protein of Helicobacter pylori is associated with increased virulence and gastric cancer risk. CagA is translocated into the host cell by a H. pylori type IV secretion system via mechanisms that are poorly understood. Translocated CagA interacts with numerous host factors, altering a variety of host signalling pathways. The recently determined crystal structure of C-terminally-truncated CagA indicated the presence of two domains: the smaller, flexible N-terminal domain and the larger, middle domain. In this study, we have investigated the conformation, oligomeric state and stability of the N-terminal, middle and glutamate-proline-isoleucine-tyrosine-alanine (EPIYA-repeats domains. All three domains are monomeric, suggesting that the multimerisation of CagA observed in infected cells is likely to be mediated not by CagA itself but by its interacting partners. The middle and the C-terminal domains, but not the N-terminal domain, are capable of refolding spontaneously upon heat denaturation, lending support to the hypothesis that unfolded CagA is threaded C-terminus first through the type IV secretion channel with its N-terminal domain, which likely requires interactions with other domains to refold, being threaded last. Our findings also revealed that the C-terminal EPIYA-repeats domain of CagA exists in an intrinsically disordered premolten globule state with regions in PPII conformation--a feature that is shared by many scaffold proteins that bind multiple protein components of signalling pathways. Taken together, these results provide a deeper understanding of the physicochemical properties of CagA that underpin its complex cellular and oncogenic functions.

The number of genes encoding repeat domain-containing proteins positively correlates with genome size in amoebal giant viruses

Science.gov (United States)

Shukla, Avi; Chatterjee, Anirvan

2018-01-01

Abstract Curiously, in viruses, the virion volume appears to be predominantly driven by genome length rather than the number of proteins it encodes or geometric constraints. With their large genome and giant particle size, amoebal viruses (AVs) are ideally suited to study the relationship between genome and virion size and explore the role of genome plasticity in their evolutionary success. Different genomic regions of AVs exhibit distinct genealogies. Although the vertically transferred core genes and their functions are universally conserved across the nucleocytoplasmic large DNA virus (NCLDV) families and are essential for their replication, the horizontally acquired genes are variable across families and are lineage-specific. When compared with other giant virus families, we observed a near–linear increase in the number of genes encoding repeat domain-containing proteins (RDCPs) with the increase in the genome size of AVs. From what is known about the functions of RDCPs in bacteria and eukaryotes and their prevalence in the AV genomes, we envisage important roles for RDCPs in the life cycle of AVs, their genome expansion, and plasticity. This observation also supports the evolution of AVs from a smaller viral ancestor by the acquisition of diverse gene families from the environment including RDCPs that might have helped in host adaption. PMID:29308275

National Coral Reef Monitoring Program: Shallow Water Conductivity-Temperature-Depth (CTD) Profiles for selected locations across the Hawaiian Archipelago in 2013 (NCEI Accession 0161327)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Near-shore shallow water Conductivity-Temperature-Depth (CTD) surveys provided vertical profiles of temperature, salinity, and turbidity providing indications for...

Repeat-Associated Plasticity in the Helicobacter pylori RD Gene Family▿ †

Science.gov (United States)

Shak, Joshua R.; Dick, Jonathan J.; Meinersmann, Richard J.; Perez-Perez, Guillermo I.; Blaser, Martin J.

2009-01-01

The bacterium Helicobacter pylori is remarkable for its ability to persist in the human stomach for decades without provoking sterilizing immunity. Since repetitive DNA can facilitate adaptive genomic flexibility via increased recombination, insertion, and deletion, we searched the genomes of two H. pylori strains for nucleotide repeats. We discovered a family of genes with extensive repetitive DNA that we have termed the H. pylori RD gene family. Each gene of this family is composed of a conserved 3′ region, a variable mid-region encoding 7 and 11 amino acid repeats, and a 5′ region containing one of two possible alleles. Analysis of five complete genome sequences and PCR genotyping of 42 H. pylori strains revealed extensive variation between strains in the number, location, and arrangement of RD genes. Furthermore, examination of multiple strains isolated from a single subject's stomach revealed intrahost variation in repeat number and composition. Despite prior evidence that the protein products of this gene family are expressed at the bacterial cell surface, enzyme-linked immunosorbent assay and immunoblot studies revealed no consistent seroreactivity to a recombinant RD protein by H. pylori-positive hosts. The pattern of repeats uncovered in the RD gene family appears to reflect slipped-strand mispairing or domain duplication, allowing for redundancy and subsequent diversity in genotype and phenotype. This novel family of hypervariable genes with conserved, repetitive, and allelic domains may represent an important locus for understanding H. pylori persistence in its natural host. PMID:19749042

Molecular Mechanics of the α-Actinin Rod Domain: Bending, Torsional, and Extensional Behavior

Science.gov (United States)

Golji, Javad; Collins, Robert; Mofrad, Mohammad R. K.

2009-01-01

α-Actinin is an actin crosslinking molecule that can serve as a scaffold and maintain dynamic actin filament networks. As a crosslinker in the stressed cytoskeleton, α-actinin can retain conformation, function, and strength. α-Actinin has an actin binding domain and a calmodulin homology domain separated by a long rod domain. Using molecular dynamics and normal mode analysis, we suggest that the α-actinin rod domain has flexible terminal regions which can twist and extend under mechanical stress, yet has a highly rigid interior region stabilized by aromatic packing within each spectrin repeat, by electrostatic interactions between the spectrin repeats, and by strong salt bridges between its two anti-parallel monomers. By exploring the natural vibrations of the α-actinin rod domain and by conducting bending molecular dynamics simulations we also predict that bending of the rod domain is possible with minimal force. We introduce computational methods for analyzing the torsional strain of molecules using rotating constraints. Molecular dynamics extension of the α-actinin rod is also performed, demonstrating transduction of the unfolding forces across salt bridges to the associated monomer of the α-actinin rod domain. PMID:19436721

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...

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...

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...

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...

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...

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...

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...

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...

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...

CRED Shallow CTD Profiles; Maro Reef, Northwestern Hawaiian Islands (Papahanaumokuakea Marine National Monument); Cruise: HI0809, Data Date Range: 20080919-20080920 (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...

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...

CRED Shallow CTD Profiles; Kure Atoll, Northwestern Hawaiian Islands (Papahanaumokuakea Marine National Monument); Cruise: HI0611, Data Date Range: 20060919-20060919 (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...

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...

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...

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...

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...

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...

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...

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...

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 are...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

CRED Shallow CTD Profiles; Lisianski Island, Northwestern Hawaiian Islands (Papahanaumokuakea Marine National Monument); Cruise: HI0611, Data Date Range: 20060926-20060926 (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...

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...

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...

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...

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...

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...

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...

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...

CTD data from the northeast Atlantic Ocean 22 deg N - 33 deg N, 19 deg W - 24 deg W, July 1983 during RRS DISCOVERY Cruises 138, 139

International Nuclear Information System (INIS)

Saunders, P.M.; Manning, A.

1984-01-01

This report presents lists and graphs of CTD data obtained aboard RRS Discovery during July 1983. A series of approximately 27 stations were made in the vicinity of 32 deg 30' N 20 deg W, 150 miles West of Madeira, in support of an experiment to investigate the benthic boundary layer on the lower continental rise (in water depths approximately 4000 to 5000 m). South of this location stations were occupied along longitude 24 deg W culminating in a series on the lower continental rise near 23 deg N. All CTD data were reconciled with reversing thermometer observations and with measurements of salinity and dissolved oxygen derived from samples. (author)

Temperature and other data bottle and CTD casts and other instruments in the Mediterranean Sea from 01 January 1901 - 31 December 1995 (NODC Accession 9900172)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Temperature, pressure, salinity, and dissolved oxygen were collected using theromsalinograph, bathythermograph (XBT and MBT), CTD, and bottle casts in the...

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.

History, rare, and multiple events of mechanical unfolding of repeat proteins

Science.gov (United States)

Sumbul, Fidan; Marchesi, Arin; Rico, Felix

2018-03-01

Mechanical unfolding of proteins consisting of repeat domains is an excellent tool to obtain large statistics. Force spectroscopy experiments using atomic force microscopy on proteins presenting multiple domains have revealed that unfolding forces depend on the number of folded domains (history) and have reported intermediate states and rare events. However, the common use of unspecific attachment approaches to pull the protein of interest holds important limitations to study unfolding history and may lead to discarding rare and multiple probing events due to the presence of unspecific adhesion and uncertainty on the pulling site. Site-specific methods that have recently emerged minimize this uncertainty and would be excellent tools to probe unfolding history and rare events. However, detailed characterization of these approaches is required to identify their advantages and limitations. Here, we characterize a site-specific binding approach based on the ultrastable complex dockerin/cohesin III revealing its advantages and limitations to assess the unfolding history and to investigate rare and multiple events during the unfolding of repeated domains. We show that this approach is more robust, reproducible, and provides larger statistics than conventional unspecific methods. We show that the method is optimal to reveal the history of unfolding from the very first domain and to detect rare events, while being more limited to assess intermediate states. Finally, we quantify the forces required to unfold two molecules pulled in parallel, difficult when using unspecific approaches. The proposed method represents a step forward toward more reproducible measurements to probe protein unfolding history and opens the door to systematic probing of rare and multiple molecule unfolding mechanisms.

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...

Preservice science teachers' experiences with repeated, guided inquiry

Science.gov (United States)

Slack, Amy B.

The purpose of this study was to examine preservice science teachers' experiences with repeated scientific inquiry (SI) activities. The National Science Education Standards (National Research Council, 1996) stress students should understand and possess the abilities to do SI. For students to meet these standards, science teachers must understand and be able to perform SI; however, previous research demonstrated that many teachers have naive understandings in this area. Teacher preparation programs provide an opportunity to facilitate the development of inquiry understandings and abilities. In this study, preservice science teachers had experiences with two inquiry activities that were repeated three times each. The research questions for this study were (a) How do preservice science teachers' describe their experiences with repeated, guided inquiry activities? (b) What are preservice science teachers' understandings and abilities of SI? This study was conducted at a large, urban university in the southeastern United States. The 5 participants had bachelor's degrees in science and were enrolled in a graduate science education methods course. The researcher was one of the course instructors but did not lead the activities. Case study methodology was used. Data was collected from a demographic survey, an open-ended questionnaire with follow-up interviews, the researcher's observations, participants' lab notes, personal interviews, and participants' journals. Data were coded and analyzed through chronological data matrices to identify patterns in participants' experiences. The five domains identified in this study were understandings of SI, abilities to conduct SI, personal feelings about the experience, science content knowledge, and classroom implications. Through analysis of themes identified within each domain, the four conclusions made about these preservice teachers' experiences with SI were that the experience increased their abilities to conduct inquiry

EX1103: Exploration and Mapping, Galapagos Spreading Center: Mapping, CTD, Tow-Yo, and ROV on NOAA Ship Okeanos Explorer between 20110608 and 20110728

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — This cruise will be composed of two separate legs. The first leg will be a transit from San Diego, CA to the Galapagos Spreading Center, where multibeam mapping, CTD...

Deletion of Repeats in the Alpha C Protein Enhances the Pathogenicity of Group B Streptococci in Immune Mice

OpenAIRE

Gravekamp, C.; Rosner, Bernard; Madoff, L. C.

1998-01-01

The alpha C protein is a protective surface-associated antigen of group B streptococci (GBS). The prototype alpha C protein of GBS (strain A909) contains nine identical tandem repeats, each comprising 82 amino acids, flanked by N- and C-terminal domains. Clinical isolates of GBS show variable numbers of repeats with a normal distribution and a median of 9 to 10 repeats. Here, we show that escape mutants of GBS expressing one-repeat alpha C protein were 100-fold more pathogenic than GBS expres...

Assessment of Cumulative Trauma Disorder (CTD) Risk for 3 Different Tasks Constructing and Repairing Multi-Layer Insulation (MLI) Blankets, Preparing the Dough for a Pizza, and Operating the Becton-Dickinson FACSAria Flow Cytometer

Science.gov (United States)

Gentzler, Marc; Kline, Martin; Palmer, Andrew; Terrone, Mark

2007-01-01

The Cumulative Trauma Disorder (CTD) risks for three different tasks using McCauley-Bell and Badiru's (1993) formula based on task, personal, and organizational factors were examined. For the Multi-Layer Insulation (MLI) blanket task, the results showed that the task, personal, and organizational risks were at about the same level. The personal risk factors for this task were evaluated using a hypothetical female employee age 52. For the pizza dough task, it was shown that the organizational risk was particularly high, with task related factors also at quite dangerous levels. On the other hand, there was a very low level of personal risk factors, based on a female age 17. The flow cytometer task was assessed with three different participants, a11 of whom had quite disparate levels of personal risk, which slightly affected the overall CTD risk. This reveals how individual difference variables certainly need to be considered. The task and organizational risks for this task were rated at about the same moderate level. The overall CTD risk averaged across the three participants was .335, indicating some risk. Compruing across the tasks revealed that the pizza dough task created the greatest overall CTD risk by far (.568), with the MLI (.325) and flow cytometer task (.335) having some risk associated with them. Future research should look into different tasks for more of a comparison

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...

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...

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...

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...

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...

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...

Domain structures and magnetization reversal in Co/Pd and CoFeB/Pd multilayers

Energy Technology Data Exchange (ETDEWEB)

Sbiaa, R., E-mail: rachid@squ.edu.om [Department of Physics, Sultan Qaboos University, P.O. Box 36, PC 123 (Oman); Ranjbar, M. [Physics Department, University of Gothenburg, 412 96 Gothenburg (Sweden); Åkerman, J. [Physics Department, University of Gothenburg, 412 96 Gothenburg (Sweden); Materials Physics, School of ICT, Royal Institute of Technology (KTH), 164 40 Kista (Sweden)

2015-05-07

Domain structures and magnetization reversal of (Co/Pd) and (CoFeB/Pd) multilayers with 7 and 14 repeats were investigated. The Co-based multilayers show much larger coercivities, a better squareness, and a sharper magnetization switching than CoFeB-based multilayers. From magnetic force microscopy observations, both structures show strong reduction in domains size as the number of repeats increases but the magnetic domains for Co-based multilayers are more than one order of magnitude larger than for CoFeB-based multilayers. By imaging domains at different times, breaks in the (CoFeB/Pd) multilayer stripes were observed within only few hours, while no change could be seen for (Co/Pd) multilayers. Although CoFeB single layers are suitable for magnetoresistive devices due to their large spin polarization and low damping constants, their lamination with Pd suffers mainly from thermal instability.

Functional and topological characteristics of mammalian regulatory domains

Science.gov (United States)

Symmons, Orsolya; Uslu, Veli Vural; Tsujimura, Taro; Ruf, Sandra; Nassari, Sonya; Schwarzer, Wibke; Ettwiller, Laurence; Spitz, François

2014-01-01

Long-range regulatory interactions play an important role in shaping gene-expression programs. However, the genomic features that organize these activities are still poorly characterized. We conducted a large operational analysis to chart the distribution of gene regulatory activities along the mouse genome, using hundreds of insertions of a regulatory sensor. We found that enhancers distribute their activities along broad regions and not in a gene-centric manner, defining large regulatory domains. Remarkably, these domains correlate strongly with the recently described TADs, which partition the genome into distinct self-interacting blocks. Different features, including specific repeats and CTCF-binding sites, correlate with the transition zones separating regulatory domains, and may help to further organize promiscuously distributed regulatory influences within large domains. These findings support a model of genomic organization where TADs confine regulatory activities to specific but large regulatory domains, contributing to the establishment of specific gene expression profiles. PMID:24398455

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...

SeaSoar CTD Observations from the Central Oregon Shelf, Cruise W9907C, 13-31 Jul 1999. A Component of Prediction of Wind-Driven Coastal Circulation Project

National Research Council Canada - National Science Library

Barth, J

2001-01-01

This report summarizes observations taken with a conductivity-temperature-depth (CTD) instrument aboard the towed, undulating vehicle SeaSoar during the 1999 National Oceanographic Partnership Program...

Crystal structure of the second fibronectin type III (FN3) domain from human collagen α1 type XX.

Science.gov (United States)

Zhao, Jingfeng; Ren, Jixia; Wang, Nan; Cheng, Zhong; Yang, Runmei; Lin, Gen; Guo, Yi; Cai, Dayong; Xie, Yong; Zhao, Xiaohong

2017-12-01

Collagen α1 type XX, which contains fibronectin type III (FN3) repeats involving six FN3 domains (referred to as the FN#1-FN#6 domains), is an unusual member of the fibril-associated collagens with interrupted triple helices (FACIT) subfamily of collagens. The results of standard protein BLAST suggest that the FN3 repeats might contribute to collagen α1 type XX acting as a cytokine receptor. To date, solution NMR structures of the FN#3, FN#4 and FN#6 domains have been determined. To obtain further structural evidence to understand the relationship between the structure and function of the FN3 repeats from collagen α1 type XX, the crystal structure of the FN#2 domain from human collagen α1 type XX (residues Pro386-Pro466; referred to as FN2-HCXX) was solved at 2.5 Å resolution. The crystal structure of FN2-HCXX shows an immunoglobulin-like fold containing a β-sandwich structure, which is formed by a three-stranded β-sheet (β1, β2 and β5) packed onto a four-stranded β-sheet (β3, β4, β6 and β7). Two consensus domains, tencon and fibcon, are structural analogues of FN2-HCXX. Fn8, an FN3 domain from human oncofoetal fibronectin, is the closest structural analogue of FN2-HCXX derived from a naturally occurring sequence. Based solely on the structural similarity of FN2-HCXX to other FN3 domains, the detailed functions of FN2-HCXX and the FN3 repeats in collagen α1 type XX cannot be identified.

Crystal structure of a PFU-PUL domain pair of Saccharomyces cerevisiae Doa1/Ufd3.

Science.gov (United States)

Nishimasu, Rieko; Komori, Hirofumi; Higuchi, Yoshiki; Nishimasu, Hiroshi; Hiroaki, Hidekazu

2010-10-21

Doa1/Ufd3 is involved in ubiquitin (Ub)-dependent cellular processes in Saccharomyces cerevisiae, and consists of WD40, PFU, and PUL domains. Previous studies showed that the PFU and PUL domains interact with Ub and Hse1, and Cdc48, respectively. However, their detailed functional interactions with Doa1 remained elusive. We report the crystal structure of the PFU-PUL domain pair of yeast Doa1 at 1.9 Å resolution. The conserved surface of the PFU domain may be involved in binding to Ub and Hse1. Unexpectedly, the PUL domain consists of an Armadillo (ARM)-like repeat structure. The positively charged concave surface of the PUL domain may bind to the negatively charged C-terminal region of Cdc48. A structural comparison of Doa1 with Ufd2 revealed that they share a similar ARM-like repeat, supporting a model in which Doa1 and Ufd2 compete for Cdc48 binding and may dictate the fate of ubiquitinated proteins in the proteasome pathway.

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...

A TALE-inspired computational screen for proteins that contain approximate tandem repeats.

Science.gov (United States)

Perycz, Malgorzata; Krwawicz, Joanna; Bochtler, Matthias

2017-01-01

TAL (transcription activator-like) effectors (TALEs) are bacterial proteins that are secreted from bacteria to plant cells to act as transcriptional activators. TALEs and related proteins (RipTALs, BurrH, MOrTL1 and MOrTL2) contain approximate tandem repeats that differ in conserved positions that define specificity. Using PERL, we screened ~47 million protein sequences for TALE-like architecture characterized by approximate tandem repeats (between 30 and 43 amino acids in length) and sequence variability in conserved positions, without requiring sequence similarity to TALEs. Candidate proteins were scored according to their propensity for nuclear localization, secondary structure, repeat sequence complexity, as well as covariation and predicted structural proximity of variable residues. Biological context was tentatively inferred from co-occurrence of other domains and interactome predictions. Approximate repeats with TALE-like features that merit experimental characterization were found in a protein of chestnut blight fungus, a eukaryotic plant pathogen.

Temperature and salinity profiles from CTD casts from NOAA Ship RONALD H. BROWN in the SE Pacific (limit -140 W) as part of the East Pacific Investigations of Climate Processes in the Coupled Ocean-Atmosphere from 2001-02-01 to 2001-03-08 (NODC Accession 0000660)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — CTD and other data were collected from NOAA Ship RONALD H. BROWN in the SE Pacific (limit-140 W) from from 01 February 2001 to 08 March 2001. CTD data consist of...

Temperature and salinity profiles from CTD casts from NOAA Ship RONALD H. BROWN in the NE and SE Pacific as part of the East Pacific Investigations of Climate Processes in support of the Coupled Ocean-Atmosphere from 2001-09-05 to 2001-10-25 (NODC Accession 0000657)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — CTD and other data were collected from NOAA Ship RONALD H. BROWN in the NE and SE Pacific from 05 September 2001 to 25 October 2001. CTD data consist of temperature...

Temperature, salinity, sigma_t, pressure measurement collected using CTD from an unknown platform in the Min Fang Bay from 1984 to 1985 (NODC Accession 0048830)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Southern Ocean data - Min Fang Bay , temperature and salinity measurements collected using CTD from unknown platform in the Min Fang Bay from 1984 to 1985

The Jasmonate-ZIM-Domain Proteins Interact with the WD-Repeat/bHLH/MYB Complexes to Regulate Jasmonate-Mediated Anthocyanin Accumulation and Trichome Initiation in Arabidopsis thaliana[C][W

Science.gov (United States)

Qi, Tiancong; Song, Susheng; Ren, Qingcuo; Wu, Dewei; Huang, Huang; Chen, Yan; Fan, Meng; Peng, Wen; Ren, Chunmei; Xie, Daoxin

2011-01-01

Jasmonates (JAs) mediate plant responses to insect attack, wounding, pathogen infection, stress, and UV damage and regulate plant fertility, anthocyanin accumulation, trichome formation, and many other plant developmental processes. Arabidopsis thaliana Jasmonate ZIM-domain (JAZ) proteins, substrates of the CORONATINE INSENSITIVE1 (COI1)–based SCFCOI1 complex, negatively regulate these plant responses. Little is known about the molecular mechanism for JA regulation of anthocyanin accumulation and trichome initiation. In this study, we revealed that JAZ proteins interact with bHLH (Transparent Testa8, Glabra3 [GL3], and Enhancer of Glabra3 [EGL3]) and R2R3 MYB transcription factors (MYB75 and Glabra1), essential components of WD-repeat/bHLH/MYB transcriptional complexes, to repress JA-regulated anthocyanin accumulation and trichome initiation. Genetic and physiological evidence showed that JA regulates WD-repeat/bHLH/MYB complex-mediated anthocyanin accumulation and trichome initiation in a COI1-dependent manner. Overexpression of the MYB transcription factor MYB75 and bHLH factors (GL3 and EGL3) restored anthocyanin accumulation and trichome initiation in the coi1 mutant, respectively. We speculate that the JA-induced degradation of JAZ proteins abolishes the interactions of JAZ proteins with bHLH and MYB factors, allowing the transcriptional function of WD-repeat/bHLH/MYB complexes, which subsequently activate respective downstream signal cascades to modulate anthocyanin accumulation and trichome initiation. PMID:21551388

Oceanographic temperature, salinity, oxygen and meteorology measurements collected using CTD from multiple ships in the Sea of Azov from 1999 to 2006 (NODC Accession 0037021)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Temperature, salinity and other measurements found in dataset CTD taken from the ZODIAK (Motor boat), GROZA (Motor felucca) and other platforms in the Black Sea from...

Stabilization of Nucleosomes by Histone Tails and by FACT Revealed by spFRET Microscopy

Directory of Open Access Journals (Sweden)

Maria E. Valieva

2017-01-01

Full Text Available A correct chromatin structure is important for cell viability and is tightly regulated by numerous factors. Human protein complex FACT (facilitates chromatin transcription is an essential factor involved in chromatin transcription and cancer development. Here FACT-dependent changes in the structure of single nucleosomes were studied with single-particle Förster resonance energy transfer (spFRET microscopy using nucleosomes labeled with a donor-acceptor pair of fluorophores, which were attached to the adjacent gyres of DNA near the contact between H2A-H2B dimers. Human FACT and its version without the C-terminal domain (CTD and the high mobility group (HMG domain of the structure-specific recognition protein 1 (SSRP1 subunit did not change the structure of the nucleosomes, while FACT without the acidic C-terminal domains of the suppressor of Ty 16 (Spt16 and the SSRP1 subunits caused nucleosome aggregation. Proteolytic removal of histone tails significantly disturbed the nucleosome structure, inducing partial unwrapping of nucleosomal DNA. Human FACT reduced DNA unwrapping and stabilized the structure of tailless nucleosomes. CTD and/or HMG domains of SSRP1 are required for this FACT activity. In contrast, previously it has been shown that yeast FACT unfolds (reorganizes nucleosomes using the CTD domain of SSRP1-like Pol I-binding protein 3 subunit (Pob3. Thus, yeast and human FACT complexes likely utilize the same domains for nucleosome reorganization and stabilization, respectively, and these processes are mechanistically similar.

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...

Wives Domain-Specific "Marriage Work" with Friends and Spouses: Links to Marital Quality

Science.gov (United States)

Proulx, Christine M.; Helms, Heather M.; Payne, C. Chris

2004-01-01

This study examined the friendship experiences of 52 wives and mothers, with particular attention given to wives' marriage work (discussions about concerns and problems in the marriage) in 10 domains with friends and spouses. A series of within-subjects repeated measures analyses of variance (ANOVAs) indicated that in all but two domains, wives…

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...

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 are...

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...

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...

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...

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...

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...

Residues 240-250 in the C-terminus of the Pirh2 protein complement the function of the RING domain in self-ubiquitination of the Pirh2 protein.

Directory of Open Access Journals (Sweden)

Rami Abou Zeinab

Full Text Available Pirh2 is a p53 inducible gene that encodes a RING-H2 domain and is proposed to be a main regulator of p53 protein, thus fine tuning the DNA damage response. Pirh2 interacts physically with p53 and promotes its MDM2-independent ubiquitination and subsequent degradation as well as participates in an auto-regulatory feedback loop that controls p53 function. Pirh2 also self-ubiquitinates. Interestingly, Pirh2 is overexpressed in a wide range of human tumors. In this study, we investigated the domains and residues essential for Pirh2 self-ubiquitination. Deletions were made in each of the three major domains of Pirh2: the N-terminal domain (NTD, Ring domain (RING, and C-terminal domain (CTD. The effects of these deletions on Pirh2 self-ubiquitination were then assessed using in vitro ubiquitination assays. Our results demonstrate that the RING domain is essential, but not sufficient, for Pirh2 self-ubiquitination and that residues 240-250 of the C-terminal domain are also essential. Our results demonstrate that Pirh2 mediated p53 polyubiquitination occurs mainly through the K48 residue of ubiquitin in vitro. Our data further our understanding of the mechanism of Pirh2 self-ubiquitination and may help identify valuable therapeutic targets that play roles in reducing the effects of the overexpression of Pirh2, thus maximizing p53's response to DNA damage.

Structure and evolution of N-domains in AAA metalloproteases.

Science.gov (United States)

Scharfenberg, Franka; Serek-Heuberger, Justyna; Coles, Murray; Hartmann, Marcus D; Habeck, Michael; Martin, Jörg; Lupas, Andrei N; Alva, Vikram

2015-02-27

Metalloproteases of the AAA (ATPases associated with various cellular activities) family play a crucial role in protein quality control within the cytoplasmic membrane of bacteria and the inner membrane of eukaryotic organelles. These membrane-anchored hexameric enzymes are composed of an N-terminal domain with one or two transmembrane helices, a central AAA ATPase module, and a C-terminal Zn(2+)-dependent protease. While the latter two domains have been well studied, so far, little is known about the N-terminal regions. Here, in an extensive bioinformatic and structural analysis, we identified three major, non-homologous groups of N-domains in AAA metalloproteases. By far, the largest one is the FtsH-like group of bacteria and eukaryotic organelles. The other two groups are specific to Yme1: one found in plants, fungi, and basal metazoans and the other one found exclusively in animals. Using NMR and crystallography, we determined the subunit structure and hexameric assembly of Escherichia coli FtsH-N, exhibiting an unusual α+β fold, and the conserved part of fungal Yme1-N from Saccharomyces cerevisiae, revealing a tetratricopeptide repeat fold. Our bioinformatic analysis showed that, uniquely among these proteins, the N-domain of Yme1 from the cnidarian Hydra vulgaris contains both the tetratricopeptide repeat region seen in basal metazoans and a region of homology to the N-domains of animals. Thus, it is a modern-day representative of an intermediate in the evolution of animal Yme1 from basal eukaryotic precursors. Copyright © 2015. Published by Elsevier Ltd.

Temperature, salinity, oxygen and nutrients bottle and CTD data collected in the northern North Atlantic, Nordic and Arctic Seas from 1901 to 2011 (NODC Accession 0105532)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Historical temperature, salinity, oxygen and nutrients bottle and CTD data collected in the Arctic Ocean, Barents Sea, Greenland Sea, Kara Sea, North Atlantic Ocean,...

Synergistic enhancement of cellulase pairs linked by consensus ankyrin repeats: Determination of the roles of spacing, orientation, and enzyme identity.

Science.gov (United States)

Cunha, Eva S; Hatem, Christine L; Barrick, Doug

2016-08-01

Biomass deconstruction to small simple sugars is a potential approach to biofuels production; however, the highly recalcitrant nature of biomass limits the economic viability of this approach. Thus, research on efficient biomass degradation is necessary to achieve large-scale production of biofuels. Enhancement of cellulolytic activity by increasing synergism between cellulase enzymes holds promise in achieving high-yield biofuels production. Here we have inserted cellulase pairs from extremophiles into hyperstable α-helical consensus ankyrin repeat domain scaffolds. Such chimeric constructs allowed us to optimize arrays of enzyme pairs against a variety of cellulolytic substrates. We found that endocellulolytic domains CelA (CA) and Cel12A (C12A) act synergistically in the context of ankyrin repeats, with both three and four repeat spacing. The extent of synergy differs for different substrates. Also, having C12A N-terminal to CA provides greater synergy than the reverse construct, especially against filter paper. In contrast, we do not see synergy for these enzymes in tandem with CelK (CK) catalytic domain, a larger exocellulase, demonstrating the importance of enzyme identity in synergistic enhancement. Furthermore, we found endocellulases CelD and CA with three repeat spacing to act synergistically against filter paper. Importantly, connecting CA and C12A with a disordered linker of similar contour length shows no synergistic enhancement, indicating that synergism results from connecting these domains with folded ankyrin repeats. These results show that ankyrin arrays can be used to vary spacing and orientation between enzymes, helping to design and optimize artificial cellulosomes, providing a novel architecture for synergistic enhancement of enzymatic cellulose degradation. Proteins 2016; 84:1043-1054. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Control of coercive field in lithium niobate crystals with repeated polarization reversal

International Nuclear Information System (INIS)

Ro, Jung Hoon; Jeong, Doun; Park, Taeyong; Kim, Chulhan; Kwon, Soon-Bok; Cha, Myoungsik; Choi, Byeong Cheol; Yu, Nanei; Kurimura, Sunao; Jeon, Gyerok

2005-01-01

In this study, the amount of decrease in coercive field of congruent lithium niobate during repeated poling and back-poling was measured. The polarization is reversed in 300 ms and then back-poled during the rest period. The coercive field can be decreased around 1 kV/mm with a repeated poling interval of 5 s. As the interval prolonged, the poling field decrease became smaller, and a stretched exponential function is suggested for the experimental fitting resulting in a set of meaningful parameters. These values are essential for the design of high quality domain engineering

The polymorphic integumentary mucin B.1 from Xenopus laevis contains the short consensus repeat.

Science.gov (United States)

Probst, J C; Hauser, F; Joba, W; Hoffmann, W

1992-03-25

The frog integumentary mucin B.1 (FIM-B.1), discovered by molecular cloning, contains a cysteine-rich C-terminal domain which is homologous with von Willebrand factor. With the help of the polymerase chain reaction, we now characterize a contiguous region 5' to the von Willebrand factor domain containing the short consensus repeat typical of many proteins from the complement system. Multiple transcripts have been cloned, which originate from a single animal and differ by a variable number of tandem repeats (rep-33 sequences). These different transcripts probably originate solely from two genes and are generated presumably by alternative splicing of an huge array of functional cassettes. This model is supported by analysis of genomic FIM-B.1 sequences from Xenopus laevis. Here, rep-33 sequences are arranged in an interrupted array of individual units. Additionally, results of Southern analysis revealed genetic polymorphism between different animals which is predicted to be within the tandem repeats. A first investigation of the predicted mucins with the help of a specific antibody against a synthetic peptide determined the molecular mass of FIM-B.1 to greater than 200 kDa. Here again, genetic polymorphism between different animals is detected.

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...

Salinity and sigma-t data from CTD casts in the TOGA Area - Pacific Ocean from 1994-01-06 to 1995-08-03 (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....

The Role of Parental Perceptions of Tic Frequency and Intensity in Predicting Tic-Related Functional Impairment in Youth with Chronic Tic Disorders

OpenAIRE

Espil, Flint M.; Capriotti, Matthew R.; Conelea, Christine A.; Woods, Douglas W.

2014-01-01

Tic severity is composed of several dimensions. Tic frequency and intensity are two such dimensions, but little empirical data exist regarding their relative contributions to functional impairment in those with Chronic Tic Disorders (CTD). The present study examined the relative contributions of these dimensions in predicting tic-related impairment across several psychosocial domains. Using data collected from parents of youth with CTD, multivariate regression analyses revealed that both tic ...

Phytoplankton, chemical, and other data from bottle and CTD casts in the North Atlantic Ocean from 04 August 1989 to 07 September 1989 (NODC Accession 0000399)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Phytoplankton, chemical, nutrients, salinity, and other data from August 4, 1989 to September 7, 1989. Data were collected using bottle and CTD casts in the North...

Expression of human PQBP-1 in Drosophila impairs long-term memory and induces abnormal courtship.

Science.gov (United States)

Yoshimura, Natsue; Horiuchi, Daisuke; Shibata, Masao; Saitoe, Minoru; Qi, Mei-Ling; Okazawa, Hitoshi

2006-04-17

Frame shift mutations of the polyglutamine binding protein-1 (PQBP1) gene lead to total or partial truncation of the C-terminal domain (CTD) and cause mental retardation in human patients. Interestingly, normal Drosophila homologue of PQBP-1 lacks CTD. As a model to analyze the molecular network of PQBP-1 affecting intelligence, we generated transgenic flies expressing human PQBP-1 with CTD. Pavlovian olfactory conditioning revealed that the transgenic flies showed disturbance of long-term memory. In addition, they showed abnormal courtship that male flies follow male flies. Abnormal functions of PQBP-1 or its binding partner might be linked to these symptoms.

The TIR domain of TIR-NB-LRR resistance proteins is a signaling domain involved in cell death induction.

Science.gov (United States)

Swiderski, Michal R; Birker, Doris; Jones, Jonathan D G

2009-02-01

In plants, the TIR (toll interleukin 1 receptor) domain is found almost exclusively in nucleotide-binding (NB) leucine-rich repeat resistance proteins and their truncated homologs, and has been proposed to play a signaling role during resistance responses mediated by TIR containing R proteins. Transient expression in Nicotiana benthamiana leaves of "TIR + 80", the RPS4 truncation without the NB-ARC domain, leads to EDS1-, SGT1-, and HSP90-dependent cell death. Transgenic Arabidopsis plants expressing the RPS4 TIR+80 from either dexamethasone or estradiol-inducible promoters display inducer-dependent cell death. Cell death is also elicited by transient expression of similarly truncated constructs from two other R proteins, RPP1A and At4g19530, but is not elicited by similar constructs representing RPP2A and RPP2B proteins. Site-directed mutagenesis of the RPS4 TIR domain identified many loss-of-function mutations but also revealed several gain-of function substitutions. Lack of cell death induction by the E160A substitution suggests that amino acids outside of the TIR domain contribute to cell death signaling in addition to the TIR domain itself. This is consistent with previous observations that the TIR domain itself is insufficient to induce cell death upon transient expression.

Deletion of intragenic tandem repeats in unit C of FLO1 of Saccharomyces cerevisiae increases the conformational stability of flocculin under acidic and alkaline conditions.

Directory of Open Access Journals (Sweden)

Ee Li

Full Text Available Flocculation is an attractive property for Saccaromyces cerevisiae, which plays important roles in fermentation industry and environmental remediation. The process of flocculation is mediated by a family of cell surface flocculins. As one member of flocculins, Flo1 is characterized by four families of repeats (designated as repeat units A, B, C and D in the central domain. It is generally accepted that variation of repeat unit A in length in Flo1 influences the degree of flocculation or specificity for sugar recognization. However, no reports were observed for other repeat units. Here, we compared the flocculation ability and its sensitivity to environmental factors between yeast strain YSF1 carrying the intact FLO1 gene and yeast strains carrying the derived forms of FLO1 with partial or complete deletion of repeats in unit C. No obvious differences in flocculation ability and specificity of carbohydrate recognition were observed among these yeast strains, which indicates the truncated flocculins can stride across the cell wall and cluster the N-terminal domain on the surface of yeast cells as the intact Flo1 thereby improving intercellular binding. However, yeast strains with the truncated flocculins required more mannose to inhibit completely the flocculation, displayed broad tolerance of flocculation to pH fluctuation, and the fewer the repeats in unit C, the stronger adaptability of flocculation to pH change, which was not relevant to the position of deletion. This suggests that more stable active conformation is obtained for flocculin by deletion the repeat unit C in the central domain of Flo1, which was validated further by the higher hydrophobicity on the surface of cells of YSF1c with complete deletion of unit C under neutral and alkaline conditions and the stabilization of GFP conformation by fusion with flocculin with complete deletion of unit C in the central domain.

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)

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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...

Temperature, salinity, oxygen, and phosphate profiles collected by CTD or bottle in the World-wide Oceans from 11/4/1902 to 12/17/1998 (NODC Accession 0000198)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Temperature profile, meteorological, and nutrients data were collected using CTD and bottle casts from the HOLLAND and other platforms in a world wide distribution....

Temperature and salinity profiles from CTD casts from NOAA Ship RONALD H. BROWN and NOAA Ship KA'IMIMOANA in the NE and SW Pacific as part of the Global Ocean-Atmosphere-Land System (GOALS) / Pan American Climate Studies (PACS) from 2001-01-14 to 2001-12-05 (NODC Accession 0000658)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — CTD and other data were collected from NOAA Ship RONALD H. BROWN and NOAA Ship KA'IMIMOANA in the NE and SW Pacific from 14 January 2001 to 05 December 2001. CTD...

Dominant integration locus drives continuous diversification of plant immune receptors with exogenous domain fusions.

Science.gov (United States)

Bailey, Paul C; Schudoma, Christian; Jackson, William; Baggs, Erin; Dagdas, Gulay; Haerty, Wilfried; Moscou, Matthew; Krasileva, Ksenia V

2018-02-19

The plant immune system is innate and encoded in the germline. Using it efficiently, plants are capable of recognizing a diverse range of rapidly evolving pathogens. A recently described phenomenon shows that plant immune receptors are able to recognize pathogen effectors through the acquisition of exogenous protein domains from other plant genes. We show that plant immune receptors with integrated domains are distributed unevenly across their phylogeny in grasses. Using phylogenetic analysis, we uncover a major integration clade, whose members underwent repeated independent integration events producing diverse fusions. This clade is ancestral in grasses with members often found on syntenic chromosomes. Analyses of these fusion events reveals that homologous receptors can be fused to diverse domains. Furthermore, we discover a 43 amino acid long motif associated with this dominant integration clade which is located immediately upstream of the fusion site. Sequence analysis reveals that DNA transposition and/or ectopic recombination are the most likely mechanisms of formation for nucleotide binding leucine rich repeat proteins with integrated domains. The identification of this subclass of plant immune receptors that is naturally adapted to new domain integration will inform biotechnological approaches for generating synthetic receptors with novel pathogen "baits."

WD-repeat instability and diversification of the Podospora anserina hnwd non-self recognition gene family.

Science.gov (United States)

Chevanne, Damien; Saupe, Sven J; Clavé, Corinne; Paoletti, Mathieu

2010-05-06

Genes involved in non-self recognition and host defence are typically capable of rapid diversification and exploit specialized genetic mechanism to that end. Fungi display a non-self recognition phenomenon termed heterokaryon incompatibility that operates when cells of unlike genotype fuse and leads to the cell death of the fusion cell. In the fungus Podospora anserina, three genes controlling this allorecognition process het-d, het-e and het-r are paralogs belonging to the same hnwd gene family. HNWD proteins are STAND proteins (signal transduction NTPase with multiple domains) that display a WD-repeat domain controlling recognition specificity. Based on genomic sequence analysis of different P. anserina isolates, it was established that repeat regions of all members of the gene family are extremely polymorphic and undergoing concerted evolution arguing for frequent recombination within and between family members. Herein, we directly analyzed the genetic instability and diversification of this allorecognition gene family. We have constituted a collection of 143 spontaneous mutants of the het-R (HNWD2) and het-E (hnwd5) genes with altered recognition specificities. The vast majority of the mutants present rearrangements in the repeat arrays with deletions, duplications and other modifications as well as creation of novel repeat unit variants. We investigate the extreme genetic instability of these genes and provide a direct illustration of the diversification strategy of this eukaryotic allorecognition gene family.

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...

Human TRPA1 is intrinsically cold- and chemosensitive with and without its N-terminal ankyrin repeat domain.

Science.gov (United States)

Moparthi, Lavanya; Survery, Sabeen; Kreir, Mohamed; Simonsen, Charlotte; Kjellbom, Per; Högestätt, Edward D; Johanson, Urban; Zygmunt, Peter M

2014-11-25

We have purified and reconstituted human transient receptor potential (TRP) subtype A1 (hTRPA1) into lipid bilayers and recorded single-channel currents to understand its inherent thermo- and chemosensory properties as well as the role of the ankyrin repeat domain (ARD) of the N terminus in channel behavior. We report that hTRPA1 with and without its N-terminal ARD (Δ1-688 hTRPA1) is intrinsically cold-sensitive, and thus, cold-sensing properties of hTRPA1 reside outside the N-terminal ARD. We show activation of hTRPA1 by the thiol oxidant 2-((biotinoyl)amino)ethyl methanethiosulfonate (MTSEA-biotin) and that electrophilic compounds activate hTRPA1 in the presence and absence of the N-terminal ARD. The nonelectrophilic compounds menthol and the cannabinoid Δ(9)-tetrahydrocannabiorcol (C16) directly activate hTRPA1 at different sites independent of the N-terminal ARD. The TRPA1 antagonist HC030031 inhibited cold and chemical activation of hTRPA1 and Δ1-688 hTRPA1, supporting a direct interaction with hTRPA1 outside the N-terminal ARD. These findings show that hTRPA1 is an intrinsically cold- and chemosensitive ion channel. Thus, second messengers, including Ca(2+), or accessory proteins are not needed for hTRPA1 responses to cold or chemical activators. We suggest that conformational changes outside the N-terminal ARD by cold, electrophiles, and nonelectrophiles are important in hTRPA1 channel gating and that targeting chemical interaction sites outside the N-terminal ARD provides possibilities to fine tune TRPA1-based drug therapies (e.g., for treatment of pain associated with cold hypersensitivity and cardiovascular disease).

Solution structure of leptospiral LigA4 Big domain

Energy Technology Data Exchange (ETDEWEB)

Mei, Song; Zhang, Jiahai [Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026 (China); Zhang, Xuecheng [School of Life Sciences, Anhui University, Hefei, Anhui 230039 (China); Tu, Xiaoming, E-mail: xmtu@ustc.edu.cn [Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026 (China)

2015-11-13

Pathogenic Leptospiraspecies express immunoglobulin-like proteins which serve as adhesins to bind to the extracellular matrices of host cells. Leptospiral immunoglobulin-like protein A (LigA), a surface exposed protein containing tandem repeats of bacterial immunoglobulin-like (Big) domains, has been proved to be involved in the interaction of pathogenic Leptospira with mammalian host. In this study, the solution structure of the fourth Big domain of LigA (LigA4 Big domain) from Leptospira interrogans was solved by nuclear magnetic resonance (NMR). The structure of LigA4 Big domain displays a similar bacterial immunoglobulin-like fold compared with other Big domains, implying some common structural aspects of Big domain family. On the other hand, it displays some structural characteristics significantly different from classic Ig-like domain. Furthermore, Stains-all assay and NMR chemical shift perturbation revealed the Ca{sup 2+} binding property of LigA4 Big domain. - Highlights: • Determining the solution structure of a bacterial immunoglobulin-like domain from a surface protein of Leptospira. • The solution structure shows some structural characteristics significantly different from the classic Ig-like domains. • A potential Ca{sup 2+}-binding site was identified by strains-all and NMR chemical shift perturbation.

Solution structure of leptospiral LigA4 Big domain

International Nuclear Information System (INIS)

Mei, Song; Zhang, Jiahai; Zhang, Xuecheng; Tu, Xiaoming

2015-01-01

Pathogenic Leptospiraspecies express immunoglobulin-like proteins which serve as adhesins to bind to the extracellular matrices of host cells. Leptospiral immunoglobulin-like protein A (LigA), a surface exposed protein containing tandem repeats of bacterial immunoglobulin-like (Big) domains, has been proved to be involved in the interaction of pathogenic Leptospira with mammalian host. In this study, the solution structure of the fourth Big domain of LigA (LigA4 Big domain) from Leptospira interrogans was solved by nuclear magnetic resonance (NMR). The structure of LigA4 Big domain displays a similar bacterial immunoglobulin-like fold compared with other Big domains, implying some common structural aspects of Big domain family. On the other hand, it displays some structural characteristics significantly different from classic Ig-like domain. Furthermore, Stains-all assay and NMR chemical shift perturbation revealed the Ca"2"+ binding property of LigA4 Big domain. - Highlights: • Determining the solution structure of a bacterial immunoglobulin-like domain from a surface protein of Leptospira. • The solution structure shows some structural characteristics significantly different from the classic Ig-like domains. • A potential Ca"2"+-binding site was identified by strains-all and NMR chemical shift perturbation.

Molecular dynamics of Middle East Respiratory Syndrome Coronavirus (MERS CoV) fusion heptad repeat trimers

KAUST Repository

Kandeel, Mahmoud; Al-Taher, Abdulla; Li, Huifang; Schwingenschlö gl, Udo; Alnazawi, Mohamed

2018-01-01

Structural studies related to Middle East Respiratory Syndrome Coronavirus (MERS CoV) infection process are so limited. In this study, molecular dynamics (MD) simulation was carried out to unravel changes in the MERS CoV heptad repeat domains (HRs

Novel anti-HIV peptides containing multiple copies of artificially designed heptad repeat motifs

International Nuclear Information System (INIS)

Shi Weiguo; Qi Zhi; Pan Chungen; Xue Na; Debnath, Asim K.; Qie Jiankun; Jiang Shibo; Liu Keliang

2008-01-01

The peptidic anti-HIV drug T20 (Fuzeon) and its analog C34 share a common heptad repeat (HR) sequence, but they have different functional domains, i.e., pocket- and lipid-binding domains (PBD and LBD, respectively). We hypothesize that novel anti-HIV peptides may be designed by using artificial sequences containing multiple copies of HR motifs plus zero, one or two functional domains. Surprisingly, we found that the peptides containing only the non-natural HR sequences could significantly inhibit HIV-1 infection, while addition of PBD and/or LBD to the peptides resulted in significant improvement of anti-HIV-1 activity. These results suggest that these artificial HR sequences, which may serve as structural domains, could be used as templates for the design of novel antiviral peptides against HIV and other viruses with class I fusion proteins

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...

Size matters: Associations between the androgen receptor CAG repeat length and the intrafollicular hormone milieu

DEFF Research Database (Denmark)

Borgbo, T; Macek, M; Chrudimska, J

2015-01-01

Granulosa cell (GC) expressed androgen receptors (AR) and intrafollicular androgens are central to fertility. The transactivating domain of the AR contains a polymorphic CAG repeat sequence, which is linked to the transcriptional activity of AR and may influence the GC function. This study aims...... to evaluate the effects of the AR CAG repeat length on the intrafollicular hormone profiles, and the gene expression profiles of GC from human small antral follicles. In total, 190 small antral follicles (3-11 mm in diameter) were collected from 58 women undergoing ovarian cryopreservation for fertility...... expression compared to medium CAG repeat lengths (P = 0.03). In conclusion, long CAG repeat lengths in the AR were associated to significant attenuated levels of androgens and an increased conversion of testosterone into oestradiol, in human small antral follicles....

Structure of the Siz/PIAS SUMO E3 Ligase Siz1 and Determinants Required for SUMO Modification of PCNA

Energy Technology Data Exchange (ETDEWEB)

Yunus, Ali A.; Lima, Christopher D.; (SKI)

2010-01-12

Siz1 is a founding member of the Siz/PIAS RING family of SUMO E3 ligases. The X-ray structure of an active Siz1 ligase revealed an elongated tripartite architecture comprised of an N-terminal PINIT domain, a central zinc-containing RING-like SP-RING domain, and a C-terminal domain we term the SP-CTD. Structure-based mutational analysis and biochemical studies show that the SP-RING and SP-CTD are required for activation of the E2SUMO thioester, while the PINIT domain is essential for redirecting SUMO conjugation to the proliferating cell nuclear antigen (PCNA) at lysine 164, a nonconsensus lysine residue that is not modified by the SUMO E2 in the absence of Siz1. Mutational analysis of Siz1 and PCNA revealed surfaces on both proteins that are required for efficient SUMO modification of PCNA in vitro and in vivo.

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...

National Coral Reef Monitoring Program: Shallow Water Conductivity-Temperature-Depth (CTD) Profiles for selected locations across Wake Island from 2014-03-16 to 2014-03-19 (NCEI Accession 0162248)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Near-shore shallow water Conductivity-Temperature-Depth (CTD) surveys provided vertical profiles of temperature, salinity, and turbidity providing indications for...

National Coral Reef Monitoring Program: Shallow Water Conductivity-Temperature-Depth (CTD) Profiles for selected locations across Jarvis Island from 2016-05-19 to 2016-05-23 (NCEI Accession 0162245)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Near-shore shallow water Conductivity-Temperature-Depth (CTD) surveys provided vertical profiles of temperature, salinity, and turbidity providing indications for...

National Coral Reef Monitoring Program: Shallow Water Conductivity-Temperature-Depth (CTD) Profiles for selected locations across American Samoa from 2015-02-15 to 2015-03-28 (NCEI Accession 0161169)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Near-shore shallow water Conductivity-Temperature-Depth (CTD) surveys provided vertical profiles of temperature, salinity, and turbidity providing indications for...

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...

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....

Potential Role of the Last Half Repeat in TAL Effectors Revealed by a Molecular Simulation Study

Directory of Open Access Journals (Sweden)

Hua Wan

2016-01-01

Full Text Available TAL effectors (TALEs contain a modular DNA-binding domain that is composed of tandem repeats. In all naturally occurring TALEs, the end of tandem repeats is invariantly a truncated half repeat. To investigate the potential role of the last half repeat in TALEs, we performed comparative molecular dynamics simulations for the crystal structure of DNA-bound TALE AvrBs3 lacking the last half repeat and its modeled structure having the last half repeat. The structural stability analysis indicates that the modeled system is more stable than the nonmodeled system. Based on the principle component analysis, it is found that the AvrBs3 increases its structural compactness in the presence of the last half repeat. The comparison of DNA groove parameters of the two systems implies that the last half repeat also causes the change of DNA major groove binding efficiency. The following calculation of hydrogen bond reveals that, by stabilizing the phosphate binding with DNA at the C-terminus, the last half repeat helps to adopt a compact conformation at the protein-DNA interface. It further mediates more contacts between TAL repeats and DNA nucleotide bases. Finally, we suggest that the last half repeat is required for the high-efficient recognition of DNA by TALE.

Temperature profile data collected using CTD casts from NOAA Ship RESEARCHER in the North Atlantic Ocean from 1981-11-21 to 1981-12-07 (NODC Accession 8200194)

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 North Atlantic Ocean from 21 November 1981 to 07 December 1981....

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...

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...

Interdomain Contacts Control Native State Switching of RfaH on a Dual-Funneled Landscape.

Directory of Open Access Journals (Sweden)

César A Ramírez-Sarmiento

2015-07-01

Full Text Available RfaH is a virulence factor from Escherichia coli whose C-terminal domain (CTD undergoes a dramatic α-to-β conformational transformation. The CTD in its α-helical fold is stabilized by interactions with the N-terminal domain (NTD, masking an RNA polymerase binding site until a specific recruitment site is encountered. Domain dissociation is triggered upon binding to DNA, allowing the NTD to interact with RNA polymerase to facilitate transcription while the CTD refolds into the β-barrel conformation that interacts with the ribosome to activate translation. However, structural details of this transformation process in the context of the full protein remain to be elucidated. Here, we explore the mechanism of the α-to-β conformational transition of RfaH in the full-length protein using a dual-basin structure-based model. Our simulations capture several features described experimentally, such as the requirement of disruption of interdomain contacts to trigger the α-to-β transformation, confirms the roles of previously indicated residues E48 and R138, and suggests a new important role for F130, in the stability of the interdomain interaction. These native basins are connected through an intermediate state that builds up upon binding to the NTD and shares features from both folds, in agreement with previous in silico studies of the isolated CTD. We also examine the effect of RNA polymerase binding on the stabilization of the β fold. Our study shows that native-biased models are appropriate for interrogating the detailed mechanisms of structural rearrangements during the dramatic transformation process of RfaH.

The Acquisition, Calibration, and Analysis of CTD Data. Unesco Technical Papers in Marine Science No. 54. (A Report of SCOR Working Group 51).

Science.gov (United States)

United Nations Educational, Scientific, and Cultural Organization, Paris (France). Div. of Marine Sciences.

In this report the members of the Scientific Committee on Ocean Research Working Group 51 have attempted to describe the total process involved in obtaining salinity and temperature profiles with modern conductivity-temperature-depth (CTD) instruments. Their objective has been to provide a guide to procedures which will, if allowed, lead to the…

Interactions between the S-domain receptor kinases and AtPUB-ARM E3 ubiquitin ligases suggest a conserved signaling pathway in Arabidopsis.

Science.gov (United States)

Samuel, Marcus A; Mudgil, Yashwanti; Salt, Jennifer N; Delmas, Frédéric; Ramachandran, Shaliny; Chilelli, Andrea; Goring, Daphne R

2008-08-01

The Arabidopsis (Arabidopsis thaliana) genome encompasses multiple receptor kinase families with highly variable extracellular domains. Despite their large numbers, the various ligands and the downstream interacting partners for these kinases have been deciphered only for a few members. One such member, the S-receptor kinase, is known to mediate the self-incompatibility (SI) response in Brassica. S-receptor kinase has been shown to interact and phosphorylate a U-box/ARM-repeat-containing E3 ligase, ARC1, which, in turn, acts as a positive regulator of the SI response. In an effort to identify conserved signaling pathways in Arabidopsis, we performed yeast two-hybrid analyses of various S-domain receptor kinase family members with representative Arabidopsis plant U-box/ARM-repeat (AtPUB-ARM) E3 ligases. The kinase domains from S-domain receptor kinases were found to interact with ARM-repeat domains from AtPUB-ARM proteins. These kinase domains, along with M-locus protein kinase, a positive regulator of SI response, were also able to phosphorylate the ARM-repeat domains in in vitro phosphorylation assays. Subcellular localization patterns were investigated using transient expression assays in tobacco (Nicotiana tabacum) BY-2 cells and changes were detected in the presence of interacting kinases. Finally, potential links to the involvement of these interacting modules to the hormone abscisic acid (ABA) were investigated. Interestingly, AtPUB9 displayed redistribution to the plasma membrane of BY-2 cells when either treated with ABA or coexpressed with the active kinase domain of ARK1. As well, T-DNA insertion mutants for ARK1 and AtPUB9 lines were altered in their ABA sensitivity during germination and acted at or upstream of ABI3, indicating potential involvement of these proteins in ABA responses.

Crystal Structure of the HEAT Domain from the Pre-mRNA Processing Factor Symplekin

Energy Technology Data Exchange (ETDEWEB)

Kennedy, Sarah A.; Frazier, Monica L.; Steiniger, Mindy; Mast, Ann M.; Marzluff, William F.; Redinbo, Matthew R.; (UNC)

2010-09-30

The majority of eukaryotic pre-mRNAs are processed by 3'-end cleavage and polyadenylation, although in metazoa the replication-dependent histone mRNAs are processed by 3'-end cleavage but not polyadenylation. The macromolecular complex responsible for processing both canonical and histone pre-mRNAs contains the {approx} 1160-residue protein Symplekin. Secondary-structural prediction algorithms identified putative HEAT domains in the 300 N-terminal residues of all Symplekins of known sequence. The structure and dynamics of this domain were investigated to begin elucidating the role Symplekin plays in mRNA maturation. The crystal structure of the Drosophila melanogaster Symplekin HEAT domain was determined to 2.4 {angstrom} resolution with single-wavelength anomalous dispersion phasing methods. The structure exhibits five canonical HEAT repeats along with an extended 31-amino-acid loop (loop 8) between the fourth and fifth repeat that is conserved within closely related Symplekin sequences. Molecular dynamics simulations of this domain show that the presence of loop 8 dampens correlated and anticorrelated motion in the HEAT domain, therefore providing a neutral surface for potential protein-protein interactions. HEAT domains are often employed for such macromolecular contacts. The Symplekin HEAT region not only structurally aligns with several established scaffolding proteins, but also has been reported to contact proteins essential for regulating 3'-end processing. Together, these data support the conclusion that the Symplekin HEAT domain serves as a scaffold for protein-protein interactions essential to the mRNA maturation process.

Temperature, salinity, oxygen and fluorescence profiles collected by CTD from the Norseman II in Bering Strait from 2013-07-04 to 2013-07-10 (NCEI Accession 0136939)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — This archive is of data from 150 CTD casts taken during the 2013 Norseman II cruise to the Bering Strait. For positions, see file headers or the cruise report...

Temperature profile data collected using CTD casts from NOAA Ship RESEARCHER in the TOGA area - Indian from 1979-04-15 to 1979-06-02 (NODC Accession 8200199)

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 TOGA Area - Indian from 15 April 1979 to 02 June 1979. Data were...

National Coral Reef Monitoring Program: Shallow Water Conductivity-Temperature-Depth (CTD) Profiles for selected locations across the Mariana Archipelago from 2014-03-24 to 2014-05-05 (NCEI Accession 0161168)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Near-shore shallow water Conductivity-Temperature-Depth (CTD) surveys provided vertical profiles of temperature, salinity, and turbidity providing indications for...

National Coral Reef Monitoring Program: Shallow Water Conductivity-Temperature-Depth (CTD) Profiles for selected locations across the Hawaiian Archipelago from 2016-09-01 to 2016-09-27 (NCEI Accession 0161171)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Near-shore shallow water Conductivity-Temperature-Depth (CTD) surveys provided vertical profiles of temperature, salinity, and turbidity providing indications for...

A conserved Mediator–CDK8 kinase module association regulates Mediator–RNA polymerase II interaction

Science.gov (United States)

Tsai, Kuang-Lei; Sato, Shigeo; Tomomori-Sato, Chieri; Conaway, Ronald C.; Conaway, Joan W.; Asturias, Francisco J.

2013-01-01

The CDK8 kinase module (CKM) is a conserved, dissociable Mediator subcomplex whose component subunits were genetically linked to the RNA polymerase II (RNAPII) carboxy-terminal domain (CTD) and individually recognized as transcriptional repressors before Mediator was identified as a preeminent complex in eukaryotic transcription regulation. We used macromolecular electron microscopy and biochemistry to investigate the subunit organization, structure, and Mediator interaction of the Saccharomyces cerevisiae CKM. We found that interaction of the CKM with Mediator’s Middle module interferes with CTD-dependent RNAPII binding to a previously unknown Middle module CTD-binding site targeted early on in a multi-step holoenzyme formation process. Taken together, our results reveal the basis for CKM repression, clarify the origin of the connection between CKM subunits and the CTD, and suggest that a combination of competitive interactions and conformational changes that facilitate holoenzyme formation underlie the Mediator mechanism. PMID:23563140

[Family of ribosomal proteins S1 contains unique conservative domain].

Science.gov (United States)

Deriusheva, E I; Machulin, A V; Selivanova, O M; Serdiuk, I N

2010-01-01

Different representatives of bacteria have different number of amino acid residues in the ribosomal proteins S1. This number varies from 111 (Spiroplasma kunkelii) to 863 a.a. (Treponema pallidum). Traditionally and for lack of this protein three-dimensional structure, its architecture is represented as repeating S1 domains. Number of these domains depends on the protein's length. Domain's quantity and its boundaries data are contained in the specialized databases, such as SMART, Pfam and PROSITE. However, for the same object these data may be very different. For search of domain's quantity and its boundaries, new approach, based on the analysis of dicted secondary structure (PsiPred), was used. This approach allowed us to reveal structural domains in amino acid sequences of S1 proteins and at that number varied from one to six. Alignment of S1 proteins, containing different domain's number, with the S1 RNAbinding domain of Escherichia coli PNPase elicited a fact that in family of ribosomal proteins SI one domain has maximal homology with S1 domain from PNPase. This conservative domain migrates along polypeptide chain and locates in proteins, containing different domain's number, according to specified pattern. In this domain as well in the S1 domain from PNPase, residues Phe-19, Phe-22, His-34, Asp-64 and Arg-68 are clustered on the surface and formed RNA binding site.

t2prhd: a tool to study the patterns of repeat evolution

Directory of Open Access Journals (Sweden)

Pénzes Zsolt

2008-01-01

Full Text Available Abstract Background The models developed to characterize the evolution of multigene families (such as the birth-and-death and the concerted models have also been applied on the level of sequence repeats inside a gene/protein. Phylogenetic reconstruction is the method of choice to study the evolution of gene families and also sequence repeats in the light of these models. The characterization of the gene family evolution in view of the evolutionary models is done by the evaluation of the clustering of the sequences with the originating loci in mind. As the locus represents positional information, it is straightforward that in the case of the repeats the exact position in the sequence should be used, as the simple numbering according to repeat order can be misleading. Results We have developed a novel rapid visual approach to study repeat evolution, that takes into account the exact repeat position in a sequence. The "pairwise repeat homology diagram" visualizes sequence repeats detected by a profile HMM in a pair of sequences and highlights their homology relations inferred by a phylogenetic tree. The method is implemented in a Perl script (t2prhd available for downloading at http://t2prhd.sourceforge.net and is also accessible as an online tool at http://t2prhd.brc.hu. The power of the method is demonstrated on the EGF-like and fibronectin-III-like (Fn-III domain repeats of three selected mammalian Tenascin sequences. Conclusion Although pairwise repeat homology diagrams do not carry all the information provided by the phylogenetic tree, they allow a rapid and intuitive assessment of repeat evolution. We believe, that t2prhd is a helpful tool with which to study the pattern of repeat evolution. This method can be particularly useful in cases of large datasets (such as large gene families, as the command line interface makes it possible to automate the generation of pairwise repeat homology diagrams with the aid of scripts.

Structure of the Siz/PIAS SUMO E3 ligase Siz1 and determinants required for SUMO modification of PCNA

Science.gov (United States)

Yunus, Ali A.; Lima, Christopher D.

2009-01-01

Summary Siz1 is a founding member of the Siz/PIAS RING family of SUMO E3 ligases. The x-ray structure of an active Siz1 ligase revealed an elongated tripartite architecture comprised of an N-terminal PINIT domain, a central zinc-containing RING-like SP-RING domain, and a C-terminal domain we term the SP-CTD. Structure-based mutational analysis and biochemical studies show that the SP-RING and SP-CTD are required for activation of the E2~SUMO thioester while the PINIT domain is essential for redirecting SUMO conjugation to the proliferating cell nuclear antigen (PCNA) at lysine 164, a non-consensus lysine residue that is not modified by the SUMO E2 in the absence of Siz1. Mutational analysis of Siz1 and PCNA revealed surfaces on both proteins that are required for efficient SUMO modification of PCNA in vitro and in vivo. PMID:19748360

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...

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...

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...

Stratification and space-time variability of Red Sea hot brines

Energy Technology Data Exchange (ETDEWEB)

Monin, A S; Plakhin, E A

1982-11-01

The results of hydrophysical studies in Red Sea hot brines prefaced with historical information are presented. The CTD-recorder readings show stratification of the upper brine in the Atlantis II Deep into meter-scale layers, in agreement with laboratory findings. Repeated soundings with the AIST CTD meter of the upper brine interface in the Valdivia Deep recorded internal waves of 3 to 4-h periods. The observations show the different nature of brines in the four deeps studied and the lack of contact between the brine layers of the Chain and Discovery deeps.

Phospho-Ser/Thr-binding domains: navigating the cell cycle and DNA damage response.

Science.gov (United States)

Reinhardt, H Christian; Yaffe, Michael B

2013-09-01

Coordinated progression through the cell cycle is a complex challenge for eukaryotic cells. Following genotoxic stress, diverse molecular signals must be integrated to establish checkpoints specific for each cell cycle stage, allowing time for various types of DNA repair. Phospho-Ser/Thr-binding domains have emerged as crucial regulators of cell cycle progression and DNA damage signalling. Such domains include 14-3-3 proteins, WW domains, Polo-box domains (in PLK1), WD40 repeats (including those in the E3 ligase SCF(βTrCP)), BRCT domains (including those in BRCA1) and FHA domains (such as in CHK2 and MDC1). Progress has been made in our understanding of the motif (or motifs) that these phospho-Ser/Thr-binding domains connect with on their targets and how these interactions influence the cell cycle and DNA damage response.

Physical profile data from CTD casts in the Gulf of Alaska from the R/V ALPHA HELIX from 2001-04-18 to 2001-12-11 (NODC Accession 0000739)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Physical profile data were collected from CTD casts in the Gulf of Alaska from the R/V Alpha Helix. Data were collected by Western Washington University (WWU) and...

Temperature profile and other data from CTD casts in the South Pacific Ocean from NOAA Ship RESEARCHER from 1982-11-21 to 1983-07-24 (NODC Accession 8400113)

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 South Pacific Ocean from 21 November 1982 to 24 July 1983. Data...

Temperature profile data collected using CTD casts from NOAA Ship RESEARCHER in the TOGA area - Atlantic Ocean from 1980-02-21 to 1980-03-07 (NODC Accession 8200239)

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 TOGA area - Atlantic Ocean from 21 February 1980 to 07 March 1980....

Temperature and salinity profile data from CTD casts from NOAA Ship RAINIER west of Sitka Island, Alaska, from 2008-05-18 to 2008-06-18 (NODC Accession 0043263)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Physical oceanographic data were collected from NOAA Ship RAINIER west of Sitka Island, Alaska, from 18 May 2008 to 18 June 2008. Data were collected from CTD casts...

Oceanographic profile temperature, salinity, and oxygen measurements collected using CTD/XBT from NOAA Ship Ronald H. Brown in the Pacific Ocean from 2007 to 2008 (NODC Accession 0046077)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — XBT/CTD profile comparison data from the oceanographic line P18 2007/2008. XBT Deployments XBTs provided by Prof. Dean Roemmich of SIO were dropped during the cruise...

CTD data collected as part of a long-term monitoring program of the water properties in the Ilulissat Ice Fjord (Greenland), June 7 - 9, 2007 (NODC Accession 0038810)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Basic hydrographic data was collected in the Ilulissat Ice Fjord and adjacent Disko Bay during the summer of 2007. In Disko Bay, data was collected using a CTD...

Expression, crystallization and preliminary crystallographic data analysis of filamin A repeats 14–16

International Nuclear Information System (INIS)

Aguda, Adeleke Halilu; Sakwe, Amos Malle; Rask, Lars; Robinson, Robert Charles

2007-01-01

The crystallization and crystallographic data analysis of filamin repeats 14–16 are reported. Human filamin A is a 280 kDa protein involved in actin-filament cross-linking. It is structurally divided into an actin-binding headpiece (ABD) and a rod domain containing 24 immunoglobulin-like (Ig) repeats. A fragment of human filamin A (Ig repeats 14–16) was cloned and expressed in Escherichia coli and the purified protein was crystallized in 1.6 M ammonium sulfate, 2% PEG 1000 and 100 mM HEPES pH 7.5. The crystals diffracted to 1.95 Å and belong to space group P2 1 2 1 2 1 , with unit-cell parameters a = 50.63, b = 52.10, c = 98.46 Å, α = β = γ = 90°

National Coral Reef Monitoring Program: Shallow Water Conductivity-Temperature-Depth (CTD) Profiles for selected locations across the Northwestern Hawaiian Islands from 2015-07-31 to 2015-08-19 (NCEI Accession 0161170)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Near-shore shallow water Conductivity-Temperature-Depth (CTD) surveys provided vertical profiles of temperature, salinity, and turbidity providing indications for...

PASTA repeats of the protein kinase StkP interconnect cell constriction and separation of Streptococcus pneumoniae.

Science.gov (United States)

Zucchini, Laure; Mercy, Chryslène; Garcia, Pierre Simon; Cluzel, Caroline; Gueguen-Chaignon, Virginie; Galisson, Frédéric; Freton, Céline; Guiral, Sébastien; Brochier-Armanet, Céline; Gouet, Patrice; Grangeasse, Christophe

2018-02-01

Eukaryotic-like serine/threonine kinases (eSTKs) with extracellular PASTA repeats are key membrane regulators of bacterial cell division. How PASTA repeats govern eSTK activation and function remains elusive. Using evolution- and structural-guided approaches combined with cell imaging, we disentangle the role of each PASTA repeat of the eSTK StkP from Streptococcus pneumoniae. While the three membrane-proximal PASTA repeats behave as interchangeable modules required for the activation of StkP independently of cell wall binding, they also control the septal cell wall thickness. In contrast, the fourth and membrane-distal PASTA repeat directs StkP localization at the division septum and encompasses a specific motif that is critical for final cell separation through interaction with the cell wall hydrolase LytB. We propose a model in which the extracellular four-PASTA domain of StkP plays a dual function in interconnecting the phosphorylation of StkP endogenous targets along with septal cell wall remodelling to allow cell division of the pneumococcus.

Salinity and sigma-t data from moored current meter and CTD casts in the North Pacific Ocean from 1979-08-26 to 1982-06-07 (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...

CTD data from Rhode Island Sound collected from R/V Hope Hudner in 2009-2010 in support of Rhode Island Ocean Special Area Management Plan (NODC Accession 0109929)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — The dataset consists of 173 CTD casts in Rhode Island and Block Island Sounds obtained during 4 surveys. The surveys were performed during 22-24 September 2009, 7-8...

Surfzone Coastal Oil Pathway Experiment (SCOPE) CTD casts taken near Santa Rosa Island, Florida in the Gulf of Mexico from 2013-12-06 to 2013-12-17 (NCEI Accession 0161175)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — This dataset contains temperature, conductivity, specific conductance, salinity, sound velocity, and density data collected with CTD casts on 6-17 December 2013 off...

Oceanographic temperature and salinity profile data from bottle and CTD casts aboard multiple platforms in the South Atlantic Ocean from 1995-01-04 to 1998-12-19 (NCEI Accession 0143331)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Bottle and CTD data collected in the Southwestern Atlantic Ocean during fisheries research cruises organized by the Instituto Nacional de Investigacion y Desarrollo...

Water temperature, salinity, and sound speed data collected by CTD and XBT from the R/V Falkor in the NW Hawaiian Islands 2014-03 to 2014-06 (NCEI Accession 0137765)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Physical parameters (water temperature, salinity, and sound speed) were measured as high-resolution profiles at select locations and times using CTD and XBT...

Temperature profile and other data from CTD casts in the Pacific Ocean as part of the Vents Program from 01 June 1985 to 31 August 2001 (NODC Accession 0000656)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Temperature profile, conductivity, pressure, and other data were collected using CTD casts in the Pacific Ocean from 01 June 1985 to 31 August 2001. Data were...

Physical and nutrient data from bottle and CTD casts from the THOMAS THOMPSON from the equatorial Pacific Ocean from 30 January 1992 to 09 March 1992 (NODC Accession 9600091)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Physical and nutrient data were collected from bottle and CTD casts from the THOMAS THOMPSON from the equatorial Pacific Ocean. Data were collected by the Bigelow...

Oceanographic temperature and salinity measurements collected using CTD and XBT from NOAA Ship Nancy Foster/Ronald H Brown in the North Atlantic from 1998 to 2007 (NODC Accession 0043165)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Temperature, salinity and other measurements found in datasets XBT and CTD taken from NOAA Ship RONALD H. BROWN (NOAA SHIP - Call Sign WTEC)(formerly NOAA Ship...

Replication Stalling and Heteroduplex Formation within CAG/CTG Trinucleotide Repeats by Mismatch Repair

KAUST Repository

Viterbo, David; Michoud, Gregoire; Mosbach, Valentine; Dujon, Bernard; Richard, Guy-Franck

2016-01-01

Trinucleotide repeat expansions are responsible for at least two dozen neurological disorders. Mechanisms leading to these large expansions of repeated DNA are still poorly understood. It was proposed that transient stalling of the replication fork by the repeat tract might trigger slippage of the newly-synthesized strand over its template, leading to expansions or contractions of the triplet repeat. However, such mechanism was never formally proven. Here we show that replication fork pausing and CAG/CTG trinucleotide repeat instability are not linked, stable and unstable repeats exhibiting the same propensity to stall replication forks when integrated in a yeast natural chromosome. We found that replication fork stalling was dependent on the integrity of the mismatch-repair system, especially the Msh2p-Msh6p complex, suggesting that direct interaction of MMR proteins with secondary structures formed by trinucleotide repeats in vivo, triggers replication fork pauses. We also show by chromatin immunoprecipitation that Msh2p is enriched at trinucleotide repeat tracts, in both stable and unstable orientations, this enrichment being dependent on MSH3 and MSH6. Finally, we show that overexpressing MSH2 favors the formation of heteroduplex regions, leading to an increase in contractions and expansions of CAG/CTG repeat tracts during replication, these heteroduplexes being dependent on both MSH3 and MSH6. These heteroduplex regions were not detected when a mutant msh2-E768A gene in which the ATPase domain was mutated was overexpressed. Our results unravel two new roles for mismatch-repair proteins: stabilization of heteroduplex regions and transient blocking of replication forks passing through such repeats. Both roles may involve direct interactions between MMR proteins and secondary structures formed by trinucleotide repeat tracts, although indirect interactions may not be formally excluded.

Replication Stalling and Heteroduplex Formation within CAG/CTG Trinucleotide Repeats by Mismatch Repair

KAUST Repository

Viterbo, David

2016-03-16

Trinucleotide repeat expansions are responsible for at least two dozen neurological disorders. Mechanisms leading to these large expansions of repeated DNA are still poorly understood. It was proposed that transient stalling of the replication fork by the repeat tract might trigger slippage of the newly-synthesized strand over its template, leading to expansions or contractions of the triplet repeat. However, such mechanism was never formally proven. Here we show that replication fork pausing and CAG/CTG trinucleotide repeat instability are not linked, stable and unstable repeats exhibiting the same propensity to stall replication forks when integrated in a yeast natural chromosome. We found that replication fork stalling was dependent on the integrity of the mismatch-repair system, especially the Msh2p-Msh6p complex, suggesting that direct interaction of MMR proteins with secondary structures formed by trinucleotide repeats in vivo, triggers replication fork pauses. We also show by chromatin immunoprecipitation that Msh2p is enriched at trinucleotide repeat tracts, in both stable and unstable orientations, this enrichment being dependent on MSH3 and MSH6. Finally, we show that overexpressing MSH2 favors the formation of heteroduplex regions, leading to an increase in contractions and expansions of CAG/CTG repeat tracts during replication, these heteroduplexes being dependent on both MSH3 and MSH6. These heteroduplex regions were not detected when a mutant msh2-E768A gene in which the ATPase domain was mutated was overexpressed. Our results unravel two new roles for mismatch-repair proteins: stabilization of heteroduplex regions and transient blocking of replication forks passing through such repeats. Both roles may involve direct interactions between MMR proteins and secondary structures formed by trinucleotide repeat tracts, although indirect interactions may not be formally excluded.

Water temperature, salinity and other profiles from CTD taken from near-shore well in Puerto Morelos from 2014-03-27 to 2014-03-28 (NCEI Accession 0163741)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — This is a 12-hr time series of CTD profiles of water temperature and salinity taken from near-shore well in Puerto Morelos from 2014-03-27 to 2014-03-28. Data were...

Temperature, salinity, and other data collected using bottle, CTD, and XBT casts in the Pacific and Atlantic Ocean from 12 April 1960 to 27 October 1999 (NODC Accession 0000214)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Temperature, salinity, and other data were collected using bottle, CTD, and XBT casts in the North/South Atlantic Ocean and North/South Pacific Ocean from April 12,...

Temperature profile and other data collected using CTD casts in the North Atlantic Ocean from NOAA Ship RESEARCHER from 1980-01-22 to 1980-02-03 (NODC Accession 8900302)

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 North Atlantic Ocean from 22 January 1980 to 03 February 1980....

The 1.75 Å resolution structure of fission protein Fis1 from Saccharomyces cerevisiae reveals elusive interactions of the autoinhibitory domain

International Nuclear Information System (INIS)

Tooley, James E.; Khangulov, Victor; Lees, Jonathan P. B.; Schlessman, Jamie L.; Bewley, Maria C.; Heroux, Annie; Bosch, Jürgen; Hill, R. Blake

2011-01-01

A 1.75 Å resolution crystal structure of the Fis1 cytoplasmic domain from Saccharomyces cerevisiae is reported which adopts a tetratricopeptide-repeat fold. Fis1 mediates mitochondrial and peroxisomal fission. It is tail-anchored to these organelles by a transmembrane domain, exposing a soluble cytoplasmic domain. Previous studies suggested that Fis1 is autoinhibited by its N-terminal region. Here, a 1.75 Å resolution crystal structure of the Fis1 cytoplasmic domain from Saccharomyces cerevisiae is reported which adopts a tetratricopeptide-repeat fold. It is observed that this fold creates a concave surface important for fission, but is sterically occluded by its N-terminal region. Thus, this structure provides a physical basis for autoinhibition and allows a detailed examination of the interactions that stabilize the inhibited state of this molecule

Temperature profile and nutrients data collected using bottle and CTD casts from the HESPERIDES in the South Atlantic Ocean from 11 February 1995 to 20 February 1995 (NODC Accession 0000870)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Temperature profile and nutrients data were collected using bottle and CTD casts in the South Atlantic Ocean from HESPERIDES. Data were collected from 11 February...

Temperature profile and nutrients data collected using bottle and CTD casts from the HESPERIDES in the South Atlantic Ocean from 15 February 1996 to 21 February 1996 (NODC Accession 0000871)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Temperature profile and nutrients data were collected using bottle and CTD casts in the South Atlantic Ocean from HESPERIDES. Data were collected from 15 February...

Salinity, sigma-t, and temperature data from moored current meter and CTD casts in the North Atlantic Ocean from 1981-08-29 to 1981-12-07 (NODC Accession 8300048)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Salinity, sigma-t, and temperature data were collected using moored current meter and CTD casts in the North Atlantic Ocean from August 29, 1981 to December 7, 1981....

Temperature and salinity profile data from CTD casts from the NOAA ship WHITING from the North Atlantic Ocean from 5 April 1995 to 1 June 1995 (NODC Accession 9500092)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Temperature and salinity profile data were collected from CTD cast from the NOAA ship WHITING from the North Atlantic Ocean. Data were collected from 5 April 1995 to...

Solution structure of telomere binding domain of AtTRB2 derived from Arabidopsis thaliana

International Nuclear Information System (INIS)

Yun, Ji-Hye; Lee, Won Kyung; Kim, Heeyoun; Kim, Eunhee; Cheong, Chaejoon; Cho, Myeon Haeng; Lee, Weontae

2014-01-01

Highlights: • We have determined solution structure of Myb domain of AtTRB2. • The Myb domain of AtTRB2 is located in the N-terminal region. • The Myb domain of AtTRB2 binds to plant telomeric DNA without fourth helix. • Helix 2 and 3 of the Myb domain of AtTRB2 are involved in DNA recognition. • AtTRB2 is a novel protein distinguished from other known plant TBP. - Abstract: Telomere homeostasis is regulated by telomere-associated proteins, and the Myb domain is well conserved for telomere binding. AtTRB2 is a member of the SMH (Single-Myb-Histone)-like family in Arabidopsis thaliana, having an N-terminal Myb domain, which is responsible for DNA binding. The Myb domain of AtTRB2 contains three α-helices and loops for DNA binding, which is unusual given that other plant telomere-binding proteins have an additional fourth helix that is essential for DNA binding. To understand the structural role for telomeric DNA binding of AtTRB2, we determined the solution structure of the Myb domain of AtTRB2 (AtTRB2 1–64 ) using nuclear magnetic resonance (NMR) spectroscopy. In addition, the inter-molecular interaction between AtTRB2 1–64 and telomeric DNA has been characterized by the electrophoretic mobility shift assay (EMSA) and NMR titration analyses for both plant (TTTAGGG)n and human (TTAGGG)n telomere sequences. Data revealed that Trp28, Arg29, and Val47 residues located in Helix 2 and Helix 3 are crucial for DNA binding, which are well conserved among other plant telomere binding proteins. We concluded that although AtTRB2 is devoid of the additional fourth helix in the Myb-extension domain, it is able to bind to plant telomeric repeat sequences as well as human telomeric repeat sequences

National Coral Reef Monitoring Program: Shallow Water Conductivity-Temperature-Depth (CTD) Profiles for selected locations across the Pacific Remote Island Areas from 2015-01-26 to 2015-04-28 (NCEI Accession 0162247)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Near-shore shallow water Conductivity-Temperature-Depth (CTD) surveys provided vertical profiles of temperature, salinity, and turbidity providing indications for...

Identification of TTAGGG-binding proteins in Neurospora crassa, a fungus with vertebrate-like telomere repeats.

Science.gov (United States)

Casas-Vila, Núria; Scheibe, Marion; Freiwald, Anja; Kappei, Dennis; Butter, Falk

2015-11-17

To date, telomere research in fungi has mainly focused on Saccharomyces cerevisiae and Schizosaccharomyces pombe, despite the fact that both yeasts have degenerated telomeric repeats in contrast to the canonical TTAGGG motif found in vertebrates and also several other fungi. Using label-free quantitative proteomics, we here investigate the telosome of Neurospora crassa, a fungus with canonical telomeric repeats. We show that at least six of the candidates detected in our screen are direct TTAGGG-repeat binding proteins. While three of the direct interactors (NCU03416 [ncTbf1], NCU01991 [ncTbf2] and NCU02182 [ncTay1]) feature the known myb/homeobox DNA interaction domain also found in the vertebrate telomeric factors, we additionally show that a zinc-finger protein (NCU07846) and two proteins without any annotated DNA-binding domain (NCU02644 and NCU05718) are also direct double-strand TTAGGG binders. We further find two single-strand binders (NCU02404 [ncGbp2] and NCU07735 [ncTcg1]). By quantitative label-free interactomics we identify TTAGGG-binding proteins in Neurospora crassa, suggesting candidates for telomeric factors that are supported by phylogenomic comparison with yeast species. Intriguingly, homologs in yeast species with degenerated telomeric repeats are also TTAGGG-binding proteins, e.g. in S. cerevisiae Tbf1 recognizes the TTAGGG motif found in its subtelomeres. However, there is also a subset of proteins that is not conserved. While a rudimentary core TTAGGG-recognition machinery may be conserved across yeast species, our data suggests Neurospora as an emerging model organism with unique features.

CTD, Oxygen, Fluorescence, Turbidity, and others collected in the DeSoto Canyon and Shelf, Gulf of Mexico, on the Weatherbird II-1411 cruise 2014-05 to 2014-06 (NCEI Accession 0159187)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — This multidisciplinary cruise will occupy sites for collection of multicores, CTD/Rosette bottom imaging transects, and piston coring. The cruise will depart St....

Dissection and Manipulation of LRR Domains in Plant Disease Resistance Gene Products.

Energy Technology Data Exchange (ETDEWEB)

Bent, Andrew [Univ. of Wisconsin, Madison, WI (United States)

2012-11-28

Leucine-rich repeat (LRR) protein domains offer a readily diversifiable platform - literally, an extended protein surface - for specific binding of very diverse ligands. The project addressed the following overlapping research questions: How do leucine-rich repeat proteins recognize their cognate ligands? What are the intra- and inter-molecular transitions that occur that cause transmembrane LRR proteins to switch between off and on states? How do plants use LRR receptor proteins to activate disease resistance? Can we synthetically evolve new LRR proteins that have acquired new ligand specificities?

Temperature profile and other data collected using CTD casts in the SE Pacific Ocean from NOAA Ship RESEARCHER from 1984-06-12 to 1984-06-30 (NODC Accession 8500249)

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 SE Pacific Ocean from 12 June 1984 to 30 June 1984. Data were...

Regulation of the transient receptor potential channel TRPA1 by its N-terminal ankyrin repeat domain

Czech Academy of Sciences Publication Activity Database

Zayats, Vasilina; Samad, Abdul; Minofar, Babak; Roelofs, K. E.; Stockner, T.; Ettrich, Rüdiger

2012-01-01

Roč. 19, č. 11 (2012), s. 4689-4700 ISSN 1610-2940 R&D Projects: GA ČR GAP207/10/1934 Institutional research plan: CEZ:AV0Z60870520 Keywords : ankyrin repeat * EF-hand * familial episodic pain syndrom * TRPA1 Subject RIV: CE - Biochemistry Impact factor: 1.984, year: 2012

The Role of Parental Perceptions of Tic Frequency and Intensity in Predicting Tic-Related Functional Impairment in Youth with Chronic Tic Disorders

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Espil, Flint M.; Capriotti, Matthew R.; Conelea, Christine A.; Woods, Douglas W.

2014-01-01

Tic severity is composed of several dimensions. Tic frequency and intensity are two such dimensions, but little empirical data exist regarding their relative contributions to functional impairment in those with Chronic Tic Disorders (CTD). The present study examined the relative contributions of these dimensions in predicting tic-related impairment across several psychosocial domains. Using data collected from parents of youth with CTD, multivariate regression analyses revealed that both tic frequency and intensity predicted tic-related impairment in several areas; including family and peer relationships, school interference, and social endeavors, even when controlling for the presence of comorbid anxiety symptoms and Attention Deficit Hyperactivity Disorder diagnostic status. Results showed that tic intensity predicted more variance across more domains than tic frequency. PMID:24395287

The role of parental perceptions of tic frequency and intensity in predicting tic-related functional impairment in youth with chronic tic disorders.

Science.gov (United States)

Espil, Flint M; Capriotti, Matthew R; Conelea, Christine A; Woods, Douglas W

2014-12-01

Tic severity is composed of several dimensions. Tic frequency and intensity are two such dimensions, but little empirical data exist regarding their relative contributions to functional impairment in those with chronic tic disorders (CTD). The present study examined the relative contributions of these dimensions in predicting tic-related impairment across several psychosocial domains. Using data collected from parents of youth with CTD, multivariate regression analyses revealed that both tic frequency and intensity predicted tic-related impairment in several areas; including family and peer relationships, school interference, and social endeavors, even when controlling for the presence of comorbid anxiety symptoms and Attention Deficit Hyperactivity Disorder diagnostic status. Results showed that tic intensity predicted more variance across more domains than tic frequency.

Por secretion system-dependent secretion and glycosylation of Porphyromonas gingivalis hemin-binding protein 35.

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Mikio Shoji

Full Text Available The anaerobic Gram-negative bacterium Porphyromonas gingivalis is a major pathogen in severe forms of periodontal disease and refractory periapical perodontitis. We have recently found that P. gingivalis has a novel secretion system named the Por secretion system (PorSS, which is responsible for secretion of major extracellular proteinases, Arg-gingipains (Rgps and Lys-gingipain. These proteinases contain conserved C-terminal domains (CTDs in their C-termini. Hemin-binding protein 35 (HBP35, which is one of the outer membrane proteins of P. gingivalis and contributes to its haem utilization, also contains a CTD, suggesting that HBP35 is translocated to the cell surface via the PorSS. In this study, immunoblot analysis of P. gingivalis mutants deficient in the PorSS or in the biosynthesis of anionic polysaccharide-lipopolysaccharide (A-LPS revealed that HBP35 is translocated to the cell surface via the PorSS and is glycosylated with A-LPS. From deletion analysis with a GFP-CTD[HBP35] green fluorescent protein fusion, the C-terminal 22 amino acid residues of CTD[HBP35] were found to be required for cell surface translocation and glycosylation. The GFP-CTD fusion study also revealed that the CTDs of CPG70, peptidylarginine deiminase, P27 and RgpB play roles in PorSS-dependent translocation and glycosylation. However, CTD-region peptides were not found in samples of glycosylated HBP35 protein by peptide map fingerprinting analysis, and antibodies against CTD-regions peptides did not react with glycosylated HBP35 protein. These results suggest both that the CTD region functions as a recognition signal for the PorSS and that glycosylation of CTD proteins occurs after removal of the CTD region. Rabbits were used for making antisera against bacterial proteins in this study.

Leucine-rich repeat kinase-1 regulates osteoclast function by modulating RAC1/Cdc42 Small GTPase phosphorylation and activation.

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Zeng, Canjun; Goodluck, Helen; Qin, Xuezhong; Liu, Bo; Mohan, Subburaman; Xing, Weirong

2016-10-01

Leucine-rich repeat kinase-1 (Lrrk1) consists of ankyrin repeats (ANK), leucine-rich repeats (LRR), a GTPase-like domain of Roc (ROC), a COR domain, a serine/threonine kinase domain (KD), and WD40 repeats (WD40). Previous studies have revealed that knockout (KO) of Lrrk1 in mice causes severe osteopetrosis, and a human mutation of Lrrk1 leads to osteosclerotic metaphysial dysplasia. The molecular mechanism by which Lrrk1 regulates osteoclast function is unknown. In this study, we generated a series of Lrrk1 mutants and evaluated their ability to rescue defective bone resorption in Lrrk1-deficient osteoclasts by use of pit formation assays. Overexpression of Lrrk1 or LRR-truncated Lrrk1, but not ANK-truncated Lrrk1, WD40-truncated Lrrk1, Lrrk1-KD, or K651A mutant Lrrk1, rescued bone resorption function of Lrrk1 KO osteoclasts. We next examined whether RAC1/Cdc42 small GTPases are direct substrates of Lrrk1 in osteoclasts. Western blot and pull-down assays revealed that Lrrk1 deficiency in osteoclasts resulted in reduced phosphorylation and activation of RAC1/Cdc42. In vitro kinase assays confirmed that recombinant Lrrk1 phosphorylated RAC1-GST protein, and immunoprecipitation showed that the interaction of Lrrk1 with RAC1 occurred within 10 min after RANKL treatment. Overexpression of constitutively active Q61L RAC1 partially rescued the resorptive function of Lrrk1-deficient osteoclasts. Furthermore, lack of Lrrk1 in osteoclasts led to reduced autophosphorylation of p21 protein-activated kinase-1 at Ser 144 , catalyzed by RAC1/Cdc42 binding and activation. Our data indicate that Lrrk1 regulates osteoclast function by directly modulating phosphorylation and activation of small GTPase RAC1/Cdc42 and that its function depends on ANK, ROC, WD40, and kinase domains. Copyright © 2016 the American Physiological Society.

Meteorological and other data collected from CTD, XBT casts, and other instruments in the TOGA Area - Pacific Ocean by NATSUSHIMA from 23 January 1993 to 11 March 1993 (NODC Accession 9400083)

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National Oceanic and Atmospheric Administration, Department of Commerce — Meteorological, temperature, and salinity data were collected using CTD, BT, XBT casts, and other instruments from the NATSUSHIMA in the TOGA Area - Pacific Ocean....

Temperature profile and other data from CTD casts from NOAA Ship OCEANOGRAPHER in the TOGA area of Pacific Ocean from 1987-05-28 to 1987-07-27 (NODC Accession 9000149)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — The Conductivity, Temperature and Depth (CTD); and other data were collected using NOAA Ship Oceanographer from TOGA Area-Pacific (30 N to 30 S) under the Transport...