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Sample records for homolog connector domain

  1. Time domain calculation of connector loads of a very large floating structure

    Science.gov (United States)

    Gu, Jiayang; Wu, Jie; Qi, Enrong; Guan, Yifeng; Yuan, Yubo

    2015-06-01

    Loads generated after an air crash, ship collision, and other accidents may destroy very large floating structures (VLFSs) and create additional connector loads. In this study, the combined effects of ship collision and wave loads are considered to establish motion differential equations for a multi-body VLFS. A time domain calculation method is proposed to calculate the connector load of the VLFS in waves. The Longuet-Higgins model is employed to simulate the stochastic wave load. Fluid force and hydrodynamic coefficient are obtained with DNV Sesam software. The motion differential equation is calculated by applying the time domain method when the frequency domain hydrodynamic coefficient is converted into the memory function of the motion differential equation of the time domain. As a result of the combined action of wave and impact loads, high-frequency oscillation is observed in the time history curve of the connector load. At wave directions of 0° and 75°, the regularities of the time history curves of the connector loads in different directions are similar and the connector loads of C1 and C2 in the X direction are the largest. The oscillation load is observed in the connector in the Y direction at a wave direction of 75° and not at 0°. This paper presents a time domain calculation method of connector load to provide a certain reference function for the future development of Chinese VLFS

  2. Membrane and Protein Interactions of the Pleckstrin Homology Domain Superfamily

    Directory of Open Access Journals (Sweden)

    Marc Lenoir

    2015-10-01

    Full Text Available The human genome encodes about 285 proteins that contain at least one annotated pleckstrin homology (PH domain. As the first phosphoinositide binding module domain to be discovered, the PH domain recruits diverse protein architectures to cellular membranes. PH domains constitute one of the largest protein superfamilies, and have diverged to regulate many different signaling proteins and modules such as Dbl homology (DH and Tec homology (TH domains. The ligands of approximately 70 PH domains have been validated by binding assays and complexed structures, allowing meaningful extrapolation across the entire superfamily. Here the Membrane Optimal Docking Area (MODA program is used at a genome-wide level to identify all membrane docking PH structures and map their lipid-binding determinants. In addition to the linear sequence motifs which are employed for phosphoinositide recognition, the three dimensional structural features that allow peripheral membrane domains to approach and insert into the bilayer are pinpointed and can be predicted ab initio. The analysis shows that conserved structural surfaces distinguish which PH domains associate with membrane from those that do not. Moreover, the results indicate that lipid-binding PH domains can be classified into different functional subgroups based on the type of membrane insertion elements they project towards the bilayer.

  3. Membrane and Protein Interactions of the Pleckstrin Homology Domain Superfamily.

    Science.gov (United States)

    Lenoir, Marc; Kufareva, Irina; Abagyan, Ruben; Overduin, Michael

    2015-10-23

    The human genome encodes about 285 proteins that contain at least one annotated pleckstrin homology (PH) domain. As the first phosphoinositide binding module domain to be discovered, the PH domain recruits diverse protein architectures to cellular membranes. PH domains constitute one of the largest protein superfamilies, and have diverged to regulate many different signaling proteins and modules such as Dbl homology (DH) and Tec homology (TH) domains. The ligands of approximately 70 PH domains have been validated by binding assays and complexed structures, allowing meaningful extrapolation across the entire superfamily. Here the Membrane Optimal Docking Area (MODA) program is used at a genome-wide level to identify all membrane docking PH structures and map their lipid-binding determinants. In addition to the linear sequence motifs which are employed for phosphoinositide recognition, the three dimensional structural features that allow peripheral membrane domains to approach and insert into the bilayer are pinpointed and can be predicted ab initio. The analysis shows that conserved structural surfaces distinguish which PH domains associate with membrane from those that do not. Moreover, the results indicate that lipid-binding PH domains can be classified into different functional subgroups based on the type of membrane insertion elements they project towards the bilayer.

  4. Chemical Shift Assignments of the C-terminal Eps15 Homology Domain-3 EH Domain*

    Science.gov (United States)

    Caplan, Steve; Sorgen, Paul L.

    2013-01-01

    The C-terminal Eps15 homology (EH) domain 3 (EHD3) belongs to a eukaryotic family of endocytic regulatory proteins and is involved in the recycling of various receptors from the early endosome to the endocytic recycling compartment or in retrograde transport from the endosomes to the Golgi. EH domains are highly conserved in the EHD family and function as protein-protein interaction units that bind to Asn-Pro-Phe (NPF) motif-containing proteins. The EH domain of EHD1 was the first C-terminal EH domain from the EHD family to be solved by NMR. The differences observed between this domain and proteins with N-terminal EH domains helped describe a mechanism for the differential binding of NPF-containing proteins. Here, structural studies were expanded to include the EHD3 EH domain. While the EHD1 and EHD3 EH domains are highly homologous, they have different protein partners. A comparison of these structures will help determine the selectivity in protein binding between the EHD family members and lead to a better understanding of their unique roles in endocytic regulation. PMID:23754701

  5. Flexible connector

    Science.gov (United States)

    Savage, Mark E.; Simpson, Walter W.

    1999-01-01

    An electrical connector accommodates high current, is not labor intensive to assemble and disassemble, and allows a wide range of motion to accommodate mechanical variations and movement of connected components. The connector comprises several parts with joints therebetween, wherein each joint provides electrical connection between and allows relative motion of the joined parts. The combination of parts and joints maintains electrical connection between two electrical components even if the components are misaligned or move after connection.

  6. Pleckstrin Homology Domain Diffusion in Dictyostelium Cytoplasm Studied Using Fluorescence Correlation Spectroscopy

    NARCIS (Netherlands)

    Engel, Ruchira; Hink, Mark A.; Bosgraaf, Leonard; Haastert, Peter J.M. van; Visser, Antonie J.W.G.

    2004-01-01

    The translocation of pleckstrin homology (PH) domain-containing proteins from the cytoplasm to the plasma membrane plays an important role in the chemotaxis mechanism of Dictyostelium cells. The diffusion of three PH domain-green fluorescent protein (GFP) fusions (PH2-GFP, PH10-GFP, and PH-CRAC

  7. Pleckstrin homology domain diffusion in Dictyostelium cytoplasm studied using fluorescence correlation spectroscopy

    NARCIS (Netherlands)

    Ruchira, A.; Hink, M.A.; Bosgraaf, L.; Haastert, van P.J.M.; Visser, A.J.W.G.

    2004-01-01

    The translocation of pleckstrin homology (PH) domain-containing proteins from the cytoplasm to the plasma membrane plays an important role in the chemotaxis mechanism of Dictyostelium cells. The diffusion of three PH domain-green fluorescent protein (GFP) fusions (PH2-GFP, PH10-GFP, and PH-CRAC

  8. The crystal structures of EAP domains from Staphylococcus aureus reveal an unexpected homology to bacterial superantigens.

    Science.gov (United States)

    Geisbrecht, Brian V; Hamaoka, Brent Y; Perman, Benjamin; Zemla, Adam; Leahy, Daniel J

    2005-04-29

    The Eap (extracellular adherence protein) of Staphylococcus aureus functions as a secreted virulence factor by mediating interactions between the bacterial cell surface and several extracellular host proteins. Eap proteins from different Staphylococcal strains consist of four to six tandem repeats of a structurally uncharacterized domain (EAP domain). We have determined the three-dimensional structures of three different EAP domains to 1.8, 2.2, and 1.35 A resolution, respectively. These structures reveal a core fold that is comprised of an alpha-helix lying diagonally across a five-stranded, mixed beta-sheet. Comparison of EAP domains with known structures reveals an unexpected homology with the C-terminal domain of bacterial superantigens. Examination of the structure of the superantigen SEC2 bound to the beta-chain of a T-cell receptor suggests a possible ligand-binding site within the EAP domain (Fields, B. A., Malchiodi, E. L., Li, H., Ysern, X., Stauffacher, C. V., Schlievert, P. M., Karjalainen, K., and Mariuzza, R. (1996) Nature 384, 188-192). These results provide the first structural characterization of EAP domains, relate EAP domains to a large class of bacterial toxins, and will guide the design of future experiments to analyze EAP domain structure/function relationships.

  9. The PLAC1-homology region of the ZP domain is sufficient for protein polymerisation

    Directory of Open Access Journals (Sweden)

    Litscher Eveline S

    2006-04-01

    Full Text Available Abstract Background Hundreds of extracellular proteins polymerise into filaments and matrices by using zona pellucida (ZP domains. ZP domain proteins perform highly diverse functions, ranging from structural to receptorial, and mutations in their genes are responsible for a number of severe human diseases. Recently, PLAC1, Oosp1-3, Papillote and CG16798 proteins were identified that share sequence homology with the N-terminal half of the ZP domain (ZP-N, but not with its C-terminal half (ZP-C. The functional significance of this partial conservation is unknown. Results By exploiting a highly engineered bacterial strain, we expressed in soluble form the PLAC1-homology region of mammalian sperm receptor ZP3 as a fusion to maltose binding protein. Mass spectrometry showed that the 4 conserved Cys residues within the ZP-N moiety of the fusion protein adopt the same disulfide bond connectivity as in full-length native ZP3, indicating that it is correctly folded, and electron microscopy and biochemical analyses revealed that it assembles into filaments. Conclusion These findings provide a function for PLAC1-like proteins and, by showing that ZP-N is a biologically active folding unit, prompt a re-evaluation of the architecture of the ZP domain and its polymers. Furthermore, they suggest that ZP-C might play a regulatory role in the assembly of ZP domain protein complexes.

  10. The K Domain Mediates Homologous and Heterologous Interactions Between FLC and SVP Proteins of Brassica juncea

    Directory of Open Access Journals (Sweden)

    Ma Guanpeng

    2015-07-01

    Full Text Available The transcription factors FLOWERING LOCUS C (FLC and SHORT VEGETATIVE PHASE (SVP can interact to form homologous and heterologous protein complexes that regulate flowering time in Brassica juncea Coss. (Mustard.Previous studies showed that protein interactions were mediated by the K domain, which contains the subdomains K1, K2 and K3. However, it remains unknown how the subdomains mediate the interactions between FLC and SVP. In the present study, we constructed several mutants of subdomains K1–K3 and investigated the mechanisms involved in the heterologous interaction of BjFLC/BjSVP and in the homologous interaction of BjFLC/BjFLC or BjSVP/BjSVP. Yeast two-hybrid and β-Galactosidase activity assays showed that the 19 amino acids of the K1 subdomain in BjSVP and the 17 amino acids of the K1 subdomain in BjFLC were functional subdomains that interact with each other to mediate hetero-dimerization. The heterologous interaction was enhanced by the K2 subdomain of BjSVP protein, but weakened by its interhelical domain L2. The heterologous interaction was also enhanced by the K2 subdomain of BjFLC protein, but weakened by its K3 subdomain. The homologous interaction of BjSVP was mediated by the full K-domain. However, the homologous interaction of BjFLC was regulated only by its K1 and weakened by its K2 and K3 subdomains. The results provided new insights into the interactions between FLC and SVP, which will be valuable for further studies on the molecular regulation mechanisms of the regulation of flowering time in B. juncea and other Brassicaceae.

  11. The insulin receptor substrate (IRS)-1 pleckstrin homology domain functions in downstream signaling.

    Science.gov (United States)

    Vainshtein, I; Kovacina, K S; Roth, R A

    2001-03-16

    The pleckstrin homology (PH) domain of the insulin receptor substrate-1 (IRS-1) plays a role in directing this molecule to the insulin receptor, thereby regulating its tyrosine phosphorylation. In this work, the role of the PH domain in subsequent signaling was studied by constructing constitutively active forms of IRS-1 in which the inter-SH2 domain of the p85 subunit of phosphatidylinositol 3-kinase was fused to portions of the IRS-1 molecule. Chimeric molecules containing the PH domain were found to activate the downstream response of stimulating the Ser/Thr kinase Akt. A chimera containing point mutations in the PH domain that abolished the ability of this domain to bind phosphatidylinositol 4,5-bisphosphate prevented these molecules from activating Akt. These mutations also decreased by about 70% the amount of the constructs present in a particulate fraction of the cells. These results indicate that the PH domain of IRS-1, in addition to directing this protein to the receptor for tyrosine phosphorylation, functions in the ability of this molecule to stimulate subsequent responses. Thus, compromising the function of the PH domain, e.g. in insulin-resistant states, could decrease both the ability of IRS-1 to be tyrosine phosphorylated by the insulin receptor and to link to subsequent downstream targets.

  12. Modes of Interaction of Pleckstrin Homology Domains with Membranes: Toward a Computational Biochemistry of Membrane Recognition.

    Science.gov (United States)

    Naughton, Fiona B; Kalli, Antreas C; Sansom, Mark S P

    2018-02-02

    Pleckstrin homology (PH) domains mediate protein-membrane interactions by binding to phosphatidylinositol phosphate (PIP) molecules. The structural and energetic basis of selective PH-PIP interactions is central to understanding many cellular processes, yet the molecular complexities of the PH-PIP interactions are largely unknown. Molecular dynamics simulations using a coarse-grained model enables estimation of free-energy landscapes for the interactions of 12 different PH domains with membranes containing PIP 2 or PIP 3 , allowing us to obtain a detailed molecular energetic understanding of the complexities of the interactions of the PH domains with PIP molecules in membranes. Distinct binding modes, corresponding to different distributions of cationic residues on the PH domain, were observed, involving PIP interactions at either the "canonical" (C) and/or "alternate" (A) sites. PH domains can be grouped by the relative strength of their C- and A-site interactions, revealing that a higher affinity correlates with increased C-site interactions. These simulations demonstrate that simultaneous binding of multiple PIP molecules by PH domains contributes to high-affinity membrane interactions, informing our understanding of membrane recognition by PH domains in vivo. Copyright © 2017. Published by Elsevier Ltd.

  13. Evolution of Src Homology 2 (SH2) Domain to Recognize Sulfotyrosine.

    Science.gov (United States)

    Ju, Tong; Niu, Wei; Guo, Jiantao

    2016-09-16

    Protein tyrosine O-sulfation is considered as the most common type of post-translational tyrosine modification in nature and plays important roles in extracellular biomolecular interactions. To facilitate the mapping, biological study, and medicinal application of this type of post-translational modification, we seek to evolve a small protein scaffold that recognizes sulfotyrosine with high affinity. We focused our efforts on the engineering of the Src Homology 2 (SH2) domain, which represents the largest class of known phosphotyrosine-recognition domain in nature and has a highly evolvable binding pocket. By using phage display, we successfully engineered the SH2 domain to recognize sulfotyrosine with high affinity. The best mutant, SH2-60.1, displayed more than 1700 fold higher sulfotyrosine-binding affinity than that of the wild-type SH2 domain. We also demonstrated that the evolved SH2 domain mutants could be used to detect sulfoprotein levels on the cell surface. These evolved SH2 domain mutants can be potentially applied to the study of protein tyrosine O-sulfation with proper experimental designs.

  14. Akt1 binds focal adhesion kinase via the Akt1 kinase domain independently of the pleckstrin homology domain.

    Science.gov (United States)

    Basson, M D; Zeng, B; Wang, S

    2015-10-01

    Akt1 and focal adhesion kinase (FAK) are protein kinases that play key roles in normal cell signaling. Individually, aberrant expression of these kinases has been linked to a variety of cancers. Together, Akt1/FAK interactions facilitate cancer metastasis by increasing cell adhesion under conditions of increased extracellular pressure. Pathological and iatrogenic sources of pressure arise from tumor growth against constraining stroma or direct perioperative manipulation. We previously reported that 15 mmHg increased extracellular pressure causes Akt1 to both directly interact with FAK and to phosphorylate and activate it. We investigated the nature of the Akt1/FAK binding by creating truncations of recombinant FAK, conjugated to glutathione S-transferase (GST), to pull down full-length Akt1. Western blots probing for Akt1 showed that FAK/Akt1 binding persisted in FAK truncations consisting of only amino acids 1-126, FAK(NT1), which contains the F1 subdomain of its band 4.1, ezrin, radixin, and moesin (FERM) domain. Using FAK(NT1) as bait, we then pulled down truncated versions of recombinant Akt1 conjugated to HA (human influenza hemagglutinin). Probes for GST-FAK(NT1) showed Akt1-FAK binding to occur in the absence of the both the Akt1 (N)-terminal pleckstrin homology (PH) domain and its adjacent hinge region. The Akt1 (C)-terminal regulatory domain was equally unnecessary for Akt1/FAK co-immunoprecipitation. Truncations involving the Akt1 catalytic domain showed that the domain by itself was enough to pull down FAK. Additionally, a fragment spanning from the PH domain to half way through the catalytic domain demonstrated increased FAK binding compared to full length Akt1. These results begin to delineate the Akt1/FAK interaction and can be used to manipulate their force-activated signal interactions. Furthermore, the finding that the N-terminal half of the Akt1 catalytic domain binds so strongly to FAK when cleaved from the rest of the protein may suggest a means

  15. CareerConnector

    Data.gov (United States)

    US Agency for International Development — CareerConnector is USAID's premiere recruiting tool. It is powered by Monster and integrated with www.usajobs.gov. CareerConnector tracks the progression of a...

  16. Aquilegia B gene homologs promote petaloidy of the sepals and maintenance of the C domain boundary

    Directory of Open Access Journals (Sweden)

    Bharti Sharma

    2017-11-01

    Full Text Available Abstract The model Aquilegia coerulea x “Origami” possesses several interesting floral features, including petaloid sepals that are morphologically distinct from the true petals and a broad domain containing many whorls of stamens. We undertook the current study in an effort to understand the former trait, but additionally uncovered data that inform on the latter. The Aquilegia B gene homolog AqPI is shown to contribute to the production of anthocyanin in the first whorl sepals, although it has no major role in their morphology. Surprisingly, knockdown of AqPI in Aquilegia coerulea x “Origami” also reveals a role for the B class genes in maintaining the expression of the C gene homolog AqAG1 in the outer whorls of stamens. These findings suggest that the transference of pollinator function to the first whorl sepals included a non-homeotic recruitment of the B class genes to promote aspects of petaloidy. They also confirm results in several other Ranunculales that have revealed an unexpected regulatory connection between the B and C class genes.

  17. Determination and validation of mTOR kinase-domain 3D structure by homology modeling

    Directory of Open Access Journals (Sweden)

    Lakhlili W

    2015-07-01

    Full Text Available Wiame Lakhlili,1 Gwénaël Chevé,2 Abdelaziz Yasri,2 Azeddine Ibrahimi1 1Laboratoire de Biotechnologie (MedBiotech, Faculté de Médecine et de Pharmacie de Rabat, Université Mohammed V de Rabat, Rabat, Morroco; 2OriBase Pharma, Cap Gamma, Parc Euromédecine, Montpellier, France Abstract: The AKT/mammalian target of rapamycin (mTOR pathway is considered as one of the commonly activated and deregulated signaling pathways in human cancer. mTOR is associated with other proteins in two molecular complexes: mTOR complex 1/Raptor and the mTOR complex 2/Rictor. Using the crystal structure of the related lipid kinase PI3Kγ, we built a model of the catalytic region of mTOR. The modeling of the three-dimensional (3D structure of the mTOR was performed by homology modeling program SWISS-MODEL. The quality and validation of the obtained model were performed using PROCHECK and PROVE softwares. The overall stereochemical property of the protein was assessed by the Ramachandran plot. The model validation was also done by docking of known inhibitors. In this paper, we describe and validate a 3D model for the mTOR catalytic site.Keywords: mTOR, homology modeling, mTOR kinase-domain, docking

  18. Remote connector development study

    International Nuclear Information System (INIS)

    Parazin, R.J.

    1995-05-01

    Plutonium-uranium extraction (PUREX) connectors, the most common connectors used at the Hanford site, offer a certain level of flexibility in pipe routing, process system configuration, and remote equipment/instrument replacement. However, these desirable features have inherent shortcomings like leakage, high pressure drop through the right angle bends, and a limited range of available pipe diameters that can be connect by them. Costs for construction, maintenance, and operation of PUREX connectors seem to be very high. The PUREX connector designs include a 90 degree bend in each connector. This increases the pressure drop and erosion effects. Thus, each jumper requires at least two 90 degree bends. PUREX connectors have not been practically used beyond 100 (4 in.) inner diameter. This study represents the results of a survey on the use of remote pipe-connection systems in US and foreign plants. This study also describes the interdependence between connectors, remote handling equipment, and the necessary skills of the operators

  19. A snapshot of the physical and functional wiring of the Eps15 homology domain network in the nematode

    DEFF Research Database (Denmark)

    Tsushima, Hanako; Malabarba, Maria Grazia; Confalonieri, Stefano

    2013-01-01

    Protein interaction modules coordinate the connections within and the activity of intracellular signaling networks. The Eps15 Homology (EH) module, a protein-protein interaction domain that is a key feature of the EH-network, was originally identified in a few proteins involved in endocytosis and...

  20. Eps homology domain endosomal transport proteins differentially localize to the neuromuscular junction

    Directory of Open Access Journals (Sweden)

    Mate Suzanne E

    2012-09-01

    Full Text Available Abstract Background Recycling of endosomes is important for trafficking and maintenance of proteins at the neuromuscular junction (NMJ. We have previously shown high expression of the endocytic recycling regulator Eps15 homology domain-containing (EHD1 proteinin the Torpedo californica electric organ, a model tissue for investigating a cholinergic synapse. In this study, we investigated the localization of EHD1 and its paralogs EHD2, EHD3, and EHD4 in mouse skeletal muscle, and assessed the morphological changes in EHD1−/− NMJs. Methods Localization of the candidate NMJ protein EHD1 was assessed by confocal microscopy analysis of whole-mount mouse skeletal muscle fibers after direct gene transfer and immunolabeling. The potential function of EHD1 was assessed by specific force measurement and α-bungarotoxin-based endplate morphology mapping in EHD1−/− mouse skeletal muscle. Results Endogenous EHD1 localized to primary synaptic clefts of murine NMJ, and this localization was confirmed by expression of recombinant green fluorescent protein labeled-EHD1 in murine skeletal muscle in vivo. EHD1−/− mouse skeletal muscle had normal histology and NMJ morphology, and normal specific force generation during muscle contraction. The EHD 1–4 proteins showed differential localization in skeletal muscle: EHD2 to muscle vasculature, EHD3 to perisynaptic regions, and EHD4 to perinuclear regions and to primary synaptic clefts, but at lower levels than EHD1. Additionally, specific antibodies raised against mammalian EHD1-4 recognized proteins of the expected mass in the T. californica electric organ. Finally, we found that EHD4 expression was more abundant in EHD1−/− mouse skeletal muscle than in wild-type skeletal muscle. Conclusion EHD1 and EHD4 localize to the primary synaptic clefts of the NMJ. Lack of obvious defects in NMJ structure and muscle function in EHD1−/− muscle may be due to functional compensation by other EHD paralogs.

  1. Crystallization and preliminary X-ray crystallographic characterization of a cyclic nucleotide-binding homology domain from the mouse EAG potassium channel

    International Nuclear Information System (INIS)

    Marques-Carvalho, Maria João; Morais-Cabral, João Henrique

    2012-01-01

    The crystallization conditions and preliminary crystal characterization of the cytoplasmic cyclic nucleotide-binding homology domain from the mouse EAG potassium channel are reported. The members of the family of voltage-gated KCNH potassium channels play important roles in cardiac and neuronal repolarization, tumour proliferation and hormone secretion. These channels have a C-terminal cytoplasmic domain which is homologous to cyclic nucleotide-binding domains (CNB-homology domains), but it has been demonstrated that channel function is not affected by cyclic nucleotides and that the domain does not bind nucleotides in vitro. Here, the crystallization and preliminary crystallographic analysis of a CNB-homology domain from a member of the KCNH family, the mouse EAG channel, is reported. X-ray diffraction data were collected to 2.2 Å resolution and the crystal belonged to the hexagonal space group P3 1 21

  2. Intrinsic Pleckstrin Homology (PH) Domain Motion in Phospholipase C-β Exposes a Gβγ Protein Binding Site*

    OpenAIRE

    Kadamur, Ganesh; Ross, Elliott M.

    2016-01-01

    Mammalian phospholipase C-β (PLC-β) isoforms are stimulated by heterotrimeric G protein subunits and members of the Rho GTPase family of small G proteins. Although recent structural studies showed how Gαq and Rac1 bind PLC-β, there is a lack of consensus regarding the Gβγ binding site in PLC-β. Using FRET between cerulean fluorescent protein-labeled Gβγ and the Alexa Fluor 594-labeled PLC-β pleckstrin homology (PH) domain, we demonstrate that the PH domain is the minimal Gβγ binding region in...

  3. Src-homology 2 domain-containing tyrosine phosphatase 2 promotes oral cancer invasion and metastasis

    Science.gov (United States)

    2014-01-01

    Background Tumor invasion and metastasis represent a major unsolved problem in cancer pathogenesis. Recent studies have indicated the involvement of Src-homology 2 domain-containing tyrosine phosphatase 2 (SHP2) in multiple malignancies; however, the role of SHP2 in oral cancer progression has yet to be elucidated. We propose that SHP2 is involved in the progression of oral cancer toward metastasis. Methods SHP2 expression was evaluated in paired oral cancer tissues by using immunohistochemical staining and real-time reverse transcription polymerase chain reaction. Isogenic highly invasive oral cancer cell lines from their respective low invasive parental lines were established using a Boyden chamber assay, and changes in the hallmarks of the epithelial-mesenchymal transition (EMT) were assessed to evaluate SHP2 function. SHP2 activity in oral cancer cells was reduced using si-RNA knockdown or enforced expression of a catalytically deficient mutant to analyze migratory and invasive ability in vitro and metastasis toward the lung in mice in vivo. Results We observed the significant upregulation of SHP2 in oral cancer tissues and cell lines. Following SHP2 knockdown, the oral cancer cells markedly attenuated migratory and invasion ability. We observed similar results in phosphatase-dead SHP2 C459S mutant expressing cells. Enhanced invasiveness was associated with significant upregulation of E-cadherin, vimentin, Snail/Twist1, and matrix metalloproteinase-2 in the highly invasive clones. In addition, we determined that SHP2 activity is required for the downregulation of phosphorylated ERK1/2, which modulates the downstream effectors, Snail and Twist1 at a transcript level. In lung tissue sections of mice, we observed that HSC3 tumors with SHP2 deletion exhibited significantly reduced metastatic capacity, compared with tumors administered control si-RNA. Conclusions Our data suggest that SHP2 promotes the invasion and metastasis of oral cancer cells. These results

  4. Increased Eps15 homology domain 1 and RAB11FIP3 expression regulate breast cancer progression via promoting epithelial growth factor receptor recycling.

    Science.gov (United States)

    Tong, Dandan; Liang, Ya-Nan; Stepanova, A A; Liu, Yu; Li, Xiaobo; Wang, Letian; Zhang, Fengmin; Vasilyeva, N V

    2017-02-01

    Recent research indicates that the C-terminal Eps15 homology domain 1 is associated with epithelial growth factor receptor-mediated endocytosis recycling in non-small-cell lung cancer. The aim of this study was to determine the clinical significance of Eps15 homology domain 1 gene expression in relation to phosphorylation of epithelial growth factor receptor expression in patients with breast cancer. Primary breast cancer samples from 306 patients were analyzed for Eps15 homology domain 1, RAB11FIP3, and phosphorylation of epithelial growth factor receptor expression via immunohistochemistry. The clinical significance was assessed via a multivariate Cox regression analysis, Kaplan-Meier curves, and the log-rank test. Eps15 homology domain 1 and phosphorylation of epithelial growth factor receptor were upregulated in 60.46% (185/306) and 53.92% (165/306) of tumor tissues, respectively, as assessed by immunohistochemistry. The statistical correlation analysis indicated that Eps15 homology domain 1 overexpression was positively correlated with the increases in phosphorylation of epithelial growth factor receptor ( r = 0.242, p breast cancer for the overall survival in the total, chemotherapy, and human epidermal growth factor receptor 2 (-) groups. However, the use of combined expression of Eps15 homology domain 1 and phosphorylation of epithelial growth factor receptor markers is more effective for the disease-free survival in the overall population, chemotherapy, and human epidermal growth factor receptor 2 (-) groups. Moreover, the combined markers are also significant prognostic markers of breast cancer in the human epidermal growth factor receptor 2 (+), estrogen receptor (+), and estrogen receptor (-) groups. Eps15 homology domain 1 has a tumor suppressor function, and the combined marker of Eps15 homology domain 1/phosphorylation of epithelial growth factor receptor expression was identified as a better prognostic marker in breast cancer diagnosis

  5. Modular Connector Keying Concept

    Science.gov (United States)

    Ishman, Scott; Dukes, Scott; Warnica, Gary; Conrad, Guy; Senigla, Steven

    2013-01-01

    For panel-mount-type connectors, keying is usually "built-in" to the connector body, necessitating different part numbers for each key arrangement. This is costly for jobs that require small quantities. This invention was driven to provide a cost savings and to reduce documentation of individual parts. The keys are removable and configurable in up to 16 combinations. Since the key parts are separate from the connector body, a common design can be used for the plug, receptacle, and key parts. The keying can then be set at the next higher assembly.

  6. Novel inhibitors induce large conformational changes of GAB1 pleckstrin homology domain and kill breast cancer cells.

    Directory of Open Access Journals (Sweden)

    Lu Chen

    2015-01-01

    Full Text Available The Grb2-associated binding protein 1 (GAB1 integrates signals from different signaling pathways and is over-expressed in many cancers, therefore representing a new therapeutic target. In the present study, we aim to target the pleckstrin homology (PH domain of GAB1 for cancer treatment. Using homology models we derived, high-throughput virtual screening of five million compounds resulted in five hits which exhibited strong binding affinities to GAB1 PH domain. Our prediction of ligand binding affinities is also in agreement with the experimental KD values. Furthermore, molecular dynamics studies showed that GAB1 PH domain underwent large conformational changes upon ligand binding. Moreover, these hits inhibited the phosphorylation of GAB1 and demonstrated potent, tumor-specific cytotoxicity against MDA-MB-231 and T47D breast cancer cell lines. This effort represents the discovery of first-in-class GAB1 PH domain inhibitors with potential for targeted breast cancer therapy and provides novel insights into structure-based approaches to targeting this protein.

  7. Yeast Fex1p Is a Constitutively Expressed Fluoride Channel with Functional Asymmetry of Its Two Homologous Domains*

    Science.gov (United States)

    Smith, Kathryn D.; Gordon, Patricia B.; Rivetta, Alberto; Allen, Kenneth E.; Berbasova, Tetyana; Slayman, Clifford; Strobel, Scott A.

    2015-01-01

    Fluoride is a ubiquitous environmental toxin with which all biological species must cope. A recently discovered family of fluoride export (FEX) proteins protects organisms from fluoride toxicity by removing it from the cell. We show here that FEX proteins in Saccharomyces cerevisiae function as ion channels that are selective for fluoride over chloride and that these proteins are constitutively expressed at the yeast plasma membrane. Continuous expression is in contrast to many other toxin exporters in yeast, and this, along with the fact that two nearly duplicate proteins are encoded in the yeast genome, suggests that the threat posed by fluoride ions is frequent and detrimental. Structurally, eukaryotic FEX proteins consist of two homologous four-transmembrane helix domains folded into an antiparallel dimer, where the orientation of the two domains is fixed by a single transmembrane linker helix. Using phylogenetic sequence conservation as a guide, we have identified several functionally important residues. There is substantial functional asymmetry in the effect of mutation at corresponding sites in the two domains. Specifically, mutations to residues in the C-terminal domain proved significantly more detrimental to function than did similar mutations in the N-terminal domain. Our data suggest particular residues that may be important to anion specificity, most notably the necessity of a positive charge near the end of TMH1 in the C-terminal domain. It is possible that a cationic charge at this location may create an electrostatic well for fluoride ions entering the channel from the cytoplasm. PMID:26055717

  8. Tyrosine Phosphorylation of the Lyn Src Homology 2 (SH2) Domain Modulates Its Binding Affinity and Specificity*

    Science.gov (United States)

    Jin, Lily L.; Wybenga-Groot, Leanne E.; Tong, Jiefei; Taylor, Paul; Minden, Mark D.; Trudel, Suzanne; McGlade, C. Jane; Moran, Michael F.

    2015-01-01

    Src homology 2 (SH2) domains are modular protein structures that bind phosphotyrosine (pY)-containing polypeptides and regulate cellular functions through protein-protein interactions. Proteomics analysis showed that the SH2 domains of Src family kinases are themselves tyrosine phosphorylated in blood system cancers, including acute myeloid leukemia, chronic lymphocytic leukemia, and multiple myeloma. Using the Src family kinase Lyn SH2 domain as a model, we found that phosphorylation at the conserved SH2 domain residue Y194 impacts the affinity and specificity of SH2 domain binding to pY-containing peptides and proteins. Analysis of the Lyn SH2 domain crystal structure supports a model wherein phosphorylation of Y194 on the EF loop modulates the binding pocket that engages amino acid side chains at the pY+2/+3 position. These data indicate another level of regulation wherein SH2-mediated protein-protein interactions are modulated by SH2 kinases and phosphatases. PMID:25587033

  9. Tyrosine phosphorylation of the Lyn Src homology 2 (SH2) domain modulates its binding affinity and specificity.

    Science.gov (United States)

    Jin, Lily L; Wybenga-Groot, Leanne E; Tong, Jiefei; Taylor, Paul; Minden, Mark D; Trudel, Suzanne; McGlade, C Jane; Moran, Michael F

    2015-03-01

    Src homology 2 (SH2) domains are modular protein structures that bind phosphotyrosine (pY)-containing polypeptides and regulate cellular functions through protein-protein interactions. Proteomics analysis showed that the SH2 domains of Src family kinases are themselves tyrosine phosphorylated in blood system cancers, including acute myeloid leukemia, chronic lymphocytic leukemia, and multiple myeloma. Using the Src family kinase Lyn SH2 domain as a model, we found that phosphorylation at the conserved SH2 domain residue Y(194) impacts the affinity and specificity of SH2 domain binding to pY-containing peptides and proteins. Analysis of the Lyn SH2 domain crystal structure supports a model wherein phosphorylation of Y(194) on the EF loop modulates the binding pocket that engages amino acid side chains at the pY+2/+3 position. These data indicate another level of regulation wherein SH2-mediated protein-protein interactions are modulated by SH2 kinases and phosphatases. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  10. Intrinsic Pleckstrin Homology (PH) Domain Motion in Phospholipase C-β Exposes a Gβγ Protein Binding Site*

    Science.gov (United States)

    Kadamur, Ganesh

    2016-01-01

    Mammalian phospholipase C-β (PLC-β) isoforms are stimulated by heterotrimeric G protein subunits and members of the Rho GTPase family of small G proteins. Although recent structural studies showed how Gαq and Rac1 bind PLC-β, there is a lack of consensus regarding the Gβγ binding site in PLC-β. Using FRET between cerulean fluorescent protein-labeled Gβγ and the Alexa Fluor 594-labeled PLC-β pleckstrin homology (PH) domain, we demonstrate that the PH domain is the minimal Gβγ binding region in PLC-β3. We show that the isolated PH domain can compete with full-length PLC-β3 for binding Gβγ but not Gαq, Using sequence conservation, structural analyses, and mutagenesis, we identify a hydrophobic face of the PLC-β PH domain as the Gβγ binding interface. This PH domain surface is not solvent-exposed in crystal structures of PLC-β, necessitating conformational rearrangement to allow Gβγ binding. Blocking PH domain motion in PLC-β by cross-linking it to the EF hand domain inhibits stimulation by Gβγ without altering basal activity or Gαq response. The fraction of PLC-β cross-linked is proportional to the fractional loss of Gβγ response. Cross-linked PLC-β does not bind Gβγ in a FRET-based Gβγ-PLC-β binding assay. We propose that unliganded PLC-β exists in equilibrium between a closed conformation observed in crystal structures and an open conformation where the PH domain moves away from the EF hands. Therefore, intrinsic movement of the PH domain in PLC-β modulates Gβγ access to its binding site. PMID:27002154

  11. Intrinsic Pleckstrin Homology (PH) Domain Motion in Phospholipase C-β Exposes a Gβγ Protein Binding Site.

    Science.gov (United States)

    Kadamur, Ganesh; Ross, Elliott M

    2016-05-20

    Mammalian phospholipase C-β (PLC-β) isoforms are stimulated by heterotrimeric G protein subunits and members of the Rho GTPase family of small G proteins. Although recent structural studies showed how Gαq and Rac1 bind PLC-β, there is a lack of consensus regarding the Gβγ binding site in PLC-β. Using FRET between cerulean fluorescent protein-labeled Gβγ and the Alexa Fluor 594-labeled PLC-β pleckstrin homology (PH) domain, we demonstrate that the PH domain is the minimal Gβγ binding region in PLC-β3. We show that the isolated PH domain can compete with full-length PLC-β3 for binding Gβγ but not Gαq, Using sequence conservation, structural analyses, and mutagenesis, we identify a hydrophobic face of the PLC-β PH domain as the Gβγ binding interface. This PH domain surface is not solvent-exposed in crystal structures of PLC-β, necessitating conformational rearrangement to allow Gβγ binding. Blocking PH domain motion in PLC-β by cross-linking it to the EF hand domain inhibits stimulation by Gβγ without altering basal activity or Gαq response. The fraction of PLC-β cross-linked is proportional to the fractional loss of Gβγ response. Cross-linked PLC-β does not bind Gβγ in a FRET-based Gβγ-PLC-β binding assay. We propose that unliganded PLC-β exists in equilibrium between a closed conformation observed in crystal structures and an open conformation where the PH domain moves away from the EF hands. Therefore, intrinsic movement of the PH domain in PLC-β modulates Gβγ access to its binding site. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  12. Two amino acid residues confer different binding affinities of Abelson family kinase SRC homology 2 domains for phosphorylated cortactin.

    Science.gov (United States)

    Gifford, Stacey M; Liu, Weizhi; Mader, Christopher C; Halo, Tiffany L; Machida, Kazuya; Boggon, Titus J; Koleske, Anthony J

    2014-07-11

    The closely related Abl family kinases, Arg and Abl, play important non-redundant roles in the regulation of cell morphogenesis and motility. Despite similar N-terminal sequences, Arg and Abl interact with different substrates and binding partners with varying affinities. This selectivity may be due to slight differences in amino acid sequence leading to differential interactions with target proteins. We report that the Arg Src homology (SH) 2 domain binds two specific phosphotyrosines on cortactin, a known Abl/Arg substrate, with over 10-fold higher affinity than the Abl SH2 domain. We show that this significant affinity difference is due to the substitution of arginine 161 and serine 187 in Abl to leucine 207 and threonine 233 in Arg, respectively. We constructed Abl SH2 domains with R161L and S187T mutations alone and in combination and find that these substitutions are sufficient to convert the low affinity Abl SH2 domain to a higher affinity "Arg-like" SH2 domain in binding to a phospho-cortactin peptide. We crystallized the Arg SH2 domain for structural comparison to existing crystal structures of the Abl SH2 domain. We show that these two residues are important determinants of Arg and Abl SH2 domain binding specificity. Finally, we expressed Arg containing an "Abl-like" low affinity mutant Arg SH2 domain (L207R/T233S) and find that this mutant, although properly localized to the cell periphery, does not support wild type levels of cell edge protrusion. Together, these observations indicate that these two amino acid positions confer different binding affinities and cellular functions on the distinct Abl family kinases. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

  13. Inhibition of tumor metastasis by a growth factor receptor bound protein 2 Src homology 2 domain-binding antagonist.

    Science.gov (United States)

    Giubellino, Alessio; Gao, Yang; Lee, Sunmin; Lee, Min-Jung; Vasselli, James R; Medepalli, Sampath; Trepel, Jane B; Burke, Terrence R; Bottaro, Donald P

    2007-07-01

    Metastasis, the primary cause of death in most forms of cancer, is a multistep process whereby cells from the primary tumor spread systemically and colonize distant new sites. Blocking critical steps in this process could potentially inhibit tumor metastasis and dramatically improve cancer survival rates; however, our understanding of metastasis at the molecular level is still rudimentary. Growth factor receptor binding protein 2 (Grb2) is a widely expressed adapter protein with roles in epithelial cell growth and morphogenesis, as well as angiogenesis, making it a logical target for anticancer drug development. We have previously shown that a potent antagonist of Grb2 Src homology-2 domain-binding, C90, blocks growth factor-driven cell motility in vitro and angiogenesis in vivo. We now report that C90 inhibits metastasis in vivo in two aggressive tumor models, without affecting primary tumor growth rate. These results support the potential efficacy of this compound in reducing the metastatic spread of primary solid tumors and establish a critical role for Grb2 Src homology-2 domain-mediated interactions in this process.

  14. Jumper connector analysis

    Science.gov (United States)

    Kanjilal, S. K.; Lindquist, M. R.; Ulbricht, L. E.

    1994-02-01

    Jumper connectors are used for remotely connecting pipe lines containing transfer fluids ranging from hazardous chemicals to other nonhazardous liquids. The jumper connector assembly comprises hooks, hookpins, a block, a nozzle, an operating screw, and a nut. The hooks are tightened against the nozzle flanges by the operating screw that is tightened with a remotely connected torque wrench. Stress analysis for the jumper connector assembly (used extensively on the US Department of Energy's Hanford Site, near Richland, Washington) is performed by using hand calculation and finite-element techniques to determine the stress levels resulting from operating and seismic loads on components of the assembly. The analysis addresses loading conditions such as prestress, seismic, operating, thermal, and leakage. The preload torque-generated forces at which each component reaches its stress limits are presented in a tabulated format. Allowable operating loads for the jumper assembly are provided to prevent leakage of the assembly during operating cycles.

  15. Flat-port connectors

    KAUST Repository

    Alrashed, Mohammed

    2017-05-26

    Disclosed are various embodiments for connectors used with electronic devices, such as input and/or output ports to connect peripheral equipment or accessories. More specifically, various flat-port are provided that can be used in place of standard connectors including, but not limited to, audio jacks and Universal Serial Bus (USB) ports. The flat-port connectors are an alternate connection design to replace the traditional receptacle port (female-port), making the device more sealed creation more dust and water resistant. It is unique in the way of using the outer surfaces of the device for the electrical connection between the ports. Flat-port design can allow the manufacture of extremely thin devices by eliminating the side ports slots that take a lot of space and contribute to the increase thickness of the device. The flat-port receptacle improves the overall appearance of the device and makes it more resistant to dust and water.

  16. Fiber optic connector

    Science.gov (United States)

    Rajic, Slobodan; Muhs, Jeffrey D.

    1996-01-01

    A fiber optic connector and method for connecting composite materials within which optical fibers are imbedded. The fiber optic connector includes a capillary tube for receiving optical fibers at opposing ends. The method involves inserting a first optical fiber into the capillary tube and imbedding the unit in the end of a softened composite material. The capillary tube is injected with a coupling medium which subsequently solidifies. The composite material is machined to a desired configuration. An external optical fiber is then inserted into the capillary tube after fluidizing the coupling medium, whereby the optical fibers are coupled.

  17. The ubiquitin-homology protein, DAP-1, associates with tumor necrosis factor receptor (p60) death domain and induces apoptosis.

    Science.gov (United States)

    Liou, M L; Liou, H C

    1999-04-09

    The tumor necrosis factor receptor, p60 (TNF-R1), transduces death signals via the association of its cytoplasmic domain with several intracellular proteins. By screening a mammalian cDNA library using the yeast two-hybrid cloning technique, we isolated a ubiquitin-homology protein, DAP-1, which specifically interacts with the cytoplasmic death domain of TNF-R1. Sequence analysis reveals that DAP-1 shares striking sequence homology with the yeast SMT3 protein that is essential for the maintenance of chromosome integrity during mitosis (Meluh, P. B., and Koshland, D. (1995) Mol. Biol. Cell 6, 793-807). DAP-1 is nearly identical to PIC1, a protein that interacts with the PML tumor suppressor implicated in acute promyelocytic leukemia (Boddy, M. N., Howe, K., Etkin, L. D., Solomon, E., and Freemont, P. S. (1996) Oncogene 13, 971-982), and the sentrin protein, which associates with the Fas death receptor (Okura, T., Gong, L., Kamitani, T., Wada, T., Okura, I., Wei, C. F., Chang, H. M., and Yeh, E. T. (1996) J. Immunol. 157, 4277-4281). The in vivo interaction between DAP-1 and TNF-R1 was further confirmed in mammalian cells. In transient transfection assays, overexpression of DAP-1 suppresses NF-kappaB/Rel activity in 293T cells, a human kidney embryonic carcinoma cell line. Overexpression of either DAP-1 or sentrin causes apoptosis of TNF-sensitive L929 fibroblast cell line, as well as TNF-resistant osteosarcoma cell line, U2OS. Furthermore, the dominant negative Fas-associated death domain protein (FADD) protein blocks the cell death induced by either DAP-1 or FADD. Collectively, these observations highly suggest a role for DAP-1 in mediating TNF-induced cell death signaling pathways, presumably through the recruitment of FADD death effector.

  18. Analysis of the hormone-binding domain of steroid receptors using chimeras generated by homologous recombination

    International Nuclear Information System (INIS)

    Martinez, Elisabeth D.; Pattabiraman, Nagarajan; Danielsen, Mark

    2005-01-01

    The glucocorticoid receptor and the mineralocorticoid receptor are members of the steroid receptor family that exhibit ligand cross-reactivity. Specificity of steroid receptor action is investigated in the present work by the construction and characterization of chimeras between the glucocorticoid receptor and the mineralocorticoid receptor. We used an innovative approach to make novel steroid receptor proteins in vivo that in general, contrary to our expectations, show increased ligand specificity compared to the parental receptors. We describe a receptor that is specific for the potent synthetic glucocorticoid triamcinolone acetonide and does not bind aldosterone. A further set of chimeras has an increased ability to discriminate between ligands, responding potently to mineralocorticoids and only very weakly to synthetic glucocorticoids. A chimera with the fusion site in the hinge highlights the importance of the region between the DNA-binding and the hormone-binding domains since, unlike both the glucocorticoid and mineralocorticoid receptors, it only responds to mineralocorticoids. One chimera has reduced specificity in that it acts as a general corticoid receptor, responding to glucocorticoids and mineralocorticoids with similar potency and efficacy. Our data suggest that regions of the glucocorticoid and mineralocorticoid receptor hormone-binding domains are functionally non-reciprocal. We present transcriptional, hormone-binding, and structure-modeling evidence that suggests that receptor-specific interactions within and across domains mediate aspects of specificity in transcriptional responses to steroids

  19. Regulation of embryonic hematopoiesis by a cytokine-inducible SH2 domain homolog in zebrafish.

    Science.gov (United States)

    Lewis, Rowena S; Noor, Suzita M; Fraser, Fiona W; Sertori, Robert; Liongue, Clifford; Ward, Alister C

    2014-06-15

    Cytokine-inducible SH2 domain-containing protein (CISH), a member of the suppressor of cytokine signaling family of negative feedback regulators, is induced by cytokines that activate STAT5 and can inhibit STAT5 signaling in vitro. However, demonstration of a definitive in vivo role for CISH during development has remained elusive. This study employed expression analysis and morpholino-mediated knockdown in zebrafish in concert with bioinformatics and biochemical approaches to investigate CISH function. Two zebrafish CISH paralogs were identified, cish.a and cish.b, with high overall conservation (43-46% identity) with their mammalian counterparts. The cish.a gene was maternally derived, with transcripts present throughout embryogenesis, and increasing at 4-5 d after fertilization, whereas cish.b expression commenced at 8 h after fertilization. Expression of cish.a was regulated by the JAK2/STAT5 pathway via conserved tetrameric STAT5 binding sites (TTCN3GAA) in its promoter. Injection of morpholinos targeting cish.a, but not cish.b or control morpholinos, resulted in enhanced embryonic erythropoiesis, myelopoiesis, and lymphopoiesis, including a 2- 3-fold increase in erythrocytic markers. This occurred concomitantly with increased activation of STAT5. This study indicates that CISH functions as a conserved in vivo target and regulator of STAT5 in the control of embryonic hematopoiesis. Copyright © 2014 by The American Association of Immunologists, Inc.

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

    Directory of Open Access Journals (Sweden)

    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.

  1. NGF-Dependent neurite outgrowth in PC12 cells overexpressing the Src homology 2-domain protein shb requires activation of the Rap1 pathway

    NARCIS (Netherlands)

    Lu, L.; Annerén, C.; Reedquist, K. A.; Bos, J. L.; Welsh, M.

    2000-01-01

    The Src homology 2 (SH2) domain adaptor protein Shb has been shown to transmit NGF- and FGF-2-dependent differentiation signals in PC12 cells. To study if this involves signaling through the small GTPase Rap1, Rap1 activity was assessed in Shb-overexpressing PC12 cells. We demonstrate that NGF and

  2. Purification, crystallization, small-angle X-ray scattering and preliminary X-ray diffraction analysis of the SH2 domain of the Csk-homologous kinase

    International Nuclear Information System (INIS)

    Gunn, Natalie J.; Gorman, Michael A.; Dobson, Renwick C. J.; Parker, Michael W.; Mulhern, Terrence D.

    2011-01-01

    The Src-homology 2 (SH2) domain of Csk-family protein tyrosine kinases acts as a conformational switch to regulate their catalytic activity, which in turn promotes the inhibition of their proto-oncogenic targets, the Src-family kinases. Here, the expression, purification, small-angle X-ray scattering and preliminary diffraction analysis of the SH2 domain of the Csk-homologous kinase is reported. The C-terminal Src kinase (Csk) and Csk-homologous kinase (CHK) are endogenous inhibitors of the proto-oncogenic Src family of protein tyrosine kinases (SFKs). Phosphotyrosyl peptide binding to their Src-homology 2 (SH2) domains activates Csk and CHK, enhancing their ability to suppress SFK signalling; however, the detailed mechanistic basis of this activation event is unclear. The CHK SH2 was expressed in Escherichia coli and the purified protein was characterized as monomeric by synchrotron small-angle X-ray scattering in-line with size-exclusion chromatography. The CHK SH2 crystallized in 0.2 M sodium bromide, 0.1 M bis-Tris propane pH 6.5 and 20% polyethylene glycol 3350 and the best crystals diffracted to ∼1.6 Å resolution. The crystals belonged to space group P2, with unit-cell parameters a = 25.8, b = 34.6, c = 63.2 Å, β = 99.4°

  3. Structure of the interleukin-2 tyrosine kinase Src homology 2 domain; comparison between X-ray and NMR-derived structures

    International Nuclear Information System (INIS)

    Joseph, Raji E.; Ginder, Nathaniel D.; Hoy, Julie A.; Nix, Jay C.; Fulton, D. Bruce; Honzatko, Richard B.; Andreotti, Amy H.

    2012-01-01

    The interleukin-2 tyrosine kinase Src homology 2 domain was crystallized and its structure was solved to 2.35 Å resolution. The structure reveals a domain-swapped dimer that is related to other dimeric SH2 domains solved previously. The cis–trans-prolyl isomerization that is evident from solution studies of Itk SH2 cannot be observed in the crystal structure. The crystal structure of the interleukin-2 tyrosine kinase Src homology domain (Itk SH2) is described and it is found that unlike in studies of this domain using NMR spectroscopy, cis–trans-prolyl isomerization is not readily detected in the crystal structure. Based on similarities between the Itk SH2 crystal form and the cis form of the Itk SH2 NMR structure, it is concluded that it is likely that the prolyl imide bond at least in part adopts the cis conformation in the crystal form. However, the lack of high-resolution data and the dynamic nature of the proline-containing loop mean that the precise imide-bond conformation cannot be determined and prolyl cis–trans isomerization in the crystal cannot be ruled out. Given the preponderance of structures that have been solved by X-ray crystallography in the Protein Data Bank, this result supports the notion that prolyl isomerization in folded proteins has been underestimated among known structures. Interestingly, while the precise status of the proline residue is ambiguous, Itk SH2 crystallizes as a domain-swapped dimer. The domain-swapped structure of Itk SH2 is similar to the domain-swapped SH2 domains of Grb2 and Nck, with domain swapping occurring at the β-meander region of all three SH2 domains. Thus, for Itk SH2 structural analysis by NMR spectroscopy and X-ray crystallography revealed very different structural features: proline isomerization versus domain-swapped dimerization, respectively

  4. Myosin-1A Targets to Microvilli Using Multiple Membrane Binding Motifs in the Tail Homology 1 (TH1) Domain*

    Science.gov (United States)

    Mazerik, Jessica N.; Tyska, Matthew J.

    2012-01-01

    One of the most abundant components of the enterocyte brush border is the actin-based monomeric motor, myosin-1a (Myo1a). Within brush border microvilli, Myo1a carries out a number of critical functions at the interface between membrane and actin cytoskeleton. Proper physiological function of Myo1a depends on its ability to bind to microvillar membrane, an interaction mediated by a C-terminal tail homology 1 (TH1) domain. However, little is known about the mechanistic details of the Myo1a-TH1/membrane interaction. Structure-function analysis of Myo1a-TH1 targeting in epithelial cells revealed that an N-terminal motif conserved among class I myosins and a C-terminal motif unique to Myo1a-TH1 are both required for steady state microvillar enrichment. Purified Myo1a bound to liposomes composed of phosphatidylserine and phosphoinositol 4,5-bisphosphate, with moderate affinity in a charge-dependent manner. Additionally, peptides of the N- and C-terminal regions required for targeting were able to compete with Myo1a for binding to highly charged liposomes in vitro. Single molecule total internal reflection fluorescence microscopy showed that these motifs are also necessary for slowing the membrane detachment rate in cells. Finally, Myo1a-TH1 co-localized with both lactadherin-C2 (a phosphatidylserine-binding protein) and PLCδ1-PH (a phosphoinositol 4,5-bisphosphate-binding protein) in microvilli, but only lactaderin-C2 expression reduced brush border targeting of Myo1a-TH1. Together, our results suggest that Myo1a targeting to microvilli is driven by membrane binding potential that is distributed throughout TH1 rather than localized to a single motif. These data highlight the diversity of mechanisms that enable different class I myosins to target membranes in distinct biological contexts. PMID:22367206

  5. The Structures of Coiled-Coil Domains from Type III Secretion System Translocators Reveal Homology to Pore-Forming Toxins

    Energy Technology Data Exchange (ETDEWEB)

    Barta, Michael L.; Dickenson, Nicholas E.; Patil, Mrinalini; Keightley, Andrew; Wyckoff, Gerald J.; Picking, William D.; Picking, Wendy L.; Geisbrecht, Brian V. (UMKC); (OKLU)

    2012-03-26

    Many pathogenic Gram-negative bacteria utilize type III secretion systems (T3SSs) to alter the normal functions of target cells. Shigella flexneri uses its T3SS to invade human intestinal cells to cause bacillary dysentery (shigellosis) that is responsible for over one million deaths per year. The Shigella type III secretion apparatus is composed of a basal body spanning both bacterial membranes and an exposed oligomeric needle. Host altering effectors are secreted through this energized unidirectional conduit to promote bacterial invasion. The active needle tip complex of S. flexneri is composed of a tip protein, IpaD, and two pore-forming translocators, IpaB and IpaC. While the atomic structure of IpaD has been elucidated and studied, structural data on the hydrophobic translocators from the T3SS family remain elusive. We present here the crystal structures of a protease-stable fragment identified within the N-terminal regions of IpaB from S. flexneri and SipB from Salmonella enterica serovar Typhimurium determined at 2.1 {angstrom} and 2.8 {angstrom} limiting resolution, respectively. These newly identified domains are composed of extended-length (114 {angstrom} in IpaB and 71 {angstrom} in SipB) coiled-coil motifs that display a high degree of structural homology to one another despite the fact that they share only 21% sequence identity. Further structural comparisons also reveal substantial similarity to the coiled-coil regions of pore-forming proteins from other Gram-negative pathogens, notably, colicin Ia. This suggests that these mechanistically separate and functionally distinct membrane-targeting proteins may have diverged from a common ancestor during the course of pathogen-specific evolutionary events.

  6. Double-plug seismic connector

    International Nuclear Information System (INIS)

    Annoot, I.R.

    1984-01-01

    The double-plug seismic electric connector comprises an elongated insulating body. A male connector plug is at one end of the body and a female connector plug is at the opposite end of the body. Each plug has a pair of male and female contacts. A pair of spaced axial conductors is embedded within the insulating body for interconnecting the opposite male and female contacts. The inner end of a double-wire cable is embedded within the insulating body and each wire inner end is connected to one of the conductors

  7. HCV NS5A protein containing potential ligands for both Src homology 2 and 3 domains enhances autophosphorylation of Src family kinase Fyn in B cells.

    Science.gov (United States)

    Nakashima, Kenji; Takeuchi, Kenji; Chihara, Kazuyasu; Horiguchi, Tomoko; Sun, Xuedong; Deng, Lin; Shoji, Ikuo; Hotta, Hak; Sada, Kiyonao

    2012-01-01

    Hepatitis C virus (HCV) infects B lymphocytes and induces mixed cryoglobulinemia and B cell non-Hodgkin's lymphoma. The molecular mechanism for the pathogenesis of HCV infection-mediated B cell disorders remains obscure. To identify the possible role for HCV nonstructural 5A (NS5A) protein in B cells, we generated the stable B cell lines expressing Myc-His tagged NS5A. Immunoprecipitation study in the presence or absence of pervanadate (PV) implied that NS5A was tyrosine phosphorylated by pervanadate (PV) treatment of the cells. Therefore we examined pull-down assay by using glutathione S-transferase (GST)-fusion proteins of various Src homology 2 (SH2) domains, which associates with phosphotyrosine within a specific amino acid sequence. The results showed that NS5A specifically bound to SH2 domain of Fyn from PV-treated B cells in addition to Src homology 3 (SH3) domain. Substitution of Arg(176) to Lys in the SH2 domain of Fyn abrogated this interaction. Deletion mutational analysis demonstrated that N-terminal region of NS5A was not required for the interaction with the SH2 domain of Fyn. Tyr(334) was identified as a tyrosine phosphorylation site in NS5A. Far-western analysis revealed that SH2 domain of Fyn directly bound to NS5A. Fyn and NS5A were colocalized in the lipid raft. These results suggest that NS5A directly binds to the SH2 domain of Fyn in a tyrosine phosphorylation-dependent manner. Lastly, we showed that the expression of NS5A in B cells increased phosphorylation of activation loop tyrosine in the kinase domain of Fyn. NS5A containing ligand for both SH2 and SH3 domains enhances an aberrant autophosphorylation and kinase activity of Fyn in B cells.

  8. HCV NS5A protein containing potential ligands for both Src homology 2 and 3 domains enhances autophosphorylation of Src family kinase Fyn in B cells.

    Directory of Open Access Journals (Sweden)

    Kenji Nakashima

    Full Text Available Hepatitis C virus (HCV infects B lymphocytes and induces mixed cryoglobulinemia and B cell non-Hodgkin's lymphoma. The molecular mechanism for the pathogenesis of HCV infection-mediated B cell disorders remains obscure. To identify the possible role for HCV nonstructural 5A (NS5A protein in B cells, we generated the stable B cell lines expressing Myc-His tagged NS5A. Immunoprecipitation study in the presence or absence of pervanadate (PV implied that NS5A was tyrosine phosphorylated by pervanadate (PV treatment of the cells. Therefore we examined pull-down assay by using glutathione S-transferase (GST-fusion proteins of various Src homology 2 (SH2 domains, which associates with phosphotyrosine within a specific amino acid sequence. The results showed that NS5A specifically bound to SH2 domain of Fyn from PV-treated B cells in addition to Src homology 3 (SH3 domain. Substitution of Arg(176 to Lys in the SH2 domain of Fyn abrogated this interaction. Deletion mutational analysis demonstrated that N-terminal region of NS5A was not required for the interaction with the SH2 domain of Fyn. Tyr(334 was identified as a tyrosine phosphorylation site in NS5A. Far-western analysis revealed that SH2 domain of Fyn directly bound to NS5A. Fyn and NS5A were colocalized in the lipid raft. These results suggest that NS5A directly binds to the SH2 domain of Fyn in a tyrosine phosphorylation-dependent manner. Lastly, we showed that the expression of NS5A in B cells increased phosphorylation of activation loop tyrosine in the kinase domain of Fyn. NS5A containing ligand for both SH2 and SH3 domains enhances an aberrant autophosphorylation and kinase activity of Fyn in B cells.

  9. Contribution of the first K-homology domain of poly(C)-binding protein 1 to its affinity and specificity for C-rich oligonucleotides

    OpenAIRE

    Yoga, Yano M. K.; Traore, Daouda A. K.; Sidiqi, Mahjooba; Szeto, Chris; Pendini, Nicole R.; Barker, Andrew; Leedman, Peter J.; Wilce, Jacqueline A.; Wilce, Matthew C. J.

    2012-01-01

    Poly-C-binding proteins are triple KH (hnRNP K homology) domain proteins with specificity for single stranded C-rich RNA and DNA. They play diverse roles in the regulation of protein expression at both transcriptional and translational levels. Here, we analyse the contributions of individual αCP1 KH domains to binding C-rich oligonucleotides using biophysical and structural methods. Using surface plasmon resonance (SPR), we demonstrate that KH1 makes the most stable interactions with both RNA...

  10. Selective anticancer activity of a hexapeptide with sequence homology to a non-kinase domain of Cyclin Dependent Kinase 4

    Directory of Open Access Journals (Sweden)

    Agarwala Usha

    2011-06-01

    Full Text Available Abstract Background Cyclin-dependent kinases 2, 4 and 6 (Cdk2, Cdk4, Cdk6 are closely structurally homologous proteins which are classically understood to control the transition from the G1 to the S-phases of the cell cycle by combining with their appropriate cyclin D or cyclin E partners to form kinase-active holoenzymes. Deregulation of Cdk4 is widespread in human cancer, CDK4 gene knockout is highly protective against chemical and oncogene-mediated epithelial carcinogenesis, despite the continued presence of CDK2 and CDK6; and overexpresssion of Cdk4 promotes skin carcinogenesis. Surprisingly, however, Cdk4 kinase inhibitors have not yet fulfilled their expectation as 'blockbuster' anticancer agents. Resistance to inhibition of Cdk4 kinase in some cases could potentially be due to a non-kinase activity, as recently reported with epidermal growth factor receptor. Results A search for a potential functional site of non-kinase activity present in Cdk4 but not Cdk2 or Cdk6 revealed a previously-unidentified loop on the outside of the C'-terminal non-kinase domain of Cdk4, containing a central amino-acid sequence, Pro-Arg-Gly-Pro-Arg-Pro (PRGPRP. An isolated hexapeptide with this sequence and its cyclic amphiphilic congeners are selectively lethal at high doses to a wide range of human cancer cell lines whilst sparing normal diploid keratinocytes and fibroblasts. Treated cancer cells do not exhibit the wide variability of dose response typically seen with other anticancer agents. Cancer cell killing by PRGPRP, in a cyclic amphiphilic cassette, requires cells to be in cycle but does not perturb cell cycle distribution and is accompanied by altered relative Cdk4/Cdk1 expression and selective decrease in ATP levels. Morphological features of apoptosis are absent and cancer cell death does not appear to involve autophagy. Conclusion These findings suggest a potential new paradigm for the development of broad-spectrum cancer specific therapeutics with

  11. Human alpha2-macroglobulin is composed of multiple domains, as predicted by homology with complement component C3.

    Science.gov (United States)

    Doan, Ninh; Gettins, Peter G W

    2007-10-01

    Human alpha2M (alpha2-macroglobulin) and the complement components C3 and C4 are thiol ester-containing proteins that evolved from the same ancestral gene. The recent structure determination of human C3 has allowed a detailed prediction of the location of domains within human alpha2M to be made. We describe here the expression and characterization of three alpha(2)M domains predicted to be involved in the stabilization of the thiol ester in native alpha2M and in its activation upon bait region proteolysis. The three newly expressed domains are MG2 (macroglobulin domain 2), TED (thiol ester-containing domain) and CUB (complement protein subcomponents C1r/C1s, urchin embryonic growth factor and bone morphogenetic protein 1) domain. Together with the previously characterized RBD (receptor-binding domain), they represent approx. 42% of the alpha2M polypeptide. Their expression as folded domains strongly supports the predicted domain organization of alpha2M. An X-ray crystal structure of MG2 shows it to have a fibronectin type-3 fold analogous to MG1-MG8 of C3. TED is, as predicted, an alpha-helical domain. CUB is a spliced domain composed of two stretches of polypeptide that flank TED in the primary structure. In intact C3 TED interacts with RBD, where it is in direct contact with the thiol ester, and with MG2 and CUB on opposite, flanking sides. In contrast, these alpha2M domains, as isolated species, show negligible interaction with one another, suggesting that the native conformation of alpha2M, and the consequent thiol ester-stabilizing domain-domain interactions, result from additional restraints imposed by the physical linkage of these domains or by additional domains in the protein.

  12. Human α2-macroglobulin is composed of multiple domains, as predicted by homology with complement component C3

    Science.gov (United States)

    Doan, Ninh; Gettins, Peter G. W.

    2007-01-01

    Human α2M (α2-macroglobulin) and the complement components C3 and C4 are thiol ester-containing proteins that evolved from the same ancestral gene. The recent structure determination of human C3 has allowed a detailed prediction of the location of domains within human α2M to be made. We describe here the expression and characterization of three α2M domains predicted to be involved in the stabilization of the thiol ester in native α2M and in its activation upon bait region proteolysis. The three newly expressed domains are MG2 (macroglobulin domain 2), TED (thiol ester-containing domain) and CUB (complement protein subcomponents C1r/C1s, urchin embryonic growth factor and bone morphogenetic protein 1) domain. Together with the previously characterized RBD (receptor-binding domain), they represent approx. 42% of the α2M polypeptide. Their expression as folded domains strongly supports the predicted domain organization of α2M. An X-ray crystal structure of MG2 shows it to have a fibronectin type-3 fold analogous to MG1–MG8 of C3. TED is, as predicted, an α-helical domain. CUB is a spliced domain composed of two stretches of polypeptide that flank TED in the primary structure. In intact C3 TED interacts with RBD, where it is in direct contact with the thiol ester, and with MG2 and CUB on opposite, flanking sides. In contrast, these α2M domains, as isolated species, show negligible interaction with one another, suggesting that the native conformation of α2M, and the consequent thiol ester-stabilizing domain–domain interactions, result from additional restraints imposed by the physical linkage of these domains or by additional domains in the protein. PMID:17608619

  13. Data Base On Cables And Connectors

    Science.gov (United States)

    Bowen, Arlen R.; Oliver, John D.

    1995-01-01

    Report describes Connector Adapter Cable Information Data Base (CONNAID) computer program, managing data base containing necessary information concerning electrical connectors, breakout boxes, adapter cables, backshells, and pertinent torque specifications for engineering project.

  14. Evaluation of fiber-optic connectors

    International Nuclear Information System (INIS)

    Reedy, R.P.

    1981-01-01

    Two fiber optic connectors for field use in high efficiency, long distance systems are described and evaluated in this report. The transmission testing arrangement and other considerations are included with the test results. Techniques for optimizing the transmission through these connectors are also described and the results are reported. Many desirable characteristics of connectors for field use are considered and compared to the ITT and Amphenol connectors tested here

  15. The SRC homology 2 domain of Rin1 mediates its binding to the epidermal growth factor receptor and regulates receptor endocytosis.

    Science.gov (United States)

    Barbieri, M Alejandro; Kong, Chen; Chen, Pin-I; Horazdovsky, Bruce F; Stahl, Philip D

    2003-08-22

    Activated epidermal growth factor receptors (EGFRs) recruit intracellular proteins that mediate receptor signaling and endocytic trafficking. Rin1, a multifunctional protein, has been shown to regulate EGFR internalization (1). Here we show that EGF stimulation induces a specific, rapid, and transient membrane recruitment of Rin1 and that recruitment is dependent on the Src homology 2 (SH2) domain of Rin1. Immunoprecipitation of EGFR is accompanied by co-immunoprecipitation of Rin1 in a time- and ligand-dependent manner. Association of Rin1 and specifically the SH2 domain of Rin1 with the EGFR was dependent on tyrosine phosphorylation of the intracellular domain of the EGFR. The recruitment of Rin1, observed by light microscopy, indicated that although initially cytosolic, Rin1 was recruited to both plasma membrane and endosomes following EGF addition. Moreover, the expression of the SH2 domain of Rin1 substantially impaired the internalization of EGF without affecting internalization of transferrin. Finally, we found that Rin1 co-immunoprecipitated with a number of tyrosine kinase receptors but not with cargo endocytic receptors. These results indicate that Rin1 provides a link via its SH2 domain between activated tyrosine kinase receptors and the endocytic pathway through the recruitment and activation of Rab5a.

  16. The Surface Layer Homology Domain-Containing Proteins of Alkaliphilic Bacillus pseudofirmus OF4 Play an Important Role in Alkaline Adaptation via Peptidoglycan Synthesis.

    Science.gov (United States)

    Fujinami, Shun; Ito, Masahiro

    2018-01-01

    It is well known that the Na + cycle and the cell wall are essential for alkaline adaptation of Na + -dependent alkaliphilic Bacillus species. In Bacillus pseudofirmus OF4, surface layer protein A (SlpA), the most abundant protein in the surface layer (S-layer) of the cell wall, is involved in alkaline adaptation, especially under low Na + concentrations. The presence of a large number of genes that encode S-layer homology (SLH) domain-containing proteins has been suggested from the genome sequence of B. pseudofirmus OF4. However, other than SlpA, the functions of SLH domain-containing proteins are not well known. Therefore, a deletion mutant of the csaB gene, required for the retention of SLH domain-containing proteins on the cell wall, was constructed to investigate its physiological properties. The csaB mutant strain of B. pseudofirmus OF4 had a chained morphology and alkaline sensitivity even under a 230 mM Na + concentration at which there is no growth difference between the parental strain and the slpA mutant strain. Ultra-thin section transmission electron microscopy showed that a csaB mutant strain lacked an S-layer part, and its peptidoglycan (PG) layer was disturbed. The slpA mutant strain also lacked an S-layer part, although its PG layer was not disturbed. These results suggested that the surface layer homology domain-containing proteins of B. pseudofirmus OF4 play an important role in alkaline adaptation via peptidoglycan synthesis.

  17. Proposed superscreened cables and connectors

    International Nuclear Information System (INIS)

    Fowler, E.P.

    1975-11-01

    The paper summarises the present availability of superscreened cables and proposes the specification of a family of cables to meet the foreseeable needs of the nuclear power industry. The cable numbering system is described, special tests outlined and important details given for the chosen cables. Appropriate connectors are also discussed and listed with an outline of their required screening performance. (author)

  18. Changes in signal transducer and activator of transcription 3 (STAT3) dynamics induced by complexation with pharmacological inhibitors of Src homology 2 (SH2) domain dimerization.

    Science.gov (United States)

    Resetca, Diana; Haftchenary, Sina; Gunning, Patrick T; Wilson, Derek J

    2014-11-21

    The activity of the transcription factor signal transducer and activator of transcription 3 (STAT3) is dysregulated in a number of hematological and solid malignancies. Development of pharmacological STAT3 Src homology 2 (SH2) domain interaction inhibitors holds great promise for cancer therapy, and a novel class of salicylic acid-based STAT3 dimerization inhibitors that includes orally bioavailable drug candidates has been recently developed. The compounds SF-1-066 and BP-1-102 are predicted to bind to the STAT3 SH2 domain. However, given the highly unstructured and dynamic nature of the SH2 domain, experimental confirmation of this prediction was elusive. We have interrogated the protein-ligand interaction of STAT3 with these small molecule inhibitors by means of time-resolved electrospray ionization hydrogen-deuterium exchange mass spectrometry. Analysis of site-specific evolution of deuterium uptake induced by the complexation of STAT3 with SF-1-066 or BP-1-102 under physiological conditions enabled the mapping of the in silico predicted inhibitor binding site to the STAT3 SH2 domain. The binding of both inhibitors to the SH2 domain resulted in significant local decreases in dynamics, consistent with solvent exclusion at the inhibitor binding site and increased rigidity of the inhibitor-complexed SH2 domain. Interestingly, inhibitor binding induced hot spots of allosteric perturbations outside of the SH2 domain, manifesting mainly as increased deuterium uptake, in regions of STAT3 important for DNA binding and nuclear localization. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

  19. A phospho-sugar binding domain homologous to NagB enzymes regulates the activity of the central glycolytic genes repressor.

    Science.gov (United States)

    Doan, Thierry; Martin, Laetitia; Zorrilla, Silvia; Chaix, Denis; Aymerich, Stéphane; Labesse, Gilles; Declerck, Nathalie

    2008-06-01

    CggR belongs to the SorC family of bacterial transcriptional regulators which control the expression of genes and operons involved in carbohydrate catabolism. CggR was first identified in Bacillus subtilis where it represses the gapA operon encoding the five enzymes that catalyze the central part of glycolysis. Here we present a structure/function study demonstrating that the C-terminal region of CggR regulates the DNA binding activity of this repressor in response to binding of a phosphorylated sugar. Molecular modeling of CggR revealed a winged-helix DNA-binding motif followed by a C-terminal domain presenting weak but significant homology with glucosamine-6-phosphate deaminases from the NagB family. In silico ligand screening suggested that the CggR C-terminal domain would bind preferentially bi-phosphorylated compounds, in agreement with previous studies that proposed fructuose-1,6-biphosphate (FBP) as the inducer metabolite. In vitro, FBP was the only sugar compound capable of interfering with CggR cooperative binding to DNA. FBP was also found to protect CggR against trypsin degradation at two arginine residues predicted to reside in a mobile loop forming the active site lid of the NagB enzymes. Replacement of residues predicted to interact with FBP led to mutant CggR with altered repressor activity in vivo but retaining their structural integrity and DNA binding activity in vitro. Interestingly, some of the mutant repressors responded with different specificity towards mono- and di-phospho-fructosides. Based on these results, we propose that the activity of the CggR-like repressors is controlled by a phospho-sugar binding (PSB) domain presenting structural and functional homology with NagB enzymes. (c) 2008 Wiley-Liss, Inc.

  20. Jumper connector analysis: 2-inch by 2-inch connector

    International Nuclear Information System (INIS)

    Kanjilal, S.K.; Ulbricht, L.E.; Lindquist, M.R.

    1994-01-01

    Jumper connectors are used for remotely connecting pipe lines containing transfer fluids ranging from hazardous chemicals to other nonhazardous liquids. The jumper connector assembly comprises hooks, hookpins, a block, a nozzle, an operating screw, and a nut. The hooks are tightened against the nozzle flanges by the operating screw, and a nut. The hooks are tightened against the nozzle flanges by the operating screw that is tightened with a remotely connected torque wrench. Stress analysis for the jumper connector assembly (used extensively on the US Department of Energy's Hanford Site, near Richland, Washington) is performed by using hand calculation and finite-element techniques to determine the stress levels resulting from operating and seismic loads on components of the assembly. The analysis addresses loading conditions such as prestress, seismic, operating, thermal, and leakage. The preload torque-generated forces at which each component reaches its stress limits are presented in a tabulated format. Allowable operating loads for the jumper assembly are provided to prevent leakage of the assembly during operating cycles

  1. The PAS fold: A redefinition of the PAS domain based upon structural prediction. A large-scale homology modelling study

    NARCIS (Netherlands)

    Hefti, M.H.; Francoijs, C.J.J.; Vries, de S.C.; Dixon, R.; Vervoort, J.J.M.

    2004-01-01

    In the postgenomic era it is essential that protein sequences are annotated correctly in order to help in the assignment of their putative functions. Over 1300 proteins in current protein sequence databases are predicted to contain a PAS domain based upon amino acid sequence alignments. One of the

  2. Time-resolved multimodal analysis of Src Homology 2 (SH2) domain binding in signaling by receptor tyrosine kinases.

    Science.gov (United States)

    Jadwin, Joshua A; Oh, Dongmyung; Curran, Timothy G; Ogiue-Ikeda, Mari; Jia, Lin; White, Forest M; Machida, Kazuya; Yu, Ji; Mayer, Bruce J

    2016-04-12

    While the affinities and specificities of SH2 domain-phosphotyrosine interactions have been well characterized, spatio-temporal changes in phosphosite availability in response to signals, and their impact on recruitment of SH2-containing proteins in vivo, are not well understood. To address this issue, we used three complementary experimental approaches to monitor phosphorylation and SH2 binding in human A431 cells stimulated with epidermal growth factor (EGF): 1) phospho-specific mass spectrometry; 2) far-Western blotting; and 3) live cell single-molecule imaging of SH2 membrane recruitment. Far-Western and MS analyses identified both well-established and previously undocumented EGF-dependent tyrosine phosphorylation and binding events, as well as dynamic changes in binding patterns over time. In comparing SH2 binding site phosphorylation with SH2 domain membrane recruitment in living cells, we found in vivo binding to be much slower. Delayed SH2 domain recruitment correlated with clustering of SH2 domain binding sites on the membrane, consistent with membrane retention via SH2 rebinding.

  3. Lightning Arrestor Connectors Production Readiness

    Energy Technology Data Exchange (ETDEWEB)

    Marten, Steve; Linder, Kim; Emmons, Jim; Gomez, Antonio; Hasam, Dawud; Maurer, Michelle

    2008-10-20

    The Lightning Arrestor Connector (LAC), part “M”, presented opportunities to improve the processes used to fabricate LACs. The A## LACs were the first production LACs produced at the KCP, after the product was transferred from Pinnellas. The new LAC relied on the lessons learned from the A## LACs; however, additional improvements were needed to meet the required budget, yield, and schedule requirements. Improvement projects completed since 2001 include Hermetic Connector Sealing Improvement, Contact Assembly molding Improvement, development of a second vendor for LAC shells, general process improvement, tooling improvement, reduction of the LAC production cycle time, and documention of the LAC granule fabrication process. This report summarizes the accomplishments achieved in improving the LAC Production Readiness.

  4. Loop connectors in dentogenic diastema

    Directory of Open Access Journals (Sweden)

    Sanjna Nayar

    2015-01-01

    Full Text Available Patients with a missing tooth along with diastema have limited treatment options to restore the edentulous space. The use of a conventional fixed partial denture (FPD to replace the missing tooth may result in too wide anterior teeth leading to poor esthetics. Loss of anterior teeth with existing diastema may result in excess space available for pontic. This condition presents great esthetic challenge for prosthodontist. If implant supported prosthesis is not possible because of inadequate bone support, FPD along with loop connector may be a treatment option to maintain the diastema and provide optimal esthetic restoration. Here, we report a clinical case where FPD along with loop connector was used to achieve esthetic rehabilitation in maxillary anterior region in which midline diastema has been maintained.

  5. High current capacity electrical connector

    International Nuclear Information System (INIS)

    Bettis, E.S.; Watts, H.L.

    1976-01-01

    An electrical connector is provided for coupling high current capacity electrical conductors such as copper busses or the like. The connector is arranged in a ''sandwiched'' configuration in which a conductor plate contacts the busses along major surfaces clamped between two stainless steel backing plates. The conductor plate is provided with contact buttons in a spaced array such that the caps of the buttons extend above the conductor plate surface to contact the busses. When clamping bolts provided through openings in the sandwiched arrangement are tightened, Belleville springs provided under the rim of each button cap are compressed and resiliently force the caps into contact with the busses' contacting surfaces to maintain a predetermined electrical contact area provided by the button cap tops. The contact area does not change with changing thermal or mechanical stresses applied to the coupled conductors

  6. Phorbol ester and hydrogen peroxide synergistically induce the interaction of diacylglycerol kinase gamma with the Src homology 2 and C1 domains of beta2-chimaerin.

    Science.gov (United States)

    Yasuda, Satoshi; Kai, Masahiro; Imai, Shin-ichi; Kanoh, Hideo; Sakane, Fumio

    2008-01-01

    DGKgamma (diacylglycerol kinase gamma) was reported to interact with beta2-chimaerin, a GAP (GTPase-activating protein) for Rac, in response to epidermal growth factor. Here we found that PMA and H2O2 also induced the interaction of DGKgamma with beta2-chimaerin. It is noteworthy that simultaneous addition of PMA and H2O2 synergistically enhanced the interaction. In this case, PMA was replaceable by DAG (diacylglycerol). The beta2-chimaerin translocation from the cytoplasm to the plasma membrane caused by PMA plus H2O2 was further enhanced by the expression of DGKgamma. Moreover, DGKgamma apparently enhanced the beta2-chimaerin GAP activity upon cell stimulation with PMA. PMA was found to be mainly required for a conversion of beta2-chimaerin into an active form. On the other hand, H2O2 was suggested to induce a release of Zn2+ from the C1 domain of beta2-chimaerin. By stepwise deletion analysis, we demonstrated that the SH2 (Src homology 2) and C1 domains of beta2-chimaerin interacted with the N-terminal half of catalytic region of DGKgamma. Unexpectedly, the SH2 domain of beta2-chimaerin contributes to the interaction independently of phosphotyrosine. Taken together, these results suggest that the functional link between DGKgamma and beta2-chimaerin has a broad significance in response to a wide range of cell stimuli. Our work offers a novel mechanism of protein-protein interaction, that is, the phosphotyrosine-independent interaction of the SH2 domain acting in co-operation with the C1 domain.

  7. Heteronuclear multidimensional NMR and homology modelling studies of the C-terminal nucleotide-binding domain of the human mitochondrial ABC transporter ABCB6

    Energy Technology Data Exchange (ETDEWEB)

    Kurashima-Ito, Kaori [RIKEN, Cellular and Molecular Biology Laboratory (Japan); Ikeya, Teppei [National Institute of Advanced Industrial Science and Technology (AIST), (Japan); Senbongi, Hiroshi [Mitochondrial Diseases Group, MRC Dunn Human NutritionUnit (United Kingdom); Tochio, Hidehito [International Graduate School of Arts and Sciences, Supramolecular Biology, Yokohama City University, Molecular Biophysics Laboratory (Japan); Mikawa, Tsutomu [RIKEN, Cellular and Molecular Biology Laboratory (Japan); Shibata, Takehiko [RIKEN, Shibata Distinguished Senior Scientist Laboratory (Japan); Ito, Yutaka [RIKEN, Cellular and Molecular Biology Laboratory (Japan)], E-mail: ito-yutaka@center.tmu.ac.jp

    2006-05-15

    Human ATP-binding cassette, sub-family B, member 6 (ABCB6) is a mitochondrial ABC transporter, and presumably contributes to iron homeostasis. Aimed at understanding the structural basis for the conformational changes accompanying the substrate-transportation cycle, we have studied the C-terminal nucleotide-binding domain of ABCB6 (ABCB6-C) in both the nucleotide-free and ADP-bound states by heteronuclear multidimensional NMR and homology modelling. A non-linear sampling scheme was utilised for indirectly acquired {sup 13}C and {sup 15}N dimensions of all 3D triple-resonance NMR experiments, in order to overcome the instability and the low solubility of ABCB6-C. The backbone resonances for approximately 25% of non-proline residues, which are mostly distributed around the functionally important loops and in the Helical domain, were not observed for nucleotide-free form of ABCB6-C. From the pH, temperature and magnetic field strength dependencies of the resonance intensities, we concluded that this incompleteness in the assignments is mainly due to the exchange between multiple conformations at an intermediate rate on the NMR timescale. These localised conformational dynamics remained in ADP-bound ABCB6-C except for the loops responsible for adenine base and {alpha}/{beta}-phosphate binding. These results revealed that the localised dynamic cooperativity, which was recently proposed for a prokaryotic ABC MJ1267, also exists in a higher eukaryotic ABC, and is presumably shared by all members of the ABC family. Since the Helical domain is the putative interface to the transmembrane domain, this cooperativity may explain the coupled functions between domains in the substrate-transportation cycle.

  8. Purification, crystallization, small-angle X-ray scattering and preliminary X-ray diffraction analysis of the SH2 domain of the Csk-homologous kinase.

    Science.gov (United States)

    Gunn, Natalie J; Gorman, Michael A; Dobson, Renwick C J; Parker, Michael W; Mulhern, Terrence D

    2011-03-01

    The C-terminal Src kinase (Csk) and Csk-homologous kinase (CHK) are endogenous inhibitors of the proto-oncogenic Src family of protein tyrosine kinases (SFKs). Phosphotyrosyl peptide binding to their Src-homology 2 (SH2) domains activates Csk and CHK, enhancing their ability to suppress SFK signalling; however, the detailed mechanistic basis of this activation event is unclear. The CHK SH2 was expressed in Escherichia coli and the purified protein was characterized as monomeric by synchrotron small-angle X-ray scattering in-line with size-exclusion chromatography. The CHK SH2 crystallized in 0.2 M sodium bromide, 0.1 M bis-Tris propane pH 6.5 and 20% polyethylene glycol 3350 and the best crystals diffracted to ∼1.6 Å resolution. The crystals belonged to space group P2, with unit-cell parameters a=25.8, b=34.6, c=63.2 Å, β=99.4°.

  9. The Three-Dimensional Solution Structure of the Src Homology Domain-2 of the Growth Factor Receptor-Bound Protein-2

    International Nuclear Information System (INIS)

    Senior, Mary M.; Frederick, Anne F.; Black, Stuart; Murgolo, Nicholas J.; Perkins, Louise M.; Wilson, Oswald; Snow, Mark E.; Wang Yusen

    1998-01-01

    A set of high-resolution three-dimensional solution structures of the Src homology region-2 (SH2) domain of the growth factor receptor-bound protein-2 was determined using heteronuclear NMR spectroscopy. The NMR data used in this study were collected on a stable monomeric protein solution that was free of protein aggregates and proteolysis. The solution structure was determined based upon a total of 1439 constraints, which included 1326 nuclear Overhauser effect distance constraints, 70 hydrogen bond constraints, and 43 dihedral angle constraints. Distance geometry-simulated annealing calculations followed by energy minimization yielded a family of 18 structures that converged to a root-mean-square deviation of 1.09 A for all backbone atoms and 0.40 A for the backbone atoms of the central β-sheet. The core structure of the SH2 domain contains an antiparallel β-sheet flanked by two parallel α-helices displaying an overall architecture that is similar to other known SH2 domain structures. This family of NMR structures is compared to the X-ray structure and to another family of NMR solution structures determined under different solution conditions

  10. Contribution of the first K-homology domain of poly(C)-binding protein 1 to its affinity and specificity for C-rich oligonucleotides.

    Science.gov (United States)

    Yoga, Yano M K; Traore, Daouda A K; Sidiqi, Mahjooba; Szeto, Chris; Pendini, Nicole R; Barker, Andrew; Leedman, Peter J; Wilce, Jacqueline A; Wilce, Matthew C J

    2012-06-01

    Poly-C-binding proteins are triple KH (hnRNP K homology) domain proteins with specificity for single stranded C-rich RNA and DNA. They play diverse roles in the regulation of protein expression at both transcriptional and translational levels. Here, we analyse the contributions of individual αCP1 KH domains to binding C-rich oligonucleotides using biophysical and structural methods. Using surface plasmon resonance (SPR), we demonstrate that KH1 makes the most stable interactions with both RNA and DNA, KH3 binds with intermediate affinity and KH2 only interacts detectibly with DNA. The crystal structure of KH1 bound to a 5'-CCCTCCCT-3' DNA sequence shows a 2:1 protein:DNA stoichiometry and demonstrates a molecular arrangement of KH domains bound to immediately adjacent oligonucleotide target sites. SPR experiments, with a series of poly-C-sequences reveals that cytosine is preferred at all four positions in the oligonucleotide binding cleft and that a C-tetrad binds KH1 with 10 times higher affinity than a C-triplet. The basis for this high affinity interaction is finally detailed with the structure determination of a KH1.W.C54S mutant bound to 5'-ACCCCA-3' DNA sequence. Together, these data establish the lead role of KH1 in oligonucleotide binding by αCP1 and reveal the molecular basis of its specificity for a C-rich tetrad.

  11. A role for the malignant brain tumour (MBT domain protein LIN-61 in DNA double-strand break repair by homologous recombination.

    Directory of Open Access Journals (Sweden)

    Nicholas M Johnson

    Full Text Available Malignant brain tumour (MBT domain proteins are transcriptional repressors that function within Polycomb complexes. Some MBT genes are tumour suppressors, but how they prevent tumourigenesis is unknown. The Caenorhabditis elegans MBT protein LIN-61 is a member of the synMuvB chromatin-remodelling proteins that control vulval development. Here we report a new role for LIN-61: it protects the genome by promoting homologous recombination (HR for the repair of DNA double-strand breaks (DSBs. lin-61 mutants manifest numerous problems associated with defective HR in germ and somatic cells but remain proficient in meiotic recombination. They are hypersensitive to ionizing radiation and interstrand crosslinks but not UV light. Using a novel reporter system that monitors repair of a defined DSB in C. elegans somatic cells, we show that LIN-61 contributes to HR. The involvement of this MBT protein in HR raises the possibility that MBT-deficient tumours may also have defective DSB repair.

  12. A Ferredoxin- and F420H2-Dependent, Electron-Bifurcating, Heterodisulfide Reductase with Homologs in the Domains Bacteria and Archaea

    Directory of Open Access Journals (Sweden)

    Zhen Yan

    2017-02-01

    Full Text Available Heterodisulfide reductases (Hdr of the HdrABC class are ancient enzymes and a component of the anaerobic core belonging to the prokaryotic common ancestor. The ancient origin is consistent with the widespread occurrence of genes encoding putative HdrABC homologs in metabolically diverse prokaryotes predicting diverse physiological functions; however, only one HdrABC has been characterized and that was from a narrow metabolic group of obligate CO2-reducing methanogenic anaerobes (methanogens from the domain Archaea. Here we report the biochemical characterization of an HdrABC homolog (HdrA2B2C2 from the acetate-utilizing methanogen Methanosarcina acetivorans with unusual properties structurally and functionally distinct from the only other HdrABC characterized. Homologs of the HdrA2B2C2 archetype are present in phylogenetically and metabolically diverse species from the domains Bacteria and Archaea. The expression of the individual HdrA2, HdrB2, and HdrB2C2 enzymes in Escherichia coli, and reconstitution of an active HdrA2B2C2 complex, revealed an intersubunit electron transport pathway dependent on ferredoxin or coenzyme F420 (F420H2 as an electron donor. Remarkably, HdrA2B2C2 couples the previously unknown endergonic oxidation of F420H2 and reduction of ferredoxin with the exergonic oxidation of F420H2 and reduction of the heterodisulfide of coenzyme M and coenzyme B (CoMS-SCoB. The unique electron bifurcation predicts a role for HdrA2B2C2 in Fe(III-dependent anaerobic methane oxidation (ANME by M. acetivorans and uncultured species from ANME environments. HdrA2B2C2, ubiquitous in acetotrophic methanogens, was shown to participate in electron transfer during acetotrophic growth of M. acetivorans and proposed to be essential for growth in the environment when acetate is limiting.

  13. The S-layer homology domain-containing protein SlhA from Paenibacillus alvei CCM 2051(T) is important for swarming and biofilm formation.

    Science.gov (United States)

    Janesch, Bettina; Koerdt, Andrea; Messner, Paul; Schäffer, Christina

    2013-01-01

    Swarming and biofilm formation have been studied for a variety of bacteria. While this is well investigated for Gram-negative bacteria, less is known about Gram-positive bacteria, including Paenibacillus alvei, a secondary invader of diseased honeybee colonies infected with Melissococcus pluton, the causative agent of European foulbrood (EFB). Paenibacillus alvei CCM 2051(T) is a Gram-positive bacterium which was recently shown to employ S-layer homology (SLH) domains as cell wall targeting modules to display proteins on its cell surface. This study deals with the newly identified 1335-amino acid protein SlhA from P. alvei which carries at the C‑terminus three consecutive SLH-motifs containing the predicted binding sequences SRGE, VRQD, and LRGD instead of the common TRAE motif. Based on the proof of cell surface location of SlhA by fluorescence microscopy using a SlhA-GFP chimera, the binding mechanism was investigated in an in vitro assay. To unravel a putative function of the SlhA protein, a knockout mutant was constructed. Experimental data indicated that one SLH domain is sufficient for anchoring of SlhA to the cell surface, and the SLH domains of SlhA recognize both the peptidoglycan and the secondary cell wall polymer in vitro. This is in agreement with previous data from the S-layer protein SpaA, pinpointing a wider utilization of that mechanism for cell surface display of proteins in P. alvei. Compared to the wild-type bacterium ΔslhA revealed changed colony morphology, loss of swarming motility and impaired biofilm formation. The phenotype was similar to that of the flagella knockout Δhag, possibly due to reduced EPS production influencing the functionality of the flagella of ΔslhA. This study demonstrates the involvement of the SLH domain-containing protein SlhA in swarming and biofilm formation of P. alvei CCM 2051(T).

  14. The S-layer homology domain-containing protein SlhA from Paenibacillus alvei CCM 2051(T is important for swarming and biofilm formation.

    Directory of Open Access Journals (Sweden)

    Bettina Janesch

    Full Text Available Swarming and biofilm formation have been studied for a variety of bacteria. While this is well investigated for Gram-negative bacteria, less is known about Gram-positive bacteria, including Paenibacillus alvei, a secondary invader of diseased honeybee colonies infected with Melissococcus pluton, the causative agent of European foulbrood (EFB.Paenibacillus alvei CCM 2051(T is a Gram-positive bacterium which was recently shown to employ S-layer homology (SLH domains as cell wall targeting modules to display proteins on its cell surface. This study deals with the newly identified 1335-amino acid protein SlhA from P. alvei which carries at the C‑terminus three consecutive SLH-motifs containing the predicted binding sequences SRGE, VRQD, and LRGD instead of the common TRAE motif. Based on the proof of cell surface location of SlhA by fluorescence microscopy using a SlhA-GFP chimera, the binding mechanism was investigated in an in vitro assay. To unravel a putative function of the SlhA protein, a knockout mutant was constructed. Experimental data indicated that one SLH domain is sufficient for anchoring of SlhA to the cell surface, and the SLH domains of SlhA recognize both the peptidoglycan and the secondary cell wall polymer in vitro. This is in agreement with previous data from the S-layer protein SpaA, pinpointing a wider utilization of that mechanism for cell surface display of proteins in P. alvei. Compared to the wild-type bacterium ΔslhA revealed changed colony morphology, loss of swarming motility and impaired biofilm formation. The phenotype was similar to that of the flagella knockout Δhag, possibly due to reduced EPS production influencing the functionality of the flagella of ΔslhA.This study demonstrates the involvement of the SLH domain-containing protein SlhA in swarming and biofilm formation of P. alvei CCM 2051(T.

  15. Inline Electrical Connector Mate/Demate Pliers

    Science.gov (United States)

    Yutko, Brian; Dininny, Michael; Moscoso, Gerand; Dokos, Adam

    2010-01-01

    Military and aerospace industries use Mil-Spec type electrical connections on bulkhead panels that require inline access for mate and demate operations. These connectors are usually in tight proximity to other connectors, or recessed within panels. The pliers described here have been designed to work in such tight spaces, and consist of a mirrored set of parallel handles, two cross links, two return springs, and replaceable polyurethane-coated end effectors. The polyurethane eliminates metal-to-metal contact and provides a high-friction surface between the jaw and the connector. Operationally, the user would slide the pliers over the connector shell until the molded polyurethane lip makes contact with the connector shell edge. Then, by squeezing the handles, the end effector jaws grip the connector shell, allowing the connector to be easily disconnected by rotating the pliers. Mating the connector occurs by reversing the prescribed procedure, except the connector shell is placed into the jaws by hand. The molded lip within the jaw allows the user to apply additional force for difficult-to-mate connectors. Handle design has been carefully examined to maximize comfort, limit weight, incorporate tether locations, and improve ergonomics. They have been designed with an off-axis offset for wiring harness clearance, while placing the connector axis of rotation close to the user s axis of wrist rotation. This was done to eliminate fatigue during multiple connector panel servicing. To limit handle opening width, with user ergonomics in mind, the pliers were designed using a parallel jaw mechanism. A cross-link mechanism was used to complete this task, while ensuring smooth operation.

  16. Gene transfer and expression in human neutrophils. The phox homology domain of p47phox translocates to the plasma membrane but not to the membrane of mature phagosomes

    Directory of Open Access Journals (Sweden)

    Brzezinska Agnieszka A

    2006-12-01

    Full Text Available Abstract Background Neutrophils are non-dividing cells with poor survival after isolation. Consequently, exogenous gene expression in neutrophils is challenging. We report here the transfection of genes and expression of active proteins in human primary peripheral neutrophils using nucleofection. Results Exogenous gene expression in human neutrophils was achieved 2 h post-transfection. We show that neutrophils transfected by nucleofection are functional cells, able to respond to soluble and particulate stimuli. They conserved the ability to undergo physiological processes including phagocytosis. Using this technique, we were able to show that the phox homology (PX domain of p47phox localizes to the plasma membrane in human neutrophils. We also show that RhoB, but not the PX domain of p47phox, is translocated to the membrane of mature phagosomes. Conclusion We demonstrated that cDNA transfer and expression of exogenous protein in human neutrophils is compatible with cell viability and is no longer a limitation for the study of protein function in human neutrophils.

  17. Activation of phosphatidylinositol-3 kinase by nerve growth factor involves indirect coupling of the trk proto-oncogene with src homology 2 domains.

    Science.gov (United States)

    Ohmichi, M; Decker, S J; Saltiel, A R

    1992-10-01

    Growth factor receptor tyrosine kinases can form stable associations with intracellular proteins that contain src homology (SH) 2 domains, including the p85 regulatory subunit of phosphatidylinositol (PI)-3 kinase. The activation of this enzyme by growth factors is evaluated in PC12 pheochromocytoma cells and NIH 3T3 fibroblasts expressing the pp140c-trk nerve growth factor (NGF) receptor (3T3-c-trk). NGF causes the rapid stimulation of PI-3 kinase activity detected in anti-phosphotyrosine, but not in anti-trk, immunoprecipitates. This effect coincides with the tyrosine phosphorylation of two proteins, with molecular masses of of 100 kd and 110 kd, that coimmunoprecipitate with p85. Similar phosphorylation patterns are induced when an immobilized fusion protein containing the amino-terminal SH2 domain of p85 is used to precipitate tyrosine-phosphorylated proteins. Thus, although NGF produces the rapid activation of PI-3 kinase through a mechanism that involves tyrosine phosphorylation, there is no evidence for tyrosine phosphorylation of p85, or for its ligand-dependent association with the NGF receptor. Perhaps another phosphoprotein may link the NGF receptor to this enzyme.

  18. Absence of SUN-domain protein Slp1 blocks karyogamy and switches meiotic recombination and synapsis from homologs to sister chromatids

    Science.gov (United States)

    Vasnier, Christelle; de Muyt, Arnaud; Zhang, Liangran; Tessé, Sophie; Kleckner, Nancy E.; Zickler, Denise; Espagne, Eric

    2014-01-01

    Karyogamy, the process of nuclear fusion is required for two haploid gamete nuclei to form a zygote. Also, in haplobiontic organisms, karyogamy is required to produce the diploid nucleus/cell that then enters meiosis. We identify sun like protein 1 (Slp1), member of the mid–Sad1p, UNC-84–domain ubiquitous family, as essential for karyogamy in the filamentous fungus Sordaria macrospora, thus uncovering a new function for this protein family. Slp1 is required at the last step, nuclear fusion, not for earlier events including nuclear movements, recognition, and juxtaposition. Correspondingly, like other family members, Slp1 localizes to the endoplasmic reticulum and also to its extensions comprising the nuclear envelope. Remarkably, despite the absence of nuclear fusion in the slp1 null mutant, meiosis proceeds efficiently in the two haploid “twin” nuclei, by the same program and timing as in diploid nuclei with a single dramatic exception: the normal prophase program of recombination and synapsis between homologous chromosomes, including loading of recombination and synaptonemal complex proteins, occurs instead between sister chromatids. Moreover, the numbers of recombination-initiating double-strand breaks (DSBs) and ensuing recombinational interactions, including foci of the essential crossover factor Homo sapiens enhancer of invasion 10 (Hei10), occur at half the diploid level in each haploid nucleus, implying per-chromosome specification of DSB formation. Further, the distribution of Hei10 foci shows interference like in diploid meiosis. Centromere and spindle dynamics, however, still occur in the diploid mode during the two meiotic divisions. These observations imply that the prophase program senses absence of karyogamy and/or absence of a homolog partner and adjusts the interchromosomal interaction program accordingly. PMID:25210014

  19. Interactive roles of Ras, insulin receptor substrate-1, and proteins with Src homology-2 domains in insulin signaling in Xenopus oocytes.

    Science.gov (United States)

    Chuang, L M; Hausdorff, S F; Myers, M G; White, M F; Birnbaum, M J; Kahn, C R

    1994-11-04

    Insulin receptor substrate-1 (IRS-1) serves as the major immediate substrate of insulin/insulin-like growth factor (IGF)-1 receptors and following tyrosine phosphorylation binds to specific Src homology-2 (SH2) domain-containing proteins including the p85 subunit of phosphatidylinositol (PI) 3-kinase and GRB2, a molecule believed to link IRS-1 to the Ras pathway. To investigate how these SH2-containing signaling molecules interact to regulate insulin/IGF-1 action, IRS-1, glutathione S-transferase (GST)-SH2 domain fusion proteins and Ras proteins were microinjected into Xenopus oocytes. We found that pleiotropic insulin actions are mediated by IRS-1 through two independent, but convergent, pathways involving PI 3-kinase and GRB2. Thus, microinjection of GST-fusion proteins of either p85 or GRB2 inhibited IRS-1-dependent activation of mitogen-activated protein (MAP) and S6 kinases and oocyte maturation, although only the GST-SH2 of p85 reduced insulin-stimulated PI 3-kinase activation. Co-injection of a dominant negative Ras (S17N) with IRS-1 inhibited insulin-stimulated MAP and S6 kinase activation. Micro-injection of activated [Arg12,Thr59]Ras increased basal MAP and S6 kinase activities and sensitized the oocytes to insulin-stimulated maturation without altering insulin-stimulated PI 3-kinase. The Ras-enhanced oocyte maturation response, but not the elevated basal level of MAP and S6 kinase, was partially blocked by the SH2-p85, but not SH2-GRB2. These data strongly suggest that IRS-1 can mediate many of insulin's actions on cellular enzyme activation and cell cycle progression requires binding and activation of multiple different SH2-domain proteins.

  20. C-terminal β9-strand of the cyclic nucleotide-binding homology domain stabilizes activated states of Kv11.1 channels.

    Directory of Open Access Journals (Sweden)

    Chai Ann Ng

    Full Text Available Kv11.1 potassium channels are important for regulation of the normal rhythm of the heartbeat. Reduced activity of Kv11.1 channels causes long QT syndrome type 2, a disorder that increases the risk of cardiac arrhythmias and sudden cardiac arrest. Kv11.1 channels are members of the KCNH subfamily of voltage-gated K(+ channels. However, they also share many similarities with the cyclic nucleotide gated ion channel family, including having a cyclic nucleotide-binding homology (cNBH domain. Kv11.1 channels, however, are not directly regulated by cyclic nucleotides. Recently, crystal structures of the cNBH domain from mEAG and zELK channels, both members of the KCNH family of voltage-gated potassium channels, revealed that a C-terminal β9-strand in the cNBH domain occupied the putative cyclic nucleotide-binding site thereby precluding binding of cyclic nucleotides. Here we show that mutations to residues in the β9-strand affect the stability of the open state relative to the closed state of Kv11.1 channels. We also show that disrupting the structure of the β9-strand reduces the stability of the inactivated state relative to the open state. Clinical mutations located in this β9-strand result in reduced trafficking efficiency, which suggests that binding of the C-terminal β9-strand to the putative cyclic nucleotide-binding pocket is also important for assembly and trafficking of Kv11.1 channels.

  1. Crystal Structures and Thermodynamic Analysis Reveal Distinct Mechanisms of CD28 Phosphopeptide Binding to the Src Homology 2 (SH2) Domains of Three Adaptor Proteins*

    Science.gov (United States)

    Inaba, Satomi; Numoto, Nobutaka; Ogawa, Shuhei; Morii, Hisayuki; Ikura, Teikichi; Abe, Ryo; Ito, Nobutoshi; Oda, Masayuki

    2017-01-01

    Full activation of T cells and differentiation into effector T cells are essential for many immune responses and require co-stimulatory signaling via the CD28 receptor. Extracellular ligand binding to CD28 recruits protein-tyrosine kinases to its cytoplasmic tail, which contains a YMNM motif. Following phosphorylation of the tyrosine, the proteins growth factor receptor-bound protein 2 (Grb2), Grb2-related adaptor downstream of Shc (Gads), and p85 subunit of phosphoinositide 3-kinase may bind to pYMNM (where pY is phosphotyrosine) via their Src homology 2 (SH2) domains, leading to downstream signaling to distinct immune pathways. These three adaptor proteins bind to the same site on CD28 with variable affinity, and all are important for CD28-mediated co-stimulatory function. However, the mechanism of how these proteins recognize and compete for CD28 is unclear. To visualize their interactions with CD28, we have determined the crystal structures of Gads SH2 and two p85 SH2 domains in complex with a CD28-derived phosphopeptide. The high resolution structures obtained revealed that, whereas the CD28 phosphopeptide bound to Gads SH2 is in a bent conformation similar to that when bound to Grb2 SH2, it adopts a more extended conformation when bound to the N- and C-terminal SH2 domains of p85. These differences observed in the peptide-protein interactions correlated well with the affinity and other thermodynamic parameters for each interaction determined by isothermal titration calorimetry. The detailed insight into these interactions reported here may inform the development of compounds that specifically inhibit the association of CD28 with these adaptor proteins to suppress excessive T cell responses, such as in allergies and autoimmune diseases. PMID:27927989

  2. Crystal Structures and Thermodynamic Analysis Reveal Distinct Mechanisms of CD28 Phosphopeptide Binding to the Src Homology 2 (SH2) Domains of Three Adaptor Proteins.

    Science.gov (United States)

    Inaba, Satomi; Numoto, Nobutaka; Ogawa, Shuhei; Morii, Hisayuki; Ikura, Teikichi; Abe, Ryo; Ito, Nobutoshi; Oda, Masayuki

    2017-01-20

    Full activation of T cells and differentiation into effector T cells are essential for many immune responses and require co-stimulatory signaling via the CD28 receptor. Extracellular ligand binding to CD28 recruits protein-tyrosine kinases to its cytoplasmic tail, which contains a YMNM motif. Following phosphorylation of the tyrosine, the proteins growth factor receptor-bound protein 2 (Grb2), Grb2-related adaptor downstream of Shc (Gads), and p85 subunit of phosphoinositide 3-kinase may bind to pYMNM (where pY is phosphotyrosine) via their Src homology 2 (SH2) domains, leading to downstream signaling to distinct immune pathways. These three adaptor proteins bind to the same site on CD28 with variable affinity, and all are important for CD28-mediated co-stimulatory function. However, the mechanism of how these proteins recognize and compete for CD28 is unclear. To visualize their interactions with CD28, we have determined the crystal structures of Gads SH2 and two p85 SH2 domains in complex with a CD28-derived phosphopeptide. The high resolution structures obtained revealed that, whereas the CD28 phosphopeptide bound to Gads SH2 is in a bent conformation similar to that when bound to Grb2 SH2, it adopts a more extended conformation when bound to the N- and C-terminal SH2 domains of p85. These differences observed in the peptide-protein interactions correlated well with the affinity and other thermodynamic parameters for each interaction determined by isothermal titration calorimetry. The detailed insight into these interactions reported here may inform the development of compounds that specifically inhibit the association of CD28 with these adaptor proteins to suppress excessive T cell responses, such as in allergies and autoimmune diseases. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  3. Functional Analysis of the Tomato Immune Receptor Ve1 through Domain Swaps with Its Non-Functional Homolog Ve2

    Science.gov (United States)

    Rovenich, Hanna; Song, Yin; Liebrand, Thomas W. H.; Masini, Laura; van den Berg, Grardy C. M.; Joosten, Matthieu H. A. J.; Thomma, Bart P. H. J.

    2014-01-01

    Resistance in tomato against race 1 strains of the fungal vascular wilt pathogens Verticillium dahliae and V. albo-atrum is mediated by the Ve locus. This locus comprises two closely linked inversely oriented genes, Ve1 and Ve2, which encode cell surface receptors of the extracellular leucine-rich repeat receptor-like protein (eLRR-RLP) type. While Ve1 mediates Verticillium resistance through monitoring the presence of the recently identified V. dahliae Ave1 effector, no functionality for Ve2 has been demonstrated in tomato. Ve1 and Ve2 contain 37 eLRRs and share 84% amino acid identity, facilitating investigation of Ve protein functionality through domain swapping. In this study it is shown that Ve chimeras in which the first thirty eLRRs of Ve1 were replaced by those of Ve2 remain able to induce HR and activate Verticillium resistance, and that deletion of these thirty eLRRs from Ve1 resulted in loss of functionality. Also the region between eLRR30 and eLRR35 is required for Ve1-mediated resistance, and cannot be replaced by the region between eLRR30 and eLRR35 of Ve2. We furthermore show that the cytoplasmic tail of Ve1 is required for functionality, as truncation of this tail results in loss of functionality. Moreover, the C-terminus of Ve2 fails to activate immune signaling as chimeras containing the C-terminus of Ve2 do not provide Verticillium resistance. Furthermore, Ve1 was found to interact through its C-terminus with the eLRR-containing receptor-like kinase (eLRR-RLK) interactor SOBIR1 that was recently identified as an interactor of eLRR-RLP (immune) receptors. Intriguingly, also Ve2 was found to interact with SOBIR1. PMID:24505431

  4. Different Principles of ADP-Ribose-Mediated Activation and Opposite Roles of the NUDT9 Homology Domain in the TRPM2 Orthologs of Man and Sea Anemone

    Directory of Open Access Journals (Sweden)

    Frank Kühn

    2017-10-01

    Full Text Available A decisive element in the human cation channel TRPM2 is a region in its cytosolic C-terminus named NUDT9H because of its homology to the NUDT9 enzyme, a pyrophosphatase degrading ADP-ribose (ADPR. In hTRPM2, however, the NUDT9H domain has lost its enzymatic activity but serves as a binding domain for ADPR. As consequence of binding, gating of the channel is initiated. Since ADPR is produced after oxidative DNA damage, hTRPM2 mediates Ca2+ influx in response to oxidative stress which may lead to cell death. In the genome of the sea anemone Nematostella vectensis (nv, a preferred model organism for the evolution of key bilaterian features, a TRPM2 ortholog has been identified that contains a NUDT9H domain as well. Heterologous expression of nvTRPM2 in HEK-293 cells reveals a cation channel with many close similarities to the human counterpart. Most notably, nvTRPM2 is activated by ADPR, and Ca2+ is a co-agonist. However, the intramolecular mechanisms of ADPR gating as well as the role of NUDT9H are strikingly different in the two species. Whereas already subtle changes of NUDT9H abolish ADPR gating in hTRPM2, the region can be completely removed from nvTRPM2 without loss of responses to ADPR. An alternative ADPR binding site seems to be present but has not yet been characterized. The ADP-ribose pyrophosphatase (ADPRase function of nvNUDT9H has been preserved but can be abolished by numerous genetic manipulations. All these manipulations create channels that are sensitive to hydrogen peroxide which fails to induce channel activity in wild-type nvTRPM2. Therefore, the function of NUDT9H in nvTRPM2 is the degradation of ADPR, thereby reducing agonist concentration in the presence of oxidative stress. Thus, the two TRPM2 orthologs have evolved divergently but nevertheless gained analogous functional properties, i.e., gating by ADPR with Ca2+ as co-factor. Opposite roles are played by the respective NUDT9H domains, either binding of ADPR and mediating

  5. A Ferredoxin- and F420H2-Dependent, Electron-Bifurcating, Heterodisulfide Reductase with Homologs in the Domains Bacteria and Archaea.

    Science.gov (United States)

    Yan, Zhen; Wang, Mingyu; Ferry, James G

    2017-02-07

    Heterodisulfide reductases (Hdr) of the HdrABC class are ancient enzymes and a component of the anaerobic core belonging to the prokaryotic common ancestor. The ancient origin is consistent with the widespread occurrence of genes encoding putative HdrABC homologs in metabolically diverse prokaryotes predicting diverse physiological functions; however, only one HdrABC has been characterized and that was from a narrow metabolic group of obligate CO 2 -reducing methanogenic anaerobes (methanogens) from the domain Archaea Here we report the biochemical characterization of an HdrABC homolog (HdrA2B2C2) from the acetate-utilizing methanogen Methanosarcina acetivorans with unusual properties structurally and functionally distinct from the only other HdrABC characterized. Homologs of the HdrA2B2C2 archetype are present in phylogenetically and metabolically diverse species from the domains Bacteria and Archaea The expression of the individual HdrA2, HdrB2, and HdrB2C2 enzymes in Escherichia coli, and reconstitution of an active HdrA2B2C2 complex, revealed an intersubunit electron transport pathway dependent on ferredoxin or coenzyme F 420 (F 420 H 2 ) as an electron donor. Remarkably, HdrA2B2C2 couples the previously unknown endergonic oxidation of F 420 H 2 and reduction of ferredoxin with the exergonic oxidation of F 420 H 2 and reduction of the heterodisulfide of coenzyme M and coenzyme B (CoMS-SCoB). The unique electron bifurcation predicts a role for HdrA2B2C2 in Fe(III)-dependent anaerobic methane oxidation (ANME) by M. acetivorans and uncultured species from ANME environments. HdrA2B2C2, ubiquitous in acetotrophic methanogens, was shown to participate in electron transfer during acetotrophic growth of M. acetivorans and proposed to be essential for growth in the environment when acetate is limiting. Discovery of the archetype HdrA2B2C2 heterodisulfide reductase with categorically unique properties extends the understanding of this ancient family beyond CO 2

  6. Behavior of Tilted Angle Shear Connectors

    Science.gov (United States)

    Khorramian, Koosha; Maleki, Shervin; Shariati, Mahdi; Ramli Sulong, N. H.

    2015-01-01

    According to recent researches, angle shear connectors are appropriate to transfer longitudinal shear forces across the steel-concrete interface. Angle steel profile has been used in different positions as L-shaped or C-shaped shear connectors. The application of angle shear connectors in tilted positions is of interest in this study. This study investigates the behaviour of tilted-shaped angle shear connectors under monotonic loading using experimental push out tests. Eight push-out specimens are tested to investigate the effects of different angle parameters on the ultimate load capacity of connectors. Two different tilted angles of 112.5 and 135 degrees between the angle leg and steel beam are considered. In addition, angle sizes and lengths are varied. Two different failure modes were observed consisting of concrete crushing-splitting and connector fracture. By increasing the size of connector, the maximum load increased for most cases. In general, the 135 degrees tilted angle shear connectors have a higher strength and stiffness than the 112.5 degrees type. PMID:26642193

  7. Behavior of Tilted Angle Shear Connectors.

    Directory of Open Access Journals (Sweden)

    Koosha Khorramian

    Full Text Available According to recent researches, angle shear connectors are appropriate to transfer longitudinal shear forces across the steel-concrete interface. Angle steel profile has been used in different positions as L-shaped or C-shaped shear connectors. The application of angle shear connectors in tilted positions is of interest in this study. This study investigates the behaviour of tilted-shaped angle shear connectors under monotonic loading using experimental push out tests. Eight push-out specimens are tested to investigate the effects of different angle parameters on the ultimate load capacity of connectors. Two different tilted angles of 112.5 and 135 degrees between the angle leg and steel beam are considered. In addition, angle sizes and lengths are varied. Two different failure modes were observed consisting of concrete crushing-splitting and connector fracture. By increasing the size of connector, the maximum load increased for most cases. In general, the 135 degrees tilted angle shear connectors have a higher strength and stiffness than the 112.5 degrees type.

  8. Solution Structure and Backbone Dynamics of the Pleckstrin Homology Domain of the Human Protein Kinase B (PKB/Akt). Interaction with Inositol Phosphates

    International Nuclear Information System (INIS)

    Auguin, Daniel; Barthe, Philippe; Auge-Senegas, Marie-Therese; Stern, Marc-Henri; Noguchi, Masayuki; Roumestand, Christian

    2004-01-01

    The programmed cell death occurs as part of normal mammalian development. The induction of developmental cell death is a highly regulated process and can be suppressed by a variety of extracellular stimuli. Recently, the ability of trophic factors to promote survival have been attributed, at least in part, to the phosphatidylinositide 3'-OH kinase (PI3K)/Protein Kinase B (PKB, also named Akt) cascade. Several targets of the PI3K/PKB signaling pathway have been identified that may underlie the ability of this regulatory cascade to promote cell survival. PKB possesses a N-terminal Pleckstrin Homology (PH) domain that binds specifically and with high affinity to PtIns(3,4,5)P 3 and PtIns(3,4)P 2 , the PI3K second messengers. PKB is then recruited to the plasma membrane by virtue of its interaction with 3'-OH phosphatidylinositides and activated. Recent evidence indicates that PKB is active in various types of human cancer; constitutive PKB signaling activation is believed to promote proliferation and increased cell survival, thereby contributing to cancer progression. Thus, it has been shown that induction of PKB activity is augmented by the TCL1/MTCP1 oncoproteins through a physical association requiring the PKB PH domain. Here we present the three-dimensional solution structure of the PH domain of the human protein PKB (isoform β). PKBβ-PH is an electrostatically polarized molecule that adopts the same fold and topology as other PH-domains, consisting of a β-sandwich of seven strands capped on one top by an α-helix. The opposite face presents three variable loops that appear poorly defined in the NMR structure. Measurements of 15 N spin relaxation times and heteronuclear 15 N{ 1 H}NOEs showed that this poor definition is due to intrinsic flexibility, involving complex motions on different time scales. Chemical shift mapping studies correctly defined the binding site of Ins(1,3,4,5)P 4 (the head group of PtIns(3,4,5)P 3 ), as was previously proposed from a

  9. Homology-modeled ligand-binding domains of medaka estrogen receptors and androgen receptors: A model system for the study of reproduction

    International Nuclear Information System (INIS)

    Cui Jianzhou; Shen Xueyan; Yan Zuowei; Zhao Haobin; Nagahama, Yoshitaka

    2009-01-01

    Estrogen and androgen and their receptors play critical roles in physiological processes such as sexual differentiation and development. Using the available structural models for the human estrogen receptors alpha and beta and androgen receptor as templates, we designed in silico agonist and antagonist models of medaka estrogen receptor (meER) alpha, beta-1, and beta-2, and androgen receptor (meAR) alpha and beta. Using these models, we studied (1) the structural relationship between the ligand-binding domains (LBDs) of ERs and ARs of human and medaka, and (2) whether medaka ER and AR can be potential models for studying the ligand-binding activities of various agonists and antagonists of these receptors by docking analysis. A high level of conservation was observed between the sequences of the ligand-binding domains of meERα and huERα, meERβ1 and huERβ, meERβ2, and huERβ with 62.8%, 66.4%, and 65.1% identity, respectively. The sequence conservation between meARα and huAR, meARβ, and huAR was found with 70.1% and 61.0% of identity, respectively. Thirty-three selected endocrine disrupting chemicals (EDCs), including both agonists and antagonists, were docked into the LBD of ER and AR, and the corresponding docking score for medaka models and human templates were calculated. In order to confirm the conservation of the overall geometry and the binding pocket, the backbone root mean square deviation (RMSD) for Cα atoms was derived from the structure superposition of all 10 medaka homology models to the six human templates. Our results suggested conformational conservation between the ERs and ARs of medaka and human, Thus, medaka could be highly useful as a model system for studies involving estrogen and androgen interaction with their receptors.

  10. Pleckstrin homology-like domain family A, member 3 (PHLDA3 deficiency improves islets engraftment through the suppression of hypoxic damage.

    Directory of Open Access Journals (Sweden)

    Naoaki Sakata

    Full Text Available Islet transplantation is a useful cell replacement therapy that can restore the glycometabolic function of severe diabetic patients. It is known that many transplanted islets failed to engraft, and thus, new approaches for overcoming graft loss that may improve the outcome of future clinical islet transplantations are necessary. Pleckstrin homology-like domain family A, member 3 (PHLDA3 is a known suppressor of neuroendocrine tumorigenicity, yet deficiency of this gene increases islet proliferation, prevents islet apoptosis, and improves their insulin-releasing function without causing tumors. In this study, we examined the potential use of PHLDA3-deficient islets in transplantation. We observed that: 1 transplanting PHLDA3-deficient islets into diabetic mice significantly improved their glycometabolic condition, 2 the improved engraftment of PHLDA3-deficient islets resulted from increased cell survival during early transplantation, and 3 Akt activity was elevated in PHLDA3-deficient islets, especially under hypoxic conditions. Thus, we determined that PHLDA3-deficient islets are more resistant against stresses induced by islet isolation and transplantation. We conclude that use of islets with suppressed PHLDA3 expression could be a novel and promising treatment for improving engraftment and consequent glycemic control in islet transplantation.

  11. Remote process connectors for the NWCF

    International Nuclear Information System (INIS)

    Jacobs, R.T.; Carter, J.A.; Hohback, A.C.

    1978-01-01

    The remote process connectors developed, used, and tested at the Remote Maintenance Development Facility are described. These connectors, including the 3-bolt kinematic-graphite flange and watertight-electrical connectors, are assembled on master jigs (holding-welding fixture) to form interchangeable pump and valve loop assemblies. These assemblies, with their guide-in platforms make possible a method of performing remote maintenance at the New Waste Calcining Facility that is a departure from methods which until now have been the standard of the industry

  12. Evaluation of remote piping connectors for fusion applications

    International Nuclear Information System (INIS)

    Welland, H.J.

    1985-08-01

    Four types of remotely actuated piping connectors were evaluated for their application to the fusion energy program. The evaluations are part of a study being performed by EG and G Idaho, Inc., for the fusion program at Kernforschungszentrum, Karlsruhe, GmbH. Results of the connector evaluation will be used to develop preliminary concepts for connector improvements and new connector configurations

  13. Waste Feed Delivery Purex Process Connector Design Pressure

    International Nuclear Information System (INIS)

    BRACKENBURY, P.J.

    2000-01-01

    The pressure retaining capability of the PUREX process connector is documented. A context is provided for the connector's current use within existing Projects. Previous testing and structural analyses campaigns are outlined. The deficient condition of the current inventory of connectors and assembly wrenches is highlighted. A brief history of the connector is provided. A bibliography of pertinent references is included

  14. The Nance-Horan syndrome protein encodes a functional WAVE homology domain (WHD) and is important for co-ordinating actin remodelling and maintaining cell morphology.

    Science.gov (United States)

    Brooks, Simon P; Coccia, Margherita; Tang, Hao R; Kanuga, Naheed; Machesky, Laura M; Bailly, Maryse; Cheetham, Michael E; Hardcastle, Alison J

    2010-06-15

    Nance-Horan syndrome (NHS) is an X-linked developmental disorder, characterized by bilateral congenital cataracts, dental anomalies, facial dysmorphism and mental retardation. Null mutations in a novel gene, NHS, cause the syndrome. The NHS gene appears to have multiple isoforms as a result of alternative transcription, but a cellular function for the NHS protein has yet to be defined. We describe NHS as a founder member of a new protein family (NHS, NHSL1 and NHSL2). Here, we demonstrate that NHS is a novel regulator of actin remodelling and cell morphology. NHS localizes to sites of cell-cell contact, the leading edge of lamellipodia and focal adhesions. The N-terminus of isoforms NHS-A and NHS-1A, implicated in the pathogenesis of NHS, have a functional WAVE homology domain that interacts with the Abi protein family, haematopoietic stem/progenitor cell protein 300 (HSPC300), Nap1 and Sra1. NHS knockdown resulted in the disruption of the actin cytoskeleton. We show that NHS controls cell morphology by maintaining the integrity of the circumferential actin ring and controlling lamellipod formation. NHS knockdown led to a striking increase in cell spreading. Conversely, ectopic overexpression of NHS inhibited lamellipod formation. Remodelling of the actin cytoskeleton and localized actin polymerization into branched actin filaments at the plasma membrane are essential for mediating changes in cell shape, migration and cell contact. Our data identify NHS as a new regulator of actin remodelling. We suggest that NHS orchestrates actin regulatory protein function in response to signalling events during development.

  15. The Nance–Horan syndrome protein encodes a functional WAVE homology domain (WHD) and is important for co-ordinating actin remodelling and maintaining cell morphology

    Science.gov (United States)

    Brooks, Simon P.; Coccia, Margherita; Tang, Hao R.; Kanuga, Naheed; Machesky, Laura M.; Bailly, Maryse; Cheetham, Michael E.; Hardcastle, Alison J.

    2010-01-01

    Nance–Horan syndrome (NHS) is an X-linked developmental disorder, characterized by bilateral congenital cataracts, dental anomalies, facial dysmorphism and mental retardation. Null mutations in a novel gene, NHS, cause the syndrome. The NHS gene appears to have multiple isoforms as a result of alternative transcription, but a cellular function for the NHS protein has yet to be defined. We describe NHS as a founder member of a new protein family (NHS, NHSL1 and NHSL2). Here, we demonstrate that NHS is a novel regulator of actin remodelling and cell morphology. NHS localizes to sites of cell–cell contact, the leading edge of lamellipodia and focal adhesions. The N-terminus of isoforms NHS-A and NHS-1A, implicated in the pathogenesis of NHS, have a functional WAVE homology domain that interacts with the Abi protein family, haematopoietic stem/progenitor cell protein 300 (HSPC300), Nap1 and Sra1. NHS knockdown resulted in the disruption of the actin cytoskeleton. We show that NHS controls cell morphology by maintaining the integrity of the circumferential actin ring and controlling lamellipod formation. NHS knockdown led to a striking increase in cell spreading. Conversely, ectopic overexpression of NHS inhibited lamellipod formation. Remodelling of the actin cytoskeleton and localized actin polymerization into branched actin filaments at the plasma membrane are essential for mediating changes in cell shape, migration and cell contact. Our data identify NHS as a new regulator of actin remodelling. We suggest that NHS orchestrates actin regulatory protein function in response to signalling events during development. PMID:20332100

  16. PD-1 immunoreceptor inhibits B cell receptor-mediated signaling by recruiting src homology 2-domain-containing tyrosine phosphatase 2 to phosphotyrosine

    Science.gov (United States)

    Okazaki, Taku; Maeda, Akito; Nishimura, Hiroyuki; Kurosaki, Tomohiro; Honjo, Tasuku

    2001-01-01

    PD-1 is an immunoreceptor that belongs to the immunoglobulin (Ig) superfamily and contains two tyrosine residues in the cytoplasmic region. Studies on PD-1-deficient mice have shown that PD-1 plays critical roles in establishment and/or maintenance of peripheral tolerance, but the mode of action is totally unknown. To study the molecular mechanism for negative regulation of lymphocytes through the PD-1 receptor, we generated chimeric molecules composed of the IgG Fc receptor type IIB (FcγRIIB) extracellular region and the PD-1 cytoplasmic region and expressed them in a B lymphoma cell line, IIA1.6. Coligation of the cytoplasmic region of PD-1 with the B cell receptor (BCR) in IIA1.6 transformants inhibited BCR-mediated growth retardation, Ca2+ mobilization, and tyrosine phosphorylation of effector molecules, including Igβ, Syk, phospholipase C-γ2 (PLCγ2), and ERK1/2, whereas phosphorylation of Lyn and Dok was not affected. Mutagenesis studies indicated that these inhibitory effects do not require the N-terminal tyrosine in the immunoreceptor tyrosine-based inhibitory motif-like sequence, but do require the other tyrosine residue in the C-terminal tail. This tyrosine was phosphorylated and recruited src homology 2-domain-containing tyrosine phosphatase 2 (SHP-2) on coligation of PD-1 with BCR. These results show that PD-1 can inhibit BCR signaling by recruiting SHP-2 to its phosphotyrosine and dephosphorylating key signal transducers of BCR signaling. PMID:11698646

  17. On-line intermittent connector anomaly detection

    Data.gov (United States)

    National Aeronautics and Space Administration — This paper investigates a non-traditional use of differential current sensor and current sensor to detect intermittent disconnection problems in connectors. An...

  18. Inflatable Air Beam Standard Interface Connector

    Data.gov (United States)

    National Aeronautics and Space Administration — The project will develop a system of 3D-printed connectors that can be used as a kit of parts to connect inflatable air beams to form a variety of spacecraft...

  19. Aesthetic rehabilitation with multiple loop connectors

    Directory of Open Access Journals (Sweden)

    Ashish Kalra

    2013-01-01

    Full Text Available Patients with a missing tooth along with diastema have limited treatment options to restore the edentulous space. The use of a conventional fixed partial denture (FPD to replace the missing tooth may result in too wide anterior teeth leading to poor esthetics. The diastema resulting from the missing central incisors can be managed with implant-supported prosthesis or FPD with loop connectors. An old lady reported with chief complaints of missing upper anterior teeth due to trauma. Her past dental history revealed that she was having generalized spacing between her upper anterior teeth. Considering her esthetic requirement of maintaining the diastema between 12, 11, 22, and 21, the treatment option of 06 units porcelain fused to metal FPD from canine to canine with intermittent loop connectors between 21, 22, 11, 12 was planned. Connectors basically link different parts of FPDs. The modified FPD with loop connectors enhanced the natural appearance of the restoration, maintained the diastemas and the proper emergence profile, and preserve the remaining tooth structure of abutment teeth. This clinical report discussed a method for fabrication of a modified FPD with loop connectors to restore the wide span created by missing central incisors.

  20. Phylogenetic analysis of the diacylglycerol kinase family of proteins and identification of multiple highly-specific conserved inserts and deletions within the catalytic domain that are distinctive characteristics of different classes of DGK homologs.

    Directory of Open Access Journals (Sweden)

    Radhey S Gupta

    Full Text Available Diacylglycerol kinase (DGK family of proteins, which phosphorylates diacylglycerol into phosphatidic acid, play important role in controlling diverse cellular processes in eukaryotic organisms. Most vertebrate species contain 10 different DGK isozymes, which are grouped into 5 different classes based on the presence or absence of specific functional domains. However, the relationships among different DGK isozymes or how they have evolved from a common ancestor is unclear. The catalytic domain constitutes the single largest sequence element within the DGK proteins that is commonly and uniquely shared by all family members, but there is limited understanding of the overall function of this domain. In this work, we have used the catalytic domain sequences to construct a phylogenetic tree for the DGK family members from representatives of the main vertebrate classes and have also examined the distributions of various DGK isozymes in eukaryotic phyla. In a tree based on catalytic domain sequences, the DGK homologs belonging to different classes formed strongly supported clusters which were separated by long branches, and the different isozymes within each class also generally formed monophyletic groupings. Further, our analysis of the sequence alignments of catalytic domains has identified >10 novel sequence signatures consisting of conserved signature indels (inserts or deletions, CSIs that are distinctive characteristics of either particular classes of DGK isozymes, or are commonly shared by members of two or more classes of DGK isozymes. The conserved indels in protein sequences are known to play important functional roles in the proteins/organisms where they are found. Thus, our identification of multiple highly specific CSIs that are distinguishing characteristics of different classes of DGK homologs points to the existence of important differences in the catalytic domain function among the DGK isozymes. The identified CSIs in conjunction with

  1. GMI1, a structural-maintenance-of-chromosomes-hinge domain-containing protein, is involved in somatic homologous recombination in Arabidopsis

    Czech Academy of Sciences Publication Activity Database

    Bohmdorfer, G.; Schleiffer, A.; Brunmeir, R.; Ferscha, S.; Nizhynska, V.; Kozák, Jaroslav; Angelis, Karel; Kreil, D. P.; Schweizer, D.

    2011-01-01

    Roč. 67, č. 3 (2011), s. 420-433 ISSN 0960-7412 R&D Projects: GA MŠk 1M0505; GA MŠk(CZ) LC06004 Institutional research plan: CEZ:AV0Z50380511 Keywords : structural maintenance of chromosomes * DNA repair * somatic homologous recombination Subject RIV: EI - Biotechnology ; Bionics Impact factor: 6.160, year: 2011

  2. Functional Independence and Interdependence of the Src Homology Domains of Phospholipase C-γ1 in B-Cell Receptor Signal Transduction

    Science.gov (United States)

    DeBell, Karen E.; Stoica, Bogdan A.; Verí, Maria-Concetta; Di Baldassarre, Angela; Miscia, Sebastiano; Graham, Laurie J.; Rellahan, Barbara L.; Ishiai, Masamichi; Kurosaki, Tomohiro; Bonvini, Ezio

    1999-01-01

    B-cell receptor (BCR)-induced activation of phospholipase C-γ1 (PLCγ1) and PLCγ2 is crucial for B-cell function. While several signaling molecules have been implicated in PLCγ activation, the mechanism coupling PLCγ to the BCR remains undefined. The role of PLCγ1 SH2 and SH3 domains at different steps of BCR-induced PLCγ1 activation was examined by reconstitution in a PLCγ-negative B-cell line. PLCγ1 membrane translocation required a functional SH2 N-terminal [SH2(N)] domain, was decreased by mutation of the SH3 domain, but was unaffected by mutation of the SH2(C) domain. Tyrosine phosphorylation did not require the SH2(C) or SH3 domains but depended exclusively on a functional SH2(N) domain, which mediated the association of PLCγ1 with the adapter protein, BLNK. Forcing PLCγ1 to the membrane via a myristoylation signal did not bypass the SH2(N) domain requirement for phosphorylation, indicating that the phosphorylation mediated by this domain is not due to membrane anchoring alone. Mutation of the SH2(N) or the SH2(C) domain abrogated BCR-stimulated phosphoinositide hydrolysis and signaling events, while mutation of the SH3 domain partially decreased signaling. PLCγ1 SH domains, therefore, have interrelated but distinct roles in BCR-induced PLCγ1 activation. PMID:10523627

  3. Enhanced Prediction of Src Homology 2 (SH2) Domain Binding Potentials Using a Fluorescence Polarization-derived c-Met, c-Kit, ErbB, and Androgen Receptor Interactome*

    Science.gov (United States)

    Leung, Kin K.; Hause, Ronald J.; Barkinge, John L.; Ciaccio, Mark F.; Chuu, Chih-Pin; Jones, Richard B.

    2014-01-01

    Many human diseases are associated with aberrant regulation of phosphoprotein signaling networks. Src homology 2 (SH2) domains represent the major class of protein domains in metazoans that interact with proteins phosphorylated on the amino acid residue tyrosine. Although current SH2 domain prediction algorithms perform well at predicting the sequences of phosphorylated peptides that are likely to result in the highest possible interaction affinity in the context of random peptide library screens, these algorithms do poorly at predicting the interaction potential of SH2 domains with physiologically derived protein sequences. We employed a high throughput interaction assay system to empirically determine the affinity between 93 human SH2 domains and phosphopeptides abstracted from several receptor tyrosine kinases and signaling proteins. The resulting interaction experiments revealed over 1000 novel peptide-protein interactions and provided a glimpse into the common and specific interaction potentials of c-Met, c-Kit, GAB1, and the human androgen receptor. We used these data to build a permutation-based logistic regression classifier that performed considerably better than existing algorithms for predicting the interaction potential of several SH2 domains. PMID:24728074

  4. 'Daisy petal' connectors for the ATLAS detector

    CERN Multimedia

    Laurent Guiraud

    1997-01-01

    These daisy-petal structures are conducting connectors embedded in kapton film. This was an innovative solution to the demands of the ATLAS detector. Straws are pushed through the petals and held in contact using plugs. The flexible kapton film allows as many petals to be built in any configuration, while acting as a printed circuit carrying the high voltage between circles.

  5. Expression, refolding and spectroscopic characterization of fibronectin type III (FnIII)-homology domains derived from human fibronectin leucine rich transmembrane protein (FLRT)-1,-2, and-3

    DEFF Research Database (Denmark)

    Yang, Lila; Falkesgaard, Maria Hansen; Thulstrup, Peter Waaben

    2017-01-01

    various species have been determined, the expression and purification of recombinant FLRT FnIII domains, important steps for further structural and functional characterizations of the proteins, have not yet been described. Here we present a protocol for expressing recombinant FLRT-FnIII domains...... that a strand-strand cystine bridge has significant effect on the stability of the FLRT FnIII fold. We further show by Surface Plasmon Resonance that all three FnIII domains bind to FGFR1, and roughly estimate a Kd for each domain, all Kds being in the µM range....

  6. Annual report 1999. Energy and connectors

    International Nuclear Information System (INIS)

    1999-01-01

    This report presents the industrial activities and the financial results of Framatome in 1999. Framatome's activities are divided into 2 sectors: energy and connectors, which represents respectively 54% and 46% of the turnover and 40% and 60% of the staff (26000 people). In 1999 the turnover reached 4.2 milliard euros. Framatome and Siemens have decided to merge their nuclear activities in a common company (66% for Framatome, 34% for Siemens). (A.C.)

  7. Identification of a New Interaction Mode between the Src Homology 2 Domain of C-terminal Src Kinase (Csk) and Csk-binding Protein/Phosphoprotein Associated with Glycosphingolipid Microdomains♦

    Science.gov (United States)

    Tanaka, Hiroaki; Akagi, Ken-ichi; Oneyama, Chitose; Tanaka, Masakazu; Sasaki, Yuichi; Kanou, Takashi; Lee, Young-Ho; Yokogawa, Daisuke; Dobenecker, Marc-Werner; Nakagawa, Atsushi; Okada, Masato; Ikegami, Takahisa

    2013-01-01

    Proteins with Src homology 2 (SH2) domains play major roles in tyrosine kinase signaling. Structures of many SH2 domains have been studied, and the regions involved in their interactions with ligands have been elucidated. However, these analyses have been performed using short peptides consisting of phosphotyrosine followed by a few amino acids, which are described as the canonical recognition sites. Here, we report the solution structure of the SH2 domain of C-terminal Src kinase (Csk) in complex with a longer phosphopeptide from the Csk-binding protein (Cbp). This structure, together with biochemical experiments, revealed the existence of a novel binding region in addition to the canonical phosphotyrosine 314-binding site of Cbp. Mutational analysis of this second region in cells showed that both canonical and novel binding sites are required for tumor suppression through the Cbp-Csk interaction. Furthermore, the data indicate an allosteric connection between Cbp binding and Csk activation that arises from residues in the βB/βC loop of the SH2 domain. PMID:23548896

  8. In vitro incorporation of the phage Phi29 connector complex

    International Nuclear Information System (INIS)

    Fu Chiyu; Prevelige, Peter E.

    2009-01-01

    The incorporation of the DNA packaging connector complex during lambdoid phage assembly in vivo is strictly controlled-one and only one of the twelve identical icosahedral vertices is differentiated by the inclusion of a portal or connector dodecamer. Proposed control mechanisms include obligate nucleation from a connector containing complex, addition of the connector as the final step during assembly, and a connector-mediated increase in the growth rate. The inability to recapitulate connector incorporation in vitro has made it difficult to obtain direct biochemical evidence in support of one model over another. Here we report the development an in vitro assembly system for the well characterized dsDNA phage Phi29 which results in the co-assembly of connector with capsid and scaffolding proteins to form procapsid-like particles (PLPs). Immuno-electron microscopy demonstrates the specific incorporation of connector vertex in PLPs. The connector protein increases both the yield and the rate of capsid assembly suggesting that the incorporation of the connector in Phi29 likely promotes nucleation of assembly.

  9. Critical role of the Src homology 2 (SH2) domain of neuronal SH2B1 in the regulation of body weight and glucose homeostasis in mice.

    Science.gov (United States)

    Morris, David L; Cho, Kae Won; Rui, Liangyou

    2010-08-01

    SH2B1 is an SH2 domain-containing adaptor protein that plays a key role in the regulation of energy and glucose metabolism in both rodents and humans. Genetic deletion of SH2B1 in mice results in obesity and type 2 diabetes. Single-nucleotide polymorphisms in the SH2B1 loci and chromosomal deletions of the SH2B1 loci associate with obesity and insulin resistance in humans. In cultured cells, SH2B1 promotes leptin and insulin signaling by binding via its SH2 domain to phosphorylated tyrosines in Janus kinase 2 and the insulin receptor, respectively. Here we generated three lines of mice to analyze the role of the SH2 domain of SH2B1 in the central nervous system. Transgenic mice expressing wild-type, SH2 domain-defective (R555E), or SH2 domain-alone (DeltaN503) forms of SH2B1 specifically in neurons were crossed with SH2B1 knockout mice to generate KO/SH2B1, KO/R555E, or KO/DeltaN503 compound mutant mice. R555E had a replacement of Arg(555) with Glu within the SH2 domain. DeltaN503 contained an intact SH2 domain but lacked amino acids 1-503. Neuron-specific expression of recombinant SH2B1, but not R555E or DeltaN503, corrected hyperphagia, obesity, glucose intolerance, and insulin resistance in SH2B1 null mice. Neuron-specific expression of R555E in wild-type mice promoted obesity and insulin resistance. These results indicate that in addition to the SH2 domain, N-terminal regions of neuronal SH2B1 are also required for the maintenance of normal body weight and glucose metabolism. Additionally, mutations in the SH2 domain of SH2B1 may increase the susceptibility to obesity and type 2 diabetes in a dominant-negative manner.

  10. Exon organization of the mouse entactin gene corresponds to the structural domains of the polypeptide and has regional homology to the low-density lipoprotein receptor gene

    DEFF Research Database (Denmark)

    Durkin, M E; Wewer, U M; Chung, A E

    1995-01-01

    of the mouse entactin gene closely corresponds to the organization of the polypeptide into distinct structural and functional domains. The two amino-terminal globular domains are encoded by three exons each. Single exons encode the two protease-sensitive, O-glycosylated linking regions. The six EGF......Entactin is a widespread basement membrane protein of 150 kDa that binds to type IV collagen and laminin. The complete exon-intron structure of the mouse entactin gene has been determined from lambda genomic DNA clones. The gene spans at least 65 kb and contains 20 exons. The exon organization...

  11. Critical Role of the Src Homology 2 (SH2) Domain of Neuronal SH2B1 in the Regulation of Body Weight and Glucose Homeostasis in Mice

    OpenAIRE

    Morris, David L.; Cho, Kae Won; Rui, Liangyou

    2010-01-01

    SH2B1 is an SH2 domain-containing adaptor protein that plays a key role in the regulation of energy and glucose metabolism in both rodents and humans. Genetic deletion of SH2B1 in mice results in obesity and type 2 diabetes. Single-nucleotide polymorphisms in the SH2B1 loci and chromosomal deletions of the SH2B1 loci associate with obesity and insulin resistance in humans. In cultured cells, SH2B1 promotes leptin and insulin signaling by binding via its SH2 domain to phosphorylated tyrosines ...

  12. Association between receptor protein-tyrosine phosphatase RPTPalpha and the Grb2 adaptor. Dual Src homology (SH) 2/SH3 domain requirement and functional consequences

    DEFF Research Database (Denmark)

    Su, J; Yang, L T; Sap, J

    1996-01-01

    domain in Grb2 (, ). We show here that association of Grb2 with RPTPalpha also involves a critical function for the C-terminal SH3 domain of Grb2. Furthermore, Grb2 SH3 binding peptides interfere with RPTPalpha-Grb2 association in vitro, and the RPTPalpha protein can dissociate the Grb2-Sos complex...... in vivo. These observations constitute a novel mode of Grb2 association and suggest a model in which association with a tyrosine-phosphorylated protein restricts the repertoire of SH3 binding proteins with which Grb2 can simultaneously interact. The function of the Tyr798 tyrosine phosphorylation/Grb2...... binding site in RPTPalpha was studied further by expression of wild type or mutant RPTPalpha proteins in PC12 cells. In these cells, wild type RPTPalpha interferes with acidic fibroblast growth factor-induced neurite outgrowth; this effect requires both the catalytic activity and the Grb2 binding Tyr798...

  13. Semantic integration of gene expression analysis tools and data sources using software connectors

    Science.gov (United States)

    2013-01-01

    Background The study and analysis of gene expression measurements is the primary focus of functional genomics. Once expression data is available, biologists are faced with the task of extracting (new) knowledge associated to the underlying biological phenomenon. Most often, in order to perform this task, biologists execute a number of analysis activities on the available gene expression dataset rather than a single analysis activity. The integration of heteregeneous tools and data sources to create an integrated analysis environment represents a challenging and error-prone task. Semantic integration enables the assignment of unambiguous meanings to data shared among different applications in an integrated environment, allowing the exchange of data in a semantically consistent and meaningful way. This work aims at developing an ontology-based methodology for the semantic integration of gene expression analysis tools and data sources. The proposed methodology relies on software connectors to support not only the access to heterogeneous data sources but also the definition of transformation rules on exchanged data. Results We have studied the different challenges involved in the integration of computer systems and the role software connectors play in this task. We have also studied a number of gene expression technologies, analysis tools and related ontologies in order to devise basic integration scenarios and propose a reference ontology for the gene expression domain. Then, we have defined a number of activities and associated guidelines to prescribe how the development of connectors should be carried out. Finally, we have applied the proposed methodology in the construction of three different integration scenarios involving the use of different tools for the analysis of different types of gene expression data. Conclusions The proposed methodology facilitates the development of connectors capable of semantically integrating different gene expression analysis tools

  14. Characterization of Mycobacterium smegmatis PolD2 and PolD1 as RNA/DNA polymerases homologous to the POL domain of bacterial DNA ligase D.

    Science.gov (United States)

    Zhu, Hui; Bhattarai, Hitesh; Yan, Han-Guang; Shuman, Stewart; Glickman, Michael S

    2012-12-21

    Mycobacteria exploit nonhomologous end-joining (NHEJ) to repair DNA double-strand breaks. The core NHEJ machinery comprises the homodimeric DNA end-binding protein Ku and DNA ligase D (LigD), a modular enzyme composed of a C-terminal ATP-dependent ligase domain (LIG), a central 3'-phosphoesterase domain (PE), and an N-terminal polymerase domain (POL). LigD POL is proficient at adding templated and nontemplated deoxynucleotides and ribonucleotides to DNA ends in vitro and is the catalyst in vivo of unfaithful NHEJ events involving nontemplated single-nucleotide additions to blunt DSB ends. Here, we identify two mycobacterial proteins, PolD1 and PolD2, as stand-alone homologues of the LigD POL domain. Biochemical characterization of PolD1 and PolD2 shows that they resemble LigD POL in their monomeric quaternary structures, their ability to add templated and nontemplated nucleotides to primer-templates and blunt ends, and their preference for rNTPs versus dNTPs. Deletion of polD1, polD2, or both from a Mycobacterium smegmatis strain carrying an inactivating mutation in LigD POL failed to reveal a role for PolD1 or PolD2 in templated nucleotide additions during NHEJ of 5'-overhang DSBs or in clastogen resistance. Whereas our results document the existence and characteristics of new stand-alone members of the LigD POL family of RNA/DNA polymerases, they imply that other polymerases can perform fill-in synthesis during mycobacterial NHEJ.

  15. ITP Hanford Type 40 pin electrical connector failure analysis

    International Nuclear Information System (INIS)

    Imrich, K.J.

    1993-01-01

    Corrosion products observed on the ITP Hanford Type 40 pin electrical connectors would be expected to adversely affect the power and control signals supplied to process equipment in the filter cell by the connectors. Corrosion products were consistent with those found on similar pins in DWPF. The recommendations based on the findings in this investigation are as follows: (1) Replace male and female rhodium plated pins with gold plated pins. (2) Replace the galvanized carbon steel spring on the male connector with a stainless steel spring. (3) Install protective caps over Hanford connectors when jumpers are removed

  16. Effect of NADPH oxidase inhibitor-apocynin on the expression of Src homology-2 domain-containing phosphatase-1 (SHP-1 exposed renal ischemia/reperfusion injury in rats

    Directory of Open Access Journals (Sweden)

    Zhiming Li

    2015-01-01

    Full Text Available This study was designed to evaluate whether NADPH oxidase inhibitor (apocynin preconditioning induces expression of Src homology-2 domain-containing phosphatase-1 (SHP-1 to protect against renal ischemia/reperfusion (I/R injury (RI/RI in rats. Rats were pretreated with 50 mg/kg apocynin, then subjected to 45 min ischemia and 24 h reperfusion. The results indicated that apocynin preconditioning improved the recovery of renal function and nitroso-redox balance, reduced oxidative stress injury and inflammation damage, and upregulated expression of SHP-1 as compared to RI/RI group. Therefore our study demonstrated that apocynin preconditioning provided a protection to the kidney against I/R injury in rats partially through inducing expression of SHP-1.

  17. Expression and crystallographic studies of the D1D2 domains of C4.4A, a homologous protein to the urokinase receptor

    DEFF Research Database (Denmark)

    Chen, Shanli; Lin, Lin; Yuan, Cai

    2017-01-01

    -diffusion method. The crystals diffracted to 2.7 Å resolution and belonged to space group C2221, with unit-cell parameters a = 55.49, b = 119.63, c = 168.54 Å. The statistics indicated good quality of the data, which form a solid basis for the determination of the C4.4A structure.The two amino-terminal LU domains...... of C4.4A were excised by limited proteolysis and were crystallized using the sitting-drop vapour-diffusion method. The crystals diffracted to 2.7 Å resolution, giving good-quality data....

  18. Low resistance, low-inductance power connectors

    Science.gov (United States)

    Coteus, Paul W.; Ferencz, Andrew; Hall, Shawn Anthony; Takken, Todd Edward

    2018-01-16

    An electrical connector includes an anode assembly for conducting an electrical supply current from a source to a destination, the anode assembly includes an anode formed into a first shape from sheet metal or other sheet-like conducting material. A cathode assembly conducts an electrical return current from the destination to the source, the cathode assembly includes a cathode formed into a second shape from sheet metal or other sheet-like conducting material. An insulator prevents electrical conduction between the anode and the cathode. The first and second shapes are such as to provide a conformity of one to the other, with the insulator therebetween having a predetermined relatively thin thickness. A predetermined low-resistance path for the supply current is provided by the anode, a predetermined low-resistance path for the return current is provided by the cathode, and the proximity of the anode to the cathode along these paths provides a predetermined low self-inductance of the connector, where the proximity is afforded by the conformity of the first and second shapes.

  19. Critical element development of standard pipe connector for remote handling

    International Nuclear Information System (INIS)

    Taguchi, Kou; Kakudate, Satoshi; Kanamori, Naokazu; Oka, Kiyoshi; Nakahira, Masataka; Obara, Kenjiro; Tada, Eisuke; Shibanuma, Kiyoshi; Seki, Masahiro

    1994-08-01

    In fusion experimental reactors such as ITER, the in-vessel components such as blanket and divertor are actively cooled and a large number of cooling pipes are located around the core of reactor, where personnel access is prohibited. Mechanical pipe connectors are highly required as standard components for easy and reliable connection/disconnection of cooling pipe by remote handling. For this purpose, a clamping chain type connector has been developed with special mechanisms such as plate springs and guide structures so as to enable concentric and axial movement of clamping chain for easy mounting and dismounting. The basic performance test of a prototypical connector for a 80-A pipe shows sufficient leak tightness and proof pressure capability as well as simple connection/disconnection operation. In addition to the clamp chain type connector, design efforts have been made to develop a quick coupling type connector and a preliminary model of air-actuated quick connector has been fabricated for further investigations. This paper gives the design concept of mechanical pipe connectors such as clamping chain type and quick coupler type, and the basic performance tests results of clamping chain type connector. (author)

  20. A member of a new plant gene family encoding a meprin and TRAF homology (MATH) domain-containing protein is involved in restriction of long distance movement of plant viruses

    Science.gov (United States)

    Cosson, Patrick; Sofer, Luc; Schurdi-Levraud, Valérie

    2010-01-01

    Restriction of long distance movement of several potyviruses in Arabidopsis thaliana is controlled by at least three dominant restricted TEV movement (RTM) genes, named RTM1, RTM2 and RTM3 and acts as a non-conventional resistance. RTM1 encodes a protein belonging to the jacalin family and RTM2 encodes a protein which has similarities to small heat shock proteins. The recent cloning of RTM3 which encodes a protein belonging to an unknown protein family of 29 members that has a meprin and TRAF homology (MATH) domain in its N-terminal region and a coiled-coil (CC) domain at its C-terminal end is an important breakthrough for a better understanding of this resistance process. Not only the third gene involved in this resistance has been identified and has allowed revealing a new gene family in plant but the discovery that the RTM3 protein interacts directly with RTM1 strongly suggests that the RTM proteins form a multimeric complex. However, these data also highlight striking similarities of the RTM resistance with the well known R-gene mediated resistance. PMID:20930558

  1. Arabidopsis KHZ1 and KHZ2, two novel non-tandem CCCH zinc-finger and K-homolog domain proteins, have redundant roles in the regulation of flowering and senescence.

    Science.gov (United States)

    Yan, Zongyun; Jia, Jianheng; Yan, Xiaoyuan; Shi, Huiying; Han, Yuzhen

    2017-12-01

    The two novel CCCH zinc-finger and K-homolog (KH) proteins, KHZ1 and KHZ2, play important roles in regulating flowering and senescence redundantly in Arabidopsis. The CCCH zinc-finger proteins and K-homolog (KH) proteins play important roles in plant development and stress responses. However, the biological functions of many CCCH zinc-finger proteins and KH proteins remain uncharacterized. In Arabidopsis, KHZ1 and KHZ2 are characterized as two novel CCCH zinc-finger and KH domain proteins which belong to subfamily VII in CCCH family. We obtained khz1, khz2 mutants and khz1 khz2 double mutants, as well as overexpression (OE) lines of KHZ1 and KHZ2. Compared with the wild type (WT), the khz2 mutants displayed no defects in growth and development, and the khz1 mutants were slightly late flowering, whereas the khz1 khz2 double mutants showed a pronounced late flowering phenotype. In contrast, artificially overexpressing KHZ1 and KHZ2 led to the early flowering. Consistent with the late flowering phenotype, the expression of flowering repressor gene FLC was up-regulated, while the expression of flowering integrator and floral meristem identity (FMI) genes were down-regulated significantly in khz1 khz2. In addition, we also observed that the OE plants of KHZ1 and KHZ2 showed early leaf senescence significantly, whereas the khz1 khz2 double mutants showed delayed senescence of leaf and the whole plant. Both KHZ1 and KHZ2 were ubiquitously expressed throughout the tissues of Arabidopsis. KHZ1 and KHZ2 were localized to the nucleus, and possessed both transactivation activities and RNA-binding abilities. Taken together, we conclude that KHZ1 and KHZ2 have redundant roles in the regulation of flowering and senescence in Arabidopsis.

  2. A disease-causing mutation illuminates the protein membrane topology of the kidney-expressed prohibitin homology (PHB) domain protein podocin.

    Science.gov (United States)

    Schurek, Eva-Maria; Völker, Linus A; Tax, Judit; Lamkemeyer, Tobias; Rinschen, Markus M; Ungrue, Denise; Kratz, John E; Sirianant, Lalida; Kunzelmann, Karl; Chalfie, Martin; Schermer, Bernhard; Benzing, Thomas; Höhne, Martin

    2014-04-18

    Mutations in the NPHS2 gene are a major cause of steroid-resistant nephrotic syndrome, a severe human kidney disorder. The NPHS2 gene product podocin is a key component of the slit diaphragm cell junction at the kidney filtration barrier and part of a multiprotein-lipid supercomplex. A similar complex with the podocin ortholog MEC-2 is required for touch sensation in Caenorhabditis elegans. Although podocin and MEC-2 are membrane-associated proteins with a predicted hairpin-like structure and amino and carboxyl termini facing the cytoplasm, this membrane topology has not been convincingly confirmed. One particular mutation that causes kidney disease in humans (podocin(P118L)) has also been identified in C. elegans in genetic screens for touch insensitivity (MEC-2(P134S)). Here we show that both mutant proteins, in contrast to the wild-type variants, are N-glycosylated because of the fact that the mutant C termini project extracellularly. Podocin(P118L) and MEC-2(P134S) did not fractionate in detergent-resistant membrane domains. Moreover, mutant podocin failed to activate the ion channel TRPC6, which is part of the multiprotein-lipid supercomplex, indicative of the fact that cholesterol recruitment to the ion channels, an intrinsic function of both proteins, requires C termini facing the cytoplasmic leaflet of the plasma membrane. Taken together, this study demonstrates that the carboxyl terminus of podocin/MEC-2 has to be placed at the inner leaflet of the plasma membrane to mediate cholesterol binding and contribute to ion channel activity, a prerequisite for mechanosensation and the integrity of the kidney filtration barrier.

  3. A Compositional Semantics for Stochastic Reo Connectors

    Directory of Open Access Journals (Sweden)

    Young-Joo Moon

    2010-07-01

    Full Text Available In this paper we present a compositional semantics for the channel-based coordination language Reo which enables the analysis of quality of service (QoS properties of service compositions. For this purpose, we annotate Reo channels with stochastic delay rates and explicitly model data-arrival rates at the boundary of a connector, to capture its interaction with the services that comprise its environment. We propose Stochastic Reo automata as an extension of Reo automata, in order to compositionally derive a QoS-aware semantics for Reo. We further present a translation of Stochastic Reo automata to Continuous-Time Markov Chains (CTMCs. This translation enables us to use third-party CTMC verification tools to do an end-to-end performance analysis of service compositions.

  4. A decking for erecting an insulating connector

    Energy Technology Data Exchange (ETDEWEB)

    Chuprikov, A Ye; Lagutin, V I; Sklyarov, A A; Sukhanov, G V

    1983-01-01

    The decking includes a parachute like dome, made of a material impenetrable to air, an air penetrable hood, attachment elements and a branch pipe for supplying the filler. To improve the sealing of the insulating connector upon contact with the walls and the roof of the drift being isolated and to reduce the labor intensity of operations, it is equipped with a housing made in the form of a cylinder from a material impenetrable to water, an advancible vertical upright and a spring loaded panel. The housing is installed between the parachute like dome and the air penetrable hood. The extendible vertical upright is installed on the side of the air penetrable hood and by means of a movable rack mechanism is kinematically linked with the spring loaded panel, installed with the capability of interacting with the air penetrable hood. The spring loaded plate is made in the form of perforated plates which have a telescopic disengagement in the horizontal plane.

  5. Remote process connectors for the new waste calcining facility

    International Nuclear Information System (INIS)

    Jacobs, R.T.; Carter, J.A.; Hohback, A.C.

    1978-01-01

    The remote process connectors developed, used, and tested at the Remote Maintenance Development Facility are described. These connectors, including the three-bolt kinematic-graphite flange and watertight electrical connectors, are assembled on master jigs (holding-welding fixture) to form interchangeable pump and valve loop assemblies. These assemblies, with their guide-in platforms, make possible a method of performing remote maintenance at the New Waste Calcining Facility which is a departure from methods that until now have been the standard of the industry

  6. Mutations in the FHA-domain of ectopically expressed NBS1 lead to radiosensitization and to no increase in somatic mutation rates via a partial suppression of homologous recombination

    International Nuclear Information System (INIS)

    Ohara, Maki; Funyu, Yumi; Ebara, Shunsuke

    2014-01-01

    Ionizing radiation induces DNA double-strand breaks (DSBs). Mammalian cells repair DSBs through multiple pathways, and the repair pathway that is utilized may affect cellular radiation sensitivity. In this study, we examined effects on cellular radiosensitivity resulting from functional alterations in homologous recombination (HR). HR was inhibited by overexpression of the forkhead-associated (FHA) domain-mutated NBS1 (G27D/R28D: FHA-2D) protein in HeLa cells or in hamster cells carrying a human X-chromosome. Cells expressing FHA-2D presented partially (but significantly) HR-deficient phenotypes, which were assayed by the reduction of gene conversion frequencies measured with a reporter assay, a decrease in radiation-induced Mre11 foci formation, and hypersensitivity to camptothecin treatments. Interestingly, ectopic expression of FHA-2D did not increase the frequency of radiation-induced somatic mutations at the HPRT locus, suggesting that a partial reduction of HR efficiency has only a slight effect on genomic stability. The expression of FHA-2D rendered the exponentially growing cell population slightly (but significantly) more sensitive to ionizing radiation. This radiosensitization effect due to the expression of FHA-2D was enhanced when the cells were irradiated with split doses delivered at 24-h intervals. Furthermore, enhancement of radiation sensitivity by split dose irradiation was not seen in contact-inhibited G0/G1 populations, even though the cells expressed FHA-2D. These results suggest that the FHA domain of NBS1 might be an effective molecular target that can be used to induce radiosensitization using low molecular weight chemicals, and that partial inhibition of HR might improve the effectiveness of cancer radiotherapy. (author)

  7. B cell lymphoma-2 (BCL-2) homology domain 3 (BH3) mimetics demonstrate differential activities dependent upon the functional repertoire of pro- and anti-apoptotic BCL-2 family proteins.

    Science.gov (United States)

    Renault, Thibaud T; Elkholi, Rana; Bharti, Archana; Chipuk, Jerry E

    2014-09-19

    The B cell lymphoma-2 (BCL-2) family is the key mediator of cellular sensitivity to apoptosis during pharmacological interventions for numerous human pathologies, including cancer. There is tremendous interest to understand how the proapoptotic BCL-2 effector members (e.g. BCL-2-associated X protein, BAX) cooperate with the BCL-2 homology domain only (BH3-only) subclass (e.g. BCL-2 interacting mediator of death, BIM; BCL-2 interacting-domain death agonist, BID) to induce mitochondrial outer membrane permeabilization (MOMP) and apoptosis and whether these mechanisms may be pharmacologically exploited to enhance the killing of cancer cells. Indeed, small molecule inhibitors of the anti-apoptotic BCL-2 family members have been designed rationally. However, the success of these "BH3 mimetics" in the clinic has been limited, likely due to an incomplete understanding of how these drugs function in the presence of multiple BCL-2 family members. To increase our mechanistic understanding of how BH3 mimetics cooperate with multiple BCL-2 family members in vitro, we directly compared the activity of several BH3-mimetic compounds (i.e. ABT-263, ABT-737, GX15-070, HA14.1, TW-37) in biochemically defined large unilamellar vesicle model systems that faithfully recapitulate BAX-dependent mitochondrial outer membrane permeabilization. Our investigations revealed that the presence of BAX, BID, and BIM differentially regulated the ability of BH3 mimetics to derepress proapoptotic molecules from anti-apoptotic proteins. Using mitochondria loaded with fluorescent BH3 peptides and cells treated with inducers of cell death, these differences were supported. Together, these data suggest that although the presence of anti-apoptotic BCL-2 proteins primarily dictates cellular sensitivity to BH3 mimetics, additional specificity is conferred by proapoptotic BCL-2 proteins. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

  8. Cell surface expression of channel catfish leukocyte immune-type receptors (IpLITRs) and recruitment of both Src homology 2 domain-containing protein tyrosine phosphatase (SHP)-1 and SHP-2.

    Science.gov (United States)

    Montgomery, Benjamin C S; Mewes, Jacqueline; Davidson, Chelsea; Burshtyn, Deborah N; Stafford, James L

    2009-04-01

    Channel catfish leukocyte immune-type receptors (IpLITRs) are immunoglobulin superfamily (IgSF) members believed to play a role in the control and coordination of cellular immune responses in teleost. Putative stimulatory and inhibitory IpLITRs are co-expressed by different types of catfish immune cells (e.g. NK cells, T cells, B cells, and macrophages) but their signaling potential has not been determined. Following cationic polymer-mediated transfections into human cell lines we examined the surface expression, tyrosine phosphorylation, and phosphatase recruitment potential of two types of putative inhibitory IpLITRs using 'chimeric' expression constructs and an epitope-tagged 'native' IpLITR. We also cloned and expressed the teleost Src homology 2 domain-containing protein tyrosine phosphatases (SHP)-1 and SHP-2 and examined their expression in adult tissues and developing zebrafish embryos. Co-immunoprecipitation experiments support the inhibitory signaling potential of distinct IpLITR-types that bound both SHP-1 and SHP-2 following the phosphorylation of tyrosine residues within their cytoplasmic tail (CYT) regions. Phosphatase recruitment by IpLITRs represents an important first step in understanding their influence on immune cell effector functions and suggests that certain inhibitory signaling pathways are conserved among vertebrates.

  9. Small form factor optical fiber connector evaluation for harsh environments

    Science.gov (United States)

    Ott, Melanie N.; Thomes, W. Joe, Jr.; Chuska, Richard F.; Switzer, Robert; Blair, Diana E.

    2011-09-01

    For the past decade NASA programs have utilized the Diamond AVIM connector for optical fiber assemblies on space flight instrumentation. These connectors have been used in communications, sensing and LIDAR systems where repeatability and high performance are required. Recently Diamond has released a smaller form factor optical fiber connector called the "Mini-AVIM" which although more compact still includes the tight tolerances and the ratcheting feature of the heritage AVIM. NASA Goddard Space Flight Center Photonics Group in the Parts, Packaging and Assembly Technologies Office has been performing evaluations of this connector to determine how it compares to the performance of the AVIM connector and to assess its feasibility for harsh environmental applications. Vibration and thermal testing were performed on the Mini-AVIM with both multi-mode and single-mode optical fiber using insitu optical transmission monitoring. Random vibration testing was performed using typical launch condition profiles for most NASA missions but extended to 35 Grms, which is much higher than most requirements. Thermal testing was performed incrementally up to a range of -55°C to +125°C. The test results include both unjacketed fiber and cabled assembly evaluations. The data presented here indicate that the Mini-AVIM provides a viable option for small form factor applications that require a high performance optical fiber connector.

  10. Pure homology of algebraic varieties

    OpenAIRE

    Weber, Andrzej

    2003-01-01

    We show that for a complete complex algebraic variety the pure component of homology coincides with the image of intersection homology. Therefore pure homology is topologically invariant. To obtain slightly more general results we introduce "image homology" for noncomplete varieties.

  11. Lectures on functor homology

    CERN Document Server

    Touzé, Antoine

    2015-01-01

    This book features a series of lectures that explores three different fields in which functor homology (short for homological algebra in functor categories) has recently played a significant role. For each of these applications, the functor viewpoint provides both essential insights and new methods for tackling difficult mathematical problems. In the lectures by Aurélien Djament, polynomial functors appear as coefficients in the homology of infinite families of classical groups, e.g. general linear groups or symplectic groups, and their stabilization. Djament’s theorem states that this stable homology can be computed using only the homology with trivial coefficients and the manageable functor homology. The series includes an intriguing development of Scorichenko’s unpublished results. The lectures by Wilberd van der Kallen lead to the solution of the general cohomological finite generation problem, extending Hilbert’s fourteenth problem and its solution to the context of cohomology. The focus here is o...

  12. Nuclear transfer alters placental gene expression and associated histone modifications of the placental-specific imprinted gene pleckstrin homology-like domain, family A, member 2 (PHLDA2) in cattle.

    Science.gov (United States)

    Arnold, Daniel R; Gaspar, Roberta C; da Rocha, Carlos V; Sangalli, Juliano R; de Bem, Tiago H C; Corrêa, Carolina A P; Penteado, João C T; Meirelles, Flavio V; Lopes, Flavia L

    2017-03-01

    Abnormal placental development is frequent in nuclear transfer (NT) pregnancies and is likely to be associated with altered epigenetic reprogramming. In the present study, fetal and placental measurements were taken on Day 60 of gestation in cows with pregnancies produced by AI, IVF and NT. Placentas were collected and subjected to histological evaluation, the expression of genes important in trophoblast differentiation and expression of the placental imprinted gene pleckstrin homology-like domain, family A, member 2 (PHLDA2), as well as chromatin immunoprecipitation (ChIP) for histone marks within the promoter of PHLDA2. Fewer binucleated cells were observed in NT cotyledons, followed by IVF and AI cotyledons (P<0.05). Expression of heart and neural crest derivatives expressed 1 (HAND1), placental lactogen (PL), pregnancy-associated glycoprotein 9 (PAG-9) and PHLDA2 was elevated in NT cotyledons compared with AI cotyledons. Expression of PHLDA2 was higher in IVF than AI samples (P<0.05). ChIP revealed an increase in the permissive mark dimethylation of lysine 4 on histone H3 (H3K4me2), surprisingly associated with the silent allele of PHLDA2, and a decrease in the inhibitory mark H3K9me2 in NT samples. Thus, genes critical for placental development were altered in NT placentas, including an imprinted gene. Allele-specific changes in the permissive histone mark in the PHLDA2 promoter indicate misregulation of imprinting in clones. Abnormal trophoblast differentiation could have resulted in lower numbers of binucleated cells following NT. These results suggest that the altered expression of imprinted genes associated with NT are also caused by changes in histone modifications.

  13. Performance of Grouted Splice Sleeve Connector under Tensile Load

    Directory of Open Access Journals (Sweden)

    A. Alias

    2016-05-01

    Full Text Available The grouted splice sleeve connector system takes advantage of the bond-slip resistance of the grout and the mechanical gripping of reinforcement bars to provide resistance to tensile force. In this system, grout acts as a load-transferring medium and bonding material between the bars and sleeve. This study adopted the end-to-end rebars connection method to investigate the effect of development length and sleeve diameter on the bonding performance of the sleeve connector. The end-to-end method refers to the condition where reinforcement bars are inserted into the sleeve from both ends and meet at the centre before grout is filled. Eight specimens of grouted splice sleeve connector were tested under tensile load to determine their performance. The sleeve connector was designed using 5 mm thick circular hollow section (CHS steel pipe and consisted of one external and two internal sleeves. The tensile test results show that connectors with a smaller external and internal sleeve diameter appear to provide better bonding performance. Three types of failure were observed in this research, which are bar fracture (outside the sleeve, bar pullout, and internal sleeve pullout. With reference to these failure types, the development length of 200 mm is the optimum value due to its bar fracture type, which indicates that the tensile capacity of the connector is higher than the reinforcement bar. It is found that the performance of the grouted splice sleeve connector is influenced by the development length of the reinforcement bar and the diameter of the sleeve.

  14. Structural health monitoring of compression connectors for overhead transmission lines

    Science.gov (United States)

    Wang, Hong; Wang, Jy-An John; Swindeman, Joseph P.; Ren, Fei; Chan, John

    2017-04-01

    Two-stage aluminum conductor steel-reinforced (ACSR) compression connectors are extensively used in US overhead transmission lines. The connectors are made by crimping a steel sleeve onto a steel core and an aluminum sleeve over electrical conducting aluminum strands. The connectors are designed to operate at temperatures up to 125°C, but their performance is increasingly degrading because of overloading of lines. Currently, electric utilities conduct routine line inspections using thermal and electrical measurements, but these methods do not provide information about the structural integrity of connectors. In this work, structural health monitoring (SHM) of compression connectors was studied using electromechanical impedance (EMI) analysis. Lead zirconate titanate (PZT)-5A was identified as a smart material for SHM. A flexible high-temperature bonding layer was used to address challenges in PZT integration due to a significant difference in the coefficients of thermal expansion of PZT and the aluminum substrate. The steel joint on the steel core was investigated because it is responsible for the ultimate tensile strength of the connector. Tensile testing was used to induce structural damage to the joint, or steel core pullout, and thermal cycling introduced additional structural perturbations. EMI measurements were conducted between the tests. The root mean square deviation (RMSD) of EMI was identified as a damage index. The use of steel joints has been shown to enable SHM under simulated conditions. The EMI signature is sensitive to variations in structural conditions. RMSD can be correlated to the structural health of a connector and has potential for use in the SHM and structural integrity evaluation.

  15. Homogeneous and single-side-operational connector mechanism for self-reconfigurable, self-assembly and self-healing systems

    Science.gov (United States)

    Shen, Wei-Min (Inventor); Kovac, Robert M. (Inventor)

    2012-01-01

    Designs of single-end-operative reconfigurable genderless connectors that include a base, a plurality of movable jaws that are formed on the base and can engage to the jaws of another connector, and an actuator that is mounted on the base and can engage and move the jaws of the reconfigurable connector to connect the reconfigurable connector with another connector.

  16. Catheter Occlusion in Home Infusion: The Influence of Needleless Connector Design on Central Catheter Occlusion.

    Science.gov (United States)

    Williams, Ann

    Thrombotic catheter occlusion is a common complication associated with central venous catheters (CVCs). A wide variety of needleless connectors that differ greatly in design and function are available for use with CVCs; however, there are a limited number of studies comparing the catheter occlusion rate associated with differently designed needleless connectors. This retrospective observational study compared occlusion rates associated with a split-septum neutral-displacement needleless connector versus those of a solid-surface neutral-reflux needleless connector in patients undergoing home infusion therapy. The neutral-reflux needleless connector was associated with a significant reduction in occlusion rate and thrombolytic use versus the neutral-displacement needleless connector.

  17. Homological stabilizer codes

    Energy Technology Data Exchange (ETDEWEB)

    Anderson, Jonas T., E-mail: jonastyleranderson@gmail.com

    2013-03-15

    In this paper we define homological stabilizer codes on qubits which encompass codes such as Kitaev's toric code and the topological color codes. These codes are defined solely by the graphs they reside on. This feature allows us to use properties of topological graph theory to determine the graphs which are suitable as homological stabilizer codes. We then show that all toric codes are equivalent to homological stabilizer codes on 4-valent graphs. We show that the topological color codes and toric codes correspond to two distinct classes of graphs. We define the notion of label set equivalencies and show that under a small set of constraints the only homological stabilizer codes without local logical operators are equivalent to Kitaev's toric code or to the topological color codes. - Highlights: Black-Right-Pointing-Pointer We show that Kitaev's toric codes are equivalent to homological stabilizer codes on 4-valent graphs. Black-Right-Pointing-Pointer We show that toric codes and color codes correspond to homological stabilizer codes on distinct graphs. Black-Right-Pointing-Pointer We find and classify all 2D homological stabilizer codes. Black-Right-Pointing-Pointer We find optimal codes among the homological stabilizer codes.

  18. Electrical connectors for blanket modules in ITER

    Energy Technology Data Exchange (ETDEWEB)

    Poddubnyi, I., E-mail: poddubnyyii@nikiet.ru [Open Joint-Stock Company “N.A. Dollezhal Research and Development Institute of Power Engineering”, 107140, Malaya Krasnoselskaya Street 2/8, Moscow (Russian Federation); Khomiakov, S.; Kolganov, V. [Open Joint-Stock Company “N.A. Dollezhal Research and Development Institute of Power Engineering”, 107140, Malaya Krasnoselskaya Street 2/8, Moscow (Russian Federation); Sadakov, S.; Calcagno, B.; Chappuis, Ph.; Roccella, R.; Raffray, R. [ITER Organization, Route de Vinon sur Verdon, 13115 St. Paul-Lez-Durance (France); Danilov, I.; Leshukov, A.; Strebkov, Y. [Open Joint-Stock Company “N.A. Dollezhal Research and Development Institute of Power Engineering”, 107140, Malaya Krasnoselskaya Street 2/8, Moscow (Russian Federation); Ulrickson, M. [Sandia National Laboratories MS-1129, PO Box 5800, Albuquerque, NM 87185 (United States)

    2014-10-15

    Highlights: • Analysis of static and cyclic strength for L-shaped and Z-shaped ES has been performed. • Analysis results do show that for L-shaped ES static and cyclic strength criteria are not satisfied. • Static and cyclic strength criteria are met well by ES with Z-shaped elastic elements. • ES with Z-shaped elastic elements has been adopted as a new baseline design for ITER. - Abstract: Blanket electrical connectors (E-straps, ES) are low-impedance electrical bridges crossing gaps between blanket modules (BMs) and vacuum vessel (VV). Similar ES are used between two parts on each BM: the first wall panel (FW) and shield block (SB). The main functions of E-straps are to: (a) conduct halo currents intercepting some rows of BM, (b) provide grounding paths for all BMs, and (c) operate as electrical shunts which protect water cooling pipes (branch pipes) from excessive halo and eddy currents. E-straps should be elastic enough to absorb 3-D imposed displacements of BM relative VV in a scale of ±2 mm and at the same time strong enough to not be damaged by EM loads. Each electrical strap is a package of flexible conductive sheets made of CuCrZr bronze. Halo current up to 137 kA and some components of eddy currents do pass through one E-strap for a few tens or hundreds milliseconds during the plasma vertical displacement events (VDE) and disruptions. These currents deposit Joule heat and cause rather high electromagnetic loads in a strong external magnetic field, reaching 9 T. A gradual failure of ES to conduct Halo and Eddy currents with low enough impedance gradually redistributes these currents into branch pipes and cause excessive EM loads. When branch pipes will be bent so much that will touch surrounding structures, the Joule heating in accidental electrical contact spots will cause local melting and may lead to a water leak. The paper presents and compares two design options of E-straps: with L-shaped and Z-shaped elastic elements. The latter option was

  19. Fibre optic connectors with high-return-loss performance

    Science.gov (United States)

    Knott, Michael P.; Johnson, R.; Cooke, K.; Longhurst, P. C.

    1990-09-01

    This paper describes the development of a single mode fibre optic connector with high return loss performance without the use of index matching. Partial reflection of incident light at a fibre optic connector interface is a recognised problem where the result can be increased noise and waveform distortion. This is particularly important for video transmission in subscriber networks which requires a high signal to noise ratio. A number of methods can be used to improve the return loss. The method described here uses a process which angles the connector endfaces. Measurements show typical return losses of -55dB can be achieved for an end angle of 6 degrees. Insertion loss results are also presented.

  20. Safety grade pressurizer heater power supply connector assembly

    International Nuclear Information System (INIS)

    Burnett, J.M.; Daftari, R.M.; Reyns, R.M.

    1987-01-01

    This patent describes a pressurizer heater power supply connector assembly for attaching a power cable to an electric heater within a pressurizer of a pressurized water nuclear reactor system, the electric heater having pin contacts. The assembly comprises: a pin-socket type connector including a tubular body having a first open end carrying a pin-socket contact member and an insert intermediate a shell and the pin-socket contact member, the contact member having socket means for electrically receiving and contacting the pin contacts, and a second open end; a flexible sealed conduit including a flexible corrugated tube having one end connected to the second open end of the pin-socket type connector, and another end; and a shop splice assembly including a header adapter and a hose clamp interconnected between the header adapter and another end of the flexible corrugated tube

  1. Friction mediated by redox-active supramolecular connector molecules.

    Science.gov (United States)

    Bozna, B L; Blass, J; Albrecht, M; Hausen, F; Wenz, G; Bennewitz, R

    2015-10-06

    We report on a friction study at the nanometer scale using atomic force microscopy under electrochemical control. Friction arises from the interaction between two surfaces functionalized with cyclodextrin molecules. The interaction is mediated by connector molecules with (ferrocenylmethyl)ammonium end groups forming supramolecular complexes with the cyclodextrin molecules. With ferrocene connector molecules in solution, the friction increases by a factor of up to 12 compared to control experiments without connector molecules. The electrochemical oxidation of ferrocene to ferrocenium causes a decrease in friction owing to the lower stability of ferrocenium-cyclodextrin complex. Upon switching between oxidative and reduction potentials, a change in friction by a factor of 1.2-1.8 is observed. Isothermal titration calorimetry reveals fast dissociation and rebinding kinetics and thus an equilibrium regime for the friction experiments.

  2. MPO-type single-mode multi-fiber connector: Low-loss and high-return-loss intermateability of APC-MPO connectors

    Science.gov (United States)

    Satake, Toshiaki; Nagasawa, Shinji; Hughes, Mike; Lutz, Sharon

    2011-01-01

    The electrical communication laboratory of NTT started the research of MT (Mechanically Transferable) connector in early 1980s. The initial goal was to realize a multi-fiber connector which can repeat low loss, stable, reliable and low-cost connections of subscriber optical fiber cable networks for more than 20 years period in the field. We review the multi-fiber alignment design with two guide pins, and following several technical improvements toward the final MT connector used in the commercial telecommunication networks. And then, we review development histories to reach to the low-loss, high-return-loss and reliable APC-MPO (Angled Physical Contact Multi-fiber Push On) connectors introduced in NTT COs and in Verizon's FTTH (Fiber To The Home) networks. In the latter half, we propose the low-loss intermateability design for connectors made by different suppliers in order to enable mass introductions into large scale systems. In addition we also describe an accurate connector loss presumption method for different lots' ferrules based on the MT ferrule dimension data before assembling the connectors. We believe with a wide intermateability of APC-MPO connector will increase its use in the fields. The APC-MPO connector manufactured based on the proposed design had low insertion losses of less than 0.25 dB at the same level of simplex connectors and the higher level of return losses higher than 65 dB.

  3. Design and experimental analysis of a new shear connector for steel and concrete composite structures

    OpenAIRE

    Veríssimo, G. S.; Paes, J. L. R.; Valente, Isabel; Cruz, Paulo J. S.; Fakury, R. H.

    2006-01-01

    This work presents the design of a new shear connector and the corresponding results obtained on push-out tests. This new shear connector consists on a steel rib with indented cut shape that provides resistance to longitudinal shear and prevents transversal separation between the concrete slab and the steel profile (uplift). Adding to this, the connector openings cut makes easier the arrangement of transversal reinforcement bars. The installation of the connectors is simple and requires only ...

  4. Geometric homology revisited

    OpenAIRE

    Ruffino, Fabio Ferrari

    2013-01-01

    Given a cohomology theory, there is a well-known abstract way to define the dual homology theory using the theory of spectra. In [4] the author provides a more geometric construction of the homology theory, using a generalization of the bordism groups. Such a generalization involves in its definition the vector bundle modification, which is a particular case of the Gysin map. In this paper we provide a more natural variant of that construction, which replaces the vector bundle modification wi...

  5. Influence of Cable Vibrations on Connectors Used in Automotive Applications

    Directory of Open Access Journals (Sweden)

    AMEL Bouzera

    2012-10-01

    Full Text Available In order to determine the influence of cable vibrations on the contact resistance of connectors, the cable resonant frequency and the resulting movement of both parts of the connector have been studied. The increase of contact voltage, followed by rapidfluctuations generated by wear particles, has been analysed. A test bench designed to monitor wire vibrations was used while the transferred amplitude was measured by a high sensitivity displacement sensor. The contact interface was made of copper alloy and tin coated. The connector was connected to a resistive power supplytransmitting different currents and voltage values. Two investigations were performed on the contact voltage measured with a fast sampling oscilloscope which enabled histograms and a Fast FourierTransform analysis to be obtained. The appearance of contact fluctuations observed during the fretting generated by cable vibrations, and depending upon the wear effect, is attributed toelectromechanical phenomena. Some slow fluctuations are well correlated to the vibration period while the rapid ones are linked to an electrical conduction perturbation in the granular interface caused by the connector movement.

  6. Endotracheal tube connector defect causing airway obstruction in an ...

    African Journals Online (AJOL)

    detected during routine visual inspection before their use, while some go unnoticed during such inspection and can lead to partial or complete airway obstruction in intubated patients. We report one case of partial airway obstruction resulting from manufacturing defect in the ET connector. A 3-month-old infant girl weighing 5 ...

  7. Electro-optics laboratory evaluation: Deutsch optical waveguide connectors

    Science.gov (United States)

    1980-01-01

    A description of a test program evaluating the performance of an optical waveguide connector system is presented. Both quality and effectiveness of connections made in an optical fiber, performance of the equipment used and applicability of equipment and components to field conditions are reviewed.

  8. Trichloroacetimidates as Alkylating Reagents and Their Application in the Synthesis of Pyrroloindoline Natural Products and Synthesis of Small Molecule Inhibitors of Src Homology 2 Domain-Containing Inositol Phosphatase (SHIP)

    Science.gov (United States)

    Adhikari, Arijit A.

    was applied towards the synthesis of natural products and their analogs. The pyrroloindoline ring system is found in many alkaloids and cyclic peptides which mainly differ in the substitution at the C3a position. To provide rapid access to these natural products a diversity-oriented strategy was established via displacement of C3a-trichloroacetimidate pyrroloindoline. Carbon, oxygen, sulfur and nitrogen nucleophiles were all shown to undergo substitution reactions with these trichloroacetimidates in the presence of a Lewis acid catalyst. In order to demonstrate the utility of this new method it was applied towards the synthesis of arundinine and a formal synthesis of psychotriasine. Current investigations involve the application of this method towards the synthesis of a complex pyrroloindoline natural product kapakahine C and the progress made therein has been discussed. The reactivity of trichloroacetimidates was also investigated for the selective C3-alkylation of 2,3-disubstituted indoles to provide indolenines. Indolenines serve as useful intermediates in the synthesis of many complex alkaloids. Different benzylic and allylic trichloroacetimidates were shown to provide 3,3'-disubstituted indolenines with high yields in the presence of catalytic amounts of Lewis acids. Various substituted indoles were evaluated under these reaction conditions. This methodology was also applied towards the synthesis of the core tetracyclic ring system found in communesin natural products. In addition to the above work, synthesis of small molecule inhibitors of Src Homology 2 Domain-Containing Inositol Phosphatase (SHIP) has also been described. Aberrations in the phosphoinositide 3-kinase (PI3K) cellular signaling pathway can lead to diseased cellular states like cancer. Herein we have reported stereoselective synthesis of two quinoline based small molecule SHIP inhibitors. The lead compounds and their analogs were tested for their activities against SHIP by Malachite green assay

  9. Development Of Remote Hanford Connector Gasket Replacement Tooling For DWPF

    International Nuclear Information System (INIS)

    Krementz, D.; Coughlin, Jeffrey

    2009-01-01

    The Defense Waste Processing Facility (DWPF) requested the Savannah River National Laboratory (SRNL) to develop tooling and equipment to remotely replace gaskets in mechanical Hanford connectors to reduce personnel radiation exposure as compared to the current hands-on method. It is also expected that radiation levels will continually increase with future waste streams. The equipment is operated in the Remote Equipment Decontamination Cell (REDC), which is equipped with compressed air, two master-slave manipulators (MSM's) and an electro-mechanical manipulator (EMM) arm for operation of the remote tools. The REDC does not provide access to electrical power, so the equipment must be manually or pneumatically operated. The MSM's have a load limit at full extension of ten pounds, which limited the weight of the installation tool. In order to remotely replace Hanford connector gaskets several operations must be performed remotely, these include: removal of the spent gasket and retaining ring (retaining ring is also called snap ring), loading the new snap ring and gasket into the installation tool and installation of the new gasket into the Hanford connector. SRNL developed and tested tools that successfully perform all of the necessary tasks. Removal of snap rings from horizontal and vertical connectors is performed by separate air actuated retaining ring removal tools and is manipulated in the cell by the MSM. In order install a new gasket, the snap ring loader is used to load a new snap ring into a groove in the gasket installation tool. A new gasket is placed on the installation tool and retained by custom springs. An MSM lifts the installation tool and presses the mounted gasket against the connector block. Once the installation tool is in position, the gasket and snap ring are installed onto the connector by pneumatic actuation. All of the tools are located on a custom work table with a pneumatic valve station that directs compressed air to the desired tool and

  10. A Dissipative Connector for CLT Buildings: Concept, Design and Testing

    Science.gov (United States)

    Scotta, Roberto; Marchi, Luca; Trutalli, Davide; Pozza, Luca

    2016-01-01

    This paper deals with the conception and characterization of an innovative connection for cross-laminated timber (CLT) panels. The connection is designed to provide an adequate level of dissipative capacity to CLT structures also when realized with large horizontal panels and therefore prone to fragile shear sliding failure. The connector, named X-bracket, has been theorized and designed by means of numerical parametric analyses. Furthermore, its cyclic behavior has been verified with experimental tests and compared to that of traditional connectors. Numerical simulations of cyclic tests of different CLT walls anchored to the foundation with X-brackets were also performed to assess their improved seismic performances. Finally, the analysis of the response of a 6 m × 3 m squat wall demonstrates that the developed connection provides good ductility and dissipation capacities also to shear walls realized with a single CLT panel. PMID:28773265

  11. A Dissipative Connector for CLT Buildings: Concept, Design and Testing.

    Science.gov (United States)

    Scotta, Roberto; Marchi, Luca; Trutalli, Davide; Pozza, Luca

    2016-02-26

    This paper deals with the conception and characterization of an innovative connection for cross-laminated timber (CLT) panels. The connection is designed to provide an adequate level of dissipative capacity to CLT structures also when realized with large horizontal panels and therefore prone to fragile shear sliding failure. The connector, named X-bracket, has been theorized and designed by means of numerical parametric analyses. Furthermore, its cyclic behavior has been verified with experimental tests and compared to that of traditional connectors. Numerical simulations of cyclic tests of different CLT walls anchored to the foundation with X-brackets were also performed to assess their improved seismic performances. Finally, the analysis of the response of a 6 m × 3 m squat wall demonstrates that the developed connection provides good ductility and dissipation capacities also to shear walls realized with a single CLT panel.

  12. The Integrity of ACSR Full Tension Single-Stage Splice Connector at Higher Operation Temperature

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Jy-An John [ORNL; Lara-Curzio, Edgar [ORNL; King Jr, Thomas J [ORNL

    2008-10-01

    Due to increases in power demand and limited investment in new infrastructure, existing overhead power transmission lines often need to operate at temperatures higher than those used for the original design criteria. This has led to the accelerated aging and degradation of splice connectors. It is manifested by the formation of hot-spots that have been revealed by infrared imaging during inspection. The implications of connector aging is two-fold: (1) significant increases in resistivity of the splice connector (i.e., less efficient transmission of electricity) and (2) significant reductions in the connector clamping strength, which could ultimately result in separation of the power transmission line at the joint. Therefore, the splice connector appears to be the weakest link in electric power transmission lines. This report presents a protocol for integrating analytical and experimental approaches to evaluate the integrity of full tension single-stage splice connector assemblies and the associated effective lifetime at high operating temperature.

  13. Domain architecture conservation in orthologs

    Science.gov (United States)

    2011-01-01

    Background As orthologous proteins are expected to retain function more often than other homologs, they are often used for functional annotation transfer between species. However, ortholog identification methods do not take into account changes in domain architecture, which are likely to modify a protein's function. By domain architecture we refer to the sequential arrangement of domains along a protein sequence. To assess the level of domain architecture conservation among orthologs, we carried out a large-scale study of such events between human and 40 other species spanning the entire evolutionary range. We designed a score to measure domain architecture similarity and used it to analyze differences in domain architecture conservation between orthologs and paralogs relative to the conservation of primary sequence. We also statistically characterized the extents of different types of domain swapping events across pairs of orthologs and paralogs. Results The analysis shows that orthologs exhibit greater domain architecture conservation than paralogous homologs, even when differences in average sequence divergence are compensated for, for homologs that have diverged beyond a certain threshold. We interpret this as an indication of a stronger selective pressure on orthologs than paralogs to retain the domain architecture required for the proteins to perform a specific function. In general, orthologs as well as the closest paralogous homologs have very similar domain architectures, even at large evolutionary separation. The most common domain architecture changes observed in both ortholog and paralog pairs involved insertion/deletion of new domains, while domain shuffling and segment duplication/deletion were very infrequent. Conclusions On the whole, our results support the hypothesis that function conservation between orthologs demands higher domain architecture conservation than other types of homologs, relative to primary sequence conservation. This supports the

  14. MWTF jumper connector integral seal block development and leak testing

    International Nuclear Information System (INIS)

    Ruff, E.S.; Jordan, S.R.

    1995-01-01

    In fiscal year 1993, tests of an o-ring/tetraseal retainer designed to replace a gasket-type seal used in PUREX-type process jumper connectors encouraged the design of an improved seal block. This new seal block combines several parts into one unitized component called an integral seal block. This report summarizes development and leak testing of the new integral seal block. The integral seal block uses a standard o-ring nested in a groove to accomplish leak tightness. This seal block eliminates the need to machine acme threads into the lower skirt casting and seal retainers, eliminates tolerance stack-up, reduces parts inventory, and eliminates an unnecessary leak path in the jumper connector assembly. This report also includes test data on various types of o-ring materials subjected to heat and pressure. Materials tested included Viton, Kalrez, and fluorosilicone, with some incidental data on teflon coated silicone o-rings. Test experience clearly demonstrates the need to test each seal material for temperature and pressure in its intended application. Some materials advertised as being open-quotes betterclose quotes at higher temperatures did not perform up to expectations. Inspection of the fluorosilicone and Kalrez seals after thermal testing indicates that they are much more susceptible to heat softening than Viton

  15. Gamma irradiation effects in optical fibres, splitters, and connectors

    Directory of Open Access Journals (Sweden)

    Srećković Milesa Ž.

    2017-01-01

    Full Text Available The paper presents a brief overview of contemporary ELION techniques with stress on their use for material modification and dosimetry. In the attempt to avoid some common misjudges of irradiation effects, special attention is paid to exact definition of irradiation geometry and careful adjustment of dose rates, which enable a proper elaboration of experimental results. In particular, effects of g-rays irradiation on properties of commercial optical fibres, splitters, connectors, and fibre joints are examined, which enables monitoring of irradiation effects in complex configurations made of materials with different radiation hardness (resistance. It has been established that g-rays irradiation of the investigated elements influences, in different ways, the transmission of laser beam signals of various wavelengths, under different modulation regimes. After irradiation, the signal attenuation is noticeably larger, both in optical connectors and optical splitter, than before it, and the effect increases in time. The effects are more pronounced at the 99 % than at the 1 % Y-splitter output at both measured wavelengths, and are more pronounced at 1310 nm than at 1550 nm. [Project of the Serbian Ministry of Education, Science and Technological Development, Grant no. III43009 and Grant no. III45012

  16. Fluid moderator control system fuel assembly seal connector

    International Nuclear Information System (INIS)

    Veronesi, L.; Tower, S.N.; Klassen, W.E.

    1987-01-01

    A nuclear reactor is described comprising fuel assemblies having one or more flow channels therethrough, a core support plate having one or more flow channels therethrough, and seal connectors for sealingly connecting the one or more flow channels in the core support plate with the one or more flow channels in the fuel assemblies. The seal connectors each comprises a first portion and second portion each comprising an elongated member having a flow channel therethrough and being in substantial axial alignment with each other and being separated by a space therebetween, means for sealingly connecting the first portion o one or the one or more flow channels in the fuel assemblies, means for sealingly connecting the second portion to the first portion and for allowing relative motion between the portions, means for limiting the relative motion of the first and second portion in directions toward and away from each other, means for reconnectingly connecting and resealingly sealing the second portion to one of the one or more flow channels in the core support plate. It comprises a slip fit connection whereby the remote end of the second portion fits within whereby the remote end of the second portion fits within an opening in the core support plate which is in flow communication with the one or more flow channels in the core support plate and further comprises a ball and cones seal in series with axially spaced ring seals

  17. Evolution of low-profile and lightweight electrical connectors for soldier-worn applications

    Science.gov (United States)

    Gans, Eric; Lee, Kang; Jannson, Tomasz; Walter, Kevin

    2011-06-01

    In addition to military radios, modern warfighters carry cell phones, GPS devices, computers, and night-vision aids, all of which require electrical cables and connectors for data and power transmission. Currently each electrical device operates via independent cables using conventional cable and connector technology. Conventional cables are stiff and difficult to integrate into a soldier-worn garment. Conventional connectors are tall and heavy, as they were designed to ensure secure connections to bulkhead-type panels, and being tall, represent significant snag-hazards in soldier-worn applications. Physical Optics Corporation has designed a new, lightweight and low-profile electrical connector that is more suitable for body-worn applications and operates much like a standard garment snap. When these connectors are mated, the combined height is <0.3 in. - a significant reduction from the 2.5 in. average height of conventional connectors. Electrical connections can be made with one hand (gloved or bare) and blindly (without looking). Furthermore, POC's connectors are integrated into systems that distribute data or power from a central location on the soldier's vest, reducing the length and weight of the cables necessary to interconnect various mission-critical electronic systems. The result is a lightweight power/data distribution system offering significant advantages over conventional electrical connectors in soldier-worn applications.

  18. Non-rigid connector: The wand to allay the stresses on abutment

    OpenAIRE

    Banerjee, Saurav; Khongshei, Arlingstone; Gupta, Tapas; Banerjee, Ardhendu

    2011-01-01

    The use of rigid connectors in 5-unit fixed dental prosthesis with a pier abutment can result in failure of weaker retainer in the long run as the pier abutment acts as a fulcrum. Non-rigid connector placed on the distal aspect of pier seems to reduce potentially excess stress concentration on the pier abutment.

  19. Comparison of Adaptation between the Major Connectors Fabricated from Intraoral Digital Impressions and Extraoral Digital Impressions.

    Science.gov (United States)

    Gan, Ning; Ruan, Yaye; Sun, Jian; Xiong, Yaoyang; Jiao, Ting

    2018-01-11

    The objective was to compare the adaptation between the major connectors of removable partial dentures derived from intraoral digital impressions and extraoral digital impressions. Twenty-four volunteers were enrolled. Each volunteer received an intraoral digital impression and one extraoral digital impression digitized from conventional gypsum impression. A software was used to create the major connectors on digital impression datasets. After all the virtual major connectors designed from Group intraoral digital impressions (Group I) and Group extraoral digital impressions (Group E) were directly fabricated by 3D printing technique, the adaptation of the final major connectors in volunteers' mouths were measured. The adaptation ranged from 159.87 to 577.99 μm in Group I while from 120.83 to 536.17 μm in Group E. The adaptation of major connectors in Group I were found better at the midline palatine suture while the adaptation of major connectors in Group E were found better at the two sides of the palatal vault. In both groups, the highest accuracy in adaptation was revealed at the anterior margin of the major connectors. It is feasible to manufacture the major connectors by digital impression and 3D printing technique. Both the adaptation of the two kinds of digital impressions were clinical acceptable.

  20. MEMS and EFF technology based micro connector for future miniature devices

    International Nuclear Information System (INIS)

    Bhuiyan, M M I; Alamgir, T; Bhuiyan, M; Kajihara, M

    2013-01-01

    The development of a miniature; size, light and high performance electronic devices; has been accelerated for further development. In commercial stamping method, connector pitch size (radius) is more than 300μm due to its size limitation. Therefore, the stamped contact hertz stress becomes lower and less suitable for fine pitch connector. To overcome this pitch size problem a narrow pitch Board-to-Board (BtoB) interface connectors are in demand for the current commercial design. Therefore, this paper describes a fork type micro connector design with high Hertz-Stress using MEMS and Electro Fine Forming (EFF) fabrication techniques. The connector is designed high aspect ratio and high-density packaging using UV thick resist and electroforming. In this study a newly fabricated micro connector's maximum aspect ratio is 50μm and pitch is 80μm is designed successfully which is most compact fork-type connector in the world. When these connectors are connected, a contact resistance of less than 50mΩ has been attained by using four-point probe technique

  1. Open Source GIS Connectors to NASA GES DISC Satellite Data

    Science.gov (United States)

    Kempler, Steve; Pham, Long; Yang, Wenli

    2014-01-01

    The NASA Goddard Earth Sciences Data and Information Services Center (GES DISC) houses a suite of high spatiotemporal resolution GIS data including satellite-derived and modeled precipitation, air quality, and land surface parameter data. The data are valuable to various GIS research and applications at regional, continental, and global scales. On the other hand, many GIS users, especially those from the ArcGIS community, have difficulties in obtaining, importing, and using our data due to factors such as the variety of data products, the complexity of satellite remote sensing data, and the data encoding formats. We introduce a simple open source ArcGIS data connector that significantly simplifies the access and use of GES DISC data in ArcGIS.

  2. A PHF8 homolog in C. elegans promotes DNA repair via homologous recombination.

    Directory of Open Access Journals (Sweden)

    Changrim Lee

    Full Text Available PHF8 is a JmjC domain-containing histone demethylase, defects in which are associated with X-linked mental retardation. In this study, we examined the roles of two PHF8 homologs, JMJD-1.1 and JMJD-1.2, in the model organism C. elegans in response to DNA damage. A deletion mutation in either of the genes led to hypersensitivity to interstrand DNA crosslinks (ICLs, while only mutation of jmjd-1.1 resulted in hypersensitivity to double-strand DNA breaks (DSBs. In response to ICLs, JMJD-1.1 did not affect the focus formation of FCD-2, a homolog of FANCD2, a key protein in the Fanconi anemia pathway. However, the dynamic behavior of RPA-1 and RAD-51 was affected by the mutation: the accumulations of both proteins at ICLs appeared normal, but their subsequent disappearance was retarded, suggesting that later steps of homologous recombination were defective. Similar changes in the dynamic behavior of RPA-1 and RAD-51 were seen in response to DSBs, supporting a role of JMJD-1.1 in homologous recombination. Such a role was also supported by our finding that the hypersensitivity of jmjd-1.1 worms to ICLs was rescued by knockdown of lig-4, a homolog of Ligase 4 active in nonhomologous end-joining. The hypersensitivity of jmjd-1.1 worms to ICLs was increased by rad-54 knockdown, suggesting that JMJD-1.1 acts in parallel with RAD-54 in modulating chromatin structure. Indeed, the level of histone H3 Lys9 tri-methylation, a marker of heterochromatin, was higher in jmjd-1.1 cells than in wild-type cells. We conclude that the histone demethylase JMJD-1.1 influences homologous recombination either by relaxing heterochromatin structure or by indirectly regulating the expression of multiple genes affecting DNA repair.

  3. Chemical shift homology in proteins

    International Nuclear Information System (INIS)

    Potts, Barbara C.M.; Chazin, Walter J.

    1998-01-01

    The degree of chemical shift similarity for homologous proteins has been determined from a chemical shift database of over 50 proteins representing a variety of families and folds, and spanning a wide range of sequence homologies. After sequence alignment, the similarity of the secondary chemical shifts of C α protons was examined as a function of amino acid sequence identity for 37 pairs of structurally homologous proteins. A correlation between sequence identity and secondary chemical shift rmsd was observed. Important insights are provided by examining the sequence identity of homologous proteins versus percentage of secondary chemical shifts that fall within 0.1 and 0.3 ppm thresholds. These results begin to establish practical guidelines for the extent of chemical shift similarity to expect among structurally homologous proteins

  4. Shear Capacity of C-Shaped and L-Shaped Angle Shear Connectors

    Science.gov (United States)

    Tahmasbi, Farzad; Maleki, Shervin; Shariati, Mahdi; Ramli Sulong, N. H.; Tahir, M. M.

    2016-01-01

    This paper investigates the behaviour of C-shaped and L-shaped angle shear connectors embedded in solid concrete slabs. An effective finite element model is proposed to simulate the push out tests of these shear connectors that encompass nonlinear material behaviour, large displacement and damage plasticity. The finite element models are validated against test results. Parametric studies using this nonlinear model are performed to investigate the variations in concrete strength and connector dimensions. The finite element analyses also confirm the test results that increasing the length of shear connector increases their shear strength proportionately. It is observed that the maximum stress in L-shaped angle connectors takes place in the weld attachment to the beam, whereas in the C-shaped angle connectors, it is in the attached leg. The location of maximum concrete compressive damage is rendered in each case. Finally, a new equation for prediction of the shear capacity of C-shaped angle connectors is proposed. PMID:27478894

  5. Study of light transmission through optical fiber-to-fiber connector assemblies

    International Nuclear Information System (INIS)

    Chung, M.; Gutowski, M.; Adams, M.; Solomon, J.

    1998-01-01

    Optical fiber-to-fiber connectors are now being used widely in particle tracking detectors. We describe the properties of the connectors, their production, and measurements of the light transmission through the gap of the connector assembly. We studied light transmission for various types of connectors illuminated by several different light sources. The light transmission was found to be dependent on the angular distribution of the light rays passing through a connector assembly. Two arrangements were studied, a point source and a diffuse source. A green LED with a diffuser is believed to best reproduce the angular distributions of light in the real detector applications. We also studied the transmission as a function of the index of refraction of the optical couplants. The light transmission depends on the index of refraction of an optical couplant placed in the gap, and improves as it approaches the index of refraction of the fiber core. Light transmissions of 80%∼88% were obtained without any optical couplant in the connector gap and transmissions of 89%∼99% with various optical couplants. A Monte Carlo study using measured light distributions from a fiber end produced a reasonable agreement with the transmission measurements made on a connector assembly

  6. Shear Capacity of C-Shaped and L-Shaped Angle Shear Connectors.

    Directory of Open Access Journals (Sweden)

    Farzad Tahmasbi

    Full Text Available This paper investigates the behaviour of C-shaped and L-shaped angle shear connectors embedded in solid concrete slabs. An effective finite element model is proposed to simulate the push out tests of these shear connectors that encompass nonlinear material behaviour, large displacement and damage plasticity. The finite element models are validated against test results. Parametric studies using this nonlinear model are performed to investigate the variations in concrete strength and connector dimensions. The finite element analyses also confirm the test results that increasing the length of shear connector increases their shear strength proportionately. It is observed that the maximum stress in L-shaped angle connectors takes place in the weld attachment to the beam, whereas in the C-shaped angle connectors, it is in the attached leg. The location of maximum concrete compressive damage is rendered in each case. Finally, a new equation for prediction of the shear capacity of C-shaped angle connectors is proposed.

  7. Study of light transmission through optical fiber-to-fiber connector assemblies

    International Nuclear Information System (INIS)

    Chung, M.; Gutowski, M.; Adams, M.; Solomon, J.

    1998-01-01

    Optical fiber-to-fiber connectors are now being used widely in particle tracking detectors. We describe the properties of the connectors, their production, and measurements of the light transmission through the gap of the connector assembly. We studied light transmission for various types of connectors illuminated by several different light sources. The light transmission was found to be dependent on the angular distribution of the light rays passing through a connector assembly. Two arrangements were studied, a point source and a diffuse source. A green LED with a diffuser is believed to best reproduce the angular distributions of light in the real detector applications. We also studied the transmission as a function of the index of refraction of the optical couplants. The light transmission depends on the index of refraction of an optical couplant placed in the gap, and improves as it approaches the index of refraction of the fiber core. Light transmissions of 80%∼88% were obtained without any optical couplant in the connector gap and transmissions of 89%∼99% with various optical couplants. A Monte Carlo study using measured light distributions from a fiber end produced a reasonable agreement with the transmission measurements made on a connector assembly. copyright 1998 American Institute of Physics

  8. Influence of Connector Width on the Stress Distribution of Posterior Bridges under Loading

    Directory of Open Access Journals (Sweden)

    A. Azary

    2011-06-01

    Full Text Available Objective: In all ceramic fixed partial dentures the connector area is a common fracture location. The survival time of three-unit fixed partial dentures may be improved by altering the connector design in regions of maximum tension. The purpose of this study was to determine the effect of buccolingual increase of the connector width on the stress distribution in posterior fixed partial dentures made of IPS Empress 2. To simulate the anatomical condition, we used three-dimensional finite element analysis to generate.Materials and Methods: Three models of three-unit bridges replacing the first molar were prepared. The buccolingual connector width varied from 3.0 to 5.0 mm. Bridges were vertically loaded with 600 N at one point on the central fossa of the pontic, at 12 points along the cusp-fossa contact (50 N each, or at eight points along the cusp-marginal ridge contact (75 N each. Alternatively, a load of 225 N was applied at a 45º angle from the lingual side.Results: Stress concentrations were observed within or near the connectors. The von Mises stress decreased by increasing connector width, regardless of whether the loading was applied vertically or at an angle.Conclusion: Within the limitations of this study, we conclude that increasing the connector width decreases the failure probability when a vertical or angled load is applied.

  9. Use of monolingual and comparable corpora in the classroom to translate adverbial connectors

    Directory of Open Access Journals (Sweden)

    Beatriz Sánchez Cárdenas

    2016-06-01

    Full Text Available Research in terminology has traditionally focused on nouns. Considerably less attention has been paid to other grammatical categories such as adverbs. However, these words can also be problematic for the novice translator, who tends to use the translation correspondences in bilingual dictionaries without realizing that formal equivalence is not necessarily the same as textual equivalence. However, semantic values, acquired in context, go far beyond dictionary meaning and are related to phenomena such as semantic prosody and preferences of lexical selection that can vary, depending on text type and specialized domain. This research explored the reasons why certain adverbial discourse connectors, apparently easy to translate, are a source of translation problems that cannot be easily resolved with a bilingual dictionary. Moreover, this study analyzed the use of parallel corpora in the translation classroom and how it can increase the quality of text production. For this purpose, we compared student translations before and after receiving training on the use of corpus analysis tools

  10. Analysis of the Shear Behavior of Stubby Y-Type Perfobond Rib Shear Connectors for a Composite Frame Structure.

    Science.gov (United States)

    Kim, Sang-Hyo; Kim, Kun-Soo; Lee, Do-Hoon; Park, Jun-Seung; Han, Oneil

    2017-11-22

    Shear connectors are used in steel beam-concrete slabs of composite frame and bridge structures to transfer shear force according to design loads. The existing Y-type perfobond rib shear connectors are designed for girder slabs of composite bridges. Therefore, the rib and transverse rebars of the conventional Y-type perfobond rib shear connectors are extremely large for the composite frames of building structures. Thus, this paper proposes stubby Y-type perfobond rib shear connectors, redefining the existing connectors, for composite frames of building structures; these were used to perform push-out tests. These shear connectors have relatively small ribs compared to the conventional Y-type perfobond rib shear connectors. To confirm the shear resistance of these stubby shear connectors, we performed an experiment by using transverse rebars D13 and D16. The results indicate that these shear connectors have suitable shear strength and ductility for application in composite frame structures. The shear strengths obtained using D13 and D16 were not significantly different. However, the ductility of the shear connectors with D16 was 45.1% higher than that of the shear connectors with D13.

  11. Mod two homology and cohomology

    CERN Document Server

    Hausmann, Jean-Claude

    2014-01-01

    Cohomology and homology modulo 2 helps the reader grasp more readily the basics of a major tool in algebraic topology. Compared to a more general approach to (co)homology this refreshing approach has many pedagogical advantages: It leads more quickly to the essentials of the subject, An absence of signs and orientation considerations simplifies the theory, Computations and advanced applications can be presented at an earlier stage, Simple geometrical interpretations of (co)chains. Mod 2 (co)homology was developed in the first quarter of the twentieth century as an alternative to integral homology, before both became particular cases of (co)homology with arbitrary coefficients. The first chapters of this book may serve as a basis for a graduate-level introductory course to (co)homology. Simplicial and singular mod 2 (co)homology are introduced, with their products and Steenrod squares, as well as equivariant cohomology. Classical applications include Brouwer's fixed point theorem, Poincaré duality, Borsuk-Ula...

  12. Compositional Homology and Creative Thinking

    Directory of Open Access Journals (Sweden)

    Salvatore Tedesco

    2015-05-01

    Full Text Available The concept of homology is the most solid theoretical basis elaborated by the morphological thinking during its history. The enucleation of some general criteria for the interpretation of homology is today a fundamental tool for life sciences, and for restoring their own opening to the question of qualitative innovation that arose so powerfully in the original Darwinian project. The aim of this paper is to verify the possible uses of the concept of compositional homology in order to provide of an adequate understanding of the dynamics of creative thinking.

  13. Combined effects of fretting and pollutant particles on the contact resistance of the electrical connectors

    Directory of Open Access Journals (Sweden)

    Zhigang Kong

    2017-06-01

    Full Text Available Usually, when electrical connectors operate in vibration environments, fretting will be produced at the contact interfaces. In addition, serious environmental pollution particles will affect contact resistance of the connectors. The fretting will worsen the reliability of connectors with the pollutant particles. The combined effects of fretting and quartz particles on the contact resistance of the gold plating connectors are studied with a fretting test system. The results show that the frequencies have obvious effect on the contact resistance. The higher the frequency, the higher the contact resistance is. The quartz particles cause serious wear of gold plating, which make the nickel and copper layer exposed quickly to increase the contact resistance. Especially in high humidity environments, water supply certain adhesion function and make quartz particles easy to insert or cover the contact surfaces, and even cause opening resistance.

  14. Homology building as a means to define antigenic epitopes on dihydrofolate reductase (DHFR) from Plasmodium falciparum

    DEFF Research Database (Denmark)

    Alifrangis, Michael; Christensen, Inge T; Jørgensen, Flemming S

    2004-01-01

    in the gene coding for Pf-DHFR. Furthermore, we wanted to study the potential use of homology models in general and of Pf-DHFR in particular in predicting antigenic malarial surface epitopes. METHODS: A homology model of Pf-DHFR domain was employed to define an epitope for the development of site...

  15. A conceptual framework for designing micro electrical connectors for hearing aid instruments

    OpenAIRE

    Doagou Rad, Saeed; Islam, Aminul; Fuglsang-Philip, M.

    2016-01-01

    Electrical connectors play vital roles in modern electronic instruments. Hearing aid devices as advanced combinations of micro mechanics and electronics comprise various electrical connectors for different purposes. However, the current trend in the miniaturization along with the sharp technological advancements have urged them to incorporate increased number of electrical contacts. The current paper presents a conceptual framework for designing and manufacturing novel plug and socket systems...

  16. Development of a Skewed Pipe Shear Connector for Precast Concrete Structures.

    Science.gov (United States)

    Kim, Sang-Hyo; Choi, Jae-Gu; Park, Sejun; Lee, Hyunmin; Heo, And Won-Ho

    2017-05-13

    Joint connection methods, such as shear key and loop bar, improve the structural performance of precast concrete structures; consequently, there is usually decreased workability or constructional efficiency. This paper proposes a high-efficiency skewed pipe shear connector. To resist shear and pull-out forces, the proposed connectors are placed diagonally between precast concrete segments and a cast-in-place concrete joint part on a girder. Design variables (such as the pipe diameter, length, and insertion angle) have been examined to investigate the connection performance of the proposed connector. The results of our testing indicate that the skewed pipe shear connectors have 50% higher ductility and a 15% higher ratio of maximum load to yield strength as compared to the corresponding parameters of the loop bar. Finite element analysis was used for validation. The resulting validation indicates that, compared to the loop bar, the skewed pipe shear connector has a higher ultimate shear and pull-out resistance. These results indicate that the skewed pipe shear connector demonstrates more idealized behavior than the loop bar in precast concrete structures.

  17. Modular glovebox connector and associated good practices for control of radioactive and chemically toxic materials

    International Nuclear Information System (INIS)

    Hoover, M.D.; Mewhinney, C.J.; Newton, G.J.

    1999-01-01

    Design and associated good practices are described for a modular glovebox connector to improve control of radioactive and chemically toxic materials. The connector consists of an anodized aluminum circular port with a mating spacer, gaskets, and retaining rings for joining two parallel ends of commercially available or custom-manufactured glovebox enclosures. Use of the connector allows multiple gloveboxes to be quickly assembled or reconfigured in functional units. Connector dimensions can be scaled to meet operational requirements for access between gloveboxes. Options for construction materials are discussed, along with recommendations for installation of the connector in new or retrofitted systems. Associated good practices include application of surface coatings and caulking, use of disposable glovebags, and proper selection and protection of gasket and glove materials. Use of the connector at an inhalation toxicology research facility has reduced the time and expense required to reconfigure equipment for changing operational requirements, the dispersion of contamination during reconfigurations, and the need for decommissioning and disposal of contaminated enclosures

  18. NRC Information No. 89-23: Environmental qualification of Litton-Veam CIR series electrical connectors

    International Nuclear Information System (INIS)

    Rossi, C.E.

    1992-01-01

    Litton-Veam CIR series multi-pin electrical connectors are used in core exit thermocouple (CET) and reactor vessel level monitoring (RVLM) systems supplied to numerous plants by Combustion Engineering, Inc., and are used in other applications in at least three additional plants. A proprietary qualification test report has been used to document environmental qualification of the connectors for loss of coolant accident (LOCA) conditions in the CE-supplied systems. During LOCA testing, the connector face seal gasket was completely degraded and elastomeric inserts interacted with simulated containment spray solution which leaked into the connector. Insulation resistances near 1,000 ohms were measured. CE has performed analyses to show that resultant errors are acceptable in CE-supplied CET and RVLM system thermocouple circuits. However, the moisture ingress and resultant low insulation resistances are not acceptable for heater circuits in the RVLM. For that application, CE developed two remedies; one is a clamp, and the other is a new connector design. CE has advised that one of these remedies has been used for all of the RVLM heater circuits. Unmodified CIR connectors are believed to be still in use in other applications

  19. Behaviour of C-shaped angle shear connectors under monotonic and fully reversed cyclic loading: An experimental study

    International Nuclear Information System (INIS)

    Shariati, Mahdi; Ramli Sulong, N.H.; Suhatril, Meldi; Shariati, Ali; Arabnejad Khanouki, M.M.; Sinaei, Hamid

    2012-01-01

    Highlights: ► C-shaped angle connectors show 8.8–33.1% strength degradation under cyclic loading. ► Connector fracture type of failure was experienced in C-shaped angle shear connectors. ► In push-out samples, more cracking was observed in those slabs with longer angles. ► C-shaped angle connectors show good behaviour in terms of the ultimate shear capacity. ► C-shaped angle connectors did not fulfil the requirements for ductility criteria. -- Abstract: This paper presents an evaluation of the structural behaviour of C-shaped angle shear connectors in composite beams, suitable for transferring shear force in composite structures. The results of the experimental programme, including eight push-out tests, are presented and discussed. The results include resistance, strength degradation, ductility, and failure modes of C-shaped angle shear connectors, under monotonic and fully reversed cyclic loading. The results show that connector fracture type of failure was experienced in C-shaped angle connectors and after the failure, more cracking was observed in those slabs with longer angles. On top of that, by comparing the shear resistance of C-shaped angle shear connectors under monotonic and cyclic loading, these connectors showed 8.8–33.1% strength degradation, under fully reversed cyclic loading. Furthermore, it was concluded that the mentioned shear connector shows a proper behaviour, in terms of the ultimate shear capacity, but it does not satisfy the ductility criteria, imposed by the Eurocode 4, to perform a plastic distribution of the shear force between different connectors along the beam length.

  20. Formin homology 2 domains occur in multiple contexts in angiosperms

    Czech Academy of Sciences Publication Activity Database

    Cvrčková, F.; Novotný, M.; Pícková, Denisa; Žárský, Viktor

    2004-01-01

    Roč. 5, č. 44 (2004), s. 1-18 ISSN 1471-2164 R&D Projects: GA AV ČR KSK5052113 Keywords : Formin * angiosperms * Arabidopsis Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.250, year: 2004

  1. Persistent homology of complex networks

    International Nuclear Information System (INIS)

    Horak, Danijela; Maletić, Slobodan; Rajković, Milan

    2009-01-01

    Long-lived topological features are distinguished from short-lived ones (considered as topological noise) in simplicial complexes constructed from complex networks. A new topological invariant, persistent homology, is determined and presented as a parameterized version of a Betti number. Complex networks with distinct degree distributions exhibit distinct persistent topological features. Persistent topological attributes, shown to be related to the robust quality of networks, also reflect the deficiency in certain connectivity properties of networks. Random networks, networks with exponential connectivity distribution and scale-free networks were considered for homological persistency analysis

  2. The ontology-based answers (OBA) service: a connector for embedded usage of ontologies in applications.

    Science.gov (United States)

    Dönitz, Jürgen; Wingender, Edgar

    2012-01-01

    The semantic web depends on the use of ontologies to let electronic systems interpret contextual information. Optimally, the handling and access of ontologies should be completely transparent to the user. As a means to this end, we have developed a service that attempts to bridge the gap between experts in a certain knowledge domain, ontologists, and application developers. The ontology-based answers (OBA) service introduced here can be embedded into custom applications to grant access to the classes of ontologies and their relations as most important structural features as well as to information encoded in the relations between ontology classes. Thus computational biologists can benefit from ontologies without detailed knowledge about the respective ontology. The content of ontologies is mapped to a graph of connected objects which is compatible to the object-oriented programming style in Java. Semantic functions implement knowledge about the complex semantics of an ontology beyond the class hierarchy and "partOf" relations. By using these OBA functions an application can, for example, provide a semantic search function, or (in the examples outlined) map an anatomical structure to the organs it belongs to. The semantic functions relieve the application developer from the necessity of acquiring in-depth knowledge about the semantics and curation guidelines of the used ontologies by implementing the required knowledge. The architecture of the OBA service encapsulates the logic to process ontologies in order to achieve a separation from the application logic. A public server with the current plugins is available and can be used with the provided connector in a custom application in scenarios analogous to the presented use cases. The server and the client are freely available if a project requires the use of custom plugins or non-public ontologies. The OBA service and further documentation is available at http://www.bioinf.med.uni-goettingen.de/projects/oba.

  3. A sensitive short read homology search tool for paired-end read sequencing data.

    Science.gov (United States)

    Techa-Angkoon, Prapaporn; Sun, Yanni; Lei, Jikai

    2017-10-16

    Homology search is still a significant step in functional analysis for genomic data. Profile Hidden Markov Model-based homology search has been widely used in protein domain analysis in many different species. In particular, with the fast accumulation of transcriptomic data of non-model species and metagenomic data, profile homology search is widely adopted in integrated pipelines for functional analysis. While the state-of-the-art tool HMMER has achieved high sensitivity and accuracy in domain annotation, the sensitivity of HMMER on short reads declines rapidly. The low sensitivity on short read homology search can lead to inaccurate domain composition and abundance computation. Our experimental results showed that half of the reads were missed by HMMER for a RNA-Seq dataset. Thus, there is a need for better methods to improve the homology search performance for short reads. We introduce a profile homology search tool named Short-Pair that is designed for short paired-end reads. By using an approximate Bayesian approach employing distribution of fragment lengths and alignment scores, Short-Pair can retrieve the missing end and determine true domains. In particular, Short-Pair increases the accuracy in aligning short reads that are part of remote homologs. We applied Short-Pair to a RNA-Seq dataset and a metagenomic dataset and quantified its sensitivity and accuracy on homology search. The experimental results show that Short-Pair can achieve better overall performance than the state-of-the-art methodology of profile homology search. Short-Pair is best used for next-generation sequencing (NGS) data that lack reference genomes. It provides a complementary paired-end read homology search tool to HMMER. The source code is freely available at https://sourceforge.net/projects/short-pair/ .

  4. An elastic elements calculation in the construction of electrical connectors based on flexible printed cables

    Directory of Open Access Journals (Sweden)

    Yefimenko A. A.

    2016-05-01

    Full Text Available In this article we consider the method of constructive parameters calculation of the elastic elements, which are used in electrical connectors of flexible printed cables. Electrical connectors characterized by the fact that the contact pair is needed to provide pressure. It is also important to know the optimum ratio between stability of the contact connection and the necessary value of the transition resistance. These ratios are studied sufficiently for discrete electrical connectors, however for connectors of flexible printed cables this theme is not explored enough. The purpose of this work is to develop methods that will allow to carry out calculations for elastic elements, which provide communication, and to determine the size of case elements for electrical connectors. We consider two types of connectors. First are removable electrical connections where it is necessary to find a compromise between the resistance value and the separating (engaging force. Second are permanent connections, where counts only the value of the transition resistance. For the first type of connectors were considered a simple form of the liner, in the shape of a rubber block, as in this case, the pressure should be created only by the compression of the liner and fixing it. It is important to get accurate results of the pressure calculation for removable electrical connections, because in this case we consider especial shape of elastomeric liner, which allows to create the pressure not only by compression of the liner, but by deformation it as a spring. For this task, the engaging force was specified on the basis of already known facts. It was important to set the amount of deformation that defines the shape and size of the liner and the case. We solved the problem of transition from the units of measuring hardness, specified in the technical specifications of rubber, to the value of the Young's modulus used in the calculations of constructive parameters of

  5. Same but not alike: Structure, flexibility and energetics of domains in multi-domain proteins are influenced by the presence of other domains.

    Science.gov (United States)

    Vishwanath, Sneha; de Brevern, Alexandre G; Srinivasan, Narayanaswamy

    2018-02-01

    The majority of the proteins encoded in the genomes of eukaryotes contain more than one domain. Reasons for high prevalence of multi-domain proteins in various organisms have been attributed to higher stability and functional and folding advantages over single-domain proteins. Despite these advantages, many proteins are composed of only one domain while their homologous domains are part of multi-domain proteins. In the study presented here, differences in the properties of protein domains in single-domain and multi-domain systems and their influence on functions are discussed. We studied 20 pairs of identical protein domains, which were crystallized in two forms (a) tethered to other proteins domains and (b) tethered to fewer protein domains than (a) or not tethered to any protein domain. Results suggest that tethering of domains in multi-domain proteins influences the structural, dynamic and energetic properties of the constituent protein domains. 50% of the protein domain pairs show significant structural deviations while 90% of the protein domain pairs show differences in dynamics and 12% of the residues show differences in the energetics. To gain further insights on the influence of tethering on the function of the domains, 4 pairs of homologous protein domains, where one of them is a full-length single-domain protein and the other protein domain is a part of a multi-domain protein, were studied. Analyses showed that identical and structurally equivalent functional residues show differential dynamics in homologous protein domains; though comparable dynamics between in-silico generated chimera protein and multi-domain proteins were observed. From these observations, the differences observed in the functions of homologous proteins could be attributed to the presence of tethered domain. Overall, we conclude that tethered domains in multi-domain proteins not only provide stability or folding advantages but also influence pathways resulting in differences in

  6. Using Three-Dimensional Printing to Fabricate a Tubing Connector for Dilation and Evacuation.

    Science.gov (United States)

    Stitely, Michael L; Paterson, Helen

    2016-02-01

    This is a proof-of-concept study to show that simple instrumentation problems encountered in surgery can be solved by fabricating devices using a three-dimensional printer. The device used in the study is a simple tubing connector fashioned to connect two segments of suction tubing used in a surgical procedure where no commercially available product for this use is available through our usual suppliers in New Zealand. A cylindrical tubing connector was designed using three-dimensional printing design software. The tubing connector was fabricated using the Makerbot Replicator 2X three-dimensional printer. The connector was used in 15 second-trimester dilation and evacuation procedures. Data forms were completed by the primary operating surgeon. Descriptive statistics were used with the expectation that the device would function as intended in all cases. The three-dimensional printed tubing connector functioned as intended in all 15 instances. Commercially available three-dimensional printing technology can be used to overcome simple instrumentation problems encountered during gynecologic surgical procedures.

  7. MIL-L-87177 and CLT:X-10 Lubricants Improve Electrical Connector Fretting Corrosion Behavior

    International Nuclear Information System (INIS)

    AUKLAND, NEIL R.; HANLON, JAMES T.

    1999-01-01

    We have conducted a fretting research project using MIL-L-87177 and CLT: X-10 lubricants on Nano-miniature connectors. When they were fretted without lubricant, individual connectors first exceeded our 0.5 ohm failure criteria from 2,341 to 45,238 fretting cycles. With additional fretting, their contact resistance increased to more than 100,000 ohms. Unmodified MIL-L-87177 lubricant delayed the onset of first failure to between 430,000 and over 20,000,000 fretting cycles. MIL-L-87177 modified by addition of Teflon powder delayed first failure to beyond 5 million fretting cycles. Best results were obtained when Teflon was used and also when both the straight and modified lubricants were poured into and then out of the connector. CLT: X-10 lubricant delayed the onset of first failure to beyond 55 million cycles in one test where a failure was actually observed and to beyond 20 million cycles in another that was terminated without failure. CLT: X-10 recovered an unlubricated connector driven deeply into failure, with six failed pins recovering immediately and four more recovering during an additional 420 thousand fretting cycles. MIL-L-87177 was not able to recover a connector under similar conditions

  8. Effect of shear connectors on local buckling and composite action in steel concrete composite walls

    International Nuclear Information System (INIS)

    Zhang, Kai; Varma, Amit H.; Malushte, Sanjeev R.; Gallocher, Stewart

    2014-01-01

    Steel concrete composite (SC) walls are being used for the third generation nuclear power plants, and also being considered for small modular reactors. SC walls consist of thick concrete walls with exterior steel faceplates serving as reinforcement. These steel faceplates are anchored to the concrete infill using shear connectors, for example, headed steel studs. The steel faceplate thickness (t p ) and yield stress (F y ), and the shear connector spacing (s), stiffness (k s ), and strength (Q n ) determine: (a) the level of composite action between the steel plates and the concrete infill, (b) the development length of steel faceplates, and (c) the local buckling of the steel faceplates. Thus, the shear connectors have a significant influence on the behavior of composite SC walls, and should be designed accordingly. This paper presents the effects of shear connector design on the level of composite action and development length of steel faceplates in SC walls. The maximum steel plate slenderness, i.e., ratio of shear connector spacing-to-plate thickness (s/t p ) ratio to prevent local buckling before yielding is also developed based on the existing experimental database and additional numerical analysis

  9. Effect of shear connectors on local buckling and composite action in steel concrete composite walls

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Kai, E-mail: kai-zh@purdue.edu [School of Civil Engineering, Purdue University, West Lafayette, IN (United States); Varma, Amit H., E-mail: ahvarma@purdue.edu [School of Civil Engineering, Purdue University, West Lafayette, IN (United States); Malushte, Sanjeev R., E-mail: smalusht@bechtel.com [Bechtel Power Corporation, Frederick, MD (United States); Gallocher, Stewart, E-mail: stewart.gallocher@steelbricks.com [Modular Walling Systems Ltd., Glasgow (United Kingdom)

    2014-04-01

    Steel concrete composite (SC) walls are being used for the third generation nuclear power plants, and also being considered for small modular reactors. SC walls consist of thick concrete walls with exterior steel faceplates serving as reinforcement. These steel faceplates are anchored to the concrete infill using shear connectors, for example, headed steel studs. The steel faceplate thickness (t{sub p}) and yield stress (F{sub y}), and the shear connector spacing (s), stiffness (k{sub s}), and strength (Q{sub n}) determine: (a) the level of composite action between the steel plates and the concrete infill, (b) the development length of steel faceplates, and (c) the local buckling of the steel faceplates. Thus, the shear connectors have a significant influence on the behavior of composite SC walls, and should be designed accordingly. This paper presents the effects of shear connector design on the level of composite action and development length of steel faceplates in SC walls. The maximum steel plate slenderness, i.e., ratio of shear connector spacing-to-plate thickness (s/t{sub p}) ratio to prevent local buckling before yielding is also developed based on the existing experimental database and additional numerical analysis.

  10. Homological stability of diffeomorphism groups

    DEFF Research Database (Denmark)

    Berglund, Alexander; Madsen, Ib Henning

    2013-01-01

    In this paper we prove a stability theorem for block diffeomorphisms of 2d -dimensional manifolds that are connected sums of S d ×S d . Combining this with a recent theorem of S. Galatius and O. Randal-Williams and Morlet’s lemma of disjunction, we determine the homology of the classifying space ...

  11. RPA homologs and ssDNA processing during meiotic recombination.

    Science.gov (United States)

    Ribeiro, Jonathan; Abby, Emilie; Livera, Gabriel; Martini, Emmanuelle

    2016-06-01

    Meiotic homologous recombination is a specialized process that involves homologous chromosome pairing and strand exchange to guarantee proper chromosome segregation and genetic diversity. The formation and repair of DNA double-strand breaks (DSBs) during meiotic recombination differs from those during mitotic recombination in that the homologous chromosome rather than the sister chromatid is the preferred repair template. The processing of single-stranded DNA (ssDNA) formed on intermediate recombination structures is central to driving the specific outcomes of DSB repair during meiosis. Replication protein A (RPA) is the main ssDNA-binding protein complex involved in DNA metabolism. However, the existence of RPA orthologs in plants and the recent discovery of meiosis specific with OB domains (MEIOB), a widely conserved meiosis-specific RPA1 paralog, strongly suggest that multiple RPA complexes evolved and specialized to subdivide their roles during DNA metabolism. Here we review ssDNA formation and maturation during mitotic and meiotic recombination underlying the meiotic specific features. We describe and discuss the existence and properties of MEIOB and multiple RPA subunits in plants and highlight how they can provide meiosis-specific fates to ssDNA processing during homologous recombination. Understanding the functions of these RPA homologs and how they interact with the canonical RPA subunits is of major interest in the fields of meiosis and DNA repair.

  12. Multiresolution persistent homology for excessively large biomolecular datasets

    Energy Technology Data Exchange (ETDEWEB)

    Xia, Kelin; Zhao, Zhixiong [Department of Mathematics, Michigan State University, East Lansing, Michigan 48824 (United States); Wei, Guo-Wei, E-mail: wei@math.msu.edu [Department of Mathematics, Michigan State University, East Lansing, Michigan 48824 (United States); Department of Electrical and Computer Engineering, Michigan State University, East Lansing, Michigan 48824 (United States); Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 (United States)

    2015-10-07

    Although persistent homology has emerged as a promising tool for the topological simplification of complex data, it is computationally intractable for large datasets. We introduce multiresolution persistent homology to handle excessively large datasets. We match the resolution with the scale of interest so as to represent large scale datasets with appropriate resolution. We utilize flexibility-rigidity index to access the topological connectivity of the data set and define a rigidity density for the filtration analysis. By appropriately tuning the resolution of the rigidity density, we are able to focus the topological lens on the scale of interest. The proposed multiresolution topological analysis is validated by a hexagonal fractal image which has three distinct scales. We further demonstrate the proposed method for extracting topological fingerprints from DNA molecules. In particular, the topological persistence of a virus capsid with 273 780 atoms is successfully analyzed which would otherwise be inaccessible to the normal point cloud method and unreliable by using coarse-grained multiscale persistent homology. The proposed method has also been successfully applied to the protein domain classification, which is the first time that persistent homology is used for practical protein domain analysis, to our knowledge. The proposed multiresolution topological method has potential applications in arbitrary data sets, such as social networks, biological networks, and graphs.

  13. Domains and domain loss

    DEFF Research Database (Denmark)

    Haberland, Hartmut

    2005-01-01

    politicians and in the media, especially in the discussion whether some languages undergo ‘domain loss’ vis-à-vis powerful international languages like English. An objection that has been raised here is that domains, as originally conceived, are parameters of language choice and not properties of languages...

  14. Domain requirements for the Dock adapter protein in growth- cone signaling

    OpenAIRE

    Rao, Yong; Zipursky, S. Lawrence

    1998-01-01

    Tyrosine phosphorylation has been implicated in growth-cone guidance through genetic, biochemical, and pharmacological studies. Adapter proteins containing src homology 2 (SH2) domains and src homology 3 (SH3) domains provide a means of linking guidance signaling through phosphotyrosine to downstream effectors regulating growth-cone motility. The Drosophila adapter, Dreadlocks (Dock), the homolog of mammalian Nck containing three N-terminal SH3 domains and a single SH2 domain, is highly speci...

  15. Src homology domain 2-containing protein-tyrosine phosphatase-1 (SHP-1) binds and dephosphorylates G(alpha)-interacting, vesicle-associated protein (GIV)/Girdin and attenuates the GIV-phosphatidylinositol 3-kinase (PI3K)-Akt signaling pathway.

    Science.gov (United States)

    Mittal, Yash; Pavlova, Yelena; Garcia-Marcos, Mikel; Ghosh, Pradipta

    2011-09-16

    GIV (Gα-interacting vesicle-associated protein, also known as Girdin) is a bona fide enhancer of PI3K-Akt signals during a diverse set of biological processes, e.g. wound healing, macrophage chemotaxis, tumor angiogenesis, and cancer invasion/metastasis. We recently demonstrated that tyrosine phosphorylation of GIV by receptor and non-receptor-tyrosine kinases is a key step that is required for GIV to directly bind and enhance PI3K activity. Here we report the discovery that Src homology 2-containing phosphatase-1 (SHP-1) is the major protein-tyrosine phosphatase that targets two critical phosphotyrosines within GIV and antagonizes phospho-GIV-dependent PI3K enhancement in mammalian cells. Using phosphorylation-dephosphorylation assays, we demonstrate that SHP-1 is the major and specific protein-tyrosine phosphatase that catalyzes the dephosphorylation of tyrosine-phosphorylated GIV in vitro and inhibits ligand-dependent tyrosine phosphorylation of GIV downstream of both growth factor receptors and GPCRs in cells. In vitro binding and co-immunoprecipitation assays demonstrate that SHP-1 and GIV interact directly and constitutively and that this interaction occurs between the SH2 domain of SHP-1 and the C terminus of GIV. Overexpression of SHP-1 inhibits tyrosine phosphorylation of GIV and formation of phospho-GIV-PI3K complexes, and specifically suppresses GIV-dependent activation of Akt. Consistently, depletion of SHP-1 enhances peak tyrosine phosphorylation of GIV, which coincides with an increase in peak Akt activity. We conclude that SHP-1 antagonizes the action of receptor and non-receptor-tyrosine kinases on GIV and down-regulates the phospho-GIV-PI3K-Akt axis of signaling.

  16. Effect of Temperature and Vibration on Electrical Connectors with Different Number of Contact Cores

    Directory of Open Access Journals (Sweden)

    Song W. L.

    2016-01-01

    Full Text Available In this paper, we presented the results from three related analysis performed by adopting the failure models, which provided an explanation of performance influencing factors caused by different number of contact cores, for the purpose of measuring the temperature change and deformation value, which were the factors causing contact failure. The failures were localized in contact parts of the connectors. Performed investigations included thermal analysis, modal analysis, harmonic response analysis and contact failure analysis. From the results of these simulations, related temperature and vibration analysis nephograms were got respectively. And the correctness of results of thermal analysis was verified by Fourier law. The research results of this paper provide a reference for thermal analysis and vibration analysis of electrical connectors, which is important for ensuring the reliability and safety of electrical connectors.

  17. Push-out tests and evaluation of FRP perfobond rib shear connectors performance

    Science.gov (United States)

    Kolpasky, Ludvik; Ryjacek, Pavel

    2017-09-01

    The behavioural characteristics of FRP (fibre-reinforced polymer) perfobond rib shear connector was examined through push-out tests in order to verify the applicability for pedestrian bridge structure. The aim of this study is to determine interaction between high performance concrete slab and handmade FRP plate which represent web of the composite beam. Combination of these modern materials leads to structural system with both great load bearing capacity and also sufficient flexural stiffness of the composite element. Openings cut into the GFRP plate at a variable spacing allow GFRP reinforcement bars to be inserted to act as shear studs. Hand lay-up process can increase suitable properties of FRP for connection by perfobond rib shear connectors. In this study, three push-out tests on fiber-reinforced polymer were performed to investigate their shear behaviour. The results of the push-out tests on FRP perfobond rib shear connector indicates great promise for application in full scale structures.

  18. Impedance Discontinuity Reduction Between High-Speed Differential Connectors and PCB Interfaces

    Science.gov (United States)

    Navidi, Sal; Agdinaoay, Rodell; Walter, Keith

    2013-01-01

    High-speed serial communication (i.e., Gigabit Ethernet) requires differential transmission and controlled impedances. Impedance control is essential throughout cabling, connector, and circuit board construction. An impedance discontinuity arises at the interface of a high-speed quadrax and twinax connectors and the attached printed circuit board (PCB). This discontinuity usually is lower impedance since the relative dielectric constant of the board is higher (i.e., polyimide approx. = 4) than the connector (Teflon approx. = 2.25). The discontinuity can be observed in transmit or receive eye diagrams, and can reduce the effective link margin of serial data networks. High-speed serial data network transmission improvements can be made at the connector-to-board interfaces as well as improving differential via hole impedances. The impedance discontinuity was improved by 10 percent by drilling a 20-mil (approx. = 0.5-mm) hole in between the pin of a differential connector spaced 55 mils (approx. = 1.4 mm) apart as it is attached to the PCB. The effective dielectric constant of the board can be lowered by drilling holes into the board material between the differential lines in a quadrax or twinax connector attachment points. The differential impedance is inversely proportional to the square root of the relative dielectric constant. This increases the differential impedance and thus reduces the above described impedance discontinuity. The differential via hole impedance can also be increased in the same manner. This technique can be extended to multiple smaller drilled holes as well as tapered holes (i.e., big in the middle followed by smaller ones diagonally).

  19. Facilitating the Easy Use of Earth Observation Data in Earth System Models through CyberConnector

    Science.gov (United States)

    Di, L.; Sun, Z.; Zhang, C.

    2017-12-01

    Earth system models (ESM) are an important tool used to understand the Earth system and predict its future states. On other hand, Earth observations (EO) provides the current state of the system. EO data are very useful in ESM initialization, verification, validation, and inter-comparison. However, EO data often cannot directly be consumed by ESMs because of the syntactic and semantic mismatches between EO products and ESM requirements. In order to remove the mismatches, scientists normally spend long time to customize EO data for ESM consumption. CyberConnector, a NSF EarthCube building block, is intended to automate the data customization so that scientists can be relieved from the laborious EO data customization. CyberConnector uses web-service-based geospatial processing models (GPM) as the mechanism to automatically customize the EO data into the right products in the right form needed by ESMs. It can support many different ESMs through its standard interfaces. It consists of seven modules: GPM designer, GPM binder, GPM runner, GPM monitor, resource register, order manager, and result display. In CyberConnector, EO data instances and GPMs are independent and loosely coupled. A modeler only needs to create a GPM in the GMP designer for EO data customization. Once the modeler specifies a study area, the designed GPM will be activated and take the temporal and spatial extents as constraints to search the data sources and customize the available EO data into the ESM-acceptable form. The execution of GMP is completely automatic. Currently CyberConnector has been fully developed. In order to validate the feasibility, flexibility, and ESM independence of CyberConnector, three ESMs from different geoscience disciplines, including the Cloud-Resolving Model (CRM), the Finite Volume Coastal Ocean Model (FVCOM), and the Community Multiscale Air Quality Model (CMAQ), have been experimented with CyberConnector through closely collaborating with modelers. In the experiment

  20. The Effective Lifetime of ACSR Full Tension Splice Connector Operated at Higher Temperature

    International Nuclear Information System (INIS)

    Wang, Jy-An John; Lara-Curzio, Edgar; King Jr, Thomas J.; Graziano, Joe; Chan, John; Goodwin, Tip

    2009-01-01

    This paper is to address the issues related to integrity of ACSR full tension splice connectors operated at high temperatures. A protocol of integrating analytical and experimental approaches to evaluate the integrity of a full tension single-stage splice connector (SSC) assembly during service at high operating temperature was developed. Based on the developed protocol the effective lifetime evaluation was demonstrated with ACSR Drake conductor SSC systems. The investigation indicates that thermal cycling temperature and frequency, conductor cable tension loading, and the compressive residual stress field within a SSC system have significant impact on the SSC integrity and the associated effective lifetime

  1. USING PARAMETERIZATION OF OBJECTS IN AUTODESK INVENTOR IN DESIGNING STRUCTURAL CONNECTORS

    Directory of Open Access Journals (Sweden)

    Gabriel Borowski

    2015-05-01

    Full Text Available The article presents the parameterization of objects used for designing the type of elements as structural connectors and making modifications of their characteristics. The design process was carried out using Autodesk Inventor 2015. We show the latest software tools, which were used for parameterization and modeling selected types of structural connectors. We also show examples of the use of parameterization facilities in the process of constructing some details and making changes to geometry with holding of the shape the element. The presented method of Inventor usage has enabled fast and efficient creation of new objects based on sketches created.

  2. Distinguishability and identifiability of products with small bore connectors according to ISO DIS 80369 series: risk analysis and summative evaluation

    Directory of Open Access Journals (Sweden)

    Ibenthal Elisabeth

    2017-09-01

    Full Text Available The ISO 80369-series replace Luer-connectors in five application areas to fight misconnections. Although the standard avoids the mechanical problem of misconnections, the design of products and packages remains arbitrary. So, packages and products with same functions but different connectors could have similar designs and hence could be mixed-up.

  3. Homological algebra in -abelian categories

    Indian Academy of Sciences (India)

    Deren Luo

    2017-08-16

    Aug 16, 2017 ... Homological algebra in n-abelian categories. 627. We recall the Comparison lemma, together with its dual, plays a central role in the sequel. Lemma 2.1 [13, Comparison lemma 2.1]. Let C be an additive category and X ∈ Ch. ≥0(C) a complex such that for all k ≥ 0the morphism dk+1. X is a weak cokernel ...

  4. Partial amino acid sequence of apolipoprotein(a) shows that it is homologous to plasminogen

    International Nuclear Information System (INIS)

    Eaton, D.L.; Fless, G.M.; Kohr, W.J.; McLean, J.W.; Xu, Q.T.; Miller, C.G.; Lawn, R.M.; Scanu, A.M.

    1987-01-01

    Apolipoprotein(a) [apo(a)] is a glycoprotein with M/sub r/ ∼ 280,000 that is disulfide linked to apolipoprotein B in lipoprotein(a) particles. Elevated plasma levels of lipoprotein(a) are correlated with atherosclerosis. Partial amino acid sequence of apo(a) shows that it has striking homology to plasminogen. Plasminogen is a plasma serine protease zymogen that consists of five homologous and tandemly repeated domains called kringles and a trypsin-like protease domain. The amino-terminal sequence obtained for apo(a) is homologous to the beginning of kringle 4 but not the amino terminus of plasminogen. Apo(a) was subjected to limited proteolysis by trypsin or V8 protease, and fragments generated were isolated and sequenced. Sequences obtained from several of these fragments are highly (77-100%) homologous to plasminogen residues 391-421, which reside within kringle 4. Analysis of these internal apo(a) sequences revealed that apo(a) may contain at least two kringle 4-like domains. A sequence obtained from another tryptic fragment also shows homology to the end of kringle 4 and the beginning of kringle 5. Sequence data obtained from the two tryptic fragments shows homology with the protease domain of plasminogen. One of these sequences is homologous to the sequences surrounding the activation site of plasminogen. Plasminogen is activated by the cleavage of a specific arginine residue by urokinase and tissue plasminogen activator; however, the corresponding site in apo(a) is a serine that would not be cleaved by tissue plasminogen activator or urokinase. Using a plasmin-specific assay, no proteolytic activity could be demonstrated for lipoprotein(a) particles. These results suggest that apo(a) contains kringle-like domains and an inactive protease domain

  5. Chronic, percutaneous connector for electrical recording and stimulation with microelectrode arrays.

    Science.gov (United States)

    Shah, Kedar G; Lee, Kye Young; Tolosa, Vanessa; Tooker, Angela; Felix, Sarah; Benett, William; Pannu, Satinderpall

    2014-01-01

    The translation of advances in neural stimulation and recording research into clinical practice hinges on the ability to perform chronic experiments in awake and behaving animal models. Advances in microelectrode array technology, most notably flexible polymer arrays, have significantly improved reliability of the neural interface. However, electrical connector technology has lagged and is prone to failure from non-biocompatibility, large size, contamination, corrosion, and difficulty of use. We present a novel chronic, percutaneous electrical connector system that is suitable for neural stimulation and recording. This system features biocompatible materials, low connect and disconnect forces, passive alignment, and a protective cap during non-use. We have successfully designed, assembled, and tested in vitro both a 16-channel system and a high density 64-channel system. Custom, polyimide, 16-channel, microelectrode arrays were electrically assembled with the connector system and tested using cyclic voltammetry and electrochemical impedance spectroscopy. This connector system is versatile and can be used with a variety of microelectrode array technologies for chronic studies.

  6. Exploring the impact of the care sport connector in the Netherlands

    NARCIS (Netherlands)

    Leenaars, Karlijn E.F.; Smit, Eva; Wagemakers, Annemarie; Molleman, Gerard R.M.; Koelen, Maria A.

    2017-01-01

    Background: Regular physical activity (PA) is deemed to contribute to the primary and secondary prevention of several chronic diseases, like diabetes mellitus, cancer, cardiovascular diseases, and osteoporosis. In 2012, Care Sport Connectors (CSC), to whom a broker has been ascribed, were introduced

  7. Exploring the impact of the care sport connector in the Netherlands

    NARCIS (Netherlands)

    Leenaars, K.E.; Smit, E.; Wagemakers, A.; Molleman, G.R.M.; Koelen, Maria

    2017-01-01

    BACKGROUND: Regular physical activity (PA) is deemed to contribute to the primary and secondary prevention of several chronic diseases, like diabetes mellitus, cancer, cardiovascular diseases, and osteoporosis. In 2012, Care Sport Connectors (CSC), to whom a broker has been ascribed, were introduced

  8. Discourse Connector Usage in Argumentative Essays by American and Thai University Students

    Science.gov (United States)

    Jangarun, Kamolphan; Luksaneeyanawin, Sudaporn

    2016-01-01

    This study investigated the similarities and differences in the use of discourse connectors (DCs) in argumentative essays of American undergraduate students (AMs), Thai with high-English exposure (THHs) and Thai with low-English exposure (THLs). The data of these three groups were collected from 60 essays; 20 essays were from the corpus of…

  9. Innovative, wearable snap connector technology for improved device networking in electronic garments

    Science.gov (United States)

    Kostrzewski, Andrew A.; Lee, Kang S.; Gans, Eric; Winterhalter, Carole A.; Jannson, Tomasz P.

    2007-04-01

    This paper discusses Physical Optics Corporation's (POC) wearable snap connector technology that provides for the transfer of data and power throughout an electronic garment (e-garment). These connectors resemble a standard garment button and can be mated blindly with only one hand. Fully compatible with military clothing, their application allows for the networking of multiple electronic devices and an intuitive method for adding/removing existing components from the system. The attached flexible cabling also permits the rugged snap connectors to be fed throughout the standard webbing found in military garments permitting placement in any location within the uniform. Variations of the snap electronics/geometry allow for integration with USB 2.0 devices, RF antennas, and are capable of transferring high bandwidth data streams such as the 221 Mbps required for VGA video. With the trend towards providing military officers with numerous electronic devices (i.e., heads up displays (HMD), GPS receiver, PDA, etc), POC's snap connector technology will greatly improve cable management resulting in a less cumbersome uniform. In addition, with electronic garments gaining widespread adoption in the commercial marketplace, POC's technology is finding applications in such areas as sporting good manufacturers and video game technology.

  10. Magnetic Actuation Connector Between Extension Shaft and Armature for Bottom Mounted Control Rod Drive Mechanism

    Energy Technology Data Exchange (ETDEWEB)

    Huh, Hyung; Cho, Yeong Garp; Kim, Jong In [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

    2013-10-15

    The electromagnet and armature inside the guide tube interact and produce magnetism, thus making the armature, connecting extension shaft and control rod move up and down to control the power of reactor. During the overhaul, the control absorber rod (CAR), extension shaft, and armature of BMCRDM are lifted together for closing a seal valve. But total length of CAR assembly is so long that it cannot be lifted due to exposure above the water level of pool which is strictly controlled. In addition to this, it is difficult to calibrate a position indicator and lifting force of electromagnet without armature assembly as a seal valve is closed. For this reason, it is necessary to install a disconnecting system between armature and extension shaft. Therefore, KAERI has developed magnetic actuation connector using plunger between armature and extension shaft for the bottom mounted control rod drive mechanism in research reactor. The results of a FEM and the experiments in this work lead to the following conclusions: The FEM result for the design of the magnetic actuation connector is compared with the measured lifting force of prototype production. As a result, it is shown that the lifting force of the prototype connector has a good agreement with the result of the FEM. A newly developed technique of prototype magnetic actuation connector which is designed by FEM analysis result is proposed.

  11. Irradiation test on connector part for nuclear instrumentation of nuclear powered ship 'Mutsu'

    International Nuclear Information System (INIS)

    Kudo, Takahiro; Mizushima, Toshihiko; Tsunoda, Tsunemi; Nakazawa, Toshio

    1991-01-01

    The nuclear instrumetnation facility of the nuclear powered ship 'Mutsu' is composed of neutron detectors, signal cables and the circuits for measurement, and ocntinuously monitors neutron flux. Since this facility treats very faint signals, for the signal cables, coaxial cables and triple coaxial cables are used. The coaxial cables for the nuclear instrumentation are equipped with connectors at both ends, and those are called prefabricated cable. The prefabricated cables are connected to neutron detectors, and installed in the detection holes of the primary shielding tank in the containment vessel. Therefore, at the time of reactor operation, they are exposed to high radiation, and the deterioration of the characteristics of the prefabricated cables is feared. For the purpose of confirming that the part of deteriorating the insulation of the prefabricated cables is connectors, and clarifying the cause of the deterioration of insulation in connector part, the irradiation test of this time was carried out. The environment in which the prefabricated cables are laid, the specifications of the cables and connectors, the materials, gamma ray irradiation and the test results are reported. (K.I.)

  12. ESCC standards, evaluation and qualification of optical fiber connectors for space application

    Science.gov (United States)

    Taugwalder, Frédéric

    2017-11-01

    Optical fiber connectors have been used for the past fifteen years in space application. Reviewing the heritage left from past and current mission, the status of ESCC standards for these components and assemblies will help future use of fiber in space applications. In the frame of the ESA ECI program, Diamond has evaluated and is currently qualifying according to ESCC standards the AVIM and Mini-AVIM connectors. The configuration retained to qualify the connector sets is using a polarization maintaining fiber at 1550nm with a loose tube in PEEK as cable structure. The evaluation has been used to step-stress specific characteristics of the optical fiber connectors with a particular aim at possible failure modes to establish a safety factor for the qualification. The evaluation results presented can be used on a case by case to evaluate special applications that would require to extend the specification. The qualification components can be extended further and a structure for assemblies is proposed in order to simplify fiber optics implementation in space projects.

  13. 24-ch microlens-integrated no-polish connector for optical interconnection with polymer waveguides

    Science.gov (United States)

    Shiraishi, Takashi; Yagisawa, Takatoshi; Ikeuchi, Tadashi; Daikuhara, Osamu; Tanaka, Kazuhiro

    2013-02-01

    We successfully developed a new 24-ch optical connector for polymer waveguides. The connector consists of a transparent thermoplastic resin that has two rectangular slits on one side for alignment of the waveguide films and integrated microlens arrays on the other side for coupling to the MT connector. Two 12-ch waveguide films were cut to a 3-mm width. The thickness of each waveguide film was controlled at 100 μm. The waveguide films were inserted into the slits until they touched the bottom face of the slit. Ultraviolet curing adhesive was used to achieve a short hardening process. The expanded beam in the transparent material is focused by the microlens arrays formed on the connector surface. This lens structure enables assembly without the need for a polishing process. We designed the lens for coupling between a step-index 40-μm rectangular waveguide and a graded-index 50-μm fiber. We achieved low-loss optical coupling by designing a method of providing asymmetric magnification between the horizontal and vertical directions in order to compensate for the asymmetric numerical aperture of the waveguide. The typical measured coupling losses from/to the waveguide to/from the fiber were 1.2 dB and 0.6 dB, respectively. The total coupling loss was as small as that of a physical contact connection.

  14. Magnetic Actuation Connector Between Extension Shaft and Armature for Bottom Mounted Control Rod Drive Mechanism

    International Nuclear Information System (INIS)

    Huh, Hyung; Cho, Yeong Garp; Kim, Jong In

    2013-01-01

    The electromagnet and armature inside the guide tube interact and produce magnetism, thus making the armature, connecting extension shaft and control rod move up and down to control the power of reactor. During the overhaul, the control absorber rod (CAR), extension shaft, and armature of BMCRDM are lifted together for closing a seal valve. But total length of CAR assembly is so long that it cannot be lifted due to exposure above the water level of pool which is strictly controlled. In addition to this, it is difficult to calibrate a position indicator and lifting force of electromagnet without armature assembly as a seal valve is closed. For this reason, it is necessary to install a disconnecting system between armature and extension shaft. Therefore, KAERI has developed magnetic actuation connector using plunger between armature and extension shaft for the bottom mounted control rod drive mechanism in research reactor. The results of a FEM and the experiments in this work lead to the following conclusions: The FEM result for the design of the magnetic actuation connector is compared with the measured lifting force of prototype production. As a result, it is shown that the lifting force of the prototype connector has a good agreement with the result of the FEM. A newly developed technique of prototype magnetic actuation connector which is designed by FEM analysis result is proposed

  15. Divergent Roles of RPA Homologs of the Model Archaeon Halobacterium salinarum in Survival of DNA Damage.

    Science.gov (United States)

    Evans, Jessica J; Gygli, Patrick E; McCaskill, Julienne; DeVeaux, Linda C

    2018-04-20

    The haloarchaea are unusual in possessing genes for multiple homologs to the ubiquitous single-stranded DNA binding protein (SSB or replication protein A, RPA) found in all three domains of life. Halobacterium salinarum contains five homologs: two are eukaryotic in organization, two are prokaryotic and are encoded on the minichromosomes, and one is uniquely euryarchaeal. Radiation-resistant mutants previously isolated show upregulation of one of the eukaryotic-type RPA genes. Here, we have created deletions in the five RPA operons. These deletion mutants were exposed to DNA-damaging conditions: ionizing radiation, UV radiation, and mitomycin C. Deletion of the euryarchaeal homolog, although not lethal as in Haloferax volcanii , causes severe sensitivity to all of these agents. Deletion of the other RPA/SSB homologs imparts a variable sensitivity to these DNA-damaging agents, suggesting that the different RPA homologs have specialized roles depending on the type of genomic insult encountered.

  16. Rational Homological Stability for Automorphisms of Manifolds

    DEFF Research Database (Denmark)

    Grey, Matthias

    In this thesis we prove rational homological stability for the classifying spaces of the homotopy automorphisms and block di↵eomorphisms of iterated connected sums of products of spheres of a certain connectivity.The results in particular apply to the manifolds       Npg,q  = (#g(Sp x Sq)) - int...... with coefficients in the homology of the universal covering, which is studied using rational homology theory. The result for the block di↵eomorphisms is deduced from the homological stability for the homotopy automorphisms upon using Surgery theory. Themain theorems of this thesis extend the homological stability...

  17. Development of an electrical connector for liquid sodium environment. Final Report

    International Nuclear Information System (INIS)

    Kataoka, Hajime; Noguchi, Koichi; Takatsudo, Hiroshi; Miyakawa, Shun-ichi

    1998-07-01

    The INstrumented irradiation Test Assembly (INTA) has been used to conduct precision on-line instrumented irradiation tests in the experimental fast reactor JOYO. In INTA, direct instrumentation wiring between the irradiation test section in the core and the upper structure section in the rotating plug makes INTA structurally complex and expensive. Instead of direct wiring, if an electrical connector capable of withstanding a heated liquid sodium environment could be used between the irradiation test section and the upper structure section, the upper mechanism of INTA could be reused and testing costs would be drastically reduced. Moreover, the reactor load factor would be improved because of reduced handling time for INTA. In an attempt to gain this advantage, research and development of an electric connector in a sodium environment was carried out from 1988 to 1996 at PNC. As no previous R and D had been conducted in this area, this development activity was conducted in a boot strap manner. The first test was carried out for a small model fabrication, the second was for a water partial model, and the third was for a sodium partial model. Based on those tests, a prototype design specification of the connector was determined. In the sodium partial model test, the resilience of the electrical connector insulation to the sodium environment was investigated. However, severe cracking in the ceramic insulator caused by the high temperature sodium environment was discovered at the junction of ceramic insulator and metallic electrode. Although additional sodium partial tests were performed for various material combinations of ceramic insulators, metallic electrodes, brazing materials and metallization materials, the results of the tests were unsatisfactory. Therefore, it was decided that the development of the connector in sodium should cease at PNC in 1997. (J.P.N.)

  18. Kuranishi homology and Kuranishi cohomology

    OpenAIRE

    Joyce, Dominic

    2007-01-01

    A Kuranishi space is a topological space with a Kuranishi structure, defined by Fukaya and Ono. Kuranishi structures occur naturally on moduli spaces of J-holomorphic curves in symplectic geometry. Let Y be an orbifold and R a commutative ring or Q-algebra. We define two kinds of Kuranishi homology KH_*(Y;R). The chain complex KC_*(Y;R) defining KH_*(Y;R) is spanned over R by [X,f,G], for X a compact oriented Kuranishi space with corners, f : X --> Y smooth, and G "gauge-fixing data" which ma...

  19. Csk Homologous Kinase, a Potential Regulator of CXCR4-mediated Breast Cancer Cell Metastasis

    Science.gov (United States)

    2010-08-31

    SH2 ) and SH3 domains and lacks the consensus tyrosine phosphorylation and myristylation sites found in Src family kinases . CHK has been shown to...0350 TITLE: Csk Homologous Kinase , a Potential Regulator of CXCR4-mediated Breast Cancer Cell Metastasis PRINCIPAL INVESTIGATOR: Byeong-Chel...1 AUG 2009 - 31 JUL 2010 4. TITLE AND SUBTITLE 5a. CONTRACT NUMBER W81XWH-09-1-0350 Csk Homologous Kinase , a Potential Regulator

  20. The biomechanical effect of transverse connectors use in a pre- and postlaminectomy model of the posterior cervical spine: an in vitro cadaveric study.

    Science.gov (United States)

    Majid, Kamran; Gudipally, Manasa; Hussain, Mir; Moldavsky, Mark; Khalil, Saif

    2011-12-15

    An in vitro biomechanical study investigating the effect of transverse connectors on posterior cervical stabilization system in a laminectomy model. To evaluate the optimal design, number, and location of the transverse connectors in stabilizing long segment posterior instrumentation in the cervical spine. In the cervical spine, lateral mass screw (LMS) fixation is used for providing stability after decompression. Transverse connectors have been used to augment segmental posterior instrumentation. However, in the cervical region the optimal design, number, and the location of transverse connectors is not known. Seven fresh human cervicothoracic cadaveric spines (C2-T1) were tested by applying ±1.5 Nm moments in flexion (F), extension (E), lateral bending (LB), and axial rotation (AR). After testing the intact condition, LMS/rods were placed and then were tested with two different transverse connectors (top-loading connector [TL] and the head-to-head [HH] connector) in multiple levels, pre- and postlaminectomy (PL). LMS significantly reduced segmental motion by 77.2% in F, 75.6% in E, 86.6% in LB, and 86.1% in AR prelaminectomy and by 75.4% in F, 76% in E, 80.6% in LB, and 76.4% in AR postlaminectomy compared to intact (P transverse connectors is significant in AR, when using two connectors at the proximal and distal ends, compared to one connector. In a clinical setting, this data may guide surgeons on transverse connector configurations to consider during posterior cervical instrumentation.

  1. Qualified measurement setup of polarization extinction ratio for Panda PMF with LC/UPC connector

    Science.gov (United States)

    Thongdaeng, Rutsuda; Worasucheep, Duang-rudee; Ngiwprom, Adisak

    2018-03-01

    Polarization Extinction Ratio (PER) is one of the key parameters for Polarization Maintaining Fiber (PMF) connector. Based on our previous studies, the bending radius of fiber greater than 1.5 cm will not affect the insertion loss of PMF [1]. Moreover, the measured PER of Panda PMF with LC/UPC connectors is more stable when that PMF is coiled around a hot rod with a minimum of 3-cm in diameter at 75°C temperature [2]. Hence, the hot rod with less constrained 6-cm in diameter at constant 75°C was selected for this PER measurement. Two PER setups were verified and compared for measuring LC/UPC PMF connectors. The Polarized Laser Source (PLS) at 1550 nm wavelength and PER meter from OZ Optics were used in both setups, in which the measured connector was connected to PLS at 0° angle while the other end was connected to PER meter. In order to qualify our setups, the percentage of Repeatability and Reproducibility (%R&R) were tested and calculated. In each setup, the PER measurement was repeated 3 trials by 3 appraisers using 10 LC/UPC PMF connectors (5 LC/UPC PMF patchcords with 3.5+/-0.5 meters in length) in random order. The 1st setup, PMF was coiled at a larger 20-cm diameter for 3 to 5 loops and left in room temperature during the test. The 2nd setup, PMF was coiled around a hot rod at constant 75°C with 6-cm diameter for 8 to 10 loops for at least 5 minutes before testing. There are 3 ranges of %R&R acceptation guide line: <10% is acceptable, between 10% - 30% is marginal, and <30% is unacceptable. According to our results, the %R&R of the 1st PER test setup was 16.2% as marginality, and the 2nd PER test setup was 8.9% as acceptance. Thus, providing the better repeatability and reproducibility, this 2nd PER test setup having PMF coiled around a hot rod at constant 75°C with 6-cm diameter was selected for our next study of the impact of hot temperature on PER in LC/UPC PMF connector.

  2. Persistent homology and string vacua

    Energy Technology Data Exchange (ETDEWEB)

    Cirafici, Michele [Center for Mathematical Analysis, Geometry and Dynamical Systems,Instituto Superior Técnico, Universidade de Lisboa,Av. Rovisco Pais, 1049-001 Lisboa (Portugal); Institut des Hautes Études Scientifiques,Le Bois-Marie, 35 route de Chartres, F-91440 Bures-sur-Yvette (France)

    2016-03-08

    We use methods from topological data analysis to study the topological features of certain distributions of string vacua. Topological data analysis is a multi-scale approach used to analyze the topological features of a dataset by identifying which homological characteristics persist over a long range of scales. We apply these techniques in several contexts. We analyze N=2 vacua by focusing on certain distributions of Calabi-Yau varieties and Landau-Ginzburg models. We then turn to flux compactifications and discuss how we can use topological data analysis to extract physical information. Finally we apply these techniques to certain phenomenologically realistic heterotic models. We discuss the possibility of characterizing string vacua using the topological properties of their distributions.

  3. Equivariant ordinary homology and cohomology

    CERN Document Server

    Costenoble, Steven R

    2016-01-01

    Filling a gap in the literature, this book takes the reader to the frontiers of equivariant topology, the study of objects with specified symmetries. The discussion is motivated by reference to a list of instructive “toy” examples and calculations in what is a relatively unexplored field. The authors also provide a reading path for the first-time reader less interested in working through sophisticated machinery but still desiring a rigorous understanding of the main concepts. The subject’s classical counterparts, ordinary homology and cohomology, dating back to the work of Henri Poincaré in topology, are calculational and theoretical tools which are important in many parts of mathematics and theoretical physics, particularly in the study of manifolds. Similarly powerful tools have been lacking, however, in the context of equivariant topology. Aimed at advanced graduate students and researchers in algebraic topology and related fields, the book assumes knowledge of basic algebraic topology and group act...

  4. Homology in Electromagnetic Boundary Value Problems

    Directory of Open Access Journals (Sweden)

    Pellikka Matti

    2010-01-01

    Full Text Available We discuss how homology computation can be exploited in computational electromagnetism. We represent various cellular mesh reduction techniques, which enable the computation of generators of homology spaces in an acceptable time. Furthermore, we show how the generators can be used for setting up and analysis of an electromagnetic boundary value problem. The aim is to provide a rationale for homology computation in electromagnetic modeling software.

  5. Stress analysis of single port (ISB) jumper connectors for 2-, 3-, and 4-in. sizes

    International Nuclear Information System (INIS)

    Islam, M.A.; Julyk, J.L.; Weiner, E.O.

    1995-01-01

    Jumper connectors are used in the Hanford site for remotely connecting jumper pipe lines in the radioactive zones. The jumper pipes are used for transporting radioactive fluids and hazardous chemicals. This report evaluates the adequacy and the integrity of the 2-, 3-, and 4-in. single-port integral seal block (ISB) jumper connector assemblies, as well as the three-way 2-in. configuration. The evaluation considers limiting forces from the piping to the nozzle. A stress evaluation of the jumper components (hook, hook pin, operating screw, nozzle and nozzle flange, and block) under operational (pressure, thermal, dead weight, and axial torquing of the jumper) and seismic loading is addressed in the report

  6. Structural insights into the backbone-circularized granulocyte colony-stimulating factor containing a short connector.

    Science.gov (United States)

    Miyafusa, Takamitsu; Shibuya, Risa; Honda, Shinya

    2018-06-02

    Backbone circularization is a powerful approach for enhancing the structural stability of polypeptides. Herein, we present the crystal structure of the circularized variant of the granulocyte colony-stimulating factor (G-CSF) in which the terminal helical region was circularized using a short, two-amino acid connector. The structure revealed that the N- and C-termini were indeed connected by a peptide bond. The local structure of the C-terminal region transited from an α helix to 3 10 helix with a bend close to the N-terminal region, indicating that the structural change offset the insufficient length of the connector. This is the first-ever report of a crystal structure of the backbone of a circularized protein. It will facilitate the development of backbone circularization methodology. Copyright © 2018 Elsevier Inc. All rights reserved.

  7. Stress analysis of single port (ISB) jumper connectors for 2-, 3-, and 4-in. sizes

    Energy Technology Data Exchange (ETDEWEB)

    Islam, M A; Julyk, J L; Weiner, E O [ICF Kaiser Hanford Co., Richland, WA (United States)

    1995-05-26

    Jumper connectors are used in the Hanford site for remotely connecting jumper pipe lines in the radioactive zones. The jumper pipes are used for transporting radioactive fluids and hazardous chemicals. This report evaluates the adequacy and the integrity of the 2-, 3-, and 4-in. single-port integral seal block (ISB) jumper connector assemblies, as well as the three-way 2-in. configuration. The evaluation considers limiting forces from the piping to the nozzle. A stress evaluation of the jumper components (hook, hook pin, operating screw, nozzle and nozzle flange, and block) under operational (pressure, thermal, dead weight, and axial torquing of the jumper) and seismic loading is addressed in the report.

  8. Use of monolingual and comparable corpora in the classroom to translate adverbial connectors

    Directory of Open Access Journals (Sweden)

    Beatriz Sánchez Cárdenas

    2016-04-01

    This research explored the reasons why certain adverbial discourse connectors, apparently easy to translate, are a source of translation problems that cannot be easily resolved with a bilingual dictionary. Moreover, this study analyzed the use of parallel corpora in the translation classroom and how it can increase the quality of text production. For this purpose, we compared student translations before and after receiving training on the use of corpus analysis tools.

  9. Experimental study on AR fiberglass connectors for bridges made of composite materials

    Directory of Open Access Journals (Sweden)

    Tolosana, N.

    2006-06-01

    Full Text Available One highly relevant aspect in composite material bridgedesing is the study of the shear connectors to be used.Composite material bridges most commonly comprise acomposite deck resting on steel or reinforced concrete girders.This article analyzes the connectors most frequentlyused in such bridges.It also reviews the connectors used in the King StormwaterChannel Bridge, whose fibreglass deck is supported bygirders made of concrete-filled carbon fibre girders.The paper advances proposals for several types of connectorsand discusses the results of push-out test run ona number of prototypes with different geometries.The results are analyzed to identify the optimum model forthe “Autovia del Cantabrico” Overpass, with its 46-m span,carbon fibre girders and AR glass shear connectors.Un aspecto relevante dentro del proyecto de un puenterealizado en materiales compuestos es el estudio de losconectores. El caso mas frecuente de puente en materialescompuestos es aquel que presenta un tablero de materialescompuestos soportado por vigas metalicas o de hormigonarmado. En este trabajo se analizaran los tipos deconectores mas utilizados en este tipo de puentesSe analizaran tambien los conectores utilizados en elKing Stormwater Channel Bridge, donde ademas deltablero en fibra de vidrio, se fabricaron las vigas en fibrasde carbono rellenas de hormigon.En este articulo se propondran varios tipos de conectoresy se presentaran los resultados experimentales correspondientesal ensayo de “push-out” de varios prototipos condiferentes geometrias.Tras evaluar los resultados, se determinara el mas idoneopara su implantacion en el Paso Superior de la Autovia delCantabrico, de 46 metros de luz y que presenta las vigasen fibra de carbono y los conectores de vidrio AR.

  10. Annual report 1999. Energy and connectors; Rapport annuel 1999. Energie connectique

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1999-07-01

    This report presents the industrial activities and the financial results of Framatome in 1999. Framatome's activities are divided into 2 sectors: energy and connectors, which represents respectively 54% and 46% of the turnover and 40% and 60% of the staff (26000 people). In 1999 the turnover reached 4.2 milliard euros. Framatome and Siemens have decided to merge their nuclear activities in a common company (66% for Framatome, 34% for Siemens). (A.C.)

  11. Compact and Robust Refilling and Connectorization of Hollow Core Photonic Crystal Fiber Gas Reference Cells

    Science.gov (United States)

    Poberezhskiy, Ilya Y.; Meras, Patrick; Chang, Daniel H.; Spiers, Gary D.

    2007-01-01

    This slide presentation reviews a method for refilling and connectorization of hollow core photonic crystal fiber gas reference cells. Thees hollow-core photonic crystal fiber allow optical propagation in air or vacuum and are for use as gas reference cell is proposed and demonstrated. It relies on torch-sealing a quartz filling tube connected to a mechanical splice between regular and hollow-core fibers.

  12. Annual report 1999. Energy and connectors; Rapport annuel 1999. Energie connectique

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1999-07-01

    This report presents the industrial activities and the financial results of Framatome in 1999. Framatome's activities are divided into 2 sectors: energy and connectors, which represents respectively 54% and 46% of the turnover and 40% and 60% of the staff (26000 people). In 1999 the turnover reached 4.2 milliard euros. Framatome and Siemens have decided to merge their nuclear activities in a common company (66% for Framatome, 34% for Siemens). (A.C.)

  13. Nuclear qualified in-containment electrical connectors and method of connecting electrical conductors

    Science.gov (United States)

    Powell, J. G.

    1991-01-01

    A nuclear qualified in-containment electrical connection comprises an insulated, sheathed instrument lead having electrical conductors extending from one end thereof to provide two exposed lead wires, a watertight cable having electrical conducting wires therein and extending from one end of the cable to provide two lead wires therefrom, two butt splice connectors each connecting the ends of respective ones of the lead wires from the instrument lead and cable, a length of heat shrinkable plastic tubing positioned over each butt splice connector and an adjacent portion of a respective lead wire from the cable and heat shrunk into position, a length of heat shrinkable plastic tubing on the end portion of the instrument lead adjacent the lead wires therefrom and heat shrunk thereon and a length of outer heat shrinkable plastic tubing extending over the end portion of the instrument lead and the heat shrinkable tubing thereon and over the butt splice connectors and a portion of the cable adjacent the cable lead lines, the outer heat shrinkable tubing being heat shrunk into sealing position on the instrument lead and cable.

  14. Behaviour of steel-concrete composite beams using bolts as shear connectors

    Science.gov (United States)

    Tran, Minh-Tung; Nguyen Van Do, Vuong; Nguyen, Tuan-Anh

    2018-04-01

    The paper presents an experimental program on the application of bolts as shear connectors for steel-composite beams. Four steel- concrete composite beams and a reference steel beam were made and tested. The aim of the testing program is to examine which forms of the steel bolts can be used effectively for steel-composite beams. The four types of the bolts include: Type 1 the bolt with the nut at the end; Type 2 the bolt bending at 900 hook; Type 3 the bolt without the nut at the end and Type 4 the bolt with the nut at the end but connected with the steel beam by hand welding in other to be connected with the steel beam by bolt connection as in the first three types. The test results showed that beside the traditional shear connectors like shear studs, angle type, channel type, bolts can be used effectively as the shear connectors in steel-composite beams and the application of bolts in Types 1 and 2 in the composite beams gave the better performance for the tested beam.

  15. Experimental analysis of reinforced concrete columns strengthened with self-compacting concrete and connectors

    Directory of Open Access Journals (Sweden)

    P. P. Nascimento

    Full Text Available There are many problems involving cases of destruction of buildings and other structures. The columns can deteriorate for several reasons such as the evolution and changing habits of the loads. The experimental phase of this work was based on a test involving nine reinforced concrete columns under combined bending and axial compression, at an initial eccentricity of 60 mm. Two columns were used as reference, one having the original dimensions of the column and the other, monolithic, had been cast along the thickness of the strengthened piece. The remaining columns received a 35 mm thick layer of self-compacting concrete on their compressed face. For the preparation of the interface between the two materials, this surface was scarified and furrowed and connectors were inserted onto the columns' shear reinforcement in various positions and amounts.As connectors, 5 mm diameter steel bars were used (the same as for stirrups, bent in the shape of a "C" with 25 mm coatings. >As a conclusion, not only the quantity, but mainly, the location of the connectors used in the link between substrate and reinforcement is crucial to increase strength and to change failure mode.

  16. Plasma treatment of fiber facets for increased (de)mating endurance in physical contact fiber connectors

    Science.gov (United States)

    Van Erps, Jürgen; Voss, Kevin; De Witte, Martijn; Radulescu, Radu; Beri, Stefano; Watté, Jan; Thienpont, Hugo

    2016-04-01

    It is known that cleaving an optical fiber introduces a number of irregularities and defects to the fiber's end-face, such as hackles and shockwaves. These defects can act as failure initiators when stress is applied to the end-face. Given the fiber's small diameter of 125 ffm, a large amount of mechanical stress can be expected to be applied on its end-face during the mating-demating cycle. In addition, a connector in a fiber-to-the-home (FTTH) network can be expected to be mated and demated more than 30 times during its lifetime for purposes such as testing, churning, or provisioning. For this reason, the performance of a connector that displays low optical loss when first installed can dramatically degrade after few mating-demating cycles and catastrophic connector failure due to end-face breakage is likely. We present plasma discharge shaping of cleaved fiber tips to strongly improve the endurance of the fibers to repeated mating-demating cycles. We quantify the dependency of the plasma-induced surface curvature of the fiber tip on the plasma duration and on the position of the fiber tip within the plasma cloud. Finally we present data showing the improved endurance of fibers that are exposed to plasma compared to conventional as-cleaved fibers.

  17. Flexural Strengthening of RC Slabs Using a Hybrid FRP-UHPC System Including Shear Connector

    Directory of Open Access Journals (Sweden)

    Jiho Moon

    2017-01-01

    Full Text Available A polymeric hybrid composite system made of UHPC and CFRP was proposed as a retrofit system to enhance flexural strength and ductility of RC slabs. While the effectiveness of the proposed system was confirmed previously through testing three full-scale one-way slabs having two continuous spans, the slabs retrofitted with the hybrid system failed in shear. This sudden shear failure would stem from the excessive enhancement of the flexural strength over the shear strength. In this study, shear connectors were installed between the hybrid system and a RC slab. Using simple beam, only positive moment section was examined. Two full-scale RC slabs were cast and tested to failure: the first as a control and the second using this new strengthening technique. The proposed strengthening system increased the ultimate load carrying capacity of the slab by 70%, the stiffness by 60%, and toughness by 128%. The efficiency of shear connectors on ductile behavior of the retrofitted slab was also confirmed. After the UHPC top is separated from the slab, the shear connector transfer shear load and the slab system were in force equilibrium by compression in UHPC and tension in CFRP.

  18. Domain analysis

    DEFF Research Database (Denmark)

    Hjørland, Birger

    2017-01-01

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

  19. Salt Spray Test to Determine Galvanic Corrosion Levels of Electroless Nickel Connectors Mounted on an Aluminum Bracket

    Science.gov (United States)

    Rolin, T. D.; Hodge, R. E.; Torres, P. D.; Jones, D. D.; Laird, K. R.

    2014-01-01

    During preliminary vehicle design reviews, requests were made to change flight termination systems from an electroless nickel (EN) connector coating to a zinc-nickel (ZN) plating. The reason for these changes was due to a new NASA-STD-6012 corrosion requirement where connectors must meet the performance requirement of 168 hr of exposure to salt spray. The specification for class F connectors, MIL-DTL-38999, certifies the EN coating will meet a 48-hr salt spray test, whereas the ZN is certified to meet a 168-hr salt spray test. The ZN finish is a concern because Marshall Space Flight Center has no flight experience with ZN-finished connectors, and MSFC-STD-3012 indicates that zinc and zinc alloys should not be used. The purpose of this test was to run a 168-hr salt spray test to verify the electrical and mechanical integrity of the EN connectors and officially document the results. The salt spray test was conducted per ASTM B117 on several MIL-DTL-38999 flight-like connectors mounted to an aluminum 6061-T6 bracket that was alodined. The configuration, mounting techniques, electrical checks, and materials used were typical of flight and ground support equipment.

  20. Homotopic Chain Maps Have Equal s-Homology and d-Homology

    Directory of Open Access Journals (Sweden)

    M. Z. Kazemi-Baneh

    2016-01-01

    Full Text Available The homotopy of chain maps on preabelian categories is investigated and the equality of standard homologies and d-homologies of homotopic chain maps is established. As a special case, if X and Y are the same homotopy type, then their nth d-homology R-modules are isomorphic, and if X is a contractible space, then its nth d-homology R-modules for n≠0 are trivial.

  1. Relative K-homology and normal operators

    DEFF Research Database (Denmark)

    Manuilov, Vladimir; Thomsen, Klaus

    2009-01-01

    -term exact sequence which generalizes the excision six-term exact sequence in the first variable of KK-theory. Subsequently we investigate the relative K-homology which arises from the group of relative extensions by specializing to abelian $C^*$-algebras. It turns out that this relative K-homology carries...

  2. Molecular Cloning And Sequencing Of Disintegrin Like Domain ...

    African Journals Online (AJOL)

    Disintegrin-like domain was cloned and sequenced from Cerastes cerastes venom gland tissue. Nested RT-PCR was performed using initial primers designed based on the homology of disintegrins from Trimeresurus flavoviridis, Glodius halys , Agkistrodon halys and Trimeresurus macrosquamatus. The homology was ...

  3. Lectures on homology with internal symmetries

    International Nuclear Information System (INIS)

    Solovyov, Yu.

    1993-09-01

    Homology with internal symmetries is a natural generalization of cyclic homology introduced, independently, by Connes and Tsygan, which has turned out to be a very useful tool in a number of problems of algebra, geometry topology, analysis and mathematical physics. It suffices to say cycling homology and cohomology are successfully applied in the index theory of elliptic operators on foliations, in the description of the homotopy type of pseudoisotopy spaces, in the theory of characteristic classes in algebraic K-theory. They are also applied in noncommutative differential geometry and in the cohomology of Lie algebras, the branches of mathematics which brought them to life in the first place. Essentially, we consider dihedral homology, which was successfully applied for the description of the homology type of groups of homeomorphisms and diffeomorphisms of simply connected manifolds. (author). 27 refs

  4. Concrete domains

    OpenAIRE

    Kahn, G.; Plotkin, G.D.

    1993-01-01

    This paper introduces the theory of a particular kind of computation domains called concrete domains. The purpose of this theory is to find a satisfactory framework for the notions of coroutine computation and sequentiality of evaluation.

  5. Domain Engineering

    Science.gov (United States)

    Bjørner, Dines

    Before software can be designed we must know its requirements. Before requirements can be expressed we must understand the domain. So it follows, from our dogma, that we must first establish precise descriptions of domains; then, from such descriptions, “derive” at least domain and interface requirements; and from those and machine requirements design the software, or, more generally, the computing systems.

  6. TJC: plan and prepare for the transition to new tubing connectors to minimize the risk of dangerous misconnections, clinician frustration.

    Science.gov (United States)

    2014-12-01

    To reduce the risk of dangerous tubing misconnections, the ISO is rolling out new tubing connector standards that will eventually make it nearly impossible for tubing associated with one delivery system to be connected to a delivery system that serves a different purpose. Experts welcome the change, noting that tubing misconnections that cause injury and even death have been happening for years. However, TJC has issued a Sentinel Event Alert, warning that health care organizations need to be vigilant in managing the risk posed by these misconnections during the phased-in transition to the new connectors. Experts explain that tubing misconnections occur because many different types of tubing utilize the same Leur connector, making it possible for a clinician to mistakenly connect a tube to the wrong delivery system. The most common type of tubing misconnection reported to the ISMP is when a clinician wants to administer something to a patient through a feeding tube, but accidently administers the substance through an IV tube instead. The first new connector, called the ENFit, is going to be for enteral feeding tubes. It will not connect to IV tubing, making that type of misconnection unlikely. The new connector should be available early next year. Since hospitals will continue to use older tubing until their supplies are exhausted, manufacturers will temporarily provide adapters capable of making new administration sets compatible with older tubing.

  7. Arranging ISO 13606 archetypes into a knowledge base using UML connectors.

    Science.gov (United States)

    Kopanitsa, Georgy

    2014-01-01

    To enable the efficient reuse of standard based medical data we propose to develop a higher-level information model that will complement the archetype model of ISO 13606. This model will make use of the relationships that are specified in UML to connect medical archetypes into a knowledge base within a repository. UML connectors were analysed for their ability to be applied in the implementation of a higher-level model that will establish relationships between archetypes. An information model was developed using XML Schema notation. The model allows linking different archetypes of one repository into a knowledge base. Presently it supports several relationships and will be advanced in future.

  8. Microorganisms present on peripheral intravenous needleless connectors in the clinical environment.

    Science.gov (United States)

    Slater, Karen; Cooke, Marie; Whitby, Michael; Fullerton, Fiona; Douglas, Joel; Hay, Jennine; Rickard, Claire

    2017-08-01

    The aim of this study was to quantify culturable microorganisms on needleless connectors (NCs) attached to peripheral intravenous catheters in hospitalized adult medical patients. Half (50%) of 40 NCs were contaminated with microorganisms commonly found on the skin or mouth. Staphylococcus capitis and Staphylococcus epidermidis were most commonly isolated. Emergency department insertion and higher patient dependency were statistically associated with positive NC microorganism growth. These results reaffirm the need for NC decontamination prior to access. Crown Copyright © 2017. Published by Elsevier Inc. All rights reserved.

  9. Open Source GIS Connectors to the NASA GES DISC Satellite Data

    Science.gov (United States)

    Pham, L.; Kempler, S. J.; Yang, W.

    2014-12-01

    The NASA Goddard Earth Sciences Data and Information Services Center (GES DISC) houses a suite of satellite-derived GIS data including high spatiotemporal resolution precipitation, air quality, and modeled land surface parameter data. The data are extremely useful to various GIS research and applications at regional, continental, and global scales, as evidenced by the growing GIS user requests to the data. On the other hand, we also found that some GIS users, especially those from the ArcGIS community, having difficulties in obtaining, importing, and using our data, primarily due to the unfamiliarity of the users with our products and GIS software's lack of capabilities in dealing with the predominately raster form data in various sometimes very complicated formats. In this presentation, we introduce a set of open source ArcGIS data connectors that significantly simplify the access and use of our data in ArcGIS. With the connectors, users do not need to know the data access URLs, the access protocols or syntaxes, and data formats. Nor do they need to browse through a long list of variables that are often embedded into one single science data file and whose names may sometimes be confusing to those not familiar with the file (such as variable CH4_VMR_D for "CH4 Volume mixing ratio from the descending orbit" and variable EVPsfc for "Total Evapotranspiration"). The connectors will expose most GIS-related variables to the users with easy to understand names. User can simply define the spatiotemporal range of their study, select interested parameter(s), and have the needed data be downloaded, imported, and displayed in ArcGIS. The connectors are python text files and there is no installation process. They can be placed at any user directory and be started by simply clicking on it. In the presentation, we'll also demonstrate how to use the tools to load GES DISC time series air quality data with a few clicks and how such data depict the spatial and temporal patterns of

  10. The Lifetime Estimate for ACSR Single-Stage Splice Connector Operating at Higher Temperatures

    International Nuclear Information System (INIS)

    Wang, Jy-An John; Graziano, Joe; Chan, John

    2011-01-01

    This paper is the continuation of Part I effort to develop a protocol of integrating analytical and experimental approaches to evaluate the integrity of a full tension single-stage splice connector (SSC) assembly during service at high operating temperature.1The Part II efforts are mainly focused on the thermal mechanical testing, thermal-cycling simulation and its impact on the effective lifetime of the SSC system. The investigation indicates that thermal cycling temperature and frequency, conductor cable tension loading, and the compressive residual stress field within a SSC system have significant impact on the SSC integrity and the associated effective lifetime.

  11. Preserved irradiated homologous cartilage for orbital reconstruction

    International Nuclear Information System (INIS)

    Linberg, J.V.; Anderson, R.L.; Edwards, J.J.; Panje, W.R.; Bardach, J.

    1980-01-01

    Human costal cartilage is an excellent implant material for orbital and periorbital reconstruction because of its light weight, strength, homogeneous consistency and the ease with which it can be carved. Its use has been limited by the necessity of a separate surgical procedure to obtain the material. Preserved irradiated homologous cartilage has been shown to have almost all the autogenous cartilage and is convenient to use. Preserved irradiated homologous cartilage transplants do not elicit rejection reactions, resist infection and rarely undergo absorption

  12. Dualities in persistent (co)homology

    International Nuclear Information System (INIS)

    De Silva, Vin; Morozov, Dmitriy; Vejdemo-Johansson, Mikael

    2011-01-01

    We consider sequences of absolute and relative homology and cohomology groups that arise naturally for a filtered cell complex. We establish algebraic relationships between their persistence modules, and show that they contain equivalent information. We explain how one can use the existing algorithm for persistent homology to process any of the four modules, and relate it to a recently introduced persistent cohomology algorithm. We present experimental evidence for the practical efficiency of the latter algorithm

  13. Crystal structure of Src-like adaptor protein 2 reveals close association of SH3 and SH2 domains through β-sheet formation.

    Science.gov (United States)

    Wybenga-Groot, Leanne E; McGlade, C Jane

    2013-12-01

    The Src-like adaptor proteins (SLAP/SLAP2) are key components of Cbl-dependent downregulation of antigen receptor, cytokine receptor, and receptor tyrosine kinase signaling in hematopoietic cells. SLAP and SLAP2 consist of adjacent SH3 and SH2 domains that are most similar in sequence to Src family kinases (SFKs). Notably, the SH3-SH2 connector sequence is significantly shorter in SLAP/SLAP2 than in SFKs. To understand the structural implication of a short SH3-SH2 connector sequence, we solved the crystal structure of a protein encompassing the SH3 domain, SH3-SH2 connector, and SH2 domain of SLAP2 (SLAP2-32). While both domains adopt typical folds, the short SH3-SH2 connector places them in close association. Strand βe of the SH3 domain interacts with strand βA of the SH2 domain, resulting in the formation of a continuous β sheet that spans the length of the protein. Disruption of the SH3/SH2 interface through mutagenesis decreases SLAP-32 stability in vitro, consistent with inter-domain binding being an important component of SLAP2 structure and function. The canonical peptide binding pockets of the SH3 and SH2 domains are fully accessible, in contrast to other protein structures that display direct interaction between SH3 and SH2 domains, in which either peptide binding surface is obstructed by the interaction. Our results reveal potential sites of novel interaction for SH3 and SH2 domains, and illustrate the adaptability of SH2 and SH3 domains in mediating interactions. As well, our results suggest that the SH3 and SH2 domains of SLAP2 function interdependently, with implications on their mode of substrate binding. © 2013.

  14. Pipe connector

    International Nuclear Information System (INIS)

    Sullivan, T.E.; Pardini, J.A.

    1978-01-01

    A safety test facility for testing sodium-cooled nuclear reactor components includes a reactor vessel and a heat exchanger submerged in sodium in the tank. The reactor vessel and heat exchanger are connected by an expansion/deflection pipe coupling comprising a pair of coaxially and slidably engaged tubular elements having radially enlarged opposed end portions of which at least a part is of spherical contour adapted to engage conical sockets in the ends of pipes leading out of the reactor vessel and in to the heat exchanger. A spring surrounding the pipe coupling urges the end portions apart and into engagement with the spherical sockets. Since the pipe coupling is submerged in liquid a limited amount of leakage of sodium from the pipe can be tolerated

  15. SH2 domains: modulators of nonreceptor tyrosine kinase activity

    OpenAIRE

    Filippakopoulos, Panagis; Müller, Susanne; Knapp, Stefan

    2009-01-01

    The Src homology 2 (SH2) domain is a sequence-specific phosphotyrosine-binding module present in many signaling molecules. In cytoplasmic tyrosine kinases, the SH2 domain is located N-terminally to the catalytic kinase domain (SH1) where it mediates cellular localization, substrate recruitment, and regulation of kinase activity. Initially, structural studies established a role of the SH2 domain stabilizing the inactive state of Src family members. However, biochemical characterization showed ...

  16. Searching remote homology with spectral clustering with symmetry in neighborhood cluster kernels.

    Directory of Open Access Journals (Sweden)

    Ujjwal Maulik

    Full Text Available Remote homology detection among proteins utilizing only the unlabelled sequences is a central problem in comparative genomics. The existing cluster kernel methods based on neighborhoods and profiles and the Markov clustering algorithms are currently the most popular methods for protein family recognition. The deviation from random walks with inflation or dependency on hard threshold in similarity measure in those methods requires an enhancement for homology detection among multi-domain proteins. We propose to combine spectral clustering with neighborhood kernels in Markov similarity for enhancing sensitivity in detecting homology independent of "recent" paralogs. The spectral clustering approach with new combined local alignment kernels more effectively exploits the unsupervised protein sequences globally reducing inter-cluster walks. When combined with the corrections based on modified symmetry based proximity norm deemphasizing outliers, the technique proposed in this article outperforms other state-of-the-art cluster kernels among all twelve implemented kernels. The comparison with the state-of-the-art string and mismatch kernels also show the superior performance scores provided by the proposed kernels. Similar performance improvement also is found over an existing large dataset. Therefore the proposed spectral clustering framework over combined local alignment kernels with modified symmetry based correction achieves superior performance for unsupervised remote homolog detection even in multi-domain and promiscuous domain proteins from Genolevures database families with better biological relevance. Source code available upon request.sarkar@labri.fr.

  17. Research on Poppers Used as Electrical Connectors in High Speed Textile Transmission Lines

    Directory of Open Access Journals (Sweden)

    Leśnikowski Jacek

    2016-12-01

    Full Text Available This paper presents results of research on poppers used as electrical connectors connecting fragments of textile signal lines. These lines can be used in intelligent clothing for connecting electronic modules implemented in it. Intelligent (smart clothing can be used, among others, in the health monitoring of the elderly, newborn babies, or people working in hazardous conditions, for example, firefighters and soldiers. The aim of the present study was to examine the usefulness of poppers, widely used in clothing, as electrical connectors connecting parts of the textile signal lines designed for transmission of high-speed digital signals. The paper presents examples of measured parameters characterizing transmission properties of two fragments of the coplanar, textile transmission line connected to each other using conventional poppers. The presented measurement results contain the so-called s parameters, characteristic impedance of the poppers, and eye measurements characterizing distortions of digital signals passing through the tested line. In the article, the effect of temperature and humidity of air surrounding the tested poppers on their characteristic impedance was also presented. This property and its stability are important in signal lines designed for high-speed data transmission.

  18. Metallurgical failure investigation of a pipe connector fracture of an expansion vessel

    International Nuclear Information System (INIS)

    Neidel, Andreas

    2016-01-01

    A pipe connector of an expansion vessel of a safety heat exchanger was torn off in a test facility's natural gas compressor. From a material point of view, the cause of the damage is a fatigue fracture induced by pulsating bending stress. The fatigue fracture originated from both, the pipe's outer surface as well as from its inner surface, which is consistent with the given stress situation (pulsating bending stress). Material defects or welding-induced flaws were not observed. Corrosion, wear, or thermal overload which may have promoted the damage, were not observed either. The primary cause was a major design error. Cases of dynamic load were obviously not duly taken into account during designing, so that the free-swinging mass of the expansion vessel which was mounted to a pipe of a diameter of only half an inch and, furthermore, installed in an angle of 45 (additional static preload.), could cause the fatigue failure induced by pulsating bending stress in the zone of highest stresses at the transition of the expansion vessel and the the pipe connector due to dynamic operating loads which always occur in plants like these.

  19. Experiment on Behavior of a New Connector Used in Bamboo (Timber Frame Structure under Cyclic Loading

    Directory of Open Access Journals (Sweden)

    Junwen Zhou

    2018-01-01

    Full Text Available Connection is an important part of the bamboo and timber structure, and it directly influences the overall structural performance and safety. Based on a comprehensive analysis of the mechanical performance of several wood connections, a new connector for the bamboo (timber frame joint was proposed in this paper. Three full-scale T-type joint specimens were designed to study the mechanical performance under cyclic loading. The thickness of the hollow steel column was different among three specimens. The specimens were loaded under displacement control with a rate of 10 mm per minute until the specimens reach failure. It was observed that the failures of three specimens were caused by the buckling of flanges in the compression and that the steel of connections does not yield. The load-displacement hysteretic curve for three specimens is relatively plump, and the stiffness of connection degenerates with the increasing of cyclic load. The maximum rotation is 0.049 rad, and the energy dissipation coefficient is 1.77. The thickness of the hollow steel column of the connector has significant impact on the energy dissipation capacity and the strength of the connection. A simplified moment-rotation hysteresis model for the joint was proposed.

  20. Investigating homology between proteins using energetic profiles.

    Science.gov (United States)

    Wrabl, James O; Hilser, Vincent J

    2010-03-26

    Accumulated experimental observations demonstrate that protein stability is often preserved upon conservative point mutation. In contrast, less is known about the effects of large sequence or structure changes on the stability of a particular fold. Almost completely unknown is the degree to which stability of different regions of a protein is generally preserved throughout evolution. In this work, these questions are addressed through thermodynamic analysis of a large representative sample of protein fold space based on remote, yet accepted, homology. More than 3,000 proteins were computationally analyzed using the structural-thermodynamic algorithm COREX/BEST. Estimated position-specific stability (i.e., local Gibbs free energy of folding) and its component enthalpy and entropy were quantitatively compared between all proteins in the sample according to all-vs.-all pairwise structural alignment. It was discovered that the local stabilities of homologous pairs were significantly more correlated than those of non-homologous pairs, indicating that local stability was indeed generally conserved throughout evolution. However, the position-specific enthalpy and entropy underlying stability were less correlated, suggesting that the overall regional stability of a protein was more important than the thermodynamic mechanism utilized to achieve that stability. Finally, two different types of statistically exceptional evolutionary structure-thermodynamic relationships were noted. First, many homologous proteins contained regions of similar thermodynamics despite localized structure change, suggesting a thermodynamic mechanism enabling evolutionary fold change. Second, some homologous proteins with extremely similar structures nonetheless exhibited different local stabilities, a phenomenon previously observed experimentally in this laboratory. These two observations, in conjunction with the principal conclusion that homologous proteins generally conserved local stability, may

  1. Investigating homology between proteins using energetic profiles.

    Directory of Open Access Journals (Sweden)

    James O Wrabl

    2010-03-01

    Full Text Available Accumulated experimental observations demonstrate that protein stability is often preserved upon conservative point mutation. In contrast, less is known about the effects of large sequence or structure changes on the stability of a particular fold. Almost completely unknown is the degree to which stability of different regions of a protein is generally preserved throughout evolution. In this work, these questions are addressed through thermodynamic analysis of a large representative sample of protein fold space based on remote, yet accepted, homology. More than 3,000 proteins were computationally analyzed using the structural-thermodynamic algorithm COREX/BEST. Estimated position-specific stability (i.e., local Gibbs free energy of folding and its component enthalpy and entropy were quantitatively compared between all proteins in the sample according to all-vs.-all pairwise structural alignment. It was discovered that the local stabilities of homologous pairs were significantly more correlated than those of non-homologous pairs, indicating that local stability was indeed generally conserved throughout evolution. However, the position-specific enthalpy and entropy underlying stability were less correlated, suggesting that the overall regional stability of a protein was more important than the thermodynamic mechanism utilized to achieve that stability. Finally, two different types of statistically exceptional evolutionary structure-thermodynamic relationships were noted. First, many homologous proteins contained regions of similar thermodynamics despite localized structure change, suggesting a thermodynamic mechanism enabling evolutionary fold change. Second, some homologous proteins with extremely similar structures nonetheless exhibited different local stabilities, a phenomenon previously observed experimentally in this laboratory. These two observations, in conjunction with the principal conclusion that homologous proteins generally conserved

  2. Proposal for the award of a blanket purchase agreement, without competitive tendering, for the supply of Burndy connectors

    CERN Document Server

    2004-01-01

    This document concerns the award of a blanket purchase agreement, without competitive tendering, for the supply of Burndy connectors. The Finance Committee is invited to agree to the negotiation of a blanket purchase agreement, without competitive tendering, with SOURIAU (CH), for the supply of Burndy connectors over a period of three years, for a total amount not exceeding 600 000 euros (932 000 Swiss francs), subject to revision for inflation from 1st January 2006. The amount in Swiss francs has been calculated using the present rate of exchange.

  3. Phylogeny of the TRAF/MATH domain.

    Science.gov (United States)

    Zapata, Juan M; Martínez-García, Vanesa; Lefebvre, Sophie

    2007-01-01

    The TNF-receptor associated factor (TRAF) domain (TD), also known as the meprin and TRAF-C homology (MATH) domain is a fold of seven anti-parallel p-helices that participates in protein-protein interactions. This fold is broadly represented among eukaryotes, where it is found associated with a discrete set of protein-domains. Virtually all protein families encompassing a TRAF/MATH domain seem to be involved in the regulation of protein processing and ubiquitination, strongly suggesting a parallel evolution of the TRAF/MATH domain and certain proteolysis pathways in eukaryotes. The restricted number of living organisms for which we have information of their genetic and protein make-up limits the scope and analysis of the MATH domain in evolution. However, the available information allows us to get a glimpse on the origins, distribution and evolution of the TRAF/MATH domain, which will be overviewed in this chapter.

  4. Homological methods, representation theory, and cluster algebras

    CERN Document Server

    Trepode, Sonia

    2018-01-01

    This text presents six mini-courses, all devoted to interactions between representation theory of algebras, homological algebra, and the new ever-expanding theory of cluster algebras. The interplay between the topics discussed in this text will continue to grow and this collection of courses stands as a partial testimony to this new development. The courses are useful for any mathematician who would like to learn more about this rapidly developing field; the primary aim is to engage graduate students and young researchers. Prerequisites include knowledge of some noncommutative algebra or homological algebra. Homological algebra has always been considered as one of the main tools in the study of finite-dimensional algebras. The strong relationship with cluster algebras is more recent and has quickly established itself as one of the important highlights of today’s mathematical landscape. This connection has been fruitful to both areas—representation theory provides a categorification of cluster algebras, wh...

  5. Structural analysis of zwitterionic liquids vs. homologous ionic liquids

    Science.gov (United States)

    Wu, Boning; Kuroda, Kosuke; Takahashi, Kenji; Castner, Edward W.

    2018-05-01

    Zwitterionic liquids (Zw-ILs) have been developed that are homologous to monovalent ionic liquids (ILs) and show great promise for controlled dissolution of cellulosic biomass. Using both high energy X-ray scattering and atomistic molecular simulations, this article compares the bulk liquid structural properties for novel Zw-ILs with their homologous ILs. It is shown that the significant localization of the charges on Zw-ILs leads to charge ordering similar to that observed for conventional ionic liquids with monovalent anions and cations. A low-intensity first sharp diffraction peak in the liquid structure factor S(q) is observed for both the Zw-IL and the IL. This is unexpected since both the Zw-IL and IL have a 2-(2-methoxyethoxy)ethyl (diether) functional group on the cationic imidazolium ring and ether functional groups are known to suppress this peak. Detailed analyses show that this intermediate range order in the liquid structure arises for slightly different reasons in the Zw-IL vs. the IL. For the Zw-IL, the ether tails in the liquid are shown to aggregate into nanoscale domains.

  6. A homology theory for smale spaces

    CERN Document Server

    Putnam, Ian F

    2014-01-01

    The author develops a homology theory for Smale spaces, which include the basics sets for an Axiom A diffeomorphism. It is based on two ingredients. The first is an improved version of Bowen's result that every such system is the image of a shift of finite type under a finite-to-one factor map. The second is Krieger's dimension group invariant for shifts of finite type. He proves a Lefschetz formula which relates the number of periodic points of the system for a given period to trace data from the action of the dynamics on the homology groups. The existence of such a theory was proposed by Bowen in the 1970s.

  7. FBH1 helicase disrupts RAD51 filaments in vitro and modulates homologous recombination in mammalian cells

    DEFF Research Database (Denmark)

    Simandlova, Jitka; Zagelbaum, Jennifer; Payne, Miranda J

    2013-01-01

    Efficient repair of DNA double strand breaks and interstrand cross-links requires the homologous recombination (HR) pathway, a potentially error-free process that utilizes a homologous sequence as a repair template. A key player in HR is RAD51, the eukaryotic ortholog of bacterial RecA protein. RAD......51 can polymerize on DNA to form a nucleoprotein filament that facilitates both the search for the homologous DNA sequences and the subsequent DNA strand invasion required to initiate HR. Because of its pivotal role in HR, RAD51 is subject to numerous positive and negative regulatory influences...... filaments on DNA through its ssDNA translocase function. Consistent with this, a mutant mouse embryonic stem cell line with a deletion in the FBH1 helicase domain fails to limit RAD51 chromatin association and shows hyper-recombination. Our data are consistent with FBH1 restraining RAD51 DNA binding under...

  8. Development of radiation-hard electric connector with ball bearing for in-vessel remote maintenance equipment of ITER

    International Nuclear Information System (INIS)

    Ito, Akira; Obara, Kenjiro; Tada, Eisuke; Morita, Yousuke; Yagi, Toshiaki; Iida, Kazuhisa; Sato, Masaru.

    1997-12-01

    Development of radiation-hard electric connector with ball bearing for in-vessel remote maintenance equipment of ITER (International Thermonuclear Experimental Reactor) has been conducted. Since the in-vessel remote maintenance equipment is operated under the condition of 10 6 R/h gamma ray dose rate, the electric connector has to be radiation hard for an accumulation dose of 10 10 R. In addition, the simple attachment/removal mechanism is essential for remote operation. For this, the alumina (Al203) ceramics and a ball bearing were adopted to electric insulator and plug (male) of connector, respectively. The handling tests on attachment/removal of the connector were conducted by using master slave manipulator and general purpose robot with handling tool, and as a result, the validity of the attachment/removal mechanism was verified. In the gamma ray irradiation tests, which are under way, no degradation in break down voltage (1000V 1min.) up to 10 10 R was confirmed. However insulation resistance and contact resistance between contact pin and contact socket were deteriorated in proportion to the accumulation dose. Increase of contact resistance is considered due to an erosion of contact pin. (author)

  9. The influence of charge injection from intermediate connectors on the performance of tandem organic light-emitting devices

    Energy Technology Data Exchange (ETDEWEB)

    Zhou, Dong-Ying [Institute of Functional Nano and Soft Materials (FUNSOM), Soochow University, Suzhou, Jiangsu 215123 (China); Department of Electrical and Computer Engineering and Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1 (Canada); Siboni, Hossein Zamani; Wang, Qi; Aziz, Hany, E-mail: lsliao@suda.edu.cn, E-mail: h2aziz@uwaterloo.ca [Department of Electrical and Computer Engineering and Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1 (Canada); Liao, Liang-Sheng, E-mail: lsliao@suda.edu.cn, E-mail: h2aziz@uwaterloo.ca [Institute of Functional Nano and Soft Materials (FUNSOM), Soochow University, Suzhou, Jiangsu 215123 (China)

    2014-12-14

    Charge generation in a typical intermediate connector, composed of “n-type doped layer/transition metal oxide (TMO)/hole transporting layer (HTL),” of a tandem organic light-emitting device (OLED) has recently been found to arise from charge transfer at the TMO/HTL interfaces. In this paper, we investigate the effect of hole injection barriers from intermediate connectors on the performance of tandem OLEDs. The hole injection barriers are caused by the offset of the highest occupied molecular orbital (HOMO) energy levels between HTLs contained in the intermediate connector and the top electroluminescence (EL) unit. We also find that although charge generation can occur at the interfaces between the TMO and a wide variety of HTLs of different HOMO values, an increase in the hole injection barrier however limits the electroluminescence efficiency of the top EL units. In the case of large hole injection barriers, significant charge accumulation in the HTLs makes the intermediate connector lose its functionality gradually over operating time, and limits device stability.

  10. Developing a Domain Model for Relay Circuits

    DEFF Research Database (Denmark)

    Haxthausen, Anne Elisabeth

    2009-01-01

    In this paper we stepwise develop a domain model for relay circuits as used in railway control systems. First we provide an abstract, property-oriented model of networks consisting of components that can be glued together with connectors. This model is strongly inspired by a network model...... for railways madeby Bjørner et.al., however our model is more general: the components can be of any kind and can later be refined to e.g. railway components or circuit components. Then we show how the abstract network model can be refined into an explicit model for relay circuits. The circuit model describes...... the statics as well as the dynamics of relay circuits, i.e. how a relay circuit can be composed legally from electrical components as well as how the components may change state over time. Finally the circuit model is transformed into an executable model, and we show how a concrete circuit can be defined...

  11. Running CMS remote analysis builder jobs on advanced resource connector middleware

    International Nuclear Information System (INIS)

    Edelmann, E; Happonen, K; Koivumäki, J; Lindén, T; Välimaa, J

    2011-01-01

    CMS user analysis jobs are distributed over the grid with the CMS Remote Analysis Builder application (CRAB). According to the CMS computing model the applications should run transparently on the different grid flavours in use. In CRAB this is handled with different plugins that are able to submit to different grids. Recently a CRAB plugin for submitting to the Advanced Resource Connector (ARC) middleware has been developed. The CRAB ARC plugin enables simple and fast job submission with full job status information available. CRAB can be used with a server which manages and monitors the grid jobs on behalf of the user. In the presentation we will report on the CRAB ARC plugin and on the status of integrating it with the CRAB server and compare this with using the gLite ARC interoperability method for job submission.

  12. Low background materials and fabrication techniques for cables and connectors in the Majorana Demonstrator

    Science.gov (United States)

    Busch, M.; Abgrall, N.; Alvis, S. I.; Arnquist, I. J.; Avignone, F. T.; Barabash, A. S.; Barton, C. J.; Bertrand, F. E.; Bode, T.; Bradley, A. W.; Brudanin, V.; Buuck, M.; Caldwell, T. S.; Chan, Y.-D.; Christofferson, C. D.; Chu, P.-H.; Cuesta, C.; Detwiler, J. A.; Dunagan, C.; Efremenko, Yu.; Ejiri, H.; Elliott, S. R.; Gilliss, T.; Giovanetti, G. K.; Green, M. P.; Gruszko, J.; Guinn, I. S.; Guiseppe, V. E.; Haufe, C. R.; Hehn, L.; Henning, R.; Hoppe, E. W.; Howe, M. A.; Keeter, K. J.; Kidd, M. F.; Konovalov, S. I.; Kouzes, R. T.; Lopez, A. M.; Martin, R. D.; Massarczyk, R.; Meijer, S. J.; Mertens, S.; Myslik, J.; O'Shaughnessy, C.; Othman, G.; Poon, A. W. P.; Radford, D. C.; Rager, J.; Reine, A. L.; Rielage, K.; Robertson, R. G. H.; Rouf, N. W.; Shanks, B.; Shirchenko, M.; Suriano, A. M.; Tedeschi, D.; Trimble, J. E.; Varner, R. L.; Vasilyev, S.; Vetter, K.; Vorren, K.; White, B. R.; Wilkerson, J. F.; Wiseman, C.; Xu, W.; Yakushev, E.; Yu, C.-H.; Yumatov, V.; Zhitnikov, I.; Zhu, B. X.

    2018-01-01

    The Majorana Collaboration is searching for the neutrinoless double-beta decay of the nucleus 76Ge. The Majorana Demonstrator is an array of germanium detectors deployed with the aim of implementing background reduction techniques suitable for a tonne scale 76Ge-based search (the LEGEND collaboration). In the Demonstrator, germanium detectors operate in an ultra-pure vacuum cryostat at 80 K. One special challenge of an ultra-pure environment is to develop reliable cables, connectors, and electronics that do not significantly contribute to the radioactive background of the experiment. This paper highlights the experimental requirements and how these requirements were met for the Majorana Demonstrator, including plans to upgrade the wiring for higher reliability in the summer of 2018. Also described are requirements for LEGEND R&D efforts underway to meet these additional requirements

  13. Homology and cohomology of Rees semigroup algebras

    DEFF Research Database (Denmark)

    Grønbæk, Niels; Gourdeau, Frédéric; White, Michael C.

    2011-01-01

    Let S by a Rees semigroup, and let 1¹(S) be its convolution semigroup algebra. Using Morita equivalence we show that bounded Hochschild homology and cohomology of l¹(S) is isomorphic to those of the underlying discrete group algebra....

  14. Induction of homologous recombination in Saccharomyces cerevisiae.

    Science.gov (United States)

    Simon, J R; Moore, P D

    1988-09-01

    We have investigated the effects of UV irradiation of Saccharomyces cerevisiae in order to distinguish whether UV-induced recombination results from the induction of enzymes required for homologous recombination, or the production of substrate sites for recombination containing regions of DNA damage. We utilized split-dose experiments to investigate the induction of proteins required for survival, gene conversion, and mutation in a diploid strain of S. cerevisiae. We demonstrate that inducing doses of UV irradiation followed by a 6 h period of incubation render the cells resistant to challenge doses of UV irradiation. The effects of inducing and challenge doses of UV irradiation upon interchromosomal gene conversion and mutation are strictly additive. Using the yeast URA3 gene cloned in non-replicating single- and double-stranded plasmid vectors that integrate into chromosomal genes upon transformation, we show that UV irradiation of haploid yeast cells and homologous plasmid DNA sequences each stimulate homologous recombination approximately two-fold, and that these effects are additive. Non-specific DNA damage has little effect on the stimulation of homologous recombination, as shown by studies in which UV-irradiated heterologous DNA was included in transformation/recombination experiments. We further demonstrate that the effect of competing single- and double-stranded heterologous DNA sequences differs in UV-irradiated and unirradiated cells, suggesting an induction of recombinational machinery in UV-irradiated S. cerevisiae cells.

  15. Threading homology through algebra selected patterns

    CERN Document Server

    Boffi, Giandomenico

    2006-01-01

    Aimed at graduate students and researchers in mathematics, this book takes homological themes, such as Koszul complexes and their generalizations, and shows how these can be used to clarify certain problems in selected parts of algebra, as well as their success in solving a number of them.

  16. Cell biology of homologous recombination in yeast

    DEFF Research Database (Denmark)

    Eckert-Boulet, Nadine Valerie; Rothstein, Rodney; Lisby, Michael

    2011-01-01

    Homologous recombination is an important pathway for error-free repair of DNA lesions, such as single- and double-strand breaks, and for rescue of collapsed replication forks. Here, we describe protocols for live cell imaging of single-lesion recombination events in the yeast Saccharomyces...

  17. 3D Architecture of the Trypanosoma brucei Flagella Connector, a Mobile Transmembrane Junction.

    Directory of Open Access Journals (Sweden)

    Johanna L Höög

    2016-01-01

    Full Text Available Cellular junctions are crucial for the formation of multicellular organisms, where they anchor cells to each other and/or supportive tissue and enable cell-to-cell communication. Some unicellular organisms, such as the parasitic protist Trypanosoma brucei, also have complex cellular junctions. The flagella connector (FC is a three-layered transmembrane junction that moves with the growing tip of a new flagellum and attaches it to the side of the old flagellum. The FC moves via an unknown molecular mechanism, independent of new flagellum growth. Here we describe the detailed 3D architecture of the FC suggesting explanations for how it functions and its mechanism of motility.We have used a combination of electron tomography and cryo-electron tomography to reveal the 3D architecture of the FC. Cryo-electron tomography revealed layers of repetitive filamentous electron densities between the two flagella in the interstitial zone. Though the FC does not change in length and width during the growth of the new flagellum, the interstitial zone thickness decreases as the FC matures. This investigation also shows interactions between the FC layers and the axonemes of the new and old flagellum, sufficiently strong to displace the axoneme in the old flagellum. We describe a novel filament, the flagella connector fibre, found between the FC and the axoneme in the old flagellum.The FC is similar to other cellular junctions in that filamentous proteins bridge the extracellular space and are anchored to underlying cytoskeletal structures; however, it is built between different portions of the same cell and is unique because of its intrinsic motility. The detailed description of its structure will be an important tool to use in attributing structure / function relationships as its molecular components are discovered in the future. The FC is involved in the inheritance of cell shape, which is important for the life cycle of this human parasite.

  18. Design and fabrication of advanced fiber alignment structures for field-installable fiber connectors

    Science.gov (United States)

    Van Erps, Jürgen; Vervaeke, Michael; Sánchez Martínez, Alberto; Beri, Stefano; Debaes, Christof; Watté, Jan; Thienpont, Hugo

    2012-06-01

    Fiber-To-The-Home (FTTH) networks have been adopted as a potential replacement of traditional electrical connections for the 'last mile' transmission of information at bandwidths over 1Gb/s. However, the success and adoption of optical access networks critically depend on the quality and reliability of connections between optical fibers. In particular a further reduction of insertion loss of field-installable connectors must be achieved without a significant increase in component cost. This requires precise alignment of fibers that can differ in terms of ellipticity, eccentricity or diameter and seems hardly achievable using today's widespread ferrule-based alignment systems. Novel low-cost structures for bare fiber alignment with outstanding positioning accuracies are strongly desired as they would allow reducing loss beyond the level achievable with ferrule-bore systems. However, the realization of such alignment system is challenging as it should provide sufficient force to position the fiber with sub-micron accuracy required in positioning the fiber. In this contribution we propose, design and prototype a bare-fiber alignment system which makes use of deflectable/compressible micro-cantilevers. Such cantilevers behave as springs and provide self-centering functionality to the structure. Simulations of the mechanical properties of the cantilevers are carried out in order to get an analytical approximation and a mathematical model of the spring constant and stress in the structure. Elastic constants of the order of 104 to 105N/m are found out to be compatible with a proof stress of 70 MPa. Finally a first self-centering structure is prototyped in PMMA using our Deep Proton Writing technology. The spring constants of the fabricated cantilevers are in the range of 4 to 6 × 104N/m and the stress is in the range 10 to 20 MPa. These self-centering structures have the potential to become the basic building blocks for a new generation of field-installable connectors.

  19. Polar representation of centrifugal pump homologous curves

    International Nuclear Information System (INIS)

    Veloso, Marcelo Antonio; Mattos, Joao Roberto Loureiro de

    2008-01-01

    Essential for any mathematical model designed to simulate flow transient events caused by pump operations is the pump performance data. The performance of a centrifugal pump is characterized by four basic parameters: the rotational speed, the volumetric flow rate, the dynamic head, and the hydraulic torque. Any one of these quantities can be expressed as a function of any two others. The curves showing the relationships between these four variables are called the pump characteristic curves, also referred to as four-quadrant curves. The characteristic curves are empirically developed by the pump manufacturer and uniquely describe head and torque as functions of volumetric flow rate and rotation speed. Because of comprising a large amount of points, the four-quadrant configuration is not suitable for computational purposes. However, it can be converted to a simpler form by the development of the homologous curves, in which dynamic head and hydraulic torque ratios are expressed as functions of volumetric flow and rotation speed ratios. The numerical use of the complete set of homologous curves requires specification of sixteen partial curves, being eight for the dynamic head and eight for the hydraulic torque. As a consequence, the handling of homologous curves is still somewhat complicated. In solving flow transient problems that require the pump characteristic data for all the operation zones, the polar form appears as the simplest way to represent the homologous curves. In the polar method, the complete characteristics of a pump can be described by only two closed curves, one for the dynamic head and other for the hydraulic torque, both in function of a single angular coordinate defined adequately in terms of the quotient between volumetric flow ratio and rotation speed ratio. The usefulness and advantages of this alternative method are demonstrated through a practical example in which the homologous curves for a pump of the type used in the main coolant loops of a

  20. Parametric representation of centrifugal pump homologous curves

    International Nuclear Information System (INIS)

    Veloso, Marcelo A.; Mattos, Joao R.L. de

    2015-01-01

    Essential for any mathematical model designed to simulate flow transient events caused by pump operations is the pump performance data. The performance of a centrifugal pump is characterized by four basic quantities: the rotational speed, the volumetric flow rate, the dynamic head, and the hydraulic torque. The curves showing the relationships between these four variables are called the pump characteristic curves. The characteristic curves are empirically developed by the pump manufacturer and uniquely describe head and torque as functions of volumetric flow rate and rotation speed. Because of comprising a large amount of points, this configuration is not suitable for computational purposes. However, it can be converted to a simpler form by the development of the homologous curves, in which dynamic head and hydraulic torque ratios are expressed as functions of volumetric flow and rotation speed ratios. The numerical use of the complete set of homologous curves requires specification of sixteen partial curves, being eight for the dynamic head and eight for the hydraulic torque. As a consequence, the handling of homologous curves is still somewhat complicated. In solving flow transient problems that require the pump characteristic data for all the operation zones, the parametric form appears as the simplest way to deal with the homologous curves. In this approach, the complete characteristics of a pump can be described by only two closed curves, one for the dynamic head and other for the hydraulic torque, both in function of a single angular coordinate defined adequately in terms of the quotient between volumetric flow ratio and rotation speed ratio. The usefulness and advantages of this alternative method are demonstrated through a practical example in which the homologous curves for a pump of the type used in the main coolant loops of a pressurized water reactor (PWR) are transformed to the parametric form. (author)

  1. EH domain of EHD1

    Energy Technology Data Exchange (ETDEWEB)

    Kieken, Fabien; Jovic, Marko; Naslavsky, Naava; Caplan, Steve, E-mail: scaplan@unmc.edu; Sorgen, Paul L. [University of Nebraska Medical Center, Department of Biochemistry and Molecular Biology and Eppley Cancer Center (United States)], E-mail: psorgen@unmc.edu

    2007-12-15

    EHD1 is a member of the mammalian C-terminal Eps15 homology domain (EH) containing protein family, and regulates the recycling of various receptors from the endocytic recycling compartment to the plasma membrane. The EH domain of EHD1 binds to proteins containing either an Asn-Pro-Phe or Asp-Pro-Phe motif, and plays an important role in the subcellular localization and function of EHD1. Thus far, the structures of five N-terminal EH domains from other proteins have been solved, but to date, the structure of the EH domains from the four C-terminal EHD family paralogs remains unknown. In this study, we have assigned the 133 C-terminal residues of EHD1, which includes the EH domain, and solved its solution structure. While the overall structure resembles that of the second of the three N-terminal Eps15 EH domains, potentially significant differences in surface charge and the structure of the tripeptide-binding pocket are discussed.

  2. EH domain of EHD1

    International Nuclear Information System (INIS)

    Kieken, Fabien; Jovic, Marko; Naslavsky, Naava; Caplan, Steve; Sorgen, Paul L.

    2007-01-01

    EHD1 is a member of the mammalian C-terminal Eps15 homology domain (EH) containing protein family, and regulates the recycling of various receptors from the endocytic recycling compartment to the plasma membrane. The EH domain of EHD1 binds to proteins containing either an Asn-Pro-Phe or Asp-Pro-Phe motif, and plays an important role in the subcellular localization and function of EHD1. Thus far, the structures of five N-terminal EH domains from other proteins have been solved, but to date, the structure of the EH domains from the four C-terminal EHD family paralogs remains unknown. In this study, we have assigned the 133 C-terminal residues of EHD1, which includes the EH domain, and solved its solution structure. While the overall structure resembles that of the second of the three N-terminal Eps15 EH domains, potentially significant differences in surface charge and the structure of the tripeptide-binding pocket are discussed

  3. Classification and Lineage Tracing of SH2 Domains Throughout Eukaryotes.

    Science.gov (United States)

    Liu, Bernard A

    2017-01-01

    Today there exists a rapidly expanding number of sequenced genomes. Cataloging protein interaction domains such as the Src Homology 2 (SH2) domain across these various genomes can be accomplished with ease due to existing algorithms and predictions models. An evolutionary analysis of SH2 domains provides a step towards understanding how SH2 proteins integrated with existing signaling networks to position phosphotyrosine signaling as a crucial driver of robust cellular communication networks in metazoans. However organizing and tracing SH2 domain across organisms and understanding their evolutionary trajectory remains a challenge. This chapter describes several methodologies towards analyzing the evolutionary trajectory of SH2 domains including a global SH2 domain classification system, which facilitates annotation of new SH2 sequences essential for tracing the lineage of SH2 domains throughout eukaryote evolution. This classification utilizes a combination of sequence homology, protein domain architecture and the boundary positions between introns and exons within the SH2 domain or genes encoding these domains. Discrete SH2 families can then be traced across various genomes to provide insight into its origins. Furthermore, additional methods for examining potential mechanisms for divergence of SH2 domains from structural changes to alterations in the protein domain content and genome duplication will be discussed. Therefore a better understanding of SH2 domain evolution may enhance our insight into the emergence of phosphotyrosine signaling and the expansion of protein interaction domains.

  4. Structural analysis of the Csk homologous kinase CHK

    International Nuclear Information System (INIS)

    Mulhern, T.; Chong, Y.-P.; Cheng, H.-C.

    2003-01-01

    Full text: CHK (Csk homologous kinase) is an intracellular protein tyrosine kinase, which is highly expressed in the haematopoietic system and the brain. The in vivo role of CHK is to specifically phosphorylate and deactivate the Src family of protein tyrosine kinases. The members of the Src family: Src, Blk, Fyn, Fgr, Hck, Lck, Lyn, Yes and Yrk are major players in numerous cell signalling pathways and exquisitely tuned control of Src family activity is fundamental to many processes in normal cells (reviewed in Lowell and Soriano, 1996). For example, the Src family kinase Fyn is highly expressed in the brain and its activity is vital for memory and learning. In the haematopoietic system, the Src family kinase Hck controls cytoskeletal reorganization, cell motility and immunologic activation. While the Csk family enzymes are closely related to the Src proteins (∼37% identity), the x-ray crystal structures of Src (Xu et al., 1997) and Csk (Ogawa et al., 2002) do display several important differences. Unlike Src, the Csk the SH2 and SH3 domains do not bind intramolecular ligands and they adopt a strikingly different disposition to that observed in Src. Another interesting feature is that the linkers between the SH3 and SH2 domains and between the SH2 and kinase domains, are in intimate contact with the N-lobe of kinase and both appear to play important roles in regulation of the kinase activity. However, the structural and functional basis of how this can be altered is still unclear. We describe the results of biochemical analyses of CHK mediated deactivation of Hck, which suggest that in addition to direct tail-phosphorylation, protein-protein interactions are important. We also describe heteronuclear NMR studies of the structure and ligand binding properties of the CHK SH2 and SH3 domains with a particular emphasis on the transmission of regulatory signals from the ligand binding sites to the interdomain linkers

  5. Csk Homologous Kinase, a Potential Regulator of CXCR4-Medicated Breast Cancer Cell Metastasis

    Science.gov (United States)

    2011-08-01

    is a non-receptor tyrosine kinase and a second member of the Csk family. Like Csk, CHK has Src homology 2 ( SH2 ) and SH3 domains and lacks the...MSCV-retroviral vectors encoding either wild-type CHK or kinase -dead CHK or wild type SH2 domain or SH2 -R147A or SH2 -G129A. All these constructs were... Kinase , a Potential Regulator of CXCR4-Medicated Breast Cancer Cell Metastasis Byeong-Chel Lee The University of Pittsburgh Pittsburgh, PA 15213

  6. Domain crossing

    DEFF Research Database (Denmark)

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

    2012-01-01

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

  7. Homologation Reaction of Ketones with Diazo Compounds.

    Science.gov (United States)

    Candeias, Nuno R; Paterna, Roberta; Gois, Pedro M P

    2016-03-09

    This review covers the addition of diazo compounds to ketones to afford homologated ketones, either in the presence or in the absence of promoters or catalysts. Reactions with diazoalkanes, aryldiazomethanes, trimethylsilyldiazomethane, α-diazo esters, and disubstituted diazo compounds are covered, commenting on the complex regiochemistry of the reaction and the nature of the catalysts and promoters. The recent reports on the enantioselective version of ketone homologation reactions are gathered in one section, followed by reports on the use of cyclic ketones ring expansion in total synthesis. Although the first reports of this reaction appeared in the literature almost one century ago, the recent achievements, in particular, for the asymmetric version, forecast the development of new breakthroughs in the synthetically valuable field of diazo chemistry.

  8. Homological mirror symmetry and tropical geometry

    CERN Document Server

    Catanese, Fabrizio; Kontsevich, Maxim; Pantev, Tony; Soibelman, Yan; Zharkov, Ilia

    2014-01-01

    The relationship between Tropical Geometry and Mirror Symmetry goes back to the work of Kontsevich and Y. Soibelman (2000), who applied methods of non-archimedean geometry (in particular, tropical curves) to Homological Mirror Symmetry. In combination with the subsequent work of Mikhalkin on the “tropical” approach to Gromov-Witten theory, and the work of Gross and Siebert, Tropical Geometry has now become a powerful tool. Homological Mirror Symmetry is the area of mathematics concentrated around several categorical equivalences connecting symplectic and holomorphic (or algebraic) geometry. The central ideas first appeared in the work of Maxim Kontsevich (1993). Roughly speaking, the subject can be approached in two ways: either one uses Lagrangian torus fibrations of Calabi-Yau manifolds (the so-called Strominger-Yau-Zaslow picture, further developed by Kontsevich and Soibelman) or one uses Lefschetz fibrations of symplectic manifolds (suggested by Kontsevich and further developed by Seidel). Tropical Ge...

  9. Homological stability for unordered configuration spaces

    DEFF Research Database (Denmark)

    Randal-Williams, Oscar

    2013-01-01

    This paper consists of two related parts. In the first part we give a self-contained proof of homological stability for the spaces C_n(M;X) of configurations of n unordered points in a connected open manifold M with labels in a path-connected space X, with the best possible integral stability range...... of the spaces C_n(M) can be considered stable when M is a closed manifold. In this case there are no stabilisation maps, but one may still ask if the dimensions of the homology groups over some field stabilise with n. We prove that this is true when M is odd-dimensional, or when the field is F_2 or Q...

  10. Regulation of homologous recombination in eukaryotes

    OpenAIRE

    Heyer, Wolf-Dietrich; Ehmsen, Kirk T.; Liu, Jie

    2010-01-01

    Homologous recombination is required for accurate chromosome segregation during the first meiotic division and constitutes a key repair and tolerance pathway for complex DNA damage including DNA double-stranded breaks, interstrand crosslinks, and DNA gaps. In addition, recombination and replication are inextricably linked, as recombination recovers stalled and broken replication forks enabling the evolution of larger genomes/replicons. Defects in recombination lead to genomic instability and ...

  11. Khovanov homology of graph-links

    Energy Technology Data Exchange (ETDEWEB)

    Nikonov, Igor M [M. V. Lomonosov Moscow State University, Faculty of Mechanics and Mathematics, Moscow (Russian Federation)

    2012-08-31

    Graph-links arise as the intersection graphs of turning chord diagrams of links. Speaking informally, graph-links provide a combinatorial description of links up to mutations. Many link invariants can be reformulated in the language of graph-links. Khovanov homology, a well-known and useful knot invariant, is defined for graph-links in this paper (in the case of the ground field of characteristic two). Bibliography: 14 titles.

  12. Quandle and Biquandle Homology Calculation in R

    Directory of Open Access Journals (Sweden)

    Roger Fenn

    2018-01-01

    Full Text Available In knot theory several knot invariants have been found over the last decades. This paper concerns itself with invariants of several of those invariants, namely the Homology of racks, quandles, biracks and biquandles. The software described in this paper calculates the rack, quandle and degenerate homology groups of racks and biracks. It works for any rack/quandle with finite elements where there are homology coefficients in 'Z'k. The up and down actions can be given either as a function of the elements of 'Z'k or provided as a matrix. When calculating a rack, the down action should coincide with the identity map. We have provided actions for both the general dihedral quandle and the group quandle over 'S'3. We also provide a second function to test if a set with a given action (or with both actions gives rise to a quandle or biquandle. The program is provided as an R package and can be found at https://github.com/ansgarwenzel/quhomology.   AMS subject classification: 57M27; 57M25

  13. Several aspects of some techniques avoiding homologous blood transfusions

    NARCIS (Netherlands)

    E.C.S.M. van Woerkens (Liesbeth)

    1998-01-01

    textabstractThe use of homologous blood products during anesthesia and surgery is not without risks. Complications due to homologous blood transfusions include transfusion reactions, isosensitization, transmission of infections (including HIV, hepatitis, CMV) and immunosuppression (resuiting in

  14. Computing Homology Group Generators of Images Using Irregular Graph Pyramids

    OpenAIRE

    Peltier , Samuel; Ion , Adrian; Haxhimusa , Yll; Kropatsch , Walter; Damiand , Guillaume

    2007-01-01

    International audience; We introduce a method for computing homology groups and their generators of a 2D image, using a hierarchical structure i.e. irregular graph pyramid. Starting from an image, a hierarchy of the image is built, by two operations that preserve homology of each region. Instead of computing homology generators in the base where the number of entities (cells) is large, we first reduce the number of cells by a graph pyramid. Then homology generators are computed efficiently on...

  15. 机械设计中联接件的自动选用%Autoselection of the Connector in Mechanical Design

    Institute of Scientific and Technical Information of China (English)

    徐静; 翁慧燕; 董雁

    2001-01-01

    介绍机械静联接在机械设计中的选用方法。建立了联接件的国标数据库及其查询、维护程序;编制了对所选联接件的计算校核程序;并开发了自动绘制联接件的软件,从而实现了机械CAD中联接件自动选用、校核、绘图的集成。%This paper deals with the selection of connector in mechanical design. Database of connector and its corresponding function for indexing, safekeeping and proof calculating are built up. Software for the drawing of connector on the environment of AutoCAD is also developed. So automatics selection, proof calculating and drawing of connector are achieved in mechanical computer aided design.

  16. The SiBI connector: a new medical device to facilitate preoxygenation and reduce waste anesthetic gases during inhaled induction with sevoflurane.

    Science.gov (United States)

    Colas, M J; Tétrault, J P; Dumais, L; Truong, P; Claprood, Y; Martin, R

    2000-12-01

    The SiBI connector is a new medical device used for vital capacity inhaled induction with sevoflurane. It allows efficient preoxygenation of patients and reduces waste anesthetic gases in the operation room during induction.

  17. Development of 30-pin connectors for electronic modules of C and I systems for NPP's confirming to customized MIL STD-1344 requirements

    International Nuclear Information System (INIS)

    Marathe, P.P.; Madala, Kalyan C.; Ramakrishna, P.

    2014-01-01

    The electrical connectors form an important constituent of C and I system where customized circuits and hardware is required to be configured meeting the Nuclear Power Plant regulatory requirements. C and I hardware has to handle multiple hundreds of I/O's and the system architectures are made in modular construction having C and I system hardware packaged in plug-in electronic modules in the required form factors. In addition if the system has to satisfy customized JSS 55555 requirements meeting stringent shock, vibration and environmental specifications, the connectors used for the electronic modules shall meet the customized MIL STD-1344 requirements and meet reliability target for the system. 30-pin type special connectors for electronic modules and 2x30 (60) pin field cabling connectors were developed meeting the required qualification specifications. (author)

  18. A new mode of SAM domain mediated oligomerization observed in the CASKIN2 neuronal scaffolding protein

    KAUST Repository

    Smirnova, Ekaterina; Kwan, Jamie J.; Siu, Ryan; Gao, Xin; Zoidl, Georg; Demeler, Borries; Saridakis, Vivian; Donaldson, Logan W.

    2016-01-01

    Background: CASKIN2 is a homolog of CASKIN1, a scaffolding protein that participates in a signaling network with CASK (calcium/calmodulin-dependent serine kinase). Despite a high level of homology between CASKIN2 and CASKIN1, CASKIN2 cannot bind CASK due to the absence of a CASK Interaction Domain and consequently, may have evolved undiscovered structural and functional distinctions.

  19. A new mode of SAM domain mediated oligomerization observed in the CASKIN2 neuronal scaffolding protein

    KAUST Repository

    Smirnova, Ekaterina

    2016-08-22

    Background: CASKIN2 is a homolog of CASKIN1, a scaffolding protein that participates in a signaling network with CASK (calcium/calmodulin-dependent serine kinase). Despite a high level of homology between CASKIN2 and CASKIN1, CASKIN2 cannot bind CASK due to the absence of a CASK Interaction Domain and consequently, may have evolved undiscovered structural and functional distinctions.

  20. Membrane localization is critical for activation of the PICK1 BAR domain

    DEFF Research Database (Denmark)

    Madsen, Kenneth L; Eriksen, Jacob; Milan-Lobo, Laura

    2008-01-01

    The PSD-95/Discs-large/ZO-1 homology (PDZ) domain protein, protein interacting with C kinase 1 (PICK1) contains a C-terminal Bin/amphiphysin/Rvs (BAR) domain mediating recognition of curved membranes; however, the molecular mechanisms controlling the activity of this domain are poorly understood....

  1. Trusted Domain

    DEFF Research Database (Denmark)

    Hjorth, Theis Solberg; Torbensen, Rune

    2012-01-01

    remote access via IP-based devices such as smartphones. The Trusted Domain platform fits existing legacy technologies by managing their interoperability and access controls, and it seeks to avoid the security issues of relying on third-party servers outside the home. It is a distributed system...... of wireless standards, limited resources of embedded systems, etc. Taking these challenges into account, we present a Trusted Domain home automation platform, which dynamically and securely connects heterogeneous networks of Short-Range Wireless devices via simple non-expert user. interactions, and allows......In the digital age of home automation and with the proliferation of mobile Internet access, the intelligent home and its devices should be accessible at any time from anywhere. There are many challenges such as security, privacy, ease of configuration, incompatible legacy devices, a wealth...

  2. DEVELOPMENT OF REMOTE HANFORD CONNECTOR GASKET REPLACEMENT TOOLING FOR THE SAVANNAH RIVER SITE'S DEFENSE WASTE PROCESSING FACILITY

    International Nuclear Information System (INIS)

    Krementz, D

    2007-01-01

    The Savannah River Site's (SRS) Defense Waste Processing Facility (DWPF) requested development of tooling for remote replacement of gaskets in mechanical Hanford connectors. The facility has compressed air supply, two master-slave manipulators (MSM's) and a lightweight robotic arm for operation of the remote tools. The Savannah River National Laboratory (SRNL) developed and tested multiple tools to perform the gasket replacement tasks. Separate pneumatic snap-ring removal tools that use the connector skirt as a reaction surface were developed for removal of the snap ring and spent gasket on both vertical and horizontal Hanford connectors. A pneumatic tool that clamps and centers on the jumper pipe ID was developed to simultaneously install the new gasket and snap ring. A pneumatic snap-ring-loading tool was developed that compresses the snap ring and places it in a groove in the installation tool. All of the tools are located on a custom work table with a pneumatic valve station that directs compressed air to the desired tool and vents the tools as needed. The entire system has been successfully tested using MSM's to manipulate the various tools. Deployment of the entire system is expected during FY08. The Hanford connector gasket replacement tooling has been successfully tested using MSM's to manipulate the various tools. Nitric acid is used in many of the decontamination processes performed in the REDC, where the tooling will be deployed. Although most of the tool components were fabricated/purchased with nitric acid and radioactive service in mind, some of the prototype parts must be replaced with parts that are more compatible with nitric acid/radioactive service. Several modifications to the various tools are needed to facilitate maintenance and replacement of failed components. Development of installation tools for replacement of 1-inch, 2-inch and multi-hole gaskets is being considered. Deployment of the existing system in the DWPF REDC is expected during FY

  3. 1 GSPS digitizer based on the FPGA Mezzanine Card (FMC) standard with low-count pin connector.

    CERN Document Server

    Vasilyev, Mikhail

    2015-01-01

    Under the scope of a CERN summer student project, the schematic for ADC based on FMC mezzanine card with 1 GSPS sampling rate and 8 bit resolution was developed. The mezzanine is fully compatible with the standard: FPGA Mezzanine Card (FMC) [1]. A low-pin count connector was used to connect the mezzanine with the “carrier”. The carrier was an Open Hardware project: Simple PCIe FMC carrier (SPEC).

  4. Mould insert fabrication of a single-mode fibre connector alignment structure optimized by justified partial metallization

    International Nuclear Information System (INIS)

    Wissmann, Markus; Barié, Nicole; Guttmann, Markus; Schneider, Marc; Kolew, Alexander; Besser, Heino; Pfleging, Wilhelm; Hofmann, Andreas; Van Erps, Jürgen; Beri, Stefano; Watté, Jan

    2015-01-01

    For mass production of multiscale-optical components, microstructured moulding tools are needed. Metal tools are used for hot embossing or injection moulding of microcomponents made of a thermoplastic polymer. Microstructures with extremely tight specifications, e.g. low side wall roughness and high aspect ratios are generally made by lithographic procedures such as x-ray lithography or deep proton writing. However, these processes are unsuitable for low-cost mass production. An alternative manufacturing method of moulding tools has been developed at the Karlsruhe Institute of Technology (KIT). This article describes a mould insert fabrication and a new replication process for self-centring fibre alignment structures for low loss field installable single-mode fibre connectors, developed and fabricated by the Vrije Universiteit Brussel (VUB) in collaboration with TE Connectivity. These components are to be used in fibre-to-the-home networks and support the deployment and maintenance of fibre optic links. The special feature of this particular fibre connector is a self-centring fibre alignment, achieved by means of a through hole with deflectable cantilevers acting as micro-springs. The particular challenge is the electroforming of through holes with a centre hole diameter smaller than 125 µm. The fibre connector structure is prototyped by deep proton writing in polymethylmethacrylate and used as a sacrificial part. Using joining, physical vapour deposition and electroforming technology, a negative copy of the prototyped connector is transferred into nickel to be used as a moulding tool. The benefits of this replication technique are a rapid and economical fabrication of moulding tools with high-precision microstructures and a long tool life. With these moulding tools low-cost mass production is possible. We present the manufacturing chain we have established. Each individual manufacturing step of the mould insert fabrication will be shown in this report. The

  5. A prospective clinical trial to assess peripheral venous catheter-related phlebitis using needleless connectors in a surgery department.

    Science.gov (United States)

    Ronen, Ohad; Shlomo, Fanny; Ben-Adiva, Gila; Edri, Zehava; Shema-Didi, Lilach

    2017-10-01

    The use of intravascular catheters is often complicated by phlebitis, which is associated with increased morbidity and extended duration of hospitalization. We conducted a study to investigate the impact of needleless intravenous access devices on the rate of phlebitis in peripheral venous catheters (PVCs). We prospectively recruited patients in 2 phases. The first group was treated with a regular cap, and the second group was treated with a needleless connector. The incidence of catheter-related phlebitis (CRP) was recorded as the primary end point. A total of 620 PVCs using regular caps were inserted into 340 patients and CRP rates were recorded. In the second phase of the study, 169 PVCs using needleless connectors were inserted into 135 patients. In the group treated with the regular cap, the CRP rate was 60% compared with 7% in the group treated with the needleless cap (P phlebitis had a statistically significant longer mean hospitalization period (P <.001), as were patients in the regular cap group (P <.01). The use of needleless connectors was found to be associated with a significant reduction of CRP in peripheral veins in a surgery department setting. The decreased morbidity resulted in a lower number of catheter replacements and duration of hospitalization. Copyright © 2017 Association for Professionals in Infection Control and Epidemiology, Inc. Published by Elsevier Inc. All rights reserved.

  6. Failure Analysis of a Nickel-Plated Electronic Connector Due to Salt-Induced Corrosion (ENGE 2014).

    Science.gov (United States)

    Lee, Na-Ri; Choi, Hyoung-Seuk; Choi, Duck-Kyun

    2015-10-01

    When electronic connectors in mobile devices are miniaturized, the thickness of plating decreases. However, this thin plating is expected to decrease the life of the connector due to problems with corrosion. In this study, salt spray aging tests were performed on miniaturized nickel-plated stainless steel electronic connectors to observe failure mechanisms in realistic environments. The tests were performed three times using a 5% NaCl solution in an atmosphere of 45 °C; each test included several cycles where one cycle was one 24-h period consisting of 8 h of salt spray and 16 h without salt spray. The nickel-plating layers were periodically observed by electron probe X-ray micro-analyzer, wavelength dispersive spectroscopy, and field-emission scanning electron microscopy to analyze and identify the corrosion mechanism. We found that the primary failure mode of the nickel plating is blistering and delamination. The corrosion mechanism is typically a chain reaction of several corrosion mechanisms: pitting corrosion --> stress corrosion cracking --> hydrogen-induced cracking --> blistering and delamination. Finally, we discuss countermeasures to prevent corrosion of the nickel layer based on the corrosion mechanisms identified in this study.

  7. Evaluating the efficacy of a structure-derived amino acid substitution matrix in detecting protein homologs by BLAST and PSI-BLAST

    Directory of Open Access Journals (Sweden)

    Nalin CW Goonesekere

    2009-06-01

    Full Text Available Nalin CW GoonesekereDepartment of Chemistry and Biochemistry, University of Northern iowa, Cedar Falls, IA, USAAbstract: The large numbers of protein sequences generated by whole genome sequencing projects require rapid and accurate methods of annotation. The detection of homology through computational sequence analysis is a powerful tool in determining the complex evolutionary and functional relationships that exist between proteins. Homology search algorithms employ amino acid substitution matrices to detect similarity between proteins sequences. The substitution matrices in common use today are constructed using sequences aligned without reference to protein structure. Here we present amino acid substitution matrices constructed from the alignment of a large number of protein domain structures from the structural classification of proteins (SCOP database. We show that when incorporated into the homology search algorithms BLAST and PSI-blaST, the structure-based substitution matrices enhance the efficacy of detecting remote homologs. Keywords: computational biology, protein homology, amino acid substitution matrix, protein structure

  8. Carrier behavior in special multilayer device composed of different transition metal oxide-based intermediate connectors

    International Nuclear Information System (INIS)

    Deng, Yan-Hong; Chen, Xiang-Yu; Ou, Qing-Dong; Wang, Qian-Kun; Jiang, Xiao-Cheng; Zhang, Dan-Dan; Li, Yan-Qing

    2014-01-01

    The impact of illumination on the connection part of the tandem organic light-emitting diodes was studied by using a special organic multilayer sample consisted of two organic active layers coupled with different transition metal oxide (TMO)-based intermediate connectors (ICs). Through measuring the current density-voltage characteristic, interfacial electronic structures, and capacitance-voltage characteristic, we observe an unsymmetrical phenomenon in current density-voltage and capacitance-voltage curves of Mg:Alq 3 /MoO 3 and MoO 3 composed devices, which was induced by the charge spouting zone near the ICs region and the recombination state in the MoO 3 layer. Moreover, Mg:Alq 3 /MoO 3 composed device displays a photovoltaic effect and the V oc shifts to forward bias under illumination. Our results demonstrate that the TMO-based IC structure coupled with photovoltaic effect can be a good approach for the study of photodetector, light sensor, and so on.

  9. Optimization of traceable coaxial RF reflection standards with 7-mm-N-connector using genetic algorithms

    Directory of Open Access Journals (Sweden)

    T. Schrader

    2003-01-01

    Full Text Available A new coaxial device with 7-mm-N-connector was developed providing calculable complex reflection coefficients for traceable calibration of vector network analyzers (VNA. It was specifically designed to fill the gap between 0 Hz (DC, direct current and 250MHz, though the device was tested up to 10GHz. The frequency dependent reflection coefficient of this device can be described by a model, which is characterized by traceable measurements. It is therefore regarded as a “traceable model". The new idea of using such models for traceability has been verified, found to be valid and was used for these investigations. The DC resistance value was extracted from RF measurements up to 10 GHz by means of Genetic Algorithms (GA. The GA was used to obtain the elements of the model describing the reflection coefficient Γ of a network of SMD resistors. The DC values determined with the GA from RF measurements match the traceable value at DC within 3·10-3, which is in good agreement with measurements using reference air lines at GHz frequencies.

  10. Expression of TGF-β in Fractures Fixed by Nitinol Swan-like Memory Compressive Connectors

    Science.gov (United States)

    Li, M.; Zhang, C. C.; Xu, S. G.; Fu, Q. G.

    2011-07-01

    In this article, the effect of internal fixation of a Nitinol swan-like memory compressive connector (SMC) on the temporal expression of transforming growth factor-β (TGF-β) at fracture sites is evaluated. Specimens were collected from 35 New Zealand rabbits modeled for bilateral humeral fracture fixed with either SMC or stainless dynamic compression plate (DCP). Five rabbits each were killed at day 1, 3, 7, 14, 21, 28, and 56. The local positive staining potency, positive area ratio, and positive index of TGF-β were measured using an immunohistochemistry approach (EnVision) in combination with a computerized image analysis system. TGF-β staining was seen in mesenchymal cells, osteoblasts, chondrocytes, and in the extracellular matrix of fractures fixed in both the SMC and the DCP samples without a significant difference in staining at both the early stages (days 1 and 3) and day 56. A higher TGF-β content was observed in the fractures fixed with SMC when compared to that of DCP from day 7 to 28. As a conclusion, TGF-β is highly expressed in fractures fixed with SMC during chondrogenesis stage and entochondrostosis stage. Finally, the mechanism of how SMC promoting synthesis and secretion of TGF-β in the process of fracture healing has been discussed.

  11. Experimental investigation on the electrical contact behavior of rolling contact connector

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Junxing; Yang, Fei, E-mail: yfei2007@mail.xjtu.edu.cn; Luo, Kaiyu; Zhu, Mingliang; Wu, Yi; Rong, Mingzhe [State Key Laboratory of Electrical Insulation and Power Equipment, Xi’an Jiaotong University, Xi’an 710049 (China)

    2015-12-15

    Rolling contact connector (RCC) is a new technology utilized in high performance electric power transfer systems with one or more rotating interfaces, such as radars, satellites, wind generators, and medical computed tomography machines. Rolling contact components are used in the RCC instead of traditional sliding contacts to transfer electrical power and/or signal. Since the requirement of the power transmission is increasing in these years, the rolling electrical contact characteristics become more and more important for the long-life design of RCC. In this paper, a typical form of RCC is presented. A series of experimental work are carried out to investigate the rolling electrical contact characteristics during its lifetime. The influence of a variety of factors on the electrical contact degradation behavior of RCC is analyzed under both vacuum and air environment. Based on the surface morphology and elemental composition changes in the contact zone, which are assessed by field emission scanning electron microscope and confocal laser scanning microscope, the mechanism of rolling electrical contact degradation is discussed.

  12. Homology analyses of the protein sequences of fatty acid synthases from chicken liver, rat mammary gland, and yeast

    International Nuclear Information System (INIS)

    Chang, Soo-Ik; Hammes, G.G.

    1989-01-01

    Homology analyses of the protein sequences of chicken liver and rat mammary gland fatty acid synthases were carried out. The amino acid sequences of the chicken and rat enzymes are 67% identical. If conservative substitutions are allowed, 78% of the amino acids are matched. A region of low homologies exists between the functional domains, in particular around amino acid residues 1059-1264 of the chicken enzyme. Homologies between the active sites of chicken and rat and of chicken and yeast enzymes have been analyzed by an alignment method. A high degree of homology exists between the active sites of the chicken and rat enzymes. However, the chicken and yeast enzymes show a lower degree of homology. The DADPH-binding dinucleotide folds of the β-ketoacyl reductase and the enoyl reductase sites were identified by comparison with a known consensus sequence for the DADP- and FAD-binding dinucleotide folds. The active sites of all of the enzymes are primarily in hydrophobic regions of the protein. This study suggests that the genes for the functional domains of fatty acid synthase were originally separated, and these genes were connected to each other by using different connecting nucleotide sequences in different species. An alternative explanation for the differences in rat and chicken is a common ancestry and mutations in the joining regions during evolution

  13. Molecular characterization of DnaJ 5 homologs in silkworm Bombyx mori and its expression during egg diapause.

    Science.gov (United States)

    Sirigineedi, Sasibhushan; Vijayagowri, Esvaran; Murthy, Geetha N; Rao, Guruprasada; Ponnuvel, Kangayam M

    2014-12-01

    A comparison of the cDNA sequences (1 056 bp) of Bombyx mori DnaJ 5 homolog with B. mori genome revealed that unlike in other Hsps, it has an intron of 234 bp. The DnaJ 5 homolog contains 351 amino acids, of which 70 contain the conserved DnaJ domain at the N-terminal end. This homolog of B. mori has all desirable functional domains similar to other insects, and the 13 different DnaJ homologs identified in B. mori genome were distributed on different chromosomes. The expressed sequence tag database analysis of Hsp40 gene expression revealed higher expression in wing disc followed by diapause-induced eggs. Microarray analysis revealed higher expression of DnaJ 5 homolog at 18th h after oviposition in diapause-induced eggs. Further validation of DnaJ 5 expression through qPCR in diapause-induced and nondiapause eggs at different time intervals revealed higher expression in diapause eggs at 18 and 24 h after oviposition, which coincided with the expression of Hsp70 as the Hsp 40 is its co-chaperone. This study thus provides an outline of the genome organization of Hsp40 gene, and its role in egg diapause induction in B. mori. © 2013 Institute of Zoology, Chinese Academy of Sciences.

  14. Hochschild Homology and Cohomology of Klein Surfaces

    Directory of Open Access Journals (Sweden)

    Frédéric Butin

    2008-09-01

    Full Text Available Within the framework of deformation quantization, a first step towards the study of star-products is the calculation of Hochschild cohomology. The aim of this article is precisely to determine the Hochschild homology and cohomology in two cases of algebraic varieties. On the one hand, we consider singular curves of the plane; here we recover, in a different way, a result proved by Fronsdal and make it more precise. On the other hand, we are interested in Klein surfaces. The use of a complex suggested by Kontsevich and the help of Groebner bases allow us to solve the problem.

  15. Homology in vertebrates bone mineral structure

    International Nuclear Information System (INIS)

    Batdehmbehrehl, G.; Chultehm, D.; Sangaa, D.

    1999-01-01

    Using the neutron diffraction method a domination of low crystal syngonic (sp. gr. P63/m) phase Ca 5 [PO 4 ] 3 (OH, F, Cl) in bull and sheep bones as well as in the fossil dinosaur bone has been established and crystal phases in all the bones have identical structure (homology). The result becomes to be an important contribution to fundamental science such as biological evolution and to be useful in medical practice and solution of radiobiological problems connected with vertebrates and man. (author)

  16. Homological Perturbation Theory for Nonperturbative Integrals

    Science.gov (United States)

    Johnson-Freyd, Theo

    2015-11-01

    We use the homological perturbation lemma to produce explicit formulas computing the class in the twisted de Rham complex represented by an arbitrary polynomial. This is a non-asymptotic version of the method of Feynman diagrams. In particular, we explain that phenomena usually thought of as particular to asymptotic integrals in fact also occur exactly: integrals of the type appearing in quantum field theory can be reduced in a totally algebraic fashion to integrals over an Euler-Lagrange locus, provided this locus is understood in the scheme-theoretic sense, so that imaginary critical points and multiplicities of degenerate critical points contribute.

  17. SANSparallel: interactive homology search against Uniprot.

    Science.gov (United States)

    Somervuo, Panu; Holm, Liisa

    2015-07-01

    Proteins evolve by mutations and natural selection. The network of sequence similarities is a rich source for mining homologous relationships that inform on protein structure and function. There are many servers available to browse the network of homology relationships but one has to wait up to a minute for results. The SANSparallel webserver provides protein sequence database searches with immediate response and professional alignment visualization by third-party software. The output is a list, pairwise alignment or stacked alignment of sequence-similar proteins from Uniprot, UniRef90/50, Swissprot or Protein Data Bank. The stacked alignments are viewed in Jalview or as sequence logos. The database search uses the suffix array neighborhood search (SANS) method, which has been re-implemented as a client-server, improved and parallelized. The method is extremely fast and as sensitive as BLAST above 50% sequence identity. Benchmarks show that the method is highly competitive compared to previously published fast database search programs: UBLAST, DIAMOND, LAST, LAMBDA, RAPSEARCH2 and BLAT. The web server can be accessed interactively or programmatically at http://ekhidna2.biocenter.helsinki.fi/cgi-bin/sans/sans.cgi. It can be used to make protein functional annotation pipelines more efficient, and it is useful in interactive exploration of the detailed evidence supporting the annotation of particular proteins of interest. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  18. Functional Coverage of the Human Genome by Existing Structures, Structural Genomics Targets, and Homology Models.

    Directory of Open Access Journals (Sweden)

    2005-08-01

    Full Text Available The bias in protein structure and function space resulting from experimental limitations and targeting of particular functional classes of proteins by structural biologists has long been recognized, but never continuously quantified. Using the Enzyme Commission and the Gene Ontology classifications as a reference frame, and integrating structure data from the Protein Data Bank (PDB, target sequences from the structural genomics projects, structure homology derived from the SUPERFAMILY database, and genome annotations from Ensembl and NCBI, we provide a quantified view, both at the domain and whole-protein levels, of the current and projected coverage of protein structure and function space relative to the human genome. Protein structures currently provide at least one domain that covers 37% of the functional classes identified in the genome; whole structure coverage exists for 25% of the genome. If all the structural genomics targets were solved (twice the current number of structures in the PDB, it is estimated that structures of one domain would cover 69% of the functional classes identified and complete structure coverage would be 44%. Homology models from existing experimental structures extend the 37% coverage to 56% of the genome as single domains and 25% to 31% for complete structures. Coverage from homology models is not evenly distributed by protein family, reflecting differing degrees of sequence and structure divergence within families. While these data provide coverage, conversely, they also systematically highlight functional classes of proteins for which structures should be determined. Current key functional families without structure representation are highlighted here; updated information on the "most wanted list" that should be solved is available on a weekly basis from http://function.rcsb.org:8080/pdb/function_distribution/index.html.

  19. Homologous Recombination—Experimental Systems, Analysis and Significance

    Science.gov (United States)

    Kuzminov, Andrei

    2014-01-01

    Homologous recombination is the most complex of all recombination events that shape genomes and produce material for evolution. Homologous recombination events are exchanges between DNA molecules in the lengthy regions of shared identity, catalyzed by a group of dedicated enzymes. There is a variety of experimental systems in E. coli and Salmonella to detect homologous recombination events of several different kinds. Genetic analysis of homologous recombination reveals three separate phases of this process: pre-synapsis (the early phase), synapsis (homologous strand exchange) and post-synapsis (the late phase). In E. coli, there are at least two independent pathway of the early phase and at least two independent pathways of the late phase. All this complexity is incongruent with the originally ascribed role of homologous recombination as accelerator of genome evolution: there is simply not enough duplication and repetition in enterobacterial genomes for homologous recombination to have a detectable evolutionary role, and therefore not enough selection to maintain such a complexity. At the same time, the mechanisms of homologous recombination are uniquely suited for repair of complex DNA lesions called chromosomal lesions. In fact, the two major classes of chromosomal lesions are recognized and processed by the two individual pathways at the early phase of homologous recombination. It follows, therefore, that homologous recombination events are occasional reflections of the continual recombinational repair, made possible in cases of natural or artificial genome redundancy. PMID:26442506

  20. Evaluation of using ferrofluid as an interface material for a field-reversible thermal connector

    Science.gov (United States)

    Yousif, Ahmed S.

    The electrical functionality of an avionics chassis is limited due to heat dissipation limits. The limits arise due to the fact that components in an avionic computer boxes are packed very compactly, with the components mounted onto plug-in cards, and the harsh environment experienced by the chassis limits how heat can be dissipated from the cards. Convective and radiative heat transfer to the ambient are generally not possible. Therefore it is necessary to have heat transferred from the components conducted to the edge of the plug-in cards. The heat then needs to conduct from the card edge to a cold block that not only holds the card in place, but also removes the generated heat by some heat transfer fluid that is circulated through the cold block. The interface between the plug-in card and the cold block typically has a high thermal resistance since it is necessary for the card to have the capability to be re-workable, meaning that the card can be removed and then returned to the chassis. Reducing the thermal resistance of the interface is the objective of the current study and the topic of this thesis. The current design uses a pressure interface between the card and cold block. The contact pressure is increased through the addition of a wedgelock, which is a field-reversible mechanical connector. To use a wedgelock, the cold block has channels milled on the surface with widths that are larger than the thickness of the plug-in card and the un-expanded wedgelock. The card edge is placed in the channel and placed against one of the channel walls. A wedgelock is then placed between the card and the other channel wall. The wedgelock is then expanded by using either a screw or a lever. As the wedgelock expands it fills in the remaining channel gap and bears against the other face of the plug-in card. The majority of heat generated by the components on the plug-in card is forced to conduct from the card into the wall of the cold block, effectively a single sided, dry

  1. Automated Inspection of Defects in Optical Fiber Connector End Face Using Novel Morphology Approaches.

    Science.gov (United States)

    Mei, Shuang; Wang, Yudan; Wen, Guojun; Hu, Yang

    2018-05-03

    Increasing deployment of optical fiber networks and the need for reliable high bandwidth make the task of inspecting optical fiber connector end faces a crucial process that must not be neglected. Traditional end face inspections are usually performed by manual visual methods, which are low in efficiency and poor in precision for long-term industrial applications. More seriously, the inspection results cannot be quantified for subsequent analysis. Aiming at the characteristics of typical defects in the inspection process for optical fiber end faces, we propose a novel method, “difference of min-max ranking filtering” (DO2MR), for detection of region-based defects, e.g., dirt, oil, contamination, pits, and chips, and a special model, a “linear enhancement inspector” (LEI), for the detection of scratches. The DO2MR is a morphology method that intends to determine whether a pixel belongs to a defective region by comparing the difference of gray values of pixels in the neighborhood around the pixel. The LEI is also a morphology method that is designed to search for scratches at different orientations with a special linear detector. These two approaches can be easily integrated into optical inspection equipment for automatic quality verification. As far as we know, this is the first time that complete defect detection methods for optical fiber end faces are available in the literature. Experimental results demonstrate that the proposed DO2MR and LEI models yield good comprehensive performance with high precision and accepted recall rates, and the image-level detection accuracies reach 96.0 and 89.3%, respectively.

  2. Smart patch integration development of compression connector structural health monitoring in overhead transmission lines

    Science.gov (United States)

    Wang, Hong; Wang, Jy-An J.; Ren, Fei; Chan, John

    2016-04-01

    Integration of smart patches into full-tension splice connectors in overhead power transmission lines was investigated. Lead zirconate titanate (PZT) -5A was used as a smart material and an aluminum beam was used as a host structure. Negative electrode termination was examined by using copper adhesive tape and direct bonding methods. Various commercial adhesives were studied for PZT integration onto the host structure. Aluminum beam specimens with integrated PZT smart patches were tested under thermal cycling at a temperature of 125°C, which is the higher-end temperature experienced by in-service aluminum conductor steel-reinforced cables. Electromechanical impedance (EMI) measurements were conducted at room temperature, and the root mean square deviation (RMSD) of the conductance signals was used to analyze the EMI data. It has been shown that the negative electrode method has an important effect on the performance of the integrated PZT. The PZT displayed more susceptibility to cracking when copper tape was used than when direct bonding was used. The reliability of PZT in direct bonding depended on the adhesives used in bonding layers. Although a hard alumina-based adhesive can lead to cracking of the PZT, a high-temperature epoxy with adequate flexibility, such as Duralco 4538D, can provide the desired performance under target thermal cycling conditions. The RMSD parameter can characterize conductance signatures effectively. It also was demonstrated that RMSD can be used to quantify the fatigue of the PZT integration system, although RMSD is used primarily as a damage index in monitoring structural health.

  3. Automated Inspection of Defects in Optical Fiber Connector End Face Using Novel Morphology Approaches

    Directory of Open Access Journals (Sweden)

    Shuang Mei

    2018-05-01

    Full Text Available Increasing deployment of optical fiber networks and the need for reliable high bandwidth make the task of inspecting optical fiber connector end faces a crucial process that must not be neglected. Traditional end face inspections are usually performed by manual visual methods, which are low in efficiency and poor in precision for long-term industrial applications. More seriously, the inspection results cannot be quantified for subsequent analysis. Aiming at the characteristics of typical defects in the inspection process for optical fiber end faces, we propose a novel method, “difference of min-max ranking filtering” (DO2MR, for detection of region-based defects, e.g., dirt, oil, contamination, pits, and chips, and a special model, a “linear enhancement inspector” (LEI, for the detection of scratches. The DO2MR is a morphology method that intends to determine whether a pixel belongs to a defective region by comparing the difference of gray values of pixels in the neighborhood around the pixel. The LEI is also a morphology method that is designed to search for scratches at different orientations with a special linear detector. These two approaches can be easily integrated into optical inspection equipment for automatic quality verification. As far as we know, this is the first time that complete defect detection methods for optical fiber end faces are available in the literature. Experimental results demonstrate that the proposed DO2MR and LEI models yield good comprehensive performance with high precision and accepted recall rates, and the image-level detection accuracies reach 96.0 and 89.3%, respectively.

  4. Acetylcholine Receptor: Complex of Homologous Subunits

    Science.gov (United States)

    Raftery, Michael A.; Hunkapiller, Michael W.; Strader, Catherine D.; Hood, Leroy E.

    1980-06-01

    The acetylcholine receptor from the electric ray Torpedo californica is composed of five subunits; two are identical and the other three are structurally related to them. Microsequence analysis of the four polypeptides demonstrates amino acid homology among the subunits. Further sequence analysis of both membrane-bound and Triton-solubilized, chromatographically purified receptor gave the stoichiometry of the four subunits (40,000:50,000:60,000:65,000 daltons) as 2:1:1:1, indicating that this protein is a pentameric complex with a molecular weight of 255,000 daltons. Genealogical analysis suggests that divergence from a common ancestral gene occurred early in the evolution of the receptor. This shared ancestry argues that each of the four subunits plays a functional role in the receptor's physiological action.

  5. Regulation of Homologous Recombination by SUMOylation

    DEFF Research Database (Denmark)

    Pinela da Silva, Sonia Cristina

    factors such as the homologous recombination (HR) machinery. HR constitutes the main DSB repair pathway in Saccharomyces cerevisiae and despite being largely considered an error-free process and essential for genome stability, uncontrolled recombination can lead to loss of heterozygosity, translocations......, deletions, and genome rearrangements that can lead to cell death or cancer in humans. The post-translational modification by SUMO (small ubiquitinlike modifier) has proven to be an important regulator of HR and genome integrity, but the molecular mechanisms responsible for these roles are still unclear....... In this study I present new insights for the role of SUMOylation in regulating HR by dissecting the role of SUMO in the interaction between the central HR-mediator protein Rad52 and its paralogue Rad59 and the outcome of recombination. This data provides evidence for the importance of SUMO in promoting protein...

  6. Homological mirror symmetry. New developments and perspectives

    International Nuclear Information System (INIS)

    Kapustin, Anton; Kreuzer, Maximilian; Schlesinger, Karl-Georg

    2009-01-01

    Homological Mirror Symmetry, the study of dualities of certain quantum field theories in a mathematically rigorous form, has developed into a flourishing subject on its own over the past years. The present volume bridges a gap in the literature by providing a set of lectures and reviews that both introduce and representatively review the state-of-the art in the field from different perspectives. With contributions by K. Fukaya, M. Herbst, K. Hori, M. Huang, A. Kapustin, L. Katzarkov, A. Klemm, M. Kontsevich, D. Page, S. Quackenbush, E. Sharpe, P. Seidel, I. Smith and Y. Soibelman, this volume will be a reference on the topic for everyone starting to work or actively working on mathematical aspects of quantum field theory. (orig.)

  7. HOMOLOGOUS CYCLONES IN THE QUIET SUN

    Energy Technology Data Exchange (ETDEWEB)

    Yu, Xinting; Zhang, Jun; Li, Ting; Zhang, Yuzong; Yang, Shuhong, E-mail: yxt27272@mail.ustc.edu.cn, E-mail: zjun@nao.cas.cn, E-mail: liting@nao.cas.cn, E-mail: yuzong@nao.cas.cn, E-mail: shuhongyang@nao.cas.cn [Key Laboratory of Solar Activity, National Astronomical Observatories, Chinese Academy of Sciences, Beijing 100012 (China)

    2014-02-20

    Through observations with the Solar Dynamics Observatory Atmospheric Imaging Assembly (AIA) and Helioseismic and Magnetic Imager, we tracked one rotating network magnetic field (RNF) near the solar equator. It lasted for more than 100 hr, from 2013 February 23 to 28. During its evolution, three cyclones were found to be rooted in this structure. Each cyclone event lasted for about 8 to 10 hr. While near the polar region, another RNF was investigated. It lasted for a shorter time (∼70 hr), from 2013 July 7 to 9. There were two cyclones rooted in the RNF and each lasted for 8 and 11 hr, respectively. For the two given examples, the cyclones have a similar dynamic evolution, and thus we put forward a new term: homologous cyclones. The detected brightening in AIA 171 Å maps indicates the release of energy, which is potentially available to heat the corona.

  8. Modeling Non-homologous End Joining

    Science.gov (United States)

    Li, Yongfeng

    2013-01-01

    Non-homologous end joining (NHEJ) is the dominant DNA double strand break (DSB) repair pathway and involves several NHEJ proteins such as Ku, DNA-PKcs, XRCC4, Ligase IV and so on. Once DSBs are generated, Ku is first recruited to the DNA end, followed by other NHEJ proteins for DNA end processing and ligation. Because of the direct ligation of break ends without the need for a homologous template, NHEJ turns out to be an error-prone but efficient repair pathway. Some mechanisms have been proposed of how the efficiency of NHEJ repair is affected. The type of DNA damage is an important factor of NHEJ repair. For instance, the length of DNA fragment may determine the recruitment efficiency of NHEJ protein such as Ku [1], or the complexity of the DNA breaks [2] is accounted for the choice of NHEJ proteins and subpathway of NHEJ repair. On the other hand, the chromatin structure also plays a role of the accessibility of NHEJ protein to the DNA damage site. In this talk, some mathematical models of NHEJ, that consist of series of biochemical reactions complying with the laws of chemical reaction (e.g. mass action, etc.), will be introduced. By mathematical and numerical analysis and parameter estimation, the models are able to capture the qualitative biological features and show good agreement with experimental data. As conclusions, from the viewpoint of modeling, how the NHEJ proteins are recruited will be first discussed for connection between the classical sequential model [4] and recently proposed two-phase model [5]. Then how the NHEJ repair pathway is affected, by the length of DNA fragment [6], the complexity of DNA damage [7] and the chromatin structure [8], will be addressed

  9. More on homological supersymmetric quantum mechanics

    Science.gov (United States)

    Behtash, Alireza

    2018-03-01

    In this work, we first solve complex Morse flow equations for the simplest case of a bosonic harmonic oscillator to discuss localization in the context of Picard-Lefschetz theory. We briefly touch on the exact non-BPS solutions of the bosonized supersymmetric quantum mechanics on algebraic geometric grounds and report that their complex phases can be accessed through the cohomology of WKB 1-form of the underlying singular spectral curve subject to necessary cohomological corrections for nonzero genus. Motivated by Picard-Lefschetz theory, we write down a general formula for the index of N =4 quantum mechanics with background R -symmetry gauge fields. We conjecture that certain symmetries of the refined Witten index and singularities of the moduli space may be used to determine the correct intersection coefficients. A few examples, where this conjecture holds, are shown in both linear and closed quivers with rank-one quiver gauge groups. The R -anomaly removal along the "Morsified" relative homology cycles also called "Lefschetz thimbles" is shown to lead to the appearance of Stokes lines. We show that the Fayet-Iliopoulos parameters appear in the intersection coefficients for the relative homology of the quiver quantum mechanics resulting from dimensional reduction of 2 d N =(2 ,2 ) gauge theory on a circle and explicitly calculate integrals along the Lefschetz thimbles in N =4 C Pk -1 model. The Stokes jumping of coefficients and its relation to wall crossing phenomena is briefly discussed. We also find that the notion of "on-the-wall" index is related to the invariant Lefschetz thimbles under Stokes phenomena. An implication of the Lefschetz thimbles in constructing knots from quiver quantum mechanics is indicated.

  10. Clustering evolving proteins into homologous families.

    Science.gov (United States)

    Chan, Cheong Xin; Mahbob, Maisarah; Ragan, Mark A

    2013-04-08

    Clustering sequences into groups of putative homologs (families) is a critical first step in many areas of comparative biology and bioinformatics. The performance of clustering approaches in delineating biologically meaningful families depends strongly on characteristics of the data, including content bias and degree of divergence. New, highly scalable methods have recently been introduced to cluster the very large datasets being generated by next-generation sequencing technologies. However, there has been little systematic investigation of how characteristics of the data impact the performance of these approaches. Using clusters from a manually curated dataset as reference, we examined the performance of a widely used graph-based Markov clustering algorithm (MCL) and a greedy heuristic approach (UCLUST) in delineating protein families coded by three sets of bacterial genomes of different G+C content. Both MCL and UCLUST generated clusters that are comparable to the reference sets at specific parameter settings, although UCLUST tends to under-cluster compositionally biased sequences (G+C content 33% and 66%). Using simulated data, we sought to assess the individual effects of sequence divergence, rate heterogeneity, and underlying G+C content. Performance decreased with increasing sequence divergence, decreasing among-site rate variation, and increasing G+C bias. Two MCL-based methods recovered the simulated families more accurately than did UCLUST. MCL using local alignment distances is more robust across the investigated range of sequence features than are greedy heuristics using distances based on global alignment. Our results demonstrate that sequence divergence, rate heterogeneity and content bias can individually and in combination affect the accuracy with which MCL and UCLUST can recover homologous protein families. For application to data that are more divergent, and exhibit higher among-site rate variation and/or content bias, MCL may often be the better

  11. K-homology and K-cohomology constructions of relations

    International Nuclear Information System (INIS)

    Abd El-Sattar, A. Dabbour; Bayoumy, F.M.

    1990-08-01

    One of the important homology (cohomology) theories, based on systems of covering of the space, is the homology (cohomology) theory of relations. In the present work, by using the idea of K-homology and K-cohomology groups different varieties of the Dowker's theory are introduced and studied. These constructions are defined on the category of pairs of topological spaces and over a pair of coefficient groups. (author). 14 refs

  12. A local homology theory for linearly compact modules

    International Nuclear Information System (INIS)

    Nguyen Tu Cuong; Tran Tuan Nam

    2004-11-01

    We introduce a local homology theory for linearly modules which is in some sense dual to the local cohomology theory of A. Grothendieck. Some basic properties of local homology modules are shown such as: the vanishing and non-vanishing, the noetherianness of local homology modules. By using duality, we extend some well-known results in theory of local cohomology of A. Grothendieck. (author)

  13. On (co)homology of Frobenius Poisson algebras

    OpenAIRE

    Zhu, Can; Van Oystaeyen, Fred; ZHANG, Yinhuo

    2014-01-01

    In this paper, we study Poisson (co)homology of a Frobenius Poisson algebra. More precisely, we show that there exists a duality between Poisson homology and Poisson cohomology of Frobenius Poisson algebras, similar to that between Hochschild homology and Hochschild cohomology of Frobenius algebras. Then we use the non-degenerate bilinear form on a unimodular Frobenius Poisson algebra to construct a Batalin-Vilkovisky structure on the Poisson cohomology ring making it into a Batalin-Vilkovisk...

  14. A geometric model for Hochschild homology of Soergel bimodules

    DEFF Research Database (Denmark)

    Webster, Ben; Williamson, Geordie

    2008-01-01

    An important step in the calculation of the triply graded link homology of Khovanov and Rozansky is the determination of the Hochschild homology of Soergel bimodules for SL(n). We present a geometric model for this Hochschild homology for any simple group G, as B–equivariant intersection cohomology...... on generators whose degree is explicitly determined by the geometry of the orbit closure, and to describe its Hilbert series, proving a conjecture of Jacob Rasmussen....

  15. Heteromorphic Sex Chromosomes: Navigating Meiosis without a Homologous Partner

    OpenAIRE

    Checchi, Paula M.; Engebrecht, JoAnne

    2011-01-01

    Accurate chromosome segregation during meiosis relies on homology between the maternal and paternal chromosomes. Yet by definition, sex chromosomes of the heterogametic sex lack a homologous partner. Recent studies in a number of systems have shed light on the unique meiotic behavior of heteromorphic sex chromosomes, and highlight both the commonalities and differences in divergent species. During meiotic prophase, the homology-dependent processes of pairing, synapsis, and recombination have ...

  16. Domain requirements for the Dock adapter protein in growth- cone signaling.

    Science.gov (United States)

    Rao, Y; Zipursky, S L

    1998-03-03

    Tyrosine phosphorylation has been implicated in growth-cone guidance through genetic, biochemical, and pharmacological studies. Adapter proteins containing src homology 2 (SH2) domains and src homology 3 (SH3) domains provide a means of linking guidance signaling through phosphotyrosine to downstream effectors regulating growth-cone motility. The Drosophila adapter, Dreadlocks (Dock), the homolog of mammalian Nck containing three N-terminal SH3 domains and a single SH2 domain, is highly specialized for growth-cone guidance. In this paper, we demonstrate that Dock can couple signals in either an SH2-dependent or an SH2-independent fashion in photoreceptor (R cell) growth cones, and that Dock displays different domain requirements in different neurons.

  17. Membrane Localization is Critical for Activation of the PICK1 BAR Domain

    OpenAIRE

    Madsen, Kenneth L.; Eriksen, Jacob; Milan-Lobo, Laura; Han, Daniel S.; Niv, Masha Y.; Ammendrup-Johnsen, Ina; Henriksen, Ulla; Bhatia, Vikram K.; Stamou, Dimitrios; Sitte, Harald H.; McMahon, Harvey T.; Weinstein, Harel; Gether, Ulrik

    2008-01-01

    The PSD-95/Discs-large/ZO-1 homology (PDZ) domain protein, protein interacting with C kinase 1 (PICK1) contains a C-terminal Bin/amphiphysin/Rvs (BAR) domain mediating recognition of curved membranes; however, the molecular mechanisms controlling the activity of this domain are poorly understood. In agreement with negative regulation of the BAR domain by the N-terminal PDZ domain, PICK1 distributed evenly in the cytoplasm, whereas truncation of the PDZ domain caused BAR domain-dependent redis...

  18. An evaluation of the spring finger solder joints on SA1358-10 and SA2052-4 connector assemblies (MC3617,W87)

    International Nuclear Information System (INIS)

    Kilgo, Alice C.; Vianco, Paul Thomas; Hlava, Paul Frank; Zender, Gary L.

    2006-01-01

    The SA1358-10 and SA2052-4 circular JT Type plug connectors are used on a number of nuclear weapons and Joint Test Assembly (JTA) systems. Prototype units were evaluated for the following specific defects associated with the 95Sn-5Sb (Sn-Sb, wt.%) solder joint used to attach the beryllium-copper (BeCu) spring fingers to the aluminum (Al) connector shell: (1) extended cracking within the fillet; (2) remelting of the solder joint during the follow-on, soldering step that attached the EMR adapter ring to the connector shell (and/or soldering the EMR shell to the adapter ring) that used the lower melting temperature 63Sn-37Pb (Sn-Pb) alloy; and (3) spalling of the Cd (Cr) layer overplating layer from the fillet surface. Several pedigrees of connectors were evaluated, which represented older fielded units as well as those assemblies that were recently constructed at Kansas City Plant. The solder joints were evaluated that were in place on connectors made with the current soldering process as well as an alternative induction soldering process for attaching the EMR adapter ring to the shell. Very similar observations were made, which crossed the different pedigrees of parts and processes. The extent of cracking in the top side fillets varied between the different connector samples and likely the EMR adapter ring to the shell. Very similar observations were made, which crossed the different pedigrees of parts and processes. The extent of cracking in the top side fillets varied between the different connector samples and likely reflected the different extents to which the connector was mated to its counterpart assembly. In all cases, the spring finger solder joints on the SA1358-10 connectors were remelted as a result of the subsequent EMR adapter ring attachment process. Spalling of the Cd (Cr) overplating layer was also observed for these connectors, which was a consequence of the remelting activity. On the other hand, the SA2052-4 connector did not exhibit evidence of

  19. Colored Kauffman homology and super-A-polynomials

    International Nuclear Information System (INIS)

    Nawata, Satoshi; Ramadevi, P.; Zodinmawia

    2014-01-01

    We study the structural properties of colored Kauffman homologies of knots. Quadruple-gradings play an essential role in revealing the differential structure of colored Kauffman homology. Using the differential structure, the Kauffman homologies carrying the symmetric tensor products of the vector representation for the trefoil and the figure-eight are determined. In addition, making use of relations from representation theory, we also obtain the HOMFLY homologies colored by rectangular Young tableaux with two rows for these knots. Furthermore, the notion of super-A-polynomials is extended in order to encompass two-parameter deformations of PSL(2,ℂ) character varieties

  20. Influence of the width and cross-sectional shape of major connectors of maxillary dentures on the accuracy of speech production.

    Science.gov (United States)

    Wada, Junichiro; Hideshima, Masayuki; Inukai, Shusuke; Matsuura, Hiroshi; Wakabayashi, Noriyuki

    2014-01-01

    To investigate the effects of the width and cross-sectional shape of the major connectors of maxillary dentures located in the middle area of the palate on the accuracy of phonetic output of consonants using an originally developed speech recognition system. Nine adults (4 males and 5 females, aged 24-26 years) with sound dentition were recruited. The following six sounds were considered: [∫i], [t∫i], [ɾi], [ni], [çi], and [ki]. The experimental connectors were fabricated to simulate bars (narrow, 8-mm width) and plates (wide, 20-mm width). Two types of cross-sectional shapes in the sagittal plane were specified: flat and plump edge. The appearance ratio of phonetic segment labels was calculated with the speech recognition system to indicate the accuracy of phonetic output. Statistical analysis was conducted using one-way ANOVA and Tukey's test. The mean appearance ratio of correct labels (MARC) significantly decreased for [ni] with the plump edge (narrow connector) and for [ki] with both the flat and plump edge (wide connectors). For [çi], the MARCs tended to be lower with flat plates. There were no significant differences for the other consonants. The width and cross-sectional shape of the connectors had limited effects on the articulation of consonants at the palate. © 2015 S. Karger AG, Basel.

  1. An in vitro comparison of standard cleaning to a continuous passive disinfection cap for the decontamination of needle-free connectors.

    Science.gov (United States)

    Casey, Anna L; Karpanen, Tarja J; Nightingale, Peter; Elliott, Tom S J

    2018-01-01

    The optimal decontamination method for needle-free connectors is still unresolved. The objective of this study was to determine if a continuous passive disinfection cap is as effective as standard cleaning for the microbial decontamination of injection ports of two types of needle-free connectors. The injection ports of needle-free connectors were inoculated with Staphylococcus aureus and allowed to dry. Disinfection caps containing 70% ( v / v ) isopropyl alcohol (IPA) were attached to the connectors for one, three or 7 days and were compared with needle-free connectors cleaned with 2% ( w / v ) chlorhexidine gluconate (CHG) in 70% ( v/v ) IPA. The number of S. aureus remaining on the injection ports was evaluated. Median log 10 reductions and 95% confidence interval (CI) were calculated and data analyzed using the Mann-Whitney test. The application of the disinfection cap resulted in a significantly higher reduction in S. aureus than the 2% ( w / v ) CHG in 70% ( v / v ) IPA wipe, achieving a > 5 Log 10 reduction in CFU at each time point. The disinfection caps resulted in a significantly higher reduction in S.aureus on the injection ports when compared to the use of a 2% ( w/v ) CHG in 70% ( v/v ) IPA wipe. This offers an explanation for the lower rates of central-line associated bloodstream infection (CLABSI) associated with the use of disinfection caps reported in clinical studies.

  2. .Gov Domains API

    Data.gov (United States)

    General Services Administration — This dataset offers the list of all .gov domains, including state, local, and tribal .gov domains. It does not include .mil domains, or other federal domains outside...

  3. Membrane-sculpting BAR domains generate stable lipid microdomains

    DEFF Research Database (Denmark)

    Zhao, Hongxia; Michelot, Alphée; Koskela, Essi V.

    2013-01-01

    Bin-Amphiphysin-Rvs (BAR) domain proteins are central regulators of many cellular processes involving membrane dynamics. BAR domains sculpt phosphoinositide-rich membranes to generate membrane protrusions or invaginations. Here, we report that, in addition to regulating membrane geometry, BAR...... domains can generate extremely stable lipid microdomains by "freezing" phosphoinositide dynamics. This is a general feature of BAR domains, because the yeast endocytic BAR and Fes/CIP4 homology BAR (F-BAR) domains, the inverse BAR domain of Pinkbar, and the eisosomal BAR protein Lsp1 induced...... phosphoinositide clustering and halted lipid diffusion, despite differences in mechanisms of membrane interactions. Lsp1 displays comparable low diffusion rates in vitro and in vivo, suggesting that BAR domain proteins also generate stable phosphoinositide microdomains in cells. These results uncover a conserved...

  4. Introduction: History of SH2 Domains and Their Applications.

    Science.gov (United States)

    Liu, Bernard A; Machida, Kazuya

    2017-01-01

    The Src Homology 2 (SH2) domain is the prototypical protein interaction module that lies at the heart of phosphotyrosine signaling. Since its serendipitous discovery, there has been a tremendous advancement in technologies and an array of techniques available for studying SH2 domains and phosphotyrosine signaling. In this chapter, we provide a glimpse of the history of SH2 domains and describe many of the tools and techniques that have been developed along the way and discuss future directions for SH2 domain studies. We highlight the gist of each chapter in this volume in the context of: the structural biology and phosphotyrosine binding; characterizing SH2 specificity and generating prediction models; systems biology and proteomics; SH2 domains in signal transduction; and SH2 domains in disease, diagnostics, and therapeutics. Many of the individual chapters provide an in-depth approach that will allow scientists to interrogate the function and role of SH2 domains.

  5. Exploring the impact of the care sport connector in the Netherlands.

    Science.gov (United States)

    Leenaars, Karlijn E F; Smit, Eva; Wagemakers, Annemarie; Molleman, Gerard R M; Koelen, Maria A

    2017-10-16

    Regular physical activity (PA) is deemed to contribute to the primary and secondary prevention of several chronic diseases, like diabetes mellitus, cancer, cardiovascular diseases, and osteoporosis. In 2012, Care Sport Connectors (CSC), to whom a broker has been ascribed, were introduced in the Netherlands to stimulate PA and guide primary care patients towards local sport facilities. The aim of this study was to explore which structural embedding is the most promising for CSCs' work. In three rounds of interviews, 13 CSCs were followed for 2 years in their work. In these interviews, a network survey was used to identify organisations in the CSCs' network, whether they collaborated with these organisations, and the role of the organisations in the connection. Data from the network survey were analysed using the RE-AIM framework and disaggregated into how CSCs were structurally embedded (Type A: only PA sector; Type B: different sectors; Type C: partnership). A related samples Wilcoxon signed rank test was performed to study how the CSCs' network developed between 2014 and 2016. All CSCs established a connection between the primary care and the PA sector in which the average number of organisations with which CSCs collaborated increased significantly between 2014 (8.3) and 2016 (19.8) (p = 0.002). However, differences were identified in the way CSCs were structurally embedded and in the way they established the connection. Type A CSCs established the connection mostly around their own activities, supported PA organisations with their activities, and collaborated with primary care and welfare professionals around their own activities. Type B and Type C CSCs established the connection by organising, supporting, and implementing different kinds of activities targeting different kinds of audiences, and collaborated mostly with primary care professionals around the referral of professionals' patients. The results of this study suggest that adopting an integral approach

  6. Exploring the impact of the care sport connector in the Netherlands

    Directory of Open Access Journals (Sweden)

    Karlijn E. F. Leenaars

    2017-10-01

    Full Text Available Abstract Background Regular physical activity (PA is deemed to contribute to the primary and secondary prevention of several chronic diseases, like diabetes mellitus, cancer, cardiovascular diseases, and osteoporosis. In 2012, Care Sport Connectors (CSC, to whom a broker has been ascribed, were introduced in the Netherlands to stimulate PA and guide primary care patients towards local sport facilities. The aim of this study was to explore which structural embedding is the most promising for CSCs’ work. Methods In three rounds of interviews, 13 CSCs were followed for 2 years in their work. In these interviews, a network survey was used to identify organisations in the CSCs’ network, whether they collaborated with these organisations, and the role of the organisations in the connection. Data from the network survey were analysed using the RE-AIM framework and disaggregated into how CSCs were structurally embedded (Type A: only PA sector; Type B: different sectors; Type C: partnership. A related samples Wilcoxon signed rank test was performed to study how the CSCs’ network developed between 2014 and 2016. Results All CSCs established a connection between the primary care and the PA sector in which the average number of organisations with which CSCs collaborated increased significantly between 2014 (8.3 and 2016 (19.8 (p = 0.002. However, differences were identified in the way CSCs were structurally embedded and in the way they established the connection. Type A CSCs established the connection mostly around their own activities, supported PA organisations with their activities, and collaborated with primary care and welfare professionals around their own activities. Type B and Type C CSCs established the connection by organising, supporting, and implementing different kinds of activities targeting different kinds of audiences, and collaborated mostly with primary care professionals around the referral of professionals’ patients

  7. Genetic interactions between the chromosome axis-associated protein Hop1 and homologous recombination determinants in Schizosaccharomyces pombe.

    Science.gov (United States)

    Brown, Simon David; Jarosinska, Olga Dorota; Lorenz, Alexander

    2018-03-17

    Hop1 is a component of the meiosis-specific chromosome axis and belongs to the evolutionarily conserved family of HORMA domain proteins. Hop1 and its orthologs in higher eukaryotes are a major factor in promoting double-strand DNA break formation and inter-homolog recombination. In budding yeast and mammals, they are also involved in a meiotic checkpoint kinase cascade monitoring the completion of double-strand DNA break repair. We used the fission yeast, Schizosaccharomyces pombe, which lacks a canonical synaptonemal complex to test whether Hop1 has a role beyond supporting the generation of double-strand DNA breaks and facilitating inter-homolog recombination events. We determined how mutants of homologous recombination factors genetically interact with hop1, studied the role(s) of the HORMA domain of Hop1, and characterized a bio-informatically predicted interactor of Hop1, Aho1 (SPAC688.03c). Our observations indicate that in fission yeast, Hop1 does require its HORMA domain to support wild-type levels of meiotic recombination and localization to meiotic chromatin. Furthermore, we show that hop1∆ only weakly interacts genetically with mutants of homologous recombination factors, and in fission yeast likely has no major role beyond break formation and promoting inter-homolog events. We speculate that after the evolutionary loss of the synaptonemal complex, Hop1 likely has become less important for modulating recombination outcome during meiosis in fission yeast, and that this led to a concurrent rewiring of genetic pathways controlling meiotic recombination.

  8. Beauty is in the eye of the beholder: proteins can recognize binding sites of homologous proteins in more than one way.

    Directory of Open Access Journals (Sweden)

    Juliette Martin

    2010-06-01

    Full Text Available Understanding the mechanisms of protein-protein interaction is a fundamental problem with many practical applications. The fact that different proteins can bind similar partners suggests that convergently evolved binding interfaces are reused in different complexes. A set of protein complexes composed of non-homologous domains interacting with homologous partners at equivalent binding sites was collected in 2006, offering an opportunity to investigate this point. We considered 433 pairs of protein-protein complexes from the ABAC database (AB and AC binary protein complexes sharing a homologous partner A and analyzed the extent of physico-chemical similarity at the atomic and residue level at the protein-protein interface. Homologous partners of the complexes were superimposed using Multiprot, and similar atoms at the interface were quantified using a five class grouping scheme and a distance cut-off. We found that the number of interfacial atoms with similar properties is systematically lower in the non-homologous proteins than in the homologous ones. We assessed the significance of the similarity by bootstrapping the atomic properties at the interfaces. We found that the similarity of binding sites is very significant between homologous proteins, as expected, but generally insignificant between the non-homologous proteins that bind to homologous partners. Furthermore, evolutionarily conserved residues are not colocalized within the binding sites of non-homologous proteins. We could only identify a limited number of cases of structural mimicry at the interface, suggesting that this property is less generic than previously thought. Our results support the hypothesis that different proteins can interact with similar partners using alternate strategies, but do not support convergent evolution.

  9. Photoperiodic regulation of flowering in perennial ryegrass involving a CONSTANS-like homolog

    DEFF Research Database (Denmark)

    Martin, J.; Storgaard, M.; Andersen, C.H.

    2004-01-01

    Photoperiod and vernalization are the two key environmental factors of the. oral induction of perennial ryegrass (Lolium perenne L.). Transition from vegetative to reproductive growth will only occur after an extended vernalization period, followed by an increase in day length and temperature. Here...... we report on the isolation and characterization of a L. perenne gene (LpCO) that is homologous to CONSTANS, and which is tightly coupled to the. oral inductive long day signal. Like other monocot CO-like proteins, the LpCO contains a zinc finger domain with a non-conserved B-Box2. Although the B-Box2...

  10. CBH1 homologs and varian CBH1 cellulase

    Energy Technology Data Exchange (ETDEWEB)

    Goedegebuur, Frits; Gualfetti, Peter; Mitchinson, Colin; Neefe, Paulien

    2014-07-01

    Disclosed are a number of homologs and variants of Hypocrea jecorina Cel7A (formerly Trichoderma reesei cellobiohydrolase I or CBH1), nucleic acids encoding the same and methods for producing the same. The homologs and variant cellulases have the amino acid sequence of a glycosyl hydrolase of family 7A wherein one or more amino acid residues are substituted and/or deleted.

  11. The Causes of Quasi-homologous CMEs

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Lijuan; Wang, Yuming; Liu, Rui; Zhou, Zhenjun; Liu, Jiajia; Liu, Kai; Shen, Chenglong; Zhang, Quanhao [CAS Key Laboratory of Geospace Environment, Department of Geophysics and Planetary Sciences, University of Science and Technology of China, Hefei, Anhui, 230026 (China); Temmer, M.; Thalmann, J. K.; Veronig, A. M., E-mail: ymwang@ustc.edu.cn, E-mail: ljliu@mail.ustc.edu.cn [Institute of Physics/IGAM, University of Graz, Universitätsplatz 5/II, A-8010 Graz (Austria)

    2017-08-01

    In this paper, we identified the magnetic source locations of 142 quasi-homologous (QH) coronal mass ejections (CMEs), of which 121 are from solar cycle (SC) 23 and 21 from SC 24. Among those CMEs, 63% originated from the same source location as their predecessor (defined as S-type), while 37% originated from a different location within the same active region as their predecessor (defined as D-type). Their distinctly different waiting time distributions, peaking around 7.5 and 1.5 hr for S- and D-type CMEs, suggest that they might involve different physical mechanisms with different characteristic timescales. Through detailed analysis based on nonlinear force-free coronal magnetic field modeling of two exemplary cases, we propose that the S-type QH CMES might involve a recurring energy release process from the same source location (by magnetic free energy replenishment), whereas the D-type QH CMEs can happen when a flux tube system is disturbed by a nearby CME.

  12. Torus actions, combinatorial topology, and homological algebra

    International Nuclear Information System (INIS)

    Bukhshtaber, V M; Panov, T E

    2000-01-01

    This paper is a survey of new results and open problems connected with fundamental combinatorial concepts, including polytopes, simplicial complexes, cubical complexes, and arrangements of subspaces. Attention is concentrated on simplicial and cubical subdivisions of manifolds, and especially on spheres. Important constructions are described that enable one to study these combinatorial objects by using commutative and homological algebra. The proposed approach to combinatorial problems is based on the theory of moment-angle complexes recently developed by the authors. The crucial construction assigns to each simplicial complex K with m vertices a T m -space Z K with special bigraded cellular decomposition. In the framework of this theory, well-known non-singular toric varieties arise as orbit spaces of maximally free actions of subtori on moment-angle complexes corresponding to simplicial spheres. It is shown that diverse invariants of simplicial complexes and related combinatorial-geometric objects can be expressed in terms of bigraded cohomology rings of the corresponding moment-angle complexes. Finally, it is shown that the new relationships between combinatorics, geometry, and topology lead to solutions of some well-known topological problems

  13. Metallurgical failure investigation of a pipe connector fracture of an expansion vessel; Werkstofftechnische Schadensuntersuchung des Abrisses einer Rohrverschraubung eines Ausgleichsbehaelters

    Energy Technology Data Exchange (ETDEWEB)

    Neidel, Andreas [Siemens AG, Power and Gas, Gas Turbines and Generators, Gasturbinenwerk Berlin (Germany). Werkstoffprueflabor

    2016-08-15

    A pipe connector of an expansion vessel of a safety heat exchanger was torn off in a test facility's natural gas compressor. From a material point of view, the cause of the damage is a fatigue fracture induced by pulsating bending stress. The fatigue fracture originated from both, the pipe's outer surface as well as from its inner surface, which is consistent with the given stress situation (pulsating bending stress). Material defects or welding-induced flaws were not observed. Corrosion, wear, or thermal overload which may have promoted the damage, were not observed either. The primary cause was a major design error. Cases of dynamic load were obviously not duly taken into account during designing, so that the free-swinging mass of the expansion vessel which was mounted to a pipe of a diameter of only half an inch and, furthermore, installed in an angle of 45 (additional static preload.), could cause the fatigue failure induced by pulsating bending stress in the zone of highest stresses at the transition of the expansion vessel and the the pipe connector due to dynamic operating loads which always occur in plants like these.

  14. Lithium hydride doped intermediate connector for high-efficiency and long-term stable tandem organic light-emitting diodes.

    Science.gov (United States)

    Ding, Lei; Tang, Xun; Xu, Mei-Feng; Shi, Xiao-Bo; Wang, Zhao-Kui; Liao, Liang-Sheng

    2014-10-22

    Lithium hydride (LiH) is employed as a novel n-dopant in the intermediate connector for tandem organic light-emitting diodes (OLEDs) because of its easy coevaporation with other electron transporting materials. The tandem OLEDs with two and three electroluminescent (EL) units connected by a combination of LiH doped 8-hydroxyquinoline aluminum (Alq3) and 1,4,5,8,9,11-hexaazatriphenylene-hexacarbonitrile (HAT-CN) demonstrate approximately 2-fold and 3-fold enhancement in current efficiency, respectively. In addition, no extra voltage drop across the intermediate connector is observed. Particularly, the lifetime (T75%) in the tandem OLED with two and three EL units is substantially improved by 3.8 times and 7.4 times, respectively. The doping effect of LiH into Alq3, the charge injection, and transport characteristics of LiH-doped Alq3 are further investigated by ultraviolet photoelectron spectroscopy (UPS) and X-ray photoemission spectroscopy (XPS).

  15. Statistical Inference for Porous Materials using Persistent Homology.

    Energy Technology Data Exchange (ETDEWEB)

    Moon, Chul [Univ. of Georgia, Athens, GA (United States); Heath, Jason E. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Mitchell, Scott A. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

    2017-12-01

    We propose a porous materials analysis pipeline using persistent homology. We rst compute persistent homology of binarized 3D images of sampled material subvolumes. For each image we compute sets of homology intervals, which are represented as summary graphics called persistence diagrams. We convert persistence diagrams into image vectors in order to analyze the similarity of the homology of the material images using the mature tools for image analysis. Each image is treated as a vector and we compute its principal components to extract features. We t a statistical model using the loadings of principal components to estimate material porosity, permeability, anisotropy, and tortuosity. We also propose an adaptive version of the structural similarity index (SSIM), a similarity metric for images, as a measure to determine the statistical representative elementary volumes (sREV) for persistence homology. Thus we provide a capability for making a statistical inference of the uid ow and transport properties of porous materials based on their geometry and connectivity.

  16. Two appendages homologous between basal bodies and centrioles are formed using distinct Odf2 domains.

    Science.gov (United States)

    Tateishi, Kazuhiro; Yamazaki, Yuji; Nishida, Tomoki; Watanabe, Shin; Kunimoto, Koshi; Ishikawa, Hiroaki; Tsukita, Sachiko

    2013-11-11

    Ciliogenesis is regulated by context-dependent cellular cues, including some transduced through appendage-like structures on ciliary basal bodies called transition fibers and basal feet. However, the molecular basis for this regulation is not fully understood. The Odf2 gene product, ODF2/cenexin, is essential for both ciliogenesis and the formation of the distal and subdistal appendages on centrioles, which become basal bodies. We examined the effects of Odf2 deletion constructs on ciliogenesis in Odf2-knockout F9 cells. Electron microscopy revealed that ciliogenesis and transition fiber formation required the ODF2/cenexin fragment containing amino acids (aa) 188-806, whereas basal foot formation required aa 1-59 and 188-806. These sequences also formed distal and subdistal appendages, respectively, indicating that the centriole appendages are molecularly analogous to those on basal bodies. We used the differential formation of appendages by Odf2 deletion constructs to study the incorporation and function of molecules associated with each appendage type. We found that transition fibers and distal appendages were required for ciliogenesis and subdistal appendages stabilized the centrosomal microtubules.

  17. A divergent calponin homology (NN–CH) domain defines a novel family

    DEFF Research Database (Denmark)

    Schou, Kenneth Bødtker; Andersen, Jens S.; Pedersen, Lotte Bang

    2014-01-01

    and NUF2 share evolutionary ancestry with a novel protein family in mammals comprising, besides NDC80/HEC1 and NUF2, three Intraflagellar Transport (IFT) complex B subunits (IFT81, IFT57, CLUAP1) as well as six proteins with poorly defined function (FAM98A-C, CCDC22, CCDC93 and C14orf166). We show...

  18. Mutational definition of functional domains within the Rev homolog encoded by human endogenous retrovirus K.

    Science.gov (United States)

    Bogerd, H P; Wiegand, H L; Yang, J; Cullen, B R

    2000-10-01

    Nuclear export of the incompletely spliced mRNAs encoded by several complex retroviruses, including human immunodeficiency virus type 1 (HIV-1), is dependent on a virally encoded adapter protein, termed Rev in HIV-1, that directly binds both to a cis-acting viral RNA target site and to the cellular Crm1 export factor. Human endogenous retrovirus K, a family of ancient endogenous retroviruses that is not related to the exogenous retrovirus HIV-1, was recently shown to also encode a Crm1-dependent nuclear RNA export factor, termed K-Rev. Although HIV-1 Rev and K-Rev display little sequence identity, they share the ability not only to bind to Crm1 and to RNA but also to form homomultimers and shuttle between nucleus and cytoplasm. We have used mutational analysis to identify sequences in the 105-amino-acid K-Rev protein required for each of these distinct biological activities. While mutations in K-Rev that inactivate any one of these properties also blocked K-Rev-dependent nuclear RNA export, several K-Rev mutants were comparable to wild type when assayed for any of these individual activities yet nevertheless defective for RNA export. Although several nonfunctional K-Rev mutants acted as dominant negative inhibitors of K-Rev-, but not HIV-1 Rev-, dependent RNA export, these were not defined by their inability to bind to Crm1, as is seen with HIV-1 Rev. In total, this analysis suggests a functional architecture for K-Rev that is similar to, but distinct from, that described for HIV-1 Rev and raises the possibility that viral RNA export mediated by the approximately 25 million-year-old K-Rev protein may require an additional cellular cofactor that is not required for HIV-1 Rev function.

  19. Probing the Tyrosine Phosphorylation State in Breast Cancer by Src Homology 2 Domain Binding

    National Research Council Canada - National Science Library

    Mayer, Bruce J

    2006-01-01

    .... The overall goal of this project was to develop a novel molecular diagnostic method, termed SH2 profiling, that can classify cell samples based on their global protein tyrosine phosphorylation state...

  20. Probing the Tyrosine Phosphorylation State in Breast Cancer by Src Homology 2 Domain Binding

    National Research Council Canada - National Science Library

    Mayer, Bruce

    2004-01-01

    .... The overall goal of this project is to develop a novel molecular diagnostic method, termed SH2 profiling, that can classify cell samples based on their global protein tyrosine phosphorylation state...

  1. Evaluating the efficacy of a structure-derived amino acid substitution matrix in detecting protein homologs by BLAST and PSI-BLAST.

    Science.gov (United States)

    Goonesekere, Nalin Cw

    2009-01-01

    The large numbers of protein sequences generated by whole genome sequencing projects require rapid and accurate methods of annotation. The detection of homology through computational sequence analysis is a powerful tool in determining the complex evolutionary and functional relationships that exist between proteins. Homology search algorithms employ amino acid substitution matrices to detect similarity between proteins sequences. The substitution matrices in common use today are constructed using sequences aligned without reference to protein structure. Here we present amino acid substitution matrices constructed from the alignment of a large number of protein domain structures from the structural classification of proteins (SCOP) database. We show that when incorporated into the homology search algorithms BLAST and PSI-blast, the structure-based substitution matrices enhance the efficacy of detecting remote homologs.

  2. Crotacetin, a novel snake venom C-type lectin, is homolog of convulxin

    Directory of Open Access Journals (Sweden)

    G. Rádis-Baptista

    2005-12-01

    Full Text Available Snake venom (sv C-type lectins encompass a group of hemorrhagic toxins, which are able to interfere with hemostasis. They share significant similarity in their primary structures with C-type lectins of other animals, and also present a conserved carbohydrate recognition domain (CRD. A very well studied sv C-type lectin is the heterodimeric toxin, convulxin (CVX, from the venoms of South American rattlesnakes, Crotalus durissus terrificus and C. d. cascavella. It consists of two subunits, alfa (CVXalpha , 13.9 kDa and beta (CVXbeta , 12.6 kDa, joined by inter and intra-chain disulfide bounds, and is arranged in a tetrameric alpha4beta4 conformation. Convulxin is able to activate platelet and induce their aggregation by acting via p62/GPVI collagen receptor. Several cDNA precursors, homolog of CVX subunits, were cloned by PCR homology screening. As determined by computational analysis, one of them, named crotacetin beta subunit, was predicted as a polypeptide with a tridimensional conformation very similar to other subunits of convulxin-like snake toxins. Crotacetin was purified from C. durissus venoms by gel permeation and reverse phase high performance liquid chromatography. The heterodimeric crotacetin is expressed in the venoms of several C. durissus subspecies, but it is prevalent in the venom of C. durissus cascavella. As inferred from homology modeling, crotacetin induces platelet aggregation but noticeably exhibits antimicrobial activity against Gram-positive and Gram-negative bacteria.

  3. Resolving RAD51C function in late stages of homologous recombination

    Directory of Open Access Journals (Sweden)

    Kuznetsov Sergey G

    2007-06-01

    Full Text Available Abstract DNA double strand breaks are efficiently repaired by homologous recombination. One of the last steps of this process is resolution of Holliday junctions that are formed at the sites of genetic exchange between homologous DNA. Although various resolvases with Holliday junctions processing activity have been identified in bacteriophages, bacteria and archaebacteria, eukaryotic resolvases have been elusive. Recent biochemical evidence has revealed that RAD51C and XRCC3, members of the RAD51-like protein family, are involved in Holliday junction resolution in mammalian cells. However, purified recombinant RAD51C and XRCC3 proteins have not shown any Holliday junction resolution activity. In addition, these proteins did not reveal the presence of a nuclease domain, which raises doubts about their ability to function as a resolvase. Furthermore, oocytes from infertile Rad51C mutant mice exhibit precocious separation of sister chromatids at metaphase II, a phenotype that reflects a defect in sister chromatid cohesion, not a lack of Holliday junction resolution. Here we discuss a model to explain how a Holliday junction resolution defect can lead to sister chromatid separation in mouse oocytes. We also describe other recent in vitro and in vivo evidence supporting a late role for RAD51C in homologous recombination in mammalian cells, which is likely to be resolution of the Holliday junction.

  4. [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.

  5. Homologous series of induced early mutants in indican rice. Pt.1. The production of homologous series of early mutants

    International Nuclear Information System (INIS)

    Chen Xiulan; Yang Hefeng; He Zhentian; Han Yuepeng; Liu Xueyu

    1999-01-01

    The percentage of homologous series of early mutants induced from the same Indican rice variety were almost the same (1.37%∼1.64%) in 1983∼1993, but the ones from the different eco-typical varieties were different. The early variety was 0.73%, the mid variety was 1.51%, and the late variety was 1.97%. The percentage of homologous series of early mutants from the varieties with the same pedigree and relationship were similar, but the one from the cog nation were lower than those from distant varieties. There are basic laws and characters in the homologous series of early mutants: 1. The inhibited phenotype is the basic of the homologous series of early mutants; 2. The production of the homologous series of early mutants is closely related with the growing period of the parent; 3. The parallel mutation of the stem and leaves are simultaneously happened with the variation of early or late maturing; 4. The occurrence of the homologous series of early mutants is in a state of imbalance. According to the law of parallel variability, the production of homologous series of early mutants can be predicted as long as the parents' classification of plant, pedigree and ecological type are identified. Therefore, the early breeding can be guided by the law of homologous series of early mutants

  6. Waggawagga-CLI: A command-line tool for predicting stable single α-helices (SAH-domains, and the SAH-domain distribution across eukaryotes.

    Directory of Open Access Journals (Sweden)

    Dominic Simm

    Full Text Available Stable single-alpha helices (SAH-domains function as rigid connectors and constant force springs between structural domains, and can provide contact surfaces for protein-protein and protein-RNA interactions. SAH-domains mainly consist of charged amino acids and are monomeric and stable in polar solutions, characteristics which distinguish them from coiled-coil domains and intrinsically disordered regions. Although the number of reported SAH-domains is steadily increasing, genome-wide analyses of SAH-domains in eukaryotic genomes are still missing. Here, we present Waggawagga-CLI, a command-line tool for predicting and analysing SAH-domains in protein sequence datasets. Using Waggawagga-CLI we predicted SAH-domains in 24 datasets from eukaryotes across the tree of life. SAH-domains were predicted in 0.5 to 3.5% of the protein-coding content per species. SAH-domains are particularly present in longer proteins supporting their function as structural building block in multi-domain proteins. In human, SAH-domains are mainly used as alternative building blocks not being present in all transcripts of a gene. Gene ontology analysis showed that yeast proteins with SAH-domains are particular enriched in macromolecular complex subunit organization, cellular component biogenesis and RNA metabolic processes, and that they have a strong nuclear and ribonucleoprotein complex localization and function in ribosome and nucleic acid binding. Human proteins with SAH-domains have roles in all types of RNA processing and cytoskeleton organization, and are predicted to function in RNA binding, protein binding involved in cell and cell-cell adhesion, and cytoskeletal protein binding. Waggawagga-CLI allows the user to adjust the stabilizing and destabilizing contribution of amino acid interactions in i,i+3 and i,i+4 spacings, and provides extensive flexibility for user-designed analyses.

  7. Stringent homology-based prediction of H. sapiens-M. tuberculosis H37Rv protein-protein interactions.

    Science.gov (United States)

    Zhou, Hufeng; Gao, Shangzhi; Nguyen, Nam Ninh; Fan, Mengyuan; Jin, Jingjing; Liu, Bing; Zhao, Liang; Xiong, Geng; Tan, Min; Li, Shijun; Wong, Limsoon

    2014-04-08

    H. sapiens-M. tuberculosis H37Rv protein-protein interaction (PPI) data are essential for understanding the infection mechanism of the formidable pathogen M. tuberculosis H37Rv. Computational prediction is an important strategy to fill the gap in experimental H. sapiens-M. tuberculosis H37Rv PPI data. Homology-based prediction is frequently used in predicting both intra-species and inter-species PPIs. However, some limitations are not properly resolved in several published works that predict eukaryote-prokaryote inter-species PPIs using intra-species template PPIs. We develop a stringent homology-based prediction approach by taking into account (i) differences between eukaryotic and prokaryotic proteins and (ii) differences between inter-species and intra-species PPI interfaces. We compare our stringent homology-based approach to a conventional homology-based approach for predicting host-pathogen PPIs, based on cellular compartment distribution analysis, disease gene list enrichment analysis, pathway enrichment analysis and functional category enrichment analysis. These analyses support the validity of our prediction result, and clearly show that our approach has better performance in predicting H. sapiens-M. tuberculosis H37Rv PPIs. Using our stringent homology-based approach, we have predicted a set of highly plausible H. sapiens-M. tuberculosis H37Rv PPIs which might be useful for many of related studies. Based on our analysis of the H. sapiens-M. tuberculosis H37Rv PPI network predicted by our stringent homology-based approach, we have discovered several interesting properties which are reported here for the first time. We find that both host proteins and pathogen proteins involved in the host-pathogen PPIs tend to be hubs in their own intra-species PPI network. Also, both host and pathogen proteins involved in host-pathogen PPIs tend to have longer primary sequence, tend to have more domains, tend to be more hydrophilic, etc. And the protein domains from both

  8. Productive Homologous and Non-homologous Recombination of Hepatitis C Virus in Cell Culture

    Science.gov (United States)

    Li, Yi-Ping; Mikkelsen, Lotte S.; Gottwein, Judith M.; Bukh, Jens

    2013-01-01

    Genetic recombination is an important mechanism for increasing diversity of RNA viruses, and constitutes a viral escape mechanism to host immune responses and to treatment with antiviral compounds. Although rare, epidemiologically important hepatitis C virus (HCV) recombinants have been reported. In addition, recombination is an important regulatory mechanism of cytopathogenicity for the related pestiviruses. Here we describe recombination of HCV RNA in cell culture leading to production of infectious virus. Initially, hepatoma cells were co-transfected with a replicating JFH1ΔE1E2 genome (genotype 2a) lacking functional envelope genes and strain J6 (2a), which has functional envelope genes but does not replicate in culture. After an initial decrease in the number of HCV positive cells, infection spread after 13–36 days. Sequencing of recovered viruses revealed non-homologous recombinants with J6 sequence from the 5′ end to the NS2–NS3 region followed by JFH1 sequence from Core to the 3′ end. These recombinants carried duplicated sequence of up to 2400 nucleotides. HCV replication was not required for recombination, as recombinants were observed in most experiments even when two replication incompetent genomes were co-transfected. Reverse genetic studies verified the viability of representative recombinants. After serial passage, subsequent recombination events reducing or eliminating the duplicated region were observed for some but not all recombinants. Furthermore, we found that inter-genotypic recombination could occur, but at a lower frequency than intra-genotypic recombination. Productive recombination of attenuated HCV genomes depended on expression of all HCV proteins and tolerated duplicated sequence. In general, no strong site specificity was observed. Non-homologous recombination was observed in most cases, while few homologous events were identified. A better understanding of HCV recombination could help identification of natural recombinants

  9. Productive homologous and non-homologous recombination of hepatitis C virus in cell culture

    DEFF Research Database (Denmark)

    Scheel, Troels K H; Galli, Andrea; Li, Yi-Ping

    2013-01-01

    . In addition, recombination is an important regulatory mechanism of cytopathogenicity for the related pestiviruses. Here we describe recombination of HCV RNA in cell culture leading to production of infectious virus. Initially, hepatoma cells were co-transfected with a replicating JFH1ΔE1E2 genome (genotype 2a......) lacking functional envelope genes and strain J6 (2a), which has functional envelope genes but does not replicate in culture. After an initial decrease in the number of HCV positive cells, infection spread after 13-36 days. Sequencing of recovered viruses revealed non-homologous recombinants with J6...

  10. Srs2 and Mus81-Mms4 Prevent Accumulation of Toxic Inter-Homolog Recombination Intermediates.

    Directory of Open Access Journals (Sweden)

    Kenji Keyamura

    2016-07-01

    Full Text Available Homologous recombination is an evolutionally conserved mechanism that promotes genome stability through the faithful repair of double-strand breaks and single-strand gaps in DNA, and the recovery of stalled or collapsed replication forks. Saccharomyces cerevisiae ATP-dependent DNA helicase Srs2 (a member of the highly conserved UvrD family of helicases has multiple roles in regulating homologous recombination. A mutation (srs2K41A resulting in a helicase-dead mutant of Srs2 was found to be lethal in diploid, but not in haploid, cells. In diploid cells, Srs2K41A caused the accumulation of inter-homolog joint molecule intermediates, increased the levels of spontaneous Rad52 foci, and induced gross chromosomal rearrangements. Srs2K41A lethality and accumulation of joint molecules were suppressed by inactivating Rad51 or deleting the Rad51-interaction domain of Srs2, whereas phosphorylation and sumoylation of Srs2 and its interaction with sumoylated proliferating cell nuclear antigen (PCNA were not required for lethality. The structure-specific complex of crossover junction endonucleases Mus81 and Mms4 was also required for viability of diploid, but not haploid, SRS2 deletion mutants (srs2Δ, and diploid srs2Δ mus81Δ mutants accumulated joint molecule intermediates. Our data suggest that Srs2 and Mus81-Mms4 have critical roles in preventing the formation of (or in resolving toxic inter-homolog joint molecules, which could otherwise interfere with chromosome segregation and lead to genetic instability.

  11. SH3 Domains Differentially Stimulate Distinct Dynamin I Assembly Modes and G Domain Activity.

    Directory of Open Access Journals (Sweden)

    Sai Krishnan

    Full Text Available Dynamin I is a highly regulated GTPase enzyme enriched in nerve terminals which mediates vesicle fission during synaptic vesicle endocytosis. One regulatory mechanism involves its interactions with proteins containing Src homology 3 (SH3 domains. At least 30 SH3 domain-containing proteins bind dynamin at its proline-rich domain (PRD. Those that stimulate dynamin activity act by promoting its oligomerisation. We undertook a systematic parallel screening of 13 glutathione-S-transferase (GST-tagged endocytosis-related SH3 domains on dynamin binding, GTPase activity and oligomerisation. No correlation was found between dynamin binding and their potency to stimulate GTPase activity. There was limited correlation between the extent of their ability to stimulate dynamin activity and the level of oligomerisation, indicating an as yet uncharacterised allosteric coupling of the PRD and G domain. We examined the two variants, dynamin Iab and Ibb, which differ in the alternately splice middle domain α2 helix. They responded differently to the panel of SH3s, with the extent of stimulation between the splice variants varying greatly between the SH3s. This study reveals that SH3 binding can act as a heterotropic allosteric regulator of the G domain via the middle domain α2 helix, suggesting an involvement of this helix in communicating the PRD-mediated allostery. This indicates that SH3 binding both stabilises multiple conformations of the tetrameric building block of dynamin, and promotes assembly of dynamin-SH3 complexes with distinct rates of GTP hydrolysis.

  12. Detecting false positive sequence homology: a machine learning approach.

    Science.gov (United States)

    Fujimoto, M Stanley; Suvorov, Anton; Jensen, Nicholas O; Clement, Mark J; Bybee, Seth M

    2016-02-24

    Accurate detection of homologous relationships of biological sequences (DNA or amino acid) amongst organisms is an important and often difficult task that is essential to various evolutionary studies, ranging from building phylogenies to predicting functional gene annotations. There are many existing heuristic tools, most commonly based on bidirectional BLAST searches that are used to identify homologous genes and combine them into two fundamentally distinct classes: orthologs and paralogs. Due to only using heuristic filtering based on significance score cutoffs and having no cluster post-processing tools available, these methods can often produce multiple clusters constituting unrelated (non-homologous) sequences. Therefore sequencing data extracted from incomplete genome/transcriptome assemblies originated from low coverage sequencing or produced by de novo processes without a reference genome are susceptible to high false positive rates of homology detection. In this paper we develop biologically informative features that can be extracted from multiple sequence alignments of putative homologous genes (orthologs and paralogs) and further utilized in context of guided experimentation to verify false positive outcomes. We demonstrate that our machine learning method trained on both known homology clusters obtained from OrthoDB and randomly generated sequence alignments (non-homologs), successfully determines apparent false positives inferred by heuristic algorithms especially among proteomes recovered from low-coverage RNA-seq data. Almost ~42 % and ~25 % of predicted putative homologies by InParanoid and HaMStR respectively were classified as false positives on experimental data set. Our process increases the quality of output from other clustering algorithms by providing a novel post-processing method that is both fast and efficient at removing low quality clusters of putative homologous genes recovered by heuristic-based approaches.

  13. SH2 domains: modulators of nonreceptor tyrosine kinase activity.

    Science.gov (United States)

    Filippakopoulos, Panagis; Müller, Susanne; Knapp, Stefan

    2009-12-01

    The Src homology 2 (SH2) domain is a sequence-specific phosphotyrosine-binding module present in many signaling molecules. In cytoplasmic tyrosine kinases, the SH2 domain is located N-terminally to the catalytic kinase domain (SH1) where it mediates cellular localization, substrate recruitment, and regulation of kinase activity. Initially, structural studies established a role of the SH2 domain stabilizing the inactive state of Src family members. However, biochemical characterization showed that the presence of the SH2 domain is frequently required for catalytic activity, suggesting a crucial function stabilizing the active state of many nonreceptor tyrosine kinases. Recently, the structure of the SH2-kinase domain of Fes revealed that the SH2 domain stabilizes the active kinase conformation by direct interactions with the regulatory helix alphaC. Stabilizing interactions between the SH2 and the kinase domains have also been observed in the structures of active Csk and Abl. Interestingly, mutations in the SH2 domain found in human disease can be explained by SH2 domain destabilization or incorrect positioning of the SH2. Here we summarize our understanding of mechanisms that lead to tyrosine kinase activation by direct interactions mediated by the SH2 domain and discuss how mutations in the SH2 domain trigger kinase inactivation.

  14. The K-homology of nets of C∗-algebras

    Science.gov (United States)

    Ruzzi, Giuseppe; Vasselli, Ezio

    2014-12-01

    Let X be a space, intended as a possibly curved space-time, and A a precosheaf of C∗-algebras on X. Motivated by algebraic quantum field theory, we study the Kasparov and Θ-summable K-homology of A interpreting them in terms of the holonomy equivariant K-homology of the associated C∗-dynamical system. This yields a characteristic class for K-homology cycles of A with values in the odd cohomology of X, that we interpret as a generalized statistical dimension.

  15. Identification of a transformer homolog in the acorn worm, Saccoglossus kowalevskii, and analysis of its activity in insect cells.

    Science.gov (United States)

    Suzuki, Masataka G; Tochigi, Mayuko; Sakaguchi, Honami; Aoki, Fugaku; Miyamoto, Norio

    2015-06-01

    The transformer (tra) gene is an intermediate component of the sex determination hierarchy in many insect species. The homolog of tra is also found in two branchiopod crustacean species but is not known outside arthropods. We have isolated a tra homolog in the acorn worm, Saccoglossus kowalevskii, which is a hemichordate belonging to the deuterostome superphylum. The full-length complementary DNA (cDNA) of the S. kowalevskii tra homolog (Sktra) has a 3786-bp open reading frame that encodes a 1261-amino acid sequence including a TRA-CAM domain and an arginine/serine (RS)-rich domain, both of which are characteristic of TRA orthologs. Reverse transcription PCR (RT-PCR) analyses demonstrated that Sktra showed no differences in expression patterns between testes and ovaries, but its expression level was approximately 7.5-fold higher in the testes than in the ovaries. TRA, together with the protein product of the transformer-2 (tra-2) gene, assembles on doublesex (dsx) pre-messenger RNA (mRNA) via the cis-regulatory element, enhancing female-specific splicing of dsx in Drosophila. To understand functional conservation of the SkTRA protein as a dsx-splicing activator, we investigated whether SkTRA is capable of inducing female-specific splicing of the Drosophila dsx. Ectopic expression of Sktra cDNA in insect cultured cells did not induce the female-specific splicing of dsx. On the other hand, forced expression of Sktra-2 (a tra-2 homolog of S. kowalevskii) was able to induce the female-specific dsx splicing. These results demonstrate that the function as a dsx-splicing activator is not conserved in SkTRA even though SkTRA-2 is capable of functionally replacing the Drosophila TRA-2. We have also found a tra homolog in an echinoderm genome. This study provides the first evidence that that tra is conserved not only in arthropods but also in basal species of deuterostoms.

  16. Evaluation of the role of Care Sport Connectors in connecting primary care, sport, and physical activity, and residents' participation in the Netherlands

    NARCIS (Netherlands)

    Smit, E.; Leenaars, K.E.F.; Wagemakers, M.A.E.; Molleman, G.R.M.; Koelen, M.A.; Velden, Van Der J.

    2015-01-01

    Background: The number of people with one or more chronic diseases is increasing, but this trend could be reduced by promoting physical activity. Therefore, in 2012, the Dutch Ministry of Health, Welfare, and Sport introduced Care Sport Connectors (CSCs), to whom a broker role has been ascribed.

  17. Dr Marta Bajko in front of the Gold pated "half-moon" connector of an LHC dipole Diode in SM18.

    CERN Multimedia

    Maximilien Brice

    2012-01-01

    Photo 1 : Cold Diode for the LHC superconducting dipoles protection. Prepared for cryogenic powering test OFF line in SM18. - Photo 2 : A gold plated bus bar of an LHC dipole diode ready for cryogenic powering test in Sm18. - Photo 3 : The gold pated “ half-moon” connector of an LHC dipole diode. Ready for a cryogenic powering test in SM18.

  18. Novel Fiber Optic Sensor Probe with a Pair of Highly Reflected Connectors and a Vessel of Water Absorption Material for Water Leak Detection

    Directory of Open Access Journals (Sweden)

    Tae-Sik Cho

    2012-08-01

    Full Text Available The use of a fiber optic quasi-distributed sensing technique for detecting the location and severity of water leakage is suggested. A novel fiber optic sensor probe is devised with a vessel of water absorption material called as water combination soil (WCS located between two highly reflected connectors: one is a reference connector and the other is a sensing connector. In this study, the sensing output is calculated from the reflected light signals of the two connectors. The first reflected light signal is a reference and the second is a sensing signal which is attenuated by the optical fiber bending loss due to the WCS expansion absorbing water. Also, the bending loss of each sensor probe is determined by referring to the total number of sensor probes and the total power budget of an entire system. We have investigated several probe characteristics to show the design feasibility of the novel fiber sensor probe. The effects of vessel sizes of the probes on the water detection sensitivity are studied. The largest vessel probe provides the highest sensitivity of 0.267 dB/mL, while the smallest shows relatively low sensitivity of 0.067 dB/mL, and unstable response. The sensor probe with a high output value provides a high sensitivity with various detection levels while the number of total installable sensor probes decreases.

  19. Novel fiber optic sensor probe with a pair of highly reflected connectors and a vessel of water absorption material for water leak detection.

    Science.gov (United States)

    Cho, Tae-Sik; Choi, Ki-Sun; Seo, Dae-Cheol; Kwon, Il-Bum; Lee, Jung-Ryul

    2012-01-01

    The use of a fiber optic quasi-distributed sensing technique for detecting the location and severity of water leakage is suggested. A novel fiber optic sensor probe is devised with a vessel of water absorption material called as water combination soil (WCS) located between two highly reflected connectors: one is a reference connector and the other is a sensing connector. In this study, the sensing output is calculated from the reflected light signals of the two connectors. The first reflected light signal is a reference and the second is a sensing signal which is attenuated by the optical fiber bending loss due to the WCS expansion absorbing water. Also, the bending loss of each sensor probe is determined by referring to the total number of sensor probes and the total power budget of an entire system. We have investigated several probe characteristics to show the design feasibility of the novel fiber sensor probe. The effects of vessel sizes of the probes on the water detection sensitivity are studied. The largest vessel probe provides the highest sensitivity of 0.267 dB/mL, while the smallest shows relatively low sensitivity of 0.067 dB/mL, and unstable response. The sensor probe with a high output value provides a high sensitivity with various detection levels while the number of total installable sensor probes decreases.

  20. Self-centering fiber alignment structures for high-precision field installable single-mode fiber connectors

    Science.gov (United States)

    Van Erps, Jürgen; Ebraert, Evert; Gao, Fei; Vervaeke, Michael; Berghmans, Francis; Beri, Stefano; Watté, Jan; Thienpont, Hugo

    2014-05-01

    There is a steady increase in the demand for internet bandwidth, primarily driven by cloud services and high-definition video streaming. Europe's Digital Agenda states the ambitious objective that by 2020 all Europeans should have access to internet at speeds of 30Mb/s or above, with 50% or more of households subscribing to connections of 100Mb/s. Today however, internet access in Europe is mainly based on the first generation of broadband, meaning internet accessed over legacy telephone copper and TV cable networks. In recent years, Fiber-To-The-Home (FTTH) networks have been adopted as a replacement of traditional electrical connections for the `last mile' transmission of information at bandwidths over 1Gb/s. However, FTTH penetration is still very low (economies. The main reason for this is the high deployment cost of FTTH networks. Indeed, the success and adoption of optical access networks critically depend on the quality and reliability of connections between optical fibers. In particular a further reduction of insertion loss of field- installable connectors must be achieved without a significant increase in component cost. This requires precise alignment of fibers that can differ in terms of ellipticity, eccentricity or diameter and seems hardly achievable using today's widespread ferrule-based alignment systems. In this paper, we present a field-installable connector based on deflectable/compressible spring structures, providing a self-centering functionality for the fiber. This way, it can accommodate for possible fiber cladding diameter variations (the tolerance on the cladding diameter of G.652 fiber is typically +/-0.7μm). The mechanical properties of the cantilever are derived through an analytical approximation and a mathematical model of the spring constant, and finite element-based simulations are carried out to find the maximum first principal stress as well as the stress distribution distribution in the fiber alignment structure. Elastic

  1. Homology of normal chains and cohomology of charges

    CERN Document Server

    Pauw, Th De; Pfeffer, W F

    2017-01-01

    The authors consider a category of pairs of compact metric spaces and Lipschitz maps where the pairs satisfy a linearly isoperimetric condition related to the solvability of the Plateau problem with partially free boundary. It includes properly all pairs of compact Lipschitz neighborhood retracts of a large class of Banach spaces. On this category the authors define homology and cohomology functors with real coefficients which satisfy the Eilenberg-Steenrod axioms, but reflect the metric properties of the underlying spaces. As an example they show that the zero-dimensional homology of a space in our category is trivial if and only if the space is path connected by arcs of finite length. The homology and cohomology of a pair are, respectively, locally convex and Banach spaces that are in duality. Ignoring the topological structures, the homology and cohomology extend to all pairs of compact metric spaces. For locally acyclic spaces, the authors establish a natural isomorphism between their cohomology and the �...

  2. Generalized local homology and cohomology for linearly compact modules

    International Nuclear Information System (INIS)

    Tran Tuan Nam

    2006-07-01

    We study generalized local homology for linearly compact modules. By duality, we get some properties of generalized local cohomology modules and extend well-known properties of local cohomology of A. Grothendieck. (author)

  3. On the homology and the cohomology of certain polycyclic groups

    International Nuclear Information System (INIS)

    Majumdar, S.

    1987-10-01

    The homology and the cohomology of infinite non-abelian split extensions of cyclic groups by cyclic groups have been computed through construction of nice free resolutions for these groups. (author). 16 refs

  4. Inhibitory Effect of Berberine on Zeste Homolog 2 (Ezh2 ...

    African Journals Online (AJOL)

    homolog 2 (Ezh2) expressions in KYSE450 human esophageal cancer cells. Methods: ... of the AXL receptor kinase. The results of ... effects of estrogen receptor antagonists on ..... protein EZH2 is involved in progression of prostate cancer.

  5. A novel approach to fabricate silk nanofibers containing hydroxyapatite nanoparticles using a three-way stopcock connector

    Science.gov (United States)

    Sheikh, Faheem A.; Ju, Hyung Woo; Moon, Bo Mi; Park, Hyun Jung; Kim, Jung Ho; Lee, Ok Joo; Park, Chan Hum

    2013-07-01

    Electrospinning technique is commonly used to produce micro- and/or nanofibers, which utilizes electrical forces to produce polymeric fibers with diameters ranging from several micrometers down to few nanometers. Desirably, electrospun materials provide highly porous structure and appropriate pore size for initial cell attachment and proliferation and thereby enable the exchange of nutrients. Composite nanofibers consisting of silk and hydroxyapatite nanoparticles (HAp) (NPs) had been considered as an excellent choice due to their efficient biocompatibility and bone-mimicking properties. To prepare these nanofiber composites, it requires the use of acidic solutions which have serious consequences on the nature of both silk and HAp NPs. It is ideal to create these nanofibers using aqueous solutions in which the physicochemical nature of both materials can be retained. However, to create those nanofibers is often difficult to obtain because of the fact that aqueous solutions of silk and HAp NPs can precipitate before they can be ejected into fibers during the electrospinning process. In this work, we had successfully used a three-way stopcock connector to mix the two different solutions, and very shortly, this solution is ejected out to form nanofibers due to electric fields. Different blend ratios consisting HAp NPs had been electrospun into nanofibers. The physicochemical aspects of fabricated nanofiber had been characterized by different state of techniques like that of FE-SEM, EDS, TEM, TEM-EDS, TGA, FT-IR, and XRD. These characterization techniques revealed that HAp NPs can be easily introduced in silk nanofibers using a stopcock connector, and this method favorably preserves the intact nature of silk fibroin and HAp NPs. Moreover, nanofibers obtained by this strategy were tested for cell toxicity and cell attachment studies using NIH 3 T3 fibroblasts which indicated non-toxic behavior and good attachment of cells upon incubation in the presence of nanofibers.

  6. Remote erosion and corrosion monitoring of subsea pipelines using acoustic telemetry and wet-mate connector technology

    Energy Technology Data Exchange (ETDEWEB)

    Painter, Howard; Barlow, Stewart [Teledyne ODI, Thousand Oaks, CA (United States); Clarke, Daniel [Teledyne Cormon, Thousand Oaks, CA (United States); Green, Dale [Teledyne Benthos, North Falmouth, MA (United States)

    2009-07-01

    This paper will present a novel approach for monitoring erosion and corrosion using proven sub sea technologies: intrusive erosion and corrosion monitoring, acoustic telemetry and wet-mateable connector technology. Intrusive metal loss based monitoring systems on sub sea pipelines are increasingly being used because of their ability to directly measure erosion and corrosion. These systems are integrated with the sub sea production control system or located close to the platform and hard-wired. However, locations remote from a sub sea control system or platform requires a dedicated communication system and long lengths of cable that can be cost prohibitive to procure and install. The system presented consists of an intrusive erosion or corrosion monitor with pressure and temperature transmitters, a retrievable electronics module with an acoustic modem, a data storage module, and a replaceable power module. Time-stamped erosion and corrosion data can be transmitted via an acoustic link to a surface platform, a vessel of opportunity or to a relaying modem. Acoustic signals can be transmitted up to 6 km from the monitoring location. The power module along with data module and acoustic modem are mounted on the erosion and corrosion module using wet-mateable connectors, allowing retrieval by remotely operated vehicles. The collected data can be used to assess the cumulative erosion and corrosion as well as use the real-time metal loss rate data to correlate with operational parameters. Benefits include optimization of corrosion inhibitor dosage rates, mitigation of damage caused by solids production, and increased flow assurance. (author)

  7. Matrix factorizations and homological mirror symmetry on the torus

    International Nuclear Information System (INIS)

    Knapp, Johanna; Omer, Harun

    2007-01-01

    We consider matrix factorizations and homological mirror symmetry on the torus T 2 using a Landau-Ginzburg description. We identify the basic matrix factorizations of the Landau-Ginzburg superpotential and compute the full spectrum taking into account the explicit dependence on bulk and boundary moduli. We verify homological mirror symmetry by comparing three-point functions in the A-model and the B-model

  8. Regulation of homologous recombination at telomeres in budding yeast

    DEFF Research Database (Denmark)

    Eckert-Boulet, Nadine; Lisby, Michael

    2010-01-01

    Homologous recombination is suppressed at normal length telomere sequences. In contrast, telomere recombination is allowed when telomeres erode in the absence of telomerase activity or as a consequence of nucleolytic degradation or incomplete replication. Here, we review the mechanisms that contr...... that contribute to regulating mitotic homologous recombination at telomeres and the role of these mechanisms in signalling short telomeres in the budding yeast Saccharomyces cerevisiae....

  9. Zeroth Poisson Homology, Foliated Cohomology and Perfect Poisson Manifolds

    Science.gov (United States)

    Martínez-Torres, David; Miranda, Eva

    2018-01-01

    We prove that, for compact regular Poisson manifolds, the zeroth homology group is isomorphic to the top foliated cohomology group, and we give some applications. In particular, we show that, for regular unimodular Poisson manifolds, top Poisson and foliated cohomology groups are isomorphic. Inspired by the symplectic setting, we define what a perfect Poisson manifold is. We use these Poisson homology computations to provide families of perfect Poisson manifolds.

  10. Confirming the Revised C-Terminal Domain of the MscL Crystal Structure

    OpenAIRE

    Maurer, Joshua A.; Elmore, Donald E.; Clayton, Daniel; Xiong, Li; Lester, Henry A.; Dougherty, Dennis A.

    2008-01-01

    The structure of the C-terminal domain of the mechanosensitive channel of large conductance (MscL) has generated significant controversy. As a result, several structures have been proposed for this region: the original crystal structure (1MSL) of the Mycobacterium tuberculosis homolog (Tb), a model of the Escherichia coli homolog, and, most recently, a revised crystal structure of Tb-MscL (2OAR). To understand which of these structures represents a physiological conformation, we measured the ...

  11. Structural Characterization of Monomeric/Dimeric State of p59fyn SH2 Domain.

    Science.gov (United States)

    Huculeci, Radu; Kieken, Fabien; Garcia-Pino, Abel; Buts, Lieven; van Nuland, Nico; Lenaerts, Tom

    2017-01-01

    Src homology 2 (SH2) domains are key modulators in various signaling pathways allowing the recognition of phosphotyrosine sites of different proteins. Despite the fact that SH2 domains acquire their biological functions in a monomeric state, a multitude of reports have shown their tendency to dimerize. Here, we provide a technical description on how to isolate and characterize by gel filtration, circular dichroism (CD), and nuclear magnetic resonance (NMR) each conformational state of p59 fyn SH2 domain.

  12. The concept of homology as a basis for evaluating developmental mechanisms: exploring selective attention across the life-span.

    Science.gov (United States)

    Lickliter, Robert; Bahrick, Lorraine E

    2013-01-01

    Research with human infants as well as non-human animal embryos and infants has consistently demonstrated the benefits of intersensory redundancy for perceptual learning and memory for redundantly specified information during early development. Studies of infant affect discrimination, face discrimination, numerical discrimination, sequence detection, abstract rule learning, and word comprehension and segmentation have all shown that intersensory redundancy promotes earlier detection of these properties when compared to unimodal exposure to the same properties. Here we explore the idea that such intersensory facilitation is evident across the life-span and that this continuity is an example of a developmental behavioral homology. We present evidence that intersensory facilitation is most apparent during early phases of learning for a variety of tasks, regardless of developmental level, including domains that are novel or tasks that require discrimination of fine detail or speeded responses. Under these conditions, infants, children, and adults all show intersensory facilitation, suggesting a developmental homology. We discuss the challenge and propose strategies for establishing appropriate guidelines for identifying developmental behavioral homologies. We conclude that evaluating the extent to which continuities observed across development are homologous can contribute to a better understanding of the processes of development. Copyright © 2012 Wiley Periodicals, Inc.

  13. Homology modeling and in silico prediction of Ulcerative colitis associated polymorphisms of NOD1.

    Science.gov (United States)

    Majumdar, Ishani; Nagpal, Isha; Paul, Jaishree

    2017-10-01

    Cytosolic pattern recognition receptors play key roles in innate immune response. Nucleotide binding and oligomerisation domain containing protein 1 (NOD1) belonging to the Nod-like receptor C (NLRC) sub-family of Nod-like receptors (NLRs) is important for detection and clearance of intra-cellular Gram negative bacteria. NOD1 is involved in activation of pro-inflammatory pathways. Limited structural data is available for NOD1. Using different templates for each domain of NOD1, we determined the full-length homology model of NOD1. ADP binding amino acids within the nucleotide binding domain (NBD) of NOD1 were also predicted. Key residues in inter-domain interaction were identified by sequence comparison with Oryctolagus cuniculus NOD2, a related protein. Interactions between NBD and winged helix domain (WHD) were found to be conserved in NOD1. Functional and structural effect of single nucleotide polymorphisms within the NOD1 NBD domain associated with susceptibility risk to Ulcerative colitis (UC), an inflammatory disorder of the colon was evaluated by in silico studies. Mutations W219R and L349P were predicted to be damaging and disease associated by prediction programs SIFT, PolyPhen2, PANTHER, SNP&GO, PhD SNP and SNAP2. We further validated the effect of W219R and L349P mutation on NOD1 function in vitro. Elevated mRNA expression of pro-inflammatory cytokines IL8 and IL-1β was seen as compared to the wild type NOD1 in intestinal epithelial cell line HT29 when stimulated with NOD1 ligand. Thus, these mutations may indeed have a bearing on pathogenesis of inflammation during UC. Copyright © 2017 Elsevier Ltd. All rights reserved.

  14. In vivo blunt-end cloning through CRISPR/Cas9-facilitated non-homologous end-joining

    Science.gov (United States)

    Geisinger, Jonathan M.; Turan, Sören; Hernandez, Sophia; Spector, Laura P.; Calos, Michele P.

    2016-01-01

    The CRISPR/Cas9 system facilitates precise DNA modifications by generating RNA-guided blunt-ended double-strand breaks. We demonstrate that guide RNA pairs generate deletions that are repaired with a high level of precision by non-homologous end-joining in mammalian cells. We present a method called knock-in blunt ligation for exploiting these breaks to insert exogenous PCR-generated sequences in a homology-independent manner without loss of additional nucleotides. This method is useful for making precise additions to the genome such as insertions of marker gene cassettes or functional elements, without the need for homology arms. We successfully utilized this method in human and mouse cells to insert fluorescent protein cassettes into various loci, with efficiencies up to 36% in HEK293 cells without selection. We also created versions of Cas9 fused to the FKBP12-L106P destabilization domain in an effort to improve Cas9 performance. Our in vivo blunt-end cloning method and destabilization-domain-fused Cas9 variant increase the repertoire of precision genome engineering approaches. PMID:26762978

  15. Purification of SOCS (Suppressor of Cytokine Signaling) SH2 Domains for Structural and Functional Studies.

    Science.gov (United States)

    Liau, Nicholas P D; Laktyushin, Artem; Babon, Jeffrey J

    2017-01-01

    Src Homology 2 (SH2) domains are protein domains which have a high binding affinity for specific amino acid sequences containing a phosphorylated tyrosine residue. The Suppressors of Cytokine Signaling (SOCS) proteins use an SH2 domain to bind to components of certain cytokine signaling pathways to downregulate the signaling cascade. The recombinantly produced SH2 domains of various SOCS proteins have been used to undertake structural and functional studies elucidating the method of how such targeting occurs. Here, we describe the protocol for the recombinant production and purification of SOCS SH2 domains, with an emphasis on SOCS3.

  16. Multiscale analysis of nonlinear systems using computational homology

    Energy Technology Data Exchange (ETDEWEB)

    Konstantin Mischaikow; Michael Schatz; William Kalies; Thomas Wanner

    2010-05-24

    This is a collaborative project between the principal investigators. However, as is to be expected, different PIs have greater focus on different aspects of the project. This report lists these major directions of research which were pursued during the funding period: (1) Computational Homology in Fluids - For the computational homology effort in thermal convection, the focus of the work during the first two years of the funding period included: (1) A clear demonstration that homology can sensitively detect the presence or absence of an important flow symmetry, (2) An investigation of homology as a probe for flow dynamics, and (3) The construction of a new convection apparatus for probing the effects of large-aspect-ratio. (2) Computational Homology in Cardiac Dynamics - We have initiated an effort to test the use of homology in characterizing data from both laboratory experiments and numerical simulations of arrhythmia in the heart. Recently, the use of high speed, high sensitivity digital imaging in conjunction with voltage sensitive fluorescent dyes has enabled researchers to visualize electrical activity on the surface of cardiac tissue, both in vitro and in vivo. (3) Magnetohydrodynamics - A new research direction is to use computational homology to analyze results of large scale simulations of 2D turbulence in the presence of magnetic fields. Such simulations are relevant to the dynamics of black hole accretion disks. The complex flow patterns from simulations exhibit strong qualitative changes as a function of magnetic field strength. Efforts to characterize the pattern changes using Fourier methods and wavelet analysis have been unsuccessful. (4) Granular Flow - two experts in the area of granular media are studying 2D model experiments of earthquake dynamics where the stress fields can be measured; these stress fields from complex patterns of 'force chains' that may be amenable to analysis using computational homology. (5) Microstructure

  17. Multiscale analysis of nonlinear systems using computational homology

    Energy Technology Data Exchange (ETDEWEB)

    Konstantin Mischaikow, Rutgers University/Georgia Institute of Technology, Michael Schatz, Georgia Institute of Technology, William Kalies, Florida Atlantic University, Thomas Wanner,George Mason University

    2010-05-19

    This is a collaborative project between the principal investigators. However, as is to be expected, different PIs have greater focus on different aspects of the project. This report lists these major directions of research which were pursued during the funding period: (1) Computational Homology in Fluids - For the computational homology effort in thermal convection, the focus of the work during the first two years of the funding period included: (1) A clear demonstration that homology can sensitively detect the presence or absence of an important flow symmetry, (2) An investigation of homology as a probe for flow dynamics, and (3) The construction of a new convection apparatus for probing the effects of large-aspect-ratio. (2) Computational Homology in Cardiac Dynamics - We have initiated an effort to test the use of homology in characterizing data from both laboratory experiments and numerical simulations of arrhythmia in the heart. Recently, the use of high speed, high sensitivity digital imaging in conjunction with voltage sensitive fluorescent dyes has enabled researchers to visualize electrical activity on the surface of cardiac tissue, both in vitro and in vivo. (3) Magnetohydrodynamics - A new research direction is to use computational homology to analyze results of large scale simulations of 2D turbulence in the presence of magnetic fields. Such simulations are relevant to the dynamics of black hole accretion disks. The complex flow patterns from simulations exhibit strong qualitative changes as a function of magnetic field strength. Efforts to characterize the pattern changes using Fourier methods and wavelet analysis have been unsuccessful. (4) Granular Flow - two experts in the area of granular media are studying 2D model experiments of earthquake dynamics where the stress fields can be measured; these stress fields from complex patterns of 'force chains' that may be amenable to analysis using computational homology. (5) Microstructure

  18. The OGCleaner: filtering false-positive homology clusters.

    Science.gov (United States)

    Fujimoto, M Stanley; Suvorov, Anton; Jensen, Nicholas O; Clement, Mark J; Snell, Quinn; Bybee, Seth M

    2017-01-01

    Detecting homologous sequences in organisms is an essential step in protein structure and function prediction, gene annotation and phylogenetic tree construction. Heuristic methods are often employed for quality control of putative homology clusters. These heuristics, however, usually only apply to pairwise sequence comparison and do not examine clusters as a whole. We present the Orthology Group Cleaner (the OGCleaner), a tool designed for filtering putative orthology groups as homology or non-homology clusters by considering all sequences in a cluster. The OGCleaner relies on high-quality orthologous groups identified in OrthoDB to train machine learning algorithms that are able to distinguish between true-positive and false-positive homology groups. This package aims to improve the quality of phylogenetic tree construction especially in instances of lower-quality transcriptome assemblies. https://github.com/byucsl/ogcleaner CONTACT: sfujimoto@gmail.comSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  19. Primary homologies of the circumorbital bones of snakes.

    Science.gov (United States)

    Palci, Alessandro; Caldwell, Michael W

    2013-09-01

    Some snakes have two circumorbital ossifications that in the current literature are usually referred to as the postorbital and supraorbital. We review the arguments that have been proposed to justify this interpretation and provide counter-arguments that reject those conjectures of primary homology based on the observation of 32 species of lizards and 81 species of snakes (both extant and fossil). We present similarity arguments, both topological and structural, for reinterpretation of the primary homologies of the dorsal and posterior orbital ossifications of snakes. Applying the test of similarity, we conclude that the posterior orbital ossification of snakes is topologically consistent as the homolog of the lacertilian jugal, and that the dorsal orbital ossification present in some snakes (e.g., pythons, Loxocemus, and Calabaria) is the homolog of the lacertilian postfrontal. We therefore propose that the terms postorbital and supraorbital should be abandoned as reference language for the circumorbital bones of snakes, and be replaced with the terms jugal and postfrontal, respectively. The primary homology claim for the snake "postorbital" fails the test of similarity, while the term "supraorbital" is an unnecessary and inaccurate application of the concept of a neomorphic ossification, for an element that passes the test of similarity as a postfrontal. This reinterpretation of the circumorbital bones of snakes is bound to have important repercussions for future phylogenetic analyses and consequently for our understanding of the origin and evolution of snakes. Copyright © 2013 Wiley Periodicals, Inc.

  20. Towards open world software architectures with semantic architecture styles, components and connectors

    DEFF Research Database (Denmark)

    Hansen, Klaus Marius; Zhang, Weishan; Fernandes, Joao Miguel

    2009-01-01

    Planning (for example choosing most suitable servicesfor self-configuration) is one important task in selfmanagement for pervasive service computing, and can bereduced to the problem of multi-objective services selectionwith constraints. Genetic algorithms (GAs) are effectivein solving such multi.......This situation makes the application of GAs difficultin the pervasive service computing domain in which performance may be critical and the settings of parameters may have big consequences for performance. In this paper, wewill present our evaluations of two GAs, namely NSGA-IIand MOCell, in the GA framework...... JMetal2.1, for achievingmulti-objective selection of available services. From theseevaluations, suggestions on how and when to use NSGA-IIand MOCell are given in the planning for self-management.Our experiences show that to get a true Pareto front for aproblem, combining solutions set from different GAs...

  1. Structure and dynamics of the human pleckstrin DEP domain: distinct molecular features of a novel DEP domain subfamily.

    Science.gov (United States)

    Civera, Concepcion; Simon, Bernd; Stier, Gunter; Sattler, Michael; Macias, Maria J

    2005-02-01

    Pleckstrin1 is a major substrate for protein kinase C in platelets and leukocytes, and comprises a central DEP (disheveled, Egl-10, pleckstrin) domain, which is flanked by two PH (pleckstrin homology) domains. DEP domains display a unique alpha/beta fold and have been implicated in membrane binding utilizing different mechanisms. Using multiple sequence alignments and phylogenetic tree reconstructions, we find that 6 subfamilies of the DEP domain exist, of which pleckstrin represents a novel and distinct subfamily. To clarify structural determinants of the DEP fold and to gain further insight into the role of the DEP domain, we determined the three-dimensional structure of the pleckstrin DEP domain using heteronuclear NMR spectroscopy. Pleckstrin DEP shares main structural features with the DEP domains of disheveled and Epac, which belong to different DEP subfamilies. However, the pleckstrin DEP fold is distinct from these structures and contains an additional, short helix alpha4 inserted in the beta4-beta5 loop that exhibits increased backbone mobility as judged by NMR relaxation measurements. Based on sequence conservation, the helix alpha4 may also be present in the DEP domains of regulator of G-protein signaling (RGS) proteins, which are members of the same DEP subfamily. In pleckstrin, the DEP domain is surrounded by two PH domains. Structural analysis and charge complementarity suggest that the DEP domain may interact with the N-terminal PH domain in pleckstrin. Phosphorylation of the PH-DEP linker, which is required for pleckstrin function, could regulate such an intramolecular interaction. This suggests a role of the pleckstrin DEP domain in intramolecular domain interactions, which is distinct from the functions of other DEP domain subfamilies found so far.

  2. Prokaryotic caspase homologs: phylogenetic patterns and functional characteristics reveal considerable diversity.

    Directory of Open Access Journals (Sweden)

    Johannes Asplund-Samuelsson

    Full Text Available Caspases accomplish initiation and execution of apoptosis, a programmed cell death process specific to metazoans. The existence of prokaryotic caspase homologs, termed metacaspases, has been known for slightly more than a decade. Despite their potential connection to the evolution of programmed cell death in eukaryotes, the phylogenetic distribution and functions of these prokaryotic metacaspase sequences are largely uncharted, while a few experiments imply involvement in programmed cell death. Aiming at providing a more detailed picture of prokaryotic caspase homologs, we applied a computational approach based on Hidden Markov Model search profiles to identify and functionally characterize putative metacaspases in bacterial and archaeal genomes. Out of the total of 1463 analyzed genomes, merely 267 (18% were identified to contain putative metacaspases, but their taxonomic distribution included most prokaryotic phyla and a few archaea (Euryarchaeota. Metacaspases were particularly abundant in Alphaproteobacteria, Deltaproteobacteria and Cyanobacteria, which harbor many morphologically and developmentally complex organisms, and a distinct correlation was found between abundance and phenotypic complexity in Cyanobacteria. Notably, Bacillus subtilis and Escherichia coli, known to undergo genetically regulated autolysis, lacked metacaspases. Pfam domain architecture analysis combined with operon identification revealed rich and varied configurations among the metacaspase sequences. These imply roles in programmed cell death, but also e.g. in signaling, various enzymatic activities and protein modification. Together our data show a wide and scattered distribution of caspase homologs in prokaryotes with structurally and functionally diverse sub-groups, and with a potentially intriguing evolutionary role. These features will help delineate future characterizations of death pathways in prokaryotes.

  3. A Polychaete's powerful punch: venom gland transcriptomics of Glycera reveals a complex cocktail of toxin homologs.

    Science.gov (United States)

    von Reumont, Björn M; Campbell, Lahcen I; Richter, Sandy; Hering, Lars; Sykes, Dan; Hetmank, Jörg; Jenner, Ronald A; Bleidorn, Christoph

    2014-09-05

    Glycerids are marine annelids commonly known as bloodworms. Bloodworms have an eversible proboscis adorned with jaws connected to venom glands. Bloodworms prey on invertebrates, and it is known that the venom glands produce compounds that can induce toxic effects in animals. Yet, none of these putative toxins has been characterized on a molecular basis. Here we present the transcriptomic profiles of the venom glands of three species of bloodworm, Glycera dibranchiata, Glycera fallax and Glycera tridactyla, as well as the body tissue of G. tridactyla. The venom glands express a complex mixture of transcripts coding for putative toxin precursors. These transcripts represent 20 known toxin classes that have been convergently recruited into animal venoms, as well as transcripts potentially coding for Glycera-specific toxins. The toxins represent five functional categories: Pore-forming and membrane-disrupting toxins, neurotoxins, protease inhibitors, other enzymes, and CAP domain toxins. Many of the transcripts coding for putative Glycera toxins belong to classes that have been widely recruited into venoms, but some are homologs of toxins previously only known from the venoms of scorpaeniform fish and monotremes (stonustoxin-like toxin), turrid gastropods (turripeptide-like peptides), and sea anemones (gigantoxin I-like neurotoxin). This complex mixture of toxin homologs suggests that bloodworms employ venom while predating on macroscopic prey, casting doubt on the previously widespread opinion that G. dibranchiata is a detritivore. Our results further show that researchers should be aware that different assembly methods, as well as different methods of homology prediction, can influence the transcriptomic profiling of venom glands. © The Author(s) 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  4. RYBP Is a K63-Ubiquitin-Chain-Binding Protein that Inhibits Homologous Recombination Repair

    Directory of Open Access Journals (Sweden)

    Mohammad A.M. Ali

    2018-01-01

    Full Text Available Summary: Ring1-YY1-binding protein (RYBP is a member of the non-canonical polycomb repressive complex 1 (PRC1, and like other PRC1 members, it is best described as a transcriptional regulator. However, several PRC1 members were recently shown to function in DNA repair. Here, we report that RYBP preferentially binds K63-ubiquitin chains via its Npl4 zinc finger (NZF domain. Since K63-linked ubiquitin chains are assembled at DNA double-strand breaks (DSBs, we examined the contribution of RYBP to DSB repair. Surprisingly, we find that RYBP is K48 polyubiquitylated by RNF8 and rapidly removed from chromatin upon DNA damage by the VCP/p97 segregase. High expression of RYBP competitively inhibits recruitment of BRCA1 repair complex to DSBs, reducing DNA end resection and homologous recombination (HR repair. Moreover, breast cancer cell lines expressing high endogenous RYBP levels show increased sensitivity to DNA-damaging agents and poly ADP-ribose polymerase (PARP inhibition. These data suggest that RYBP negatively regulates HR repair by competing for K63-ubiquitin chain binding. : Ali et al. find that RYBP binds K63-linked ubiquitin chains and is removed from DNA damage sites. This K63-ubiquitin binding allows RYBP to hinder the recruitment of BRCA1 and Rad51 to DNA double-strand breaks, thus inhibiting homologous recombination repair. Accordingly, cancer cells expressing high RYBP are more sensitive to DNA-damaging therapies. Keywords: DNA damage response, homologous recombination, ubiquitylation, RYBP, polycomb proteins, double-strand break repair, chromatin, histone modification

  5. [Analysis of DNA-DNA homologies in obligate methylotrophic bacteria].

    Science.gov (United States)

    Doronina, N V; Govorukhina, N I; Lysenko, A M; Trotsenko, Iu A

    1988-01-01

    The genotypic affinity of 19 bacterial strains obligately dependent on methanol or methylamine as carbon and energy sources was studied by techniques of molecular DNA hybridization. The high homology level (35-88%) between motile strain Methylophilus methanolovorus V-1447D and nonmotile strain Methylobacillus sp. VSB-792 as well as other motile strains (Pseudomonas methanolica ATCC 21704, Methylomonas methanolica NRRL 5458, Pseudomonas sp. W6, strain A3) indicates that all of them belong to one genus. Rather high level of homology (62-63%) was found between Methylobacillus glycogenes ATCC 29475 and Pseudomonas insueta ATCC 21276 and strain G-10. The motile strain Methylophilus methylotrophus NCIB 10515 has a low homology (below 20%) to other of the studied obligate methylobacteria. Therefore, at least two genetically different genera of obligate methylobacteria can be distinguished, namely Methylophilus and Methylobacillus, the latter being represented by both motile and nonmotile forms.

  6. Induction of intrachromosomal homologous recombination in whole plants

    International Nuclear Information System (INIS)

    Puchta, H.; Swoboda, P.; Hohn, B.

    1995-01-01

    The influence of different factors on frequencies of intrachromosomal homologous recombination in whole Arabidopsis thaliana and tobacco plants was analyzed using a disrupted β-glucuronidase marker gene. Recombination frequencies were enhanced several fold by DNA damaging agents like UV-light or MMS (methyl methanesulfonate). Applying 3-methoxybenzamide (3-MB), an inhibitor of poly(ADP)ribose polymerase (PARP), an enzyme that is postulated to be involved in DNA repair, enhanced homologous recombination frequencies strongly. These findings indicate that homologous recombination is involved in DNA repair and can (at least partially) compensate for other DNA repair pathways. Indications that recombination in plants can be induced by environmental stress factors that are not likely to be involved in DNA metabolism were also found; Arabidopsis plants growing in a medium containing 0.1 M NaCl exhibited elevated recombination frequencies. The possible general effects of ‘environmental’ challenges on genome flexibility are discussed. (author)

  7. Khovanov homology for virtual knots with arbitrary coefficients

    International Nuclear Information System (INIS)

    Manturov, Vassily O

    2007-01-01

    The Khovanov homology theory over an arbitrary coefficient ring is extended to the case of virtual knots. We introduce a complex which is well-defined in the virtual case and is homotopy equivalent to the original Khovanov complex in the classical case. Unlike Khovanov's original construction, our definition of the complex does not use any additional prescription of signs to the edges of a cube. Moreover, our method enables us to construct a Khovanov homology theory for 'twisted virtual knots' in the sense of Bourgoin and Viro (including knots in three-dimensional projective space). We generalize a number of results of Khovanov homology theory (the Wehrli complex, minimality problems, Frobenius extensions) to virtual knots with non-orientable atoms

  8. Homology groups for particles on one-connected graphs

    Science.gov (United States)

    MaciÄ Żek, Tomasz; Sawicki, Adam

    2017-06-01

    We present a mathematical framework for describing the topology of configuration spaces for particles on one-connected graphs. In particular, we compute the homology groups over integers for different classes of one-connected graphs. Our approach is based on some fundamental combinatorial properties of the configuration spaces, Mayer-Vietoris sequences for different parts of configuration spaces, and some limited use of discrete Morse theory. As one of the results, we derive the closed-form formulae for ranks of the homology groups for indistinguishable particles on tree graphs. We also give a detailed discussion of the second homology group of the configuration space of both distinguishable and indistinguishable particles. Our motivation is the search for new kinds of quantum statistics.

  9. Exotic plant infestation is associated with decreased modularity and increased numbers of connectors in mixed-grass prairie pollination networks

    Science.gov (United States)

    Larson, Diane L.; Rabie, Paul A.; Droege, Sam; Larson, Jennifer L.; Haar, Milton

    2016-01-01

    The majority of pollinating insects are generalists whose lifetimes overlap flowering periods of many potentially suitable plant species. Such generality is instrumental in allowing exotic plant species to invade pollination networks. The particulars of how existing networks change in response to an invasive plant over the course of its phenology are not well characterized, but may shed light on the probability of long-term effects on plant-pollinator interactions and the stability of network structure. Here we describe changes in network topology and modular structure of infested and non-infested networks during the flowering season of the generalist non-native flowering plant, Cirsium arvense in mixed-grass prairie at Badlands National Park, South Dakota, USA. Objectives were to compare network-level effects of infestation as they propagate over the season in infested and non-infested (with respect to C. arvense) networks. We characterized plant-pollinator networks on 5 non-infested and 7 infested 1-ha plots during 4 sample periods that collectively covered the length of C. arvense flowering period. Two other abundantly-flowering invasive plants were present during this time: Melilotus officinalis had highly variable floral abundance in both C. arvense-infested and non-infested plots andConvolvulus arvensis, which occurred almost exclusively in infested plots and peaked early in the season. Modularity, including roles of individual species, and network topology were assessed for each sample period as well as in pooled infested and non-infested networks. Differences in modularity and network metrics between infested and non-infested networks were limited to the third and fourth sample periods, during flower senescence of C. arvenseand the other invasive species; generality of pollinators rose concurrently, suggesting rewiring of the network and a lag effect of earlier floral abundance. Modularity was lower and number of connectors higher in infested

  10. View of the inner part of the VO prototype box. The WLS fibers wrapped up in teflon strips are coupled to connectors which ensure the passage of the light outside the box and its transfer in optical fibers.

    CERN Multimedia

    2004-01-01

    View of the inner part of the VO prototype box. The WLS fibers wrapped up in teflon strips are coupled to connectors which ensure the passage of the light outside the box and its transfer in optical fibers.

  11. Structural insights into a high affinity nanobody:antigen complex by homology modelling.

    Science.gov (United States)

    Skottrup, Peter Durand

    2017-09-01

    Porphyromonas gingivalis is a major periodontitis-causing pathogens. P. gingivalis secrete a cysteine protease termed RgpB, which is specific for Arg-Xaa bonds in substrates. Recently, a nanobody-based assay was used to demonstrate that RgpB could represent a novel diagnostic target, thereby simplifying. P. gingivalis detection. The nanobody, VHH7, had a high binding affinity and was specific for RgpB, when tested towards the highly identical RgpA. In this study a homology model of VHH7 was build. The complementarity determining regions (CDR) comprising the paratope residues responsible for RgpB binding were identified and used as input to the docking. Furthermore, residues likely involved in the RgpB epitope was identified based upon RgpB:RgpA alignment and analysis of residue surface accessibility. CDR residues and putitative RgpB epitope residues were used as input to an information-driven flexible docking approach using the HADDOCK server. Analysis of the VHH7:RgpB model demonstrated that the epitope was found in the immunoglobulin-like domain and residue pairs located at the molecular paratope:epitope interface important for complex stability was identified. Collectively, the VHH7 homology model and VHH7:RgpB docking supplies knowledge of the residues involved in the high affinity interaction. This information could prove valuable in the design of an antibody-drug conjugate for specific RgpB targeting. Copyright © 2017 Elsevier Inc. All rights reserved.

  12. Promotion of BRCA2-Dependent Homologous Recombination by DSS1 via RPA Targeting and DNA Mimicry.

    Science.gov (United States)

    Zhao, Weixing; Vaithiyalingam, Sivaraja; San Filippo, Joseph; Maranon, David G; Jimenez-Sainz, Judit; Fontenay, Gerald V; Kwon, Youngho; Leung, Stanley G; Lu, Lucy; Jensen, Ryan B; Chazin, Walter J; Wiese, Claudia; Sung, Patrick

    2015-07-16

    The tumor suppressor BRCA2 is thought to facilitate the handoff of ssDNA from replication protein A (RPA) to the RAD51 recombinase during DNA break and replication fork repair by homologous recombination. However, we find that RPA-RAD51 exchange requires the BRCA2 partner DSS1. Biochemical, structural, and in vivo analyses reveal that DSS1 allows the BRCA2-DSS1 complex to physically and functionally interact with RPA. Mechanistically, DSS1 acts as a DNA mimic to attenuate the affinity of RPA for ssDNA. A mutation in the solvent-exposed acidic domain of DSS1 compromises the efficacy of RPA-RAD51 exchange. Thus, by targeting RPA and mimicking DNA, DSS1 functions with BRCA2 in a two-component homologous recombination mediator complex in genome maintenance and tumor suppression. Our findings may provide a paradigm for understanding the roles of DSS1 in other biological processes. Copyright © 2015 Elsevier Inc. All rights reserved.

  13. Interaction and dynamics of homologous pairing protein 2 (HOP2) and DNA studied by MD simulation

    Science.gov (United States)

    Moktan, Hem; Pezza, Roberto; Zhou, Donghua

    2015-03-01

    The homologous pairing protein 2 (Hop2) plays an important role in meiosis and DNA repair. Together with protein Mnd1, Hop2 enhances the strand invasion activity of recombinase Dmc1 by over 30 times, facilitating proper synapsis of homologous chromosomes. We recently determined the NMR structure of the N-terminal domain of Hop2 and proposed a model of Protein-DNA complex based on NMR chemical shift perturbations and mutagenesis studies (Moktan, J Biol Chem 2014 10.1074/jbc.M114.548180). However structure and dynamics of the complex have not been studied at the atomic level yet. Here, we used classical MD simulations to study the interactions between the N-terminal HOP2 and DNA. The simulated results indicate that helix3 (H3) interacts with DNA in major groove and wing1 (W1) interacts mostly in minor groove mainly via direct hydrogen bonds. Also it is found that binding leads to reduced fluctuations in both protein and DNA. Several water bridge interactions have been identified. The residue-wise contributions to the interaction energy were evaluated. Also the functional motion of the protein is analyzed using principal component analysis. The results confirmed the importance of H3 and W1 for the stability of the complex, which is consistent with our previous experimental studies.

  14. Mutagenic Organized Recombination Process by Homologous IN vivo Grouping (MORPHING) for directed enzyme evolution.

    Science.gov (United States)

    Gonzalez-Perez, David; Molina-Espeja, Patricia; Garcia-Ruiz, Eva; Alcalde, Miguel

    2014-01-01

    Approaches that depend on directed evolution require reliable methods to generate DNA diversity so that mutant libraries can focus on specific target regions. We took advantage of the high frequency of homologous DNA recombination in Saccharomyces cerevisiae to develop a strategy for domain mutagenesis aimed at introducing and in vivo recombining random mutations in defined segments of DNA. Mutagenic Organized Recombination Process by Homologous IN vivo Grouping (MORPHING) is a one-pot random mutagenic method for short protein regions that harnesses the in vivo recombination apparatus of yeast. Using this approach, libraries can be prepared with different mutational loads in DNA segments of less than 30 amino acids so that they can be assembled into the remaining unaltered DNA regions in vivo with high fidelity. As a proof of concept, we present two eukaryotic-ligninolytic enzyme case studies: i) the enhancement of the oxidative stability of a H2O2-sensitive versatile peroxidase by independent evolution of three distinct protein segments (Leu28-Gly57, Leu149-Ala174 and Ile199-Leu268); and ii) the heterologous functional expression of an unspecific peroxygenase by exclusive evolution of its native 43-residue signal sequence.

  15. Proposal to negotiate an amendment to an existing blanket purchase contract for the supply of Burndy connectors for the LHC project and LHC experiments

    CERN Document Server

    2006-01-01

    This document concerns the proposal to negotiate an amendment to an existing blanket purchase contract for the supply of Burndy connectors for the LHC project and LHC experiments. For the reasons explained in this document, the Finance Committee is invited to agree to the negotiation of an amendment to the blanket purchase contract for the supply of Burndy connectors for the LHC project and LHC experiments with the company SOURIAU (CH), for the next three years for up to 600 000 euros (954 600 Swiss francs), subject to revision for inflation from January 2007, bringing the total amount of the blanket purchase contract to a maximum amount of 1 200 000 euros (1 909 200 Swiss francs), subject to revision for inflation from January 2007. The amounts in Swiss francs have been calculated using the present rate of exchange. 2006/60/5/e

  16. Khovanov-Rozansky Graph Homology and Composition Product

    DEFF Research Database (Denmark)

    Wagner, Emmanuel

    2008-01-01

    In analogy with a recursive formula for the HOMFLY-PT polynomial of links given by Jaeger, we give a recursive formula for the graph polynomial introduced by Kauffman and Vogel. We show how this formula extends to the Khovanov–Rozansky graph homology.......In analogy with a recursive formula for the HOMFLY-PT polynomial of links given by Jaeger, we give a recursive formula for the graph polynomial introduced by Kauffman and Vogel. We show how this formula extends to the Khovanov–Rozansky graph homology....

  17. Macdonald operators and homological invariants of the colored Hopf link

    International Nuclear Information System (INIS)

    Awata, Hidetoshi; Kanno, Hiroaki

    2011-01-01

    Using a power sum (boson) realization for the Macdonald operators, we investigate the Gukov, Iqbal, Kozcaz and Vafa (GIKV) proposal for the homological invariants of the colored Hopf link, which include Khovanov-Rozansky homology as a special case. We prove the polynomiality of the invariants obtained by GIKV's proposal for arbitrary representations. We derive a closed formula of the invariants of the colored Hopf link for antisymmetric representations. We argue that a little amendment of GIKV's proposal is required to make all the coefficients of the polynomial non-negative integers. (paper)

  18. Phosphosite mapping of P-type plasma membrane H+-ATPase in homologous and heterologous environments

    DEFF Research Database (Denmark)

    Rudashevskaya, Elena; Ye, Juanying; Jensen, Ole Nørregaard

    2012-01-01

    Phosphorylation is an important posttranslational modification of proteins in living cells and primarily serves regulatory purposes. Several methods were employed for isolating phosphopeptides from proteolytically digested plasma membranes of Arabidopsis thaliana. After a mass spectrometric...... of the phosphosites identified in AHA2 were identical in the plant and fungal systems even though none of the target sequences in AHA2 show homology to proteins of the fungal host. These findings suggest an unexpected accessibility of the terminal regulatory domain of plasma membrane H(+)-ATPase to protein kinase...... analysis of the resulting peptides we could identify 10 different phosphorylation sites in plasma membrane H(+)-ATPases AHA1, AHA2, AHA3, and AHA4/11, five of which have not been reported before, bringing the total number of phosphosites up to 11, which is substantially higher than reported so far for any...

  19. Structural differences of matrix metalloproteinases. Homology modeling and energy minimization of enzyme-substrate complexes

    DEFF Research Database (Denmark)

    Terp, G E; Christensen, I T; Jørgensen, Flemming Steen

    2000-01-01

    Matrix metalloproteinases are extracellular enzymes taking part in the remodeling of extracellular matrix. The structures of the catalytic domain of MMP1, MMP3, MMP7 and MMP8 are known, but structures of enzymes belonging to this family still remain to be determined. A general approach...... to the homology modeling of matrix metalloproteinases, exemplified by the modeling of MMP2, MMP9, MMP12 and MMP14 is described. The models were refined using an energy minimization procedure developed for matrix metalloproteinases. This procedure includes incorporation of parameters for zinc and calcium ions...... in the AMBER 4.1 force field, applying a non-bonded approach and a full ion charge representation. Energy minimization of the apoenzymes yielded structures with distorted active sites, while reliable three-dimensional structures of the enzymes containing a substrate in active site were obtained. The structural...

  20. Quantifying the mechanisms of domain gain in animal proteins.

    Science.gov (United States)

    Buljan, Marija; Frankish, Adam; Bateman, Alex

    2010-01-01

    Protein domains are protein regions that are shared among different proteins and are frequently functionally and structurally independent from the rest of the protein. Novel domain combinations have a major role in evolutionary innovation. However, the relative contributions of the different molecular mechanisms that underlie domain gains in animals are still unknown. By using animal gene phylogenies we were able to identify a set of high confidence domain gain events and by looking at their coding DNA investigate the causative mechanisms. Here we show that the major mechanism for gains of new domains in metazoan proteins is likely to be gene fusion through joining of exons from adjacent genes, possibly mediated by non-allelic homologous recombination. Retroposition and insertion of exons into ancestral introns through intronic recombination are, in contrast to previous expectations, only minor contributors to domain gains and have accounted for less than 1% and 10% of high confidence domain gain events, respectively. Additionally, exonization of previously non-coding regions appears to be an important mechanism for addition of disordered segments to proteins. We observe that gene duplication has preceded domain gain in at least 80% of the gain events. The interplay of gene duplication and domain gain demonstrates an important mechanism for fast neofunctionalization of genes.

  1. Homology modeling, molecular docking and DNA binding studies of nucleotide excision repair UvrC protein from M. tuberculosis.

    Science.gov (United States)

    Parulekar, Rishikesh S; Barage, Sagar H; Jalkute, Chidambar B; Dhanavade, Maruti J; Fandilolu, Prayagraj M; Sonawane, Kailas D

    2013-08-01

    Mycobacterium tuberculosis is a Gram positive, acid-fast bacteria belonging to genus Mycobacterium, is the leading causative agent of most cases of tuberculosis. The pathogenicity of the bacteria is enhanced by its developed DNA repair mechanism which consists of machineries such as nucleotide excision repair. Nucleotide excision repair consists of excinuclease protein UvrABC endonuclease, multi-enzymatic complex which carries out repair of damaged DNA in sequential manner. UvrC protein is a part of this complex and thus helps to repair the damaged DNA of M. tuberculosis. Hence, structural bioinformatics study of UvrC protein from M. tuberculosis was carried out using homology modeling and molecular docking techniques. Assessment of the reliability of the homology model was carried out by predicting its secondary structure along with its model validation. The predicted structure was docked with the ATP and the interacting amino acid residues of UvrC protein with the ATP were found to be TRP539, PHE89, GLU536, ILE402 and ARG575. The binding of UvrC protein with the DNA showed two different domains. The residues from domain I of the protein VAL526, THR524 and LEU521 interact with the DNA whereas, amino acids interacting from the domain II of the UvrC protein included ARG597, GLU595, GLY594 and GLY592 residues. This predicted model could be useful to design new inhibitors of UvrC enzyme to prevent pathogenesis of Mycobacterium and so the tuberculosis.

  2. Experimental Studies of Sealing Mechanism of a Dismountable Microsystem-to-Macropart Fluidic Connector for High Pressure and a Wide Range of Temperature

    Directory of Open Access Journals (Sweden)

    Hugo Nguyen

    2010-01-01

    Full Text Available As fluidic microelectromechanical devices are developing and often attached to, or embedded in, large, complex, and expensive systems, the issues of modularity, maintenance, and subsystem replacement arise. In this work, a robust silicon connector suitable for high-pressure applications—likely with harsh fluids—in the temperature range of +100 to −100° C is demonstrated and tested together with a stainless steel nipple representing a simple and typical macropart. With a micromachined circular membrane equipped with a 5 μm high ridge, this connector is able to maintain a leak rate below 2.0×10−8 scc/s of gaseous helium with a pressure of up to 9.7 bar. Degradation of the sealing performance on reassembly is associated with the indentation of the ridge. However, the ridge makes the sealing interface less sensitive to particles in comparison with a flat reference. Most evaluation is made through the so-called heat-until-leak tests conducted to determine the maximum working temperature and the sealing mechanism of the connector. A couple of these are followed by cryogenic testing. The effect of thermal mismatch of the components is discussed and utilized as an early warning mechanism.

  3. Redox control of ferrocene-based complexes with systematically extended π-conjugated connectors: switchable and tailorable second order nonlinear optics.

    Science.gov (United States)

    Wang, Wen-Yong; Ma, Na-Na; Sun, Shi-Ling; Qiu, Yong-Qing

    2014-03-14

    The studies of geometrical structures, thermal stabilities, redox properties, nonlinear responses and optoelectronic properties have been carried out on a series of novel ferrocenyl (Fc) chromophores with the view of assessing their switchable and tailorable second order nonlinear optics (NLO). The use of a constant Fc donor and a 4,4'-bipyridinium acceptor and varied conjugated bridges makes it possible to systematically determine the contribution of organic connectors to chromophore nonlinear optical activities. The structures reveal that both the reduction reactions and organic connectors have a significant influence on 4,4'-bipyridinium. The potential energy surface maps along with plots of reduced density gradient mirror the thermal stabilities of the Fc-based chromophores. The first and second reductions take place preferentially at the 4,4'-bipyridinium moieties. Significantly, the reduction processes result in the molecular switches with large NLO contrast varying from zero or very small to a large value. Moreover, time-dependent density functional theory results indicate that the absorption peaks are mainly attributed to Fc to 4,4'-bipyridinium charge transfer and the mixture of intramolecular charge transfer within the two respective 4,4'-bipyridinium moieties coupled with interlayer charge transfer between the two 4,4'-bipyridinium moieties. This provides us with comprehensive information on the effect of organic connectors on the NLO properties.

  4. A localized interaction surface for voltage-sensing domains on the pore domain of a K+ channel.

    Science.gov (United States)

    Li-Smerin, Y; Hackos, D H; Swartz, K J

    2000-02-01

    Voltage-gated K+ channels contain a central pore domain and four surrounding voltage-sensing domains. How and where changes in the structure of the voltage-sensing domains couple to the pore domain so as to gate ion conduction is not understood. The crystal structure of KcsA, a bacterial K+ channel homologous to the pore domain of voltage-gated K+ channels, provides a starting point for addressing this question. Guided by this structure, we used tryptophan-scanning mutagenesis on the transmembrane shell of the pore domain in the Shaker voltage-gated K+ channel to localize potential protein-protein and protein-lipid interfaces. Some mutants cause only minor changes in gating and when mapped onto the KcsA structure cluster away from the interface between pore domain subunits. In contrast, mutants producing large changes in gating tend to cluster near this interface. These results imply that voltage-sensing domains interact with localized regions near the interface between adjacent pore domain subunits.

  5. Hydrophobic interaction between the SH2 domain and the kinase domain is required for the activation of Csk.

    Science.gov (United States)

    Mikkola, Esa T; Gahmberg, Carl G

    2010-06-18

    The protein tyrosine kinase C-terminal Src kinase (Csk) is activated by the engagement of its Src homology (SH) 2 domain. However, the molecular mechanism required for this is not completely understood. The crystal structure of the active Csk indicates that Csk could be activated by contact between the SH2 domain and the beta3-alphaC loop in the N-terminal lobe of the kinase domain. To study the importance of this interaction for the SH2-domain-mediated activation of Csk, we mutated the amino acid residues forming the contacts between the SH2 domain and the beta3-alphaC loop. The mutation of the beta3-alphaC loop Ala228 to glycine and of the SH2 domain Tyr116, Tyr133, Leu138, and Leu149 to alanine resulted in the inability of the SH2 domain ligand to activate Csk. Furthermore, the overexpressed Csk mutants A228G, Y133A/Y116A, L138A, and L149A were unable to efficiently inactivate endogenous Src in human embryonic kidney 293 cells. The results suggest that the SH2-domain-mediated activation of Csk is dependent on the binding of the beta3-alphaC loop Ala228 to the hydrophobic pocket formed by the side chains of Tyr116, Tyr133, Leu138, and Leu149 on the surface of the SH2 domain. Copyright (c) 2010 Elsevier Ltd. All rights reserved.

  6. Topological Hochschild homology and the Bass trace conjecture

    DEFF Research Database (Denmark)

    Berrick, A. J.; Hesselholt, Lars

    2015-01-01

    We use the methods of topological Hochschild homology to shed new light on groups satisfying the Bass trace conjecture. Factorization of the Hattori–Stallings rank map through the Bökstedt–Hsiang–Madsen cyclotomic trace map leads to Linnell's restriction on such groups. As a new consequence...

  7. The homological content of the Jones representations at $q = -1$

    DEFF Research Database (Denmark)

    Egsgaard, Jens Kristian; Fuglede Jørgensen, Søren

    We generalize a discovery of Kasahara and show that the Jones representations of braid groups, when evaluated at $q = -1$, are related to the action on homology of a branched double cover of the underlying punctured disk. As an application, we prove for a large family of pseudo-Anosov mapping...

  8. Topological quantum information, virtual Jones polynomials and Khovanov homology

    International Nuclear Information System (INIS)

    Kauffman, Louis H

    2011-01-01

    In this paper, we give a quantum statistical interpretation of the bracket polynomial state sum 〈K〉, the Jones polynomial V K (t) and virtual knot theory versions of the Jones polynomial, including the arrow polynomial. We use these quantum mechanical interpretations to give new quantum algorithms for these Jones polynomials. In those cases where the Khovanov homology is defined, the Hilbert space C(K) of our model is isomorphic with the chain complex for Khovanov homology with coefficients in the complex numbers. There is a natural unitary transformation U:C(K) → C(K) such that 〈K〉 = Trace(U), where 〈K〉 denotes the evaluation of the state sum model for the corresponding polynomial. We show that for the Khovanov boundary operator ∂:C(K) → C(K), we have the relationship ∂U + U∂ = 0. Consequently, the operator U acts on the Khovanov homology, and we obtain a direct relationship between the Khovanov homology and this quantum algorithm for the Jones polynomial. (paper)

  9. Homology of the open moduli space of curves

    DEFF Research Database (Denmark)

    Madsen, Ib Henning

    2012-01-01

    This is a survey on the proof of a generalized version of the Mumford conjecture obtained in joint work with M. Weiss stating that a certain map between some classifying spaces which a priori have different natures induces an isomorphism at the level of integral homology. We also discuss our proo...

  10. On the Cogosvili functor generated by a homology

    International Nuclear Information System (INIS)

    Abd El-Satter, A. Dabbour; Mahmoud, S.

    1991-09-01

    In the present work we discuss the Cogosvili functor generated by a homology, and study the construction of the corresponding groups and their induced homomorphisms. Moreover, we investigate the properties of this functor and prove that the set of such functors are isomorphic to the Bauer homotopy theory. (author). 19 refs

  11. Human Fanconi anemia monoubiquitination pathway promotes homologous DNA repair.

    Science.gov (United States)

    Nakanishi, Koji; Yang, Yun-Gui; Pierce, Andrew J; Taniguchi, Toshiyasu; Digweed, Martin; D'Andrea, Alan D; Wang, Zhao-Qi; Jasin, Maria

    2005-01-25

    Fanconi anemia (FA) is a recessive disorder characterized by congenital abnormalities, progressive bone-marrow failure, and cancer susceptibility. Cells from FA patients are hypersensitive to agents that produce DNA crosslinks and, after treatment with these agents, have pronounced chromosome breakage and other cytogenetic abnormalities. Eight FANC genes have been cloned, and the encoded proteins interact in a common cellular pathway. DNA-damaging agents activate the monoubiquitination of FANCD2, resulting in its targeting to nuclear foci that also contain BRCA1 and BRCA2/FANCD1, proteins involved in homology-directed DNA repair. Given the interaction of the FANC proteins with BRCA1 and BRCA2, we tested whether cells from FA patients (groups A, G, and D2) and mouse Fanca-/- cells with a targeted mutation are impaired for this repair pathway. We find that both the upstream (FANCA and FANCG) and downstream (FANCD2) FA pathway components promote homology-directed repair of chromosomal double-strand breaks (DSBs). The FANCD2 monoubiquitination site is critical for normal levels of repair, whereas the ATM phosphorylation site is not. The defect in these cells, however, is mild, differentiating them from BRCA1 and BRCA2 mutant cells. Surprisingly, we provide evidence that these proteins, like BRCA1 but unlike BRCA2, promote a second DSB repair pathway involving homology, i.e., single-strand annealing. These results suggest an early role for the FANC proteins in homologous DSB repair pathway choice.

  12. The PCNA-associated protein PARI negatively regulates homologous recombination via the inhibition of DNA repair synthesis

    DEFF Research Database (Denmark)

    Burkovics, Peter; Dome, Lili; Juhasz, Szilvia

    2016-01-01

    to inhibit homologous recombination (HR) events. Here, we describe a biochemical mechanism in which PARI functions as an HR regulator after replication fork stalling and during double-strand break repair. In our reconstituted biochemical system, we show that PARI inhibits DNA repair synthesis during...... recombination events in a PCNA interaction-dependent way but independently of its UvrD-like helicase domain. In accordance, we demonstrate that PARI inhibits HR in vivo, and its knockdown suppresses the UV sensitivity of RAD18-depleted cells. Our data reveal a novel human regulatory mechanism that limits...

  13. The N domain of somatic angiotensin-converting enzyme negatively regulates ectodomain shedding and catalytic activity

    OpenAIRE

    Woodman, Zenda L.; Schwager, Sylva L. U.; Redelinghuys, Pierre; Carmona, Adriana K.; Ehlers, Mario R. W.; Sturrock, Edward D.

    2005-01-01

    sACE (somatic angiotensin-converting enzyme) consists of two homologous, N and C domains, whereas the testis isoenzyme [tACE (testis ACE)] consists of a single C domain. Both isoenzymes are shed from the cell surface by a sheddase activity, although sACE is shed much less efficiently than tACE. We hypothesize that the N domain of sACE plays a regulatory role, by occluding a recognition motif on the C domain required for ectodomain shedding and by influencing the catalytic efficiency. To test ...

  14. Membrane-Sculpting BAR Domains Generate Stable Lipid Microdomains

    Science.gov (United States)

    Zhao, Hongxia; Michelot, Alphée; Koskela, Essi V.; Tkach, Vadym; Stamou, Dimitrios; Drubin, David G.; Lappalainen, Pekka

    2014-01-01

    SUMMARY Bin-Amphiphysin-Rvs (BAR) domain proteins are central regulators of many cellular processes involving membrane dynamics. BAR domains sculpt phosphoinositide-rich membranes to generate membrane protrusions or invaginations. Here, we report that, in addition to regulating membrane geometry, BAR domains can generate extremely stable lipid microdomains by “freezing” phosphoinositide dynamics. This is a general feature of BAR domains, because the yeast endocytic BAR and Fes/CIP4 homology BAR (F-BAR) domains, the inverse BAR domain of Pinkbar, and the eisosomal BAR protein Lsp1 induced phosphoinositide clustering and halted lipid diffusion, despite differences in mechanisms of membrane interactions. Lsp1 displays comparable low diffusion rates in vitro and in vivo, suggesting that BAR domain proteins also generate stable phosphoinositide microdomains in cells. These results uncover a conserved role for BAR superfamily proteins in regulating lipid dynamics within membranes. Stable microdomains induced by BAR domain scaffolds and specific lipids can generate phase boundaries and diffusion barriers, which may have profound impacts on diverse cellular processes. PMID:24055060

  15. Epitope mapping of the domains of human angiotensin converting enzyme.

    Science.gov (United States)

    Kugaevskaya, Elena V; Kolesanova, Ekaterina F; Kozin, Sergey A; Veselovsky, Alexander V; Dedinsky, Ilya R; Elisseeva, Yulia E

    2006-06-01

    Somatic angiotensin converting enzyme (sACE), contains in its single chain two homologous domains (called N- and C-domains), each bearing a functional zinc-dependent active site. The present study aims to define the differences between two sACE domains and to localize experimentally revealed antigenic determinants (B-epitopes) in the recently determined three-dimensional structure of testicular tACE. The predicted linear antigenic determinants of human sACE were determined by peptide scanning ("PEPSCAN") approach. Essential difference was demonstrated between locations of the epitopes in the N- and C-domains. Comparison of arrangement of epitopes in the human domains with the corresponding sequences of some mammalian sACEs enabled to classify the revealed antigenic determinants as variable or conserved areas. The location of antigenic determinants with respect to various structural elements and to functionally important sites of the human sACE C-domain was estimated. The majority of antigenic sites of the C-domain were located at the irregular elements and at the boundaries of secondary structure elements. The data show structural differences between the sACE domains. The experimentally revealed antigenic determinants were in agreement with the recently determined crystal tACE structure. New potential applications are open to successfully produce mono-specific and group-specific antipeptide antibodies.

  16. Structural and Sequence Similarities of Hydra Xeroderma Pigmentosum A Protein to Human Homolog Suggest Early Evolution and Conservation

    Directory of Open Access Journals (Sweden)

    Apurva Barve

    2013-01-01

    Full Text Available Xeroderma pigmentosum group A (XPA is a protein that binds to damaged DNA, verifies presence of a lesion, and recruits other proteins of the nucleotide excision repair (NER pathway to the site. Though its homologs from yeast, Drosophila, humans, and so forth are well studied, XPA has not so far been reported from protozoa and lower animal phyla. Hydra is a fresh-water cnidarian with a remarkable capacity for regeneration and apparent lack of organismal ageing. Cnidarians are among the first metazoa with a defined body axis, tissue grade organisation, and nervous system. We report here for the first time presence of XPA gene in hydra. Putative protein sequence of hydra XPA contains nuclear localization signal and bears the zinc-finger motif. It contains two conserved Pfam domains and various characterized features of XPA proteins like regions for binding to excision repair cross-complementing protein-1 (ERCC1 and replication protein A 70 kDa subunit (RPA70 proteins. Hydra XPA shows a high degree of similarity with vertebrate homologs and clusters with deuterostomes in phylogenetic analysis. Homology modelling corroborates the very close similarity between hydra and human XPA. The protein thus most likely functions in hydra in the same manner as in other animals, indicating that it arose early in evolution and has been conserved across animal phyla.

  17. Functional diversity of Csk, Chk, and Src SH2 domains due to a single residue variation.

    Science.gov (United States)

    Ayrapetov, Marina K; Nam, Nguyen Hai; Ye, Guofeng; Kumar, Anil; Parang, Keykavous; Sun, Gongqin

    2005-07-08

    The C-terminal Src kinase (Csk) family of protein tyrosine kinases contains two members: Csk and Csk homologous kinase (Chk). Both phosphorylate and inactivate Src family kinases. Recent reports suggest that the Src homology (SH) 2 domains of Csk and Chk may bind to different phosphoproteins, which provides a basis for different cellular functions for Csk and Chk. To verify and characterize such a functional divergence, we compared the binding properties of the Csk, Chk, and Src SH2 domains and investigated the structural basis for the functional divergence. First, the study demonstrated striking functional differences between the Csk and Chk SH2 domains and revealed functional similarities between the Chk and Src SH2 domains. Second, structural analysis and mutagenic studies revealed that the functional differences among the three SH2 domains were largely controlled by one residue, Glu127 in Csk, Ile167 in Chk, and Lys200 in Src. Mutating these residues in the Csk or Chk SH2 domain to the Src counterpart resulted in dramatic gain of function similar to Src SH2 domain, whereas mutating Lys200 in Src SH2 domain to Glu (the Csk counterpart) resulted in loss of Src SH2 function. Third, a single point mutation of E127K rendered Csk responsive to activation by a Src SH2 domain ligand. Finally, the optimal phosphopeptide sequence for the Chk SH2 domain was determined. These results provide a compelling explanation for the functional differences between two homologous protein tyrosine kinases and reveal a new structure-function relationship for the SH2 domains.

  18. Analysis of four achaete-scute homologs in Bombyx mori reveals new viewpoints of the evolution and functions of this gene family

    OpenAIRE

    Zhou, Qingxiang; Zhang, Tianyi; Xu, Weihua; Yu, Linlin; Yi, Yongzhu; Zhang, Zhifang

    2008-01-01

    Abstract Background achaete-scute complexe (AS-C) has been widely studied at genetic, developmental and evolutional levels. Genes of this family encode proteins containing a highly conserved bHLH domain, which take part in the regulation of the development of central nervous system and peripheral nervous system. Many AS-C homologs have been isolated from various vertebrates and invertebrates. Also, AS-C genes are duplicated during the evolution of Diptera. Functions besides neural development...

  19. Ensenyar els connectors al primer cicle de l’escola primària / Teaching linking words to primary students

    Directory of Open Access Journals (Sweden)

    Alícia Santolària Òrrios

    2014-10-01

    Full Text Available Resum: L’aprenentatge de la llengua escrita és un procés complex en què interaccionen diversos factors. El punt de partença amb què iniciem aquest article relaciona l’ensenyament d’elements gramaticals, com són els connectors, amb la producció textual d’infants de segon curs d’Educació Primària. En la investigació, que es duu a terme en situació d’aula, s’ha triat com a dispositiu una seqüència didàctica tot tenint en compte el model de l’escola de Ginebra. La mediació elegida demostra, d’una banda, que resulta possible i eficaç introduir aquests sabers gramaticals a l’inici de l’escolarització i, de l’altra, que la intervenció ajuda a millorar els textos dels infants. Abstract: Learning the written language is a complex process in which several factors interact. This article relates the teaching of grammar points -such as linking works- with the written texts of children in their second year of Primary Education. In this research, which was conducted in the classroom, a didactic sequence as a methodological tool has been chosen following the Geneva School. The selected device demonstrates, firstly, that introducing knowledge on grammar is not only possible but efficient at an early age; and, secondly, that the introduction of a didactic sequence helps improve children’s texts.

  20. Tracing the Evolutionary History of the CAP Superfamily of Proteins Using Amino Acid Sequence Homology and Conservation of Splice Sites.

    Science.gov (United States)

    Abraham, Anup; Chandler, Douglas E

    2017-10-01

    Proteins of the CAP superfamily play numerous roles in reproduction, innate immune responses, cancer biology, and venom toxicology. Here we document the breadth of the CAP (Cysteine-RIch Secretory Protein (CRISP), Antigen 5, and Pathogenesis-Related) protein superfamily and trace the major events in its evolution using amino acid sequence homology and the positions of exon/intron borders within their genes. Seldom acknowledged in the literature, we find that many of the CAP subfamilies present in mammals, where they were originally characterized, have distinct homologues in the invertebrate phyla. Early eukaryotic CAP genes contained only one exon inherited from prokaryotic predecessors and as evolution progressed an increasing number of introns were inserted, reaching 2-5 in the invertebrate world and 5-15 in the vertebrate world. Focusing on the CRISP subfamily, we propose that these proteins evolved in three major steps: (1) origination of the CAP/PR/SCP domain in bacteria, (2) addition of a small Hinge domain to produce the two-domain SCP-like proteins found in roundworms and anthropoids, and (3) addition of an Ion Channel Regulatory domain, borrowed from invertebrate peptide toxins, to produce full length, three-domain CRISP proteins, first seen in insects and later to diversify into multiple subtypes in the vertebrate world.

  1. Crystal structure of the Rasputin NTF2-like domain from Drosophila melanogaster

    DEFF Research Database (Denmark)

    Vognsen, Tina Reinholdt; Kristensen, Ole

    2012-01-01

    The crystal structure of the NTF2-like domain of the Drosophila homolog of Ras GTPase SH3 Binding Protein (G3BP), Rasputin, was determined at 2.7Å resolution. The overall structure is highly similar to nuclear transport factor 2: It is a homodimer comprised of a ß-sheet and three a-helices forming...

  2. CORAL: aligning conserved core regions across domain families.

    Science.gov (United States)

    Fong, Jessica H; Marchler-Bauer, Aron

    2009-08-01

    Homologous protein families share highly conserved sequence and structure regions that are frequent targets for comparative analysis of related proteins and families. Many protein families, such as the curated domain families in the Conserved Domain Database (CDD), exhibit similar structural cores. To improve accuracy in aligning such protein families, we propose a profile-profile method CORAL that aligns individual core regions as gap-free units. CORAL computes optimal local alignment of two profiles with heuristics to preserve continuity within core regions. We benchmarked its performance on curated domains in CDD, which have pre-defined core regions, against COMPASS, HHalign and PSI-BLAST, using structure superpositions and comprehensive curator-optimized alignments as standards of truth. CORAL improves alignment accuracy on core regions over general profile methods, returning a balanced score of 0.57 for over 80% of all domain families in CDD, compared with the highest balanced score of 0.45 from other methods. Further, CORAL provides E-values to aid in detecting homologous protein families and, by respecting block boundaries, produces alignments with improved 'readability' that facilitate manual refinement. CORAL will be included in future versions of the NCBI Cn3D/CDTree software, which can be downloaded at http://www.ncbi.nlm.nih.gov/Structure/cdtree/cdtree.shtml. Supplementary data are available at Bioinformatics online.

  3. Intersection spaces, spatial homology truncation, and string theory

    CERN Document Server

    Banagl, Markus

    2010-01-01

    Intersection cohomology assigns groups which satisfy a generalized form of Poincaré duality over the rationals to a stratified singular space. The present monograph introduces a method that assigns to certain classes of stratified spaces cell complexes, called intersection spaces, whose ordinary rational homology satisfies generalized Poincaré duality. The cornerstone of the method is a process of spatial homology truncation, whose functoriality properties are analyzed in detail. The material on truncation is autonomous and may be of independent interest to homotopy theorists. The cohomology of intersection spaces is not isomorphic to intersection cohomology and possesses algebraic features such as perversity-internal cup-products and cohomology operations that are not generally available for intersection cohomology. A mirror-symmetric interpretation, as well as applications to string theory concerning massless D-branes arising in type IIB theory during a Calabi-Yau conifold transition, are discussed.

  4. A homology sound-based algorithm for speech signal interference

    Science.gov (United States)

    Jiang, Yi-jiao; Chen, Hou-jin; Li, Ju-peng; Zhang, Zhan-song

    2015-12-01

    Aiming at secure analog speech communication, a homology sound-based algorithm for speech signal interference is proposed in this paper. We first split speech signal into phonetic fragments by a short-term energy method and establish an interference noise cache library with the phonetic fragments. Then we implement the homology sound interference by mixing the randomly selected interferential fragments and the original speech in real time. The computer simulation results indicated that the interference produced by this algorithm has advantages of real time, randomness, and high correlation with the original signal, comparing with the traditional noise interference methods such as white noise interference. After further studies, the proposed algorithm may be readily used in secure speech communication.

  5. The endless tale of non-homologous end-joining.

    Science.gov (United States)

    Weterings, Eric; Chen, David J

    2008-01-01

    DNA double-strand breaks (DSBs) are introduced in cells by ionizing radiation and reactive oxygen species. In addition, they are commonly generated during V(D)J recombination, an essential aspect of the developing immune system. Failure to effectively repair these DSBs can result in chromosome breakage, cell death, onset of cancer, and defects in the immune system of higher vertebrates. Fortunately, all mammalian cells possess two enzymatic pathways that mediate the repair of DSBs: homologous recombination and non-homologous end-joining (NHEJ). The NHEJ process utilizes enzymes that capture both ends of the broken DNA molecule, bring them together in a synaptic DNA-protein complex, and finally repair the DNA break. In this review, all the known enzymes that play a role in the NHEJ process are discussed and a working model for the co-operation of these enzymes during DSB repair is presented.

  6. Homology and isomorphism: Bourdieu in conversation with New Institutionalism.

    Science.gov (United States)

    Wang, Yingyao

    2016-06-01

    Bourdieusian Field Theory (BFT) provided decisive inspiration for the early conceptual formulation of New Institutionalism (NI). This paper attempts to reinvigorate the stalled intellectual dialogue between NI and BFT by comparing NI's concept of isomorphism with BFT's notion of homology. I argue that Bourdieu's understanding of domination-oriented social action, transposable habitus, and a non-linear causality, embodied in his neglected concept of homology, provides an alternative theorization of field-level convergence to New Institutionalism's central idea of institutional isomorphism. To showcase how BFT can be useful for organizational research, I postulate a habitus-informed and field-conditioned theory of transference to enrich NI's spin-off thesis of 'diffusion'. I propose that while NI can benefit from BFT's potential of bringing social structure back into organizational research, BFT can enrich its social analysis by borrowing from NI's elaboration of the symbolic system of organizations. © London School of Economics and Political Science 2016.

  7. RTEL1 maintains genomic stability by suppressing homologous recombination.

    Science.gov (United States)

    Barber, Louise J; Youds, Jillian L; Ward, Jordan D; McIlwraith, Michael J; O'Neil, Nigel J; Petalcorin, Mark I R; Martin, Julie S; Collis, Spencer J; Cantor, Sharon B; Auclair, Melissa; Tissenbaum, Heidi; West, Stephen C; Rose, Ann M; Boulton, Simon J

    2008-10-17

    Homologous recombination (HR) is an important conserved process for DNA repair and ensures maintenance of genome integrity. Inappropriate HR causes gross chromosomal rearrangements and tumorigenesis in mammals. In yeast, the Srs2 helicase eliminates inappropriate recombination events, but the functional equivalent of Srs2 in higher eukaryotes has been elusive. Here, we identify C. elegans RTEL-1 as a functional analog of Srs2 and describe its vertebrate counterpart, RTEL1, which is required for genome stability and tumor avoidance. We find that rtel-1 mutant worms and RTEL1-depleted human cells share characteristic phenotypes with yeast srs2 mutants: lethality upon deletion of the sgs1/BLM homolog, hyperrecombination, and DNA damage sensitivity. In vitro, purified human RTEL1 antagonizes HR by promoting the disassembly of D loop recombination intermediates in a reaction dependent upon ATP hydrolysis. We propose that loss of HR control after deregulation of RTEL1 may be a critical event that drives genome instability and cancer.

  8. FastBLAST: homology relationships for millions of proteins.

    Directory of Open Access Journals (Sweden)

    Morgan N Price

    Full Text Available BACKGROUND: All-versus-all BLAST, which searches for homologous pairs of sequences in a database of proteins, is used to identify potential orthologs, to find new protein families, and to provide rapid access to these homology relationships. As DNA sequencing accelerates and data sets grow, all-versus-all BLAST has become computationally demanding. METHODOLOGY/PRINCIPAL FINDINGS: We present FastBLAST, a heuristic replacement for all-versus-all BLAST that relies on alignments of proteins to known families, obtained from tools such as PSI-BLAST and HMMer. FastBLAST avoids most of the work of all-versus-all BLAST by taking advantage of these alignments and by clustering similar sequences. FastBLAST runs in two stages: the first stage identifies additional families and aligns them, and the second stage quickly identifies the homologs of a query sequence, based on the alignments of the families, before generating pairwise alignments. On 6.53 million proteins from the non-redundant Genbank database ("NR", FastBLAST identifies new families 25 times faster than all-versus-all BLAST. Once the first stage is completed, FastBLAST identifies homologs for the average query in less than 5 seconds (8.6 times faster than BLAST and gives nearly identical results. For hits above 70 bits, FastBLAST identifies 98% of the top 3,250 hits per query. CONCLUSIONS/SIGNIFICANCE: FastBLAST enables research groups that do not have supercomputers to analyze large protein sequence data sets. FastBLAST is open source software and is available at http://microbesonline.org/fastblast.

  9. Supersymmetric domain walls

    NARCIS (Netherlands)

    Bergshoeff, Eric A.; Kleinschmidt, Axel; Riccioni, Fabio

    2012-01-01

    We classify the half-supersymmetric "domain walls," i.e., branes of codimension one, in toroidally compactified IIA/IIB string theory and show to which gauged supergravity theory each of these domain walls belong. We use as input the requirement of supersymmetric Wess-Zumino terms, the properties of

  10. Homologous Recombination in Protozoan Parasites and Recombinase Inhibitors

    Directory of Open Access Journals (Sweden)

    Andrew A. Kelso

    2017-09-01

    Full Text Available Homologous recombination (HR is a DNA double-strand break (DSB repair pathway that utilizes a homologous template to fully repair the damaged DNA. HR is critical to maintain genome stability and to ensure genetic diversity during meiosis. A specialized class of enzymes known as recombinases facilitate the exchange of genetic information between sister chromatids or homologous chromosomes with the help of numerous protein accessory factors. The majority of the HR machinery is highly conserved among eukaryotes. In many protozoan parasites, HR is an essential DSB repair pathway that allows these organisms to adapt to environmental conditions and evade host immune systems through genetic recombination. Therefore, small molecule inhibitors, capable of disrupting HR in protozoan parasites, represent potential therapeutic options. A number of small molecule inhibitors were identified that disrupt the activities of the human recombinase RAD51. Recent studies have examined the effect of two of these molecules on the Entamoeba recombinases. Here, we discuss the current understandings of HR in the protozoan parasites Trypanosoma, Leishmania, Plasmodium, and Entamoeba, and we review the small molecule inhibitors known to disrupt human RAD51 activity.

  11. Phenylbutyrate inhibits homologous recombination induced by camptothecin and methyl methanesulfonate.

    Science.gov (United States)

    Kaiser, Gitte S; Germann, Susanne M; Westergaard, Tine; Lisby, Michael

    2011-08-01

    Homologous recombination is accompanied by extensive changes to chromatin organization at the site of DNA damage. Some of these changes are mediated through acetylation/deacetylation of histones. Here, we show that recombinational repair of DNA damage induced by the anti-cancer drug camptothecin (CPT) and the alkylating agent methyl methanesulfonate (MMS) is blocked by sodium phenylbutyrate (PBA) in the budding yeast Saccharomyces cerevisiae. In particular, PBA suppresses CPT- and MMS-induced genetic recombination as well as DNA double-strand break repair during mating-type interconversion. Treatment with PBA is accompanied by a dramatic reduction in histone H4 lysine 8 acetylation. Live cell imaging of homologous recombination proteins indicates that repair of CPT-induced DNA damage is redirected to a non-recombinogenic pathway in the presence of PBA without loss in cell viability. In contrast, the suppression of MMS-induced recombination by PBA is accompanied by a dramatic loss in cell viability. Taken together, our results demonstrate that PBA inhibits DNA damage-induced homologous recombination likely by mediating changes in chromatin acetylation. Moreover, the combination of PBA with genotoxic agents can lead to different cell fates depending on the type of DNA damage inflicted. 2011 Elsevier B.V. All rights reserved.

  12. Prefiltering Model for Homology Detection Algorithms on GPU.

    Science.gov (United States)

    Retamosa, Germán; de Pedro, Luis; González, Ivan; Tamames, Javier

    2016-01-01

    Homology detection has evolved over the time from heavy algorithms based on dynamic programming approaches to lightweight alternatives based on different heuristic models. However, the main problem with these algorithms is that they use complex statistical models, which makes it difficult to achieve a relevant speedup and find exact matches with the original results. Thus, their acceleration is essential. The aim of this article was to prefilter a sequence database. To make this work, we have implemented a groundbreaking heuristic model based on NVIDIA's graphics processing units (GPUs) and multicore processors. Depending on the sensitivity settings, this makes it possible to quickly reduce the sequence database by factors between 50% and 95%, while rejecting no significant sequences. Furthermore, this prefiltering application can be used together with multiple homology detection algorithms as a part of a next-generation sequencing system. Extensive performance and accuracy tests have been carried out in the Spanish National Centre for Biotechnology (NCB). The results show that GPU hardware can accelerate the execution times of former homology detection applications, such as National Centre for Biotechnology Information (NCBI), Basic Local Alignment Search Tool for Proteins (BLASTP), up to a factor of 4.

  13. Superbinder SH2 domains act as antagonists of cell signaling.

    Science.gov (United States)

    Kaneko, Tomonori; Huang, Haiming; Cao, Xuan; Li, Xing; Li, Chengjun; Voss, Courtney; Sidhu, Sachdev S; Li, Shawn S C

    2012-09-25

    Protein-ligand interactions mediated by modular domains, which often play important roles in regulating cellular functions, are generally of moderate affinities. We examined the Src homology 2 (SH2) domain, a modular domain that recognizes phosphorylated tyrosine (pTyr) residues, to investigate how the binding affinity of a modular domain for its ligand influences the structure and cellular function of the protein. We used the phage display method to perform directed evolution of the pTyr-binding residues in the SH2 domain of the tyrosine kinase Fyn and identified three amino acid substitutions that critically affected binding. We generated three SH2 domain triple-point mutants that were "superbinders" with much higher affinities for pTyr-containing peptides than the natural domain. Crystallographic analysis of one of these superbinders revealed that the superbinder SH2 domain recognized the pTyr moiety in a bipartite binding mode: A hydrophobic surface encompassed the phenyl ring, and a positively charged site engaged the phosphate. When expressed in mammalian cells, the superbinder SH2 domains blocked epidermal growth factor receptor signaling and inhibited anchorage-independent cell proliferation, suggesting that pTyr superbinders might be explored for therapeutic applications and useful as biological research tools. Although the SH2 domain fold can support much higher affinity for its ligand than is observed in nature, our results suggest that natural SH2 domains are not optimized for ligand binding but for specificity and flexibility, which are likely properties important for their function in signaling and regulatory processes.

  14. Expression and Production of SH2 Domain Proteins.

    Science.gov (United States)

    Liu, Bernard A; Ogiue-Ikeda, Mari; Machida, Kazuya

    2017-01-01

    The Src Homology 2 (SH2) domain lies at the heart of phosphotyrosine signaling, coordinating signaling events downstream of receptor tyrosine kinases (RTKs), adaptors, and scaffolds. Over a hundred SH2 domains are present in mammals, each having a unique specificity which determines its interactions with multiple binding partners. One of the essential tools necessary for studying and determining the role of SH2 domains in phosphotyrosine signaling is a set of soluble recombinant SH2 proteins. Here we describe methods, based on a broad experience with purification of all SH2 domains, for the production of SH2 domain proteins needed for proteomic and biochemical-based studies such as peptide arrays, mass-spectrometry, protein microarrays, reverse-phase microarrays, and high-throughput fluorescence polarization (HTP-FP). We describe stepwise protocols for expression and purification of SH2 domains using GST or poly His-tags, two widely adopted affinity tags. In addition, we address alternative approaches, challenges, and validation studies for assessing protein quality and provide general characteristics of purified human SH2 domains.

  15. Evolution of SH2 domains and phosphotyrosine signalling networks

    Science.gov (United States)

    Liu, Bernard A.; Nash, Piers D.

    2012-01-01

    Src homology 2 (SH2) domains mediate selective protein–protein interactions with tyrosine phosphorylated proteins, and in doing so define specificity of phosphotyrosine (pTyr) signalling networks. SH2 domains and protein-tyrosine phosphatases expand alongside protein-tyrosine kinases (PTKs) to coordinate cellular and organismal complexity in the evolution of the unikont branch of the eukaryotes. Examination of conserved families of PTKs and SH2 domain proteins provides fiduciary marks that trace the evolutionary landscape for the development of complex cellular systems in the proto-metazoan and metazoan lineages. The evolutionary provenance of conserved SH2 and PTK families reveals the mechanisms by which diversity is achieved through adaptations in tissue-specific gene transcription, altered ligand binding, insertions of linear motifs and the gain or loss of domains following gene duplication. We discuss mechanisms by which pTyr-mediated signalling networks evolve through the development of novel and expanded families of SH2 domain proteins and the elaboration of connections between pTyr-signalling proteins. These changes underlie the variety of general and specific signalling networks that give rise to tissue-specific functions and increasingly complex developmental programmes. Examination of SH2 domains from an evolutionary perspective provides insight into the process by which evolutionary expansion and modification of molecular protein interaction domain proteins permits the development of novel protein-interaction networks and accommodates adaptation of signalling networks. PMID:22889907

  16. Progress towards the development of SH2 domain inhibitors.

    Science.gov (United States)

    Kraskouskaya, Dziyana; Duodu, Eugenia; Arpin, Carolynn C; Gunning, Patrick T

    2013-04-21

    Src homology 2 (SH2) domains are 100 amino acid modular units, which recognize and bind to tyrosyl-phosphorylated peptide sequences on their target proteins, and thereby mediate intracellular protein-protein interactions. This review summarizes the progress towards the development of synthetic agents that disrupt the function of the SH2 domains in different proteins as well as the clinical relevance of targeting a specific SH2 domain. Since 1986, SH2 domains have been identified in over 110 human proteins, including kinases, transcription factors, and adaptor proteins. A number of these proteins are over-activated in many diseases, including cancer, and their function is highly dependent on their SH2 domain. Thus, inhibition of a protein's function through disrupting that of its SH2 domain has emerged as a promising approach towards the development of novel therapeutic modalities. Although targeting the SH2 domain is a challenging task in molecular recognition, the progress reported here demonstrates the feasibility of such an approach.

  17. Genetic selection and DNA sequences of 4.5S RNA homologs

    DEFF Research Database (Denmark)

    Brown, S; Thon, G; Tolentino, E

    1989-01-01

    A general strategy for cloning the functional homologs of an Escherichia coli gene was used to clone homologs of 4.5S RNA from other bacteria. The genes encoding these homologs were selected by their ability to complement a deletion of the gene for 4.5S RNA. DNA sequences of the regions encoding...

  18. Cloning and characterization of a functional human homolog of Escherichia coli endonuclease III

    Science.gov (United States)

    Aspinwall, Richard; Rothwell, Dominic G.; Roldan-Arjona, Teresa; Anselmino, Catherine; Ward, Christopher J.; Cheadle, Jeremy P.; Sampson, Julian R.; Lindahl, Tomas; Harris, Peter C.; Hickson, Ian D.

    1997-01-01

    Repair of oxidative damage to DNA bases is essential to prevent mutations and cell death. Endonuclease III is the major DNA glycosylase activity in Escherichia coli that catalyzes the excision of pyrimidines damaged by ring opening or ring saturation, and it also possesses an associated lyase activity that incises the DNA backbone adjacent to apurinic/apyrimidinic sites. During analysis of the area adjacent to the human tuberous sclerosis gene (TSC2) in chromosome region 16p13.3, we identified a gene, OCTS3, that encodes a 1-kb transcript. Analysis of OCTS3 cDNA clones revealed an open reading frame encoding a predicted protein of 34.3 kDa that shares extensive sequence similarity with E. coli endonuclease III and a related enzyme from Schizosaccharomyces pombe, including a conserved active site region and an iron/sulfur domain. The product of the OCTS3 gene was therefore designated hNTH1 (human endonuclease III homolog 1). The hNTH1 protein was overexpressed in E. coli and purified to apparent homogeneity. The recombinant protein had spectral properties indicative of the presence of an iron/sulfur cluster, and exhibited DNA glycosylase activity on double-stranded polydeoxyribonucleotides containing urea and thymine glycol residues, as well as an apurinic/apyrimidinic lyase activity. Our data indicate that hNTH1 is a structural and functional homolog of E. coli endonuclease III, and that this class of enzymes, for repair of oxidatively damaged pyrimidines in DNA, is highly conserved in evolution from microorganisms to human cells. PMID:8990169

  19. Light-Dependent Expression of Four Cryptic Archaeal Circadian Gene Homologs

    Directory of Open Access Journals (Sweden)

    Michael eManiscalco

    2014-03-01

    Full Text Available Circadian rhythms are important biological signals that have been found in almost all major groups of life from bacteria to man, yet it remains unclear if any members of the second major prokaryotic domain of life, the Archaea, also possess a biological clock. To investigate this question, we examined the regulation of four cyanobacterial-like circadian gene homologs present in the genome of the haloarchaeon Haloferax volcanii. These genes, designated cirA, cirB, cirC, and cirD, display similarity to the KaiC-family of cyanobacterial clock proteins, which act to regulate rhythmic gene expression and to control the timing of cell division. Quantitative RT-PCR analysis was used to examine the expression of each of the four cir genes in response to 12 h light/12 h dark cycles (LD 12:12 during balanced growth in H. volcanii. Our data reveal that there is an approximately two to sixteen-fold increase in cir gene expression when cells are shifted from light to constant darkness and this pattern of gene expression oscillates with the light conditions in a rhythmic manner. Targeted single- and double-gene knockouts in the H. volcanii cir genes results in disruption of light-dependent, rhythmic gene expression, although it does not lead to any significant effect on growth under these conditions. Restoration of light-dependent, rhythmic gene expression was demonstrated by introducing, in trans, a wild-type copy of individual cir genes into knockout strains. These results are noteworthy as this is the first attempt to characterize the transcriptional expression and regulation of the ubiquitous kaiC homologs found among archaeal genomes.

  20. Homologous recombination mediates functional recovery of dysferlin deficiency following AAV5 gene transfer.

    Directory of Open Access Journals (Sweden)

    William E Grose

    Full Text Available The dysferlinopathies comprise a group of untreatable muscle disorders including limb girdle muscular dystrophy type 2B, Miyoshi myopathy, distal anterior compartment syndrome, and rigid spine syndrome. As with other forms of muscular dystrophy, adeno-associated virus (AAV gene transfer is a particularly auspicious treatment strategy, however the size of the DYSF cDNA (6.5 kb negates packaging into traditional AAV serotypes known to express well in muscle (i.e. rAAV1, 2, 6, 8, 9. Potential advantages of a full cDNA versus a mini-gene include: maintaining structural-functional protein domains, evading protein misfolding, and avoiding novel epitopes that could be immunogenic. AAV5 has demonstrated unique plasticity with regards to packaging capacity and recombination of virions containing homologous regions of cDNA inserts has been implicated in the generation of full-length transcripts. Herein we show for the first time in vivo that homologous recombination following AAV5.DYSF gene transfer leads to the production of full length transcript and protein. Moreover, gene transfer of full-length dysferlin protein in dysferlin deficient mice resulted in expression levels sufficient to correct functional deficits in the diaphragm and importantly in skeletal muscle membrane repair. Intravascular regional gene transfer through the femoral artery produced high levels of transduction and enabled targeting of specific muscle groups affected by the dysferlinopathies setting the stage for potential translation to clinical trials. We provide proof of principle that AAV5 mediated delivery of dysferlin is a highly promising strategy for treatment of dysferlinopathies and has far-reaching implications for the therapeutic delivery of other large genes.

  1. Sequence homology and expression profile of genes associated with dna repair pathways in Mycobacterium leprae

    Directory of Open Access Journals (Sweden)

    Mukul Sharma

    2017-01-01

    Full Text Available Background: Survival of Mycobacterium leprae, the causative bacteria for leprosy, in the human host is dependent to an extent on the ways in which its genome integrity is retained. DNA repair mechanisms protect bacterial DNA from damage induced by various stress factors. The current study is aimed at understanding the sequence and functional annotation of DNA repair genes in M. leprae. Methods: T he genome of M. leprae was annotated using sequence alignment tools to identify DNA repair genes that have homologs in Mycobacterium tuberculosis and Escherichia coli. A set of 96 genes known to be involved in DNA repair mechanisms in E. coli and Mycobacteriaceae were chosen as a reference. Among these, 61 were identified in M. leprae based on sequence similarity and domain architecture. The 61 were classified into 36 characterized gene products (59%, 11 hypothetical proteins (18%, and 14 pseudogenes (23%. All these genes have homologs in M. tuberculosis and 49 (80.32% in E. coli. A set of 12 genes which are absent in E. coli were present in M. leprae and in Mycobacteriaceae. These 61 genes were further investigated for their expression profiles in the whole transcriptome microarray data of M. leprae which was obtained from the signal intensities of 60bp probes, tiling the entire genome with 10bp overlaps. Results: It was noted that transcripts corresponding to all the 61 genes were identified in the transcriptome data with varying expression levels ranging from 0.18 to 2.47 fold (normalized with 16SrRNA. The mRNA expression levels of a representative set of seven genes ( four annotated and three hypothetical protein coding genes were analyzed using quantitative Polymerase Chain Reaction (qPCR assays with RNA extracted from skin biopsies of 10 newly diagnosed, untreated leprosy cases. It was noted that RNA expression levels were higher for genes involved in homologous recombination whereas the genes with a low level of expression are involved in the

  2. Sequence homology and expression profile of genes associated with DNA repair pathways in Mycobacterium leprae.

    Science.gov (United States)

    Sharma, Mukul; Vedithi, Sundeep Chaitanya; Das, Madhusmita; Roy, Anindya; Ebenezer, Mannam

    2017-01-01

    Survival of Mycobacterium leprae, the causative bacteria for leprosy, in the human host is dependent to an extent on the ways in which its genome integrity is retained. DNA repair mechanisms protect bacterial DNA from damage induced by various stress factors. The current study is aimed at understanding the sequence and functional annotation of DNA repair genes in M. leprae. T he genome of M. leprae was annotated using sequence alignment tools to identify DNA repair genes that have homologs in Mycobacterium tuberculosis and Escherichia coli. A set of 96 genes known to be involved in DNA repair mechanisms in E. coli and Mycobacteriaceae were chosen as a reference. Among these, 61 were identified in M. leprae based on sequence similarity and domain architecture. The 61 were classified into 36 characterized gene products (59%), 11 hypothetical proteins (18%), and 14 pseudogenes (23%). All these genes have homologs in M. tuberculosis and 49 (80.32%) in E. coli. A set of 12 genes which are absent in E. coli were present in M. leprae and in Mycobacteriaceae. These 61 genes were further investigated for their expression profiles in the whole transcriptome microarray data of M. leprae which was obtained from the signal intensities of 60bp probes, tiling the entire genome with 10bp overlaps. It was noted that transcripts corresponding to all the 61 genes were identified in the transcriptome data with varying expression levels ranging from 0.18 to 2.47 fold (normalized with 16SrRNA). The mRNA expression levels of a representative set of seven genes ( four annotated and three hypothetical protein coding genes) were analyzed using quantitative Polymerase Chain Reaction (qPCR) assays with RNA extracted from skin biopsies of 10 newly diagnosed, untreated leprosy cases. It was noted that RNA expression levels were higher for genes involved in homologous recombination whereas the genes with a low level of expression are involved in the direct repair pathway. This study provided

  3. Study on homologous series of induced early mutants in Indica rice Ⅱ. the relationship between the homologous series of early mutants induced and the ecotype in Indica rice

    International Nuclear Information System (INIS)

    Chen Xiulan; Yang Hefeng; He Zhentian; Han Yuepeng; Liu Xueyu

    2001-01-01

    The induced mutation in light sensitivity of the Indica rice leads to induction of the homologous series of early mutants along with the variation of ecological character and the ecoclimate. The induction of mutants was closely related to the ecotype of Indica rice, the homologous series of early mutants in different level were derived from the different ecotype of the Indica rice, otherwise, the similar homologous series of early mutants were derived from the same ecotypic variety. The induction of the early ecotypic variety derived from the homologous series of early mutants provides the basis and possibility for accelerating the development of the new cultivars. (authors)

  4. A protein-binding domain, EH, identified in the receptor tyrosine kinase substrate Eps15 and conserved in evolution

    DEFF Research Database (Denmark)

    Wong, W T; Schumacher, C; Salcini, A E

    1995-01-01

    In this report we structurally and functionally define a binding domain that is involved in protein association and that we have designated EH (for Eps15 homology domain). This domain was identified in the tyrosine kinase substrate Eps15 on the basis of regional conservation with several heteroge......In this report we structurally and functionally define a binding domain that is involved in protein association and that we have designated EH (for Eps15 homology domain). This domain was identified in the tyrosine kinase substrate Eps15 on the basis of regional conservation with several...... heterogeneous proteins of yeast and nematode. The EH domain spans about 70 amino acids and shows approximately 60% overall amino acid conservation. We demonstrated the ability of the EH domain to specifically bind cytosolic proteins in normal and malignant cells of mesenchymal, epithelial, and hematopoietic...... (for Eps15-related). Structural comparison of Eps15 and Eps15r defines a family of signal transducers possessing extensive networking abilities including EH-mediated binding and association with Src homology 3-containing proteins....

  5. Mechanism of mRNA-STAR domain interaction: Molecular dynamics simulations of Mammalian Quaking STAR protein.

    Science.gov (United States)

    Sharma, Monika; Anirudh, C R

    2017-10-03

    STAR proteins are evolutionary conserved mRNA-binding proteins that post-transcriptionally regulate gene expression at all stages of RNA metabolism. These proteins possess conserved STAR domain that recognizes identical RNA regulatory elements as YUAAY. Recently reported crystal structures show that STAR domain is composed of N-terminal QUA1, K-homology domain (KH) and C-terminal QUA2, and mRNA binding is mediated by KH-QUA2 domain. Here, we present simulation studies done to investigate binding of mRNA to STAR protein, mammalian Quaking protein (QKI). We carried out conventional MD simulations of STAR domain in presence and absence of mRNA, and studied the impact of mRNA on the stability, dynamics and underlying allosteric mechanism of STAR domain. Our unbiased simulations results show that presence of mRNA stabilizes the overall STAR domain by reducing the structural deviations, correlating the 'within-domain' motions, and maintaining the native contacts information. Absence of mRNA not only influenced the essential modes of motion of STAR domain, but also affected the connectivity of networks within STAR domain. We further explored the dissociation of mRNA from STAR domain using umbrella sampling simulations, and the results suggest that mRNA binding to STAR domain occurs in multi-step: first conformational selection of mRNA backbone conformations, followed by induced fit mechanism as nucleobases interact with STAR domain.

  6. Physical and functional interactions between SH2 and SH3 domains of the Src family protein tyrosine kinase p59fyn

    NARCIS (Netherlands)

    Panchamoorthy, G.; Fukazawa, T.; Stolz, L.; Payne, G.; Reedquist, K.; Shoelson, S.; Songyang, Z.; Cantley, L.; Walsh, C.; Band, H.

    1994-01-01

    The Src family protein tyrosine kinases participate in signalling through cell surface receptors that lack intrinsic tyrosine kinase domains. All nine members of this family possess adjacent Src homology (SH2 and SH3) domains, both of which are essential for repression of the enzymatic activity. The

  7. p53 regulates the repair of DNA double-strand breaks by both homologous and non-homologous recombination

    International Nuclear Information System (INIS)

    Willers, H.; Powell, S.N.; Dahm-Daphi, J.

    2003-01-01

    Full text: p53 is known to suppress spontaneous homologous recombination (HR), while its role in non-homologous recombination (NHR) remains to be clarified. Here, we sought to determine the influence of p53 on the repair of chromosomal double-strand breaks (DSBs) by HR or NHR using specially designed recombination substrates that integrate into the genome. Isogenic mouse fibroblast pairs with or without expression of exogenous p53 protein were utilized. A reporter plasmid carrying a mutated XGPRT gene was chromosomally integrated and DSBs were generated within the plasmid by the I-SceI endonuclease. Subsequent homology-mediated repair from an episomal donor resulted in XGPRT reconstitution and cellular resistance to a selection antibiotic. Analogously, the repair of chromosomal I-SceI breaks by NHR using another novel reporter plasmid restored XGPRT translation. For p53-null cells, the mean frequency of I-SceI break repair via HR was 5.5 x 10 -4 . The p53-Val135 mutant, which previously has been shown to suppress spontaneous HR by 14-fold employing the same cell system and reporter gene, only caused a 2- to 3-fold suppression of break-induced HR. In contrast, a dramatic effect of p53 on repair via NHR was found. Preliminary sequence analysis indicated that there was at least a 1000-fold reduction of illegitimate repair events resulting in loss of sequence at the break sites. The observed effects were mediated by p53 mutants defective in regulation of the cell-cycle and apoptosis. The main findings were: (1) p53 virtually blocked illegitimate rejoining of chromosomal ends. (2) The suppression of homologous DSB repair was less pronounced than the inhibition of spontaneous HR. We hypothesize that p53 allows to a certain extent error-free homology-dependent repair to proceed, while blocking error-prone NHR. The data support and extent a previous model, in which p53 maintains genomic stability by regulating recombination independently of its transactivation function

  8. Analysis of multichannel optical rotary connectors based on the compensation operating principle with mirror and prismatic optical compensators (Part 1

    Directory of Open Access Journals (Sweden)

    V.M. Shapar

    2017-04-01

    Full Text Available Performed in this work is a comprehensive theoretical computer analysis of performances inherent to two types of multichannel optical rotary connectors (ORC of compensation operation based on mirror and prismatic compensators. This analysis relies on exact analytical expressions obtained for light ray paths in ORC models with a mirror compensator made in the form of bilateral mirror placed between two optical hemispheres and with prismatic compensator made in the form of Dove prism placed between two non-aberrational elliptic lenses. Found in ORC with the mirror compensator is the essential deficiency inherent to all these constructions, which is related with considerable rotary oscillations in the value of optical signals in mirror angular positions when the mirror halves the input light beam. In these mirror positions, the amplitude value of optical signal oscillations exceeds 95%, and optical losses are higher than –13 dB, when the rotor turns. One deficiency more in these constructions is also strict technical requirements to the accuracy of making the optical components and mechanisms at the level of 1…2 µm. Concerning the ORC construction with a prismatic compensator as well as collimator and focusing lenses common for all the channels, one should note the inadmissibly high optical losses of the signal value (higher than –30…40 dB in the case of construction with fiber-optic interfaces, and large dimensions and mass in the case of active construction with optoelectronic transducers at the inputs and outputs of ORC. For example, when the number of channels N = 10 the longitudinal dimension of optical transfer channel (prism and lenses exceeds 300 mm, and this dimension increases with increasing the number of channels. When this dimension is lower than 100 mm, the facility can be equipped with only one optical communication channel containing one LED and one photodiode located on the rotation axis. Optical losses in these

  9. Carbon-13 NMR study of switch variant anti-dansyl antibodies: Antigen binding and domain-domain interactions

    Energy Technology Data Exchange (ETDEWEB)

    Kato, Koichi; Matsunaga, Chigusa; Odaka, Asano; Yamato, Sumie; Takaha, Wakana; Shimada, Ichio; Arata, Yoji (Univ. of Tokyo (Japan))

    1991-07-02

    A {sup 13}C NMR study is reported of switch variant anti-dansyl antibodies, which possess the identical V{sub H}, V{sub L}, and C{sub L} domains in conjunction with highly homologous but not identical heavy-chain constant regions. Each of the antibodies has been selectively labeled with {sup 13}C at the carbonyl carbon of Trp, Tyr, His, or Cys residue by growing hybridoma cells in serum-free medium. Spectral assignments have been made by folowing the procedure described previously for the switch variant antibodies labeled with (1-{sup 13}C)Met. On the basis of the spectral data collected for the antibodies and their proteolytic fragments, the authors discuss how {sup 13}C NMR spectroscopy can be used for the structural analyses of antigen binding and also of domain-domain interactions in the antibody molecule.

  10. Carbon-13 NMR study of switch variant anti-dansyl antibodies: Antigen binding and domain-domain interactions

    International Nuclear Information System (INIS)

    Kato, Koichi; Matsunaga, Chigusa; Odaka, Asano; Yamato, Sumie; Takaha, Wakana; Shimada, Ichio; Arata, Yoji

    1991-01-01

    A 13 C NMR study is reported of switch variant anti-dansyl antibodies, which possess the identical V H , V L , and C L domains in conjunction with highly homologous but not identical heavy-chain constant regions. Each of the antibodies has been selectively labeled with 13 C at the carbonyl carbon of Trp, Tyr, His, or Cys residue by growing hybridoma cells in serum-free medium. Spectral assignments have been made by folowing the procedure described previously for the switch variant antibodies labeled with [1- 13 C]Met. On the basis of the spectral data collected for the antibodies and their proteolytic fragments, the authors discuss how 13 C NMR spectroscopy can be used for the structural analyses of antigen binding and also of domain-domain interactions in the antibody molecule

  11. Structure of an isolated unglycosylated antibody CH2 domain

    International Nuclear Information System (INIS)

    Prabakaran, Ponraj; Vu, Bang K.; Gan, Jianhua; Feng, Yang; Dimitrov, Dimiter S.; Ji, Xinhua

    2008-01-01

    The crystal structure of an isolated unglycosylated antibody C H 2 domain has been determined at 1.7 Å resolution. The C H 2 (C H 3 for IgM and IgE) domain of an antibody plays an important role in mediating effector functions and preserving antibody stability. It is the only domain in human immunoglobulins (Igs) which is involved in weak interchain protein–protein interactions with another C H 2 domain solely through sugar moieties. The N-linked glycosylation at Asn297 is conserved in mammalian IgGs as well as in homologous regions of other antibody isotypes. To examine the structural details of the C H 2 domain in the absence of glycosylation and other antibody domains, the crystal structure of an isolated unglycosylated antibody γ1 C H 2 domain was determined at 1.7 Å resolution and compared with corresponding C H 2 structures from intact Fc, IgG and Fc receptor complexes. Furthermore, the oligomeric state of the protein in solution was studied using size-exclusion chromatography. The results suggested that the unglycosylated human antibody C H 2 domain is a monomer and that its structure is similar to that found in the intact Fc, IgG and Fc receptor complex structures. However, certain structural variations were observed in the Fc receptor-binding sites. Owing to its small size, stability and non-immunogenic Ig template, the C H 2-domain structure could be useful for the development by protein design of antibody domains exerting effector functions and/or antigen specificity and as a robust scaffold in protein-engineering applications

  12. Conserved Domain Database (CDD)

    Data.gov (United States)

    U.S. Department of Health & Human Services — CDD is a protein annotation resource that consists of a collection of well-annotated multiple sequence alignment models for ancient domains and full-length proteins.

  13. Flat-port connectors

    KAUST Repository

    Alrashed, Mohammed

    2017-01-01

    and water resistant. It is unique in the way of using the outer surfaces of the device for the electrical connection between the ports. Flat-port design can allow the manufacture of extremely thin devices by eliminating the side ports slots that take a lot

  14. Pyrotechnic Tubing Connector

    Science.gov (United States)

    Graves, Thomas J.; Yang, Robert A.

    1988-01-01

    Tool forms mechanical seal at joint without levers or hydraulic apparatus. Proposed tool intended for use in outer space used on Earth by heavily garbed workers to join tubing in difficult environments. Called Pyrotool, used with Lokring (or equivalent) fittings. Piston slides in cylinder when pushed by gas from detonating pyrotechnic charge. Impulse of piston compresses fittings, sealing around butting ends of tubes.

  15. Crystallization and preliminary crystallographic characterization of the PAS domains of EAG and ELK potassium channels

    International Nuclear Information System (INIS)

    Adaixo, Ricardo; Morais-Cabral, João Henrique

    2010-01-01

    The N-terminal PAS domains from the eukaryotic EAG potassium channels are thought to have a regulatory function. Here the expression, purification, crystallization and preliminary crystallographic characterization of two of these domains are described. Per–Arnt–Sim (PAS) domains are ubiquitous in nature; they are ∼130-amino-acid protein domains that adopt a fairly conserved three-dimensional structure despite their low degree of sequence homology. These domains constitute the N-terminus or, less frequently, the C-terminus of a number of proteins, where they exert regulatory functions. PAS-containing proteins generally display two or more copies of this motif. In this work, the crystallization and preliminary analysis of the PAS domains of two eukaryotic potassium channels from the ether-à-go-go (EAG) family are reported

  16. The colocalization transition of homologous chromosomes at meiosis

    Science.gov (United States)

    Nicodemi, Mario; Panning, Barbara; Prisco, Antonella

    2008-06-01

    Meiosis is the specialized cell division required in sexual reproduction. During its early stages, in the mother cell nucleus, homologous chromosomes recognize each other and colocalize in a crucial step that remains one of the most mysterious of meiosis. Starting from recent discoveries on the system molecular components and interactions, we discuss a statistical mechanics model of chromosome early pairing. Binding molecules mediate long-distance interaction of special DNA recognition sequences and, if their concentration exceeds a critical threshold, they induce a spontaneous colocalization transition of chromosomes, otherwise independently diffusing.

  17. Homology and cohomology of a class of polycyclic groups

    International Nuclear Information System (INIS)

    Majumdar, S.

    1984-11-01

    The homology and the cohomology of the class of polycyclic groups G given by generators h 1 , h 2 ,..., hsub(n+1) and relations h 2 -1 h 1 h 2 =h 1 sup(m 1 ),h 3 -1 h 2 h 3 =h 2 sup(m 2 ),..., hsub(n+1) -1 hsub(n) hsub(n+1)=hsub(n)sup(msub(n)) are determined through the construction of a suitable free ZG resolution for the trivial ZG module Z. (author)

  18. Opto-mechanical design of a buckling cavity in a novel high-performance outside-plant robust field installable single-mode fibre connector

    Science.gov (United States)

    Ebraert, Evert; Van Erps, Jürgen; Beri, Stefano; Watté, Jan; Thienpont, Hugo

    2014-05-01

    Fibre-to-the-home (FTTH) networks provide an ideal means to reach the goal the European Union has set to provide 50 % of the households with a broadband connection faster than 100 Mb/s. Deployment of FTTH networks, which is still costly today, could be significantly boosted by novel ferrule-less connectors which don't require highly skilled personnel and allow installation in the field. We propose a ferrule-less connector in which two single-mode fibres (SMFs) are aligned and maintain physical contact by ensuring that at least one fibre is in a buckled state. To this end, we design a cavity in which a fibre can buckle in a controlled way. Using finite element analysis simulations to investigate the shape of the formed buckle for various buckling cavity lengths, we show that it can be accurately approximated by a cosine function. In addition, the optical performance of a buckled SMF is investigated by bending loss calculations and simulations. We show a good agreement between the analytical and the simulated bending loss results for a G.652 fibre at a wavelength of 1550 nm. Buckling cavity lengths smaller than 20 mm should be avoided to keep the optical bending loss due to buckling below 0.1 dB. In this case the cavity height should at least be 2 mm to avoid mechanical confinement of the fibre.

  19. Fatigue limit of monolithic Y-TZP three-unit-fixed dental prostheses: Effect of grinding at the gingival zone of the connector.

    Science.gov (United States)

    Amaral, Marina; Villefort, Regina F; Melo, Renata Marques; Pereira, Gabriel K R; Zhang, Yu; Valandro, Luiz Felipe; Bottino, Marco Antonio

    2017-08-01

    To determine the fatigue limits of three-unit monolithic zirconia fixed dental prosthesis (FDPs) before and after grinding of the gingival areas of connectors with diamond burs. FDPs were milled from pre-sintered blocks of zirconia simulating the absence of the first mandibular molar. Half of the specimens were subjected to grinding, simulating clinical adjustment, and all of them were subjected to glazing procedure. Additional specimens were manufactured for roughness analysis. FDPs were adhesively cemented onto glass-fiber reinforced epoxy resin abutments. Fatigue limits and standard deviations were obtained using a staircase fatigue method (n=20, 100,000 loading cycles/5Hz). The initial test load was 70% of the mean load-to-fracture (n=3) and load increments were 5% of the initial test load for both the control and ground specimens. Data were compared by Student's T-test (α≤0.05). Both the control and ground groups exhibited similar values of load-to-fracture and fatigue limits. Neither the surface treatments nor ageing affected the surface roughness of the specimens. The damage induced by grinding with fine-grit diamond bur in the gingival area of the connectors did not decrease the fatigue limit of the three-unit monolithic zirconia FDP. Copyright © 2017 Elsevier Ltd. All rights reserved.

  20. Molecular Mechanisms of SH2- and PTB-Domain-Containing Proteins in Receptor Tyrosine Kinase Signaling

    Science.gov (United States)

    Wagner, Melany J.; Stacey, Melissa M.; Liu, Bernard A.; Pawson, Tony

    2013-01-01

    Intracellular signaling is mediated by reversible posttranslational modifications (PTMs) that include phosphorylation, ubiquitination, and acetylation, among others. In response to extracellular stimuli such as growth factors, receptor tyrosine kinases (RTKs) typically dimerize and initiate signaling through phosphorylation of their cytoplasmic tails and downstream scaffolds. Signaling effectors are recruited to these phosphotyrosine (pTyr) sites primarily through Src homology 2 (SH2) domains and pTyr-binding (PTB) domains. This review describes how these conserved domains specifically recognize pTyr residues and play a major role in mediating precise downstream signaling events. PMID:24296166

  1. Molecular mechanisms of SH2- and PTB-domain-containing proteins in receptor tyrosine kinase signaling.

    Science.gov (United States)

    Wagner, Melany J; Stacey, Melissa M; Liu, Bernard A; Pawson, Tony

    2013-12-01

    Intracellular signaling is mediated by reversible posttranslational modifications (PTMs) that include phosphorylation, ubiquitination, and acetylation, among others. In response to extracellular stimuli such as growth factors, receptor tyrosine kinases (RTKs) typically dimerize and initiate signaling through phosphorylation of their cytoplasmic tails and downstream scaffolds. Signaling effectors are recruited to these phosphotyrosine (pTyr) sites primarily through Src homology 2 (SH2) domains and pTyr-binding (PTB) domains. This review describes how these conserved domains specifically recognize pTyr residues and play a major role in mediating precise downstream signaling events.

  2. Globular, Sponge-like to Layer-like Morphological Transition in 1-n-Alkyl-3-methylimidazolium Octylsulfate Ionic Liquid Homologous Series.

    Science.gov (United States)

    Kapoor, Utkarsh; Shah, Jindal K

    2018-01-11

    Segregation of polar and nonpolar domains in ionic liquids for which either the cation or anion is responsible for inducing nonpolar domains is well understood. On the other hand, information regarding the nanoscale heterogeneities originating due to the presence of nonpolar content on both the ions is rudimentary at this point. The present contribution is aimed at addressing this question and focuses on a molecular dynamics simulation study to probe nanoscale structural and aggregation features of the 1-n-alkyl-3-methylimidazolium [C n mim] octylsulfate [C 8 SO 4 ] ionic liquid homologous series (n = 2, 4, 6, 8, 10, and 12). The objective of this work is to determine the effect of increasing alkyl chain length in the cation on nonpolar domain formation, especially when the alkyl chain lengths from both the ions participate in defining such domains. The results indicate that all the ionic liquids form nonpolar domains, morphology of which gradually changes from globular, sponge-like to layer-like structure with increase in the cationic alkyl chain length. The length of the nonpolar domains calculated from the total structure factor for [C 10 mim][C 8 SO 4 ] is considerably higher than that reported for other imidazolium-based ionic liquid containing smaller anions. The structure factor for [C 12 mim][C 8 SO 4 ] ionic liquid contains multiple intermediate peaks separating the charge alternation peak and pre-peak, which points to nonpolar domains of varying lengths, an observation that remains to be validated. Analysis of the heterogeneous order parameters and orientational correlation functions of the alkyl chains further suggests an increase in the spatial heterogeneity and long-range order along the homologous series. The origin of rich diversity of structures obtained by introducing nonpolar content on both the ions is discussed.

  3. Impact of homologous recombination on individual cellular radiosensitivity

    International Nuclear Information System (INIS)

    Koch, Kerstin; Wrona, Agnieszka; Dikomey, Ekkehard; Borgmann, Kerstin

    2009-01-01

    Purpose: Individual radiosensitivity as measured with in vitro irradiated lymphocytes using metaphase analysis can predict the risk of normal tissue effects after radiotherapy. This parameter is considered to be primarily determined by the cellular repair capacity of DNA double-strand breaks (DSBs). It is now tested to which extent this capacity also depends on homologous recombination (HR), which is a pathway available when cells are in S/G2 phase. Methods: Experiments were performed with CHO K1 cells, in which HR was suppressed via knock-down of RAD51 using RNA interference (RNAi). RAD51 was measured via western and foci formation, cell survival by colony forming, DSBs by γH2AX foci formation, and chromosomal damage using PCC, G0 or G2 assay. Results: In quiescent G1 cells DSB repair is completed 6 h after irradiation. But there is still a substantial fraction of non-repaired DSBs. Most of these DSBs are repaired when G1 cells are stimulated into cell cycle. Suppression of HR by down-regulation of RAD51 did not affect this repair. In contrast, repair was inhibited when cells were irradiated in late S/G2. In line with these data down-regulation of HR did affect survival of cells irradiated in late S/G2, but not in G1. Conclusions: Individual radiosensitivity as measured for G0/1 cells using metaphase analysis does not depend on homologous recombination

  4. On discrete symmetries and torsion homology in F-theory

    Energy Technology Data Exchange (ETDEWEB)

    Mayrhofer, Christoph [Arnold-Sommerfeld-Center, Ludwig-Maximilians-Universität München,München (Germany); Palti, Eran; Till, Oskar; Weigand, Timo [Institut für Theoretische Physik, Ruprecht-Karls-Universität Heidelberg,Heidelberg (Germany)

    2015-06-04

    We study the relation between discrete gauge symmetries in F-theory compactifications and torsion homology on the associated Calabi-Yau manifold. Focusing on the simplest example of a ℤ{sub 2} symmetry, we show that there are two physically distinct ways that such a discrete gauge symmetry can arise. First, compactifications of M-Theory on Calabi-Yau threefolds which support a genus-one fibration with a bi-section are known to be dual to six-dimensional F-theory vacua with a ℤ{sub 2} gauge symmetry. We show that the resulting five-dimensional theories do not have a ℤ{sub 2} symmetry but that the latter emerges only in the F-theory decompactification limit. Accordingly the genus-one fibred Calabi-Yau manifolds do not exhibit torsion in homology. Associated to the bi-section fibration is a Jacobian fibration which does support a section. Compactifying on these related but distinct varieties does lead to a ℤ{sub 2} symmetry in five dimensions and, accordingly, we find explicitly an associated torsion cycle. We identify the expected particle and membrane system of the discrete symmetry in terms of wrapped M2 and M5 branes and present a field-theory description of the physics for both cases in terms of circle reductions of six-dimensional theories. Our results and methods generalise straightforwardly to larger discrete symmetries and to four-dimensional compactifications.

  5. Gimeracil sensitizes cells to radiation via inhibition of homologous recombination

    International Nuclear Information System (INIS)

    Takagi, Masaru; Sakata, Koh-ichi; Someya, Masanori; Tauchi, Hiroshi; Iijima, Kenta; Matsumoto, Yoshihisa; Torigoe, Toshihiko; Takahashi, Akari; Hareyama, Masato; Fukushima, Masakazu

    2010-01-01

    Background and purpose: 5-Chloro-2,4-dihydroxypyridine (Gimeracil) is a component of an oral fluoropyrimidine derivative S-1. Gimeracil is originally added to S-1 to yield prolonged 5-FU concentrations in tumor tissues by inhibiting dihydropyrimidine dehydrogenase, which degrades 5-FU. We found that Gimeracil by itself had the radiosensitizing effect. Methods and materials: We used various cell lines deficient in non-homologous end-joining (NHEJ) or homologous recombination (HR) as well as DLD-1 and HeLa in clonogenic assay. γ-H2AX focus formation and SCneo assay was performed to examine the effects of Gimeracil on DNA double strand break (DSB) repair mechanisms. Results: Results of γ-H2AX focus assay indicated that Gimeracil inhibited DNA DSB repair. It did not sensitize cells deficient in HR but sensitized those deficient in NHEJ. In SCneo assay, Gimeracil reduced the frequency of neo-positive clones. Additionally, it sensitized the cells in S-phase more than in G0/G1. Conclusions: Gimeracil inhibits HR. Because HR plays key roles in the repair of DSBH caused by radiotherapy, Gimeracil may enhance the efficacy of radiotherapy through the suppression of HR-mediated DNA repair pathways.

  6. Protein homology model refinement by large-scale energy optimization.

    Science.gov (United States)

    Park, Hahnbeom; Ovchinnikov, Sergey; Kim, David E; DiMaio, Frank; Baker, David

    2018-03-20

    Proteins fold to their lowest free-energy structures, and hence the most straightforward way to increase the accuracy of a partially incorrect protein structure model is to search for the lowest-energy nearby structure. This direct approach has met with little success for two reasons: first, energy function inaccuracies can lead to false energy minima, resulting in model degradation rather than improvement; and second, even with an accurate energy function, the search problem is formidable because the energy only drops considerably in the immediate vicinity of the global minimum, and there are a very large number of degrees of freedom. Here we describe a large-scale energy optimization-based refinement method that incorporates advances in both search and energy function accuracy that can substantially improve the accuracy of low-resolution homology models. The method refined low-resolution homology models into correct folds for 50 of 84 diverse protein families and generated improved models in recent blind structure prediction experiments. Analyses of the basis for these improvements reveal contributions from both the improvements in conformational sampling techniques and the energy function.

  7. 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.

  8. HOMOLOGY MODELING AND MOLECULAR DYNAMICS STUDY OF MYCOBACTERIUM TUBERCULOSIS UREASE

    Directory of Open Access Journals (Sweden)

    Lisnyak Yu. V.

    2017-10-01

    Full Text Available Introduction. M. tuberculosis urease (MTU is an attractive target for chemotherapeutic intervention in tuberculosis by designing new safe and efficient enzyme inhibitors. A prerequisite for designing such inhibitors is an understanding of urease's three-dimensional (3D structure organization. 3D structure of M. tuberculosis urease is unknown. When experimental three-dimensional structure of a protein is not known, homology modeling, the most commonly used computational structure prediction method, is the technique of choice. This paper aimed to build a 3D-structure of M. tuberculosis urease by homology modeling and to study its stability by molecular dynamics simulations. Materials and methods. To build MTU model, five high-resolution X-ray structures of bacterial ureases with three-subunit composition (2KAU, 5G4H, 4UBP, 4СEU, and 4EPB have been selected as templates. For each template five stochastic alignments were created and for each alignment, a three-dimensional model was built. Then, each model was energy minimized and the models were ranked by quality Z-score. The MTU model with highest quality estimation amongst 25 potential models was selected. To further improve structure quality the model was refined by short molecular dynamics simulation that resulted in 20 snapshots which were rated according to their energy and the quality Z-score. The best scoring model having minimum energy was chosen as a final homology model of 3D structure for M. tuberculosis. The final model of MTU was also validated by using PDBsum and QMEAN servers. These checks confirmed good quality of MTU homology model. Results and discussion. Homology model of MTU is a nonamer (homotrimer of heterotrimers, (αβγ3 consisting of 2349 residues. In MTU heterotrimer, sub-units α, β, and γ tightly interact with each other at a surface of approximately 3000 Å2. Sub-unit α contains the enzyme active site with two Ni atoms coordinated by amino acid residues His347, His

  9. Crystal structure of the N domain of human somatic angiotensin I-converting enzyme provides a structural basis for domain-specific inhibitor design.

    Science.gov (United States)

    Corradi, Hazel R; Schwager, Sylva L U; Nchinda, Aloysius T; Sturrock, Edward D; Acharya, K Ravi

    2006-03-31

    Human somatic angiotensin I-converting enzyme (sACE) is a key regulator of blood pressure and an important drug target for combating cardiovascular and renal disease. sACE comprises two homologous metallopeptidase domains, N and C, joined by an inter-domain linker. Both domains are capable of cleaving the two hemoregulatory peptides angiotensin I and bradykinin, but differ in their affinities for a range of other substrates and inhibitors. Previously we determined the structure of testis ACE (C domain); here we present the crystal structure of the N domain of sACE (both in the presence and absence of the antihypertensive drug lisinopril) in order to aid the understanding of how these two domains differ in specificity and function. In addition, the structure of most of the inter-domain linker allows us to propose relative domain positions for sACE that may contribute to the domain cooperativity. The structure now provides a platform for the design of "domain-specific" second-generation ACE inhibitors.

  10. 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.

  11. Organization of functional domains in the docking protein p130Cas

    International Nuclear Information System (INIS)

    Nasertorabi, Fariborz; Garcia-Guzman, Miguel; Briknarova, Klara; Larsen, Elise; Havert, Marnie L.; Vuori, Kristiina; Ely, Kathryn R.

    2004-01-01

    The docking protein p130Cas becomes phosphorylated upon cell adhesion to extracellular matrix proteins, and is thought to play an essential role in cell transformation. Cas transmits signals through interactions with the Src-homology 3 (SH3) and Src-homology 2 domains of FAK or v-Crk signaling molecules, or with 14-3-3 protein, as well as phosphatases PTP1B and PTP-PEST. The large (130 kDa), multi-domain Cas molecule contains an SH3 domain, a Src-binding domain, a serine-rich protein interaction region, and a C-terminal region that participates in protein interactions implicated in antiestrogen resistance in breast cancer. In this study, as part of a long-term goal to examine the protein interactions of Cas by X-ray crystallography and nuclear magnetic resonance spectroscopy, molecular constructs were designed to express two adjacent domains, the serine-rich domain and the Src-binding domain, that each participate in intermolecular contacts dependent on protein phosphorylation. The protein products are soluble, homogeneous, monodisperse, and highly suitable for structural studies to define the role of Cas in integrin-mediated cell signaling

  12. Structure of the GH1 domain of guanylate kinase-associated protein from Rattus norvegicus

    International Nuclear Information System (INIS)

    Tong, Junsen; Yang, Huiseon; Eom, Soo Hyun; Chun, ChangJu; Im, Young Jun

    2014-01-01

    Graphical abstract: - Highlights: • The crystal structure of GKAP homology domain 1 (GH1) was determined. • GKAP GH1 is a three-helix bundle connected by short flexible loops. • The predicted helix α4 associates weakly with the helix α3, suggesting dynamic nature of the GH1 domain. - Abstract: Guanylate-kinase-associated protein (GKAP) is a scaffolding protein that links NMDA receptor-PSD-95 to Shank–Homer complexes by protein–protein interactions at the synaptic junction. GKAP family proteins are characterized by the presence of a C-terminal conserved GKAP homology domain 1 (GH1) of unknown structure and function. In this study, crystal structure of the GH1 domain of GKAP from Rattus norvegicus was determined in fusion with an N-terminal maltose-binding protein at 2.0 Å resolution. The structure of GKAP GH1 displays a three-helix bundle connected by short flexible loops. The predicted helix α4 which was not visible in the crystal structure associates weakly with the helix α3 suggesting dynamic nature of the GH1 domain. The strict conservation of GH1 domain across GKAP family members and the lack of a catalytic active site required for enzyme activity imply that the GH1 domain might serve as a protein–protein interaction module for the synaptic protein clustering

  13. Structure of the GH1 domain of guanylate kinase-associated protein from Rattus norvegicus

    Energy Technology Data Exchange (ETDEWEB)

    Tong, Junsen; Yang, Huiseon [College of Pharmacy, Chonnam National University, Gwangju 500-757 (Korea, Republic of); Eom, Soo Hyun [School of Life Sciences, Steitz Center for Structural Biology, and Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 500-712 (Korea, Republic of); Chun, ChangJu, E-mail: cchun1130@jnu.ac.kr [College of Pharmacy, Chonnam National University, Gwangju 500-757 (Korea, Republic of); Im, Young Jun, E-mail: imyoungjun@jnu.ac.kr [College of Pharmacy, Chonnam National University, Gwangju 500-757 (Korea, Republic of)

    2014-09-12

    Graphical abstract: - Highlights: • The crystal structure of GKAP homology domain 1 (GH1) was determined. • GKAP GH1 is a three-helix bundle connected by short flexible loops. • The predicted helix α4 associates weakly with the helix α3, suggesting dynamic nature of the GH1 domain. - Abstract: Guanylate-kinase-associated protein (GKAP) is a scaffolding protein that links NMDA receptor-PSD-95 to Shank–Homer complexes by protein–protein interactions at the synaptic junction. GKAP family proteins are characterized by the presence of a C-terminal conserved GKAP homology domain 1 (GH1) of unknown structure and function. In this study, crystal structure of the GH1 domain of GKAP from Rattus norvegicus was determined in fusion with an N-terminal maltose-binding protein at 2.0 Å resolution. The structure of GKAP GH1 displays a three-helix bundle connected by short flexible loops. The predicted helix α4 which was not visible in the crystal structure associates weakly with the helix α3 suggesting dynamic nature of the GH1 domain. The strict conservation of GH1 domain across GKAP family members and the lack of a catalytic active site required for enzyme activity imply that the GH1 domain might serve as a protein–protein interaction module for the synaptic protein clustering.

  14. Molecular and Functional Characterization of FLOWERING LOCUS T Homologs in Allium cepa

    Directory of Open Access Journals (Sweden)

    Ranjith Kumar Manoharan

    2016-02-01

    Full Text Available Onion bulbing is an important agricultural trait affecting economic value and is regulated by flowering-related genes. FLOWERING LOCUS T (FT-like gene function is crucial for the initiation of flowering in various plant species and also in asexual reproduction in tuber plants. By employing various computational analysis using RNA-Seq data, we identified eight FT-like genes (AcFT encoding PEBP (phosphatidylethanolamine-binding protein domains in Allium cepa. Sequence and phylogenetic analyses of FT-like proteins revealed six proteins that were identical to previously reported AcFT1-6 proteins, as well as one (AcFT7 with a highly conserved region shared with AcFT6 and another (comp106231 with low similarity to MFT protein, but containing a PEBP domain. Homology modelling of AcFT7 proteins showed similar structures and conservation of amino acids crucial for function in AtFT (Arabidopsis and Hd3a (rice, with variation in the C-terminal region. Further, we analyzed AcFT expression patterns in different transitional stages, as well as under SD (short-day, LD (long-day, and drought treatment in two contrasting genotypic lines EM (early maturation, 36101 and LM (late maturation, 36122. The FT transcript levels were greatly affected by various environmental factors such as photoperiod, temperature and drought. Our results suggest that AcFT7 is a member of the FT-like genes in Allium cepa and may be involved in regulation of onion bulbing, similar to other FT genes. In addition, AcFT4 and AcFT7 could be involved in establishing the difference in timing of bulb maturity between the two contrasting onion lines.

  15. Homologous recombination and non-homologous end-joining repair pathways in bovine embryos with different developmental competence

    International Nuclear Information System (INIS)

    Henrique Barreta, Marcos; Garziera Gasperin, Bernardo; Braga Rissi, Vitor; Cesaro, Matheus Pedrotti de; Ferreira, Rogério; Oliveira, João Francisco de; Gonçalves, Paulo Bayard Dias; Bordignon, Vilceu

    2012-01-01

    This study investigated the expression of genes controlling homologous recombination (HR), and non-homologous end-joining (NHEJ) DNA-repair pathways in bovine embryos of different developmental potential. It also evaluated whether bovine embryos can respond to DNA double-strand breaks (DSBs) induced with ultraviolet irradiation by regulating expression of genes involved in HR and NHEJ repair pathways. Embryos with high, intermediate or low developmental competence were selected based on the cleavage time after in vitro insemination and were removed from in vitro culture before (36 h), during (72 h) and after (96 h) the expected period of embryonic genome activation. All studied genes were expressed before, during and after the genome activation period regardless the developmental competence of the embryos. Higher mRNA expression of 53BP1 and RAD52 was found before genome activation in embryos with low developmental competence. Expression of 53BP1, RAD51 and KU70 was downregulated at 72 h and upregulated at 168 h post-insemination in response to DSBs induced by ultraviolet irradiation. In conclusion, important genes controlling HR and NHEJ DNA-repair pathways are expressed in bovine embryos, however genes participating in these pathways are only regulated after the period of embryo genome activation in response to ultraviolet-induced DSBs.

  16. Homologous recombination and non-homologous end-joining repair pathways in bovine embryos with different developmental competence

    Energy Technology Data Exchange (ETDEWEB)

    Henrique Barreta, Marcos [Universidade Federal de Santa Catarina, Campus Universitario de Curitibanos, Curitibanos, SC (Brazil); Laboratorio de Biotecnologia e Reproducao Animal-BioRep, Universidade Federal de Santa Maria, Santa Maria, RS (Brazil); Garziera Gasperin, Bernardo; Braga Rissi, Vitor; Cesaro, Matheus Pedrotti de [Laboratorio de Biotecnologia e Reproducao Animal-BioRep, Universidade Federal de Santa Maria, Santa Maria, RS (Brazil); Ferreira, Rogerio [Centro de Educacao Superior do Oeste-Universidade do Estado de Santa Catarina, Chapeco, SC (Brazil); Oliveira, Joao Francisco de; Goncalves, Paulo Bayard Dias [Laboratorio de Biotecnologia e Reproducao Animal-BioRep, Universidade Federal de Santa Maria, Santa Maria, RS (Brazil); Bordignon, Vilceu, E-mail: vilceu.bordignon@mcgill.ca [Department of Animal Science, McGill University, Ste-Anne-De-Bellevue, QC (Canada)

    2012-10-01

    This study investigated the expression of genes controlling homologous recombination (HR), and non-homologous end-joining (NHEJ) DNA-repair pathways in bovine embryos of different developmental potential. It also evaluated whether bovine embryos can respond to DNA double-strand breaks (DSBs) induced with ultraviolet irradiation by regulating expression of genes involved in HR and NHEJ repair pathways. Embryos with high, intermediate or low developmental competence were selected based on the cleavage time after in vitro insemination and were removed from in vitro culture before (36 h), during (72 h) and after (96 h) the expected period of embryonic genome activation. All studied genes were expressed before, during and after the genome activation period regardless the developmental competence of the embryos. Higher mRNA expression of 53BP1 and RAD52 was found before genome activation in embryos with low developmental competence. Expression of 53BP1, RAD51 and KU70 was downregulated at 72 h and upregulated at 168 h post-insemination in response to DSBs induced by ultraviolet irradiation. In conclusion, important genes controlling HR and NHEJ DNA-repair pathways are expressed in bovine embryos, however genes participating in these pathways are only regulated after the period of embryo genome activation in response to ultraviolet-induced DSBs.

  17. The C. elegans VAPB homolog VPR-1 is a permissive signal for gonad development.

    Science.gov (United States)

    Cottee, Pauline A; Cole, Tim; Schultz, Jessica; Hoang, Hieu D; Vibbert, Jack; Han, Sung Min; Miller, Michael A

    2017-06-15

    VAMP/synaptobrevin-associated proteins (VAPs) contain an N-terminal major sperm protein domain (MSPd) that is associated with amyotrophic lateral sclerosis. VAPs have an intracellular housekeeping function, as well as an extracellular signaling function mediated by the secreted MSPd. Here we show that the C. elegans VAP homolog VPR-1 is essential for gonad development. vpr-1 null mutants are maternal effect sterile due to arrested gonadogenesis following embryo hatching. Somatic gonadal precursor cells and germ cells fail to proliferate fully and complete their respective differentiation programs. Maternal or zygotic vpr-1 expression is sufficient to induce gonadogenesis and fertility. Genetic mosaic and cell type-specific expression studies indicate that vpr-1 activity is important in the nervous system, germ line and intestine. VPR-1 acts in parallel to Notch signaling, a key regulator of germline stem cell proliferation and differentiation. Neuronal vpr-1 expression is sufficient for gonadogenesis induction during a limited time period shortly after hatching. These results support the model that the secreted VPR-1 MSPd acts at least in part on gonadal sheath cell precursors in L1 to early L2 stage hermaphrodites to permit gonadogenesis. © 2017. Published by The Company of Biologists Ltd.

  18. Direct Involvement of Retinoblastoma Family Proteins in DNA Repair by Non-homologous End-Joining

    Directory of Open Access Journals (Sweden)

    Rebecca Cook

    2015-03-01

    Full Text Available Deficiencies in DNA double-strand break (DSB repair lead to genetic instability, a recognized cause of cancer initiation and evolution. We report that the retinoblastoma tumor suppressor protein (RB1 is required for DNA DSB repair by canonical non-homologous end-joining (cNHEJ. Support of cNHEJ involves a mechanism independent of RB1’s cell-cycle function and depends on its amino terminal domain with which it binds to NHEJ components XRCC5 and XRCC6. Cells with engineered loss of RB family function as well as cancer-derived cells with mutational RB1 loss show substantially reduced levels of cNHEJ. RB1 variants disabled for the interaction with XRCC5 and XRCC6, including a cancer-associated variant, are unable to support cNHEJ despite being able to confer cell-cycle control. Our data identify RB1 loss as a candidate driver of structural genomic instability and a causative factor for cancer somatic heterogeneity and evolution.

  19. SAMHD1 Promotes DNA End Resection to Facilitate DNA Repair by Homologous Recombination

    Directory of Open Access Journals (Sweden)

    Waaqo Daddacha

    2017-08-01

    Full Text Available DNA double-strand break (DSB repair by homologous recombination (HR is initiated by CtIP/MRN-mediated DNA end resection to maintain genome integrity. SAMHD1 is a dNTP triphosphohydrolase, which restricts HIV-1 infection, and mutations are associated with Aicardi-Goutières syndrome and cancer. We show that SAMHD1 has a dNTPase-independent function in promoting DNA end resection to facilitate DSB repair by HR. SAMHD1 deficiency or Vpx-mediated degradation causes hypersensitivity to DSB-inducing agents, and SAMHD1 is recruited to DSBs. SAMHD1 complexes with CtIP via a conserved C-terminal domain and recruits CtIP to DSBs to facilitate end resection and HR. Significantly, a cancer-associated mutant with impaired CtIP interaction, but not dNTPase-inactive SAMHD1, fails to rescue the end resection impairment of SAMHD1 depletion. Our findings define a dNTPase-independent function for SAMHD1 in HR-mediated DSB repair by facilitating CtIP accrual to promote DNA end resection, providing insight into how SAMHD1 promotes genome integrity.

  20. GPCRM: a homology modeling web service with triple membrane-fitted quality assessment of GPCR models.

    Science.gov (United States)

    Miszta, Przemyslaw; Pasznik, Pawel; Jakowiecki, Jakub; Sztyler, Agnieszka; Latek, Dorota; Filipek, Slawomir

    2018-05-21

    Due to the involvement of G protein-coupled receptors (GPCRs) in most of the physiological and pathological processes in humans they have been attracting a lot of attention from pharmaceutical industry as well as from scientific community. Therefore, the need for new, high quality structures of GPCRs is enormous. The updated homology modeling service GPCRM (http://gpcrm.biomodellab.eu/) meets those expectations by greatly reducing the execution time of submissions (from days to hours/minutes) with nearly the same average quality of obtained models. Additionally, due to three different scoring functions (Rosetta, Rosetta-MP, BCL::Score) it is possible to select accurate models for the required purposes: the structure of the binding site, the transmembrane domain or the overall shape of the receptor. Currently, no other web service for GPCR modeling provides this possibility. GPCRM is continually upgraded in a semi-automatic way and the number of template structures has increased from 20 in 2013 to over 90 including structures the same receptor with different ligands which can influence the structure not only in the on/off manner. Two types of protein viewers can be used for visual inspection of obtained models. The extended sortable tables with available templates provide links to external databases and display ligand-receptor interactions in visual form.