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Sample records for phototropin lov domain

  1. Primary photophysics of the FMN binding LOV2 domain of the plant blue light receptor phototropin of Avena sativa

    NASA Astrophysics Data System (ADS)

    Schüttrigkeit, Tanja A.; Kompa, Christian K.; Salomon, Michael; Rüdiger, Wolfhart; Michel-Beyerle, Maria E.

    2003-11-01

    The temporal evolution of the initially excited singlet state of flavine mononucleotide, which is the cofactor in the LOV2 domain of the blue photoreceptor phototropin, has been studied in picosecond time-resolved fluorescence and femtosecond time-resolved absorption experiments. In the LOV2-WT protein of Avena sativa singlet-triplet intersystem crossing proceeding within 2.3 ns is the primary process which increases the triplet yield by a factor of 1.23 as compared to a mutant where cysteine 39 is replaced by alanine. This flavin triplet state is responsible for the formation of a cysteinyl-flavin adduct which triggers the unique photocycle of the LOV2 domain and thus the sensoric function of the blue light receptor phototropin.

  2. Crystallization and preliminary X-ray diffraction anaylsis of the LOV1 domains of phototropin 1 and 2 from Arabidopsis thaliana

    SciTech Connect

    Nakasako, Masayoshi; Hirata, Michihiro; Shimizu, Nobutaka; Matsuoka, Daisuke; Oka, Toshihiko; Yamamoto, Masaki; Tokutomi, Satoru

    2008-07-01

    Crystals of the LOV1 domains of phototropin 1 and 2 from A. thaliana were obtained which diffracted X-rays to a resolution of at least 2.1 Å. Phototropin is a blue-light receptor protein in plants that is responsible for phototropic responses, stomata opening and photo-induced relocation of chloroplasts. Higher plants such as Arabidopsis thaliana have two isoforms of phototropin: phototropin 1 and phototropin 2. Both isoforms comprise a tandem pair of blue-light-absorbing light–oxygen–voltage domains named LOV1 and LOV2 in the N-terminal half and a serine/threonine kinase domain in the C-terminal half. The LOV1 domain is thought to function as a dimerization site. In the present study, recombinant LOV1 domains of A. thaliana phototropin 1 and phototropin 2 were crystallized. The crystal of the LOV1 domain of phototropin 1 belonged to the orthorhombic space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 61.2, b = 64.9, c = 70.8 Å, and diffracted X-rays to a resolution of 2.1 Å. The crystal of the LOV1 domain of phototropin 2 belonged to space group P2{sub 1}, with unit-cell parameters a = 32.5, b = 66.5, c = 56.7 Å, β = 92.4°, and diffracted X-rays to beyond 2.0 Å resolution. In both crystals, two LOV1 domains occupied the crystallographic asymmetric unit.

  3. The primary photophysics of the Avena sativa phototropin 1 LOV2 domain observed with time-resolved emission spectroscopy†

    PubMed Central

    van Stokkum, Ivo H.M.; Gauden, Magdalena; Crosson, Sean; van Grondelle, Rienk; Moffat, Keith; Kennis, John T.M.

    2016-01-01

    The phototropins are blue-light receptors that base their light-dependent action on the reversible formation of a covalent bond between a flavin mononucleotide (FMN) cofactor and a conserved cysteine in light, oxygen or voltage (LOV) domains. The primary reactions of the Avena sativa phototropin 1 LOV2 domain were investigated by means of time-resolved and low-temperature fluorescence spectroscopy. Synchroscan streak camera experiments revealed a fluorescence lifetime of 2.2 ns in LOV2. A weak long-lived component with emission intensity from 600 to 650 nm was assigned to phosphorescence from the reactive FMN triplet state. This observation allowed determination of the LOV2 triplet state energy level at physiological temperature at 16600 cm−1. FMN dissolved in aqueous solution showed pH-dependent fluorescence lifetimes of 2.7 ns at pH 2 and 3.9–4.1 ns at pH 3 to 8. Here, too, a weak phosphorescence band was observed. The fluorescence quantum yield of LOV2 increased from 0.13 to 0.41 upon cooling the sample from 293 to 77 K. A pronounced phosphorescence emission around 600 nm was observed in the LOV2 domain between 77 and 120 K in the steady-state emission. PMID:21261629

  4. The primary photophysics of the Avena sativa phototropin 1 LOV2 domain observed with time-resolved emission spectroscopy.

    PubMed

    van Stokkum, Ivo H M; Gauden, Magdalena; Crosson, Sean; van Grondelle, Rienk; Moffat, Keith; Kennis, John T M

    2011-01-01

    The phototropins are blue-light receptors that base their light-dependent action on the reversible formation of a covalent bond between a flavin mononucleotide (FMN) cofactor and a conserved cysteine in light, oxygen or voltage (LOV) domains. The primary reactions of the Avena sativa phototropin 1 LOV2 domain were investigated by means of time-resolved and low-temperature fluorescence spectroscopy. Synchroscan streak camera experiments revealed a fluorescence lifetime of 2.2 ns in LOV2. A weak long-lived component with emission intensity from 600 to 650 nm was assigned to phosphorescence from the reactive FMN triplet state. This observation allowed determination of the LOV2 triplet state energy level at physiological temperature at 16600 cm(-1). FMN dissolved in aqueous solution showed pH-dependent fluorescence lifetimes of 2.7 ns at pH 2 and 3.9-4.1 ns at pH 3-8. Here, too, a weak phosphorescence band was observed. The fluorescence quantum yield of LOV2 increased from 0.13 to 0.41 upon cooling the sample from 293 to 77 K. A pronounced phosphorescence emission around 600 nm was observed in the LOV2 domain between 77 and 120 K in the steady-state emission. © 2011 The Authors. Photochemistry and Photobiology © 2011 The American Society of Photobiology.

  5. A conserved isoleucine in the LOV1 domain of a novel phototropin from the marine alga Ostreococcus tauri modulates the dark state recovery of the domain.

    PubMed

    Veetil, Sindhu Kandoth; Mittal, Chitvan; Ranjan, Peeyush; Kateriya, Suneel

    2011-07-01

    Phototropins are UV-A/blue light receptor proteins with two LOV (Light-Oxygen-Voltage) sensor domains at their N terminus and a kinase domain at the C-terminus in photoautotrophic organisms. This is the first research report of a canonical phototropin from marine algae Ostreococcus tauri. We synthesized core LOV1 (OtLOV1) domain-encoding portion of the phototropin gene of O. tauri, the domain was heterologously expressed, purified and assessed for its spectral properties and dark recovery kinetics by UV-Visible, fluorescence spectroscopy and mutational studies. Quaternary structure characteristics were studied by SEC and glutaraldehyde crosslinking. The absorption spectrum of OtLOV1 lacks the characteristic 361nm peak shown by other LOV1 domains. It undergoes a photocycle with a dark state recovery time of approximately 30min (τ=300.35s). Native OtLOV1 stayed as dimer in aqueous solution and the dimer formation was light and concentration independent. Mutating isoleucine at 43rd position to valine accelerated the dark recovery time by more than 10-fold. Mutating it to serine reduced sensitivity to blue light, but the dark recovery time remained unaltered. I43S mutation also destabilized the FMN binding to a great extent. The OtLOV1 domain of the newly identified OtPhot is functional and the isoleucine at position 43 of OtLOV1 is the key residue responsible for fine-tuning the domain properties. This is the first characterized LOV1 domain of a canonical phototropin from a marine alga and spectral properties of the domain are similar to that of the LOV1 domain of higher plants. 2011 Elsevier B.V. All rights reserved.

  6. Light-induced movement of the LOV2 domain in an Asp720Asn mutant LOV2-kinase fragment of Arabidopsis phototropin 2.

    PubMed

    Takayama, Yuki; Nakasako, Masayoshi; Okajima, Koji; Iwata, Aya; Kashojiya, Sachiko; Matsui, Yuka; Tokutomi, Satoru

    2011-02-22

    Phototropin, a blue-light receptor protein of plants, triggers phototropic responses, chloroplast relocation, and opening of stomata to maximize the efficiency of photosynthesis. Phototropin is composed of two light-oxygen-voltage sensing domains (LOV1 and LOV2) that absorb blue light and a serine/theroine kinase domain responsible for light-dependent autophosphorylation leading to cellular signaling cascades. Although the light-activated LOV2 domain is primarily responsible for subsequent activation of the kinase domain, it is unclear how conformational changes in the former transmit to the latter. To understand this molecular mechanism in Arabidopsis phototropin 2, we performed small-angle X-ray scattering analysis on a fragment composed of the LOV2 and kinase domains, which contained an Asp720Asn mutation that led to an absence of ATP binding activity. The scattering data were collected up to a resolution of 25 Å. The apparent molecular weight of the fragment estimated from scattering intensities demonstrated that the fragment existed in a monomeric form in solution. The fragment exhibited photoreversible changes in the scattering profiles, and the radii of gyration under dark and blue-light irradiation conditions were 32.4 and 34.8 Å, respectively. In the dark, the molecular shape restored from the scattering profile appeared as an elongated shape of 110 Å in length and 45 Å in width. The homology modeled LOV2 and kinase domains could be fitted to the molecular shape and appeared to make slight contact. However, under blue-light irradiation, a more extended molecular shape was observed. The changes in the molecular shape and radius of gyration were interpreted as a light-dependent positional shift of the LOV2 domain of approximately 13 Å from the kinase domain. Because the region connecting the LOV2 and kinase domains was categorized as a naturally unfolded polypeptide, we propose that the light-activated LOV2 domain triggers conformational changes in the

  7. Low-temperature and time-resolved spectroscopic characterization of the LOV2 domain of Avena sativa phototropin

    SciTech Connect

    Gauden, Magdalena; Crosson, Sean; van Stokkum, I.H.; Grondelle, Rienkvan; Moffat, Keith; Kennis, John T.

    2004-12-13

    The phototropins are plant blue-light receptors that base their light-dependent action on the reversible formation of a covalent bond between a flavin mononucleotide (FMN) cofactor and a conserved cysteine residue in light, oxygen or voltage (LOV) domains. The spectroscopic properties of the LOV2 domain of phototropin 1 of Avena sativa (oat) have been investigated by means of low-temperature absorption and fluorescence spectroscopy and by time-resolved fluorescence spectroscopy. The low-temperature absorption spectrum of the LOV2 domain showed a fine structure around 473 nm, indicating heterogeneity in the flavin binding pocket. The fluorescence quantum yield of the flavin cofactor increased from 0.13 to 0.41 upon cooling the sample from room temperature to 77 K. A pronounced phosphorescence emission around 600 nm was observed in the LOV2 domain between 77 and 120 K, allowing for an accurate positioning of the flavin triplet state in the LOV2 domain at 16900 cm{sup -1}. Fluorescence from the cryotrapped covalent adduct state was extremely weak, with a fluorescence spectrum showing a maximum at 440 nm. Time-resolved fluorescence experiments utilizing a synchroscan streak camera revealed a singlet-excited state lifetime of the LOV2 domain of 2.4 ns. FMN dissolved in aqueous solution showed a pH-dependent lifetime ranging between 2.9 ns at pH 2.0 to 4.7 ns at pH 8.0. No spectral shifting of the flavin emission was observed in the LOV2 domain nor in FMN in aqueous solution.

  8. Low-temperature and time-resolved spectroscopic characterization of the LOV2 domain of Avena sativa phototropin 1

    NASA Astrophysics Data System (ADS)

    Gauden, Magdalena; Crosson, Sean; van Stokkum, I. H. M.; van Grondelle, Rienk; Moffat, Keith; Kennis, John T. M.

    2004-09-01

    The phototropins are plant blue-light receptors that base their light-dependent action on the reversible formation of a covalent bond between a flavin mononucleotide (FMN) cofactor and a conserved cysteine residue in light, oxygen or voltage (LOV) domains. The spectroscopic properties of the LOV2 domain of phototropin 1 of Avena sativa (oat) have been investigated by means of low-temperature absorption and fluorescence spectroscopy and by time-resolved fluorescence spectroscopy. The low-temperature absorption spectrum of the LOV2 domain showed a fine structure around 473 nm, indicating heterogeneity in the flavin binding pocket. The fluorescence quantum yield of the flavin cofactor increased from 0.13 to 0.41 upon cooling the sample from room temperature to 77 K. A pronounced phosphorescence emission around 600 nm was observed in the LOV2 domain between 77 and 120 K, allowing for an accurate positioning of the flavin triplet state in the LOV2 domain at 16900 cm-1. Fluorescence from the cryotrapped covalent adduct state was extremely weak, with a fluorescence spectrum showing a maximum at 440 nm. Time-resolved fluorescence experiments utilizing a synchroscan streak camera revealed a singlet-excited state lifetime of the LOV2 domain of 2.4 ns. FMN dissolved in aqueous solution showed a pH-dependent lifetime ranging between 2.9 ns at pH 2.0 to 4.7 ns at pH 8.0. No spectral shifting of the flavin emission was observed in the LOV2 domain nor in FMN in aqueous solution.

  9. Both LOV1 and LOV2 domains of phototropin2 function as the photosensory domain for hypocotyl phototropic responses in Arabidopsis thaliana (Brassicaceae).

    PubMed

    Suetsugu, Noriyuki; Kong, Sam-Geun; Kasahara, Masahiro; Wada, Masamitsu

    2013-01-01

    Phototropins (phot) are blue light receptor proteins that mediate phototropism and control photomovement responses, such as chloroplast photorelocation movement and stomatal opening. Arabidopsis thaliana has two phototropins, phot1 and phot2. Although both phot1 and phot2 redundantly mediate photomovement responses, phot2 uniquely regulates phototropism and the chloroplast avoidance response under high-intensity blue light. However, compared to that of phot1, the mechanistic basis of phot2 function is poorly understood, and in particular, the importance of the LOV2 domain in phot2 function has not been clearly demonstrated. Indeed, photocycle-deficient LOV2 transgenic lines expressing phot2 in a phot1phot2 mutant background retained phototropism, although with less sensitivity than wild-type plants. We isolated 11 alleles of phot2 mutants and determined the molecular lesion in each allele. We analyzed hypocotyl phototropism, chloroplast photorelocation movement, and leaf flattening in the phot2 mutant and the respective phot1phot2 double mutant plants. We demonstrated that unlike the phot2 null mutant, the phot2-10 mutant, which has the defective phot2 LOV2 domain, retained the phototropic response and had unusual chloroplast movement. Mutants phot2-2 and phot2-6, which have a missense mutation in the kinase activation loop of phot2, had the phot2-null mutant phenotype. Furthermore, we convincingly demonstrated that the commonly used phot2-1 mutant allele is a phot2-null mutant. The analyses of the multiple phot2 mutant alleles provided strong evidence for the importance of both LOV domains and the kinase activation loop of phot2 in phototropism and other phot-dependent responses and also demonstrated that phot2-1 allele is a null mutant.

  10. A base-catalyzed mechanism for dark state recovery in the Avena sativa phototropin-1 LOV2 domain.

    PubMed

    Alexandre, Maxime T A; Arents, Jos C; van Grondelle, Rienk; Hellingwerf, Klaas J; Kennis, John T M

    2007-03-20

    Phototropins are autophosphorylating serine/threonine kinases responsible for blue-light perception in plants; their action gives rise to phototropism, chloroplast relocation, and opening of stomatal guard cells. The kinase domain constitutes the C-terminal part of Avena sativa phototropin 1. The N-terminal part contains two light, oxygen, or voltage (LOV) sensing domains, LOV1 and LOV2; each binds a flavin mononucleotide (FMN) chromophore (lambdamax = 447 nm, termed D447) and forms the light-sensitive domains, of which LOV2 is the principal component. Blue-light absorption produces a covalent adduct between a very conserved nearby cysteine residue and the C(4a) atom of the FMN moiety via the triplet state of the flavin. The covalent adduct thermally decays to regenerate the D447 dark state, with a rate that may vary by several orders of magnitude between different species. We report that the imidazole base can act as a very efficient enhancer of the dark recovery of A. sativa phot1 LOV2 (AsLOV2) and some other well-characterized LOV domains. Imidazole accelerates the thermal decay of AsLOV2 by 3 orders of magnitude in the submolar concentration range, via a base-catalyzed mechanism involving base abstraction of the FMN N(5)-H adduct state and subsequent reprotonation of the reactive cysteine. The LOV2 crystal structure suggests that the imidazole molecules may act from a cavity located in the vicinity of the FMN, explaining its high efficiency, populated through a channel connecting the cavity to the protein surface. Use of pH titration and chemical inactivation by diethyl pyrocarbonate (DEPC) suggests that histidines located at the surface of the LOV domain act as base catalysts via an as yet unidentified H-bond network, operating at a rate of (55 s)-1 at pH 8. In addition, molecular processes other than histidine-mediated base catalysis contibute significantly to the total thermal decay rate of the adduct and operate at a rate constant of (65 s)-1, leading to a

  11. Conformational heterogeneity and propagation of structural changes in the LOV2/Jalpha domain from Avena sativa phototropin 1 as recorded by temperature-dependent FTIR spectroscopy.

    PubMed

    Alexandre, Maxime T A; van Grondelle, Rienk; Hellingwerf, Klaas J; Kennis, John T M

    2009-07-08

    Phototropins control phototropism, chloroplast movement, stomatal opening, and leaf expansion in plants. Phototropin 1 (phot1) is composed of a kinase domain linked to two blue light-sensing domains, LOV2 and LOV1, which bind flavin mononucleotide. Disruption of the interaction between the LOV2 domain and a helical segment named Jalpha, joining LOV to the kinase domain, induces the subsequent kinase activity of phototropin 1 and further-downstream signal transduction. Here we study the effects of temperature and hydration on the light-triggered signal propagation in the phot1 LOV2 domain of Avena sativa (AsLOV2/Jalpha), using Fourier transform infrared spectroscopy to unravel part of the molecular mechanism of phototropin 1. We report that AsLOV2/Jalpha shows an intense signal in the amide I and II regions, arising mainly from beta-sheet changes and the unbinding of the Jalpha helix from the Per-ARNT-Sim core and its subsequent partial unfolding. Importantly, these structural changes only occur under conditions of full hydration and at temperatures above 280 K. We characterized a newly isolated low-hydration intermediate that shows a downshift of high-frequency amide I signals and that possibly corresponds to loop tightening, without large beta-sheet or Jalpha structural changes. In addition, we report a heterogeneity in AsLOV2/Jalpha involving two different C(4)=O conformer populations, coexisting in the dark state and characterized by C(4)=O carbonyl frequencies at 1712 cm(-1) and 1694 cm(-1) that are attributable to a single H-bond and two H-bonds at this site, respectively. Such conformers display slightly shifted absorption spectra and cause a splitting of the 475-nm band in the ultraviolet/visible spectra of LOV domains at low temperature.

  12. Conformational Heterogeneity and Propagation of Structural Changes in the LOV2/Jα Domain from Avena sativa Phototropin 1 as Recorded by Temperature-Dependent FTIR Spectroscopy

    PubMed Central

    Alexandre, Maxime T.A.; van Grondelle, Rienk; Hellingwerf, Klaas J.; Kennis, John T.M.

    2009-01-01

    Abstract Phototropins control phototropism, chloroplast movement, stomatal opening, and leaf expansion in plants. Phototropin 1 (phot1) is composed of a kinase domain linked to two blue light-sensing domains, LOV2 and LOV1, which bind flavin mononucleotide. Disruption of the interaction between the LOV2 domain and a helical segment named Jα, joining LOV to the kinase domain, induces the subsequent kinase activity of phototropin 1 and further-downstream signal transduction. Here we study the effects of temperature and hydration on the light-triggered signal propagation in the phot1 LOV2 domain of Avena sativa (AsLOV2/Jα), using Fourier transform infrared spectroscopy to unravel part of the molecular mechanism of phototropin 1. We report that AsLOV2/Jα shows an intense signal in the amide I and II regions, arising mainly from β-sheet changes and the unbinding of the Jα helix from the Per-ARNT-Sim core and its subsequent partial unfolding. Importantly, these structural changes only occur under conditions of full hydration and at temperatures above 280 K. We characterized a newly isolated low-hydration intermediate that shows a downshift of high-frequency amide I signals and that possibly corresponds to loop tightening, without large β-sheet or Jα structural changes. In addition, we report a heterogeneity in AsLOV2/Jα involving two different C(4)=O conformer populations, coexisting in the dark state and characterized by C(4)=O carbonyl frequencies at 1712 cm−1 and 1694 cm−1 that are attributable to a single H-bond and two H-bonds at this site, respectively. Such conformers display slightly shifted absorption spectra and cause a splitting of the 475-nm band in the ultraviolet/visible spectra of LOV domains at low temperature. PMID:19580761

  13. Light-induced conformational changes of LOV1 (light oxygen voltage-sensing domain 1) and LOV2 relative to the kinase domain and regulation of kinase activity in Chlamydomonas phototropin.

    PubMed

    Okajima, Koji; Aihara, Yusuke; Takayama, Yuki; Nakajima, Mihoko; Kashojiya, Sachiko; Hikima, Takaaki; Oroguchi, Tomotaka; Kobayashi, Amane; Sekiguchi, Yuki; Yamamoto, Masaki; Suzuki, Tomomi; Nagatani, Akira; Nakasako, Masayoshi; Tokutomi, Satoru

    2014-01-03

    Phototropin (phot), a blue light (BL) receptor in plants, has two photoreceptive domains named LOV1 and LOV2 as well as a Ser/Thr kinase domain (KD) and acts as a BL-regulated protein kinase. A LOV domain harbors a flavin mononucleotide that undergoes a cyclic photoreaction upon BL excitation via a signaling state in which the inhibition of the kinase activity by LOV2 is negated. To understand the molecular mechanism underlying the BL-dependent activation of the kinase, the photochemistry, kinase activity, and molecular structure were studied with the phot of Chlamydomonas reinhardtii. Full-length and LOV2-KD samples of C. reinhardtii phot showed cyclic photoreaction characteristics with the activation of LOV- and BL-dependent kinase. Truncation of LOV1 decreased the photosensitivity of the kinase activation, which was well explained by the fact that the signaling state lasted for a shorter period of time compared with that of the phot. Small angle x-ray scattering revealed monomeric forms of the proteins in solution and detected BL-dependent conformational changes, suggesting an extension of the global molecular shapes of both samples. Constructed molecular model of full-length phot based on the small angle x-ray scattering data proved the arrangement of LOV1, LOV2, and KD for the first time that showed a tandem arrangement both in the dark and under BL irradiation. The models suggest that LOV1 alters its position relative to LOV2-KD under BL irradiation. This finding demonstrates that LOV1 may interact with LOV2 and modify the photosensitivity of the kinase activation through alteration of the duration of the signaling state in LOV2.

  14. Primary Reactions of the LOV2 Domain of Phototropin Studied with Ultrafast Mid-Infrared Spectroscopy and Quantum Chemistry

    PubMed Central

    Alexandre, Maxime T.A.; Domratcheva, Tatiana; Bonetti, Cosimo; van Wilderen, Luuk J.G.W.; van Grondelle, Rienk; Groot, Marie-Louise; Hellingwerf, Klaas J.; Kennis, John T.M.

    2009-01-01

    Abstract Phototropins, major blue-light receptors in plants, are sensitive to blue light through a pair of flavin mononucleotide (FMN)-binding light oxygen and voltage (LOV) domains, LOV1 and LOV2. LOV2 undergoes a photocycle involving light-driven covalent adduct formation between a conserved cysteine and the FMN C(4a) atom. Here, the primary reactions of Avena sativa phototropin 1 LOV2 (AsLOV2) were studied using ultrafast mid-infrared spectroscopy and quantum chemistry. The singlet excited state (S1) evolves into the triplet state (T1) with a lifetime of 1.5 ns at a yield of ∼50%. The infrared signature of S1 is characterized by absorption bands at 1657 cm−1, 1495–1415 cm−1, and 1375 cm−1. The T1 state shows infrared bands at 1657 cm−1, 1645 cm−1, 1491–1438 cm−1, and 1390 cm−1. For both electronic states, these bands are assigned principally to C=O, C=N, C-C, and C-N stretch modes. The overall downshifting of C=O and C=N bond stretch modes is consistent with an overall bond-order decrease of the conjugated isoalloxazine system upon a π-π∗ transition. The configuration interaction singles (CIS) method was used to calculate the vibrational spectra of the S1 and T1 excited ππ∗ states, as well as respective electronic energies, structural parameters, electronic dipole moments, and intrinsic force constants. The harmonic frequencies of S1 and T1, as calculated by the CIS method, are in satisfactory agreement with the evident band positions and intensities. On the other hand, CIS calculations of a T1 cation that was protonated at the N(5) site did not reproduce the experimental FMN T1 spectrum. We conclude that the FMN T1 state remains nonprotonated on a nanosecond timescale, which rules out an ionic mechanism for covalent adduct formation involving cysteine-N(5) proton transfer on this timescale. Finally, we observed a heterogeneous population of singly and doubly H-bonded FMN C(4)=O conformers in the dark state, with stretch frequencies

  15. Primary reactions of the LOV2 domain of phototropin studied with ultrafast mid-infrared spectroscopy and quantum chemistry.

    PubMed

    Alexandre, Maxime T A; Domratcheva, Tatiana; Bonetti, Cosimo; van Wilderen, Luuk J G W; van Grondelle, Rienk; Groot, Marie-Louise; Hellingwerf, Klaas J; Kennis, John T M

    2009-07-08

    Phototropins, major blue-light receptors in plants, are sensitive to blue light through a pair of flavin mononucleotide (FMN)-binding light oxygen and voltage (LOV) domains, LOV1 and LOV2. LOV2 undergoes a photocycle involving light-driven covalent adduct formation between a conserved cysteine and the FMN C(4a) atom. Here, the primary reactions of Avena sativa phototropin 1 LOV2 (AsLOV2) were studied using ultrafast mid-infrared spectroscopy and quantum chemistry. The singlet excited state (S1) evolves into the triplet state (T1) with a lifetime of 1.5 ns at a yield of approximately 50%. The infrared signature of S1 is characterized by absorption bands at 1657 cm(-1), 1495-1415 cm(-1), and 1375 cm(-1). The T1 state shows infrared bands at 1657 cm(-1), 1645 cm(-1), 1491-1438 cm(-1), and 1390 cm(-1). For both electronic states, these bands are assigned principally to C=O, C=N, C-C, and C-N stretch modes. The overall downshifting of C=O and C=N bond stretch modes is consistent with an overall bond-order decrease of the conjugated isoalloxazine system upon a pi-pi* transition. The configuration interaction singles (CIS) method was used to calculate the vibrational spectra of the S1 and T1 excited pipi* states, as well as respective electronic energies, structural parameters, electronic dipole moments, and intrinsic force constants. The harmonic frequencies of S1 and T1, as calculated by the CIS method, are in satisfactory agreement with the evident band positions and intensities. On the other hand, CIS calculations of a T1 cation that was protonated at the N(5) site did not reproduce the experimental FMN T1 spectrum. We conclude that the FMN T1 state remains nonprotonated on a nanosecond timescale, which rules out an ionic mechanism for covalent adduct formation involving cysteine-N(5) proton transfer on this timescale. Finally, we observed a heterogeneous population of singly and doubly H-bonded FMN C(4)=O conformers in the dark state, with stretch frequencies at 1714

  16. Structural water cluster as a possible proton acceptor in the adduct decay reaction of oat phototropin 1 LOV2 domain.

    PubMed

    Chan, Ruby H; Bogomolni, Roberto A

    2012-09-06

    LOV domains (Light, Oxygen, Voltage) are the light-sensory modules of phototropins, the blue-light photoreceptor kinases in plants, and of a wide variety of flavoproteins found in all three domains of life. These 12 kDa modules bind a flavin chromophore (FMN or FAD) noncovalently and undergo a photochemical activation in which the sulfur atom of a conserved cysteine forms an adduct to the C(4a) carbon of the flavin. The adduct breaks spontaneously in a base-catalyzed reaction involving a rate-limiting proton-transfer step, regenerating the dark state in seconds. This photocycle involves chromophore and protein structural changes that activate the C-terminal serine/threonine kinase. Previous studies (Biochemistry 2007, 46, 7016-7021) showed that decreased hydration obtained at high glycerol concentrations stabilizes the adduct state in a manner similar to that attained at low temperatures, resulting in much longer adduct decay times. This kinetic effect was attributed to an increased protein rigidity that hindered structural fluctuations necessary for the decay reaction. In this work, we studied the adduct decay kinetics of oat phototropin 1 (phot1) LOV2 at varying hydration using a specially designed chamber that allowed for measurement of UV-visible and FTIR spectra of the same samples. Therefore, we obtained LOV protein concentrations, adduct decay kinetics, and the different populations of bound water by deconvolution of the broad water absorption peak around 3500 cm(-1). A linear dependence of the adduct decay rate constant on the concentration of double and triple hydrogen-bonded waters strongly suggests that the adduct decay is a pseudo-first-order reaction in which both the adduct and the strongly bound waters are reactants. We suggest that a cluster of strongly bound water functions as the proton acceptor in the rate-limiting step of adduct decay.

  17. Photochemically induced dynamic nuclear polarization in a C450A mutant of the LOV2 domain of the Avena sativa blue-light receptor phototropin.

    PubMed

    Richter, Gerald; Weber, Stefan; Römisch, Werner; Bacher, Adelbert; Fischer, Markus; Eisenreich, Wolfgang

    2005-12-14

    Phototropin is a blue-light receptor involved in the phototropic response of higher plants. The photoreceptor comprises a protein kinase domain and two structurally similar flavin-mononucleotide (FMN) binding domains designated LOV1 and LOV2. Blue-light irradiation of recombinant LOV2 domains induces the formation of a covalent adduct of the thiol group of a functional cysteine in the cofactor-binding pocket to C(4a) of the FMN. Cysteine-to-alanine mutants of LOV domains are unable to form that adduct but generate an FMN radical upon illumination. The recombinant C450A mutant of the LOV2 domain of Avena sativa phototropin was reconstituted with universally and site-selectively (13)C-labeled FMN and the (13)C NMR signals were unequivocally assigned. (13)C NMR spectra were acquired in darkness and under blue-light irradiation. The chemical shifts and the coupling patterns of the signals were not affected by irradiation. However, under blue-light exposure, exceptionally strong nuclear-spin polarization was developed in the resonances belonging to certain carbons of the FMN's isoalloxazine moiety. An enhancement of the NMR absorption was observed for the signals of C(5a), C(7), and C(9). NMR lines in emission were detected for the signals belonging to C(2), C(4), C(4a), C(6), C(8), and C(9a). The signal of C(10a) remained in absorption but was slightly attenuated. In contrast, the intensities of the NMR signals belonging to the carbons of the ribityl side chain of FMN were not affected by light. The observation of spin-polarized (13)C-nuclei in the NMR spectra of the mutant LOV2 domain is clear evidence for radical-pair intermediates in the reaction steps following optical sample excitation.

  18. N- and C-terminal flanking regions modulate light-induced signal transduction in the LOV2 domain of the blue light sensor phototropin 1 from Avena sativa.

    PubMed

    Halavaty, Andrei S; Moffat, Keith

    2007-12-11

    Light sensing by photoreceptors controls phototropism, chloroplast movement, stomatal opening, and leaf expansion in plants. Understanding the molecular mechanism by which these processes are regulated requires a quantitative description of photoreceptor dynamics. We focus on a light-driven signal transduction mechanism in the LOV2 domain (LOV, light, oxygen, voltage) of the blue light photoreceptor phototropin 1 from Avena sativa (oat). High-resolution crystal structures of the dark and light states of an oat LOV2 construct including residues Leu404 through Leu546 (LOV2 (404-546)) have been determined at 105 and 293 K. In all four structures, LOV2 (404-546) exhibits the typical Per-ARNT-Sim (PAS) fold, flanked by an additional conserved N-terminal turn-helix-turn motif and a C-terminal flanking region containing an amphipathic Jalpha helix. These regions dock on the LOV2 core domain and bury several hydrophobic residues of the central beta-sheet of the core domain that would otherwise be exposed to solvent. Light structures of LOV2 (404-546) reveal that formation of the covalent bond between Cys450 and the C4a atom of the flavin mononucleotide (FMN) results in local rearrangement of the hydrogen-bonding network in the FMN binding pocket. These rearrangements are associated with disruption of the Asn414-Asp515 hydrogen bond on the surface of the protein and displacement of the N- and C-terminal flanking regions of LOV2 (404-546), both of which constitute a structural signal.

  19. Photosensitivity of kinase activation by blue light involves the lifetime of a cysteinyl-flavin adduct intermediate, S390, in the photoreaction cycle of the LOV2 domain in phototropin, a plant blue light receptor.

    PubMed

    Okajima, Koji; Kashojiya, Sachiko; Tokutomi, Satoru

    2012-11-30

    Phototropin (phot) is a light-regulated protein kinase that mediates a variety of photoresponses in plants, such as phototropism, chloroplast positioning, and stomata opening. Arabidopsis has two homologues, phot1 and phot2, that share physiological functions depending on light intensity. A phot molecule has two photoreceptive light oxygen voltage-sensing domains, LOV1 and LOV2, and a Ser/Thr kinase domain. The LOV domains undergo a photocycle upon blue light (BL) stimulation, including transient adduct formation between the chromophore and a conserved cysteine (S390 intermediate) that leads to activation of the kinase. To uncover the mechanism underlying the photoactivation of the kinase, we have introduced a kinase assay system composed of a phot1 LOV2-linker-kinase polypeptide as a light-regulated kinase and its N-terminal polypeptide as an artificial substrate (Okajima, K., Matsuoka, D., and Tokutomi, S. (2011) LOV2-linker-kinase phosphorylates LOV1-containing N-terminal polypeptide substrate via photoreaction of LOV2 in Arabidopsis phototropin1. FEBS Lett. 585, 3391-3395). In the present study, we extended the assay system to phot2 and compared the photochemistry and kinase activation by BL between phot1 and phot2 to gain insight into the molecular basis for the different photosensitivities of phot1 and phot2. Photosensitivity of kinase activation by BL and the lifetime of S390 of phot1 were 10 times higher and longer, respectively, than those of phot2. This correlation was confirmed by an amino acid substitution experiment with phot1 to shorten the lifetime of S390. The present results demonstrated that the photosensitivity of kinase activation in phot involves the lifetime of S390 in LOV2, suggesting that the lifetime is one of the key factors for the different photosensitivities observed for phot1 and phot2.

  20. Designing photoswitchable peptides using the AsLOV2 domain

    PubMed Central

    Lungu, Oana I.; Hallett, Ryan A.; Choi, Eun Jung; Aiken, Mary J.; Hahn, Klaus M.; Kuhlman, Brian

    2012-01-01

    Summary Photocontrol of functional peptides is a powerful tool for spatial and temporal control of cell signaling events. We show that the genetically encoded light-sensitive LOV2 domain of Avena Sativa phototropin 1 (AsLOV2) can be used to reversibly photomodulate the affinity of peptides for their binding partners. Sequence analysis and molecular modeling were used to embed two peptides into the Ja helix of the AsLOV2 domain while maintaining AsLOV2 structure in the dark, but allowing for binding to effector proteins when the Jα helix unfolds in the light. Caged versions of the ipaA and SsrA peptides, LOV-ipaA and LOV-SsrA, bind their targets with 49-fold and 8-fold enhanced affinity in the light, respectively. These switches can be used as general tools for light dependent co-localization, which we demonstrate with photoactivable gene transcription in yeast. PMID:22520757

  1. Mechanism-Based Tuning of a LOV Domain Photoreceptor

    SciTech Connect

    Zoltowski, B.; Vaccaro, B; Crane, B

    2009-01-01

    Phototropin-like LOV domains form a cysteinyl-flavin adduct in response to blue light but show considerable variation in output signal and the lifetime of the photo-adduct signaling state. Mechanistic studies of the slow-cycling fungal LOV photoreceptor Vivid (VVD) reveal the importance of reactive cysteine conformation, flavin electronic environment and solvent accessibility for adduct scission and thermal reversion. Proton inventory, pH effects, base catalysis and structural studies implicate flavin N5 deprotonation as rate-determining for recovery. Substitutions of active site residues Ile74, Ile85, Met135 and Met165 alter photoadduct lifetimes by over four orders of magnitude in VVD, and similar changes in other LOV proteins show analogous effects. Adduct state decay rates also correlate with changes in conformational and oligomeric properties of the protein necessary for signaling. These findings link natural sequence variation of LOV domains to function and provide a means to design broadly reactive light-sensitive probes.

  2. A C-terminal membrane association domain of phototropin 2 is necessary for chloroplast movement.

    PubMed

    Kong, Sam-Geun; Kagawa, Takatoshi; Wada, Masamitsu; Nagatani, Akira

    2013-01-01

    Phototropins (phot1 and phot2), plant-specific blue light receptor kinases, mediate a range of physiological responses in Arabidopsis, including phototropism, chloroplast photorelocation movement, stomatal opening and leaf flattening. Phototropins consist of two photoreceptive domains at their N-terminus, LOV1 (light, oxygen or voltage 1) and LOV2, and a serine/threonine kinase domain at their C-terminus. Here, we determined the molecular moiety for the membrane association of phototropins using the yeast CytoTrap and Arabidopsis protoplast systems. We then examined the physiological significance of the membrane association of phototropins. This detailed study with serial deletions narrowed down the association domain to a relatively small part of the C-terminal domain of phototropin. The functional analysis of phot2 deletion mutants in the phot2-deficient Adiantum and Arabidopsis mutants revealed that the ability to mediate the chloroplast avoidance response correlated well with phot2's membrane association, especially with the Golgi apparatus. Taken together, our data suggest that a small part of the C-terminal domain of phototropins is necessary not only for membrane association but also for the physiological activities that elicit phototropin-specific responses.

  3. Photochemical properties of the flavin mononucleotide-binding domains of the phototropins from Arabidopsis, rice, and Chlamydomonas reinhardtii.

    PubMed

    Kasahara, Masahiro; Swartz, Trevor E; Olney, Margaret A; Onodera, Akihiko; Mochizuki, Nobuyoshi; Fukuzawa, Hideya; Asamizu, Erika; Tabata, Satoshi; Kanegae, Hiromi; Takano, Makoto; Christie, John M; Nagatani, Akira; Briggs, Winslow R

    2002-06-01

    Phototropins (phot1 and phot2, formerly designated nph1 and npl1) are blue-light receptors that mediate phototropism, blue light-induced chloroplast relocation, and blue light-induced stomatal opening in Arabidopsis. Phototropins contain two light, oxygen, or voltage (LOV) domains at their N termini (LOV1 and LOV2), each a binding site for the chromophore flavin mononucleotide (FMN). Their C termini contain a serine/threonine protein kinase domain. Here, we examine the kinetic properties of the LOV domains of Arabidopsis phot1 and phot2, rice (Oryza sativa) phot1 and phot2, and Chlamydomonas reinhardtii phot. When expressed in Escherichia coli, purified LOV domains from all phototropins examined bind FMN tightly and undergo a self-contained photocycle, characterized by fluorescence and absorption changes induced by blue light (T. Sakai, T. Kagawa, M. Kasahara, T.E. Swartz, J.M. Christie, W.R. Briggs, M. Wada, K. Okada [2001] Proc Natl Acad Sci USA 98: 6969-6974; M. Salomon, J.M. Christie, E. Knieb, U. Lempert, W.R. Briggs [2000] Biochemistry 39: 9401-9410). The photocycle involves the light-induced formation of a cysteinyl adduct to the C(4a) carbon of the FMN chromophore, which subsequently breaks down in darkness. In each case, the relative quantum efficiencies for the photoreaction and the rate constants for dark recovery of LOV1, LOV2, and peptides containing both LOV domains are presented. Moreover, the data obtained from full-length Arabidopsis phot1 and phot2 expressed in insect cells closely resemble those obtained for the tandem LOV-domain fusion proteins expressed in E. coli. For both Arabidopsis and rice phototropins, the LOV domains of phot1 differ from those of phot2 in their reaction kinetic properties and relative quantum efficiencies. Thus, in addition to differing in amino acid sequence, the phototropins can be distinguished on the basis of the photochemical cycles of their LOV domains. The LOV domains of C. reinhardtii phot also undergo light

  4. The LOV domain: a chromophore module servicing multiple photoreceptors.

    PubMed

    Briggs, Winslow R

    2007-07-01

    Three different families of blue-light receptors have been characterized from higher plants: three cryptochromes, two phototropins, and the three members of the ZTL/ADO family. Phototropins and the ZTL/ADO proteins have chromophore modules, designated LOV domains, that bind flavin mononucleotide and undergo formation of a C(4a) flavin-cysteinyl adduct. All contain the highly conserved amino acid motif GXNCRFLQ. Over 90 prokaryote proteins also contain LOV domains with this motif upstream from one of several different functional groups. All of these that have been investigated to date act as photoreceptors in vitro and form the adduct upon irradiation. Four members of the class LOV-histidine kinase, one from a plant pathogen (Pseudomonas syringae), one from an animal pathogen Brucella melitensis), and two from a marine bacterium (Erythrobacter litoralis) respectively, mediate light-activated histidine phosphorylation. Decay of the adduct in darkness after a blue light pulse coincides with loss of the capacity for phosphorylation upon addition of ATP. At present, the biological role(s) of these light-sensitive proteins is under investigation.

  5. Factors That Control the Chemistry of the LOV Domain Photocycle

    PubMed Central

    Zayner, Josiah P.; Sosnick, Tobin R.

    2014-01-01

    Algae, plants, bacteria and fungi contain Light-Oxygen-Voltage (LOV) domains that function as blue light sensors to control cellular responses to light. All LOV domains contain a bound flavin chromophore that is reduced upon photon absorption and forms a reversible, metastable covalent bond with a nearby cysteine residue. In Avena sativa LOV2 (AsLOV2), the photocycle is accompanied by an allosteric conformational change that activates the attached phototropin kinase in the full-length protein. Both the conformational change and formation of the cysteinyl-flavin adduct are stabilized by the reduction of the N5 atom in the flavin’s isoalloxazine ring. In this study, we perform a mutational analysis to investigate the requirements for LOV2 to photocycle. We mutated all the residues that interact with the chromophore isoalloxazine ring to inert functional groups but none could fully inhibit the photocycle except those to the active-site cysteine. However, electronegative side chains in the vicinity of the chromophore accelerate the N5 deprotonation and the return to the dark state. Mutations to the N414 and Q513 residues identify a potential water gate and H2O coordination sites. These residues affect the electronic nature of the chromophore and photocycle time by helping catalyze the N5 reduction leading to the completion of the photocycle. In addition, we demonstrate that dehydration leads to drastically slower photocycle times. Finally, to investigate the requirements of an active-site cysteine for photocycling, we moved the nearby cysteine to alternative locations and found that some variants can still photocycle. We propose a new model of the LOV domain photocycle that involves all of these components. PMID:24475227

  6. Short LOV Proteins in Methylocystis Reveal Insight into LOV Domain Photocycle Mechanisms

    PubMed Central

    El-Arab, Kaley K.; Pudasaini, Ashutosh; Zoltowski, Brian D.

    2015-01-01

    Light Oxygen Voltage (LOV) proteins are widely used in optogenetic devices, however universal signal transduction pathways and photocycle mechanisms remain elusive. In particular, short-LOV (sLOV) proteins have been discovered in bacteria and fungi, containing only the photoresponsive LOV element without any obvious signal transduction domains. These sLOV proteins may be ideal models for LOV domain function due to their ease of study as full-length proteins. Unfortunately, characterization of such proteins remains limited to select systems. Herein, we identify a family of bacterial sLOV proteins present in Methylocystis. Sequence analysis of Methylocystis LOV proteins (McLOV) demonstrates conservation with sLOV proteins from fungal systems that employ competitive dimerization as a signaling mechanism. Cloning and characterization of McLOV proteins confirms functional dimer formation and reveal unexpected photocycle mechanisms. Specifically, some McLOV photocycles are insensitive to external bases such as imidazole, in contrast to previously characterized LOV proteins. Mutational analysis identifies a key residue that imparts insensitivity to imidazole in two McLOV homologs and affects adduct decay by two orders of magnitude. The resultant data identifies a new family of LOV proteins that indicate a universal photocycle mechanism may not be present in LOV proteins. PMID:25933162

  7. Rationally improving LOV domain–based photoswitches

    PubMed Central

    Strickland, Devin; Yao, Xiaolan; Gawlak, Grzegorz; Rosen, Michael K.; Gardner, Kevin H.; Sosnick, Tobin R.

    2010-01-01

    Genetically-encoded protein photosensors, including the LOV (light, oxygen, voltage) domain, are promising tools for engineering optical control of cellular behavior. We are only beginning to understand how to couple these light detectors to effectors of choice. We report a method that increases the dynamic range of an artificial photoswitch based on the LOV2 domain of A. sativa phototropin1 (AsLOV2). This approach can potentially be used to improve many AsLOV2-based photoswitches. PMID:20562867

  8. Photochemical Reactions of the LOV and LOV-Linker Domains of the Blue Light Sensor Protein YtvA.

    PubMed

    Choi, Seokwoo; Nakasone, Yusuke; Hellingwerf, Klaas J; Terazima, Masahide

    2016-06-07

    YtvA is a blue light sensor protein composed of an N-terminal LOV (light-oxygen-voltage) domain, a linker helix, and the C-terminal sulfate transporter and anti-σ factor antagonist domain. YtvA is believed to act as a positive regulator for light and salt stress responses by regulating the σB transcription factor. Although its biological function has been studied, the reaction dynamics and molecular mechanism underlying the function are not well understood. To improve our understanding of the signaling mechanism, we studied the reaction of the LOV domain (YLOV, amino acids 26-127), the LOV domain with its N-terminal extension (N-YLOV, amino acids 1-127), the LOV domain with its C-terminal linker helix (YLOV-linker, amino acids 26-147), and the YLOV domain with the N-terminal extension and the C-terminal linker helix (N-YLOV-linker, amino acids 1-147) using the transient grating method. The signals of all constructs showed adduct formation, thermal diffusion, and molecular diffusion. YLOV showed no change in the diffusion coefficient (D), while the other three constructs showed a significant decrease in D within ∼70 μs of photoexcitation. This indicates that conformational changes in both the N- and C-terminal helices of the YLOV domain indeed do occur. The time constant in the YtvA derivatives was much faster than the corresponding dynamics of phototropins. Interestingly, an additional reaction was observed as a volume expansion as well as a slight increase in D only when both helices were included. These findings suggest that although the rearrangement of the N- and C-terminal helices occurs independently on the fast time scale, this change induces an additional conformational change only when both helices are present.

  9. Hydration and temperature similarly affect light-induced protein structural changes in the chromophoric domain of phototropin.

    PubMed

    Iwata, Tatsuya; Yamamoto, Atsushi; Tokutomi, Satoru; Kandori, Hideki

    2007-06-12

    Phototropin is a blue-light sensor protein in plants, and LOV domain binds a flavin mononucleotide (FMN) as a chromophore. A photointermediate state, S390, is formed by light-induced adduct formation between FMN and an S-H group of nearby cysteine, which triggers protein structural changes for kinase activation in phototropin. We previously studied the low-temperature Fourier transform infrared (FTIR) spectra between the S390 and unphotolyzed states for a LOV2 domain of a phototropin from Adiantum (neo1-LOV2), and found that the protein structures of the S390 intermediate are highly temperature dependent (Iwata, T., Nozaki, D., Tokutomi, S., Kagawa, T., Wada, M., and Kandori, H. (2003) Biochemistry 42, 8183-8191). At physiological temperature, amide-I vibration at 1640-1620 cm-1 is significantly changed, implying structural alteration of beta-sheet region. Such changes are largely suppressed at low temperatures, though S390 is formed. This observation suggested the presence of progressive protein structural changes in the unique active state (S390). Here we report that the hydration dependence of the amide-I vibrational bands in neo1-LOV2 is similar to the temperature dependence. As hydration of the sample is lowered, amide-I vibration at 1640-1620 cm-1 is significantly reduced. Instead, amide-I vibration at 1694 cm-1 newly emerged at low hydration as well as at low temperature, which shows a weakened hydrogen bond in the loop region. Spectral coincidence between low hydrations and temperatures strongly suggested that protein structural changes are similarly restricted under such conditions. It is likely that protein fluctuations are prerequisite for formation of the active state of neo1-LOV2.

  10. Allosterically regulated unfolding of the A'α helix exposes the dimerization site of the blue-light-sensing aureochrome-LOV domain.

    PubMed

    Herman, Elena; Kottke, Tilman

    2015-02-24

    Aureochromes have been shown to act as blue-light-regulated transcription factors in algae in the absence of phototropins. Aureochromes comprise a light-, oxygen-, or voltage-sensitive (LOV) domain as a sensory module binding the flavin chromophore and a basic region leucine zipper (bZIP) domain as an effector. The domain arrangement in aureochromes with an N-terminal effector is inversed to other LOV proteins. To clarify the role of the linking A'α helix in signaling, we have investigated the LOV domain of aureochrome1a from the diatom alga Phaeodactylum tricornutum without the N-terminal A'α helix but with the C-terminal Jα helix. Results were analyzed in comparison to those previously obtained on the LOV domain with both flanking helices and on the LOV domain with the A'α helix but without the Jα helix. Fourier transform infrared difference spectroscopy provides evidence by a band at 1656 cm(-1) that the A'α helix unfolds in response to light. This unfolding takes place only in the presence and as a consequence of the unfolding of the Jα helix, which points to an allosteric regulation. Size exclusion chromatography shows the LOV domain to be dimeric in the absence and monomeric in the presence of the A'α helix, implying that the folded helix covers the dimerization site. Therefore, the A'α helix directly modulates the oligomerization state of the LOV domain, whereas the Jα helix acts as an allosteric regulator. Both the allosteric control and the light-induced dimerization have not been observed in phototropin-LOV2 and point to a different signaling mechanism within the full-length proteins.

  11. Spatiotemporal control of small GTPases with light using the LOV domain.

    PubMed

    Wu, Yi I; Wang, Xiaobo; He, Li; Montell, Denise; Hahn, Klaus M

    2011-01-01

    Signaling networks in living systems are coordinated through subcellular compartmentalization and precise timing of activation. These spatiotemporal aspects ensure the fidelity of signaling while contributing to the diversity and specificity of downstream events. This is studied through development of molecular tools that generate localized and precisely timed protein activity in living systems. To study the molecular events responsible for cytoskeletal changes in real time, we generated versions of Rho family GTPases whose interactions with downstream effectors is controlled by light. GTPases were grafted to the phototropin LOV (light, oxygen, or voltage) domain (Huala, E., Oeller, P. W., Liscum, E., Han, I., Larsen, E., and Briggs, W. R. (1997). Arabidopsis NPH1: A protein kinase with a putative redox-sensing domain. Science278, 2120-2123.) via an alpha helix on the LOV C-terminus (Wu, Y. I., Frey, D., Lungu, O. I., Jaehrig, A., Schlichting, I., Kuhlman, B., and Hahn, K. M. (2009). A genetically encoded photoactivatable Rac controls the motility of living cells. Nature461, 104-108.). The LOV domain sterically blocked the GTPase active site until it was irradiated. Exposure to 400-500nm light caused unwinding of the helix linking the LOV domain to the GTPase, relieving steric inhibition. The change was reversible and repeatable, and the protein could be returned to its inactive state simply by turning off the light. The LOV domain incorporates a flavin as the active chromophore. This naturally occurring molecule is incorporated simply upon expression of the LOV fusion in cells or animals, permitting ready control of GTPase function in different systems. In cultured single cells, light-activated Rac leads to membrane ruffling, protrusion, and migration. In collectively migrating border cells in the Drosophila ovary, focal activation of photoactivatable Rac (PA-Rac) in a single cell is sufficient to redirect the entire group. PA-Rac in a single cell also rescues the

  12. Phototropin and light-signaling in phototropism.

    PubMed

    Kimura, Mitsuhiro; Kagawa, Takatoshi

    2006-10-01

    Blue-light-induced phototropism in higher plants is regulated by phototropin, which is a photoreceptor kinase that contains a flavin mononucleotide (FMN). Recently, it was found that this kinase is inhibited by the binding of the LOV2 (light-oxygen-voltage2) domain in the dark but that its activity is increased in the light by the release of the LOV2 domain. Phototropin-associated proteins have been identified, although the proteins that are phosphorylated by phototropin are still unknown. The asymmetrical auxin distribution caused by unilateral irradiation suggests that differential growth is induced by a difference in auxin-regulated gene expression between the shaded and illuminated sides of plant organs. Transcription-related factors, such as NPH4/ARF7, MSG2/IAA19 and SCF(TIR1), play key roles in this process.

  13. Absorption and emission spectroscopic characterisation of combined wildtype LOV1-LOV2 domain of phot from Chlamydomonas reinhardtii.

    PubMed

    Song, S-H; Dick, B; Zirak, P; Penzkofer, A; Schiereis, T; Hegemann, P

    2005-10-03

    An absorption and emission spectroscopic characterisation of the combined wild-type LOV1-LOV2 domain string (abbreviated LOV1/2) of phot from the green alga Chlamydomonas reinhardtii is carried out at pH 8. A LOV1/2-MBP fusion protein (MBP=maltose binding protein) and LOV1/2 with a His-tag at the C-terminus (LOV1/2-His) expressed in an Escherichia coli strain are investigated. Blue-light photo-excitation generates a non-fluorescent intermediate photoproduct (flavin-C(4a)-cysteinyl adduct with absorption peak at 390 nm). The photo-cycle dynamics is studied by dark-state absorption and fluorescence measurement, by following the temporal absorption and emission changes under blue and violet light exposure, and by measuring the temporal absorption and fluorescence recovery after light exposure. The fluorescence quantum yield, phi(F), of the dark adapted samples is phi(F)(LOV1/2-His) approximately 0.15 and phi(F)(LOV1/2-MBP) approximately 0.17. A bi-exponential absorption recovery after light exposure with a fast (in the several 10-s range) and a slow component (in the near 10-min range) are resolved. The quantum yield of photo-adduct formation, phi(Ad), is extracted from excitation intensity dependent absorption measurements. It decreases somewhat with rising excitation intensity. The behaviour of the combined wildtype LOV1-LOV2 double domains is compared with the behaviour of the separate LOV1 and LOV2 domains.

  14. Femtosecond to Millisecond Dynamics of Light Induced Allostery in the Avena sativa LOV Domain.

    PubMed

    Gil, Agnieszka A; Laptenok, Sergey P; French, Jarrod B; Iuliano, James N; Lukacs, Andras; Hall, Christopher R; Sazanovich, Igor V; Greetham, Gregory M; Bacher, Adelbert; Illarionov, Boris; Fischer, Markus; Tonge, Peter J; Meech, Stephen R

    2017-02-09

    The rational engineering of photosensor proteins underpins the field of optogenetics, in which light is used for spatiotemporal control of cell signaling. Optogenetic elements function by converting electronic excitation of an embedded chromophore into structural changes on the microseconds to seconds time scale, which then modulate the activity of output domains responsible for biological signaling. Using time-resolved vibrational spectroscopy coupled with isotope labeling, we have mapped the structural evolution of the LOV2 domain of the flavin binding phototropin Avena sativa (AsLOV2) over 10 decades of time, reporting structural dynamics between 100 fs and 1 ms after optical excitation. The transient vibrational spectra contain contributions from both the flavin chromophore and the surrounding protein matrix. These contributions are resolved and assigned through the study of four different isotopically labeled samples. High signal-to-noise data permit the detailed analysis of kinetics associated with the light activated structural evolution. A pathway for the photocycle consistent with the data is proposed. The earliest events occur in the flavin binding pocket, where a subpicosecond perturbation of the protein matrix occurs. In this perturbed environment, the previously characterized reaction between triplet state isoalloxazine and an adjacent cysteine leads to formation of the adduct state; this step is shown to exhibit dispersive kinetics. This reaction promotes coupling of the optical excitation to successive time-dependent structural changes, initially in the β-sheet and then α-helix regions of the AsLOV2 domain, which ultimately gives rise to Jα-helix unfolding, yielding the signaling state. This model is tested through point mutagenesis, elucidating in particular the key mediating role played by Q513.

  15. Functional and topological diversity of LOV domain photoreceptors

    PubMed Central

    Glantz, Spencer T.; Carpenter, Eric J.; Melkonian, Michael; Boyden, Edward S.; Wong, Gane Ka-Shu; Chow, Brian Y.

    2016-01-01

    Light–oxygen–voltage sensitive (LOV) flavoproteins are ubiquitous photoreceptors that mediate responses to environmental cues. Photosensory inputs are transduced into signaling outputs via structural rearrangements in sensor domains that consequently modulate the activity of an effector domain or multidomain clusters. Establishing the diversity in effector function and sensor–effector topology will inform what signaling mechanisms govern light-responsive behaviors across multiple kingdoms of life and how these signals are transduced. Here, we report the bioinformatics identification of over 6,700 candidate LOV domains (including over 4,000 previously unidentified sequences from plants and protists), and insights from their annotations for ontological function and structural arrangements. Motif analysis identified the sensors from ∼42 million ORFs, with strong statistical separation from other flavoproteins and non-LOV members of the structurally related Per-aryl hydrocarbon receptor nuclear translocator (ARNT)-Sim family. Conserved-domain analysis determined putative light-regulated function and multidomain topologies. We found that for certain effectors, sensor–effector linker length is discretized based on both phylogeny and the preservation of α-helical heptad repeats within an extended coiled-coil linker structure. This finding suggests that preserving sensor–effector orientation is a key determinant of linker length, in addition to ancestry, in LOV signaling structure–function. We found a surprisingly high prevalence of effectors with functions previously thought to be rare among LOV proteins, such as regulators of G protein signaling, and discovered several previously unidentified effectors, such as lipases. This work highlights the value of applying genomic and transcriptomic technologies to diverse organisms to capture the structural and functional variation in photosensory proteins that are vastly important in adaptation, photobiology, and

  16. Functional and topological diversity of LOV domain photoreceptors.

    PubMed

    Glantz, Spencer T; Carpenter, Eric J; Melkonian, Michael; Gardner, Kevin H; Boyden, Edward S; Wong, Gane Ka-Shu; Chow, Brian Y

    2016-03-15

    Light-oxygen-voltage sensitive (LOV) flavoproteins are ubiquitous photoreceptors that mediate responses to environmental cues. Photosensory inputs are transduced into signaling outputs via structural rearrangements in sensor domains that consequently modulate the activity of an effector domain or multidomain clusters. Establishing the diversity in effector function and sensor-effector topology will inform what signaling mechanisms govern light-responsive behaviors across multiple kingdoms of life and how these signals are transduced. Here, we report the bioinformatics identification of over 6,700 candidate LOV domains (including over 4,000 previously unidentified sequences from plants and protists), and insights from their annotations for ontological function and structural arrangements. Motif analysis identified the sensors from ∼42 million ORFs, with strong statistical separation from other flavoproteins and non-LOV members of the structurally related Per-aryl hydrocarbon receptor nuclear translocator (ARNT)-Sim family. Conserved-domain analysis determined putative light-regulated function and multidomain topologies. We found that for certain effectors, sensor-effector linker length is discretized based on both phylogeny and the preservation of α-helical heptad repeats within an extended coiled-coil linker structure. This finding suggests that preserving sensor-effector orientation is a key determinant of linker length, in addition to ancestry, in LOV signaling structure-function. We found a surprisingly high prevalence of effectors with functions previously thought to be rare among LOV proteins, such as regulators of G protein signaling, and discovered several previously unidentified effectors, such as lipases. This work highlights the value of applying genomic and transcriptomic technologies to diverse organisms to capture the structural and functional variation in photosensory proteins that are vastly important in adaptation, photobiology, and optogenetics.

  17. Unique temperature dependence in the adduct formation between FMN and cysteine S-H group in the LOV2 domain of Adiantum phytochrome3

    NASA Astrophysics Data System (ADS)

    Nozaki, Dai; Iwata, Tatsuya; Tokutomi, Satoru; Kandori, Hideki

    2005-07-01

    In a plant blue-light receptor phototropin, the primary reaction is an adduct formation between the flavin chromophore and a cysteine S-H group. In the case of a LOV2 domain of Adiantum phytochrome3 (phy3-LOV2), we found that Arrhenius plots of the efficiency of the adduct formation provide two kinks at about 190 and 270 K, and a negative activation energy was obtained between the temperatures. They are close to the transition temperatures of protein structural changes observed by the low-temperature difference FTIR spectroscopy. We concluded that the observed temperature dependence of the reaction efficiency in a restricted protein environment originates from protein fluctuation that mainly reflects secondary structure.

  18. Light-Induced Subunit Dissociation by a LOV domain Photoreceptor from Rhodobacter sphaeroides

    PubMed Central

    Conrad, Karen S.; Bilwes, Alexandrine M.; Crane, Brian R.

    2013-01-01

    Light-oxygen-voltage (LOV) domains bind a flavin chromophore to serve as blue light sensors in a wide range of eukaryotic and prokaryotic proteins. LOV domains are associated with a variable effector domain or a separate protein signaling partner to execute a wide variety of functions that include regulation of kinases, generation of antisigma-factor antagonists, and regulation of circadian clocks. Here we present the crystal structure, photocycle kinetics, association properties, and spectroscopic features of a full-length LOV protein from Rhodobacter sphaeroides (RsLOV). RsLOV exhibits N-terminal and C-terminal helical extensions that form an unusual helical bundle at its dimer interface with some resemblance to the helical transducer of sensory rhodopsin II. The blue light-induced conformational changes of RsLOV revealed from a comparison of light and dark state crystal structures support a shared signaling mechanism of LOV domain proteins that originates with the light-induced formation of a flavin-cysteinyl photoadduct. Adduct formation disrupts hydrogen bonding in the active site and propagates structural changes through the LOV domain core to the N- and C-terminal extensions. Single residue variants in the active site and dimer interface of RsLOV alter photoadduct lifetimes and induce structural changes that perturb oligomeric state. Size exclusion chromatography, multi-angle light scattering, small-angle X-ray scattering and cross-linking studies indicate that RsLOV dimerizes in the dark, but upon light excitation, dissociates into monomers. This light-induced switch in oligomeric state may prove useful for engineering molecular associations in controlled cellular settings. PMID:23252338

  19. A eukaryotic LOV-histidine kinase with circadian clock function in the picoalga Ostreococcus.

    PubMed

    Djouani-Tahri, El-Batoul; Christie, John M; Sanchez-Ferandin, Sophie; Sanchez, Frédéric; Bouget, François-Yves; Corellou, Florence

    2011-02-01

    The marine environment has unique properties of light transmission, with an attenuation of long wavelengths within the first meters of the water column. Marine organisms have therefore evolved specific blue-light receptors such as aureochromes to absorb shorter-wavelength light. Here, we identify and characterize a light, oxygen, or voltage sensing (LOV) containing histidine kinase (LOV-HK) that functions as a new class of eukaryotic blue-light receptor in the pico-phytoplanktonic cell Ostreococcus tauri. This LOV-HK is related to the large family of LOV-HKs found in prokaryotes. Phylogenetic analysis indicates that the LOV domains from LOV-HKs, including O. tauri LOV-HK, and phototropins (phot; plant and green algal LOV serine/threonine kinases) have different evolutionary histories. Photochemical analysis shows that the LOV domain of LOV-HK binds a flavin cofactor and absorbs blue light with a fast photocycle compared with its prokaryotic counterparts. Ostreococcus tauri LOV-HK expression is induced by blue light and is under circadian control. Further, both overexpression and downregulation of LOV-HK result in arrhythmia of the circadian reporter CCA1:Luc under constant blue light. In contrast, photochemical inactivation of O. tauri LOV-HK is without effect, demonstrating its importance for function of the circadian clock under blue light. Overexpression/downregulation of O. tauriLOV-HK alters CCA1 rhythmicity under constant red light, irrespective of LOV-HK's photochemical reactivity, suggesting that O. tauri LOV-HK also participates in regulation of the circadian clock independent of its blue-light-sensing property. Molecular characterization of O. tauri LOV-HK demonstrates that this type of photoreceptor family is not limited to prokaryotes. © 2011 The Authors. The Plant Journal © 2011 Blackwell Publishing Ltd.

  20. Kinetics of the LOV domain of ZEITLUPE determine its circadian function in Arabidopsis.

    PubMed

    Pudasaini, Ashutosh; Shim, Jae Sung; Song, Young Hun; Shi, Hua; Kiba, Takatoshi; Somers, David E; Imaizumi, Takato; Zoltowski, Brian D

    2017-02-28

    A LOV (Light, Oxygen, or Voltage) domain containing blue-light photoreceptor ZEITLUPE (ZTL) directs circadian timing by degrading clock proteins in plants. Functions hinge upon allosteric differences coupled to the ZTL photocycle; however, structural and kinetic information was unavailable. Herein, we tune the ZTL photocycle over two orders of magnitude. These variants reveal that ZTL complexes with targets independent of light, but dictates enhanced protein degradation in the dark. In vivo experiments definitively show photocycle kinetics dictate the rate of clock component degradation, thereby impacting circadian period. Structural studies demonstrate that photocycle dependent activation of ZTL depends on an unusual dark-state conformation of ZTL. Crystal structures of ZTL LOV domain confirm delineation of structural and kinetic mechanisms and identify an evolutionarily selected allosteric hinge differentiating modes of PAS/LOV signal transduction. The combined biochemical, genetic and structural studies provide new mechanisms indicating how PAS/LOV proteins integrate environmental variables in complex networks.

  1. Estimation of Available Free Energy in a LOV2-Jα Photoswitch

    PubMed Central

    Yao, Xiaolan; Rosen, Michael K.; Gardner, Kevin H.

    2008-01-01

    Protein photosensors provide versatile tools to study ligand-regulated allostery and signaling. Fundamental to these processes is the amount of energy that can be provided by a photosensor to control downstream signaling events. Such regulation is exemplified by the phototropins, plant serine/threonine kinases that are activated by blue light via conserved LOV (Light, Oxygen and Voltage) domains. The core photosensor of oat phototropin 1 is a LOV domain that interacts in light-dependent fashion with an adjacent α-helix (Jα) to control kinase activity. We used solution NMR measurements to quantify the free energy of the LOV domain:Jα helix binding equilibrium in the dark and lit states. These data indicate that light shifts this equilibrium by ~3.8 kcal mol−1, quantifying the energy available through LOV-Jα for light-driven allosteric regulation. This study provides insight into the energetics of light sensing by phototropins and benchmark values for engineering photoswitchable systems based on the LOV-Jα interaction. PMID:18604202

  2. Estimation of the available free energy in a LOV2-J alpha photoswitch.

    PubMed

    Yao, Xiaolan; Rosen, Michael K; Gardner, Kevin H

    2008-08-01

    Protein photosensors are versatile tools for studying ligand-regulated allostery and signaling. Fundamental to these processes is the amount of energy that can be provided by a photosensor to control downstream signaling events. Such regulation is exemplified by the phototropins--plant serine/threonine kinases that are activated by blue light via conserved LOV (light, oxygen and voltage) domains. The core photosensor of oat phototropin 1 is a LOV domain that interacts in a light-dependent fashion with an adjacent alpha-helix (J alpha) to control kinase activity. We used solution NMR measurements to quantify the free energy of the LOV domain-J alpha-helix binding equilibrium in the dark and lit states. These data indicate that light shifts this equilibrium by approximately 3.8 kcal mol(-1), thus quantifying the energy available through LOV-J alpha for light-driven allosteric regulation. This study provides insight into the energetics of light sensing by phototropins and benchmark values for engineering photoswitchable systems based on the LOV-J alpha interaction.

  3. Biochemical characterization of the minimal polyketide synthase domains in the lovastatin nonaketide synthase LovB.

    PubMed

    Ma, Suzanne M; Tang, Yi

    2007-06-01

    The biosynthesis of lovastatin in Aspergillus terreus requires two megasynthases. The lovastatin nonaketide synthase, LovB, synthesizes the intermediate dihydromonacolin L using nine malonyl-coenzyme A molecules, and is a reducing, iterative type I polyketide synthase. The iterative type I polyketide synthase is mechanistically different from bacterial type I polyketide synthases and animal fatty acid synthases. We have cloned the minimal polyketide synthase domains of LovB as standalone proteins and assayed their activities and substrate specificities. The didomain proteins ketosynthase-malonyl-coenzyme A:acyl carrier protein acyltransferase (KS-MAT) and acyl carrier protein-condensation (ACP-CON) domain were expressed solubly in Escherichia coli. The monodomains MAT, ACP and CON were also obtained as soluble proteins. The MAT domain can be readily labeled by [1,2-(14)C]malonyl-coenzyme A and can transfer the acyl group to both the cognate LovB ACP and heterologous ACPs from bacterial type I and type II polyketide synthases. Using the LovB ACP-CON didomain as an acyl acceptor, LovB MAT transferred malonyl and acetyl groups with k(cat)/K(m) values of 0.62 min(-1).mum(-1) and 0.032 min(-1).mum(-1), respectively. The LovB MAT domain was able to substitute the Streptomyces coelicolor FabD in supporting product turnover in a bacterial type II minimal polyketide synthase assay. The activity of the KS domain was assayed independently using a KS-MAT (S656A) mutant in which the MAT domain was inactivated. The KS domain displayed no activity towards acetyl groups, but was able to recognize malonyl groups in the absence of cerulenin. The relevance of these finding to the priming mechanism of fungal polyketide synthase is discussed.

  4. Fluorescence Imaging-Based High-Throughput Screening of Fast- and Slow-Cycling LOV Proteins

    PubMed Central

    Kawano, Fuun; Aono, Yuki; Suzuki, Hideyuki; Sato, Moritoshi

    2013-01-01

    Light-oxygen-voltage (LOV) domains function as blue light-inducible molecular switches. The photosensory LOV domains derived from plants and fungi have provided an indispensable tool for optogenetics. Here we develop a high-throughput screening system to efficiently improve switch-off kinetics of LOV domains. The present system is based on fluorescence imaging of thermal reversion of a flavin cofactor bound to LOV domains. We conducted multi site-directed random mutagenesis of seven amino acid residues surrounding the flavin cofactor of the second LOV domain derived from Avena sativa phototropin 1 (AsLOV2). The gene library was introduced into Escherichia coli cells. Then thermal reversion of AsLOV2 variants, respectively expressed in different bacterial colonies on agar plate, was imaged with a stereoscopic fluorescence microscope. Based on the mutagenesis and imaging-based screening, we isolated 12 different variants showing substantially faster thermal reversion kinetics than wild-type AsLOV2. Among them, AsLOV2-V416T exhibited thermal reversion with a time constant of 2.6 s, 21-fold faster than wild-type AsLOV2. With a slight modification of the present approach, we also have efficiently isolated 8 different decelerated variants, represented by AsLOV2-V416L that exhibited thermal reversion with a time constant of 4.3×103 s (78-fold slower than wild-type AsLOV2). The present approach based on fluorescence imaging of the thermal reversion of the flavin cofactor is generally applicable to a variety of blue light-inducible molecular switches and may provide a new opportunity for the development of molecular tools for emerging optogenetics. PMID:24367542

  5. Photocontrolled Exposure of Pro‐apoptotic Peptide Sequences in LOV Proteins Modulates Bcl‐2 Family Interactions

    PubMed Central

    Mart, Robert J.; Meah, Dilruba

    2015-01-01

    Abstract LOV domains act as biomolecular sensors for light, oxygen or the environment's redox potential. Conformational changes upon the formation of a covalent cysteinyl flavin adduct are propagated through hydrogen‐bonding networks in the core of designed hybrid phototropin LOV2 domains that incorporate the Bcl homology region 3 (BH3) of the key pro‐apoptotic protein BH3‐interacting‐domain death agonist (BID). The resulting change in conformation of a flanking amphiphilic α‐helix creates a light‐dependent optogenetic tool for the modulation of interactions with the anti‐apoptotic B‐cell leukaemia‐2 (Bcl‐2) family member Bcl‐xL. PMID:26493687

  6. Light-induced structural changes in the LOV2 domain of Adiantum phytochrome3 studied by low-temperature FTIR and UV-visible spectroscopy.

    PubMed

    Iwata, Tatsuya; Nozaki, Dai; Tokutomi, Satoru; Kagawa, Takatoshi; Wada, Masamitsu; Kandori, Hideki

    2003-07-15

    Phototropin (Phot) is a blue-light receptor in plants. The molecule has two FMN (flavin mononucleotide) binding domains named LOV (light-, oxygen-, and voltage-sensing), which is a subset of the PAS (Per-Arnt-Sim) superfamily. Illumination of the phot-LOV domains in the dark state (D447) produces a covalent C(4a) flavin-cysteinyl adduct (S390) via a triplet excited state (L660), which reverts to D447 in the dark. In this work, we studied the light-induced structural changes in the LOV2 domain of Adiantum phytochrome3 (phy3), which is a fusion protein of phot containing the phytochrome chromophoric domain, by low-temperature UV-visible and FTIR spectroscopy. UV-visible spectroscopy detected only one intermediate state, S390, in the temperature range from 77 to 295 K, indicating that the adduct is produced even at temperatures as low as 77 K, although a portion of D447 cannot be converted to S390 at low temperatures possibly because of motional freezing. In the whole temperature range, FTIR spectra in the S-H stretching frequency region showed that Cys966 of phy3-LOV2 is protonated in D447 and unprotonated on illumination, supporting adduct formation. The pK(a) of the S-H group in D447 is estimated to be >10. FTIR spectra also showed the light-induced appearance of a positive peak around 3621 cm(-1) in the whole temperature range, indicating that adduct formation accompanies rearrangement of a hydrogen bond of a water molecule(s), which can be either water25, water45, or both, near the chromophore. In contrast to the weak temperature dependence of the spectral changes in the UV-visible absorption and the FTIR of both S-H and O-H stretching bands, light-induced changes in the amide I vibration that probes protein backbone structure vary significantly with the increase in temperature. The spectral changes suggest that light excitation of FMN loosens the local structure around it, particularly in turns, in the early stages and that another change subsequently takes

  7. Structure of a flavin-binding plant photoreceptor domain: Insights into light-mediated signal transduction

    PubMed Central

    Crosson, Sean; Moffat, Keith

    2001-01-01

    Phototropin, a major blue-light receptor for phototropism in seed plants, exhibits blue-light-dependent autophosphorylation and contains two light, oxygen, or voltage (LOV) domains and a serine/threonine kinase domain. The LOV domains share homology with the PER-ARNT-SIM (PAS) superfamily, a diverse group of sensor proteins. Each LOV domain noncovalently binds a single FMN molecule and exhibits reversible photochemistry in vitro when expressed separately or in tandem. We have determined the crystal structure of the LOV2 domain from the phototropin segment of the chimeric fern photoreceptor phy3 to 2.7-Å resolution. The structure constitutes an FMN-binding fold that reveals how the flavin cofactor is embedded in the protein. The single LOV2 cysteine residue is located 4.2 Å from flavin atom C(4a), consistent with a model in which absorption of blue light induces formation of a covalent cysteinyl-C(4a) adduct. Residues that interact with FMN in the phototropin segment of the chimeric fern photoreceptor (phy3) LOV2 are conserved in LOV domains from phototropin of other plant species and from three proteins involved in the regulation of circadian rhythms in Arabidopsis and Neurospora. This conservation suggests that these domains exhibit the same overall fold and share a common mechanism for flavin binding and light-induced signaling. PMID:11248020

  8. Kinetics of the LOV domain of ZEITLUPE determine its circadian function in Arabidopsis

    PubMed Central

    Pudasaini, Ashutosh; Shim, Jae Sung; Song, Young Hun; Shi, Hua; Kiba, Takatoshi; Somers, David E; Imaizumi, Takato; Zoltowski, Brian D

    2017-01-01

    A LOV (Light, Oxygen, or Voltage) domain containing blue-light photoreceptor ZEITLUPE (ZTL) directs circadian timing by degrading clock proteins in plants. Functions hinge upon allosteric differences coupled to the ZTL photocycle; however, structural and kinetic information was unavailable. Herein, we tune the ZTL photocycle over two orders of magnitude. These variants reveal that ZTL complexes with targets independent of light, but dictates enhanced protein degradation in the dark. In vivo experiments definitively show photocycle kinetics dictate the rate of clock component degradation, thereby impacting circadian period. Structural studies demonstrate that photocycle dependent activation of ZTL depends on an unusual dark-state conformation of ZTL. Crystal structures of ZTL LOV domain confirm delineation of structural and kinetic mechanisms and identify an evolutionarily selected allosteric hinge differentiating modes of PAS/LOV signal transduction. The combined biochemical, genetic and structural studies provide new mechanisms indicating how PAS/LOV proteins integrate environmental variables in complex networks. DOI: http://dx.doi.org/10.7554/eLife.21646.001 PMID:28244872

  9. Lighting Up Clostridium Difficile: Reporting Gene Expression Using Fluorescent Lov Domains

    PubMed Central

    Buckley, Anthony M.; Jukes, Caitlin; Candlish, Denise; Irvine, June J.; Spencer, Janice; Fagan, Robert P.; Roe, Andrew J.; Christie, John M.; Fairweather, Neil F.; Douce, Gillian R.

    2016-01-01

    The uses of fluorescent reporters derived from green fluorescent protein have proved invaluable for the visualisation of biological processes in bacteria grown under aerobic conditions. However, their requirement for oxygen has limited their application in obligate anaerobes such as Clostridium difficile. Fluorescent proteins derived from Light, Oxygen or Voltage sensing (LOV) domains have been shown to bridge this limitation, but their utility as translational fusions to monitor protein expression and localisation in a strict anaerobic bacterium has not been reported. Here we demonstrate the utility of phiLOV in three species of Clostridium and its application as a marker of real-time protein translation and dynamics through genetic fusion with the cell division protein, FtsZ. Time lapse microscopy of dividing cells suggests that Z ring assembly arises through the extension of the FtsZ arc starting from one point on the circumference. Furthermore, through incorporation of phiLOV into the flagella subunit, FliC, we show the potential of bacterial LOV-based fusion proteins to be successfully exported to the extracellular environment. PMID:26996606

  10. Blue light-induced LOV domain dimerization enhances the affinity of Aureochrome 1a for its target DNA sequence

    PubMed Central

    Heintz, Udo; Schlichting, Ilme

    2016-01-01

    The design of synthetic optogenetic tools that allow precise spatiotemporal control of biological processes previously inaccessible to optogenetic control has developed rapidly over the last years. Rational design of such tools requires detailed knowledge of allosteric light signaling in natural photoreceptors. To understand allosteric communication between sensor and effector domains, characterization of all relevant signaling states is required. Here, we describe the mechanism of light-dependent DNA binding of the light-oxygen-voltage (LOV) transcription factor Aureochrome 1a from Phaeodactylum tricornutum (PtAu1a) and present crystal structures of a dark state LOV monomer and a fully light-adapted LOV dimer. In combination with hydrogen/deuterium-exchange, solution scattering data and DNA-binding experiments, our studies reveal a light-sensitive interaction between the LOV and basic region leucine zipper DNA-binding domain that together with LOV dimerization results in modulation of the DNA affinity of PtAu1a. We discuss the implications of these results for the design of synthetic LOV-based photosensors with application in optogenetics. DOI: http://dx.doi.org/10.7554/eLife.11860.001 PMID:26754770

  11. An auxilin-like J-domain protein, JAC1, regulates phototropin-mediated chloroplast movement in Arabidopsis.

    PubMed

    Suetsugu, Noriyuki; Kagawa, Takatoshi; Wada, Masamitsu

    2005-09-01

    The ambient-light conditions mediate chloroplast relocation in plant cells. Under the low-light conditions, chloroplasts accumulate in the light (accumulation response), while under the high-light conditions, they avoid the light (avoidance response). In Arabidopsis (Arabidopsis thaliana), the accumulation response is mediated by two blue-light receptors, termed phototropins (phot1 and phot2) that act redundantly, and the avoidance response is mediated by phot2 alone. A mutant, J-domain protein required for chloroplast accumulation response 1 (jac1), lacks the accumulation response under weak blue light but shows a normal avoidance response under strong blue light. In dark-adapted wild-type cells, chloroplasts accumulate on the bottom of cells. Both the jac1 and phot2 mutants are defective in this chloroplast movement in darkness. Positional cloning of JAC1 reveals that this gene encodes a J-domain protein, resembling clathrin-uncoating factor auxilin at its C terminus. The amounts of JAC1 transcripts and JAC1 proteins are not regulated by light and by phototropins. A green fluorescent protein-JAC1 fusion protein showed a similar localization pattern to green fluorescent protein alone in a transient expression assay using Arabidopsis mesophyll cells and onion (Allium cepa) epidermal cells, suggesting that the JAC1 protein may be a soluble cytosolic protein. Together, these results suggest that JAC1 is an essential component of phototropin-mediated chloroplast movement.

  12. First evidence for phototropin-related blue-light receptors in prokaryotes.

    PubMed Central

    Losi, Aba; Polverini, Eugenia; Quest, Benjamin; Gärtner, Wolfgang

    2002-01-01

    A prokaryotic protein, YtvA from Bacillus subtilis, was found to possess a light, oxygen, voltage (LOV) domain sharing high homology with the photoactive, flavin mononucleotide (FMN)-binding LOV domains of phototropins (phot), blue-light photoreceptors for phototropism in higher plants. Computer-based three-dimensional modeling suggests that YtvA-LOV binds FMN in a similar pocket as phot-LOVs. Recombinant YtvA indeed exhibits the same spectroscopical features and blue-light-induced photochemistry as phot-LOVs, with the reversible formation of a blue-shifted photoproduct, assigned to an FMN-cysteine thiol adduct (Thio383). By means of laser-flash photolysis and time-resolved optoacoustic experiments, we measured the quantum yield of formation for Thio383, Phi(Thio) = 0.49, and the enthalpy change, DeltaH(Thio) = 135 kJ/mol, with respect to the parent state. The formation of Thio383 is accompanied by a considerable volume contraction, DeltaV(Thio) = -13.5 ml/mol. Similar to phot-LOVs, Thio383 is formed from the decay of a red-shifted transient species, T650, within 2 micros. In both YtvA and free FMN, this transient has an enthalpy content of approximately 200 kJ/mol, and its formation is accompanied by a small contraction, DeltaV(T) approximately -1.5 ml/mol, supporting the assignment of T650 to the FMN triplet state, as suggested by spectroscopical evidences. These are the first studies indicating that phototropin-related, blue-light receptors may exist also in prokaryotes, besides constituting a steadily growing family in plants. PMID:11964249

  13. All-optical switching in plant blue light photoreceptor phototropin.

    PubMed

    Roy, Sukhdev; Kulshrestha, Kapil

    2006-12-01

    We theoretically analyze all-optical switching in the recently characterized LOV2 domain from Avena sativa (oat) phot1 phototropin, a blue-light plant photoreceptor, based on nonlinear intensity-induced excited-state absorption. The transmission of a cw probe laser beam at 660 nm corresponding to the peak absorption of the first excited L-state, through the LOV2 sample, is switched by a pulsed pump laser beam at 442 nm that corresponds to the maximum initial D state absorption. The switching characteristics have been analyzed using the rate equation approach, considering all the three intermediate states and transitions in the LOV2 photocycle. It is shown that for a given pump pulse intensity, there is an optimum pump pulsewidth for which the switching contrast is maximum. It is shown that the probe laser beam can be completely switched off (100% modulation) by the pump laser beam at 50 kW/cm2 for a concentration of 1 mM with sample thickness of 5.5 mm. The switching characteristics are sensitive to various parameters such as concentration, rate constant of L-state, peak pump intensity and pump pulse width. At typical values, the switch-off and switch-on time is 1.6 and 22.3 micros, respectively. The switching characteristics have also been used to design all-optical NOT and the universal NOR and NAND logic gates.

  14. A dominant mutation in the light-oxygen and voltage2 domain vicinity impairs phototropin1 signaling in tomato.

    PubMed

    Sharma, Sulabha; Kharshiing, Eros; Srinivas, Ankanagari; Zikihara, Kazunori; Tokutomi, Satoru; Nagatani, Akira; Fukayama, Hiroshi; Bodanapu, Reddaiah; Behera, Rajendra K; Sreelakshmi, Yellamaraju; Sharma, Rameshwar

    2014-04-01

    In higher plants, blue light (BL) phototropism is primarily controlled by the phototropins, which are also involved in stomatal movement and chloroplast relocation. These photoresponses are mediated by two phototropins, phot1 and phot2. Phot1 mediates responses with higher sensitivity than phot2, and phot2 specifically mediates chloroplast avoidance and dark positioning responses. Here, we report the isolation and characterization of a Nonphototropic seedling1 (Nps1) mutant of tomato (Solanum lycopersicum). The mutant is impaired in low-fluence BL responses, including chloroplast accumulation and stomatal opening. Genetic analyses show that the mutant locus is dominant negative in nature. In dark-grown seedlings of the Nps1 mutant, phot1 protein accumulates at a highly reduced level relative to the wild type and lacks BL-induced autophosphorylation. The mutant harbors a single glycine-1484-to-alanine transition in the Hinge1 region of a phot1 homolog, resulting in an arginine-to-histidine substitution (R495H) in a highly conserved A'α helix proximal to the light-oxygen and voltage2 domain of the translated gene product. Significantly, the R495H substitution occurring in the Hinge1 region of PHOT1 abolishes its regulatory activity in Nps1 seedlings, thereby highlighting the functional significance of the A'α helix region in phototropic signaling of tomato.

  15. Functional characterization of a constitutively active kinase variant of Arabidopsis phototropin 1.

    PubMed

    Petersen, Jan; Inoue, Shin-Ichiro; Kelly, Sharon M; Sullivan, Stuart; Kinoshita, Toshinori; Christie, John M

    2017-08-18

    Phototropins (phots) are plasma membrane-associated serine/threonine kinases that coordinate a range of processes linked to optimizing photosynthetic efficiency in plants. These photoreceptors contain two light-, oxygen-, or voltage-sensing (LOV) domains within their N terminus, with each binding one molecule of flavin mononucleotide as a UV/blue light-absorbing chromophore. Although phots contain two LOV domains, light-induced activation of the C-terminal kinase domain and subsequent receptor autophosphorylation is controlled primarily by the A'α-LOV2-Jα photosensory module. Mutations that disrupt interactions between the LOV2 core and its flanking helical segments can uncouple this mode of light regulation. However, the impact of these mutations on phot function in Arabidopsis has not been explored. Here we report that histidine substitution of Arg-472 located within the A'α-helix of Arabidopsis phot1 constitutively activates phot1 kinase activity in vitro without affecting LOV2 photochemistry. Expression analysis of phot1 R472H in the phot-deficient mutant confirmed that it is autophosphorylated in darkness in vivo but unable to initiate phot1 signaling in the absence of light. Instead, we found that phot1 R472H is poorly functional under low-light conditions but can restore phototropism, chloroplast accumulation, stomatal opening, and leaf positioning and expansion at higher light intensities. Our findings suggest that Arabidopsis can adapt to the elevated phosphorylation status of the phot1 R472H mutant in part by reducing its stability, whereas the activity of the mutant under high-light conditions can be attributed to additional increases in LOV2-mediated photoreceptor autophosphorylation. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  16. A LOV2 domain-based optogenetic tool to control protein degradation and cellular function.

    PubMed

    Renicke, Christian; Schuster, Daniel; Usherenko, Svetlana; Essen, Lars-Oliver; Taxis, Christof

    2013-04-18

    Light perception is indispensable for plants to respond adequately to external cues and is linked to proteolysis of key transcriptional regulators. To provide synthetic light control of protein stability, we developed a generic photosensitive degron (psd) module combining the light-reactive LOV2 domain of Arabidopsis thaliana phot1 with the murine ornithine decarboxylase-like degradation sequence cODC1. Functionality of the psd module was demonstrated in the model organism Saccharomyces cerevisiae. Generation of conditional mutants, light regulation of cyclin-dependent kinase activity, light-based patterning of cell growth, and yeast photography exemplified its versatility. In silico modeling of psd module behavior increased understanding of its characteristics. This engineered degron module transfers the principle of light-regulated degradation to nonplant organisms. It will be highly beneficial to control protein levels in biotechnological or biomedical applications and offers the potential to render a plethora of biological processes light-switchable. Copyright © 2013 Elsevier Ltd. All rights reserved.

  17. Variations in protein/flavin hydrogen bonding in a LOV domain produce non-Arrhenius kinetics of adduct decay†

    PubMed Central

    Zoltowski, Brian D.; Nash, Abigail I.; Gardner, Kevin H.

    2011-01-01

    Light Oxygen Voltage (LOV) domains utilize a conserved blue light-dependent mechanism to control a diverse array of effector domains in biological and engineered proteins. Variations in the kinetics and efficiency of LOV photochemistry fine tune various aspects of the photic response. Characterization of the kinetics of a key aspect of this photochemical mechanism in EL222, a blue-light responsive DNA binding protein from Erythrobacter litoralis HTCC2594, reveals unique non-Arrhenius behavior in the rate of dark state cleavage of the photochemically-generated adduct. Sequence analysis and mutagenesis studies establish that this effect stems from a Gln to Ala mutation unique to EL222 and homologous proteins from marine bacteria. Kinetic and spectroscopic analyses reveal that hydrogen bonding interactions between the FMN N1, O2 and ribityl hydroxyls with the surrounding protein regulate photocycle kinetics and stabilize the LOV active site from temperature-induced alteration in local structure. Substitution of residues interacting with the N1-O2 locus modulates adduct stability, structural flexibility and sequestration of the active site from bulk solvent without perturbation of light-activated DNA binding. Together, these variants link non-Arrhenius behavior to specific alteration of an H-bonding network, while affording tunability of photocycle kinetics. PMID:21923139

  18. Regulatory mechanism of the light-activable allosteric switch LOV-TAP for the control of DNA binding: a computer simulation study.

    PubMed

    Peter, Emanuel; Dick, Bernhard; Baeurle, Stephan A

    2013-03-01

    The spatio-temporal control of gene expression is fundamental to elucidate cell proliferation and deregulation phenomena in living systems. Novel approaches based on light-sensitive multiprotein complexes have recently been devised, showing promising perspectives for the noninvasive and reversible modulation of the DNA-transcriptional activity in vivo. This has lately been demonstrated in a striking way through the generation of the artificial protein construct light-oxygen-voltage (LOV)-tryptophan-activated protein (TAP), in which the LOV-2-Jα photoswitch of phototropin1 from Avena sativa (AsLOV2-Jα) has been ligated to the tryptophan-repressor (TrpR) protein from Escherichia coli. Although tremendous progress has been achieved on the generation of such protein constructs, a detailed understanding of their functioning as opto-genetical tools is still in its infancy. Here, we elucidate the early stages of the light-induced regulatory mechanism of LOV-TAP at the molecular level, using the noninvasive molecular dynamics simulation technique. More specifically, we find that Cys450-FMN-adduct formation in the AsLOV2-Jα-binding pocket after photoexcitation induces the cleavage of the peripheral Jα-helix from the LOV core, causing a change of its polarity and electrostatic attraction of the photoswitch onto the DNA surface. This goes along with the flexibilization through unfolding of a hairpin-like helix-loop-helix region interlinking the AsLOV2-Jα- and TrpR-domains, ultimately enabling the condensation of LOV-TAP onto the DNA surface. By contrast, in the dark state the AsLOV2-Jα photoswitch remains inactive and exerts a repulsive electrostatic force on the DNA surface. This leads to a distortion of the hairpin region, which finally relieves its tension by causing the disruption of LOV-TAP from the DNA. Copyright © 2012 Wiley Periodicals, Inc.

  19. A Native Threonine Coordinates Ordered Water to Tune Light-Oxygen-Voltage (LOV) Domain Photocycle Kinetics and Osmotic Stress Signaling in Trichoderma reesei ENVOY*

    PubMed Central

    Lokhandwala, Jameela; Silverman y de la Vega, Rafael I.; Hopkins, Hilary C.; Britton, Collin W.; Rodriguez-Iglesias, Aroa; Bogomolni, Roberto; Schmoll, Monika; Zoltowski, Brian D.

    2016-01-01

    Light-oxygen-voltage (LOV) domain-containing proteins function as small light-activated modules capable of imparting blue light control of biological processes. Their small modular nature has made them model proteins for allosteric signal transduction and optogenetic devices. Despite intense research, key aspects of their signal transduction mechanisms and photochemistry remain poorly understood. In particular, ordered water has been identified as a possible key mediator of photocycle kinetics, despite the lack of ordered water in the LOV active site. Herein, we use recent crystal structures of a fungal LOV protein ENVOY to interrogate the role of Thr101 in recruiting water to the flavin active site where it can function as an intrinsic base to accelerate photocycle kinetics. Kinetic and molecular dynamic simulations confirm a role in solvent recruitment to the active site and identify structural changes that correlate with solvent recruitment. In vivo analysis of T101I indicates a direct role of the Thr101 position in mediating adaptation to osmotic stress, thereby verifying biological relevance of ordered water in LOV signaling. The combined studies identify position 101 as a mediator of both allostery and photocycle catalysis that can impact organism physiology. PMID:27226624

  20. A Dominant Mutation in the Light-Oxygen and Voltage2 Domain Vicinity Impairs Phototropin1 Signaling in Tomato1[C][W][OPEN

    PubMed Central

    Sharma, Sulabha; Kharshiing, Eros; Srinivas, Ankanagari; Zikihara, Kazunori; Tokutomi, Satoru; Nagatani, Akira; Fukayama, Hiroshi; Bodanapu, Reddaiah; Behera, Rajendra K.; Sreelakshmi, Yellamaraju; Sharma, Rameshwar

    2014-01-01

    In higher plants, blue light (BL) phototropism is primarily controlled by the phototropins, which are also involved in stomatal movement and chloroplast relocation. These photoresponses are mediated by two phototropins, phot1 and phot2. Phot1 mediates responses with higher sensitivity than phot2, and phot2 specifically mediates chloroplast avoidance and dark positioning responses. Here, we report the isolation and characterization of a Nonphototropic seedling1 (Nps1) mutant of tomato (Solanum lycopersicum). The mutant is impaired in low-fluence BL responses, including chloroplast accumulation and stomatal opening. Genetic analyses show that the mutant locus is dominant negative in nature. In dark-grown seedlings of the Nps1 mutant, phot1 protein accumulates at a highly reduced level relative to the wild type and lacks BL-induced autophosphorylation. The mutant harbors a single glycine-1484-to-alanine transition in the Hinge1 region of a phot1 homolog, resulting in an arginine-to-histidine substitution (R495H) in a highly conserved A′α helix proximal to the light-oxygen and voltage2 domain of the translated gene product. Significantly, the R495H substitution occurring in the Hinge1 region of PHOT1 abolishes its regulatory activity in Nps1 seedlings, thereby highlighting the functional significance of the A′α helix region in phototropic signaling of tomato. PMID:24515830

  1. Absorption and emission spectroscopic characterisation of the LOV2-domain of phot from Chlamydomonas reinhardtii fused to a maltose binding protein

    NASA Astrophysics Data System (ADS)

    Holzer, W.; Penzkofer, A.; Susdorf, T.; Álvarez, M.; Islam, Sh. D. M.; Hegemann, P.

    2004-07-01

    The absorption and emission behaviour of flavin mononucleotide (FMN) in the wild-type light, oxygen and voltage-sensitive (LOV) domain LOV2 of the photoreceptor phot from the green alga Chlamydomonas reinhardtii is studied at pH 8. Actually a LOV2-MBP-fusion protein (MBP=maltose binding protein) expressed in an Escherichia coli strain is investigated. For fresh samples stored in the dark an initial fluorescence quantum yield of φF=0.08±0.01 is determined. Blue-light photo-excitation generates a non-fluorescent intermediate photoproduct (flavin-C(4a)-cysteinyl adduct with absorption peak at 390 nm). In the aqueous solutions studied approximately seven percent of the FMN molecules are not bound to the protein (free FMN in oxidized form) and about seven percent of the non-covalently bound FMN are not convertible to an adduct. Approximately two thirds of the intermediate photoproduct recovers with a time constant of 41 ± 1 s, while approximately one third recovers with a time constant of about 7 min. The photo-adduct formation is thought to proceed via singlet excited-state electron transfer and triplet formation.

  2. A phytochrome/phototropin chimeric photoreceptor of fern functions as a blue/far-red light-dependent photoreceptor for phototropism in Arabidopsis.

    PubMed

    Kanegae, Takeshi; Kimura, Izumi

    2015-08-01

    In the fern Adiantum capillus-veneris, the phototropic response of the protonemal cells is induced by blue light and partially inhibited by subsequent irradiation with far-red light. This observation strongly suggests the existence of a phytochrome that mediates this blue/far-red reversible response; however, the phytochrome responsible for this response has not been identified. PHY3/NEO1, one of the three phytochrome genes identified in Adiantum, encodes a chimeric photoreceptor composed of both a phytochrome and a phototropin domain. It was demonstrated that phy3 mediates the red light-dependent phototropic response of Adiantum, and that phy3 potentially functions as a phototropin. These findings suggest that phy3 is the phytochrome that mediates the blue/far-red response in Adiantum protonemata. In the present study, we expressed Adiantum phy3 in a phot1 phot2 phototropin-deficient Arabidopsis line, and investigated the ability of phy3 to induce phototropic responses under various light conditions. Blue light irradiation clearly induced a phototropic response in the phy3-expressing transgenic seedlings, and this effect was fully inhibited by simultaneous irradiation with far-red light. In addition, experiments using amino acid-substituted phy3 indicated that FMN-cysteinyl adduct formation in the light, oxygen, voltage (LOV) domain was not necessary for the induction of blue light-dependent phototropism by phy3. We thus demonstrate that phy3 is the phytochrome that mediates the blue/far-red reversible phototropic response in Adiantum. Furthermore, our results imply that phy3 can function as a phototropin, but that it acts principally as a phytochrome that mediates both the red/far-red and blue/far-red light responses. © 2015 The Authors The Plant Journal © 2015 John Wiley & Sons Ltd.

  3. Structural basis of a phototropin light switch.

    PubMed

    Harper, Shannon M; Neil, Lori C; Gardner, Kevin H

    2003-09-12

    Phototropins are light-activated kinases important for plant responses to blue light. Light initiates signaling in these proteins by generating a covalent protein-flavin mononucleotide (FMN) adduct within sensory Per-ARNT-Sim (PAS) domains. We characterized the light-dependent changes of a phototropin PAS domain by solution nuclear magnetic resonance spectroscopy and found that an alpha helix located outside the canonical domain plays a key role in this activation process. Although this helix associates with the PAS core in the dark, photoinduced changes in the domain structure disrupt this interaction. We propose that this mechanism couples light-dependent bond formation to kinase activation and identifies a signaling pathway conserved among PAS domains.

  4. Switching from adduct formation to electron transfer in a light-oxygen-voltage domain containing the reactive cysteine.

    PubMed

    Magerl, Kathrin; Stambolic, Ivan; Dick, Bernhard

    2017-03-08

    LOV (light-, oxygen- or voltage-sensitive) domains act as photosensory units of many prokaryotic and eukaryotic proteins. Upon blue light excitation they undergo a photocycle via the excited triplet state of their flavin chromophore yielding the flavin-cysteinyl adduct. Adduct formation is highly conserved among all LOV domains and constitutes the primary step of LOV domain signaling. But recently, it has been shown that signal propagation can also be triggered by flavin photoreduction to the neutral semiquinone offering new prospects for protein engineering. This, however, requires mutation of the photo-active Cys. Here, we report on LOV1 mutants of C. reinhardtii phototropin in which adduct formation is suppressed although the photo-active Cys is present. Introduction of a Tyr into the LOV core induces a proton coupled electron transfer towards the flavin chromophore. Flavin radical species are formed via either the excited flavin singlet or triplet state depending on the geometry of donor and acceptor. This photoreductive pathway resembles the photoreaction observed in other blue light photoreceptors, e.g. blue-light sensors using flavin adenine dinucleotide (BLUF) domains or cryptochromes. The ability to tune the photoreactivity of the flavin chromophore inside the LOV core has implications for the mechanism of adduct formation in the wild type and may be of use for protein engineering.

  5. The LovK-LovR Two-Component System Is a Regulator of the General Stress Pathway in Caulobacter crescentus

    PubMed Central

    Foreman, Robert

    2012-01-01

    A conserved set of regulators control the general stress response in Caulobacter crescentus, including σT, its anti-σ factor NepR, the anti-anti-σ factor PhyR, and the transmembrane sensor kinase PhyK. We report that the soluble histidine kinase LovK and the single-domain response regulator LovR also function within the C. crescentus general stress pathway. Our genetic data support a model in which LovK-LovR functions upstream of σT by controlling the phosphorylation state and thus anti-anti-σ activity of PhyR. Transcription of lovK and lovR is independently activated by stress through a mechanism that requires sigT and phyR. Conversely, lovK and lovR function together to repress transcription of the general stress regulon. Concordant with a functional role of the LovK-LovR two-component system as a negative regulator of the general stress pathway, lovK-lovR-null mutants exhibit increased cell survival after osmotic stress, while coordinate overexpression of lovK and lovR attenuates cell survival relative to that of the wild type. Notably, lovK can complement the transcriptional and cell survival defects of a phyK-null mutant when lovR is deleted. Moreover, in this same genetic background, σT-dependent transcription is activated in response to osmotic stress. This result suggests that flavin-binding LOV (light, oxygen, or voltage) histidine kinases are competent to perceive cytoplasmic signals in addition to the environmental signal blue light. We conclude that the PhyK-PhyR and LovK-LovR two-component signaling systems coordinately regulate stress physiology in C. crescentus. PMID:22408156

  6. Engineering a More Thermostable Blue Light Photo Receptor Bacillus subtilis YtvA LOV Domain by a Computer Aided Rational Design Method

    PubMed Central

    Shu, Zhiyu; Hong, Jingbo; Li, Tong; Yao, Lishan

    2013-01-01

    The ability to design thermostable proteins offers enormous potential for the development of novel protein bioreagents. In this work, a combined computational and experimental method was developed to increase the T m of the flavin mononucleotide based fluorescent protein Bacillus Subtilis YtvA LOV domain by 31 Celsius, thus extending its applicability in thermophilic systems. Briefly, the method includes five steps, the single mutant computer screening to identify thermostable mutant candidates, the experimental evaluation to confirm the positive selections, the computational redesign around the thermostable mutation regions, the experimental reevaluation and finally the multiple mutations combination. The adopted method is simple and effective, can be applied to other important proteins where other methods have difficulties, and therefore provides a new tool to improve protein thermostability. PMID:23861663

  7. Structure of a LOV protein in apo-state and implications for construction of LOV-based optical tools

    PubMed Central

    Arinkin, Vladimir; Granzin, Joachim; Röllen, Katrin; Krauss, Ulrich; Jaeger, Karl-Erich; Willbold, Dieter; Batra-Safferling, Renu

    2017-01-01

    Unique features of Light-Oxygen-Voltage (LOV) proteins like relatively small size (~12–19 kDa), inherent modularity, highly-tunable photocycle and oxygen-independent fluorescence have lately been exploited for the generation of optical tools. Structures of LOV domains reported so far contain a flavin chromophore per protein molecule. Here we report two new findings on the short LOV protein W619_1-LOV from Pseudomonas putida. First, the apo-state crystal structure of W619_1-LOV at 2.5 Å resolution reveals conformational rearrangements in the secondary structure elements lining the chromophore pocket including elongation of the Fα helix, shortening of the Eα-Fα loop and partial unfolding of the Eα helix. Second, the apo W619_1-LOV protein binds both natural and structurally modified flavin chromophores. Remarkably different photophysical and photochemical properties of W619_1-LOV bound to 7-methyl-8-chloro-riboflavin (8-Cl-RF) and lumichrome imply application of these variants as novel optical tools as they offer advantages such as no adduct state formation, and a broader choice of wavelengths for in vitro studies. PMID:28211532

  8. The origin and evolution of phototropins

    PubMed Central

    Li, Fay-Wei; Rothfels, Carl J.; Melkonian, Michael; Villarreal, Juan C.; Stevenson, Dennis W.; Graham, Sean W.; Wong, Gane K.-S.; Mathews, Sarah; Pryer, Kathleen M.

    2015-01-01

    Plant phototropism, the ability to bend toward or away from light, is predominantly controlled by blue-light photoreceptors, the phototropins. Although phototropins have been well-characterized in Arabidopsis thaliana, their evolutionary history is largely unknown. In this study, we complete an in-depth survey of phototropin homologs across land plants and algae using newly available transcriptomic and genomic data. We show that phototropins originated in an ancestor of Viridiplantae (land plants + green algae). Phototropins repeatedly underwent independent duplications in most major land-plant lineages (mosses, lycophytes, ferns, and seed plants), but remained single-copy genes in liverworts and hornworts—an evolutionary pattern shared with another family of photoreceptors, the phytochromes. Following each major duplication event, the phototropins differentiated in parallel, resulting in two specialized, yet partially overlapping, functional forms that primarily mediate either low- or high-light responses. Our detailed phylogeny enables us to not only uncover new phototropin lineages, but also link our understanding of phototropin function in Arabidopsis with what is known in Adiantum and Physcomitrella (the major model organisms outside of flowering plants). We propose that the convergent functional divergences of phototropin paralogs likely contributed to the success of plants through time in adapting to habitats with diverse and heterogeneous light conditions. PMID:26322073

  9. Structure and function of a short LOV protein from the marine phototrophic bacterium Dinoroseobacter shibae.

    PubMed

    Endres, Stephan; Granzin, Joachim; Circolone, Franco; Stadler, Andreas; Krauss, Ulrich; Drepper, Thomas; Svensson, Vera; Knieps-Grünhagen, Esther; Wirtz, Astrid; Cousin, Anneliese; Tielen, Petra; Willbold, Dieter; Jaeger, Karl-Erich; Batra-Safferling, Renu

    2015-02-14

    Light, oxygen, voltage (LOV) domains are widely distributed in plants, algae, fungi, bacteria, and represent the photo-responsive domains of various blue-light photoreceptor proteins. Their photocycle involves the blue-light triggered adduct formation between the C(4a) atom of a non-covalently bound flavin chromophore and the sulfur atom of a conserved cysteine in the LOV sensor domain. LOV proteins show considerable variation in the structure of N- and C-terminal elements which flank the LOV core domain, as well as in the lifetime of the adduct state. Here, we report the photochemical, structural and functional characterization of DsLOV, a LOV protein from the photoheterotrophic marine α-proteobacterium Dinoroseobacter shibae which exhibits an average adduct state lifetime of 9.6 s at 20°C, and thus represents the fastest reverting bacterial LOV protein reported so far. Mutational analysis in D. shibae revealed a unique role of DsLOV in controlling the induction of photopigment synthesis in the absence of blue-light. The dark state crystal structure of DsLOV determined at 1.5 Å resolution reveals a conserved core domain with an extended N-terminal cap. The dimer interface in the crystal structure forms a unique network of hydrogen bonds involving residues of the N-terminus and the β-scaffold of the core domain. The structure of photoexcited DsLOV suggests increased flexibility in the N-cap region and a significant shift in the Cα backbone of β strands in the N- and C-terminal ends of the LOV core domain. The results presented here cover the characterization of the unusual short LOV protein DsLOV from Dinoroseobacter shibae including its regulatory function, extremely fast dark recovery and an N-terminus mediated dimer interface. Due to its unique photophysical, structural and regulatory properties, DsLOV might thus serve as an alternative model system for studying light perception by LOV proteins and physiological responses in bacteria.

  10. An Analysis of the Solution Structure and Signaling Mechanism of LovK, a Sensor Histidine Kinase Integrating Light and Redox Signals

    SciTech Connect

    Purcell, Erin B.; McDonald, Claudia A.; Palfey, Bruce A.; Crosson, Sean

    2010-12-07

    Flavin-binding LOV domains are broadly conserved in plants, fungi, archaea, and bacteria. These {approx}100-residue photosensory modules are generally encoded within larger, multidomain proteins that control a range of blue light-dependent physiologies. The bacterium Caulobacter crescentus encodes a soluble LOV-histidine kinase, LovK, that regulates the adhesive properties of the cell. Full-length LovK is dimeric as are a series of systematically truncated LovK constructs containing only the N-terminal LOV sensory domain. Nonconserved sequence flanking the LOV domain functions to tune the signaling lifetime of the protein. Size exclusion chromatography and small-angle X-ray scattering (SAXS) demonstrate that the LOV sensor domain does not undergo a large conformational change in response to photon absorption. However, limited proteolysis identifies a sequence flanking the C-terminus of the LOV domain as a site of light-induced change in protein conformation and dynamics. On the basis of SAXS envelope reconstruction and bioinformatic prediction, we propose this dynamic region of structure is an extended C-terminal coiled coil that links the LOV domain to the histidine kinase domain. To test the hypothesis that LOV domain signaling is affected by cellular redox state in addition to light, we measured the reduction potential of the LovK FMN cofactor. The measured potential of -258 mV is congruent with the redox potential of Gram-negative cytoplasm during logarithmic growth (-260 to -280 mV). Thus, a fraction of LovK in the cytosol may be in the reduced state under typical growth conditions. Chemical reduction of the FMN cofactor of LovK attenuates the light-dependent ATPase activity of the protein in vitro, demonstrating that LovK can function as a conditional photosensor that is regulated by the oxidative state of the cellular environment.

  11. Crystal Structures of Aureochrome1 LOV Suggest New Design Strategies for Optogenetics

    SciTech Connect

    Mitra, Devrani; Yang, Xiaojing; Moffat, Keith

    2014-10-02

    Aureochrome1, a signaling photoreceptor from a eukaryotic photosynthetic stramenopile, confers blue-light-regulated DNA binding on the organism. Its topology, in which a C-terminal LOV sensor domain is linked to an N-terminal DNA-binding bZIP effector domain, contrasts with the reverse sensor-effector topology in most other known LOV-photoreceptors. How, then, is signal transmitted in Aureochrome1? The dark- and light-state crystal structures of Aureochrome1 LOV domain (AuLOV) show that its helical N- and C-terminal flanking regions are packed against the external surface of the core {beta} sheet, opposite to the FMN chromophore on the internal surface. Light-induced conformational changes occur in the quaternary structure of the AuLOV dimer and in Phe298 of the H{beta} strand in the core. The properties of AuLOV extend the applicability of LOV domains as versatile design modules that permit fusion to effector domains via either the N- or C-termini to confer blue-light sensitivity.

  12. Light-induced structural changes in a short light, oxygen, voltage (LOV) protein revealed by molecular dynamics simulations—implications for the understanding of LOV photoactivation

    PubMed Central

    Bocola, Marco; Schwaneberg, Ulrich; Jaeger, Karl-Erich; Krauss, Ulrich

    2015-01-01

    The modularity of light, oxygen, voltage (LOV) blue-light photoreceptors has recently been exploited for the design of LOV-based optogenetic tools, which allow the light-dependent control of biological functions. For the understanding of LOV sensory function and hence the optimal design of LOV-based optogentic tools it is essential to gain an in depth atomic-level understanding of the underlying photoactivation and intramolecular signal-relay mechanisms. To address this question we performed molecular dynamics simulations on both the dark- and light-adapted state of PpSB1-LOV, a short dimeric bacterial LOV-photoreceptor protein, recently crystallized under constant illumination. While LOV dimers remained globally stable during the light-state simulation with regard to the Jα coiled-coil, distinct conformational changes for a glutamine in the vicinity of the FMN chromophore are observed. In contrast, multiple Jα-helix conformations are sampled in the dark-state. These changes coincide with a displacement of the Iβ and Hβ strands relative to the light-state structure and result in a correlated rotation of both LOV core domains in the dimer. These global changes are most likely initiated by the reorientation of the conserved glutamine Q116, whose side chain flips between the Aβ (dark state) and Hβ strand (light state), while maintaining two potential hydrogen bonds to FMN-N5 and FMN-O4, respectively. This local Q116-FMN reorientation impacts on an inter-subunit salt-bridge (K117-E96), which is stabilized in the light state, hence accounting for the observed decreased mobility. Based on these findings we propose an alternative mechanism for dimeric LOV photoactivation and intramolecular signal-relay, assigning a distinct structural role for the conserved “flipping” glutamine. The proposed mechanism is discussed in light of universal applicability and its implications for the understanding of LOV-based optogenetic tools. PMID:26484348

  13. LOV-based optogenetic devices: light-driven modules to impart photoregulated control of cellular signaling

    PubMed Central

    Pudasaini, Ashutosh; El-Arab, Kaley K.; Zoltowski, Brian D.

    2015-01-01

    The Light-Oxygen-Voltage domain family of proteins is widespread in biology where they impart sensory responses to signal transduction domains. The small, light responsive LOV modules offer a novel platform for the construction of optogenetic tools. Currently, the design and implementation of these devices is partially hindered by a lack of understanding of how light drives allosteric changes in protein conformation to activate diverse signal transduction domains. Further, divergent photocycle properties amongst LOV family members complicate construction of highly sensitive devices with fast on/off kinetics. In the present review we discuss the history of LOV domain research with primary emphasis on tuning LOV domain chemistry and signal transduction to allow for improved optogenetic tools. PMID:25988185

  14. LOV-based optogenetic devices: light-driven modules to impart photoregulated control of cellular signaling.

    PubMed

    Pudasaini, Ashutosh; El-Arab, Kaley K; Zoltowski, Brian D

    2015-01-01

    The Light-Oxygen-Voltage domain family of proteins is widespread in biology where they impart sensory responses to signal transduction domains. The small, light responsive LOV modules offer a novel platform for the construction of optogenetic tools. Currently, the design and implementation of these devices is partially hindered by a lack of understanding of how light drives allosteric changes in protein conformation to activate diverse signal transduction domains. Further, divergent photocycle properties amongst LOV family members complicate construction of highly sensitive devices with fast on/off kinetics. In the present review we discuss the history of LOV domain research with primary emphasis on tuning LOV domain chemistry and signal transduction to allow for improved optogenetic tools.

  15. Light regulates attachment, exopolysaccharide production, and nodulation in Rhizobium leguminosarum through a LOV-histidine kinase photoreceptor.

    PubMed

    Bonomi, Hernán R; Posadas, Diana M; Paris, Gastón; Carrica, Mariela del Carmen; Frederickson, Marcus; Pietrasanta, Lía Isabel; Bogomolni, Roberto A; Zorreguieta, Angeles; Goldbaum, Fernando A

    2012-07-24

    Rhizobium leguminosarum is a soil bacterium that infects root hairs and induces the formation of nitrogen-fixing nodules on leguminous plants. Light, oxygen, and voltage (LOV)-domain proteins are blue-light receptors found in higher plants and many algae, fungi, and bacteria. The genome of R. leguminosarum bv. viciae 3841, a pea-nodulating endosymbiont, encodes a sensor histidine kinase containing a LOV domain at the N-terminal end (R-LOV-HK). R-LOV-HK has a typical LOV domain absorption spectrum with broad bands in the blue and UV-A regions and shows a truncated photocycle. Here we show that the R-LOV-HK protein regulates attachment to an abiotic surface and production of flagellar proteins and exopolysaccharide in response to light. Also, illumination of bacterial cultures before inoculation of pea roots increases the number of nodules per plant and the number of intranodular bacteroids. The effects of light on nodulation are dependent on a functional lov gene. The results presented in this work suggest that light, sensed by R-LOV-HK, is an important environmental factor that controls adaptive responses and the symbiotic efficiency of R. leguminosarum.

  16. Light regulates attachment, exopolysaccharide production, and nodulation in Rhizobium leguminosarum through a LOV-histidine kinase photoreceptor

    PubMed Central

    Bonomi, Hernán R.; Posadas, Diana M.; Paris, Gastón; Carrica, Mariela del Carmen; Frederickson, Marcus; Pietrasanta, Lía Isabel; Bogomolni, Roberto A.; Zorreguieta, Angeles; Goldbaum, Fernando A.

    2012-01-01

    Rhizobium leguminosarum is a soil bacterium that infects root hairs and induces the formation of nitrogen-fixing nodules on leguminous plants. Light, oxygen, and voltage (LOV)-domain proteins are blue-light receptors found in higher plants and many algae, fungi, and bacteria. The genome of R. leguminosarum bv. viciae 3841, a pea-nodulating endosymbiont, encodes a sensor histidine kinase containing a LOV domain at the N-terminal end (R-LOV-HK). R-LOV-HK has a typical LOV domain absorption spectrum with broad bands in the blue and UV-A regions and shows a truncated photocycle. Here we show that the R-LOV-HK protein regulates attachment to an abiotic surface and production of flagellar proteins and exopolysaccharide in response to light. Also, illumination of bacterial cultures before inoculation of pea roots increases the number of nodules per plant and the number of intranodular bacteroids. The effects of light on nodulation are dependent on a functional lov gene. The results presented in this work suggest that light, sensed by R-LOV-HK, is an important environmental factor that controls adaptive responses and the symbiotic efficiency of R. leguminosarum. PMID:22773814

  17. Solving Blue Light Riddles: New Lessons from Flavin-binding LOV Photoreceptors.

    PubMed

    Losi, Aba; Gärtner, Wolfgang

    2017-01-01

    Detection of blue light (BL) via flavin-binding photoreceptors (Fl-Blues) has evolved throughout all three domains of life. Although the main BL players, that is light, oxygen and voltage (LOV), blue light sensing using flavins (BLUF) and Cry (cryptochrome) proteins, have been characterized in great detail with respect to structure and function, still several unresolved issues at different levels of complexity remain and novel unexpected findings were reported. Here, we review the most prevailing riddles of LOV-based photoreceptors, for example: the relevance of water and/or small metabolites for the dynamics of the photocycle; molecular details of light-to-signal transduction events; the interplay of BL sensing by LOV domains with other environmental stimuli, such as BL plus oxygen-mediating photodamage and its impact on microbial lifestyles; the importance of the cell or chromophore redox state in determining the fate of BL-driven reactions; the evolutionary pathways of LOV-based BL sensing and associated functions through the diverse phyla. We will discuss major novelties emerged during the last few years on these intriguing aspects of LOV proteins by presenting paradigmatic examples from prokaryotic photosensors that exhibit the largest complexity and richness in associated functions. © 2016 The American Society of Photobiology.

  18. Fine tuning chloroplast movements through physical interactions between phototropins

    PubMed Central

    Sztatelman, Olga; Łabuz, Justyna; Hermanowicz, Paweł; Banaś, Agnieszka Katarzyna; Bażant, Aneta; Zgłobicki, Piotr; Aggarwal, Chhavi; Nadzieja, Marcin; Krzeszowiec, Weronika; Strzałka, Wojciech; Gabryś, Halina

    2016-01-01

    Phototropins are plant photoreceptors which regulate numerous responses to blue light, including chloroplast relocation. Weak blue light induces chloroplast accumulation, whereas strong light leads to an avoidance response. Two Arabidopsis phototropins are characterized by different light sensitivities. Under continuous light, both can elicit chloroplast accumulation, but the avoidance response is controlled solely by phot2. As well as continuous light, brief light pulses also induce chloroplast displacements. Pulses of 0.1s and 0.2s of fluence rate saturating the avoidance response lead to transient chloroplast accumulation. Longer pulses (up to 20s) trigger a biphasic response, namely transient avoidance followed by transient accumulation. This work presents a detailed study of transient chloroplast responses in Arabidopsis. Phototropin mutants display altered chloroplast movements as compared with the wild type: phot1 is characterized by weaker responses, while phot2 exhibits enhanced chloroplast accumulation, especially after 0.1s and 0.2s pulses. To determine the cause of these differences, the abundance and phosphorylation levels of both phototropins, as well as the interactions between phototropin molecules are examined. The formation of phototropin homo- and heterocomplexes is the most plausible explanation of the observed phenomena. The physiological consequences of this interplay are discussed, suggesting the universal character of this mechanism that fine-tunes plant reactions to blue light. Additionally, responses in mutants of different protein phosphatase 2A subunits are examined to assess the role of protein phosphorylation in signaling of chloroplast movements. PMID:27406783

  19. Phosphoinositides play differential roles in regulating phototropin1- and phototropin2-mediated chloroplast movements in Arabidopsis.

    PubMed

    Aggarwal, Chhavi; Labuz, Justyna; Gabryś, Halina

    2013-01-01

    Phototropins are UVA/blue-light receptors involved in controlling the light-dependent physiological responses which serve to optimize the photosynthetic activity of plants and promote growth. The phototropin-induced phosphoinositide (PI) metabolism has been shown to be essential for stomatal opening and phototropism. However, the role of PIs in phototropin-induced chloroplast movements remains poorly understood. The aim of this work is to determine which PI species are involved in the control of chloroplast movements in Arabidopsis and the nature of their involvement. We present the effects of the inactivation of phospholipase C (PLC), PI3-kinase (PI3K) and PI4-kinase (PI4K) on chloroplast relocations in Arabidopsis. The inhibition of the phosphatidylinositol 4,5-bisphospahte [PI(4,5)P2]-PLC pathway, using neomycin and U73122, suppressed the phot2-mediated chloroplast accumulation and avoidance responses, without affecting movement responses controlled by phot1. On the other hand, PI3K and PI4K activities are more restricted to phot1- and phot2-induced weak-light responses. The inactivation of PI3K and PI4K by wortmannin and LY294002 severely affected the weak blue-light-activated accumulation response but had little effect on the strong blue-light-activated avoidance response. The inhibitory effect observed with PI metabolism inhibitors is, at least partly, due to a disturbance in Ca(2+) ((c)) signaling. Using the transgenic aequorin system, we show that the application of these inhibitors suppresses the blue-light-induced transient Ca(2+) ((c)) rise. These results demonstrate the importance of PIs in chloroplast movements, with the PI(4,5)P2-PLC pathway involved in phot2 signaling while PI3K and PI4K are required for the phot1- and phot2-induced accumulation response. Our results suggest that these PIs modulate cytosolic Ca(2+) signaling during movements.

  20. Blue-light-activated phototropin2 trafficking from the cytoplasm to Golgi/post-Golgi vesicles.

    PubMed

    Aggarwal, Chhavi; Banaś, Agnieszka Katarzyna; Kasprowicz-Maluśki, Anna; Borghetti, Carolina; Labuz, Justyna; Dobrucki, Jerzy; Gabryś, Halina

    2014-07-01

    Phototropins are plasma membrane-localized UVA/blue light photoreceptors which mediate phototropism, inhibition of primary hypocotyl elongation, leaf positioning, chloroplast movements, and stomatal opening. Blue light irradiation activates the C-terminal serine/threonine kinase domain of phototropin which autophosphorylates the receptor. Arabidopsis thaliana encodes two phototropins, phot1 and phot2. In response to blue light, phot1 moves from the plasma membrane into the cytosol and phot2 translocates to the Golgi complex. In this study the molecular mechanism and route of blue-light-induced phot2 trafficking are demonstrated. It is shown that Atphot2 behaves in a similar manner when expressed transiently under 35S or its native promoter. The phot2 kinase domain but not blue-light-mediated autophosphorylation is required for the receptor translocation. Using co-localization and western blotting, the receptor was shown to move from the cytoplasm to the Golgi complex, and then to the post-Golgi structures. The results were confirmed by brefeldin A (an inhibitor of the secretory pathway) which disrupted phot2 trafficking. An association was observed between phot2 and the light chain2 of clathrin via bimolecular fluorescence complementation. The fluorescence was observed at the plasma membrane. The results were confirmed using co-immunoprecipitation. However, tyrphostin23 (an inhibitor of clathrin-mediated endocytosis) and wortmannin (a suppressor of receptor endocytosis) were not able to block phot2 trafficking, indicating no involvement of receptor endocytosis in the formation of phot2 punctuate structures. Protein turnover studies indicated that the receptor was continuously degraded in both darkness and blue light. The degradation of phot2 proceeded via a transport route different from translocation to the Golgi complex. © The Author 2014. Published by Oxford University Press on behalf of the Society for Experimental Biology.

  1. Blue-light-activated phototropin2 trafficking from the cytoplasm to Golgi/post-Golgi vesicles

    PubMed Central

    Aggarwal, Chhavi; Banaś, Agnieszka Katarzyna; Kasprowicz-Maluśki, Anna; Borghetti, Carolina; Łabuz, Justyna; Dobrucki, Jerzy; Gabryś, Halina

    2014-01-01

    Phototropins are plasma membrane-localized UVA/blue light photoreceptors which mediate phototropism, inhibition of primary hypocotyl elongation, leaf positioning, chloroplast movements, and stomatal opening. Blue light irradiation activates the C-terminal serine/threonine kinase domain of phototropin which autophosphorylates the receptor. Arabidopsis thaliana encodes two phototropins, phot1 and phot2. In response to blue light, phot1 moves from the plasma membrane into the cytosol and phot2 translocates to the Golgi complex. In this study the molecular mechanism and route of blue-light-induced phot2 trafficking are demonstrated. It is shown that Atphot2 behaves in a similar manner when expressed transiently under 35S or its native promoter. The phot2 kinase domain but not blue-light-mediated autophosphorylation is required for the receptor translocation. Using co-localization and western blotting, the receptor was shown to move from the cytoplasm to the Golgi complex, and then to the post-Golgi structures. The results were confirmed by brefeldin A (an inhibitor of the secretory pathway) which disrupted phot2 trafficking. An association was observed between phot2 and the light chain2 of clathrin via bimolecular fluorescence complementation. The fluorescence was observed at the plasma membrane. The results were confirmed using co-immunoprecipitation. However, tyrphostin23 (an inhibitor of clathrin-mediated endocytosis) and wortmannin (a suppressor of receptor endocytosis) were not able to block phot2 trafficking, indicating no involvement of receptor endocytosis in the formation of phot2 punctuate structures. Protein turnover studies indicated that the receptor was continuously degraded in both darkness and blue light. The degradation of phot2 proceeded via a transport route different from translocation to the Golgi complex. PMID:24821953

  2. Fine tuning chloroplast movements through physical interactions between phototropins.

    PubMed

    Sztatelman, Olga; Łabuz, Justyna; Hermanowicz, Paweł; Banaś, Agnieszka Katarzyna; Bażant, Aneta; Zgłobicki, Piotr; Aggarwal, Chhavi; Nadzieja, Marcin; Krzeszowiec, Weronika; Strzałka, Wojciech; Gabryś, Halina

    2016-09-01

    Phototropins are plant photoreceptors which regulate numerous responses to blue light, including chloroplast relocation. Weak blue light induces chloroplast accumulation, whereas strong light leads to an avoidance response. Two Arabidopsis phototropins are characterized by different light sensitivities. Under continuous light, both can elicit chloroplast accumulation, but the avoidance response is controlled solely by phot2. As well as continuous light, brief light pulses also induce chloroplast displacements. Pulses of 0.1s and 0.2s of fluence rate saturating the avoidance response lead to transient chloroplast accumulation. Longer pulses (up to 20s) trigger a biphasic response, namely transient avoidance followed by transient accumulation. This work presents a detailed study of transient chloroplast responses in Arabidopsis. Phototropin mutants display altered chloroplast movements as compared with the wild type: phot1 is characterized by weaker responses, while phot2 exhibits enhanced chloroplast accumulation, especially after 0.1s and 0.2s pulses. To determine the cause of these differences, the abundance and phosphorylation levels of both phototropins, as well as the interactions between phototropin molecules are examined. The formation of phototropin homo- and heterocomplexes is the most plausible explanation of the observed phenomena. The physiological consequences of this interplay are discussed, suggesting the universal character of this mechanism that fine-tunes plant reactions to blue light. Additionally, responses in mutants of different protein phosphatase 2A subunits are examined to assess the role of protein phosphorylation in signaling of chloroplast movements. © The Author 2016. Published by Oxford University Press on behalf of the Society for Experimental Biology.

  3. The Drosophila BTB Domain Protein Jim Lovell Has Roles in Multiple Larval and Adult Behaviors

    PubMed Central

    Bjorum, Sonia M.; Simonette, Rebecca A.; Alanis, Raul; Wang, Jennifer E.; Lewis, Benjamin M.; Trejo, Michael H.; Hanson, Keith A.; Beckingham, Kathleen M.

    2013-01-01

    Innate behaviors have their origins in the specification of neural fates during development. Within Drosophila, BTB (Bric-a-brac,Tramtrack, Broad) domain proteins such as Fruitless are known to play key roles in the neural differentiation underlying such responses. We previously identified a gene, which we have termed jim lovell (lov), encoding a BTB protein with a role in gravity responses. To understand more fully the behavioral roles of this gene we have investigated its function through several approaches. Transcript and protein expression patterns have been examined and behavioral phenotypes of new lov mutations have been characterized. Lov is a nuclear protein, suggesting a role as a transcriptional regulator, as for other BTB proteins. In late embryogenesis, Lov is expressed in many CNS and PNS neurons. An examination of the PNS expression indicates that lov functions in the late specification of several classes of sensory neurons. In particular, only two of the five abdominal lateral chordotonal neurons express Lov, predicting functional variation within this highly similar group. Surprisingly, Lov is also expressed very early in embryogenesis in ways that suggests roles in morphogenetic movements, amnioserosa function and head neurogenesis. The phenotypes of two new lov mutations that delete adjacent non-coding DNA regions are strikingly different suggesting removal of different regulatory elements. In lov47, Lov expression is lost in many embryonic neurons including the two lateral chordotonal neurons. lov47 mutant larvae show feeding and locomotor defects including spontaneous backward movement. Adult lov47 males perform aberrant courtship behavior distinguished by courtship displays that are not directed at the female. lov47 adults also show more defective negative gravitaxis than the previously isolated lov91Y mutant. In contrast, lov66 produces largely normal behavior but severe female sterility associated with ectopic lov expression in the ovary. We

  4. Glutamine Amide Flip Elicits Long Distance Allosteric Responses in the LOV Protein Vivid.

    PubMed

    Ganguly, Abir; Thiel, Walter; Crane, Brian R

    2017-03-01

    Light-oxygen-voltage (LOV) domains sense blue light through the photochemical formation of a cysteinyl-flavin covalent adduct. Concurrent protonation at the flavin N5 position alters the hydrogen bonding interactions of an invariant Gln residue that has been proposed to flip its amide side chain as a critical step in the propagation of conformational change. Traditional molecular dynamics (MD) and replica-exchange MD (REMD) simulations of the well-characterized LOV protein Vivid (VVD) demonstrate that the Gln182 amide indeed reorients by ∼180° in response to either adduct formation or reduction of the isoalloxazine ring to the neutral semiquinone, both of which involve N5 protonation. Free energy simulations reveal that the relative free energies of the flipped Gln conformation and the flipping barrier are significantly lower in the light-adapted state. The Gln182 flip stabilizes an important hinge-bβ region between the PAS β-sheet and the N-terminal cap helix that in turn destabilizes an N-terminal latch region against the PAS core. Release of the latch, observed both experimentally and in the simulations, is known to mediate light-induced VVD dimerization. This computational study of a LOV protein, unprecedented in its agreement with experiment, provides an atomistic view of long-range allosteric coupling in a photoreceptor.

  5. Photoactivation Reduces Side-Chain Dynamics of a LOV Photoreceptor

    PubMed Central

    Stadler, Andreas M.; Knieps-Grünhagen, Esther; Bocola, Marco; Lohstroh, Wiebke; Zamponi, Michaela; Krauss, Ulrich

    2016-01-01

    We used neutron-scattering experiments to probe the conformational dynamics of the light, oxygen, voltage (LOV) photoreceptor PpSB1-LOV from Pseudomonas putida in both the dark and light states. Global protein diffusion and internal macromolecular dynamics were measured using incoherent neutron time-of-flight and backscattering spectroscopy on the picosecond to nanosecond timescales. Global protein diffusion of PpSB1-LOV is not influenced by photoactivation. Observation-time-dependent global diffusion coefficients were found, which converge on the nanosecond timescale toward diffusion coefficients determined by dynamic light scattering. Mean-square displacements of localized internal motions and effective force constants, , describing the resilience of the proteins were determined on the respective timescales. Photoactivation significantly modifies the flexibility and the resilience of PpSB1-LOV. On the fast, picosecond timescale, small changes in the mean-square displacement and are observed, which are enhanced on the slower, nanosecond timescale. Photoactivation results in a slightly larger resilience of the photoreceptor on the fast, picosecond timescale, whereas in the nanosecond range, a significantly less resilient structure of the light-state protein is observed. For a residue-resolved interpretation of the experimental neutron-scattering data, we analyzed molecular dynamics simulations of the PpSB1-LOV X-ray structure. Based on these data, it is tempting to speculate that light-induced changes in the protein result in altered side-chain mobility mostly for residues on the protruding Jα helix and on the LOV-LOV dimer interface. Our results provide strong experimental evidence that side-chain dynamics play a crucial role in photoactivation and signaling of PpSB1-LOV via modulation of conformational entropy. PMID:26958884

  6. Phototropins mediate blue and red light-induced chloroplast movements in Physcomitrella patens.

    PubMed

    Kasahara, Masahiro; Kagawa, Takatoshi; Sato, Yoshikatsu; Kiyosue, Tomohiro; Wada, Masamitsu

    2004-07-01

    Phototropin is the blue-light receptor that mediates phototropism, chloroplast movement, and stomatal opening in Arabidopsis. Blue and red light induce chloroplast movement in the moss Physcomitrella patens. To study the photoreceptors for chloroplast movement in P. patens, four phototropin genes (PHOTA1, PHOTA2, PHOTB1, and PHOTB2) were isolated by screening cDNA libraries. These genes were classified into two groups (PHOTA and PHOTB) on the basis of their deduced amino acid sequences. Then phototropin disruptants were generated by homologous recombination and used for analysis of chloroplast movement. Data revealed that blue light-induced chloroplast movement was mediated by phototropins in P. patens. Both photA and photB groups were able to mediate chloroplast avoidance, as has been reported for Arabidopsis phot2, although the photA group contributed more to the response. Red light-induced chloroplast movement was also significantly reduced in photA2photB1photB2 triple disruptants. Because the primary photoreceptor for red light-induced chloroplast movement in P. patens is phytochrome, phototropins may be downstream components of phytochromes in the signaling pathway. To our knowledge, this work is the first to show a function for the phototropin blue-light receptor in a response to wavelengths that it does not absorb.

  7. LOV Histidine Kinase Modulates the General Stress Response System and Affects the virB Operon Expression in Brucella abortus.

    PubMed

    Sycz, Gabriela; Carrica, Mariela Carmen; Tseng, Tong-Seung; Bogomolni, Roberto A; Briggs, Winslow R; Goldbaum, Fernando A; Paris, Gastón

    2015-01-01

    Brucella is the causative agent of the zoonotic disease brucellosis, and its success as an intracellular pathogen relies on its ability to adapt to the harsh environmental conditions that it encounters inside the host. The Brucella genome encodes a sensor histidine kinase containing a LOV domain upstream from the kinase, LOVHK, which plays an important role in light-regulated Brucella virulence. In this report we study the intracellular signaling pathway initiated by the light sensor LOVHK using an integrated biochemical and genetic approach. From results of bacterial two-hybrid assays and phosphotransfer experiments we demonstrate that LOVHK functionally interacts with two response regulators: PhyR and LovR, constituting a functional two-component signal-transduction system. LOVHK contributes to the activation of the General Stress Response (GSR) system in Brucella via PhyR, while LovR is proposed to be a phosphate-sink for LOVHK, decreasing its phosphorylation state. We also show that in the absence of LOVHK the expression of the virB operon is down-regulated. In conclusion, our results suggest that LOVHK positively regulates the GSR system in vivo, and has an effect on the expression of the virB operon. The proposed regulatory network suggests a similar role for LOVHK in other microorganisms.

  8. Structure of a Light-Activated LOV Protein Dimer That Regulates Transcription

    SciTech Connect

    Vaidya, Anand T.; Chen, Chen-Hui; Dunlap, Jay C.; Loros, Jennifer J.; Crane, Brian R.

    2012-10-25

    Light, oxygen, or voltage (LOV) protein domains are present in many signaling proteins in bacteria, archaea, protists, plants, and fungi. The LOV protein VIVID (VVD) of the filamentous fungus Neurospora crassa enables the organism to adapt to constant or increasing amounts of light and facilitates proper entrainment of circadian rhythms. Here, we determined the crystal structure of the fully light-adapted VVD dimer and reveal the mechanism by which light-driven conformational change alters the oligomeric state of the protein. Light-induced formation of a cysteinyl-flavin adduct generated a new hydrogen bond network that released the amino (N) terminus from the protein core and restructured an acceptor pocket for binding of the N terminus on the opposite subunit of the dimer. Substitution of residues critical for the switch between the monomeric and the dimeric states of the protein had profound effects on light adaptation in Neurospora. The mechanism of dimerization of VVD provides molecular details that explain how members of a large family of photoreceptors convert light responses to alterations in protein-protein interactions.

  9. The LOV Protein of Xanthomonas citri subsp. citri Plays a Significant Role in the Counteraction of Plant Immune Responses during Citrus Canker

    PubMed Central

    Kraiselburd, Ivana; Daurelio, Lucas D.; Tondo, María Laura; Merelo, Paz; Cortadi, Adriana A.; Talón, Manuel; Tadeo, Francisco R.; Orellano, Elena G.

    2013-01-01

    Pathogens interaction with a host plant starts a set of immune responses that result in complex changes in gene expression and plant physiology. Light is an important modulator of plant defense response and recent studies have evidenced the novel influence of this environmental stimulus in the virulence of several bacterial pathogens. Xanthomonas citri subsp. citri is the bacterium responsible for citrus canker disease, which affects most citrus cultivars. The ability of this bacterium to colonize host plants is influenced by bacterial blue-light sensing through a LOV-domain protein and disease symptoms are considerably altered upon deletion of this protein. In this work we aimed to unravel the role of this photoreceptor during the bacterial counteraction of plant immune responses leading to citrus canker development. We performed a transcriptomic analysis in Citrus sinensis leaves inoculated with the wild type X. citri subsp. citri and with a mutant strain lacking the LOV protein by a cDNA microarray and evaluated the differentially regulated genes corresponding to specific biological processes. A down-regulation of photosynthesis-related genes (together with a corresponding decrease in photosynthesis rates) was observed upon bacterial infection, this effect being more pronounced in plants infected with the lov-mutant bacterial strain. Infection with this strain was also accompanied with the up-regulation of several secondary metabolism- and defense response-related genes. Moreover, we found that relevant plant physiological alterations triggered by pathogen attack such as cell wall fortification and tissue disruption were amplified during the lov-mutant strain infection. These results suggest the participation of the LOV-domain protein from X. citri subsp. citri in the bacterial counteraction of host plant defense response, contributing in this way to disease development. PMID:24260514

  10. Diversity of bacteria in surface ice of Austre Lovénbreen glacier, Svalbard.

    PubMed

    Zeng, Yin-Xin; Yan, Ming; Yu, Yong; Li, Hui-Rong; He, Jian-Feng; Sun, Kun; Zhang, Fang

    2013-05-01

    Two 16S rRNA gene clone libraries Cores 1U and 2U were constructed using two ice core samples collected from Austre Lovénbreen glacier in Svalbard. The two libraries yielded a total of 262 clones belonging to 59 phylotypes. Sequences fell into 10 major lineages of the domain Bacteria, including Proteobacteria (alpha, beta, gamma and delta subdivisions), Bacteroidetes, Actinobacteria, Firmicutes, Acidobacteria, Deinococcus-Thermus, Chloroflexi, Planctomycetes, Cyanobacteria and candidate division TM7. Among them, Bacteroidetes, Actinobacteria, Alphaproteobacteria and Cyanobacteria were most abundant. UniFrac data showed no significant differences in community composition between the two ice cores. A total of nineteen bacterial strains from the genera Pseudoalteromonas and Psychrobacter were isolated from the ice cores. Phylogenetic and phenotypic analyses revealed a close relationship between the ice core isolates and bacteria in marine environments, indicating a wide distribution of some bacterial phylotypes in both terrestrial and marine ecosystems.

  11. Phototropin Mediated Relocation of Myosins in Arabidopsis thaliana.

    PubMed

    Krzeszowiec, Weronika; Gabryś, Halina

    2007-09-01

    The mechanism of the light-dependent movements of chloroplasts is based on actin and myosin but its details are largely unknown. The movements are activated by blue light in terrestrial angiosperms. The aim of the present study was to determine the role of myosin associated with the chloroplast surface in the light-induced chloroplast responses in Arabidopsis thaliana. The localization of myosins was investigated under blue light intensities generating avoidance and accumulation responses of chloroplasts. The localization was compared in wild type plants and in phot2 mutant lacking the avoidance response. Wild type and phot2 mutant plants were irradiated with strong (36 microEm(-2)s(-1)) and/or weak (0.8 microEm(-2)s(-1)) blue light. The leaf tissue was immunolabeled with antimyosin antibodies. Different arrangements of myosins were observed in the mesophyll depending on the fluence rate in wild type plants. In tissue irradiated with weak blue light myosins were associated with chloroplast envelopes. In contrast, in tissue irradiated with strong blue light chloroplasts were almost myosin-free. The effect did not occur in red light and in the phot2 mutant. Myosin displacement is blue light specific, i.e., it is associated with the activation of a specific blue-light photoreceptor. We suggest that the reorganization of myosins is essential for chloroplast movement. Myosins appear to be the final step of the signal transduction pathway starting with phototropin2 and leading to chloroplast movements.

  12. REPRESSOR OF ULTRAVIOLET-B PHOTOMORPHOGENESIS function allows efficient phototropin mediated ultraviolet-B phototropism in etiolated seedlings.

    PubMed

    Vanhaelewyn, Lucas; Schumacher, Paolo; Poelman, Dirk; Fankhauser, Christian; Van Der Straeten, Dominique; Vandenbussche, Filip

    2016-11-01

    Ultraviolet B (UV-B) light is a part of the solar radiation which has significant effects on plant morphology, even at low doses. In Arabidopsis, many of these morphological changes have been attributed to a specific UV-B receptor, UV resistance locus 8 (UVR8). Recent findings showed that next to phototropin regulated phototropism, UVR8 mediated signaling is able of inducing directional bending towards UV-B light in etiolated seedlings of Arabidopsis, in a phototropin independent manner. In this study, kinetic analysis of phototropic bending was used to evaluate the relative contribution of each of these pathways in UV-B mediated phototropism. Diminishing UV-B light intensity favors the importance of phototropins. Molecular and genetic analyses suggest that UV-B is capable of inducing phototropin signaling relying on phototropin kinase activity and regulation of NPH3. Moreover, enhanced UVR8 responses in the UV-B hypersensitive rup1rup2 mutants interferes with the fast phototropin mediated phototropism. Together the data suggest that phototropins are the most important receptors for UV-B induced phototropism in etiolated seedlings, and a RUP mediated negative feedback pathway prevents UVR8 signaling to interfere with the phototropin dependent response.

  13. Identification of ASK and clock-associated proteins as molecular partners of LKP2 (LOV kelch protein 2) in Arabidopsis.

    PubMed

    Yasuhara, Masahiro; Mitsui, Shunya; Hirano, Hiroshi; Takanabe, Rieko; Tokioka, Yoko; Ihara, Norihisa; Komatsu, Akihiro; Seki, Motoaki; Shinozaki, Kazuo; Kiyosue, Tomohiro

    2004-09-01

    The ADO/FKF/LKP/ZTL family of proteins of Arabidopsis thaliana Heynh. have a LOV domain, an F-box motif, and a kelch repeat region. LKP2 is a member of this family and functions either within or very close to the circadian oscillator in Arabidopsis. Promoter-GUS fusion studies revealed that the LKP2 gene was highly active in rosette leaves. In CaMV 35S:LKP2-GFP plants, GFP-associated fluorescence was detected in nuclei, suggesting that LKP2 is a nuclear protein. Yeast two-hybrid analysis demonstrated that LKP2 interacted with some Arabidopsis Skp1-like proteins (ASK), as do other ADO/FKF/LKP/ZTL family proteins, suggesting that LKP2 can form an SCF (Skp1-Cullin-F-box protein) complex that functions as a ubiquitin E3 ligase. LKP2 interacted not only with itself but also with other members of the family, LKP1 and FKF1. The two-hybrid analysis also demonstrated that LKP2 interacted with TOC1, a clock component, but not with CCA1 or LHY, negative regulators of TOC1 gene expression. The LOV domain of LKP2 was shown to be necessary and sufficient for the interaction with TOC1. An interaction between LKP2 and APRR5, a paralogue of TOC1, was also observed, but LKP2 did not interact with APRR3, APRR7, or APRR9, other paralogues of TOC1.

  14. Antagonistic regulation of leaf flattening by phytochrome B and phototropin in Arabidopsis thaliana.

    PubMed

    Kozuka, Toshiaki; Suetsugu, Noriyuki; Wada, Masamitsu; Nagatani, Akira

    2013-01-01

    Light is one of the most important environmental factors regulating the growth and development of leaves. As the primary photosynthetic organs, leaves have a laminar structure in many dicotyledonous plants. The regulation of leaf flatness is a key mechanism for the efficient absorption of light under low light conditions. In the present study, we demonstrated that phytochrome B (phyB) promoted the development of curled leaves. Wild-type leaves gently curled downwards under white light, whereas the phyB-deficient mutant (phyB) constitutively exhibited flatter leaves. In the wild type, leaf flattening was promoted by end-of-day far-red light (EODFR) treatment, which rapidly eliminates the active Pfr phytochrome. Interestingly, the curled-leaf phenotype in a phototropin-deficient mutant was almost completely suppressed by the phyB mutation as well as by EODFR. Thus, phototropin promotes leaf flattening by suppressing the leaf-curling activity of phyB. We examined the downstream components of phyB and phototropin to assess their antagonistic regulation of leaf flatness further. Consequently, we found that a phototropin signaling transducer, NON-PHOTOTROPIC HYPOCOTYL 3 (NPH3), was required to promote leaf flattening in phyB. The present study provides new insights into a mechanism in which leaf flatness is regulated in response to different light environmental cues.

  15. A phytochrome–phototropin light signaling complex at the plasma membrane

    PubMed Central

    Jaedicke, Katharina; Lichtenthäler, Anna Lena; Meyberg, Rabea; Zeidler, Mathias; Hughes, Jon

    2012-01-01

    Phytochromes are red/far-red photochromic photoreceptors central to regulating plant development. Although they are known to enter the nucleus upon light activation and, once there, regulate transcription, this is not the complete picture. Various phytochrome effects are manifested much too rapidly to derive from changes in gene expression, whereas others seem to occur without phytochrome entering the nucleus. Phytochromes also guide directional responses to light, excluding a genetic signaling route and implying instead plasma membrane association and a direct cytoplasmic signal. However, to date, no such association has been demonstrated. Here we report that a phytochrome subpopulation indeed associates physically with another photoreceptor, phototropin, at the plasma membrane. Yeast two-hybrid methods using functional photoreceptor molecules showed that the phytochrome steering growth direction in Physcomitrella protonemata binds several phototropins specifically in the photoactivated Pfr state. Split-YFP studies in planta showed that the interaction occurs exclusively at the plasma membrane. Coimmunoprecipitation experiments provided independent confirmation of in vivo phy-phot binding. Consistent with this interaction being associated with a cellular signal, we found that phytochrome-mediated tropic responses are impaired in Physcomitrella phot− mutants. Split-YFP revealed a similar interaction between Arabidopsis phytochrome A and phototropin 1 at the plasma membrane. These associations additionally provide a functional explanation for the evolution of neochrome photoreceptors. Our results imply that the elusive phytochrome cytoplasmic signal arises through binding and coaction with phototropin at the plasma membrane. PMID:22773817

  16. Phototropins do not alter accumulation of evening-phased circadian transcripts under blue light

    PubMed Central

    Litthauer, Suzanne; Battle, Martin W.; Jones, Matthew A.

    2016-01-01

    ABSTRACT The circadian system induces rhythmic variation in a suite of biochemical and physiological processes that serve to optimise plant growth in diel cycles. To be of greatest utility, these rhythmic behaviors are coordinated with regular environmental changes such as the rising and setting of the sun. Photoreceptors, along with metabolites produced during photosynthesis, act to synchronise the internal timing mechanism with lighting cues. We have recently shown that phototropins help maintain robust rhythms of photosynthetic operating efficiency (φPSII or Fq′/Fm′) under blue light, although rhythmic accumulation of morning-phased circadian transcripts in the nucleus was unaffected. Here we report that evening-phased nuclear clock transcripts were also unaffected. We also observe that rhythms of nuclear clock transcript accumulation are maintained in phototropin mutant plants under a fluctuating lighting regime that induced a loss of Fq′/Fm′ rhythms. PMID:26653107

  17. Functional characterization of blue-light-induced responses and PHOTOTROPIN 1 gene in Welwitschia mirabilis.

    PubMed

    Ishishita, Kazuhiro; Suetsugu, Noriyuki; Hirose, Yuki; Higa, Takeshi; Doi, Michio; Wada, Masamitsu; Matsushita, Tomonao; Gotoh, Eiji

    2016-03-01

    The blue light (BL) receptor phototropin (phot) is specifically found in green plants; it regulates various BL-induced responses such as phototropism, chloroplast movement, stomatal opening, and leaf flattening. In Arabidopsis thaliana, two phototropins--phot1 and phot2--respond to blue light in overlapping but distinct ways. These BL-receptor-mediated responses enhance the photosynthetic activity of plants under weak light and minimize photodamage under strong light conditions. Welwitschia mirabilis Hook.f. found in the Namib Desert, and it has adapted to severe environmental stresses such as limiting water and strong sunlight. Although the plant has physiologically and ecologically unique features, it is unknown whether phototropin is functional in this plant. In this study, we assessed the functioning of phot-mediated BL responses in W. mirabilis. BL-dependent phototropism and stomatal opening was observed but light-dependent chloroplast movement was not detected. We performed a functional analysis of the PHOT1 gene of W. mirabilis, WmPHOT1, in Arabidopsis thaliana. We generated transgenic A. thaliana lines expressing WmPHOT1 in a phot1 phot2 double mutant background. Several Wmphot1 transgenic plants showed normal growth, although phot1 phot2 double mutant plants showed stunted growth. Furthermore, Wmphot1 transgenic plants showed normal phot1-mediated responses including phototropism, chloroplast accumulation, stomatal opening, and leaf flattening, but lacked the chloroplast avoidance response that is specifically mediated by phot2. Thus, our findings indicate that W. mirabilis possesses typical phot-mediated BL responses that were at least partially mediated by functional phototropin 1, an ortholog of Atphot1.

  18. Second Positive Phototropism Results from Coordinated Co-Action of the Phototropins and Cryptochromes1

    PubMed Central

    Whippo, Craig W.; Hangarter, Roger P.

    2003-01-01

    Phototropism and hypocotyl growth inhibition are modulated by the coaction of different blue-light photoreceptors and their signaling pathways. How seedlings integrate the activities of the different blue-light photoreceptors to coordinate these hypocotyl growth responses is still unclear. We have used time-lapse imaging and a nontraditional mathematical approach to conduct a detailed examination of phototropism in wild-type Arabidopsis and various blue-light photoreceptor mutants. Our results indicate that high fluence rates of blue light (100 μmol m–2 s–1) attenuate phototropism through the coaction of the phototropin and cryptochrome blue-light photoreceptors. In contrast, we also demonstrate that phototropins and cryptochromes function together to enhance phototropism under low fluence rates (<1.0 μmol m–2 s–1) of blue light. Based on our results, we hypothesize that phototropins and cryptochromes regulate phototropism by coordinating the balance between stimulation and inhibition of growth of the hypocotyl depending on the fluence rate of blue light. PMID:12857830

  19. Second positive phototropism results from coordinated co-action of the phototropins and cryptochromes.

    PubMed

    Whippo, Craig W; Hangarter, Roger P

    2003-07-01

    Phototropism and hypocotyl growth inhibition are modulated by the coaction of different blue-light photoreceptors and their signaling pathways. How seedlings integrate the activities of the different blue-light photoreceptors to coordinate these hypocotyl growth responses is still unclear. We have used time-lapse imaging and a nontraditional mathematical approach to conduct a detailed examination of phototropism in wild-type Arabidopsis and various blue-light photoreceptor mutants. Our results indicate that high fluence rates of blue light (100 micro mol m(-)(2) s(-)(1)) attenuate phototropism through the coaction of the phototropin and cryptochrome blue-light photoreceptors. In contrast, we also demonstrate that phototropins and cryptochromes function together to enhance phototropism under low fluence rates (<1.0 micro mol m(-)(2) s(-)(1)) of blue light. Based on our results, we hypothesize that phototropins and cryptochromes regulate phototropism by coordinating the balance between stimulation and inhibition of growth of the hypocotyl depending on the fluence rate of blue light.

  20. Tissue-Autonomous Promotion of Palisade Cell Development by Phototropin 2 in Arabidopsis[W

    PubMed Central

    Kozuka, Toshiaki; Kong, Sam-Geun; Doi, Michio; Shimazaki, Ken-ichiro; Nagatani, Akira

    2011-01-01

    Light is an important environmental information source that plants use to modify their growth and development. Palisade parenchyma cells in leaves develop cylindrical shapes in response to blue light; however, the photosensory mechanism for this response has not been elucidated. In this study, we analyzed the palisade cell response in phototropin-deficient mutants. First, we found that two different light-sensing mechanisms contributed to the response in different proportions depending on the light intensity. One response observed under lower intensities of blue light was mediated exclusively by a blue light photoreceptor, phototropin 2 (PHOT2). Another response was elicited under higher intensities of light in a phototropin-independent manner. To determine the tissue in which PHOT2 perceives the light stimulus to regulate the response, green fluorescent protein (GFP)–tagged PHOT2 (P2G) was expressed under the control of tissue-specific promoters in the phot1 phot2 mutant background. The results revealed that the expression of P2G in the mesophyll, but not in the epidermis, promoted palisade cell development. Furthermore, a constitutively active C-terminal kinase fragment of PHOT2 fused to GFP (P2CG) promoted the development of cylindrical palisade cells in the proper direction without the directional cue provided by light. Hence, in response to blue light, PHOT2 promotes the development of cylindrical palisade cells along a predetermined axis in a tissue-autonomous manner. PMID:21972260

  1. Tissue-autonomous promotion of palisade cell development by phototropin 2 in Arabidopsis.

    PubMed

    Kozuka, Toshiaki; Kong, Sam-Geun; Doi, Michio; Shimazaki, Ken-ichiro; Nagatani, Akira

    2011-10-01

    Light is an important environmental information source that plants use to modify their growth and development. Palisade parenchyma cells in leaves develop cylindrical shapes in response to blue light; however, the photosensory mechanism for this response has not been elucidated. In this study, we analyzed the palisade cell response in phototropin-deficient mutants. First, we found that two different light-sensing mechanisms contributed to the response in different proportions depending on the light intensity. One response observed under lower intensities of blue light was mediated exclusively by a blue light photoreceptor, phototropin 2 (PHOT2). Another response was elicited under higher intensities of light in a phototropin-independent manner. To determine the tissue in which PHOT2 perceives the light stimulus to regulate the response, green fluorescent protein (GFP)-tagged PHOT2 (P2G) was expressed under the control of tissue-specific promoters in the phot1 phot2 mutant background. The results revealed that the expression of P2G in the mesophyll, but not in the epidermis, promoted palisade cell development. Furthermore, a constitutively active C-terminal kinase fragment of PHOT2 fused to GFP (P2CG) promoted the development of cylindrical palisade cells in the proper direction without the directional cue provided by light. Hence, in response to blue light, PHOT2 promotes the development of cylindrical palisade cells along a predetermined axis in a tissue-autonomous manner.

  2. Optical Control of Peroxisomal Trafficking

    PubMed Central

    2015-01-01

    The blue-light-responsive LOV2 domain of Avena sativa phototropin1 (AsLOV2) has been used to regulate activity and binding of diverse protein targets with light. Here, we used AsLOV2 to photocage a peroxisomal targeting sequence, allowing light regulation of peroxisomal protein import. We generated a protein tag, LOV-PTS1, that can be appended to proteins of interest to direct their import to the peroxisome with light. This method provides a means to inducibly trigger peroxisomal protein trafficking in specific cells at user-defined times. PMID:26513473

  3. Revealing Hidden Conformational Space of LOV Protein VIVID Through Rigid Residue Scan Simulations

    PubMed Central

    Zhou, Hongyu; Zoltowski, Brian D.; Tao, Peng

    2017-01-01

    VIVID(VVD) protein is a Light-Oxygen-Voltage(LOV) domain in circadian clock system. Upon blue light activation, a covalent bond is formed between VVD residue Cys108 and its cofactor flavin adenine dinucleotide(FAD), and prompts VVD switching from Dark state to Light state with significant conformational deviation. However, the mechanism of this local environment initiated global protein conformational change remains elusive. We employed a recently developed computational approach, rigid residue scan(RRS), to systematically probe the impact of the internal degrees of freedom in each amino acid residue of VVD on its overall dynamics by applying rigid body constraint on each residue in molecular dynamics simulations. Key residues were identified with distinctive impacts on Dark and Light states, respectively. All the simulations display wide range of distribution on a two-dimensional(2D) plot upon structural root-mean-square deviations(RMSD) from either Dark or Light state. Clustering analysis of the 2D RMSD distribution leads to 15 representative structures with drastically different conformation of N-terminus, which is also a key difference between Dark and Light states of VVD. Further principle component analyses(PCA) of RRS simulations agree with the observation of distinctive impact from individual residues on Dark and Light states. PMID:28425502

  4. Revealing Hidden Conformational Space of LOV Protein VIVID Through Rigid Residue Scan Simulations

    NASA Astrophysics Data System (ADS)

    Zhou, Hongyu; Zoltowski, Brian D.; Tao, Peng

    2017-04-01

    VIVID(VVD) protein is a Light-Oxygen-Voltage(LOV) domain in circadian clock system. Upon blue light activation, a covalent bond is formed between VVD residue Cys108 and its cofactor flavin adenine dinucleotide(FAD), and prompts VVD switching from Dark state to Light state with significant conformational deviation. However, the mechanism of this local environment initiated global protein conformational change remains elusive. We employed a recently developed computational approach, rigid residue scan(RRS), to systematically probe the impact of the internal degrees of freedom in each amino acid residue of VVD on its overall dynamics by applying rigid body constraint on each residue in molecular dynamics simulations. Key residues were identified with distinctive impacts on Dark and Light states, respectively. All the simulations display wide range of distribution on a two-dimensional(2D) plot upon structural root-mean-square deviations(RMSD) from either Dark or Light state. Clustering analysis of the 2D RMSD distribution leads to 15 representative structures with drastically different conformation of N-terminus, which is also a key difference between Dark and Light states of VVD. Further principle component analyses(PCA) of RRS simulations agree with the observation of distinctive impact from individual residues on Dark and Light states.

  5. The Role of Distant Mutations and Allosteric Regulation on LovD Active Site Dynamics

    PubMed Central

    Jiménez-Osés, Gonzalo; Osuna, Sílvia; Gao, Xue; Sawaya, Michael R.; Gilson, Lynne; Collier, Steven J.; Huisman, Gjalt W.; Yeates, Todd O.; Tang, Yi; Houk, K. N.

    2014-01-01

    Natural enzymes have evolved to perform their cellular functions under complex selective pressures, which often require their catalytic activities to be regulated by other proteins. We contrasted a natural enzyme, LovD, which acts on a protein-bound (LovF) acyl substrate, with a laboratory-generated variant that was transformed by directed evolution to accept instead a small free acyl thioester, and no longer requires the acyl carrier protein. The resulting 29-mutant variant is 1000-fold more efficient in the synthesis of the drug simvastatin than the wild-type LovD. This is the first non-patent report of the enzyme currently used for the manufacture of simvastatin, as well as the intermediate evolved variants. Crystal structures and microsecond molecular dynamics simulations revealed the mechanism by which the laboratory-generated mutations free LovD from dependence on protein-protein interactions. Mutations dramatically altered conformational dynamics of the catalytic residues, obviating the need for allosteric modulation by the acyl carrier LovF. PMID:24727900

  6. Light Regulation of Swarming Motility in Pseudomonas syringae Integrates Signaling Pathways Mediated by a Bacteriophytochrome and a LOV Protein

    PubMed Central

    Wu, Liang; McGrane, Regina S.; Beattie, Gwyn A.

    2013-01-01

    ABSTRACT The biological and regulatory roles of photosensory proteins are poorly understood for nonphotosynthetic bacteria. The foliar bacterial pathogen Pseudomonas syringae has three photosensory protein-encoding genes that are predicted to encode the blue-light-sensing LOV (light, oxygen, or voltage) histidine kinase (LOV-HK) and two red/far-red-light-sensing bacteriophytochromes, BphP1 and BphP2. We provide evidence that LOV-HK and BphP1 form an integrated network that regulates swarming motility in response to multiple light wavelengths. The swarming motility of P. syringae B728a deletion mutants indicated that LOV-HK positively regulates swarming motility in response to blue light and BphP1 negatively regulates swarming motility in response to red and far-red light. BphP2 does not detectably regulate swarming motility. The histidine kinase activity of each LOV-HK and BphP1 is required for this regulation based on the loss of complementation upon mutation of residues key to their kinase activity. Surprisingly, mutants lacking both lov and bphP1 were similar in motility to a bphP1 single mutant in blue light, indicating that the loss of bphP1 is epistatic to the loss of lov and also that BphP1 unexpectedly responds to blue light. Moreover, whereas expression of bphP1 did not alter motility under blue light in a bphP1 mutant, it reduced motility in a mutant lacking lov and bphP1, demonstrating that LOV-HK positively regulates motility by suppressing negative regulation by BphP1. These results are the first to show cross talk between the LOV protein and phytochrome signaling pathways in bacteria, and the similarity of this regulatory network to that of photoreceptors in plants suggests a possible common ancestry. PMID:23760465

  7. PHYTOCHROME KINASE SUBSTRATE 1 is a phototropin 1 binding protein required for phototropism.

    PubMed

    Lariguet, Patricia; Schepens, Isabelle; Hodgson, Daniel; Pedmale, Ullas V; Trevisan, Martine; Kami, Chitose; de Carbonnel, Matthieu; Alonso, José M; Ecker, Joseph R; Liscum, Emmanuel; Fankhauser, Christian

    2006-06-27

    Phototropism, or plant growth in response to unidirectional light, is an adaptive response of crucial importance. Lateral differences in low fluence rates of blue light are detected by phototropin 1 (phot1) in Arabidopsis. Only NONPHOTOTROPIC HYPOCOTYL 3 (NPH3) and root phototropism 2, both belonging to the same family of proteins, have been previously identified as phototropin-interacting signal transducers involved in phototropism. PHYTOCHROME KINASE SUBSTRATE (PKS) 1 and PKS2 are two phytochrome signaling components belonging to a small gene family in Arabidopsis (PKS1-PKS4). The strong enhancement of PKS1 expression by blue light and its light induction in the elongation zone of the hypocotyl prompted us to study the function of this gene family during phototropism. Photobiological experiments show that the PKS proteins are critical for hypocotyl phototropism. Furthermore, PKS1 interacts with phot1 and NPH3 in vivo at the plasma membrane and in vitro, indicating that the PKS proteins may function directly with phot1 and NPH3 to mediate phototropism. The phytochromes are known to influence phototropism but the mechanism involved is still unclear. We show that PKS1 induction by a pulse of blue light is phytochrome A-dependent, suggesting that the PKS proteins may provide a molecular link between these two photoreceptor families.

  8. PHYTOCHROME KINASE SUBSTRATE 1 is a phototropin 1 binding protein required for phototropism

    PubMed Central

    Lariguet, Patricia; Schepens, Isabelle; Hodgson, Daniel; Pedmale, Ullas V.; Trevisan, Martine; Kami, Chitose; de Carbonnel, Matthieu; Alonso, José M.; Ecker, Joseph R.; Liscum, Emmanuel; Fankhauser, Christian

    2006-01-01

    Phototropism, or plant growth in response to unidirectional light, is an adaptive response of crucial importance. Lateral differences in low fluence rates of blue light are detected by phototropin 1 (phot1) in Arabidopsis. Only NONPHOTOTROPIC HYPOCOTYL 3 (NPH3) and root phototropism 2, both belonging to the same family of proteins, have been previously identified as phototropin-interacting signal transducers involved in phototropism. PHYTOCHROME KINASE SUBSTRATE (PKS) 1 and PKS2 are two phytochrome signaling components belonging to a small gene family in Arabidopsis (PKS1–PKS4). The strong enhancement of PKS1 expression by blue light and its light induction in the elongation zone of the hypocotyl prompted us to study the function of this gene family during phototropism. Photobiological experiments show that the PKS proteins are critical for hypocotyl phototropism. Furthermore, PKS1 interacts with phot1 and NPH3 in vivo at the plasma membrane and in vitro, indicating that the PKS proteins may function directly with phot1 and NPH3 to mediate phototropism. The phytochromes are known to influence phototropism but the mechanism involved is still unclear. We show that PKS1 induction by a pulse of blue light is phytochrome A-dependent, suggesting that the PKS proteins may provide a molecular link between these two photoreceptor families. PMID:16777956

  9. Both phototropin 1 and 2 localize on the chloroplast outer membrane with distinct localization activity.

    PubMed

    Kong, Sam-Geun; Suetsugu, Noriyuki; Kikuchi, Shingo; Nakai, Masato; Nagatani, Akira; Wada, Masamitsu

    2013-01-01

    Chloroplasts change their position to adapt cellular activities to fluctuating environmental light conditions. Phototropins (phot1 and phot2 in Arabidopsis) are plant-specific blue light photoreceptors that perceive changes in light intensity and direction, and mediate actin-based chloroplast photorelocation movements. Both phot1 and phot2 regulate the chloroplast accumulation response, while phot2 is mostly responsible for the regulation of the avoidance response. Although it has been widely accepted that distinct intracellular localizations of phototropins are implicated in the specificity, the mechanism underlying the phot2-specific avoidance response has remained elusive. In this study, we examined the relationship of the phot2 localization pattern to the chloroplast photorelocation movement. First, the fusion of a nuclear localization signal with phot2, which effectively reduced the amount of phot2 in the cytoplasm, retained the activity for both the accumulation and avoidance responses, indicating that membrane-localized phot2 but not cytoplasmic phot2 is functional to mediate the responses. Importantly, some fractions of phot2, and of phot1 to a lesser extent, were localized on the chloroplast outer membrane. Moreover, the deletion of the C-terminal region of phot2, which was previously shown to be defective in blue light-induced Golgi localization and avoidance response, affected the localization pattern on the chloroplast outer membrane. Taken together, these results suggest that dynamic phot2 trafficking from the plasma membrane to the Golgi apparatus and the chloroplast outer membrane might be involved in the avoidance response.

  10. Chloroplast photorelocation movement mediated by phototropin family proteins in green plants.

    PubMed

    Suetsugu, Noriyuki; Wada, Masamitsu

    2007-09-01

    Chloroplasts gather in areas irradiated with weak light to maximize photosynthesis (the accumulation response). They move away from areas irradiated with strong light to minimize damage of the photosynthetic apparatus (the avoidance response). The processes underlying these chloroplast movements can be divided into three parts: photoperception, signal transduction, and chloroplast movement. Photoreceptors for chloroplast movement have been identified recently in various plant species. A blue light receptor phototropin (phot) mediates chloroplast photorelocation movement in the seed plant Arabidopsis thaliana, the fern Adiantum capillus-veneris, the moss Physcomitrella patens and possibly the green alga Mougeotia scalaris. A chimeric photoreceptor between phytochrome and phototropin, neochrome (neo), was found in some advanced ferns and in the green alga M. scalaris. While the mechanism of chloroplast movement is not well understood, it is known that actin filaments play an important role in this process. To understand the molecular mechanisms associated with chloroplast movement, several mutants were isolated in A. thaliana (jac1 and chup1) and the corresponding genes were cloned. In this review, recent progress in photoreceptor research into chloroplast movement in various plant species and the possible factors functioning in signal transduction or the regulation of actin filaments identified in A. thaliana is discussed.

  11. Light regulation of swarming motility in Pseudomonas syringae integrates signaling pathways mediated by a bacteriophytochrome and a LOV protein.

    PubMed

    Wu, Liang; McGrane, Regina S; Beattie, Gwyn A

    2013-06-11

    The biological and regulatory roles of photosensory proteins are poorly understood for nonphotosynthetic bacteria. The foliar bacterial pathogen Pseudomonas syringae has three photosensory protein-encoding genes that are predicted to encode the blue-light-sensing LOV (light, oxygen, or voltage) histidine kinase (LOV-HK) and two red/far-red-light-sensing bacteriophytochromes, BphP1 and BphP2. We provide evidence that LOV-HK and BphP1 form an integrated network that regulates swarming motility in response to multiple light wavelengths. The swarming motility of P. syringae B728a deletion mutants indicated that LOV-HK positively regulates swarming motility in response to blue light and BphP1 negatively regulates swarming motility in response to red and far-red light. BphP2 does not detectably regulate swarming motility. The histidine kinase activity of each LOV-HK and BphP1 is required for this regulation based on the loss of complementation upon mutation of residues key to their kinase activity. Surprisingly, mutants lacking both lov and bphP1 were similar in motility to a bphP1 single mutant in blue light, indicating that the loss of bphP1 is epistatic to the loss of lov and also that BphP1 unexpectedly responds to blue light. Moreover, whereas expression of bphP1 did not alter motility under blue light in a bphP1 mutant, it reduced motility in a mutant lacking lov and bphP1, demonstrating that LOV-HK positively regulates motility by suppressing negative regulation by BphP1. These results are the first to show cross talk between the LOV protein and phytochrome signaling pathways in bacteria, and the similarity of this regulatory network to that of photoreceptors in plants suggests a possible common ancestry. IMPORTANCE Photosensory proteins enable organisms to perceive and respond to light. The biological and ecological roles of these proteins in nonphotosynthetic bacteria are largely unknown. This study discovered that a blue-light-sensing LOV (light, oxygen, or

  12. Phototropins function in high-intensity blue light-induced hypocotyl phototropism in Arabidopsis by altering cytosolic calcium.

    PubMed

    Zhao, Xiang; Wang, Yan-Liang; Qiao, Xin-Rong; Wang, Jin; Wang, Lin-Dan; Xu, Chang-Shui; Zhang, Xiao

    2013-07-01

    Phototropins (phot1 and phot2), the blue light receptors in plants, regulate hypocotyl phototropism in a fluence-dependent manner. Especially under high fluence rates of blue light (HBL), the redundant function mediated by both phot1 and phot2 drastically restricts the understanding of the roles of phot2. Here, systematic analysis of phototropin-related mutants and overexpression transgenic lines revealed that HBL specifically induced a transient increase in cytosolic Ca(2+) concentration ([Ca(2+)]cyt) in Arabidopsis (Arabidopsis thaliana) hypocotyls and that the increase in [Ca(2+)]cyt was primarily attributed to phot2. Pharmacological and genetic experiments illustrated that HBL-induced Ca(2+) increases were modulated differently by phot1 and phot2. Phot2 mediated the HBL-induced increase in [Ca(2+)]cyt mainly by an inner store-dependent Ca(2+)-release pathway, not by activating plasma membrane Ca(2+) channels. Further analysis showed that the increase in [Ca(2+)]cyt was possibly responsible for HBL-induced hypocotyl phototropism. An inhibitor of auxin efflux carrier exhibited significant inhibitions of both phototropism and increases in [Ca(2+)]cyt, which indicates that polar auxin transport is possibly involved in HBL-induced responses. Moreover, PHYTOCHROME KINASE SUBSTRATE1 (PKS1), the phototropin-related signaling element identified, interacted physically with phototropins, auxin efflux carrier PIN-FORMED1 and calcium-binding protein CALMODULIN4, in vitro and in vivo, respectively, and HBL-induced phototropism was impaired in pks multiple mutants, indicating the role of the PKS family in HBL-induced phototropism. Together, these results provide new insights into the functions of phototropins and highlight a potential integration point through which Ca(2+) signaling-related HBL modulates hypocotyl phototropic responses.

  13. Listening to Others' Voices (LOV) Project: An Empowering Strategy Incorporating Marginalized Perspectives

    ERIC Educational Resources Information Center

    Kim, Minsung; Ryu, Jae-Myong

    2014-01-01

    This study introduces the Listening to Others' Voices (LOV) project, an empowering strategy in geography education. This research aims to create a dataset detailing the perspectives of negatively stereotyped countries with respect to how their countries are portrayed in geography textbooks and to investigate the pedagogical effects of the LOV…

  14. Listening to Others' Voices (LOV) Project: An Empowering Strategy Incorporating Marginalized Perspectives

    ERIC Educational Resources Information Center

    Kim, Minsung; Ryu, Jae-Myong

    2014-01-01

    This study introduces the Listening to Others' Voices (LOV) project, an empowering strategy in geography education. This research aims to create a dataset detailing the perspectives of negatively stereotyped countries with respect to how their countries are portrayed in geography textbooks and to investigate the pedagogical effects of the LOV…

  15. Engineering an FMN-based iLOV protein for the detection of arsenic ions.

    PubMed

    Ravikumar, Yuvaraj; Nadarajan, Saravanan Prabhu; Lee, Chong-Soon; Yun, Hyungdon

    2017-05-15

    Over the past few decades, genetically encoded fluorescent proteins have been widely used as efficient probes to explore and investigate the roles of metal ions in biological processes. The discovery of small FMN-based fluorescent proteins, such as iLOV and FbFP, has enabled researchers to exploit these fluorescent reporter proteins for metal-sensing applications. In this study, we report the inherent binding properties of iLOV towards arsenic ions. The fluorescence quenching of iLOV was linearly related to the concentration of arsenic ions, and engineered proteins showed better sensitivity than the wild-type protein. Engineering key residues around the chromophore converted the iLOV protein into a highly sensitive sensor for As(3+) ions. iLOVN468S exhibited an improved binding affinity with a dissociation constant of 1.5 μM. Furthermore, the circular dichroism spectra indicated that the fluorescence quenching mechanism might be related to arsenic-protein complex formation. Thus, the reagentless sensing of arsenic can potentially be exploited to determine intracellular or environmental arsenic using a genetically encoded biosensing approach. Copyright © 2017 Elsevier Inc. All rights reserved.

  16. A wandering pathway in plant biology: from wildflowers to phototropins to bacterial virulence.

    PubMed

    Briggs, Winslow R

    2010-01-01

    The author describes the somewhat convoluted pathway he followed from amateur taxonomy of Minnesota wildflowers to identification of the phototropin family of blue-light receptors. He also mentions individuals who were important in moving his career first into plant taxonomy, then plant development, and finally plant photobiology (and out of music). He emphasizes the many twists and turns a research career can take, including a few that lead to blind ends. He also emphasizes the oscillatory nature of his career-back and forth between the Atlantic and Pacific oceans (with occasional forays to Freiburg, Germany) and back and forth between red-light receptors and blue-light receptors. There is a short intermission in which he describes his longtime relationship with California's Henry W. Coe State Park. Finally, he relates how he followed the unlikely pathway from plant blue-light receptors to a blue-light receptor required to maximize virulence of a bacterial animal pathogen.

  17. Decoding the role of phosphoinositides in phototropin signaling involved in chloroplast movements.

    PubMed

    Aggarwal, Chhavi; Labuz, Justyna; Gabryś, Halina

    2013-08-01

    In angiosperms, light-dependent chloroplast movements are exclusively mediated by UVA/blue light receptors - phototropins. The two photoreceptors of Arabidopsis thaliana, phot1 and phot2, have overlapping roles in the control of these movements. Experiments performed in different plant species point to the participation of phosphoinositides in blue light-controlled chloroplast relocations. Here, we report a summary of recent findings presenting the involvement of phosphatidylinositol 4,5-bisphosphate as well as phosphatidylinositol 3- and 4-phosphates in weak blue light-mediated (accumulation) and strong blue light-mediated (avoidance) responses of chloroplasts. The blue light-activated alterations in phosphoinositide concentration are partly responsible for cytosolic Ca (2+) changes. Ca (2+) influx from apoplast does not seem to be involved in the mechanism of movement responses. In summary, interplay between phosphoinositides and intracellular Ca (2+) regulates chloroplast redistribution in response to blue light in higher plants.

  18. Evidence of physiological phototropin1 (phot1) action in response to UV-C illumination

    PubMed Central

    Magerøy, Melissa Hamner; Kowalik, Erin H; Folta, Kevin M

    2010-01-01

    Stem growth kinetics were measured in cucumber (Cucumis sativus) and Arabidopsis thaliana using highly-sensitive monitoring with 5-minute resolution, in darkness and in response to a short, single pulse of UV-C illumination. The results show that UV-C, like blue light, induces a rapid decrease in seedling growth rate. The fluence-response kinetics and time course were similar to the phototropin1-mediated response observed following a blue pulse. Arabidopsis seedlings were used to assess the genetic mechanism of this response. The phot1 mutant exhibited defects in stem growth rate inhibition, with sustained growth inhibition completely absent following specific treatments. The cryptochrome and phytochrome mutants exhibited responses comparable to wild type, suggesting that these receptor classes do not contribute to this response. The work demonstrates in two species that UV-C has an effect on a rapid plant photomorphogenic response and that the response is partially mediated by the phot1 photoreceptor. PMID:20861684

  19. Crystal structure and biochemical studies of the trans-acting polyketide enoyl reductase LovC from lovastatin biosynthesis

    PubMed Central

    Ames, Brian D.; Nguyen, Chi; Bruegger, Joel; Smith, Peter; Xu, Wei; Ma, Suzanne; Wong, Emily; Wong, Steven; Xie, Xinkai; Li, Jesse W.-H.; Vederas, John C.; Tang, Yi; Tsai, Shiou-Chuan

    2012-01-01

    Lovastatin is an important statin prescribed for the treatment and prevention of cardiovascular diseases. Biosynthesis of lovastatin uses an iterative type I polyketide synthase (PKS). LovC is a trans-acting enoyl reductase (ER) that specifically reduces three out of eight possible polyketide intermediates during lovastatin biosynthesis. Such trans-acting ERs have been reported across a variety of other fungal PKS enzymes as a strategy in nature to diversify polyketides. How LovC achieves such specificity is unknown. The 1.9-Å structure of LovC reveals that LovC possesses a medium-chain dehydrogenase/reductase (MDR) fold with a unique monomeric assembly. Two LovC cocrystal structures and enzymological studies help elucidate the molecular basis of LovC specificity, define stereochemistry, and identify active-site residues. Sequence alignment indicates a general applicability to trans-acting ERs of fungal PKSs, as well as their potential application to directing biosynthesis. PMID:22733743

  20. Overexpression of AtLOV1 in Switchgrass Alters Plant Architecture, Lignin Content, and Flowering Time

    PubMed Central

    Xu, Bin; Sathitsuksanoh, Noppadon; Tang, Yuhong; Udvardi, Michael K.; Zhang, Ji-Yi; Shen, Zhengxing; Balota, Maria; Harich, Kim; Zhang, Percival Y.-H.; Zhao, Bingyu

    2012-01-01

    Background Switchgrass (Panicum virgatum L.) is a prime candidate crop for biofuel feedstock production in the United States. As it is a self-incompatible polyploid perennial species, breeding elite and stable switchgrass cultivars with traditional breeding methods is very challenging. Translational genomics may contribute significantly to the genetic improvement of switchgrass, especially for the incorporation of elite traits that are absent in natural switchgrass populations. Methodology/Principal Findings In this study, we constitutively expressed an Arabidopsis NAC transcriptional factor gene, LONG VEGETATIVE PHASE ONE (AtLOV1), in switchgrass. Overexpression of AtLOV1 in switchgrass caused the plants to have a smaller leaf angle by changing the morphology and organization of epidermal cells in the leaf collar region. Also, overexpression of AtLOV1 altered the lignin content and the monolignol composition of cell walls, and caused delayed flowering time. Global gene-expression analysis of the transgenic plants revealed an array of responding genes with predicted functions in plant development, cell wall biosynthesis, and flowering. Conclusions/Significance To our knowledge, this is the first report of a single ectopically expressed transcription factor altering the leaf angle, cell wall composition, and flowering time of switchgrass, therefore demonstrating the potential advantage of translational genomics for the genetic improvement of this crop. PMID:23300513

  1. Distribution and Phylogeny of Light-Oxygen-Voltage-Blue-Light-Signaling Proteins in the Three Kingdoms of Life▿ †

    PubMed Central

    Krauss, Ulrich; Minh, Bui Quang; Losi, Aba; Gärtner, Wolfgang; Eggert, Thorsten; von Haeseler, Arndt; Jaeger, Karl-Erich

    2009-01-01

    Plants and fungi respond to environmental light stimuli via the action of different photoreceptor modules. One such class, responding to the blue region of light, is constituted by photoreceptors containing so-called light-oxygen-voltage (LOV) domains as sensor modules. Four major LOV families are currently identified in eukaryotes: (i) the plant phototropins, regulating various physiological effects such as phototropism, chloroplast relocation, and stomatal opening; (ii) the aureochromes, mediating photomorphogenesis in photosynthetic stramenopile algae; (iii) the plant circadian photoreceptors of the zeitlupe (ZTL)/adagio (ADO)/flavin-binding Kelch repeat F-box protein 1 (FKF1) family; and (iv) the fungal circadian photoreceptors white-collar 1 (WC-1). Blue-light-sensitive LOV signaling modules are also widespread throughout the prokaryotic world, and physiological responses mediated by bacterial LOV photoreceptors were recently reported. Thus, the question arises as to the evolutionary relationship between the pro- and eukaryotic LOV photoreceptor systems. We used Bayesian and maximum-likelihood tree reconstruction methods to infer evolutionary scenarios that might have led to the widespread appearance of LOV domains among the pro- and eukaryotes. The phylogenetic study presented here suggests a bacterial origin for the LOV domains of the four major eukaryotic LOV photoreceptor families, whereas the LOV sensor domains were most likely recruited from the bacteria in the course of plastid and mitochondrial endosymbiosis. PMID:19783626

  2. An experimental test of the adaptive evolution of phototropins: blue-light photoreceptors controlling phototropism in Arabidopsis thaliana.

    PubMed

    Galen, Candace; Huddle, Julie; Liscum, Emmanuel

    2004-03-01

    Phototropins are blue-light photoreceptor molecules mediating the capacity for phototropism or bending toward or away from directional light. Like the red-light sensing phytochromes that control shade avoidance, phototropins modulate developmental plasticity in plant architecture. Yet, unlike phytochromes, the adaptive significance of phototropins has been largely a topic of conjecture. In Arabidopsis thaliana, phototropism of seedling and plant stems is under the control of two paralogous genes, PHOT1 and PHOT2, that encode different phototropins with partially redundant light response qualities. The PHOT1 gene product interacts with the NPH3 gene product to cause phototropic bending over a broad range of light intensity, from very weak light in the soil to stronger light in the aerial environment. The PHOT2 gene product modulates shoot bending in response to light of higher intensity only. We compared the fitness of wild-type, phot1, phot2, and nph3 genotypes over a range of light conditions in the field. Seeds were sown in the field on the soil surface and left bare or covered with either gravel or bark mulch chips. Plantings were made under full sun and dense canopy cover. Rates of seedling emergence, survival to flowering, and total seed set were measured. All mutant genotypes had significantly reduced lifetime fitness compared to wild-type. Consistent with their different fluence rate sensitivities, phot1 and phot2 signaling pathways affected fitness at discrete life-cycle stages. Fitness costs of phot1 and nph3 were expressed mainly during seedling emergence from the soil whereas that of phot2 was expressed solely after emergence. Surprisingly, the only significant genotype-by-environment interaction for fitness occurred during emergence: genotypes blind to dim blue light (phot1 and nph3) had poor emergence in the open, but not in the shade. Possibly, the loss of negative phototropism in seedling roots of mutant genotypes reduced establishment success in

  3. Phototropin 1 and dim-blue light modulate the red light de-etiolation response

    PubMed Central

    Wang, Yihai; M Folta, Kevin

    2014-01-01

    Light signals regulate seedling morphological changes during de-etiolation through the coordinated actions of multiple light-sensing pathways. Previously we have shown that red-light-induced hypocotyl growth inhibition can be reversed by addition of dim blue light through the action of phototropin 1 (phot1). Here we further examine the fluence-rate relationships of this blue light effect in short-term (hours) and long-term (days) hypocotyl growth assays. The red stem-growth inhibition and blue promotion is a low-fluence rate response, and blue light delays or attenuates both the red light and far-red light responses. These de-etiolation responses include blue light reversal of red or far-red induced apical hook opening. This response also requires phot1. Cryptochromes (cry1 and cry2) are activated by higher blue light fluence-rates and override phot1's influence on hypocotyl growth promotion. Exogenous application of auxin transport inhibitor naphthylphthalamic acid abolished the blue light stem growth promotion in both hypocotyl growth and hook opening. Results from the genetic tests of this blue light effect in auxin transporter mutants, as well as phytochrome kinase substrate mutants indicated that aux1 may play a role in blue light reversal of red light response. Together, the phot1-mediated adjustment of phytochrome-regulated photomorphogenic events is most robust in dim blue light conditions and is likely modulated by auxin transport through its transporters. PMID:25482790

  4. Phototropin 2 is involved in blue light-induced anthocyanin accumulation in Fragaria x ananassa fruits.

    PubMed

    Kadomura-Ishikawa, Yasuko; Miyawaki, Katsuyuki; Noji, Sumihare; Takahashi, Akira

    2013-11-01

    Anthocyanins are widespread, essential secondary metabolites in higher plants during color development in certain flowers and fruits. In strawberries, anthocyanins are also key contributors to fruit antioxidant capacity and nutritional value. However, the effects of different light qualities on anthocyanin accumulation in strawberry (Fragaria x ananassa, cv. Sachinoka) fruits remain elusive. In the present study, we showed the most efficient increase in anthocyanin content occurred by blue light irradiation. Light sensing at the molecular level was investigated by isolation of two phototropin (FaPHOT1 and FaPHOT2), two cryptochrome (FaCRY1 and FaCRY2), and two phytochrome (FaPHYA and FaPHYB) homologs. Expression analysis revealed only FaPHOT2 transcripts markedly increased depending on fruit developmental stage, and a corresponding increase in anthocyanin content was detected. FaPHOT2 knockdown resulted in decreased anthocyanin content; however, overexpression increased anthocyanin content. These findings suggested blue light induced anthocyanin accumulation, and FaPHOT2 may play a role in sensing blue light, and mediating anthocyanin biosynthesis in strawberry fruits. This is the first report to find a relationship between visible light sensing, and color development in strawberry fruits.

  5. Phototropin 1 and dim-blue light modulate the red light de-etiolation response.

    PubMed

    Wang, Yihai; M Folta, Kevin

    2014-01-01

    Light signals regulate seedling morphological changes during de-etiolation through the coordinated actions of multiple light-sensing pathways. Previously we have shown that red-light-induced hypocotyl growth inhibition can be reversed by addition of dim blue light through the action of phototropin 1 (phot1). Here we further examine the fluence-rate relationships of this blue light effect in short-term (hours) and long-term (days) hypocotyl growth assays. The red stem-growth inhibition and blue promotion is a low-fluence rate response, and blue light delays or attenuates both the red light and far-red light responses. These de-etiolation responses include blue light reversal of red or far-red induced apical hook opening. This response also requires phot1. Cryptochromes (cry1 and cry2) are activated by higher blue light fluence-rates and override phot1's influence on hypocotyl growth promotion. Exogenous application of auxin transport inhibitor naphthylphthalamic acid abolished the blue light stem growth promotion in both hypocotyl growth and hook opening. Results from the genetic tests of this blue light effect in auxin transporter mutants, as well as phytochrome kinase substrate mutants indicated that aux1 may play a role in blue light reversal of red light response. Together, the phot1-mediated adjustment of phytochrome-regulated photomorphogenic events is most robust in dim blue light conditions and is likely modulated by auxin transport through its transporters.

  6. The blue light receptor Phototropin 1 suppresses lateral root growth by controlling cell elongation.

    PubMed

    Moni, A; Lee, A-Y; Briggs, W R; Han, I-S

    2015-01-01

    We investigated the relationship between the blue light receptor phototropin 1 (phot1) and lateral root growth in Arabidopsis thaliana seedlings. Fluorescence and confocal microscopy images, as well as PHOT1 mRNA expression studies provide evidence that it is highly expressed in the elongation zone of lateral roots where auxin is accumulating. However, treatment with the auxin transport inhibitor N-1-naphthylphthalamic acid significantly reduced PHOT1 expression in this zone. In addition, PHOT1 expression was higher in darkness than in light. The total number of lateral roots was higher in the phot1 mutant than in wild-type Arabidopsis. Cells in the elongation zone of lateral roots of the phot1 mutant were longer than those of wild-type lateral roots. These findings suggest that PHOT1 plays a role(s) in elongation of lateral roots through the control of an auxin-related signalling pathway. © 2014 German Botanical Society and The Royal Botanical Society of the Netherlands.

  7. A LOV Protein Modulates the Physiological Attributes of Xanthomonas axonopodis pv. citri Relevant for Host Plant Colonization

    PubMed Central

    Kraiselburd, Ivana; Alet, Analía I.; Tondo, María Laura; Petrocelli, Silvana; Daurelio, Lucas D.; Monzón, Jesica; Ruiz, Oscar A.; Losi, Aba; Orellano, Elena G.

    2012-01-01

    Recent studies have demonstrated that an appropriate light environment is required for the establishment of efficient vegetal resistance responses in several plant-pathogen interactions. The photoreceptors implicated in such responses are mainly those belonging to the phytochrome family. Data obtained from bacterial genome sequences revealed the presence of photosensory proteins of the BLUF (Blue Light sensing Using FAD), LOV (Light, Oxygen, Voltage) and phytochrome families with no known functions. Xanthomonas axonopodis pv. citri is a Gram-negative bacterium responsible for citrus canker. The in silico analysis of the X. axonopodis pv. citri genome sequence revealed the presence of a gene encoding a putative LOV photoreceptor, in addition to two genes encoding BLUF proteins. This suggests that blue light sensing could play a role in X. axonopodis pv. citri physiology. We obtained the recombinant Xac-LOV protein by expression in Escherichia coli and performed a spectroscopic analysis of the purified protein, which demonstrated that it has a canonical LOV photochemistry. We also constructed a mutant strain of X. axonopodis pv. citri lacking the LOV protein and found that the loss of this protein altered bacterial motility, exopolysaccharide production and biofilm formation. Moreover, we observed that the adhesion of the mutant strain to abiotic and biotic surfaces was significantly diminished compared to the wild-type. Finally, inoculation of orange (Citrus sinensis) leaves with the mutant strain of X. axonopodis pv. citri resulted in marked differences in the development of symptoms in plant tissues relative to the wild-type, suggesting a role for the Xac-LOV protein in the pathogenic process. Altogether, these results suggest the novel involvement of a photosensory system in the regulation of physiological attributes of a phytopathogenic bacterium. A functional blue light receptor in Xanthomonas spp. has been described for the first time, showing an important

  8. A LOV protein modulates the physiological attributes of Xanthomonas axonopodis pv. citri relevant for host plant colonization.

    PubMed

    Kraiselburd, Ivana; Alet, Analía I; Tondo, María Laura; Petrocelli, Silvana; Daurelio, Lucas D; Monzón, Jesica; Ruiz, Oscar A; Losi, Aba; Orellano, Elena G

    2012-01-01

    Recent studies have demonstrated that an appropriate light environment is required for the establishment of efficient vegetal resistance responses in several plant-pathogen interactions. The photoreceptors implicated in such responses are mainly those belonging to the phytochrome family. Data obtained from bacterial genome sequences revealed the presence of photosensory proteins of the BLUF (Blue Light sensing Using FAD), LOV (Light, Oxygen, Voltage) and phytochrome families with no known functions. Xanthomonas axonopodis pv. citri is a Gram-negative bacterium responsible for citrus canker. The in silico analysis of the X. axonopodis pv. citri genome sequence revealed the presence of a gene encoding a putative LOV photoreceptor, in addition to two genes encoding BLUF proteins. This suggests that blue light sensing could play a role in X. axonopodis pv. citri physiology. We obtained the recombinant Xac-LOV protein by expression in Escherichia coli and performed a spectroscopic analysis of the purified protein, which demonstrated that it has a canonical LOV photochemistry. We also constructed a mutant strain of X. axonopodis pv. citri lacking the LOV protein and found that the loss of this protein altered bacterial motility, exopolysaccharide production and biofilm formation. Moreover, we observed that the adhesion of the mutant strain to abiotic and biotic surfaces was significantly diminished compared to the wild-type. Finally, inoculation of orange (Citrus sinensis) leaves with the mutant strain of X. axonopodis pv. citri resulted in marked differences in the development of symptoms in plant tissues relative to the wild-type, suggesting a role for the Xac-LOV protein in the pathogenic process. Altogether, these results suggest the novel involvement of a photosensory system in the regulation of physiological attributes of a phytopathogenic bacterium. A functional blue light receptor in Xanthomonas spp. has been described for the first time, showing an important

  9. Phototropin encoded by a single-copy gene mediates chloroplast photorelocation movements in the liverwort Marchantia polymorpha.

    PubMed

    Komatsu, Aino; Terai, Mika; Ishizaki, Kimitsune; Suetsugu, Noriyuki; Tsuboi, Hidenori; Nishihama, Ryuichi; Yamato, Katsuyuki T; Wada, Masamitsu; Kohchi, Takayuki

    2014-09-01

    Blue-light-induced chloroplast photorelocation movement is observed in most land plants. Chloroplasts move toward weak-light-irradiated areas to efficiently absorb light (the accumulation response) and escape from strong-light-irradiated areas to avoid photodamage (the avoidance response). The plant-specific kinase phototropin (phot) is the blue-light receptor for chloroplast movements. Although the molecular mechanisms for chloroplast photorelocation movement have been analyzed, the overall aspects of signal transduction common to land plants are still unknown. Here, we show that the liverwort Marchantia polymorpha exhibits the accumulation and avoidance responses exclusively induced by blue light as well as specific chloroplast positioning in the dark. Moreover, in silico and Southern-blot analyses revealed that the M. polymorpha genome encodes a single PHOT gene, MpPHOT, and its knockout line displayed none of the chloroplast photorelocation movements, indicating that the sole MpPHOT gene mediates all types of movement. Mpphot was localized on the plasma membrane and exhibited blue-light-dependent autophosphorylation both in vitro and in vivo. Heterologous expression of MpPHOT rescued the defects in chloroplast movement of phot mutants in the fern Adiantum capillus-veneris and the seed plant Arabidopsis (Arabidopsis thaliana). These results indicate that Mpphot possesses evolutionarily conserved regulatory activities for chloroplast photorelocation movement. M. polymorpha offers a simple and versatile platform for analyzing the fundamental processes of phototropin-mediated chloroplast photorelocation movement common to land plants.

  10. Hypocotyl growth orientation in blue light is determined by phytochrome A inhibition of gravitropism and phototropin promotion of phototropism.

    PubMed

    Lariguet, Patricia; Fankhauser, Christian

    2004-12-01

    How developing seedlings integrate gravitropic and phototropic stimuli to determine their direction of growth is poorly understood. In this study we tested whether blue light influences hypocotyl gravitropism in Arabidopsis. Phototropin1 (phot1) triggers phototropism under low fluence rates of blue light but, at least in the dark, has no effect on gravitropism. By analyzing the growth orientation of phototropism-deficient seedlings in response to gravitropic and phototropic stimulations we show that blue light not only triggers phototropism but also represses hypocotyl gravitropism. At low fluence rates of blue light phot1 mutants were agravitropic. In contrast, phyAphot1 double mutants grew exclusively according to gravity demonstrating that phytochrome A (phyA) is necessary to inhibit gravitropism. Analyses of phot1cry1cry2 triple mutants indicate that cryptochromes play a minor role in this response. Thus the optimal growth orientation of hypocotyls is determined by the action of phyA-suppressing gravitropism and the phototropin-triggering phototropism. It has long been known that phytochromes promote phototropism but the mechanism involved is still unknown. Our data show that by inhibiting gravitropism phyA acts as a positive regulator of phototropism.

  11. Phototropin Encoded by a Single-Copy Gene Mediates Chloroplast Photorelocation Movements in the Liverwort Marchantia polymorpha1[W

    PubMed Central

    Komatsu, Aino; Terai, Mika; Ishizaki, Kimitsune; Suetsugu, Noriyuki; Tsuboi, Hidenori; Nishihama, Ryuichi; Yamato, Katsuyuki T.; Wada, Masamitsu; Kohchi, Takayuki

    2014-01-01

    Blue-light-induced chloroplast photorelocation movement is observed in most land plants. Chloroplasts move toward weak-light-irradiated areas to efficiently absorb light (the accumulation response) and escape from strong-light-irradiated areas to avoid photodamage (the avoidance response). The plant-specific kinase phototropin (phot) is the blue-light receptor for chloroplast movements. Although the molecular mechanisms for chloroplast photorelocation movement have been analyzed, the overall aspects of signal transduction common to land plants are still unknown. Here, we show that the liverwort Marchantia polymorpha exhibits the accumulation and avoidance responses exclusively induced by blue light as well as specific chloroplast positioning in the dark. Moreover, in silico and Southern-blot analyses revealed that the M. polymorpha genome encodes a single PHOT gene, MpPHOT, and its knockout line displayed none of the chloroplast photorelocation movements, indicating that the sole MpPHOT gene mediates all types of movement. Mpphot was localized on the plasma membrane and exhibited blue-light-dependent autophosphorylation both in vitro and in vivo. Heterologous expression of MpPHOT rescued the defects in chloroplast movement of phot mutants in the fern Adiantum capillus-veneris and the seed plant Arabidopsis (Arabidopsis thaliana). These results indicate that Mpphot possesses evolutionarily conserved regulatory activities for chloroplast photorelocation movement. M. polymorpha offers a simple and versatile platform for analyzing the fundamental processes of phototropin-mediated chloroplast photorelocation movement common to land plants. PMID:25096976

  12. The Enhancement of Phototropin-Induced Phototropic Curvature in Arabidopsis Occurs via a Photoreversible Phytochrome A-Dependent Modulation of Auxin Responsiveness1

    PubMed Central

    Stowe-Evans, Emily L.; Luesse, Darron R.; Liscum, Emmanuel

    2001-01-01

    The induction of phototropism in etiolated (dark-grown) seedlings exposed to an unidirectional pulse or extended irradiation with low fluence rate blue light (BL) requires the action of the phototropin (nph1) BL receptor. Although cryptochromes and phytochromes are not required for phototropic induction, these photoreceptors do modulate the magnitude of curvature resulting from phototropin activation. Modulatory increases in the magnitude of phototropic curvature have been termed “enhancement.” Here, we show that phototropic enhancement is primarily a phytochrome A (phyA)-dependent red/far-red-reversible low fluence response. This phyA-dependent response is genetically separable from the basal phototropin-dependent response, as demonstrated by its retention under extended irradiation conditions in the nph4 mutant background, which normally lacks the basal BL-induced response. It is interesting that the nph4 mutants fail to exhibit the basal phototropin-dependent and phyA-dependent enhancement responses under limiting light conditions. Given that NPH4 encodes a transcriptional activator, auxin response factor 7 (ARF7), we hypothesize that the ultimate target(s) of phyA action during the phototropic enhancement response is a rate-limiting ARF-containing transcriptional complex in which the constituent ARFs can vary in identity or activity depending upon the irradiation condition. PMID:11402210

  13. Phototropins Function in High-Intensity Blue Light-Induced Hypocotyl Phototropism in Arabidopsis by Altering Cytosolic Calcium1[C][W][OA

    PubMed Central

    Zhao, Xiang; Wang, Yan-Liang; Qiao, Xin-Rong; Wang, Jin; Wang, Lin-Dan; Xu, Chang-Shui; Zhang, Xiao

    2013-01-01

    Phototropins (phot1 and phot2), the blue light receptors in plants, regulate hypocotyl phototropism in a fluence-dependent manner. Especially under high fluence rates of blue light (HBL), the redundant function mediated by both phot1 and phot2 drastically restricts the understanding of the roles of phot2. Here, systematic analysis of phototropin-related mutants and overexpression transgenic lines revealed that HBL specifically induced a transient increase in cytosolic Ca2+ concentration ([Ca2+]cyt) in Arabidopsis (Arabidopsis thaliana) hypocotyls and that the increase in [Ca2+]cyt was primarily attributed to phot2. Pharmacological and genetic experiments illustrated that HBL-induced Ca2+ increases were modulated differently by phot1 and phot2. Phot2 mediated the HBL-induced increase in [Ca2+]cyt mainly by an inner store-dependent Ca2+-release pathway, not by activating plasma membrane Ca2+ channels. Further analysis showed that the increase in [Ca2+]cyt was possibly responsible for HBL-induced hypocotyl phototropism. An inhibitor of auxin efflux carrier exhibited significant inhibitions of both phototropism and increases in [Ca2+]cyt, which indicates that polar auxin transport is possibly involved in HBL-induced responses. Moreover, PHYTOCHROME KINASE SUBSTRATE1 (PKS1), the phototropin-related signaling element identified, interacted physically with phototropins, auxin efflux carrier PIN-FORMED1 and calcium-binding protein CALMODULIN4, in vitro and in vivo, respectively, and HBL-induced phototropism was impaired in pks multiple mutants, indicating the role of the PKS family in HBL-induced phototropism. Together, these results provide new insights into the functions of phototropins and highlight a potential integration point through which Ca2+ signaling-related HBL modulates hypocotyl phototropic responses. PMID:23674105

  14. Diversity of yeasts from puddles in the vicinity of midre lovénbreen glacier, arctic and bioprospecting for enzymes and fatty acids.

    PubMed

    Pathan, Akbar Ali Khan; Bhadra, Bhaskar; Begum, Zareena; Shivaji, Sisinthy

    2010-04-01

    A total of 132 yeast strains were characterised from 4 sediment samples collected from small puddles in the vicinity of Midre Lovénbreen glacier, Arctic. Based on the D1/D2 domain sequence similarity, the isolates could be categorised into 6 groups. The nearest phylogenetic neighbour of groups I to VI were identified as Cryptococcus gastricus, Cryptococcus terricolus, Rhodotorula muscorum, Mrakia psychrophila, Mrakia gelida and Rhodotorula glacialis, respectively. Strains representative of the six groups were psychrophilic and salt tolerant but varied in their ability to produce cold-active extracellular enzymes such as lipase, protease, pectinase, cellulase and amylase. C(18:1 (w9C)) and C(18:2 (w9,12C)) were the only two fatty acids common to all the yeasts and branched and (or) unsaturated fatty acids increased in yeasts growing at 8 degrees C compared to 22 degrees C, probably as an adaptation to low temperature. The present study establishes that psychrophilic yeasts are predominant in Arctic and could be used as work horses to produce cold-active enzymes and poly unsaturated fatty acids which have been implicated in low temperature adaptation and also for their use in biotechnology.

  15. Quantum Mechanics/Molecular Mechanics Study on the Photoreactions of Dark- and Light-Adapted States of a Blue-Light YtvA LOV Photoreceptor.

    PubMed

    Chang, Xue-Ping; Gao, Yuan-Jun; Fang, Wei-Hai; Cui, Ganglong; Thiel, Walter

    2017-08-01

    The dark- and light-adapted states of YtvA LOV domains exhibit distinct excited-state behavior. We have employed high-level QM(MS-CASPT2)/MM calculations to study the photochemical reactions of the dark- and light-adapted states. The photoreaction from the dark-adapted state starts with an S1 →T1 intersystem crossing followed by a triplet-state hydrogen transfer from the thiol to the flavin moiety that produces a diradical intermediate, and a subsequent internal conversion that triggers a barrierless C-S bond formation in the S0 state. The energy profiles for these transformations are different for the four conformers of the dark-adapted state considered. The photochemistry of the light-adapted state does not involve the triplet state: photoexcitation to the S1 state triggers C-S bond cleavage followed by recombination in the S0 state; both these processes are essentially barrierless and thus ultrafast. The present work offers new mechanistic insights into the photoresponse of flavin-containing blue-light photoreceptors. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. Investigations on the photoregulation of chloroplast movement and leaf positioning in Arabidopsis.

    PubMed

    Han, In-Seob; Cho, Hae-Young; Moni, Akhi; Lee, Ah-Young; Briggs, Winslow R

    2013-01-01

    We recently investigated the roles of the phototropin 1 (PHOT1) LOV (light, oxygen or voltage) domains in mediating phototropic curvature in transgenic Arabidopsis seedlings expressing either wild-type PHOT1 or PHOT1 with one or both LOV domains inactivated by a single amino acid replacement. We have now investigated the role of the PHOT1 LOV domains in chloroplast movement and in leaf positioning in response to blue light. Low fluence rate blue light is known to mediate a chloroplast accumulation response and high fluence rate blue light an avoidance response in Arabidopsis leaves. As was the case for phototropism, LOV2 of PHOT1 is essential for chloroplast accumulation and LOV1 is dispensable. PHOT1 LOV2 is also essential to maintain developing primary leaves in a horizontal position under white light from above and LOV1 is again dispensable. A red light pulse given to dark-adapted light-grown plants followed by 2 h of darkness enhances both the chloroplast accumulation response under dim blue light and the chloroplast avoidance response under strong blue light. The effect is far-red reversible. This photoreversible response is normal in a phyB null mutant but does not appear in a phyA null mutant. These results suggest that phyA mediates the enhancement, induced by a red light pulse, of blue light-induced chloroplast movements.

  17. The Arabidopsis PHYTOCHROME KINASE SUBSTRATE2 Protein Is a Phototropin Signaling Element That Regulates Leaf Flattening and Leaf Positioning1[W][OA

    PubMed Central

    de Carbonnel, Matthieu; Davis, Phillip; Roelfsema, M. Rob G.; Inoue, Shin-ichiro; Schepens, Isabelle; Lariguet, Patricia; Geisler, Markus; Shimazaki, Ken-ichiro; Hangarter, Roger; Fankhauser, Christian

    2010-01-01

    In Arabidopsis (Arabidopsis thaliana), the blue light photoreceptor phototropins (phot1 and phot2) fine-tune the photosynthetic status of the plant by controlling several important adaptive processes in response to environmental light variations. These processes include stem and petiole phototropism (leaf positioning), leaf flattening, stomatal opening, and chloroplast movements. The PHYTOCHROME KINASE SUBSTRATE (PKS) protein family comprises four members in Arabidopsis (PKS1–PKS4). PKS1 is a novel phot1 signaling element during phototropism, as it interacts with phot1 and the important signaling element NONPHOTOTROPIC HYPOCOTYL3 (NPH3) and is required for normal phot1-mediated phototropism. In this study, we have analyzed more globally the role of three PKS members (PKS1, PKS2, and PKS4). Systematic analysis of mutants reveals that PKS2 (and to a lesser extent PKS1) act in the same subset of phototropin-controlled responses as NPH3, namely leaf flattening and positioning. PKS1, PKS2, and NPH3 coimmunoprecipitate with both phot1-green fluorescent protein and phot2-green fluorescent protein in leaf extracts. Genetic experiments position PKS2 within phot1 and phot2 pathways controlling leaf positioning and leaf flattening, respectively. NPH3 can act in both phot1 and phot2 pathways, and synergistic interactions observed between pks2 and nph3 mutants suggest complementary roles of PKS2 and NPH3 during phototropin signaling. Finally, several observations further suggest that PKS2 may regulate leaf flattening and positioning by controlling auxin homeostasis. Together with previous findings, our results indicate that the PKS proteins represent an important family of phototropin signaling proteins. PMID:20071603

  18. Light-induced nuclear export reveals rapid dynamics of epigenetic modifications

    PubMed Central

    Yumerefendi, Hayretin; Lerner, Andrew Michael; Zimmerman, Seth Parker; Hahn, Klaus; Bear, James E; Strahl, Brian D.; Kuhlman, Brian

    2016-01-01

    We engineered a photoactivatable system for rapidly and reversibly exporting proteins from the nucleus by embedding a nuclear export signal in the LOV2 domain from phototropin 1. Fusing the chromatin modifier Bre1 to the photoswitch, we achieved light-dependent control of histone H2B monoubiquitylation in yeast, revealing fast turnover of the ubiquitin mark. Moreover, this inducible system allowed us to dynamically monitor the status of epigenetic modifications dependent on H2B ubiquitylation. PMID:27089030

  19. Optogenetics: optical control of a photoactivatable Rac in living cells.

    PubMed

    Yin, Taofei; Wu, Yi I

    2015-01-01

    Recent developments in optogenetics have extended optical control of signaling to intracellular proteins, including Rac, a small G protein in the Rho family. A blue light-sensing LOV (light, oxygen, or voltage) domain derived from Avena sativa (oat) phototropin was fused to the N-terminus of a constitutively active mutant of Rac, via an α-helix (Jα) that is conserved among plant phototropins. The fused LOV domain occluded binding of downstream effectors to Rac in the dark. Exposure to blue light caused a conformational change of the LOV domain and unwinding of the Jα helix, relieving steric inhibition. The LOV domain incorporates a flavin as the photon-absorbing cofactor and can be activated by light in a reversible and repeatable fashion. In cultured cells, global illumination with blue light rapidly activated Rac and led to cell spreading and membrane ruffling. Localized and pulsed illumination generated a gradient of Rac activity and induced directional migration. In this chapter, we will describe the techniques in detail and present some examples of applications of using photoactivatable Rac (PA-Rac) in living cells.

  20. Lab on valve-multisyringe flow injection system (LOV-MSFIA) for fully automated uranium determination in environmental samples.

    PubMed

    Avivar, Jessica; Ferrer, Laura; Casas, Montserrat; Cerdà, Víctor

    2011-06-15

    The hyphenation of lab-on-valve (LOV) and multisyringe flow analysis (MSFIA), coupled to a long path length liquid waveguide capillary cell (LWCC), allows the spectrophotometric determination of uranium in different types of environmental sample matrices, without any manual pre-treatment, and achieving high selectivity and sensitivity levels. On-line separation and preconcentration of uranium is carried out by means of UTEVA resin. The potential of the LOV-MSFIA makes possible the fully automation of the system by the in-line regeneration of the column. After elution, uranium(VI) is spectrophotometrically detected after reaction with arsenazo-III. The determination of levels of uranium present in environmental samples is required in order to establish an environmental control. Thus, we propose a rapid, cheap and fully automated method to determine uranium(VI) in environmental samples. The limit of detection reached is 1.9 ηg of uranium and depending on the preconcentrated volume; it results in ppt levels (10.3 ηg L(-1)). Different water sample matrices (seawater, well water, freshwater, tap water and mineral water) and a phosphogypsum sample (with natural uranium content) were satisfactorily analyzed.

  1. The subcellular localization and blue-light-induced movement of phototropin 1-GFP in etiolated seedlings of Arabidopsis thaliana.

    PubMed

    Wan, Ying-Lang; Eisinger, William; Ehrhardt, David; Kubitscheck, Ulrich; Baluska, Frantisek; Briggs, Winslow

    2008-01-01

    Phototropin 1 (phot1) is a photoreceptor for phototropism, chloroplast movement, stomatal opening, leaf expansion, and solar tracking in response to blue light. Following earlier work with PHOT1::GFP (Sakamoto and Briggs, 2002), we investigated the pattern of cellular and subcellular localization of phot1 in 3- 4-d-old etiolated seedlings of Arabidopsis thalinana. As expressed from native upstream sequences, the PHOT1::GFP fusion protein is expressed strongly in the abaxial tissues of the cotyledons and in the elongating regions of the hypocotyl. It is moderately expressed in the shoot/root transition zone and in cells near the root apex. A fluorescence signal is undetectable in the root epidermis, root cap, and root apical meristem itself. The plasma membranes of mesophyll cells near the cotyledon margin appear labeled uniformly but cross-walls created by recent cell divisions are more strongly labeled. The pattern of labeling of individual cell types varies with cell type and developmental stage. Blue-light treatment causes PHOT1::GFP, initially relatively evenly distributed at the plasma membrane, to become reorganized into a distinct mosaic with strongly labeled punctate areas and other areas completely devoid of fluorescence--a phenomenon best observed in cortical cells in the hypocotyl elongation region. Concomitant with or following this reorganization, PHOT1::GFP moves into the cytoplasm in all cell types investigated except for guard cells. It disappears from the cytoplasm by an unidentified mechanism after several hours in darkness. Neither its appearance in the cytoplasm nor its eventual disappearance in darkness is prevented by the translation inhibitor cycloheximide, although the latter process is retarded. We hypothesize that blue-light-induced phot1 re-localization modulates blue-light-activated signal transduction.

  2. Primary Inhibition of Hypocotyl Growth and Phototropism Depend Differently on Phototropin-Mediated Increases in Cytoplasmic Calcium Induced by Blue Light1

    PubMed Central

    Folta, Kevin M.; Lieg, Erin J.; Durham, Tessa; Spalding, Edgar P.

    2003-01-01

    The phototropin photoreceptors transduce blue-light signals into several physiological and developmental responses in plants. A transient rise in cytoplasmic calcium (Ca2+) that begins within seconds of phototropin 1 (phot1) excitation is believed to be an important element in the transduction pathways leading to one or more of the phot1-dependent responses. The goal of the present work was to determine whether the Ca2+ response was necessary for (a) the inhibition of hypocotyl elongation that develops within minutes of the irradiation, and (b) hypocotyl phototropism (curved growth of the stem in response to asymmetric illumination). After determining that pulses of light delivering photon fluences of between 1 and 1,000 μmol m-2 induced growth inhibition mediated by phot1 without significant interference from other photosensory pathways, the effect of blocking the Ca2+ rise was assessed. Treatment of seedlings with a Ca2+ chelator prevented the rise in cytoplasmic Ca2+ and prevented phot1-mediated growth inhibition. However, the same chelator treatment did not impair phot1-mediated phototropism. Thus, it appears that the early, transient rise in cytoplasmic Ca2+ is an important intermediary process in at least one but not all phot1-signaling pathways. PMID:14645723

  3. Primary inhibition of hypocotyl growth and phototropism depend differently on phototropin-mediated increases in cytoplasmic calcium induced by blue light.

    PubMed

    Folta, Kevin M; Lieg, Erin J; Durham, Tessa; Spalding, Edgar P

    2003-12-01

    The phototropin photoreceptors transduce blue-light signals into several physiological and developmental responses in plants. A transient rise in cytoplasmic calcium (Ca2+) that begins within seconds of phototropin 1 (phot1) excitation is believed to be an important element in the transduction pathways leading to one or more of the phot1-dependent responses. The goal of the present work was to determine whether the Ca2+ response was necessary for (a). the inhibition of hypocotyl elongation that develops within minutes of the irradiation, and (b). hypocotyl phototropism (curved growth of the stem in response to asymmetric illumination). After determining that pulses of light delivering photon fluences of between 1 and 1000 micromol m-2 induced growth inhibition mediated by phot1 without significant interference from other photosensory pathways, the effect of blocking the Ca2+ rise was assessed. Treatment of seedlings with a Ca2+ chelator prevented the rise in cytoplasmic Ca2+ and prevented phot1-mediated growth inhibition. However, the same chelator treatment did not impair phot1-mediated phototropism. Thus, it appears that the early, transient rise in cytoplasmic Ca2+ is an important intermediary process in at least one but not all phot1-signaling pathways.

  4. Blue light-induced phototropism of inflorescence stems and petioles is mediated by phototropin family members phot1 and phot2.

    PubMed

    Kagawa, Takatoshi; Kimura, Mitsuhiro; Wada, Masamitsu

    2009-10-01

    Phototropin family photoreceptors, phot1 and phot2, in Arabidopsis thaliana control the blue light (BL)-mediated phototropic responses of the hypocotyl, chloroplast relocation movement and stomatal opening. Phototropic responses in dark-grown tissues have been well studied but those in de-etiolated green plants are not well understood. Here, we analyzed phototropic responses of inflorescence stems and petioles of wild-type and phototropin mutant plants of A. thaliana. Similar to the results obtained from dark-grown seedlings, inflorescence stems and petioles in wild-type and phot2 mutant plants showed phototropic bending towards low fluence BL, while in phot1 mutant plants, a high fluence rate of BL was required. phot1 phot2 double mutant plants did not show any phototropic responses even under very high fluence rates of BL. We further studied the photoreceptive sites for phototropic responses of stems and petioles by partial tissue irradiation. The whole part of the inflorescence stem is sensitive to BL and shows phototropism, but in the petiole only the irradiated abaxial side is sensitive. Similar to dark-grown etiolated seedlings, phot1 plays a major role in phototropic responses under weak light, but phot2 functions under high fluence rate conditions in green plants.

  5. Phototropin plays a crucial role in controlling changes in chemotaxis during the initial phase of the sexual life cycle in Chlamydomonas.

    PubMed

    Ermilova, Elena V; Zalutskaya, Zhanna M; Huang, Kaiyao; Beck, Christoph F

    2004-07-01

    During sexual differentiation, Chlamydomonas reinhardtii changes its chemotactic behavior in response to ammonium. Just like gamete formation, the change in chemotaxis mode is controlled by the sequential action of two environmental cues, removal of ammonium or nitrate from the medium and light. Thus, vegetative cells and mating incompetent pre-gametes, the latter being generated by nitrogen starvation in the dark, exhibit chemotaxis towards ammonium. Irradiation of pre-gametes results in a loss of chemotaxis and the gaining of mating competence. Incubation of these gametes in the dark resulted in their regaining chemotactic activity; re-illumination again resulted in its loss. Blue light was shown to be most effective in switching-off chemotaxis. RNA-interference strains with reduced levels of the blue-light receptor phototropin showed an attenuated inactivation of chemotaxis that could be partially compensated by the application of higher fluence rates, suggesting that these light responses are mediated by phototropin. The sharing of photoreceptor and signal transduction components as well as similar temporal patterns observed for changes in chemotaxis towards ammonium and gametic differentiation suggest an integration of the signaling pathways that control these two responses.

  6. Allosteric communication between DNA-binding and light-responsive domains of diatom class I aureochromes

    PubMed Central

    Banerjee, Ankan; Herman, Elena; Serif, Manuel; Maestre-Reyna, Manuel; Hepp, Sebastian; Pokorny, Richard; Kroth, Peter G.; Essen, Lars-Oliver; Kottke, Tilman

    2016-01-01

    The modular architecture of aureochrome blue light receptors, found in several algal groups including diatoms, is unique by having the LOV-type photoreceptor domain fused to the C-terminus of its putative effector, an N-terminal DNA-binding bZIP module. The structural and functional understanding of aureochromes’ light-dependent signaling mechanism is limited, despite their promise as an optogenetic tool. We show that class I aureochromes 1a and 1c from the diatom Phaeodactylum tricornutum are regulated in a light-independent circadian rhythm. These aureochromes are capable to form functional homo- and heterodimers, which recognize the ACGT core sequence within the canonical ‘aureo box’, TGACGT, in a light-independent manner. The bZIP domain holds a more folded and less flexible but extended conformation in the duplex DNA-bound state. FT-IR spectroscopy in the absence and the presence of DNA shows light-dependent helix unfolding in the LOV domain, which leads to conformational changes in the bZIP region. The solution structure of DNA bound to aureochrome points to a tilted orientation that was further validated by molecular dynamics simulations. We propose that aureochrome signaling relies on an allosteric pathway from LOV to bZIP that results in conformational changes near the bZIP-DNA interface without major effects on the binding affinity. PMID:27179025

  7. Penicillin-binding protein 2 is essential in wild-type Escherichia coli but not in lov or cya mutants.

    PubMed Central

    Ogura, T; Bouloc, P; Niki, H; D'Ari, R; Hiraga, S; Jaffé, A

    1989-01-01

    Penicillin-binding protein 2 (PBP2), target of the beta-lactam mecillinam, is required for rod morphology and cell wall elongation in Escherichia coli. A new temperature-sensitive PBP2 allele and an in vitro-constructed insertion deletion allele were shown to be lethal in wild-type strains, establishing that the activity of this protein is essential. Mutations in the lov or cya genes, conferring mecillinam resistance, compensated for the deleterious effect of the absence of PBP2. The resulting double mutants grew as spheres. In a cya mutant lacking PBP2, the restoration of a Cya+ phenotype by addition of cyclic AMP caused lethality and a block in cell division. These results show that in wild-type cells, PBP2 is essential for growth and division. PMID:2656638

  8. MSFIA-LOV system for (226)Ra isolation and pre-concentration from water samples previous radiometric detection.

    PubMed

    Rodríguez, Rogelio; Borràs, Antoni; Leal, Luz; Cerdà, Víctor; Ferrer, Laura

    2016-03-10

    An automatic system based on multisyringe flow injection analysis (MSFIA) and lab-on-valve (LOV) flow techniques for separation and pre-concentration of (226)Ra from drinking and natural water samples has been developed. The analytical protocol combines two different procedures: the Ra adsorption on MnO2 and the BaSO4 co-precipitation, achieving more selectivity especially in water samples with low radium levels. Radium is adsorbed on MnO2 deposited on macroporous of bead cellulose. Then, it is eluted with hydroxylamine to transform insoluble MnO2 to soluble Mn(II) thus freeing Ra, which is then coprecipitated with BaSO4. The (226)Ra can be directly detected in off-line mode using a low background proportional counter (LBPC) or through a liquid scintillation counter (LSC), after performing an on-line coprecipitate dissolution. Thus, the versatility of the proposed system allows the selection of the radiometric detection technique depending on the detector availability or the required response efficiency (sample number vs. response time and limit of detection). The MSFIA-LOV system improves the precision (1.7% RSD), and the extraction frequency (up to 3 h(-1)). Besides, it has been satisfactorily applied to different types of water matrices (tap, mineral, well and sea water). The (226)Ra minimum detectable activities (LSC: 0.004 Bq L(-1); LBPC: 0.02 Bq L(-1)) attained by this system allow to reach the guidance values proposed by the relevant international agencies e.g. WHO, EPA and EC. Copyright © 2016 Elsevier B.V. All rights reserved.

  9. Monitoring seasonal snow dynamics using ground based high resolution photography (Austre Lovénbreen, Svalbard, 79°N)

    NASA Astrophysics Data System (ADS)

    Bernard, É.; Friedt, J. M.; Tolle, F.; Griselin, M.; Martin, G.; Laffly, D.; Marlin, C.

    2013-01-01

    Arctic glaciers are reliable indicators of global climate changes. However, monitoring snow and ice dynamics in Arctic regions is challenging: some fast but key events can be missed since they are short in time but significant in the hydrological budget. In the context of long term monitoring with high temporal and spatial resolutions of the snow cover dynamics, automated digital cameras were installed around the Austre Lovénbreen glacier basin (Spitsbergen, Norway, 79°N). Despite data losses due to rough weather conditions and control electronics failure, a dataset of 2411 pictures (out of an expected 3294) was gathered over a 1 year hydrological period to assess the snow coverage of the glacier as a function of time with daily resolution. 73% of the total number of expected images was thus recorded, with gaps associated with temporary electronics or data storage failure. The six camera stations oriented so as to observe the glacier itself provide a surface coverage of 96%. Furthermore, geometric corrections of the pictures, using reference ground control points located on the glacier through GPS receivers, yield a quantitative information from initially qualitative images. Projecting the resulting mosaic of the images gathered from six cameras on a GIS allows for the precise monitoring of ice-related processes, and especially the snow coverage evolution over time. This paper summarizes our current understanding of such dynamics, based on the analysis of daily mosaics of images allowing for the observation of both long term evolution on the seasonal scale and the short term events on a weekly scale. Such results demonstrated over one typical full hydrological season (April-October 2009) that snow coverage evolves following discrete steps, either due to water precipitation or warm events, with a snow coverage ranging from 100% (april) to 37% (September).

  10. Engineering light-inducible nuclear localization signals for precise spatiotemporal control of protein dynamics in living cells.

    PubMed

    Niopek, Dominik; Benzinger, Dirk; Roensch, Julia; Draebing, Thomas; Wehler, Pierre; Eils, Roland; Di Ventura, Barbara

    2014-07-14

    The function of many eukaryotic proteins is regulated by highly dynamic changes in their nucleocytoplasmic distribution. The ability to precisely and reversibly control nuclear translocation would, therefore, allow dissecting and engineering cellular networks. Here we develop a genetically encoded, light-inducible nuclear localization signal (LINuS) based on the LOV2 domain of Avena sativa phototropin 1. LINuS is a small, versatile tag, customizable for different proteins and cell types. LINuS-mediated nuclear import is fast and reversible, and can be tuned at different levels, for instance, by introducing mutations that alter AsLOV2 domain photo-caging properties or by selecting nuclear localization signals (NLSs) of various strengths. We demonstrate the utility of LINuS in mammalian cells by controlling gene expression and entry into mitosis with blue light.

  11. TULIPs: tunable, light-controlled interacting protein tags for cell biology.

    PubMed

    Strickland, Devin; Lin, Yuan; Wagner, Elizabeth; Hope, C Matthew; Zayner, Josiah; Antoniou, Chloe; Sosnick, Tobin R; Weiss, Eric L; Glotzer, Michael

    2012-03-04

    Naturally photoswitchable proteins offer a means of directly manipulating the formation of protein complexes that drive a diversity of cellular processes. We developed tunable light-inducible dimerization tags (TULIPs) based on a synthetic interaction between the LOV2 domain of Avena sativa phototropin 1 (AsLOV2) and an engineered PDZ domain (ePDZ). TULIPs can recruit proteins to diverse structures in living yeast and mammalian cells, either globally or with precise spatial control using a steerable laser. The equilibrium binding and kinetic parameters of the interaction are tunable by mutation, making TULIPs readily adaptable to signaling pathways with varying sensitivities and response times. We demonstrate the utility of TULIPs by conferring light sensitivity to functionally distinct components of the yeast mating pathway and by directing the site of cell polarization.

  12. Engineering light-inducible nuclear localization signals for precise spatiotemporal control of protein dynamics in living cells

    PubMed Central

    Niopek, Dominik; Benzinger, Dirk; Roensch, Julia; Draebing, Thomas; Wehler, Pierre; Eils, Roland; Di Ventura, Barbara

    2014-01-01

    The function of many eukaryotic proteins is regulated by highly dynamic changes in their nucleocytoplasmic distribution. The ability to precisely and reversibly control nuclear translocation would, therefore, allow dissecting and engineering cellular networks. Here we develop a genetically encoded, light-inducible nuclear localization signal (LINuS) based on the LOV2 domain of Avena sativa phototropin 1. LINuS is a small, versatile tag, customizable for different proteins and cell types. LINuS-mediated nuclear import is fast and reversible, and can be tuned at different levels, for instance, by introducing mutations that alter AsLOV2 domain photo-caging properties or by selecting nuclear localization signals (NLSs) of various strengths. We demonstrate the utility of LINuS in mammalian cells by controlling gene expression and entry into mitosis with blue light. PMID:25019686

  13. The signal transducer NPH3 integrates the phototropin1 photosensor with PIN2-based polar auxin transport in Arabidopsis root phototropism.

    PubMed

    Wan, Yinglang; Jasik, Jan; Wang, Li; Hao, Huaiqing; Volkmann, Dieter; Menzel, Diedrik; Mancuso, Stefano; Baluška, František; Lin, Jinxing

    2012-02-01

    Under blue light (BL) illumination, Arabidopsis thaliana roots grow away from the light source, showing a negative phototropic response. However, the mechanism of root phototropism is still unclear. Using a noninvasive microelectrode system, we showed that the BL sensor phototropin1 (phot1), the signal transducer NONPHOTOTROPIC HYPOCOTYL3 (NPH3), and the auxin efflux transporter PIN2 were essential for BL-induced auxin flux in the root apex transition zone. We also found that PIN2-green fluorescent protein (GFP) localized to vacuole-like compartments (VLCs) in dark-grown root epidermal and cortical cells, and phot1/NPH3 mediated a BL-initiated pathway that caused PIN2 redistribution to the plasma membrane. When dark-grown roots were exposed to brefeldin A (BFA), PIN2-GFP remained in VLCs in darkness, and BL caused PIN2-GFP disappearance from VLCs and induced PIN2-GFP-FM4-64 colocalization within enlarged compartments. In the nph3 mutant, both dark and BL BFA treatments caused the disappearance of PIN2-GFP from VLCs. However, in the phot1 mutant, PIN2-GFP remained within VLCs under both dark and BL BFA treatments, suggesting that phot1 and NPH3 play different roles in PIN2 localization. In conclusion, BL-induced root phototropism is based on the phot1/NPH3 signaling pathway, which stimulates the shootward auxin flux by modifying the subcellular targeting of PIN2 in the root apex transition zone.

  14. Modulation of Phototropic Responsiveness in Arabidopsis through Ubiquitination of Phototropin 1 by the CUL3-Ring E3 Ubiquitin Ligase CRL3NPH3[W

    PubMed Central

    Roberts, Diana; Pedmale, Ullas V.; Morrow, Johanna; Sachdev, Shrikesh; Lechner, Esther; Tang, Xiaobo; Zheng, Ning; Hannink, Mark; Genschik, Pascal; Liscum, Emmanuel

    2011-01-01

    Plant phototropism is an adaptive response to changes in light direction, quantity, and quality that results in optimization of photosynthetic light harvesting, as well as water and nutrient acquisition. Though several components of the phototropic signal response pathway have been identified in recent years, including the blue light (BL) receptors phototropin1 (phot1) and phot2, much remains unknown. Here, we show that the phot1-interacting protein NONPHOTOTROPIC HYPOCOTYL3 (NPH3) functions as a substrate adapter in a CULLIN3-based E3 ubiquitin ligase, CRL3NPH3. Under low-intensity BL, CRL3NPH3 mediates the mono/multiubiquitination of phot1, likely marking it for clathrin-dependent internalization from the plasma membrane. In high-intensity BL, phot1 is both mono/multi- and polyubiquitinated by CRL3NPH3, with the latter event targeting phot1 for 26S proteasome-mediated degradation. Polyubiquitination and subsequent degradation of phot1 under high-intensity BL likely represent means of receptor desensitization, while mono/multiubiquitination-stimulated internalization of phot1 may be coupled to BL-induced relocalization of hormone (auxin) transporters. PMID:21990941

  15. Lipid anchoring of Arabidopsis phototropin 1 to assess the functional significance of receptor internalization: should I stay or should I go?

    PubMed

    Preuten, Tobias; Blackwood, Lisa; Christie, John M; Fankhauser, Christian

    2015-05-01

    The phototropin 1 (phot1) blue light receptor mediates a number of adaptive responses, including phototropism, that generally serve to optimize photosynthetic capacity. Phot1 is a plasma membrane-associated protein, but upon irradiation, a fraction is internalized into the cytoplasm. Although this phenomenon has been reported for more than a decade, its biological significance remains elusive. Here, we use a genetic approach to revisit the prevalent hypotheses regarding the functional importance of receptor internalization. Transgenic plants expressing lipidated versions of phot1 that are permanently anchored to the plasma membrane were used to analyse the effect of internalization on receptor turnover, phototropism and other phot1-mediated responses. Myristoylation and farnesylation effectively prevented phot1 internalization. Both modified photoreceptors were found to be fully functional in Arabidopsis, rescuing phototropism and all other phot1-mediated responses tested. Light-mediated phot1 turnover occurred as in the native receptor. Furthermore, our work does not provide any evidence of a role of phot1 internalization in the attenuation of receptor signalling during phototropism. Our results demonstrate that phot1 signalling is initiated at the plasma membrane. They furthermore indicate that release of phot1 into the cytosol is not linked to receptor turnover or desensitization. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

  16. The Signal Transducer NPH3 Integrates the Phototropin1 Photosensor with PIN2-Based Polar Auxin Transport in Arabidopsis Root Phototropism[C][W

    PubMed Central

    Wan, Yinglang; Jasik, Jan; Wang, Li; Hao, Huaiqing; Volkmann, Dieter; Menzel, Diedrik; Mancuso, Stefano; Baluška, František; Lin, Jinxing

    2012-01-01

    Under blue light (BL) illumination, Arabidopsis thaliana roots grow away from the light source, showing a negative phototropic response. However, the mechanism of root phototropism is still unclear. Using a noninvasive microelectrode system, we showed that the BL sensor phototropin1 (phot1), the signal transducer NONPHOTOTROPIC HYPOCOTYL3 (NPH3), and the auxin efflux transporter PIN2 were essential for BL-induced auxin flux in the root apex transition zone. We also found that PIN2-green fluorescent protein (GFP) localized to vacuole-like compartments (VLCs) in dark-grown root epidermal and cortical cells, and phot1/NPH3 mediated a BL-initiated pathway that caused PIN2 redistribution to the plasma membrane. When dark-grown roots were exposed to brefeldin A (BFA), PIN2-GFP remained in VLCs in darkness, and BL caused PIN2-GFP disappearance from VLCs and induced PIN2-GFP-FM4-64 colocalization within enlarged compartments. In the nph3 mutant, both dark and BL BFA treatments caused the disappearance of PIN2-GFP from VLCs. However, in the phot1 mutant, PIN2-GFP remained within VLCs under both dark and BL BFA treatments, suggesting that phot1 and NPH3 play different roles in PIN2 localization. In conclusion, BL-induced root phototropism is based on the phot1/NPH3 signaling pathway, which stimulates the shootward auxin flux by modifying the subcellular targeting of PIN2 in the root apex transition zone. PMID:22374399

  17. Phototropins but not cryptochromes mediate the blue light-specific promotion of stomatal conductance, while both enhance photosynthesis and transpiration under full sunlight.

    PubMed

    Boccalandro, Hernán E; Giordano, Carla V; Ploschuk, Edmundo L; Piccoli, Patricia N; Bottini, Rubén; Casal, Jorge J

    2012-03-01

    Leaf epidermal peels of Arabidopsis (Arabidopsis thaliana) mutants lacking either phototropins 1 and 2 (phot1 and phot2) or cryptochromes 1 and 2 (cry1 and cry2) exposed to a background of red light show severely impaired stomatal opening responses to blue light. Since phot and cry are UV-A/blue light photoreceptors, they may be involved in the perception of the blue light-specific signal that induces the aperture of the stomatal pores. In leaf epidermal peels, the blue light-specific effect saturates at low irradiances; therefore, it is considered to operate mainly under the low irradiance of dawn, dusk, or deep canopies. Conversely, we show that both phot1 phot2 and cry1 cry2 have reduced stomatal conductance, transpiration, and photosynthesis, particularly under the high irradiance of full sunlight at midday. These mutants show compromised responses of stomatal conductance to irradiance. However, the effects of phot and cry on photosynthesis were largely nonstomatic. While the stomatal conductance phenotype of phot1 phot2 was blue light specific, cry1 cry2 showed reduced stomatal conductance not only in response to blue light, but also in response to red light. The levels of abscisic acid were elevated in cry1 cry2. We conclude that considering their effects at high irradiances cry and phot are critical for the control of transpiration and photosynthesis rates in the field. The effects of cry on stomatal conductance are largely indirect and involve the control of abscisic acid levels.

  18. Phototropins But Not Cryptochromes Mediate the Blue Light-Specific Promotion of Stomatal Conductance, While Both Enhance Photosynthesis and Transpiration under Full Sunlight12[C][W][OA

    PubMed Central

    Boccalandro, Hernán E.; Giordano, Carla V.; Ploschuk, Edmundo L.; Piccoli, Patricia N.; Bottini, Rubén; Casal, Jorge J.

    2012-01-01

    Leaf epidermal peels of Arabidopsis (Arabidopsis thaliana) mutants lacking either phototropins 1 and 2 (phot1 and phot2) or cryptochromes 1 and 2 (cry1 and cry2) exposed to a background of red light show severely impaired stomatal opening responses to blue light. Since phot and cry are UV-A/blue light photoreceptors, they may be involved in the perception of the blue light-specific signal that induces the aperture of the stomatal pores. In leaf epidermal peels, the blue light-specific effect saturates at low irradiances; therefore, it is considered to operate mainly under the low irradiance of dawn, dusk, or deep canopies. Conversely, we show that both phot1 phot2 and cry1 cry2 have reduced stomatal conductance, transpiration, and photosynthesis, particularly under the high irradiance of full sunlight at midday. These mutants show compromised responses of stomatal conductance to irradiance. However, the effects of phot and cry on photosynthesis were largely nonstomatic. While the stomatal conductance phenotype of phot1 phot2 was blue light specific, cry1 cry2 showed reduced stomatal conductance not only in response to blue light, but also in response to red light. The levels of abscisic acid were elevated in cry1 cry2. We conclude that considering their effects at high irradiances cry and phot are critical for the control of transpiration and photosynthesis rates in the field. The effects of cry on stomatal conductance are largely indirect and involve the control of abscisic acid levels. PMID:22147516

  19. Variations in protein-flavin hydrogen bonding in a light, oxygen, voltage domain produce non-Arrhenius kinetics of adduct decay.

    PubMed

    Zoltowski, Brian D; Nash, Abigail I; Gardner, Kevin H

    2011-10-18

    Light, oxygen, voltage (LOV) domains utilize a conserved blue light-dependent mechanism to control a diverse array of effector domains in biological and engineered proteins. Variations in the kinetics and efficiency of LOV photochemistry fine-tune various aspects of the photic response. Characterization of the kinetics of a key aspect of this photochemical mechanism in EL222, a blue light responsive DNA binding protein from Erythrobacter litoralis HTCC2594, reveals unique non-Arrhenius behavior in the rate of dark-state cleavage of the photochemically generated adduct. Sequence analysis and mutagenesis studies establish that this effect stems from a Gln to Ala mutation unique to EL222 and homologous proteins from marine bacteria. Kinetic and spectroscopic analyses reveal that hydrogen bonding interactions between the FMN N1, O2, and ribityl hydroxyls and the surrounding protein regulate photocycle kinetics and stabilize the LOV active site from temperature-induced alteration in local structure. Substitution of residues interacting with the N1-O2 locus modulates adduct stability, structural flexibility, and sequestration of the active site from bulk solvent without perturbation of light-activated DNA binding. Together, these variants link non-Arrhenius behavior to specific alteration of an H-bonding network, while affording tunability of photocycle kinetics. © 2011 American Chemical Society

  20. Structural Insights into the HWE Histidine Kinase Family: The Brucella Blue Light-Activated Histidine Kinase Domain.

    PubMed

    Rinaldi, Jimena; Arrar, Mehrnoosh; Sycz, Gabriela; Cerutti, María Laura; Berguer, Paula M; Paris, Gastón; Estrín, Darío Ariel; Martí, Marcelo Adrián; Klinke, Sebastián; Goldbaum, Fernando Alberto

    2016-03-27

    In response to light, as part of a two-component system, the Brucella blue light-activated histidine kinase (LOV-HK) increases its autophosphorylation, modulating the virulence of this microorganism. The Brucella histidine kinase (HK) domain belongs to the HWE family, for which there is no structural information. The HWE family is exclusively present in proteobacteria and usually coupled to a wide diversity of light sensor domains. This work reports the crystal structure of the Brucella HK domain, which presents two different dimeric assemblies in the asymmetric unit: one similar to the already described canonical parallel homodimers (C) and the other, an antiparallel non-canonical (NC) dimer, each with distinct relative subdomain orientations and dimerization interfaces. Contrary to these crystallographic structures and unlike other HKs, in solution, the Brucella HK domain is monomeric and still active, showing an astonishing instability of the dimeric interface. Despite this instability, using cross-linking experiments, we show that the C dimer is the functionally relevant species. Mutational analysis demonstrates that the autophosphorylation activity occurs in cis. The different relative subdomain orientations observed for the NC and C states highlight the large conformational flexibility of the HK domain. Through the analysis of these alternative conformations by means of molecular dynamics simulations, we also propose a catalytic mechanism for Brucella LOV-HK.

  1. [The incidence of viral hepatitis A in the Hradec Králové Region in the Czech Republic in the last decade].

    PubMed

    Šošovičková, R; Smetana, J; Beranová, E; Kučerová, K; Chlíbek, R

    Viral hepatitis A continues to occur in the Czech Republic due to the high susceptibility of the population and existing opportunities for the transmission of the disease. The aim was to describe and analyse the incidence of viral hepatitis A in the Hradec Králové Region in the Czech Republic in 2005-2014, including the study of two outbreaks that required a different approach of field epidemiologists. In 2015, a retrospective analysis was carried out of the data on the incidence of viral hepatitis A in Hradec Králové Region in 2005-2014. The EPIDAT system where cases of infectious diseases and data from epidemiological investigations are reported was used as a data source for the purposes of the present analysis. In addition, two final reports on epidemic outbreaks of viral hepatitis A from 2014 were assessed. The incidence of viral hepatitis A at the regional level follows, to a certain extent, the pattern of the incidence of this disease at the national level. The highest number of cases was reported in 2010 due to a country-wide epidemic. The most affected age groups were children, adolescents, and young adults. The incidence of viral hepatitis A in individual years has a significant effect on the emergence of local outbreaks. The incidence of viral hepatitis A in the Czech Republic has a fluctuating trend, at both the national and regional levels. The highest incidence of viral hepatitis A was observed in the younger and middle-age categories. The high susceptibility of these population groups suggests the importance of vaccination against viral hepatitis A that confers specific personal protection.Key words: viral hepatitis A - incidence - outbreak - Czech Republic.

  2. Terrimonas crocea sp. nov., isolated from the till of high Arctic glacier Midtre Lovénbreen in the West Svalbard Archipelago.

    PubMed

    Kim, Myong Chol; Kang, Ok Chol; Kim, Chol Myong; Zhang, Yumin; Liu, Zuobing; Wei, Ziyan; Huang, Yao; Danzeng, Wangmu; Peng, Fang

    2016-11-24

    A yellow-pigmented bacteria strain, designated M1-33108T, was isolated from the till of high Arctic glacier Midtre Lovénbreen (MLB) near Ny-Ålesund, in the West Svalbard Archipelago, Norway. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain M1-33108T belonged to the genus Terrimonas and its closest neighbor was Terrimonas arctica R9-86T with 96.12% 16S rRNA gene sequence similarity. Strain M1-33108T was Gram-reaction-negative, aerobic, non-spore-forming, rod-shaped bacterium that lacked motility. Cells contained iso-C15:1 G, iso-C15:0, iso-C17:0 3OH, C16:0 and summed feature 3 (comprising C16:1 ω7c and/or C16:1 ω6c) as its major cellular fatty acids; and menaquinone-7 as sole respiratory quinone. The polar lipid profile of strain M1-33108T consisted of phosphatidylethanolamine, two unknown aminophospholipids, eight unknown aminolipids, an unknown glycolipid and three unknown polar lipids. The DNA G+C content was 45.0 mol %. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain M1-33108T is considered to represent a novel species in the genus Terrimonas, for which the name Terrimonas crocea sp. nov. is proposed. The type strain is M1-33108T (=CCTCC AB 2016103T=KCTC 52448T).

  3. A terrestrial laser scanning survey to derive snow volume and water equivalent on the slopes of Austre Lovén glacier basin (Svalbard - 79°N)

    NASA Astrophysics Data System (ADS)

    Tolle, Florian; Prokop, Alexander; Bernard, Eric; Friedt, Jean-Michel; Marlin, Christelle; Griselin, Madeleine

    2013-04-01

    Steep slopes represent 35% of Austre Lovén glacier basin, a small valley glacier in Svalbard (79°N). Slopes and their dynamics do have an important impact on polar glaciers. They also are of high hydrological importance in the water budget of basins. One major issue in studying slopes is the fact that they are hard to instrument and both equipment and staff have to deal with the steepness of the field and the exposure to avalanches and rock fall. In order to minimize this exposure without giving up the required spatial and temporal precision, terrestrial laser scanning (TLS) is used. A monitoring program is now starting using TLS. TLS allows for remote high quality measurements. It can be operated by small teams and scanning may be repeated as many times as needed even over short time periods. Acquired point clouds are interpolated to generate surface models. These models are used to reveal slope dynamics over short time, seasonal or interannual periods. Rock and snow movements and volumes may therefore be accounted for at a high resolution. In order to assess the volume of snow on slopes two scanning field surveys were conducted. The first one took place in April at the yearly expected maximum snow cover. The second took place in August to record the seasonal minimum. In addition density measurements were conducted in April in the safely accessible lower parts of slopes. Some of the April scans have been repeated over an 8 days interval. The results showed the high quality of the data and clearly showed snow movements including small avalanches. Subtraction of the snow minimum surface model (August) to the snow maximum acquired in spring provided a good estimation of the global snow volume on slopes. Using density values measured in April, these volumes have then been expressed in water equivalent. In addition to these measurements laser scanning was also performed on some areas of the glacier and in the moraine.

  4. Light-activated DNA binding in a designed allosteric protein

    SciTech Connect

    Strickland, Devin; Moffat, Keith; Sosnick, Tobin R.

    2008-09-03

    An understanding of how allostery, the conformational coupling of distant functional sites, arises in highly evolvable systems is of considerable interest in areas ranging from cell biology to protein design and signaling networks. We reasoned that the rigidity and defined geometry of an {alpha}-helical domain linker would make it effective as a conduit for allosteric signals. To test this idea, we rationally designed 12 fusions between the naturally photoactive LOV2 domain from Avena sativa phototropin 1 and the Escherichia coli trp repressor. When illuminated, one of the fusions selectively binds operator DNA and protects it from nuclease digestion. The ready success of our rational design strategy suggests that the helical 'allosteric lever arm' is a general scheme for coupling the function of two proteins.

  5. Investigations of human myosin VI targeting using optogenetically controlled cargo loading.

    PubMed

    French, Alexander R; Sosnick, Tobin R; Rock, Ronald S

    2017-02-28

    Myosins play countless critical roles in the cell, each requiring it to be activated at a specific location and time. To control myosin VI with this specificity, we created an optogenetic tool for activating myosin VI by fusing the light-sensitive Avena sativa phototropin1 LOV2 domain to a peptide from Dab2 (LOVDab), a myosin VI cargo protein. Our approach harnesses the native targeting and activation mechanism of myosin VI, allowing direct inferences on myosin VI function. LOVDab robustly recruits human full-length myosin VI to various organelles in vivo and hinders peroxisome motion in a light-controllable manner. LOVDab also activates myosin VI in an in vitro gliding filament assay. Our data suggest that protein and lipid cargoes cooperate to activate myosin VI, allowing myosin VI to integrate Ca(2+), lipid, and protein cargo signals in the cell to deploy in a site-specific manner.

  6. Structure and activity of JAC1 J-domain implicate the involvement of the cochaperone activity with HSC70 in chloroplast photorelocation movement.

    PubMed

    Suetsugu, Noriyuki; Takano, Akira; Kohda, Daisuke; Wada, Masamitsu

    2010-12-01

    Chloroplast photorelocation movement towards weak light and away from strong light is essential for plants to adapt to the fluctuation of ambient light conditions. In the previous study, we showed that blue light receptor phototropins mediated blue light-induced chloroplast movement in Arabidopsis by regulating short actin filaments localized at the chloroplast periphery (cp-actin filaments) rather than actin cables in the cytoplasm. However, the signaling pathway for the chloroplast photorelocation movement is still unclear. We also identified JAC1 (J-domain protein required for chloroplast accumulation response 1) as an essential component for the accumulation response and dark positioning in Arabidopsis. We recently determined the crystal structure of the J-domain of JAC1. The JAC1 J-domain has a positively charged surface, which forms a putative interface with the Hsc70 chaperone by analogy to that of bovine auxilin. Furthermore, the mutation of the highly conserved HPD motif in the JAC1 J-domain impaired the in vivo activity of JAC1. These data suggest that JAC1 cochaperone activity with HSC70 is essential for chloroplast photorelocation movement.

  7. A blue-light photoreceptor mediates the feedback regulation of photosynthesis.

    PubMed

    Petroutsos, Dimitris; Tokutsu, Ryutaro; Maruyama, Shinichiro; Flori, Serena; Greiner, Andre; Magneschi, Leonardo; Cusant, Loic; Kottke, Tilman; Mittag, Maria; Hegemann, Peter; Finazzi, Giovanni; Minagawa, Jun

    2016-09-22

    In plants and algae, light serves both as the energy source for photosynthesis and a biological signal that triggers cellular responses via specific sensory photoreceptors. Red light is perceived by bilin-containing phytochromes and blue light by the flavin-containing cryptochromes and/or phototropins (PHOTs), the latter containing two photosensory light, oxygen, or voltage (LOV) domains. Photoperception spans several orders of light intensity, ranging from far below the threshold for photosynthesis to values beyond the capacity of photosynthetic CO2 assimilation. Excess light may cause oxidative damage and cell death, processes prevented by enhanced thermal dissipation via high-energy quenching (qE), a key photoprotective response. Here we show the existence of a molecular link between photoreception, photosynthesis, and photoprotection in the green alga Chlamydomonas reinhardtii. We show that PHOT controls qE by inducing the expression of the qE effector protein LHCSR3 (light-harvesting complex stress-related protein 3) in high light intensities. This control requires blue-light perception by LOV domains on PHOT, LHCSR3 induction through PHOT kinase, and light dissipation in photosystem II via LHCSR3. Mutants deficient in the PHOT gene display severely reduced fitness under excessive light conditions, indicating that the sensing, utilization, and dissipation of light is a concerted process that plays a vital role in microalgal acclimation to environments of variable light intensities.

  8. Controlling Protein Activity and Degradation Using Blue Light.

    PubMed

    Lutz, Anne P; Renicke, Christian; Taxis, Christof

    2016-01-01

    Regulation of protein stability is a fundamental process in eukaryotic cells and pivotal to, e.g., cell cycle progression, faithful chromosome segregation, or protein quality control. Synthetic regulation of protein stability requires conditional degradation sequences (degrons) that induce a stability switch upon a specific signal. Fusion to a selected target protein permits to influence virtually every process in a cell. Light as signal is advantageous due to its precise applicability in time, space, quality, and quantity. Light control of protein stability was achieved by fusing the LOV2 photoreceptor domain of Arabidopsis thaliana phototropin1 with a synthetic degron (cODC1) derived from the carboxy-terminal degron of ornithine decarboxylase to obtain the photosensitive degron (psd) module. The psd module can be attached to the carboxy terminus of target proteins that are localized to the cytosol or nucleus to obtain light control over their stability. Blue light induces structural changes in the LOV2 domain, which in turn lead to activation of the degron and thus proteasomal degradation of the whole fusion protein. Variants of the psd module with diverse characteristics are useful to fine-tune the stability of a selected target at permissive (darkness) and restrictive conditions (blue light).

  9. Photo-sensitive degron variants for tuning protein stability by light.

    PubMed

    Usherenko, Svetlana; Stibbe, Hilke; Muscò, Massimiliano; Essen, Lars-Oliver; Kostina, Ekaterina A; Taxis, Christof

    2014-11-18

    Regulated proteolysis by the proteasome is one of the fundamental mechanisms used in eukaryotic cells to control cellular behavior. Efficient tools to regulate protein stability offer synthetic influence on molecular level on a selected biological process. Optogenetic control of protein stability has been achieved with the photo-sensitive degron (psd) module. This engineered tool consists of the photoreceptor domain light oxygen voltage 2 (LOV2) from Arabidopsis thaliana phototropin1 fused to a sequence that induces direct proteasomal degradation, which was derived from the carboxy-terminal degron of murine ornithine decarboxylase. The abundance of target proteins tagged with the psd module can be regulated by blue light if the degradation tag is exposed to the cytoplasm or the nucleus. We used the model organism Saccharomyces cerevisiae to generate psd module variants with increased and decreased stabilities in darkness or when exposed to blue light using site-specific and random mutagenesis. The variants were characterized as fusions to fluorescent reporter proteins and showed half-lives between 6 and 75 minutes in cells exposed to blue light and 14 to 187 minutes in darkness. In blue light, ten variants showed accelerated degradation and four variants increased stability compared to the original psd module. Measuring the dark/light ratio of selected constructs in yeast cells showed that two variants were obtained with ratios twice as high as in the wild type psd module. In silico modeling of photoreceptor variant characteristics suggested that for most cases alterations in behavior were induced by changes in the light-response of the LOV2 domain. In total, the mutational analysis resulted in psd module variants, which provide tuning of protein stability over a broad range by blue light. Two variants showed characteristics that are profoundly improved compared to the original construct. The modular usage of the LOV2 domain in optogenetic tools allows the usage of

  10. Light-induced protein degradation in human-derived cells.

    PubMed

    Sun, Wansheng; Zhang, Wenyao; Zhang, Chao; Mao, Miaowei; Zhao, Yuzheng; Chen, Xianjun; Yang, Yi

    2017-05-27

    Controlling protein degradation can be a valuable tool for posttranslational regulation of protein abundance to study complex biological systems. In the present study, we designed a light-switchable degron consisting of a light oxygen voltage (LOV) domain of Avena sativa phototropin 1 (AsLOV2) and a C-terminal degron. Our results showed that the light-switchable degron could be used for rapid and specific induction of protein degradation in HEK293 cells by light in a proteasome-dependent manner. Further studies showed that the light-switchable degron could also be utilized to mediate the degradation of secreted Gaussia princeps luciferase (GLuc), demonstrating the adaptability of the light-switchable degron in different types of protein. We suggest that the light-switchable degron offers a robust tool to control protein levels and may serves as a new and significant method for gene- and cell-based therapies. Copyright © 2017 Elsevier Inc. All rights reserved.

  11. Control of Protein Activity and Cell Fate Specification via Light-Mediated Nuclear Translocation

    PubMed Central

    Zimmerman, Seth P.; Bear, James E.; Goldstein, Bob; Hahn, Klaus; Kuhlman, Brian

    2015-01-01

    Light-activatable proteins allow precise spatial and temporal control of biological processes in living cells and animals. Several approaches have been developed for controlling protein localization with light, including the conditional inhibition of a nuclear localization signal (NLS) with the Light Oxygen Voltage (AsLOV2) domain of phototropin 1 from Avena sativa. In the dark, the switch adopts a closed conformation that sterically blocks the NLS motif. Upon activation with blue light the C-terminus of the protein unfolds, freeing the NLS to direct the protein to the nucleus. A previous study showed that this approach can be used to control the localization and activity of proteins in mammalian tissue culture cells. Here, we extend this result by characterizing the binding properties of a LOV/NLS switch and demonstrating that it can be used to control gene transcription in yeast. Additionally, we show that the switch, referred to as LANS (light-activated nuclear shuttle), functions in the C. elegans embryo and allows for control of nuclear localization in individual cells. By inserting LANS into the C. elegans lin-1 locus using Cas9-triggered homologous recombination, we demonstrated control of cell fate via light-dependent manipulation of a native transcription factor. We conclude that LANS can be a valuable experimental method for spatial and temporal control of nuclear localization in vivo. PMID:26083500

  12. Understanding the Public Domain.

    ERIC Educational Resources Information Center

    Russell, Carrie

    2003-01-01

    This overview of the public domain covers: defining the public domain; figuring out if a work is protected by copyright; being sure a work is in the public domain; asserting the copyright protection and term; the Creative Commons initiative; building the Information Commons; when permission is needed for using a public domain work; and special…

  13. Taxonomic characterization, adaptation strategies and biotechnological potential of cryophilic yeasts from ice cores of Midre Lovénbreen glacier, Svalbard, Arctic.

    PubMed

    Singh, Purnima; Tsuji, Masaharu; Singh, Shiv Mohan; Roy, Utpal; Hoshino, Tamotsu

    2013-04-01

    Ten strains of cryophilic yeast were studied from glacier ice cores of Svalbard, Arctic. The ice melt samples contained about 3×10(3) - 1×10(4) colony forming unit (CFUs) per ml. Sequence analysis of the isolates, using D1/D2 domain identified five species of yeasts: Cryptococcus adeliensis (MLB-18 JX192655), Cryptococcus albidosimilis (MLB-19 JX192656), Cryptococcus saitoi (MLB-22 JX192659), Rhodosporidium lusitaniae (MLB-20 JX192657), and Rhodotorula mucilaginosa (MLB-27 JX192664). Effect of temperature on growth of these isolates was studied. The strains are able to grow at temperatures ranging between 1 and 20°C. Screening of the cultures for amylase, cellulase, protease, lipase, urease and catalase activity were carried out indicating varying amounts of enzyme production at different temperatures. Characterization of lipase in strain Cryptococcus sp. MLB-24 was performed. Fatty acid methyl ester (FAME) analysis of the cultures grown at four different temperatures (1, 4, 15, and 20°C) was also done. Decrease in temperature was reported to cause increase in concentration of unsaturated fatty acids. High amount of oleic acid accumulated with increase in temperature. These fatty acids possibly help the strains to survive in glacial ice core cold environment. The extracellular and intracellular filtrate of the cultures showed negative antifreeze protein (AFP) activity. The observations indicate that probably the isolates in the present undertaking adapt to low temperatures, by enzyme and PUFA secretion rather than by antifreeze protein secretion. Copyright © 2013 Elsevier Inc. All rights reserved.

  14. Domains in multiband superconductors

    NASA Astrophysics Data System (ADS)

    Tanaka, Y.; Yanagisawa, T.; Crisan, A.; Shirage, P. M.; Iyo, A.; Tokiwa, K.; Nishio, T.; Sundaresan, A.; Terada, N.

    2011-11-01

    Multiband superconductors can have several types of domains that are inhibited in conventional single-band superconductors. These domains are phase domains and chiral domains and their domain wall are an interband phase difference soliton. In a superconductor with an odd number of electronic bands (five or more) and with positive interband Josephson interactions, we find other types of domains with different interband phase differences. We call these domains configuration domains because pseudo-order parameters for each band are dispersed in the complex plain and several configurations, which have several local minima. Fractional vortices serve as hubs for phase difference solitons (configuration domain walls). The divergence of the number of configurations with local minima would pose a serious problem for the stability of superconductivity.

  15. Internationalized Domain Names.

    ERIC Educational Resources Information Center

    Wielansky, Marc D.

    2002-01-01

    Reports on an investigation of what may appear at first to be an arcane topic--the internationalization of domain names on the Internet. Concludes that expanding domain names internationally poses challenges to the inherent open structure of the Internet; to its ease of use for those accustomed to Latin-alphabet-only domain names; and to corporate…

  16. Domains and Naive Theories.

    PubMed

    Gelman, Susan A; Noles, Nicholaus S

    2011-09-01

    Human cognition entails domain-specific cognitive processes that influence memory, attention, categorization, problem-solving, reasoning, and knowledge organization. This review examines domain-specific causal theories, which are of particular interest for permitting an examination of how knowledge structures change over time. We first describe the properties of commonsense theories, and how commonsense theories differ from scientific theories, illustrating with children's classification of biological and non-biological kinds. We next consider the implications of domain-specificity for broader issues regarding cognitive development and conceptual change. We then examine the extent to which domain-specific theories interact, and how people reconcile competing causal frameworks. Future directions for research include examining how different content domains interact, the nature of theory change, the role of context (including culture, language, and social interaction) in inducing different frameworks, and the neural bases for domain-specific reasoning.

  17. Domains and Naive Theories

    PubMed Central

    Gelman, Susan A.; Noles, Nicholaus S.

    2013-01-01

    Human cognition entails domain-specific cognitive processes that influence memory, attention, categorization, problem-solving, reasoning, and knowledge organization. This review examines domain-specific causal theories, which are of particular interest for permitting an examination of how knowledge structures change over time. We first describe the properties of commonsense theories, and how commonsense theories differ from scientific theories, illustrating with children’s classification of biological and non-biological kinds. We next consider the implications of domain-specificity for broader issues regarding cognitive development and conceptual change. We then examine the extent to which domain-specific theories interact, and how people reconcile competing causal frameworks. Future directions for research include examining how different content domains interact, the nature of theory change, the role of context (including culture, language, and social interaction) in inducing different frameworks, and the neural bases for domain-specific reasoning. PMID:24187603

  18. Phantom domain walls

    NASA Astrophysics Data System (ADS)

    Avelino, P. P.; Ferreira, V. M. C.; Menezes, J.; Sousa, L.

    2017-08-01

    We consider a model with two real scalar fields which admits phantom domain wall solutions. We investigate the structure and evolution of these phantom domain walls in an expanding homogeneous and isotropic universe. In particular, we show that the increase of the tension of the domain walls with cosmic time, associated to the evolution of the phantom scalar field, is responsible for an additional damping term in their equations of motion. We describe the macroscopic dynamics of phantom domain walls, showing that extended phantom defects whose tension varies on a cosmological time scale cannot be the dark energy.

  19. Visualizing domain wall and reverse domain superconductivity.

    PubMed

    Iavarone, M; Moore, S A; Fedor, J; Ciocys, S T; Karapetrov, G; Pearson, J; Novosad, V; Bader, S D

    2014-08-28

    In magnetically coupled, planar ferromagnet-superconductor (F/S) hybrid structures, magnetic domain walls can be used to spatially confine the superconductivity. In contrast to a superconductor in a uniform applied magnetic field, the nucleation of the superconducting order parameter in F/S structures is governed by the inhomogeneous magnetic field distribution. The interplay between the superconductivity localized at the domain walls and far from the walls leads to effects such as re-entrant superconductivity and reverse domain superconductivity with the critical temperature depending upon the location. Here we use scanning tunnelling spectroscopy to directly image the nucleation of superconductivity at the domain wall in F/S structures realized with Co-Pd multilayers and Pb thin films. Our results demonstrate that such F/S structures are attractive model systems that offer the possibility to control the strength and the location of the superconducting nucleus by applying an external magnetic field, potentially useful to guide vortices for computing application.

  20. Visualizing domain wall and reverse domain superconductivity

    PubMed Central

    Iavarone, M.; Moore, S. A.; Fedor, J.; Ciocys, S. T.; Karapetrov, G.; Pearson, J.; Novosad, V.; Bader, S. D.

    2014-01-01

    In magnetically coupled, planar ferromagnet-superconductor (F/S) hybrid structures, magnetic domain walls can be used to spatially confine the superconductivity. In contrast to a superconductor in a uniform applied magnetic field, the nucleation of the superconducting order parameter in F/S structures is governed by the inhomogeneous magnetic field distribution. The interplay between the superconductivity localized at the domain walls and far from the walls leads to effects such as re-entrant superconductivity and reverse domain superconductivity with the critical temperature depending upon the location. Here we use scanning tunnelling spectroscopy to directly image the nucleation of superconductivity at the domain wall in F/S structures realized with Co-Pd multilayers and Pb thin films. Our results demonstrate that such F/S structures are attractive model systems that offer the possibility to control the strength and the location of the superconducting nucleus by applying an external magnetic field, potentially useful to guide vortices for computing application. PMID:25164004

  1. Causal Learning Across Domains

    ERIC Educational Resources Information Center

    Schulz, Laura E.; Gopnik, Alison

    2004-01-01

    Five studies investigated (a) children's ability to use the dependent and independent probabilities of events to make causal inferences and (b) the interaction between such inferences and domain-specific knowledge. In Experiment 1, preschoolers used patterns of dependence and independence to make accurate causal inferences in the domains of…

  2. A Domain Analysis Bibliography

    DTIC Science & Technology

    1990-06-01

    Bauhaus , a prototype CASE workstation for D-SAPS development. [ARAN88A] Guillermo F. Arango. Domain Engineering for Software Reuse. PhD thesis...34 VITA90B: Domain Analysis within the ISEC Rapid Center 48 CMU/SEI-90-SR-3 Appendix III Alphabetical by Organization/Project BAUHAUS * ALLE87A

  3. Modeling Protein Domain Function

    ERIC Educational Resources Information Center

    Baker, William P.; Jones, Carleton "Buck"; Hull, Elizabeth

    2007-01-01

    This simple but effective laboratory exercise helps students understand the concept of protein domain function. They use foam beads, Styrofoam craft balls, and pipe cleaners to explore how domains within protein active sites interact to form a functional protein. The activity allows students to gain content mastery and an understanding of the…

  4. Domains of Learning.

    ERIC Educational Resources Information Center

    Gagne, Robert M.

    In planning educational research, recognition needs to be made of five domains of learning: (1) motor skills, (2) verbal information, (3) intellectual skills, (4) cognitive strategies, and (5) attitudes. In being cognizant of these domains, the researcher is able to distinguish the parts of a content area which are subject to different…

  5. Modeling Protein Domain Function

    ERIC Educational Resources Information Center

    Baker, William P.; Jones, Carleton "Buck"; Hull, Elizabeth

    2007-01-01

    This simple but effective laboratory exercise helps students understand the concept of protein domain function. They use foam beads, Styrofoam craft balls, and pipe cleaners to explore how domains within protein active sites interact to form a functional protein. The activity allows students to gain content mastery and an understanding of the…

  6. Domain wall filters

    SciTech Connect

    Baer, Oliver; Narayanan, Rajamani; Neuberger, Herbert; Witzel, Oliver

    2007-03-15

    We propose using the extra dimension separating the domain walls carrying lattice quarks of opposite handedness to gradually filter out the ultraviolet fluctuations of the gauge fields that are felt by the fermionic excitations living in the bulk. This generalization of the homogeneous domain wall construction has some theoretical features that seem nontrivial.

  7. Sac phosphatase domain proteins.

    PubMed Central

    Hughes, W E; Cooke, F T; Parker, P J

    2000-01-01

    Advances in our understanding of the roles of phosphatidylinositol phosphates in controlling cellular functions such as endocytosis, exocytosis and the actin cytoskeleton have included new insights into the phosphatases that are responsible for the interconversion of these lipids. One of these is an entirely novel class of phosphatase domain found in a number of well characterized proteins. Proteins containing this Sac phosphatase domain include the yeast Saccharomyces cerevisiae proteins Sac1p and Fig4p. The Sac phosphatase domain is also found within the mammalian phosphoinositide 5-phosphatase synaptojanin and the yeast synaptojanin homologues Inp51p, Inp52p and Inp53p. These proteins therefore contain both Sac phosphatase and 5-phosphatase domains. This review describes the Sac phosphatase domain-containing proteins and their actions, with particular reference to the genetic and biochemical insights provided by study of the yeast Saccharomyces cerevisiae. PMID:10947947

  8. Cross Domain Analogies for Learning Domain Theories

    DTIC Science & Technology

    2007-01-01

    Example Problem and Worked Solution All problems and worked solutions used in this work were taken from the same physics textbook ( Giancoli 1991...domain theory. We close with a discussion of related work and our plans for the future. Representations and Problem Solving Representing physics ...small compared to the 30,000+ concepts and 8,000+ predicates already defined in the KB. Thus, objects, relations, and events that appear in physics

  9. Visualizing Knowledge Domains.

    ERIC Educational Resources Information Center

    Borner, Katy; Chen, Chaomei; Boyack, Kevin W.

    2003-01-01

    Reviews visualization techniques for scientific disciplines and information retrieval and classification. Highlights include historical background of scientometrics, bibliometrics, and citation analysis; map generation; process flow of visualizing knowledge domains; measures and similarity calculations; vector space model; factor analysis;…

  10. Stability of domain structures in multi-domain proteins

    PubMed Central

    Bhaskara, Ramachandra M.; Srinivasan, Narayanaswamy

    2011-01-01

    Multi-domain proteins have many advantages with respect to stability and folding inside cells. Here we attempt to understand the intricate relationship between the domain-domain interactions and the stability of domains in isolation. We provide quantitative treatment and proof for prevailing intuitive ideas on the strategies employed by nature to stabilize otherwise unstable domains. We find that domains incapable of independent stability are stabilized by favourable interactions with tethered domains in the multi-domain context. Stability of such folds to exist independently is optimized by evolution. Specific residue mutations in the sites equivalent to inter-domain interface enhance the overall solvation, thereby stabilizing these domain folds independently. A few naturally occurring variants at these sites alter communication between domains and affect stability leading to disease manifestation. Our analysis provides safe guidelines for mutagenesis which have attractive applications in obtaining stable fragments and domain constructs essential for structural studies by crystallography and NMR. PMID:22355559

  11. Software architecture design domain

    SciTech Connect

    White, S.A.

    1996-12-31

    Software architectures can provide a basis for the capture and subsequent reuse of design knowledge. The goal of software architecture is to allow the design of a system to take place at a higher level of abstraction; a level concerned with components, connections, constraints, rationale. This architectural view of software adds a new layer of abstraction to the traditional design phase of software development. It has resulted in a flurry of activity towards techniques, tools, and architectural design languages developed specifically to assist with this activity. An analysis of architectural descriptions, even though they differ in notation, shows a common set of key constructs that are present across widely varying domains. These common aspects form a core set of constructs that should belong to any ADL in order to for the language to offer the ability to specify software systems at the architectural level. This analysis also revealed a second set of constructs which served to expand the first set thereby improving the syntax and semantics. These constructs are classified according to whether they provide representation and analysis support for architectures belonging to many varying application domains (domain-independent construct class) or to a particular application domain (domain-dependent constructs). This paper presents the constructs of these two classes, their placement in the architecture design domain and shows how they may be used to classify, select, and analyze proclaimed architectural design languages (ADLs).

  12. Domains in Ferroelectric Nanostructures

    NASA Astrophysics Data System (ADS)

    Gregg, Marty

    2010-03-01

    Ferroelectric materials have great potential in influencing the future of small scale electronics. At a basic level, this is because ferroelectric surfaces are charged, and so interact strongly with charge-carrying metals and semiconductors - the building blocks for all electronic systems. Since the electrical polarity of the ferroelectric can be reversed, surfaces can both attract and repel charges in nearby materials, and can thereby exert complete control over both charge distribution and movement. It should be no surprise, therefore, that microelectronics industries have already looked very seriously at harnessing ferroelectric materials in a variety of applications, from solid state memory chips (FeRAMs) to field effect transistors (FeFETs). In all such applications, switching the direction of the polarity of the ferroelectric is a key aspect of functional behavior. The mechanism for switching involves the field-induced nucleation and growth of domains. Domain coarsening, through domain wall propagation, eventually causes the entire ferroelectric to switch its polar direction. It is thus the existence and behavior of domains that determine the switching response, and ultimately the performance of the ferroelectric device. A major issue, associated with the integration of ferroelectrics into microelectronic devices, has been that the fundamental properties associated with ferroelectrics, when in bulk form, appear to change quite dramatically and unpredictably when at the nanoscale: new modes of behaviour, and different functional characteristics from those seen in bulk appear. For domains, in particular, the proximity of surfaces and boundaries have a dramatic effect: surface tension and depolarizing fields both serve to increase the equilibrium density of domains, such that minor changes in scale or morphology can have major ramifications for domain redistribution. Given the importance of domains in dictating the overall switching characteristics of a device

  13. Extending Protein Domain Boundary Predictors to Detect Discontinuous Domains

    PubMed Central

    Xue, Zhidong; Jang, Richard; Govindarajoo, Brandon; Huang, Yichu; Wang, Yan

    2015-01-01

    A variety of protein domain predictors were developed to predict protein domain boundaries in recent years, but most of them cannot predict discontinuous domains. Considering nearly 40% of multidomain proteins contain one or more discontinuous domains, we have developed DomEx to enable domain boundary predictors to detect discontinuous domains by assembling the continuous domain segments. Discontinuous domains are predicted by matching the sequence profile of concatenated continuous domain segments with the profiles from a single-domain library derived from SCOP and CATH, and Pfam. Then the matches are filtered by similarity to library templates, a symmetric index score and a profile-profile alignment score. DomEx recalled 32.3% discontinuous domains with 86.5% precision when tested on 97 non-homologous protein chains containing 58 continuous and 99 discontinuous domains, in which the predicted domain segments are within ±20 residues of the boundary definitions in CATH 3.5. Compared with our recently developed predictor, ThreaDom, which is the state-of-the-art tool to detect discontinuous-domains, DomEx recalled 26.7% discontinuous domains with 72.7% precision in a benchmark with 29 discontinuous-domain chains, where ThreaDom failed to predict any discontinuous domains. Furthermore, combined with ThreaDom, the method ranked number one among 10 predictors. The source code and datasets are available at https://github.com/xuezhidong/DomEx. PMID:26502173

  14. Axion domain wall baryogenesis

    SciTech Connect

    Daido, Ryuji; Kitajima, Naoya; Takahashi, Fuminobu

    2015-07-28

    We propose a new scenario of baryogenesis, in which annihilation of axion domain walls generates a sizable baryon asymmetry. Successful baryogenesis is possible for a wide range of the axion mass and decay constant, m≃10{sup 8}–10{sup 13} GeV and f≃10{sup 13}–10{sup 16} GeV. Baryonic isocurvature perturbations are significantly suppressed in our model, in contrast to various spontaneous baryogenesis scenarios in the slow-roll regime. In particular, the axion domain wall baryogenesis is consistent with high-scale inflation which generates a large tensor-to-scalar ratio within the reach of future CMB B-mode experiments. We also discuss the gravitational waves produced by the domain wall annihilation and its implications for the future gravitational wave experiments.

  15. Axion domain wall baryogenesis

    SciTech Connect

    Daido, Ryuji; Kitajima, Naoya; Takahashi, Fuminobu E-mail: kitajima@tuhep.phys.tohoku.ac.jp

    2015-07-01

    We propose a new scenario of baryogenesis, in which annihilation of axion domain walls generates a sizable baryon asymmetry. Successful baryogenesis is possible for a wide range of the axion mass and decay constant, m ≅ 10{sup 8}–10{sup 13} GeV and f ≅ 10{sup 13}–10{sup 16} GeV . Baryonic isocurvature perturbations are significantly suppressed in our model, in contrast to various spontaneous baryogenesis scenarios in the slow-roll regime. In particular, the axion domain wall baryogenesis is consistent with high-scale inflation which generates a large tensor-to-scalar ratio within the reach of future CMB B-mode experiments. We also discuss the gravitational waves produced by the domain wall annihilation and its implications for the future gravitational wave experiments.

  16. Optimal domain decomposition strategies

    NASA Technical Reports Server (NTRS)

    Yoon, Yonghyun; Soni, Bharat K.

    1995-01-01

    The primary interest of the authors is in the area of grid generation, in particular, optimal domain decomposition about realistic configurations. A grid generation procedure with optimal blocking strategies has been developed to generate multi-block grids for a circular-to-rectangular transition duct. The focus of this study is the domain decomposition which optimizes solution algorithm/block compatibility based on geometrical complexities as well as the physical characteristics of flow field. The progress realized in this study is summarized in this paper.

  17. Development of a Synthetic Switch to Control Protein Stability in Eukaryotic Cells with Light.

    PubMed

    Taxis, Christof

    2017-01-01

    In eukaryotic cells, virtually all regulatory processes are influenced by proteolysis. Thus, synthetic control of protein stability is a powerful approach to influence cellular behavior. To achieve this, selected target proteins are modified with a conditional degradation sequence (degron) that responds to a distinct signal. For development of a synthetic degron, an appropriate sensor domain is fused with a degron such that activity of the degron is under control of the sensor. This chapter describes the development of a light-activated, synthetic degron in the model organism Saccharomyces cerevisiae. This photosensitive degron module is composed of the light-oxygen-voltage (LOV) 2 photoreceptor domain of Arabidopsis thaliana phototropin 1 and a degron derived from murine ornithine decarboxylase (ODC). Excitation of the photoreceptor with blue light induces a conformational change that leads to exposure and activation of the degron. Subsequently, the protein is targeted for degradation by the proteasome. Here, the strategy for degron module development and optimization is described in detail together with experimental aspects, which were pivotal for successful implementation of light-controlled proteolysis. The engineering of the photosensitive degron (psd) module may well serve as a blueprint for future development of sophisticated synthetic switches.

  18. Domain Validity and Generalizability

    ERIC Educational Resources Information Center

    Kaiser, Henry F.; Michael, William B.

    1975-01-01

    An alternative derivation of Tryon's basic formula for the coefficient of domain validity or the coefficient of generalizability developed by Cronbach, Rajaratnam, and Glaser is provided. This derivation, which is also the generalized Kuder-Richardson coefficient, requires a relatively minimal number of assumptions compared with that in previously…

  19. Cellulose binding domain proteins

    DOEpatents

    Shoseyov, O.; Shpiegl, I.; Goldstein, M.; Doi, R.

    1998-11-17

    A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques. 16 figs.

  20. Cellulose binding domain proteins

    SciTech Connect

    Shoseyov, Oded; Shpiegl, Itai; Goldstein, Marc; Doi, Roy

    1998-01-01

    A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production thereof. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques.

  1. The Domains of TESOL.

    ERIC Educational Resources Information Center

    Robinett, Betty Wallace

    The domains of Teachers of English to Speakers of Other Languages (TESOL) are those spheres of concern involving persons who speak languages other than English or dialects of English other than the standard. This clientele has been classified traditionally in terms of programs in English as a foreign language, English as a second language, English…

  2. Clusters, factories and domains

    PubMed Central

    Gillespie, Peter J

    2010-01-01

    During S-phase of the cell cycle, chromosomal DNA is replicated according to a complex replication timing program, with megabase-sized domains replicating at different times. DNA fiber analysis reveals that clusters of adjacent replication origins fire near-synchronously. Analysis of replicating cells by light microscopy shows that DNA synthesis occurs in discrete foci or factories. The relationship between timing domains, origin clusters and replication foci is currently unclear. Recent work, using a hybrid Xenopus/hamster replication system, has shown that when CDK levels are manipulated during S-phase the activation of replication factories can be uncoupled from progression through the replication timing program. Here, we use data from this hybrid system to investigate potential relationships between timing domains, origin clusters and replication foci. We suggest that each timing domain typically comprises several replicon clusters, which are usually processed sequentially by replication factories. We discuss how replication might be regulated at different levels to create this complex organization and the potential involvement of CDKs in this process. PMID:20724827

  3. Magnetic domain and domain wall in Co/Pt multilayer

    NASA Astrophysics Data System (ADS)

    Talapatra, A.; Mohanty, J.

    2016-05-01

    We report systematic micromagnetic investigation of formation of magnetic domains in perpendicularly magnetized Co/Pt multilayer with the variation in magnetic anisotropy and stack thickness. The lowering of anisotropy makes the domain wall broader and domain formation less efficient. Domain sizeincreases with increasing thickness of the stack to minimize the stray field energy.The minimization of energy of the system due to domain formation makes the M-H loop narrower whereas, lower stack thickness results in a wider loop. The magnetization reversalin this system occurs due tothe nucleation and growth of reverse domains.

  4. Frequency domain measurement systems

    NASA Technical Reports Server (NTRS)

    Eischer, M. C.

    1978-01-01

    Stable frequency sources and signal processing blocks were characterized by their noise spectra, both discrete and random, in the frequency domain. Conventional measures are outlined, and systems for performing the measurements are described. Broad coverage of system configurations which were found useful is given. Their functioning and areas of application are discussed briefly. Particular attention is given to some of the potential error sources in the measurement procedures, system configurations, double-balanced-mixer-phase-detectors, and application of measuring instruments.

  5. Magnetic bubble domain memories

    NASA Technical Reports Server (NTRS)

    Ypma, J. E.

    1974-01-01

    Some attractive features of Bubble Domain Memory and its relation to existing technologies are discussed. Two promising applications are block access mass memory and tape recorder replacement. The required chip capabilities for these uses are listed, and the specifications for a block access mass memory designed to fit between core and HPT disk are presented. A feasibility model for a tape recorder replacement is introduced.

  6. Genome cartography through domain annotation

    PubMed Central

    Ponting, Chris P; Dickens, Nicholas J

    2001-01-01

    The evolutionary history of eukaryotic proteins involves rapid sequence divergence, addition and deletion of domains, and fusion and fission of genes. Although the protein repertoires of distantly related species differ greatly, their domain repertoires do not. To account for the great diversity of domain contexts and an unexpected paucity of ortholog conservation, we must categorize the coding regions of completely sequenced genomes into domain families, as well as protein families.

  7. Runaway dilatonic domain walls

    SciTech Connect

    Aguirre, Anthony; Johnson, Matthew C.; Larfors, Magdalena

    2010-02-15

    We explore the stability of domain wall and bubble solutions in theories with compact extra dimensions. The energy density stored inside of the wall can destabilize the volume modulus of a compactification, leading to solutions containing either a timelike singularity or a region where space decompactifies, depending on the metric ansatz. We determine the structure of such solutions both analytically and using numerical simulations, and analyze how they arise in compactifications of Einstein-Maxwell theory and type IIB string theory. The existence of instabilities has important implications for the formation of networks of topological defects and the population of vacua during eternal inflation.

  8. Field Evolution of Antiferromagnetic Domains and Domain Walls

    NASA Astrophysics Data System (ADS)

    Fullerton, Eric E.; Hellwig, Olav; Berger, Andreas K.

    2003-03-01

    We have used magnetron sputtered [Co(4Å)Pt(7Å)]X Co(4Å)Ru(9Å)N multiplayer films to create artificially layered antiferromagnets. In contrast to atomic antiferromagnets our model system has an antiferromagnetic (AF) exchange energy comparable to the Zeemann energy in moderate fields and allows to fine tune the relative magnitude of the different magnetic energy terms by varying the parameters X and N. With increasing X and N we observe a transition from traditionally observed sharp AF domain walls towards AF domain walls with a finite width which consist of ferromagnetic stripes, i.e. the AF domains have zero net moment whereas the domain walls carry a finite magnetic moment. Such AF domain walls have not been observed before and are a direct consequence of balancing out exchange and Zeeman energy. We also show that such domain walls are expected from theoretical energy calculations. In this contribution we study the nature and field evolution of the AF stripe domain walls by Magnetic Force Microscopy (MFM). The surface sensitivity of MFM and the finite moment of the AF domain walls allow us to image AF domains as well as domain walls. We are showing first experiments to study the AF domain wall evolution in real space while applying an external field. O.H. was supported by the Deutsche Forschungsgemeinschaft via a Forschungsstipendium under the contract number HE 3286/1-1.

  9. The YTH Domain Is a Novel RNA Binding Domain*

    PubMed Central

    Zhang, Zhaiyi; Theler, Dominik; Kaminska, Katarzyna H.; Hiller, Michael; de la Grange, Pierre; Pudimat, Rainer; Rafalska, Ilona; Heinrich, Bettina; Bujnicki, Janusz M.; Allain, Frédéric H.-T.; Stamm, Stefan

    2010-01-01

    The YTH (YT521-B homology) domain was identified by sequence comparison and is found in 174 different proteins expressed in eukaryotes. It is characterized by 14 invariant residues within an α-helix/β-sheet structure. Here we show that the YTH domain is a novel RNA binding domain that binds to a short, degenerated, single-stranded RNA sequence motif. The presence of the binding motif in alternative exons is necessary for YT521-B to directly influence splice site selection in vivo. Array analyses demonstrate that YT521-B predominantly regulates vertebrate-specific exons. An NMR titration experiment identified the binding surface for single-stranded RNA on the YTH domain. Structural analyses indicate that the YTH domain is related to the pseudouridine synthase and archaeosine transglycosylase (PUA) domain. Our data show that the YTH domain conveys RNA binding ability to a new class of proteins that are found in all eukaryotic organisms. PMID:20167602

  10. Sustained accurate recording of intracellular acidification in living tissues with a photo-controllable bioluminescent protein

    PubMed Central

    Hattori, Mitsuru; Haga, Sanae; Takakura, Hideo; Ozaki, Michitaka; Ozawa, Takeaki

    2013-01-01

    Regulation of an intracellular acidic environment plays a pivotal role in biological processes and functions. However, spatiotemporal analysis of the acidification in complex tissues of living subjects persists as an important challenge. We developed a photo-inactivatable bioluminescent indicator, based on a combination of luciferase-fragment complementation and a photoreaction of a light, oxygen, and voltage domain from Avena sativa Phototropin1 (LOV2), to visualize temporally dynamic acidification in living tissue samples. Bioluminescence of the indicator diminished upon light irradiation and it recovered gradually in the dark state thereafter. The recovery rate was remarkably sensitive to pH changes but unsusceptible to fluctuation of luciferin or ATP concentrations. Bioluminescence imaging, taken as an index of the recovery rates, enabled long-time recording of acidification in apoptotic and autophagous processes in a cell population and an ischemic condition in living mice. This technology using the indicator is widely applicable to sense organelle-specific acidic changes in target biological tissues. PMID:23690604

  11. Sustained accurate recording of intracellular acidification in living tissues with a photo-controllable bioluminescent protein.

    PubMed

    Hattori, Mitsuru; Haga, Sanae; Takakura, Hideo; Ozaki, Michitaka; Ozawa, Takeaki

    2013-06-04

    Regulation of an intracellular acidic environment plays a pivotal role in biological processes and functions. However, spatiotemporal analysis of the acidification in complex tissues of living subjects persists as an important challenge. We developed a photo-inactivatable bioluminescent indicator, based on a combination of luciferase-fragment complementation and a photoreaction of a light, oxygen, and voltage domain from Avena sativa Phototropin1 (LOV2), to visualize temporally dynamic acidification in living tissue samples. Bioluminescence of the indicator diminished upon light irradiation and it recovered gradually in the dark state thereafter. The recovery rate was remarkably sensitive to pH changes but unsusceptible to fluctuation of luciferin or ATP concentrations. Bioluminescence imaging, taken as an index of the recovery rates, enabled long-time recording of acidification in apoptotic and autophagous processes in a cell population and an ischemic condition in living mice. This technology using the indicator is widely applicable to sense organelle-specific acidic changes in target biological tissues.

  12. Swarming in bounded domains

    NASA Astrophysics Data System (ADS)

    Armbruster, Dieter; Motsch, Sébastien; Thatcher, Andrea

    2017-04-01

    The Vicsek model is a prototype for the emergence of collective motion. In free space, it is characterized by a swarm of particles all moving in the same direction. Since this dynamic does not include attraction among particles, the swarm, while aligning in velocity space, has no spatial coherence. Adding specular reflection at the boundaries generates global spatial coherence of the swarms while maintaining its velocity alignment. We investigate numerically how the geometry of the domain influences the Vicsek model using three type of geometry: a channel, a disk and a rectangle. Varying the parameters of the Vicsek model (e.g. noise levels and influence horizons), we discuss the mechanisms that generate spatial coherence and show how they create new dynamical solutions of the swarming motions in these geometries. Several observables are introduced to characterize the simulated patterns (e.g. mass profile, center of mass, connectivity of the swarm).

  13. Beyond the Number Domain

    PubMed Central

    Cantlon, Jessica F.; Platt, Michael L.; Brannon, Elizabeth M.

    2009-01-01

    In a world without numbers, we would be unable to build a skyscraper, hold a national election, plan a wedding, or pay for a chicken at the market. The numerical symbols used in all these behaviors build on the approximate number system (ANS) which represents the number of discrete objects or events as a continuous mental magnitude. In this review, we first discuss evidence that the ANS bears a set of behavioral and brain signatures that are universally displayed across animal species, human cultures, and development. We then turn to the question of whether the ANS constitutes a specialized cognitive and neural domain--a question central to understanding how this system works, the nature of its evolutionary and developmental trajectory, and its physical instantiation in the brain. PMID:19131268

  14. Multifunctionalities driven by ferroic domains

    SciTech Connect

    Yang, J. C.; Huang, Y. L.; Chu, Y. H.; He, Q.

    2014-08-14

    Considerable attention has been paid to ferroic systems in pursuit of advanced applications in past decades. Most recently, the emergence and development of multiferroics, which exhibit the coexistence of different ferroic natures, has offered a new route to create functionalities in the system. In this manuscript, we step from domain engineering to explore a roadmap for discovering intriguing phenomena and multifunctionalities driven by periodic domain patters. As-grown periodic domains, offering exotic order parameters, periodic local perturbations and the capability of tailoring local spin, charge, orbital and lattice degrees of freedom, are introduced as modeling templates for fundamental studies and novel applications. We discuss related significant findings on ferroic domain, nanoscopic domain walls, and conjunct heterostructures based on the well-organized domain patterns, and end with future prospects and challenges in the field.

  15. Ligand binding by PDZ domains.

    PubMed

    Chi, Celestine N; Bach, Anders; Strømgaard, Kristian; Gianni, Stefano; Jemth, Per

    2012-01-01

    The postsynaptic density protein-95/disks large/zonula occludens-1 (PDZ) protein domain family is one of the most common protein-protein interaction modules in mammalian cells, with paralogs present in several hundred human proteins. PDZ domains are found in most cell types, but neuronal proteins, for example, are particularly rich in these domains. The general function of PDZ domains is to bring proteins together within the appropriate cellular compartment, thereby facilitating scaffolding, signaling, and trafficking events. The many functions of PDZ domains under normal physiological as well as pathological conditions have been reviewed recently. In this review, we focus on the molecular details of how PDZ domains bind their protein ligands and their potential as drug targets in this context.

  16. Mapping the Moral Domain

    PubMed Central

    Graham, Jesse; Nosek, Brian A.; Haidt, Jonathan; Iyer, Ravi; Koleva, Spassena; Ditto, Peter H.

    2010-01-01

    The moral domain is broader than the empathy and justice concerns assessed by existing measures of moral competence, and it is not just a subset of the values assessed by value inventories. To fill the need for reliable and theoretically-grounded measurement of the full range of moral concerns, we developed the Moral Foundations Questionnaire (MFQ) based on a theoretical model of five universally available (but variably developed) sets of moral intuitions: Harm/care, Fairness/reciprocity, Ingroup/loyalty, Authority/respect, and Purity/sanctity. We present evidence for the internal and external validity of the scale and the model, and in doing so present new findings about morality: 1. Comparative model fitting of confirmatory factor analyses provides empirical justification for a five-factor structure of moral concerns. 2. Convergent/discriminant validity evidence suggests that moral concerns predict personality features and social group attitudes not previously considered morally relevant. 3. We establish pragmatic validity of the measure in providing new knowledge and research opportunities concerning demographic and cultural differences in moral intuitions. These analyses provide evidence for the usefulness of Moral Foundations Theory in simultaneously increasing the scope and sharpening the resolution of psychological views of morality. PMID:21244182

  17. Mapping the moral domain.

    PubMed

    Graham, Jesse; Nosek, Brian A; Haidt, Jonathan; Iyer, Ravi; Koleva, Spassena; Ditto, Peter H

    2011-08-01

    The moral domain is broader than the empathy and justice concerns assessed by existing measures of moral competence, and it is not just a subset of the values assessed by value inventories. To fill the need for reliable and theoretically grounded measurement of the full range of moral concerns, we developed the Moral Foundations Questionnaire on the basis of a theoretical model of 5 universally available (but variably developed) sets of moral intuitions: Harm/Care, Fairness/Reciprocity, Ingroup/Loyalty, Authority/Respect, and Purity/Sanctity. We present evidence for the internal and external validity of the scale and the model, and in doing so we present new findings about morality: (a) Comparative model fitting of confirmatory factor analyses provides empirical justification for a 5-factor structure of moral concerns; (b) convergent/discriminant validity evidence suggests that moral concerns predict personality features and social group attitudes not previously considered morally relevant; and (c) we establish pragmatic validity of the measure in providing new knowledge and research opportunities concerning demographic and cultural differences in moral intuitions. These analyses provide evidence for the usefulness of Moral Foundations Theory in simultaneously increasing the scope and sharpening the resolution of psychological views of morality.

  18. Discoidin Domain Receptor 1

    PubMed Central

    Song, Sunmi; Shackel, Nicholas A.; Wang, Xin M.; Ajami, Katerina; McCaughan, Geoffrey W.; Gorrell, Mark D.

    2011-01-01

    Discoidin domain receptor 1 (DDR1) is a receptor tyrosine kinase that binds and is activated by collagens. Transcriptional profiling of cirrhosis in human liver using a DNA array and quantitative PCR detected elevated mRNA expression of DDR1 compared with that in nondiseased liver. The present study characterized DDR1 expression in cirrhotic and nondiseased human liver and examined the cellular effects of DDR1 expression. mRNA expression of all five isoforms of DDR1 was detected in human liver, whereas DDR1a demonstrated differential expression in liver with hepatitis C virus and primary biliary cirrhosis compared with nondiseased liver. In addition, immunoblot analysis detected shed fragments of DDR1 more readily in cirrhotic liver than in nondiseased liver. Inasmuch as DDR1 is subject to protease-mediated cleavage after prolonged interaction with collagen, this differential expression may indicate more intense activation of DDR1 protein in cirrhotic compared with nondiseased liver. In situ hybridization and immunofluorescence localized intense DDR1 mRNA and protein expression to epithelial cells including hepatocytes at the portal-parenchymal interface and the luminal aspect of the biliary epithelium. Overexpression of DDR1a altered hepatocyte behavior including increased adhesion and less migration on extracelular matrix substrates. DDR1a regulated extracellular expression of matrix metalloproteinases 1 and 2. These data elucidate DDR1 function pertinent to cirrhosis and indicate the importance of epithelial cell–collagen interactions in chronic liver injury. PMID:21356365

  19. CDD: a conserved domain database for interactive domain family analysis.

    PubMed

    Marchler-Bauer, Aron; Anderson, John B; Derbyshire, Myra K; DeWeese-Scott, Carol; Gonzales, Noreen R; Gwadz, Marc; Hao, Luning; He, Siqian; Hurwitz, David I; Jackson, John D; Ke, Zhaoxi; Krylov, Dmitri; Lanczycki, Christopher J; Liebert, Cynthia A; Liu, Chunlei; Lu, Fu; Lu, Shennan; Marchler, Gabriele H; Mullokandov, Mikhail; Song, James S; Thanki, Narmada; Yamashita, Roxanne A; Yin, Jodie J; Zhang, Dachuan; Bryant, Stephen H

    2007-01-01

    The conserved domain database (CDD) is part of NCBI's Entrez database system and serves as a primary resource for the annotation of conserved domain footprints on protein sequences in Entrez. Entrez's global query interface can be accessed at http://www.ncbi.nlm.nih.gov/Entrez and will search CDD and many other databases. Domain annotation for proteins in Entrez has been pre-computed and is readily available in the form of 'Conserved Domain' links. Novel protein sequences can be scanned against CDD using the CD-Search service; this service searches databases of CDD-derived profile models with protein sequence queries using BLAST heuristics, at http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi. Protein query sequences submitted to NCBI's protein BLAST search service are scanned for conserved domain signatures by default. The CDD collection contains models imported from Pfam, SMART and COG, as well as domain models curated at NCBI. NCBI curated models are organized into hierarchies of domains related by common descent. Here we report on the status of the curation effort and present a novel helper application, CDTree, which enables users of the CDD resource to examine curated hierarchies. More importantly, CDD and CDTree used in concert, serve as a powerful tool in protein classification, as they allow users to analyze protein sequences in the context of domain family hierarchies.

  20. Hydrophobic Compounds Reshape Membrane Domains

    PubMed Central

    Barnoud, Jonathan; Rossi, Giulia; Marrink, Siewert J.; Monticelli, Luca

    2014-01-01

    Cell membranes have a complex lateral organization featuring domains with distinct composition, also known as rafts, which play an essential role in cellular processes such as signal transduction and protein trafficking. In vivo, perturbations of membrane domains (e.g., by drugs or lipophilic compounds) have major effects on the activity of raft-associated proteins and on signaling pathways, but they are difficult to characterize because of the small size of the domains, typically below optical resolution. Model membranes, instead, can show macroscopic phase separation between liquid-ordered and liquid-disordered domains, and they are often used to investigate the driving forces of membrane lateral organization. Studies in model membranes have shown that some lipophilic compounds perturb membrane domains, but it is not clear which chemical and physical properties determine domain perturbation. The mechanisms of domain stabilization and destabilization are also unknown. Here we describe the effect of six simple hydrophobic compounds on the lateral organization of phase-separated model membranes consisting of saturated and unsaturated phospholipids and cholesterol. Using molecular simulations, we identify two groups of molecules with distinct behavior: aliphatic compounds promote lipid mixing by distributing at the interface between liquid-ordered and liquid-disordered domains; aromatic compounds, instead, stabilize phase separation by partitioning into liquid-disordered domains and excluding cholesterol from the disordered domains. We predict that relatively small concentrations of hydrophobic species can have a broad impact on domain stability in model systems, which suggests possible mechanisms of action for hydrophobic compounds in vivo. PMID:25299598

  1. Ontology development for Sufism domain

    NASA Astrophysics Data System (ADS)

    Iqbal, Rizwan

    2012-01-01

    Domain ontology is a descriptive representation of any particular domain which in detail describes the concepts in a domain, the relationships among those concepts and organizes them in a hierarchal manner. It is also defined as a structure of knowledge, used as a means of knowledge sharing to the community. An Important aspect of using ontologies is to make information retrieval more accurate and efficient. Thousands of domain ontologies from all around the world are available online on ontology repositories. Ontology repositories like SWOOGLE currently have over 1000 ontologies covering a wide range of domains. It was found that up to date there was no ontology available covering the domain of "Sufism". This unavailability of "Sufism" domain ontology became a motivation factor for this research. This research came up with a working "Sufism" domain ontology as well a framework, design of the proposed framework focuses on the resolution to problems which were experienced while creating the "Sufism" ontology. The development and working of the "Sufism" domain ontology are covered in detail in this research. The word "Sufism" is a term which refers to Islamic mysticism. One of the reasons to choose "Sufism" for ontology creation is its global curiosity. This research has also managed to create some individuals which inherit the concepts from the "Sufism" ontology. The creation of individuals helps to demonstrate the efficient and precise retrieval of data from the "Sufism" domain ontology. The experiment of creating the "Sufism" domain ontology was carried out on a tool called Protégé. Protégé is a tool which is used for ontology creation, editing and it is open source.

  2. Ontology development for Sufism domain

    NASA Astrophysics Data System (ADS)

    Iqbal, Rizwan

    2011-12-01

    Domain ontology is a descriptive representation of any particular domain which in detail describes the concepts in a domain, the relationships among those concepts and organizes them in a hierarchal manner. It is also defined as a structure of knowledge, used as a means of knowledge sharing to the community. An Important aspect of using ontologies is to make information retrieval more accurate and efficient. Thousands of domain ontologies from all around the world are available online on ontology repositories. Ontology repositories like SWOOGLE currently have over 1000 ontologies covering a wide range of domains. It was found that up to date there was no ontology available covering the domain of "Sufism". This unavailability of "Sufism" domain ontology became a motivation factor for this research. This research came up with a working "Sufism" domain ontology as well a framework, design of the proposed framework focuses on the resolution to problems which were experienced while creating the "Sufism" ontology. The development and working of the "Sufism" domain ontology are covered in detail in this research. The word "Sufism" is a term which refers to Islamic mysticism. One of the reasons to choose "Sufism" for ontology creation is its global curiosity. This research has also managed to create some individuals which inherit the concepts from the "Sufism" ontology. The creation of individuals helps to demonstrate the efficient and precise retrieval of data from the "Sufism" domain ontology. The experiment of creating the "Sufism" domain ontology was carried out on a tool called Protégé. Protégé is a tool which is used for ontology creation, editing and it is open source.

  3. Fractional diffusion on bounded domains

    DOE PAGES

    Defterli, Ozlem; D'Elia, Marta; Du, Qiang; ...

    2015-03-13

    We found that the mathematically correct specification of a fractional differential equation on a bounded domain requires specification of appropriate boundary conditions, or their fractional analogue. In this paper we discuss the application of nonlocal diffusion theory to specify well-posed fractional diffusion equations on bounded domains.

  4. Parallel pseudospectral domain decomposition techniques

    NASA Technical Reports Server (NTRS)

    Gottlieb, David; Hirsh, Richard S.

    1988-01-01

    The influence of interface boundary conditions on the ability to parallelize pseudospectral multidomain algorithms is investigated. Using the properties of spectral expansions, a novel parallel two domain procedure is generalized to an arbitrary number of domains each of which can be solved on a separate processor. This interface boundary condition considerably simplifies influence matrix techniques.

  5. Parallel pseudospectral domain decomposition techniques

    NASA Technical Reports Server (NTRS)

    Gottlieb, David; Hirsch, Richard S.

    1989-01-01

    The influence of interface boundary conditions on the ability to parallelize pseudospectral multidomain algorithms is investigated. Using the properties of spectral expansions, a novel parallel two domain procedure is generalized to an arbitrary number of domains each of which can be solved on a separate processor. This interface boundary condition considerably simplifies influence matrix techniques.

  6. Optimal Transport for Domain Adaptation.

    PubMed

    Courty, Nicolas; Flamary, Remi; Tuia, Devis; Rakotomamonjy, Alain

    2017-09-01

    Domain adaptation is one of the most challenging tasks of modern data analytics. If the adaptation is done correctly, models built on a specific data representation become more robust when confronted to data depicting the same classes, but described by another observation system. Among the many strategies proposed, finding domain-invariant representations has shown excellent properties, in particular since it allows to train a unique classifier effective in all domains. In this paper, we propose a regularized unsupervised optimal transportation model to perform the alignment of the representations in the source and target domains. We learn a transportation plan matching both PDFs, which constrains labeled samples of the same class in the source domain to remain close during transport. This way, we exploit at the same time the labeled samples in the source and the distributions observed in both domains. Experiments on toy and challenging real visual adaptation examples show the interest of the method, that consistently outperforms state of the art approaches. In addition, numerical experiments show that our approach leads to better performances on domain invariant deep learning features and can be easily adapted to the semi-supervised case where few labeled samples are available in the target domain.

  7. Fractional diffusion on bounded domains

    SciTech Connect

    Defterli, Ozlem; D'Elia, Marta; Du, Qiang; Gunzburger, Max Donald; Lehoucq, Richard B.; Meerschaert, Mark M.

    2015-03-13

    We found that the mathematically correct specification of a fractional differential equation on a bounded domain requires specification of appropriate boundary conditions, or their fractional analogue. In this paper we discuss the application of nonlocal diffusion theory to specify well-posed fractional diffusion equations on bounded domains.

  8. Phase-domain photoacoustic sensing

    NASA Astrophysics Data System (ADS)

    Gao, Fei; Zhang, Ruochong; Feng, Xiaohua; Liu, Siyu; Ding, Ran; Kishor, Rahul; Qiu, Lei; Zheng, Yuanjin

    2017-01-01

    As one of the fastest-growing imaging modalities in recent years, photoacoustic imaging has attracted tremendous research interest for various applications including anatomical, functional, and molecular imaging. The majority of the photoacoustic imaging systems are based on the time-domain pulsed photoacoustic method, which utilizes a pulsed laser source to induce a wideband photoacoustic signal, revealing optical absorption contrast. An alternative way is the frequency-domain photoacoustic method utilizing the chirping modulation of laser intensity to achieve lower system cost. In this paper, we report another way of the photoacoustic method, called phase-domain photoacoustic sensing, which explores the phase difference between two consequent intensity-modulated laser pulse induced photoacoustic measurements to reveal the optical properties. The basic principle is introduced, modeled, and experimentally validated in this paper, which opens another potential pathway to perform photoacoustic sensing and imaging, eliminating acoustic detection variations beyond the conventional time-domain and frequency-domain photoacoustic methods.

  9. Diversity in protein domain superfamilies

    PubMed Central

    Das, Sayoni; Dawson, Natalie L; Orengo, Christine A

    2015-01-01

    Whilst ∼93% of domain superfamilies appear to be relatively structurally and functionally conserved based on the available data from the CATH-Gene3D domain classification resource, the remainder are much more diverse. In this review, we consider how domains in some of the most ubiquitous and promiscuous superfamilies have evolved, in particular the plasticity in their functional sites and surfaces which expands the repertoire of molecules they interact with and actions performed on them. To what extent can we identify a core function for these superfamilies which would allow us to develop a ‘domain grammar of function’ whereby a protein's biological role can be proposed from its constituent domains? Clearly the first step is to understand the extent to which these components vary and how changes in their molecular make-up modifies function. PMID:26451979

  10. Microbial starch-binding domain.

    PubMed

    Rodríguez-Sanoja, Romina; Oviedo, Norma; Sánchez, Sergio

    2005-06-01

    Glucosidic bonds from different non-soluble polysaccharides such as starch, cellulose and xylan are hydrolyzed by amylases, cellulases and xylanases, respectively. These enzymes are produced by microorganisms. They have a modular structure that is composed of a catalytic domain and at least one non-catalytic domain that is involved in polysaccharide binding. Starch-binding modules are present in microbial enzymes that are involved in starch metabolism; these are classified into several different families on the basis of their amino acid sequence similarities. Such binding domains promote attachment to the substrate and increase its concentration at the active site of the enzyme, which allows microorganisms to degrade non-soluble starch. Fold similarities are better conserved than sequences; nevertheless, it is possible to notice two evolutionary clusters of microbial starch-binding domains. These domains have enormous potential as tags for protein immobilization, as well as for the tailoring of enzymes that play a part in polysaccharide metabolism.

  11. The monocyte binding domain(s) on human immunoglobulin G.

    PubMed

    Woof, J M; Nik Jaafar, M I; Jefferis, R; Burton, D R

    1984-06-01

    Monocyte binding has previously been assigned to the C gamma 3 domain of human immunoglobulin G (IgG) largely on the ability of the pFc' fragment to inhibit the monocyte-IgG interaction. This ability is markedly reduced compared to the intact parent IgG. We find this result with a conventional pFc' preparation but this preparation is found to contain trace contamination of parent IgG as demonstrated by reactivity with monoclonal antibodies directed against C gamma 2 domain and light-chain epitopes of human IgG. Extensive immunoaffinity purification of the pFc' preparation removes its inhibitory ability indicating that this originates in the trace contamination of parent IgG (or Fc). Neither of the human IgG1 paraproteins TIM, lacking the C gamma 2 domain, or SIZ, lacking the C gamma 3 domain, are found to inhibit the monocyte-IgG interaction. The hinge-deleted IgG1 Dob protein shows little or no inhibitory ability. Indirect evidence for the involvement of the C gamma 2 domain in monocyte binding is considered. We suggest finally that the site of interaction is found either on the C gamma 2 domain alone or between the C gamma 2 and C gamma 3 domains.

  12. Failure to Burrow and Tunnel Reveals Roles for jim lovell in the Growth and Endoreplication of the Drosophila Larval Tracheae

    PubMed Central

    Qiang, Karen M.; Beckingham, Kathleen M.

    2016-01-01

    The Drosophila protein Jim Lovell (Lov) is a putative transcription factor of the BTB/POZ (Bric- a-Brac/Tramtrack/Broad/ Pox virus and Zinc finger) domain class that is expressed in many elements of the developing larval nervous system. It has roles in innate behaviors such as larval locomotion and adult courtship. In performing tissue-specific knockdown with the Gal4-UAS system we identified a new behavioral phenotype for lov: larvae failed to burrow into their food during their growth phase and then failed to tunnel into an agarose substratum during their wandering phase. We determined that these phenotypes originate in a previously unrecognized role for lov in the tracheae. By using tracheal-specific Gal4 lines, Lov immunolocalization and a lov enhancer trap line, we established that lov is normally expressed in the tracheae from late in embryogenesis through larval life. Using an assay that monitors food burrowing, substrate tunneling and death we showed that lov tracheal knockdown results in tracheal fluid-filling, producing hypoxia that activates the aberrant behaviors and inhibits development. We investigated the role of lov in the tracheae that initiates this sequence of events. We discovered that when lov levels are reduced, the tracheal cells are smaller, more numerous and show lower levels of endopolyploidization. Together our findings indicate that Lov is necessary for tracheal endoreplicative growth and that its loss in this tissue causes loss of tracheal integrity resulting in chronic hypoxia and abnormal burrowing and tunneling behavior. PMID:27494251

  13. Separated matter and antimatter domains with vanishing domain walls

    SciTech Connect

    Dolgov, A.D.; Godunov, S.I.; Rudenko, A.S.; Tkachev, I.I. E-mail: sgodunov@itep.ru E-mail: tkachev@ms2.inr.ac.ru

    2015-10-01

    We present a model of spontaneous (or dynamical) C and CP violation where it is possible to generate domains of matter and antimatter separated by cosmologically large distances. Such C(CP) violation existed only in the early universe and later it disappeared with the only trace of generated baryonic and/or antibaryonic domains. So the problem of domain walls in this model does not exist. These features are achieved through a postulated form of interaction between inflaton and a new scalar field, realizing short time C(CP) violation.

  14. Domain walls riding the wave.

    SciTech Connect

    Karapetrov, G.; Novosad, V.; Materials Science Division

    2010-11-01

    Recent years have witnessed a rapid proliferation of electronic gadgets around the world. These devices are used for both communication and entertainment, and it is a fact that they account for a growing portion of household energy consumption and overall world consumption of electricity. Increasing the energy efficiency of these devices could have a far greater and immediate impact than a gradual switch to renewable energy sources. The advances in the area of spintronics are therefore very important, as gadgets are mostly comprised of memory and logic elements. Recent developments in controlled manipulation of magnetic domains in ferromagnet nanostructures have opened opportunities for novel device architectures. This new class of memories and logic gates could soon power millions of consumer electronic devices. The attractiveness of using domain-wall motion in electronics is due to its inherent reliability (no mechanical moving parts), scalability (3D scalable architectures such as in racetrack memory), and nonvolatility (retains information in the absence of power). The remaining obstacles in widespread use of 'racetrack-type' elements are the speed and the energy dissipation during the manipulation of domain walls. In their recent contribution to Physical Review Letters, Oleg Tretiakov, Yang Liu, and Artem Abanov from Texas A&M University in College Station, provide a theoretical description of domain-wall motion in nanoscale ferromagnets due to the spin-polarized currents. They find exact conditions for time-dependent resonant domain-wall movement, which could speed up the motion of domain walls while minimizing Ohmic losses. Movement of domain walls in ferromagnetic nanowires can be achieved by application of external magnetic fields or by passing a spin-polarized current through the nanowire itself. On the other hand, the readout of the domain state is done by measuring the resistance of the wire. Therefore, passing current through the ferromagnetic wire is

  15. Mutation of domain III and domain VI in L gene conserved domain of Nipah virus

    NASA Astrophysics Data System (ADS)

    Jalani, Siti Aishah; Ibrahim, Nazlina

    2016-11-01

    Nipah virus (NiV) is the etiologic agent responsible for the respiratory illness and causes fatal encephalitis in human. NiV L protein subunit is thought to be responsible for the majority of enzymatic activities involved in viral transcription and replication. The L protein which is the viral RNA dependent RNA polymerase has high sequence homology among negative sense RNA viruses. In negative stranded RNA viruses, based on sequence alignment six conserved domain (domain I-IV) have been determined. Each domain is separated on variable regions that suggest the structure to consist concatenated functional domain. To directly address the roles of domains III and VI, site-directed mutations were constructed by the substitution of bases at sequences 2497, 2500, 5528 and 5532. Each mutated L gene can be used in future studies to test the ability for expression on in vitro translation.

  16. Modeling software systems by domains

    NASA Technical Reports Server (NTRS)

    Dippolito, Richard; Lee, Kenneth

    1992-01-01

    The Software Architectures Engineering (SAE) Project at the Software Engineering Institute (SEI) has developed engineering modeling techniques that both reduce the complexity of software for domain-specific computer systems and result in systems that are easier to build and maintain. These techniques allow maximum freedom for system developers to apply their domain expertise to software. We have applied these techniques to several types of applications, including training simulators operating in real time, engineering simulators operating in non-real time, and real-time embedded computer systems. Our modeling techniques result in software that mirrors both the complexity of the application and the domain knowledge requirements. We submit that the proper measure of software complexity reflects neither the number of software component units nor the code count, but the locus of and amount of domain knowledge. As a result of using these techniques, domain knowledge is isolated by fields of engineering expertise and removed from the concern of the software engineer. In this paper, we will describe kinds of domain expertise, describe engineering by domains, and provide relevant examples of software developed for simulator applications using the techniques.

  17. Discussion summary: Fictitious domain methods

    NASA Technical Reports Server (NTRS)

    Glowinski, Rowland; Rodrigue, Garry

    1991-01-01

    Fictitious Domain methods are constructed in the following manner: Suppose a partial differential equation is to be solved on an open bounded set, Omega, in 2-D or 3-D. Let R be a rectangle domain containing the closure of Omega. The partial differential equation is first solved on R. Using the solution on R, the solution of the equation on Omega is then recovered by some procedure. The advantage of the fictitious domain method is that in many cases the solution of a partial differential equation on a rectangular region is easier to compute than on a nonrectangular region. Fictitious domain methods for solving elliptic PDEs on general regions are also very efficient when used on a parallel computer. The reason is that one can use the many domain decomposition methods that are available for solving the PDE on the fictitious rectangular region. The discussion on fictitious domain methods began with a talk by R. Glowinski in which he gave some examples of a variational approach to ficititious domain methods for solving the Helmholtz and Navier-Stokes equations.

  18. Predicting domain-domain interaction based on domain profiles with feature selection and support vector machines

    PubMed Central

    2010-01-01

    Background Protein-protein interaction (PPI) plays essential roles in cellular functions. The cost, time and other limitations associated with the current experimental methods have motivated the development of computational methods for predicting PPIs. As protein interactions generally occur via domains instead of the whole molecules, predicting domain-domain interaction (DDI) is an important step toward PPI prediction. Computational methods developed so far have utilized information from various sources at different levels, from primary sequences, to molecular structures, to evolutionary profiles. Results In this paper, we propose a computational method to predict DDI using support vector machines (SVMs), based on domains represented as interaction profile hidden Markov models (ipHMM) where interacting residues in domains are explicitly modeled according to the three dimensional structural information available at the Protein Data Bank (PDB). Features about the domains are extracted first as the Fisher scores derived from the ipHMM and then selected using singular value decomposition (SVD). Domain pairs are represented by concatenating their selected feature vectors, and classified by a support vector machine trained on these feature vectors. The method is tested by leave-one-out cross validation experiments with a set of interacting protein pairs adopted from the 3DID database. The prediction accuracy has shown significant improvement as compared to InterPreTS (Interaction Prediction through Tertiary Structure), an existing method for PPI prediction that also uses the sequences and complexes of known 3D structure. Conclusions We show that domain-domain interaction prediction can be significantly enhanced by exploiting information inherent in the domain profiles via feature selection based on Fisher scores, singular value decomposition and supervised learning based on support vector machines. Datasets and source code are freely available on the web at http

  19. Predicting domain-domain interaction based on domain profiles with feature selection and support vector machines.

    PubMed

    González, Alvaro J; Liao, Li

    2010-10-29

    Protein-protein interaction (PPI) plays essential roles in cellular functions. The cost, time and other limitations associated with the current experimental methods have motivated the development of computational methods for predicting PPIs. As protein interactions generally occur via domains instead of the whole molecules, predicting domain-domain interaction (DDI) is an important step toward PPI prediction. Computational methods developed so far have utilized information from various sources at different levels, from primary sequences, to molecular structures, to evolutionary profiles. In this paper, we propose a computational method to predict DDI using support vector machines (SVMs), based on domains represented as interaction profile hidden Markov models (ipHMM) where interacting residues in domains are explicitly modeled according to the three dimensional structural information available at the Protein Data Bank (PDB). Features about the domains are extracted first as the Fisher scores derived from the ipHMM and then selected using singular value decomposition (SVD). Domain pairs are represented by concatenating their selected feature vectors, and classified by a support vector machine trained on these feature vectors. The method is tested by leave-one-out cross validation experiments with a set of interacting protein pairs adopted from the 3DID database. The prediction accuracy has shown significant improvement as compared to InterPreTS (Interaction Prediction through Tertiary Structure), an existing method for PPI prediction that also uses the sequences and complexes of known 3D structure. We show that domain-domain interaction prediction can be significantly enhanced by exploiting information inherent in the domain profiles via feature selection based on Fisher scores, singular value decomposition and supervised learning based on support vector machines. Datasets and source code are freely available on the web at http

  20. Anatomy of Mammalian Replication Domains

    PubMed Central

    Takebayashi, Shin-ichiro; Ogata, Masato; Okumura, Katsuzumi

    2017-01-01

    Genetic information is faithfully copied by DNA replication through many rounds of cell division. In mammals, DNA is replicated in Mb-sized chromosomal units called “replication domains.” While genome-wide maps in multiple cell types and disease states have uncovered both dynamic and static properties of replication domains, we are still in the process of understanding the mechanisms that give rise to these properties. A better understanding of the molecular basis of replication domain regulation will bring new insights into chromosome structure and function. PMID:28350365

  1. Protein domain connectivity and essentiality

    NASA Astrophysics Data System (ADS)

    da F. Costa, L.; Rodrigues, F. A.; Travieso, G.

    2006-10-01

    Protein-protein interactions can be properly modeled as scale-free complex networks, while the lethality of proteins has been correlated with the node degrees, therefore defining a lethality-centrality rule. In this work the authors revisit this relevant problem by focusing attention not on proteins as a whole, but on their functional domains, which are ultimately responsible for their binding potential. Four networks are considered: the original protein-protein interaction network, its randomized version, and two domain networks assuming different lethality hypotheses. By using formal statistical analysis, they show that the correlation between connectivity and essentiality is higher for domains than for proteins.

  2. Domain Walls in Bent Nanowires

    NASA Astrophysics Data System (ADS)

    Lofink, F.; Philippi-Kobs, A.; Rahbar Azad, M. R.; Hankemeier, S.; Hoffmann, G.; Frömter, R.; Oepen, H. P.

    2017-08-01

    The influence of geometric parameters on the magnetic fine structure of domain walls in bent nanowires is investigated. The domain pattern in the soft-magnetic Co39Fe54Si7 alloy is studied via scanning electron microscopy with polarization analysis and modeled via micromagnetic simulations. It is demonstrated that the bending angle affects details of the microstructure as well as the preponderant domain-wall type. A phenomenological model is developed that provides the global energy minimum of individual types of domain walls as a function of the geometric parameters of the wire. The results can be directly transferred to permalloy wires, as permalloy and Co39Fe54Si7 alloy have a comparable magnetostatic exchange length.

  3. Structure of axionic domain walls

    NASA Astrophysics Data System (ADS)

    Huang, M. C.; Sikivie, P.

    1985-09-01

    The structure of axionic domain walls is investigated using the low-energy effective theory of axions and pions. We derive the spatial dependence of the phases of the Peccei-Quinn scalar field and the QCD quark-antiquark condensates inside an axionic domain wall. Thence an accurate estimate of the wall surface energy density is obtained. The equations of motion for axions, photons, leptons, and baryons in the neighborhood of axionic domain walls are written down and estimates are given for the wall reflection and transmission coefficients of these particles. Finally, we discuss the energy dissipation by axionic domain walls oscillating in the early universe due to the reflection of particles in the primordial soup.

  4. Affective Domain Measuring Scale (ADMS).

    ERIC Educational Resources Information Center

    Downs, Gary E.

    The development, validation, and reliability of the Affective Domain Measuring Scale are described. Values are presented with the techniques used in calculations. The scale is included with the scale value (the median or 50th percentile) for each item. (SA)

  5. Engineered autonomous human variable domains

    PubMed Central

    Nilvebrant, Johan; Tessier, Peter M.; Sidhu, Sachdev S.

    2017-01-01

    The complex multi-chain architecture of antibodies has spurred interest in smaller derivatives that retain specificity but can be more easily produced in bacteria. Domain antibodies consisting of single variable domains are the smallest antibody fragments and have been shown to possess enhanced ability to target epitopes that are difficult to access using multidomain antibodies. However, in contrast to natural camelid antibody domains, human variable domains typically suffer from low stability and high propensity to aggregate. This review summarizes strategies to improve the biophysical properties of heavy chain variable domains from human antibodies with an emphasis on aggregation resistance. Several protein engineering approaches have targeted antibody frameworks and complementarity determining regions to stabilize the native state and prevent aggregation of the denatured state. Recent findings enable the construction of highly diverse libraries enriched in aggregation-resistant variants that are expected to provide binders to diverse antigens. Engineered domain antibodies possess unique advantages in expression, epitope preference and flexibility of formatting over conventional immunoreagents and are a promising class of antibody fragments for biomedical development. PMID:27655414

  6. Domain-to-domain coupling in voltage-sensing phosphatase

    PubMed Central

    Sakata, Souhei; Matsuda, Makoto; Kawanabe, Akira; Okamura, Yasushi

    2017-01-01

    Voltage-sensing phosphatase (VSP) consists of a transmembrane voltage sensor and a cytoplasmic enzyme region. The enzyme region contains the phosphatase and C2 domains, is structurally similar to the tumor suppressor phosphatase PTEN, and catalyzes the dephosphorylation of phosphoinositides. The transmembrane voltage sensor is connected to the phosphatase through a short linker region, and phosphatase activity is induced upon membrane depolarization. Although the detailed molecular characteristics of the voltage sensor domain and the enzyme region have been revealed, little is known how these two regions are coupled. In addition, it is important to know whether mechanism for coupling between the voltage sensor domain and downstream effector function is shared among other voltage sensor domain-containing proteins. Recent studies in which specific amino acid sites were genetically labeled using a fluorescent unnatural amino acid have enabled detection of the local structural changes in the cytoplasmic region of Ciona intestinalis VSP that occur with a change in membrane potential. The results of those studies provide novel insight into how the enzyme activity of the cytoplasmic region of VSP is regulated by the voltage sensor domain. PMID:28744425

  7. A Blue Light Inducible Two-Component Signal Transduction System in the Plant Pathogen Pseudomonas syringae pv. tomato☆

    PubMed Central

    Cao, Z.; Buttani, V.; Losi, A.; Gärtner, W.

    2008-01-01

    Abstract The open reading frame PSPTO2896 from the plant pathogen Pseudomonas syringae pv. tomato encodes a protein of 534 amino acids showing all salient features of a blue light-driven two-component system. The N-terminal LOV (light, oxygen, voltage) domain, potentially binding a flavin chromophore, is followed by a histidine kinase (HK) motif and a response regulator (RR). The full-length protein (PST-LOV) and, separately, the RR and the LOV+HK part (PST-LOVΔRR) were heterologously expressed and functionally characterized. The two LOV proteins showed typical LOV-like spectra and photochemical reactions, with the blue light-driven, reversible formation of a covalent flavin-cysteine bond. The fluorescence changes in the lit state of full-length PST-LOV, but not in PST-LOVΔRR, indicating a direct interaction between the LOV core and the RR module. Experiments performed with radioactive ATP uncover the light-driven kinase activity. For both PST-LOV and PST-LOVΔRR, much more radioactivity is incorporated when the protein is in the lit state. Furthermore, addition of the RR domain to the fully phosphorylated PST-LOVΔRR leads to a very fast transfer of radioactivity, indicating a highly efficient HK activity and a tight interaction between PST-LOVΔRR and RR, possibly facilitated by the LOV core itself. PMID:17905842

  8. Domain and Specification Models for Software Engineering

    NASA Technical Reports Server (NTRS)

    Iscoe, Neil; Liu, Zheng-Yang; Feng, Guohui

    1992-01-01

    This paper discusses our approach to representing application domain knowledge for specific software engineering tasks. Application domain knowledge is embodied in a domain model. Domain models are used to assist in the creation of specification models. Although many different specification models can be created from any particular domain model, each specification model is consistent and correct with respect to the domain model. One aspect of the system-hierarchical organization is described in detail.

  9. Localization of resistive domains in inhomogeneous superconductors

    SciTech Connect

    Gurevich, A.V.; Mints, R.G.

    1981-01-01

    The properties of resistive domains due to the Joule heating in inhomogeneous superconductors with transport currents are studied. The equilibrium of a domain at an inhomogeneity of arbitrary type and with dimensions much smaller than the dimensions of the domain is investigated. It is shown that resistive domains can become localized at inhomogeneities. The temperature distribution in a domain and the current--voltage characteristic of the domain are determined. The stability of localized domains is discussed. It is shown that such domains give rise to a hysteresis in the destruction (recovery) of the superconductivity by the transport current.

  10. Functional domain walls in multiferroics.

    PubMed

    Meier, Dennis

    2015-11-25

    During the last decade a wide variety of novel and fascinating correlation phenomena has been discovered at domain walls in multiferroic bulk systems, ranging from unusual electronic conductance to inseparably entangled spin and charge degrees of freedom. The domain walls represent quasi-2D functional objects that can be induced, positioned, and erased on demand, bearing considerable technological potential for future nanoelectronics. Most of the challenges that remain to be solved before turning related device paradigms into reality, however, still fall in the field of fundamental condensed matter physics and materials science. In this topical review seminal experimental findings gained on electric and magnetic domain walls in multiferroic bulk materials are addressed. A special focus is put on the physical properties that emerge at so-called charged domain walls and the added functionality that arises from coexisting magnetic order. The research presented in this review highlights that we are just entering a whole new world of intriguing nanoscale physics that is yet to be explored in all its details. The goal is to draw attention to the persistent challenges and identify future key directions for the research on functional domain walls in multiferroics.

  11. Faraday instability in deformable domains

    NASA Astrophysics Data System (ADS)

    Pucci, Giuseppe; Ben Amar, Martine; Couder, Yves

    2014-11-01

    We investigate the Faraday instability in floating liquid lenses, as an example of hydrodynamic instability that develops in a domain with flexible boundaries. We show that a mutual adaptation of the instability pattern and the domain shape occurs, as a result of the competition between the wave radiation pressure and the capillary response of the lens border. Two archetypes of behaviour are observed. In the first, stable shapes are obtained experimentally and predicted theoretically as the exact solutions of a Riccati equation, and they result from the equilibrium between wave radiation pressure and capillarity. In the second, the radiation pressure exceeds the capillary response of the lens border and leads to non-equilibrium behaviours, with breaking into smaller domains that have a complex dynamics including spontaneous propagation. The authors are grateful to Université Franco-Italienne (UFI) for financial support.

  12. Domain similarity based orthology detection.

    PubMed

    Bitard-Feildel, Tristan; Kemena, Carsten; Greenwood, Jenny M; Bornberg-Bauer, Erich

    2015-05-13

    Orthologous protein detection software mostly uses pairwise comparisons of amino-acid sequences to assert whether two proteins are orthologous or not. Accordingly, when the number of sequences for comparison increases, the number of comparisons to compute grows in a quadratic order. A current challenge of bioinformatic research, especially when taking into account the increasing number of sequenced organisms available, is to make this ever-growing number of comparisons computationally feasible in a reasonable amount of time. We propose to speed up the detection of orthologous proteins by using strings of domains to characterize the proteins. We present two new protein similarity measures, a cosine and a maximal weight matching score based on domain content similarity, and new software, named porthoDom. The qualities of the cosine and the maximal weight matching similarity measures are compared against curated datasets. The measures show that domain content similarities are able to correctly group proteins into their families. Accordingly, the cosine similarity measure is used inside porthoDom, the wrapper developed for proteinortho. porthoDom makes use of domain content similarity measures to group proteins together before searching for orthologs. By using domains instead of amino acid sequences, the reduction of the search space decreases the computational complexity of an all-against-all sequence comparison. We demonstrate that representing and comparing proteins as strings of discrete domains, i.e. as a concatenation of their unique identifiers, allows a drastic simplification of search space. porthoDom has the advantage of speeding up orthology detection while maintaining a degree of accuracy similar to proteinortho. The implementation of porthoDom is released using python and C++ languages and is available under the GNU GPL licence 3 at http://www.bornberglab.org/pages/porthoda .

  13. The Garrison Domain: Civil Military Relations in the Cyberspace Domain

    DTIC Science & Technology

    2015-04-01

    through the creation of the Advanced Research Projects Agency Network ( ARPANET ), and was not codified as a domain until the early part of the 21st...therefore viewed as less important . The powers of the legislative and judicial branches of government become weak in relation to the executive branch

  14. Sinh-domain complex integrators

    NASA Astrophysics Data System (ADS)

    Skotis, George-Drosos; Khanday, Farooq A.; Psychalinos, Costas

    2015-07-01

    The basic building blocks for performing complex signal processing in the Sinh-domain are introduced in this article. Attractive offered benefits are the capabilities for achieving resistorless realisations with electronic adjustment of their frequency characteristics, independent tuning of centre frequency and bandwidth and operating in a low-voltage environment. In addition, the inherent class-AB operation of Sinh-domain filters allows the handling of signals greater than the bias current, leading to a power saving. The aforementioned benefits have been evaluated through simulation results, using the Analog Design Environment of the Cadence software.

  15. The Evolution and Functional Role of Flavin-based Prokaryotic Photoreceptors.

    PubMed

    Losi, Aba; Mandalari, Carmen; Gärtner, Wolfgang

    2015-01-01

    Flavin-based photoreceptor proteins of the LOV (light, oxygen and voltage) superfamily are ubiquitous and appear to be essential blue-light sensing systems not only in plants, algae and fungi, but also in prokaryotes, where they are represented in more than 10% of known species. Despite their broad occurrence, only in few cases LOV proteins have been correlated with important phenomena such as bacterial infectivity, selective growth patterns or/and stress responses; nevertheless these few known roles are helping us understand the multiple ways by which prokaryotes can exploit these soluble blue-light photoreceptors. Given the large number of sequences now deposited in databases, it becomes meaningful to define a signature for bona fide LOV domains, a procedure that facilitates identification of proteins with new properties and phylogenetic analysis. The latter clearly evidences that a class of LOV proteins from alpha-proteobacteria is the closest prokaryotic relative of eukaryotic LOV domains, whereas cyanobacterial sequences cluster with the archaeal and the other bacterial LOV domains. Distance trees built for LOV domains suggest complex evolutionary patterns, possibly involving multiple horizontal gene transfer events. Based on available data, the in vivo relevance and evolution of prokaryotic LOV is discussed.

  16. Inferring Domain-Domain Interactions from Protein-Protein Interactions with Formal Concept Analysis

    PubMed Central

    Khor, Susan

    2014-01-01

    Identifying reliable domain-domain interactions will increase our ability to predict novel protein-protein interactions, to unravel interactions in protein complexes, and thus gain more information about the function and behavior of genes. One of the challenges of identifying reliable domain-domain interactions is domain promiscuity. Promiscuous domains are domains that can occur in many domain architectures and are therefore found in many proteins. This becomes a problem for a method where the score of a domain-pair is the ratio between observed and expected frequencies because the protein-protein interaction network is sparse. As such, many protein-pairs will be non-interacting and domain-pairs with promiscuous domains will be penalized. This domain promiscuity challenge to the problem of inferring reliable domain-domain interactions from protein-protein interactions has been recognized, and a number of work-arounds have been proposed. This paper reports on an application of Formal Concept Analysis to this problem. It is found that the relationship between formal concepts provides a natural way for rare domains to elevate the rank of promiscuous domain-pairs and enrich highly ranked domain-pairs with reliable domain-domain interactions. This piggybacking of promiscuous domain-pairs onto less promiscuous domain-pairs is possible only with concept lattices whose attribute-labels are not reduced and is enhanced by the presence of proteins that comprise both promiscuous and rare domains. PMID:24586450

  17. AIDA: ab initio domain assembly server.

    PubMed

    Xu, Dong; Jaroszewski, Lukasz; Li, Zhanwen; Godzik, Adam

    2014-07-01

    AIDA: ab initio domain assembly server, available at http://ffas.burnham.org/AIDA/ is a tool that can identify domains in multi-domain proteins and then predict their 3D structures and relative spatial arrangements. The server is free and open to all users, and there is an option for a user to provide an e-mail to get the link to result page. Domains are evolutionary conserved and often functionally independent units in proteins. Most proteins, especially eukaryotic ones, consist of multiple domains while at the same time, most experimentally determined protein structures contain only one or two domains. As a result, often structures of individual domains in multi-domain proteins can be accurately predicted, but the mutual arrangement of different domains remains unknown. To address this issue we have developed AIDA program, which combines steps of identifying individual domains, predicting (separately) their structures and assembling them into multiple domain complexes using an ab initio folding potential to describe domain-domain interactions. AIDA server not only supports the assembly of a large number of continuous domains, but also allows the assembly of domains inserted into other domains. Users can also provide distance restraints to guide the AIDA energy minimization. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  18. Exhaustive enumeration of protein domain families.

    PubMed

    Heger, Andreas; Holm, Liisa

    2003-05-02

    Domains are considered as the basic units of protein folding, evolution, and function. Decomposing each protein into modular domains is thus a basic prerequisite for accurate functional classification of biological molecules. Here, we present ADDA, an automatic algorithm for domain decomposition and clustering of all protein domain families. We use alignments derived from an all-on-all sequence comparison to define domains within protein sequences based on a global maximum likelihood model. In all, 90% of domain boundaries are predicted within 10% of domain size when compared with the manual domain definitions given in the SCOP database. A representative database of 249,264 protein sequences were decomposed into 450,462 domains. These domains were clustered on the basis of sequence similarities into 33,879 domain families containing at least two members with less than 40% sequence identity. Validation against family definitions in the manually curated databases SCOP and PFAM indicates almost perfect unification of various large domain families while contamination by unrelated sequences remains at a low level. The global survey of protein-domain space by ADDA confirms that most large and universal domain families are already described in PFAM and/or SMART. However, a survey of the complete set of mobile modules leads to the identification of 1479 new interesting domain families which shuffle around in multi-domain proteins. The data are publicly available at ftp://ftp.ebi.ac.uk/pub/contrib/heger/adda.

  19. A Method to Examine Content Domain Structures

    ERIC Educational Resources Information Center

    D'Agostino, Jerome; Karpinski, Aryn; Welsh, Megan

    2011-01-01

    After a test is developed, most content validation analyses shift from ascertaining domain definition to studying domain representation and relevance because the domain is assumed to be set once a test exists. We present an approach that allows for the examination of alternative domain structures based on extant test items. In our example based on…

  20. Domain Specificity and Variability in Cognitive Development.

    ERIC Educational Resources Information Center

    Gelman, Rochel

    2000-01-01

    Maintains that there are core-specific and non-core-specific domains of knowledge, but that only the core-specific domains benefit from innate skeletal structures. Asserts that core skeletal domains are universally shared, even though their particular foci may vary. Emphasizes that individuals vary in terms of the noncore domains they acquire.…

  1. Development in the Food Domain.

    ERIC Educational Resources Information Center

    Rozin, Paul

    1990-01-01

    Discusses problems of general interest in developmental psychology that can be successfully studied in the domain of food; these include (1) development of food likes and dislikes; (2) establishment of the edible/inedible distinction; (3) disgust and contagion; (4) transgenerational communication of preferences; and (5) transition to food…

  2. Cellulose binding domain fusion proteins

    DOEpatents

    Shoseyov, O.; Yosef, K.; Shpiegl, I.; Goldstein, M.A.; Doi, R.H.

    1998-02-17

    A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques. 16 figs.

  3. Cellulose binding domain fusion proteins

    SciTech Connect

    Shoseyov, Oded; Shpiegl, Itai; Goldstein, Marc A.; Doi, Roy H.

    1998-01-01

    A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production thereof. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques.

  4. Life sciences domain analysis model.

    PubMed

    Freimuth, Robert R; Freund, Elaine T; Schick, Lisa; Sharma, Mukesh K; Stafford, Grace A; Suzek, Baris E; Hernandez, Joyce; Hipp, Jason; Kelley, Jenny M; Rokicki, Konrad; Pan, Sue; Buckler, Andrew; Stokes, Todd H; Fernandez, Anna; Fore, Ian; Buetow, Kenneth H; Klemm, Juli D

    2012-01-01

    Meaningful exchange of information is a fundamental challenge in collaborative biomedical research. To help address this, the authors developed the Life Sciences Domain Analysis Model (LS DAM), an information model that provides a framework for communication among domain experts and technical teams developing information systems to support biomedical research. The LS DAM is harmonized with the Biomedical Research Integrated Domain Group (BRIDG) model of protocol-driven clinical research. Together, these models can facilitate data exchange for translational research. The content of the LS DAM was driven by analysis of life sciences and translational research scenarios and the concepts in the model are derived from existing information models, reference models and data exchange formats. The model is represented in the Unified Modeling Language and uses ISO 21090 data types. The LS DAM v2.2.1 is comprised of 130 classes and covers several core areas including Experiment, Molecular Biology, Molecular Databases and Specimen. Nearly half of these classes originate from the BRIDG model, emphasizing the semantic harmonization between these models. Validation of the LS DAM against independently derived information models, research scenarios and reference databases supports its general applicability to represent life sciences research. The LS DAM provides unambiguous definitions for concepts required to describe life sciences research. The processes established to achieve consensus among domain experts will be applied in future iterations and may be broadly applicable to other standardization efforts. The LS DAM provides common semantics for life sciences research. Through harmonization with BRIDG, it promotes interoperability in translational science.

  5. Protein structural domains: definition and prediction.

    PubMed

    Ezkurdia, Iakes; Tress, Michael L

    2011-11-01

    Recognition and prediction of structural domains in proteins is an important part of structure and function prediction. This unit lists the range of tools available for domain prediction, and describes sequence and structural analysis tools that complement domain prediction methods. Also detailed are the basic domain prediction steps, along with suggested strategies for different protein sequences and potential pitfalls in domain boundary prediction. The difficult problem of domain orientation prediction is also discussed. All the resources necessary for domain boundary prediction are accessible via publicly available Web servers and databases and do not require computational expertise.

  6. Domains of Awareness in Schizophrenia

    PubMed Central

    Gilleen, J.; Greenwood, K.; David, A. S.

    2011-01-01

    Patients with schizophrenia are often characterized as lacking insight or awareness into their illness and symptoms, yet despite considerable research, we still lack a full understanding of the factors involved in causing poor awareness. Within schizophrenia, there has been shown to be a fractionation across dimensions of awareness into mental illness: of being ill, of symptoms, and of treatment compliance. Recently, attention has turned to evidence of a fractionation between awareness of illness and of cognitive impairments and functioning. The current study investigated the degree of fractionation across a broad range of domains of function in schizophrenia and how each domain may be associated with neuropsychological functioning, clinical, mood, and demographic variables. Thirty-one mostly chronic stable patients with schizophrenia completed a battery of neuropsychological tests and measures of psychopathology, including mood. Cognitive insight and awareness of illness, symptoms, memory, and behavioral functioning were also measured. Insight and awareness were assessed using a combination of semistructured interview, observer-rated, self-rated, and objective measures, and included measures of the discrepancy between carer and self-ratings of impairment. Results revealed that awareness of functioning in each domain was largely independent and that awareness in each domain was predicted by different factors. Insight into symptoms was relatively poor while insight into cognitive deficits was preserved. Relative to neuropsychological variables, cognitive insight, comprising self-certainty and self-reflexivity, was a greater predictor of awareness. In conclusion, awareness is multiply fractionated and multiply determined. Therapeutic interventions could, therefore, produce beneficial changes within specific domains of awareness. PMID:20851850

  7. Domain relaxation in Langmuir films

    NASA Astrophysics Data System (ADS)

    Alexander, James C.; Bernoff, Andrew J.; Mann, Elizabeth K.; Mann, J. Adin; Wintersmith, Jacob R.; Zou, Lu

    We report on theoretical studies of molecularly thin Langmuir films on the surface of a quiescent subfluid and qualitatively compare the results to both new and previous experiments. The film covers the entire fluid surface, but domains of different phases are observed. In the absence of external forcing, the compact domains tend to relax to circles, driven by a line tension at the phase boundaries. When stretched (by a transient applied stagnation-point flow or by stirring), a compact domain elongates, creating a bola consisting of two roughly circular reservoirs connected by a thin tether. This shape will then relax slowly to the minimum-energy configuration of a circular domain. The tether is never observed to rupture, even when it is more than a hundred times as long as it is wide. We model these experiments by taking previous descriptions of the full hydrodynamics, identifying the dominant effects via dimensional analysis, and reducing the system to a more tractable form. The result is a free boundary problem for an inviscid Langmuir film whose motion is driven by the line tension of the domain and damped by the viscosity of the subfluid. Using this model we derive relaxation rates for perturbations of a uniform strip and a circular patch. We also derive a boundary integral formulation which allows an efficient numerical solution of the problem. Numerically this model replicates the formation of a bola and the subsequent relaxation observed in the experiments. Finally, we suggest physical properties of the system (such as line tension) that can be deduced by comparison of the theory and numerical simulations to the experiment. Two movies are available with the online version of the paper.

  8. DIMA 3.0: Domain Interaction Map.

    PubMed

    Luo, Qibin; Pagel, Philipp; Vilne, Baiba; Frishman, Dmitrij

    2011-01-01

    Domain Interaction MAp (DIMA, available at http://webclu.bio.wzw.tum.de/dima) is a database of predicted and known interactions between protein domains. It integrates 5807 structurally known interactions imported from the iPfam and 3did databases and 46,900 domain interactions predicted by four computational methods: domain phylogenetic profiling, domain pair exclusion algorithm correlated mutations and domain interaction prediction in a discriminative way. Additionally predictions are filtered to exclude those domain pairs that are reported as non-interacting by the Negatome database. The DIMA Web site allows to calculate domain interaction networks either for a domain of interest or for entire organisms, and to explore them interactively using the Flash-based Cytoscape Web software.

  9. Certifying Domain-Specific Policies

    NASA Technical Reports Server (NTRS)

    Lowry, Michael; Pressburger, Thomas; Rosu, Grigore; Koga, Dennis (Technical Monitor)

    2001-01-01

    Proof-checking code for compliance to safety policies potentially enables a product-oriented approach to certain aspects of software certification. To date, previous research has focused on generic, low-level programming-language properties such as memory type safety. In this paper we consider proof-checking higher-level domain -specific properties for compliance to safety policies. The paper first describes a framework related to abstract interpretation in which compliance to a class of certification policies can be efficiently calculated Membership equational logic is shown to provide a rich logic for carrying out such calculations, including partiality, for certification. The architecture for a domain-specific certifier is described, followed by an implemented case study. The case study considers consistency of abstract variable attributes in code that performs geometric calculations in Aerospace systems.

  10. Frequency domain optical parametric amplification

    PubMed Central

    Schmidt, Bruno E.; Thiré, Nicolas; Boivin, Maxime; Laramée, Antoine; Poitras, François; Lebrun, Guy; Ozaki, Tsuneyuki; Ibrahim, Heide; Légaré, François

    2014-01-01

    Today’s ultrafast lasers operate at the physical limits of optical materials to reach extreme performances. Amplification of single-cycle laser pulses with their corresponding octave-spanning spectra still remains a formidable challenge since the universal dilemma of gain narrowing sets limits for both real level pumped amplifiers as well as parametric amplifiers. We demonstrate that employing parametric amplification in the frequency domain rather than in time domain opens up new design opportunities for ultrafast laser science, with the potential to generate single-cycle multi-terawatt pulses. Fundamental restrictions arising from phase mismatch and damage threshold of nonlinear laser crystals are not only circumvented but also exploited to produce a synergy between increased seed spectrum and increased pump energy. This concept was successfully demonstrated by generating carrier envelope phase stable, 1.43 mJ two-cycle pulses at 1.8 μm wavelength. PMID:24805968

  11. Domain decomposition methods in aerodynamics

    NASA Technical Reports Server (NTRS)

    Venkatakrishnan, V.; Saltz, Joel

    1990-01-01

    Compressible Euler equations are solved for two-dimensional problems by a preconditioned conjugate gradient-like technique. An approximate Riemann solver is used to compute the numerical fluxes to second order accuracy in space. Two ways to achieve parallelism are tested, one which makes use of parallelism inherent in triangular solves and the other which employs domain decomposition techniques. The vectorization/parallelism in triangular solves is realized by the use of a recording technique called wavefront ordering. This process involves the interpretation of the triangular matrix as a directed graph and the analysis of the data dependencies. It is noted that the factorization can also be done in parallel with the wave front ordering. The performances of two ways of partitioning the domain, strips and slabs, are compared. Results on Cray YMP are reported for an inviscid transonic test case. The performances of linear algebra kernels are also reported.

  12. Gabor domain optical coherence microscopy

    NASA Astrophysics Data System (ADS)

    Murali, Supraja

    Time domain Optical Coherence Tomography (TD-OCT), first reported in 1991, makes use of the low temporal coherence properties of a NIR broadband laser to create depth sectioning of up to 2mm under the surface using optical interferometry and point to point scanning. Prior and ongoing work in OCT in the research community has concentrated on improving axial resolution through the development of broadband sources and speed of image acquisition through new techniques such as Spectral domain OCT (SD-OCT). In SD-OCT, an entire depth scan is acquired at once with a low numerical aperture (NA) objective lens focused at a fixed point within the sample. In this imaging geometry, a longer depth of focus is achieved at the expense of lateral resolution, which is typically limited to 10 to 20 mum. Optical Coherence Microscopy (OCM), introduced in 1994, combined the advantages of high axial resolution obtained in OCT with high lateral resolution obtained by increasing the NA of the microscope placed in the sample arm. However, OCM presented trade-offs caused by the inverse quadratic relationship between the NA and the DOF of the optics used. For applications requiring high lateral resolution, such as cancer diagnostics, several solutions have been proposed including the periodic manual re-focusing of the objective lens in the time domain as well as the spectral domain C-mode configuration in order to overcome the loss in lateral resolution outside the DOF. In this research, we report for the first time, high speed, sub-cellular imaging (lateral resolution of 2 mum) in OCM using a Gabor domain image processing algorithm with a custom designed and fabricated dynamic focus microscope interfaced to a Ti:Sa femtosecond laser centered at 800 nm within an SD-OCM configuration. It is envisioned that this technology will provide a non-invasive replacement for the current practice of multiple biopsies for skin cancer diagnosis. The research reported here presents three important advances

  13. Domain Processes in Ferroelectric Ceramics

    DTIC Science & Technology

    1994-04-14

    WALLS Electron holography utilizing the wave characteristics of electrons. Through a sharp emission tip, the emitted electron beam is largely coherent, or...mirostructural modulation at 25% doping. The strongly first order ferroelectric phase transition in PbTiO3 is also gradually changed to a nearly second...a new domain configuraton. 13 The end-member of the PZT solid solution, PbTiO3 , has the highest transition temperature (Tc = 490 °C) and the largest

  14. Flexible time domain averaging technique

    NASA Astrophysics Data System (ADS)

    Zhao, Ming; Lin, Jing; Lei, Yaguo; Wang, Xiufeng

    2013-09-01

    Time domain averaging(TDA) is essentially a comb filter, it cannot extract the specified harmonics which may be caused by some faults, such as gear eccentric. Meanwhile, TDA always suffers from period cutting error(PCE) to different extent. Several improved TDA methods have been proposed, however they cannot completely eliminate the waveform reconstruction error caused by PCE. In order to overcome the shortcomings of conventional methods, a flexible time domain averaging(FTDA) technique is established, which adapts to the analyzed signal through adjusting each harmonic of the comb filter. In this technique, the explicit form of FTDA is first constructed by frequency domain sampling. Subsequently, chirp Z-transform(CZT) is employed in the algorithm of FTDA, which can improve the calculating efficiency significantly. Since the signal is reconstructed in the continuous time domain, there is no PCE in the FTDA. To validate the effectiveness of FTDA in the signal de-noising, interpolation and harmonic reconstruction, a simulated multi-components periodic signal that corrupted by noise is processed by FTDA. The simulation results show that the FTDA is capable of recovering the periodic components from the background noise effectively. Moreover, it can improve the signal-to-noise ratio by 7.9 dB compared with conventional ones. Experiments are also carried out on gearbox test rigs with chipped tooth and eccentricity gear, respectively. It is shown that the FTDA can identify the direction and severity of the eccentricity gear, and further enhances the amplitudes of impulses by 35%. The proposed technique not only solves the problem of PCE, but also provides a useful tool for the fault symptom extraction of rotating machinery.

  15. InfoDOMAIN. Fall 2011

    DTIC Science & Technology

    2011-09-01

    magazine of Navy Cyber Forces that promotes the advancement of Information Dominance through an open exchange of better practices, tactics, and... Information Dominance Corps is central to that effort. For the Department of Defense and the Navy to operate freely within the cyber domain, we must...Officer (CIO) Division on the staff of the Deputy Chief of Naval Operations for Information Dominance (OPNAV N2/N6). Fleet assignments include combat

  16. Escalation of the Space Domain

    DTIC Science & Technology

    2015-04-01

    whether close or open . The close blockade for space operations equates to preventing the deployment of systems from launch facilities and to interfering...obliges the adversary either to submit or fight. In contrast, a more capable space power can impose an open blockade, occupying or interfering with the...other domains the aperture begins to open on how space fits within full spectrum dominance. Space and Full Spectrum Dominance Joint Vision 2020

  17. Building Credible Cross Domain Operators

    DTIC Science & Technology

    2010-04-01

    Clark (POL) AP-E290 C-IED Lecture (POL) Lunch Transition AFA Guest Speaker (POL) Tuskegee Airmen (POL) Transition Lunch Combined Operations Week...domain integration and operators. However, today‟s Airmen are being shortchanged the essential education to develop critical thinking skills necessary...Air Service leaders recognized the need to educate airmen in air doctrine and concepts of aviation. The first air-minded school was called the Air

  18. Maneuver from the Air Domain

    DTIC Science & Technology

    2016-05-26

    cognitive maneuver mechanisms developed in the 1980s as part of broader maneuver warfare theory. The result is a proposed definition of maneuver from the...air power employment and results from two case studies - Operation Rolling Thunder and Operation Iraqi Freedom - support that the proposed definition is...question – what is maneuver from the air domain? Simply placing the doctrinal definition of maneuver in an air power context is not enough. Ultimately

  19. Life sciences domain analysis model

    PubMed Central

    Freimuth, Robert R; Freund, Elaine T; Schick, Lisa; Sharma, Mukesh K; Stafford, Grace A; Suzek, Baris E; Hernandez, Joyce; Hipp, Jason; Kelley, Jenny M; Rokicki, Konrad; Pan, Sue; Buckler, Andrew; Stokes, Todd H; Fernandez, Anna; Fore, Ian; Buetow, Kenneth H

    2012-01-01

    Objective Meaningful exchange of information is a fundamental challenge in collaborative biomedical research. To help address this, the authors developed the Life Sciences Domain Analysis Model (LS DAM), an information model that provides a framework for communication among domain experts and technical teams developing information systems to support biomedical research. The LS DAM is harmonized with the Biomedical Research Integrated Domain Group (BRIDG) model of protocol-driven clinical research. Together, these models can facilitate data exchange for translational research. Materials and methods The content of the LS DAM was driven by analysis of life sciences and translational research scenarios and the concepts in the model are derived from existing information models, reference models and data exchange formats. The model is represented in the Unified Modeling Language and uses ISO 21090 data types. Results The LS DAM v2.2.1 is comprised of 130 classes and covers several core areas including Experiment, Molecular Biology, Molecular Databases and Specimen. Nearly half of these classes originate from the BRIDG model, emphasizing the semantic harmonization between these models. Validation of the LS DAM against independently derived information models, research scenarios and reference databases supports its general applicability to represent life sciences research. Discussion The LS DAM provides unambiguous definitions for concepts required to describe life sciences research. The processes established to achieve consensus among domain experts will be applied in future iterations and may be broadly applicable to other standardization efforts. Conclusions The LS DAM provides common semantics for life sciences research. Through harmonization with BRIDG, it promotes interoperability in translational science. PMID:22744959

  20. Dynamic optical frequency domain reflectometry.

    PubMed

    Arbel, Dror; Eyal, Avishay

    2014-04-21

    We describe a dynamic Optical Frequency Domain Reflectometry (OFDR) system which enables real time, long range, acoustic sensing at high sampling rate. The system is based on a fast scanning laser and coherent detection scheme. Distributed sensing is obtained by probing the Rayleigh backscattered light. The system was tested by interrogation of a 10 km communication type single mode fiber and successfully detected localized impulse and sinusoidal excitations.

  1. Subharmonic Fourier domain mode locking.

    PubMed

    Eigenwillig, Christoph M; Wieser, Wolfgang; Biedermann, Benjamin R; Huber, Robert

    2009-03-15

    We demonstrate a subharmonically Fourier domain mode-locked wavelength-swept laser source with a substantially reduced cavity fiber length. In contrast to a standard Fourier domain mode-locked configuration, light is recirculated repetitively in the delay line with the optical bandpass filter used as switch. The laser has a fundamental optical round trip frequency of 285 kHz and can be operated at integer fractions thereof (subharmonics). Sweep ranges up to 95 nm full width centred at 1317 nm are achieved at the 1/5th subharmonic. A maximum sensitivity of 116 dB and an axial resolution of 12 microm in air are measured at an average sweep power of 12 mW. A sensitivity roll-off of 11 dB over 4 mm and 25 dB over 10 mm is observed and optical coherence tomography imaging is demonstrated. Besides the advantage of a reduced fiber length, subharmonic Fourier domain mode locking (shFDML) enables simple scaling of the sweep speed by extracting light from the delay part of the resonator. A sweep rate of 570 kHz is achieved. Characteristic features of shFDML operation, such as power leakage during fly-back and cw breakthrough, are investigated.

  2. Mapping knowledge domains: Characterizing PNAS

    PubMed Central

    Boyack, Kevin W.

    2004-01-01

    A review of data mining and analysis techniques that can be used for the mapping of knowledge domains is given. Literature mapping techniques can be based on authors, documents, journals, words, and/or indicators. Most mapping questions are related to research assessment or to the structure and dynamics of disciplines or networks. Several mapping techniques are demonstrated on a data set comprising 20 years of papers published in PNAS. Data from a variety of sources are merged to provide unique indicators of the domain bounded by PNAS. By using funding source information and citation counts, it is shown that, on an aggregate basis, papers funded jointly by the U.S. Public Health Service (which includes the National Institutes of Health) and non-U.S. government sources outperform papers funded by other sources, including by the U.S. Public Health Service alone. Grant data from the National Institute on Aging show that, on average, papers from large grants are cited more than those from small grants, with performance increasing with grant amount. A map of the highest performing papers over the 20-year period was generated by using citation analysis. Changes and trends in the subjects of highest impact within the PNAS domain are described. Interactions between topics over the most recent 5-year period are also detailed. PMID:14963238

  3. Nicotinic Receptor Fourth Transmembrane Domain

    PubMed Central

    Bouzat, Cecilia; Barrantes, Francisco; Sine, Steven

    2000-01-01

    The fourth transmembrane domain (M4) of the nicotinic acetylcholine receptor (AChR) contributes to the kinetics of activation, yet its close association with the lipid bilayer makes it the outermost of the transmembrane domains. To investigate mechanistic and structural contributions of M4 to AChR activation, we systematically mutated αT422, a conserved residue that has been labeled by hydrophobic probes, and evaluated changes in rate constants underlying ACh binding and channel gating steps. Aromatic and nonpolar mutations of αT422 selectively affect the channel gating step, slowing the rate of opening two- to sevenfold, and speeding the rate of closing four- to ninefold. Additionally, kinetic modeling shows a second doubly liganded open state for aromatic and nonpolar mutations. In contrast, serine and asparagine mutations of αT422 largely preserve the kinetics of the wild-type AChR. Thus, rapid and efficient gating of the AChR channel depends on a hydrogen bond involving the side chain at position 422 of the M4 transmembrane domain. PMID:10779322

  4. Domain Relaxation in Langmuir Films

    NASA Astrophysics Data System (ADS)

    Bernoff, Andrew J.; Alexander, James C.; Mann, Elizabeth K.; Mann, J. Adin; Zou, Lu; Wintersmith, Jacob R.

    2007-11-01

    We report on an experimental, theoretical and computational study of a molecularly thin polymer Langmuir layer domain on the surface of a subfluid. When stretched (by a transient stagnation flow), the Langmuir layer takes the form of a bola consisting of two roughly circular reservoirs connected by a thin tether. This shape relaxes to the circular minimum energy configuration. The tether is never observed to rupture, even when it is more than a hundred times as long as it is thin. We model these experiments as a free boundary problem where motion is driven by the line tension of the domain and damped by the viscosity of the subfluid. We process the digital images of the experiment to extract the domain shape, use one of these shapes as an initial condition for the numerical solution of a boundary-integral model of the underlying hydrodynamics, and compare the subsequent images of the experiment to the numerical simulation. The numerical evolutions verify that our hydrodynamical model can reproduce the observed dynamics. They also allow us to deduce the magnitude of the line tension in the system, often to within 1%.

  5. Cross-Domain Network Fault Localization

    DTIC Science & Technology

    2009-06-01

    digest, or simply digest, for Gi. • Gj = ( n ] i6=j f(Gi) ) ] Gj , where j is a domain performing cross-domain inference and ] is a model-specific union... Gj is the cross-domain model integrating the digests from all the other domains with domain j’s undigested graph. Now, domain j may use an existing...algorithm such as SHRINK to perform inference over Gj . Before a practical graph digest design can be implemented, interoperability standards must be

  6. A novel domain-by-domain survivable mechanism in multi-domain wavelength-division-multiplexing optical networks

    NASA Astrophysics Data System (ADS)

    Guo, Lei; Wang, Xingwei; Li, Ying; Wang, Chongshan; Li, Hongming; Wang, Hongpeng; Liu, Xin

    2009-03-01

    In multi-domain wavelength-division-multiplexing (WDM) optical networks, the inter-domain routing is a challenge since each single-domain cannot view the full network topology. At the same time, survivability is also an important issue in optical networks since the failures of fiber links or network nodes may lead to a lot of traffic being blocked. In this paper, we study the survivability in multi-domain WDM optical networks, and propose a new survivable mechanism called load balanced domain-by-domain routing (LBDDR). In LBDDR, in order to obtain the efficient inter-domain survivable routes, we present the domain-by-domain routing (DDR) method which can find the intra-domain sub-working path and sub-backup path in each single-domain to form the inter-domain working path and backup path for each demand. In order to reduce the blocking probability, we present the load balanced routing method which can encourage the traffic to be uniformly distributed on the links with more free wavelengths. Simulation results show that, compared with conventional mechanism, LBDDR can obtain better performances.

  7. Characterization of lipid domains in erythrocyte membranes.

    PubMed

    Rodgers, W; Glaser, M

    1991-02-15

    Fluorescence digital imaging microscopy was used to study the lateral distribution of the lipid components in erythrocyte membranes. Intact erythrocytes labeled with phospholipids containing a fluorophore attached to one fatty acid chain showed an uneven distribution of the phospholipids in the membrane thereby demonstrating the presence of membrane domains. The enrichment of the lipotropic compound chlor-promazine in domains in intact erythrocytes also suggested that the domains are lipid-enriched regions. Similar membrane domains were present in erythrocyte ghosts. The phospholipid enrichment was increased in the domains by inducing membrane protein aggregation. Double-labeling experiments were done to determine the relative distributions of different phospholipids in the membrane. Vesicles made from extracted lipids did not show the presence of domains consistent with the conclusion that membrane proteins were responsible for creating the domains. Overall, it was found that large domains exist in the red blood cell membrane with unequal enrichment of the different phospholipid species.

  8. Generic domain models in software engineering

    NASA Technical Reports Server (NTRS)

    Maiden, Neil

    1992-01-01

    This paper outlines three research directions related to domain-specific software development: (1) reuse of generic models for domain-specific software development; (2) empirical evidence to determine these generic models, namely elicitation of mental knowledge schema possessed by expert software developers; and (3) exploitation of generic domain models to assist modelling of specific applications. It focuses on knowledge acquisition for domain-specific software development, with emphasis on tool support for the most important phases of software development.

  9. DEP domains: structurally similar but functionally different.

    PubMed

    Consonni, Sarah V; Maurice, Madelon M; Bos, Johannes L

    2014-05-01

    The Dishevelled, EGL-10 and pleckstrin (DEP) domain is a globular protein domain that is present in about ten human protein families with well-defined structural features. A picture is emerging that DEP domains mainly function in the spatial and temporal control of diverse signal transduction events by recruiting proteins to the plasma membrane. DEP domains can interact with various partners at the membrane, including phospholipids and membrane receptors, and their binding is subject to regulation.

  10. Frequency-Domain Optical Mammogram

    DTIC Science & Technology

    2002-10-01

    have performed the proposed analysis of frequency-domain optical mammograms for a clinical population of about 150 patients. This analysis has led to...model the propagation of light in tissue14-20 have led to new approaches to optical mammography. As The authors are with the Department of Electrical...Modulation Methods, and Signal Detection /406 7.2.1 Lasers and arc lamps / 407’ 7.2.2 Pulsed sources / 407 7.2.3 Laser diodes and light-emitting diodes ( LEDs

  11. The Promise of Domain Adaptation

    NASA Astrophysics Data System (ADS)

    Mahabal, Ashish A.; Li, Jingling; Vaijanapurkar, Samarth; Bue, Brian; Miller, Adam; Donalek, Ciro; Djorgovski, Stanislav G.; Drake, Andrew J.; Graham, Matthew; CRTS, iPTF

    2016-01-01

    Most new surveys spend an appreciable time in collecting data on which to train classifiers before they can be used on future observations from the same dataset. The result generating phase can start much earlier if the training could incorporate data accumulated from older surveys enhanced with a small set from the new survey. This is exactly what Domain Adaptation (DA) allows us to do. The main idea behind DAs can be summarized thus: if we have two classes of separable objects in some feature space of a Source survey (S), we can define a hyperplane to separate the two types. In a second Target survey (T), for the same features the hyperplane would be inclined differently. DA methods get the mapping between the two hyperplanes using a small fraction of data from the Target (T) survey and can then be used to predict the classes of the remaining majority of data in T. We discuss the parameters that need to be tuned, the difficulties involved, and ways to improve the results. As we move towards bigger, and deeper surveys, being able to use existing labelled information to conduct classification in future surveys will be more cost-effective and promote time efficiency as well. Starting with the light curve data of 50,000 periodic objects from Catalina Real-Time Transient Survey (CRTS), we have applied domain adaptation techniques such as Geodesic Flow Kernel (GFK) with Random forest classifier and Co-training for domain adaptation (CODA) to the CRTS data which has 35,000 points overlapping with Palomar Transient Factory (PTF), and 12,000 with Lincoln Near-Earth Asteroid Research (LINEAR). The results suggest that domain adaptation is an area worth exploring as the knowledge between these surveys is transferable and the approaches to find the mappings between these surveys can be applied to the remaining data as well as for near future surveys such as CRTS-II, Zwicky Transient Facility (ZTF) and the Large Synoptic Survey Telescope (LSST) to name a few at the optical

  12. Walking droplets in confined domains

    NASA Astrophysics Data System (ADS)

    Sáenz, Pedro; Bush, John

    2016-11-01

    A millimetric liquid drop can walk spontaneously along the surface of a vibrating fluid bath, propelled by a resonant interaction with its own wave field. These walking droplets exhibit features previously thought to be exclusive to the microscopic quantum realm. We here explore experimentally the dynamics and statistics of this macroscopic wave-particle system in confined domains, or 'corrals'. Particular attention is given to characterizing the influence of the corral geometry on the emergent probability distributions. The relation to analogous quantum systems (specifically, quantum corrals, the quantum mirage and scarring in Bose-Einstein condensates) is discussed. NSF support via CMMI-1333242.

  13. Domain wall orientation and domain shape in KTiOPO4 crystals

    NASA Astrophysics Data System (ADS)

    Shur, V. Ya.; Vaskina, E. M.; Pelegova, E. V.; Chuvakova, M. A.; Akhmatkhanov, A. R.; Kizko, O. V.; Ivanov, M.; Kholkin, A. L.

    2016-09-01

    Domain shape evolution and domain wall motion have been studied in KTiOPO4 (KTP) ferroelectric single crystals using complementary experimental methods. The in situ visualization of domain kinetics has allowed revealing: (1) qualitative change of the domain shape, (2) dependence of the domain wall velocity on its orientation, (3) jump-like domain wall motion caused by domain merging, (4) effect of domain shape stability. The model of domain wall motion driven by generation of elementary steps (kink-pair nucleation) and subsequent kink motion is presented. The decrease in the relative velocity of the approaching parallel domain walls is attributed to electrostatic interaction. The effect of polarization reversal induced by chemical etching is observed. The obtained results are important for the development of domain engineering in the crystals of KTP family.

  14. Pectin Homogalacturonans: Nanostructural Characterization of Methylesterified Domains

    USDA-ARS?s Scientific Manuscript database

    Functionality of pectic hydrocolloids is largely dependent on the two major domains commonly found in their homogalacturonan (HG) regions, i.e., methylester protected domains (MPDs)and non methylesterified domains (NMDs). MPDs can participate in hydrogen bonding and hydrophobic interactions but unli...

  15. Frequency domain photoacoustic and fluorescence microscopy

    PubMed Central

    Langer, Gregor; Buchegger, Bianca; Jacak, Jaroslaw; Klar, Thomas A.; Berer, Thomas

    2016-01-01

    We report on simultaneous frequency domain optical-resolution photoacoustic and fluorescence microscopy with sub-µm lateral resolution. With the help of a blood smear, we show that photoacoustic and fluorescence images provide complementary information. Furthermore, we compare theoretically predicted signal-to-noise ratios of sinusoidal modulation in frequency domain with pulsed excitation in time domain. PMID:27446698

  16. Teaching-Learning in the Affective Domain

    ERIC Educational Resources Information Center

    Holt, Brett J.; Hannon, James C.

    2006-01-01

    Affect is an important domain in which children learn. The affective domain of learning in physical education focuses on feelings, values, social behavior, and attitudes as they relate to human movement. Learning in the affective domain in physical education means that students learn such concepts as sportsmanship, "fair play," respect for others,…

  17. 22 CFR 120.11 - Public domain.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 22 Foreign Relations 1 2012-04-01 2012-04-01 false Public domain. 120.11 Section 120.11 Foreign Relations DEPARTMENT OF STATE INTERNATIONAL TRAFFIC IN ARMS REGULATIONS PURPOSE AND DEFINITIONS § 120.11 Public domain. (a) Public domain means information which is published and which is generally...

  18. 22 CFR 120.11 - Public domain.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 22 Foreign Relations 1 2013-04-01 2013-04-01 false Public domain. 120.11 Section 120.11 Foreign Relations DEPARTMENT OF STATE INTERNATIONAL TRAFFIC IN ARMS REGULATIONS PURPOSE AND DEFINITIONS § 120.11 Public domain. (a) Public domain means information which is published and which is generally...

  19. 22 CFR 120.11 - Public domain.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 22 Foreign Relations 1 2014-04-01 2014-04-01 false Public domain. 120.11 Section 120.11 Foreign Relations DEPARTMENT OF STATE INTERNATIONAL TRAFFIC IN ARMS REGULATIONS PURPOSE AND DEFINITIONS § 120.11 Public domain. (a) Public domain means information which is published and which is generally...

  20. AIDA: ab initio domain assembly for automated multi-domain protein structure prediction and domain–domain interaction prediction

    PubMed Central

    Xu, Dong; Jaroszewski, Lukasz; Li, Zhanwen; Godzik, Adam

    2015-01-01

    Motivation: Most proteins consist of multiple domains, independent structural and evolutionary units that are often reshuffled in genomic rearrangements to form new protein architectures. Template-based modeling methods can often detect homologous templates for individual domains, but templates that could be used to model the entire query protein are often not available. Results: We have developed a fast docking algorithm ab initio domain assembly (AIDA) for assembling multi-domain protein structures, guided by the ab initio folding potential. This approach can be extended to discontinuous domains (i.e. domains with ‘inserted’ domains). When tested on experimentally solved structures of multi-domain proteins, the relative domain positions were accurately found among top 5000 models in 86% of cases. AIDA server can use domain assignments provided by the user or predict them from the provided sequence. The latter approach is particularly useful for automated protein structure prediction servers. The blind test consisting of 95 CASP10 targets shows that domain boundaries could be successfully determined for 97% of targets. Availability and implementation: The AIDA package as well as the benchmark sets used here are available for download at http://ffas.burnham.org/AIDA/. Contact: adam@sanfordburnham.org Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25701568

  1. One Health Core Competency Domains

    PubMed Central

    Frankson, Rebekah; Hueston, William; Christian, Kira; Olson, Debra; Lee, Mary; Valeri, Linda; Hyatt, Raymond; Annelli, Joseph; Rubin, Carol

    2016-01-01

    The emergence of complex global challenges at the convergence of human, animal, and environmental health has catalyzed a movement supporting “One Health” approaches. Despite recognition of the importance of One Health approaches to address these complex challenges, little effort has been directed at identifying the seminal knowledge, skills, and attitudes necessary for individuals to successfully contribute to One Health efforts. Between 2008 and 2011, three groups independently embarked on separate initiatives to identify core competencies for professionals involved with One Health approaches. Core competencies were considered critically important for guiding curriculum development and continuing professional education, as they describe the knowledge, skills, and attitudes required to be effective. A workshop was convened in 2012 to synthesize the various strands of work on One Health competencies. Despite having different mandates, participants, and approaches, all of these initiatives identified similar core competency domains: management; communication and informatics; values and ethics; leadership; teams and collaboration; roles and responsibilities; and systems thinking. These core competency domains have been used to develop new continuing professional education programs for One Health professionals and help university curricula prepare new graduates to be able to contribute more effectively to One Health approaches. PMID:27679794

  2. One Health Core Competency Domains.

    PubMed

    Frankson, Rebekah; Hueston, William; Christian, Kira; Olson, Debra; Lee, Mary; Valeri, Linda; Hyatt, Raymond; Annelli, Joseph; Rubin, Carol

    2016-01-01

    The emergence of complex global challenges at the convergence of human, animal, and environmental health has catalyzed a movement supporting "One Health" approaches. Despite recognition of the importance of One Health approaches to address these complex challenges, little effort has been directed at identifying the seminal knowledge, skills, and attitudes necessary for individuals to successfully contribute to One Health efforts. Between 2008 and 2011, three groups independently embarked on separate initiatives to identify core competencies for professionals involved with One Health approaches. Core competencies were considered critically important for guiding curriculum development and continuing professional education, as they describe the knowledge, skills, and attitudes required to be effective. A workshop was convened in 2012 to synthesize the various strands of work on One Health competencies. Despite having different mandates, participants, and approaches, all of these initiatives identified similar core competency domains: management; communication and informatics; values and ethics; leadership; teams and collaboration; roles and responsibilities; and systems thinking. These core competency domains have been used to develop new continuing professional education programs for One Health professionals and help university curricula prepare new graduates to be able to contribute more effectively to One Health approaches.

  3. Time domain backcalculation of pavement

    NASA Astrophysics Data System (ADS)

    Matsui, Kunihito; Nishizawa, Tatsuo; Kikuta, Yukio

    1998-03-01

    Falling weight deflectometor (FWD) has been frequently used to evaluate structural integrity of pavement. The device applies an impulsive force on the surface of pavement and measure surface deflections at several locations including the place of loading. Although the test is dynamic, the data is regarded as pseudo-static data. According to common practice, using the peak load and the corresponding peak deflections, layer moduli are estimated in a static domain such that the measured peak deflections coincide with the corresponding calculated deflections based on the assumption of the theory of linear elasticity. This paper presents a method to back calculate layer moduli in dynamic domain such that the histories of both measured and calculated responses corresponding to the impulsive force coincide. Pavement is modeled by an axisymmetric linear elastic system. FEM is utilized coupled with Ritz vector to reduce a matrix and thus to improve computational efficiency. The backcalculation algorithm used is the Gauss-Newton method coupled with a truncated singular value decomposition.

  4. Domain Relaxation in Polymer Monolayers

    NASA Astrophysics Data System (ADS)

    Bernoff, Andrew J.; Alexander, James C.; Mann, J. R.; Mann, Elizabeth K.

    2004-11-01

    We report on an experimental and theoretical study of a polymer monolayer on the surface of a subfluid. When stretched (by a transient applied flow), the monolayer takes the form of a bola consisting of two roughly circular reservoirs connected by a thin tether. This shape relaxes to the minimum energy configuration of a circular domain. The tether is never observed to rupture, even when it is more than a hundred times as long as it is thin. We model these experiments by taking previous descriptions of the hydrodynamics (primarily those of Stone & McConnell and Lubensky & Goldstein ), identifying the dominant effects, and reducing the system to a more tractable form. The result is a free boundary problem where motion is driven by the line tension of the domain and damped by the viscosity of the subfluid. Using this model we derive relaxation rates for perturbations of a uniform strip and a circular patch. Lubrication theory for the tether evolution yields the thin film equation HT = -(H^2H_XXX)_X. This evolution equation appears not to manifest rupture, in agreement with the experiments. Finally, we speculate on which physical properties of the system (such as line tension) can be deduced by comparison of theory to experiment.

  5. Interfaces between Block Copolymer Domains

    NASA Astrophysics Data System (ADS)

    Kim, Jaeup; Jeong, Seong-Jun; Kim, Sang Ouk

    2011-03-01

    Block copolymers naturally form nanometer scale structures which repeat their geometry on a larger scale. Such a small scale periodic pattern can be used for various applications such as storage media, nano-circuits and optical filters. However, perfect alignment of block copolymer domains in the macroscopic scale is still a distant dream. The nanostructure formation usually occurs with spontaneously broken symmetry; hence it is easily infected by topological defects which sneak in due to entropic fluctuation and incomplete annealing. Careful annealing can gradually reduce the number of defects, but once kinetically trapped, it is extremely difficult to remove all the defects. One of the main reasons is that the defect finds a locally metastable morphology whose potential depth is large enough to prohibit further morphology evolution. In this work, the domain boundaries between differently oriented lamellar structures in thin film are studied. For the first time, it became possible to quantitatively study the block copolymer morphology in the transitional region, and it was shown that the twisted grain boundary is energetically favorable compared to the T-junction grain boundary. [Nano Letters, 9, 2300 (2010)]. This theoretical method successfully explained the experimental results.

  6. Single-domain antibodies for biomedical applications.

    PubMed

    Krah, Simon; Schröter, Christian; Zielonka, Stefan; Empting, Martin; Valldorf, Bernhard; Kolmar, Harald

    2016-01-01

    Single-domain antibodies are the smallest antigen-binding units of antibodies, consisting either only of one variable domain or one engineered constant domain that solely facilitates target binding. This class of antibody derivatives comprises naturally occurring variable domains derived from camelids and sharks as well as engineered human variable or constant antibody domains of the heavy or light chain. Because of their high affinity and specificity as well as stability, small size and benefit of multiple re-formatting opportunities, those molecules emerged as promising candidates for biomedical applications and some of these entities have already proven to be successful in clinical development.

  7. Word Domain Disambiguation via Word Sense Disambiguation

    SciTech Connect

    Sanfilippo, Antonio P.; Tratz, Stephen C.; Gregory, Michelle L.

    2006-06-04

    Word subject domains have been widely used to improve the perform-ance of word sense disambiguation al-gorithms. However, comparatively little effort has been devoted so far to the disambiguation of word subject do-mains. The few existing approaches have focused on the development of al-gorithms specific to word domain dis-ambiguation. In this paper we explore an alternative approach where word domain disambiguation is achieved via word sense disambiguation. Our study shows that this approach yields very strong results, suggesting that word domain disambiguation can be ad-dressed in terms of word sense disam-biguation with no need for special purpose algorithms.

  8. GMPLS inter-domain signaling and routing to control LSPs based on per-domain policy

    NASA Astrophysics Data System (ADS)

    Okamoto, S.; Guo, H.; Otani, T.

    2008-11-01

    GMPLS inter-domain network control was investigated by employing BGP-based inter-domain routing and flexible signaling with loose hop expansion. Per-domain based operational policy was successfully applied to the establishment of GMPLS inter-domain LSPs.

  9. Enhanced protein domain discovery using taxonomy

    PubMed Central

    Coin, Lachlan; Bateman, Alex; Durbin, Richard

    2004-01-01

    Background It is well known that different species have different protein domain repertoires, and indeed that some protein domains are kingdom specific. This information has not yet been incorporated into statistical methods for finding domains in sequences of amino acids. Results We show that by incorporating our understanding of the taxonomic distribution of specific protein domains, we can enhance domain recognition in protein sequences. We identify 4447 new instances of Pfam domains in the SP-TREMBL database using this technique, equivalent to the coverage increase given by the last 8.3% of Pfam families and to a 0.7% increase in the number of domain predictions. We use PSI-BLAST to cross-validate our new predictions. We also benchmark our approach using a SCOP test set of proteins of known structure, and demonstrate improvements relative to standard Hidden Markov model techniques. Conclusions Explicitly including knowledge about the taxonomic distribution of protein domains can enhance protein domain recognition. Our method can also incorporate other context-specific domain distributions – such as domain co-occurrence and protein localisation. PMID:15137915

  10. Domain adaptive boosting method and its applications

    NASA Astrophysics Data System (ADS)

    Geng, Jie; Miao, Zhenjiang

    2015-03-01

    Differences of data distributions widely exist among datasets, i.e., domains. For many pattern recognition, nature language processing, and content-based analysis systems, a decrease in performance caused by the domain differences between the training and testing datasets is still a notable problem. We propose a domain adaptation method called domain adaptive boosting (DAB). It is based on the AdaBoost approach with extensions to cover the domain differences between the source and target domains. Two main stages are contained in this approach: source-domain clustering and source-domain sample selection. By iteratively adding the selected training samples from the source domain, the discrimination model is able to achieve better domain adaptation performance based on a small validation set. The DAB algorithm is suitable for the domains with large scale samples and easy to extend for multisource adaptation. We implement this method on three computer vision systems: the skin detection model in single images, the video concept detection model, and the object classification model. In the experiments, we compare the performances of several commonly used methods and the proposed DAB. Under most situations, the DAB is superior.

  11. Collective magnetism at multiferroic vortex domain walls.

    PubMed

    Geng, Yanan; Lee, N; Choi, Y J; Cheong, S-W; Wu, Weida

    2012-12-12

    Cross-coupled phenomena of multiferroic domains and domain walls are of fundamental scientific and technological interest. Using cryogenic magnetic force microscopy, we find alternating net magnetic moments at ferroelectric domain walls around vortex cores in multiferroic hexagonal ErMnO(3), which correlate with each other throughout the entire vortex network. This collective nature of domain wall magnetism originates from the uncompensated Er(3+) moments at domain walls and the self-organization of the vortex network. Our results demonstrate that the collective domain wall magnetism can be controlled by external magnetic fields and represent a major advancement in the manipulation of local magnetic moments by harnessing cross-coupled domain walls.

  12. Functional innovation from changes in protein domains and their combinations.

    PubMed

    Lees, Jonathan G; Dawson, Natalie L; Sillitoe, Ian; Orengo, Christine A

    2016-06-01

    Domains are the functional building blocks of proteins. In this work we discuss how domains can contribute to the evolution of new functions. Domains themselves can evolve through various mechanisms, altering their intrinsic function. Domains can also facilitate functional innovations by combining with other domains to make novel proteins. We discuss the mechanisms by which domain and domain combinations support functional innovations. We highlight interesting examples where changes in domain combination promote changes at the domain level.

  13. Structure and function of KH domains.

    PubMed

    Valverde, Roberto; Edwards, Laura; Regan, Lynne

    2008-06-01

    The hnRNP K homology (KH) domain was first identified in the protein human heterogeneous nuclear ribonucleoprotein K (hnRNP K) 14 years ago. Since then, KH domains have been identified as nucleic acid recognition motifs in proteins that perform a wide range of cellular functions. KH domains bind RNA or ssDNA, and are found in proteins associated with transcriptional and translational regulation, along with other cellular processes. Several diseases, e.g. fragile X mental retardation syndrome and paraneoplastic disease, are associated with the loss of function of a particular KH domain. Here we discuss the progress made towards understanding both general and specific features of the molecular recognition of nucleic acids by KH domains. The typical binding surface of KH domains is a cleft that is versatile but that can typically accommodate only four unpaired bases. Van der Waals forces and hydrophobic interactions and, to a lesser extent, electrostatic interactions, contribute to the nucleic acid binding affinity. 'Augmented' KH domains or multiple copies of KH domains within a protein are two strategies that are used to achieve greater affinity and specificity of nucleic acid binding. Isolated KH domains have been seen to crystallize as monomers, dimers and tetramers, but no published data support the formation of noncovalent higher-order oligomers by KH domains in solution. Much attention has been given in the literature to a conserved hydrophobic residue (typically Ile or Leu) that is present in most KH domains. The interest derives from the observation that an individual with this Ile mutated to Asn, in the KH2 domain of fragile X mental retardation protein, exhibits a particularly severe form of the syndrome. The structural effects of this mutation in the fragile X mental retardation protein KH2 domain have recently been reported. We discuss the use of analogous point mutations at this position in other KH domains to dissect both structure and function.

  14. Structure and Function of KH Domains

    SciTech Connect

    Valverde, R.; Regan, E

    2008-01-01

    The hnRNP K homology (KH) domain was first identified in the protein human heterogeneous nuclear ribonucleoprotein K (hnRNP K) 14 years ago. Since then, KH domains have been identified as nucleic acid recognition motifs in proteins that perform a wide range of cellular functions. KH domains bind RNA or ssDNA, and are found in proteins associated with transcriptional and translational regulation, along with other cellular processes. Several diseases, e.g. fragile X mental retardation syndrome and paraneoplastic disease, are associated with the loss of function of a particular KH domain. Here we discuss the progress made towards understanding both general and specific features of the molecular recognition of nucleic acids by KH domains. The typical binding surface of KH domains is a cleft that is versatile but that can typically accommodate only four unpaired bases. Van der Waals forces and hydrophobic interactions and, to a lesser extent, electrostatic interactions, contribute to the nucleic acid binding affinity. 'Augmented' KH domains or multiple copies of KH domains within a protein are two strategies that are used to achieve greater affinity and specificity of nucleic acid binding. Isolated KH domains have been seen to crystallize as monomers, dimers and tetramers, but no published data support the formation of noncovalent higher-order oligomers by KH domains in solution. Much attention has been given in the literature to a conserved hydrophobic residue (typically Ile or Leu) that is present in most KH domains. The interest derives from the observation that an individual with this Ile mutated to Asn, in the KH2 domain of fragile X mental retardation protein, exhibits a particularly severe form of the syndrome. The structural effects of this mutation in the fragile X mental retardation protein KH2 domain have recently been reported. We discuss the use of analogous point mutations at this position in other KH domains to dissect both structure and function.

  15. Time domain electromagnetic metal detectors

    SciTech Connect

    Hoekstra, P.

    1996-04-01

    This presentation focuses on illustrating by case histories the range of applications and limitations of time domain electromagnetic (TDEM) systems for buried metal detection. Advantages claimed for TDEM metal detectors are: independent of instrument response (Geonics EM61) to surrounding soil and rock type; simple anomaly shape; mitigation of interference by ambient electromagnetic noise; and responsive to both ferrous and non-ferrous metallic targets. The data in all case histories to be presented were acquired with the Geonics EM61 TDEM system. Case histories are a test bed site on Molokai, Hawaii; Fort Monroe, Virginia; and USDOE, Rocky Flats Plant. The present limitations of this technology are: discrimination capabilities in terms of type of ordnance, and depth of burial is limited, and ability of resolving targets with small metallic ambient needs to be improved.

  16. Rapid spectral-domain localization

    PubMed Central

    van Dijk, Thomas; Mayerich, David; Bhargava, Rohit; Carney, P. Scott

    2013-01-01

    We present a method to dynamically image structures at nanometer spatial resolution with far-field instruments. We propose the use of engineered nanoprobes with distinguishable spectral responses and the measurement of coherent scattering, rather than fluorescence. Approaches such as PALM/STORM have relied on the rarity of emission events in time to distinguish signals from distinct probes. By distinguishing signals in the spectral domain, we enable the acquisition of data in a multiplex fashion and thus circumvent the fundamental problem of slow data acquisition of current techniques. The described method has the potential to image dynamic systems with a spatial resolution only limited to the size of the scattering probes. PMID:23736501

  17. Baryogenesis from unstable domain walls

    NASA Astrophysics Data System (ADS)

    Ben-Menahem, Shahar; Cooper, Adrian R.

    1992-12-01

    There exists a class of cosmic strings that turn matter into antimatter (Alice strings). In a GUT where the unbroken gauge group contains charge conjugation (C), such strings form when a phase transition renders C a discrete symmetry. They become boundaries of domain walls at a later, C-breaking transition. These ``Alice walls'' are cosmologically harmless, but can play an important role in baryogenesis. We present a three-generation toy model with scalar baryons, where a quasi-static Alice wall (or a gas of such walls) temporarily gives rise to net baryogenesis of uniform sign everywhere in space. This becomes a permanent baryon excess if the wall shrinks away early enough. We comment on the possible relevance of a similar mechanism to baryogenesis in a realistic SO(10) unification model, where Alice walls would form at the scale of left-right symmetry breaking.

  18. Functional domains in tetraspanin proteins.

    PubMed

    Stipp, Christopher S; Kolesnikova, Tatiana V; Hemler, Martin E

    2003-02-01

    Exciting new findings have emerged about the structure, function and biochemistry of tetraspanin proteins. Five distinct tetraspanin regions have now been delineated linking structural features to specific functions. Within the large extracellular loop of tetraspanins, there is a variable region that mediates specific interactions with other proteins, as well as a more highly conserved region that has been suggested to mediate homodimerization. Within the transmembrane region, the four tetraspanin transmembrane domains are probable sites of both intra- and inter-molecular interactions that are crucial during biosynthesis and assembly of the network of tetraspanin-linked membrane proteins known as the 'tetraspanin web'. In the intracellular juxtamembrane region, palmitoylation of cysteine residues also contributes to tetraspanin web assembly, and the C-terminal cytoplasmic tail region could provide specific functional links to cytoskeletal or signaling proteins.

  19. Nonlocal problems in thin domains

    NASA Astrophysics Data System (ADS)

    Pereira, Marcone C.; Rossi, Julio D.

    2017-08-01

    In this paper we consider nonlocal problems in thin domains. First, we deal with a nonlocal Neumann problem, that is, we study the behavior of the solutions to f (x) =∫Ω1×Ω2Jɛ (x - y) (uɛ (y) -uɛ (x)) dy with Jɛ (z) = J (z1 , ɛz2) and Ω =Ω1 ×Ω2 ⊂RN =R N1 ×R N2 a bounded domain. We find that there is a limit problem, that is, we show that uɛ →u0 as ɛ → 0 in Ω and this limit function verifies ∫Ω2 f (x1 ,x2) dx2 = |Ω2 |∫Ω1 J (x1 -y1 , 0) (U0 (y1) -U0 (x1)) dy1, with U0 (x1) =∫Ω2u0 (x1 ,x2) dx2. In addition, we deal with a double limit when we add to this model a rescale in the kernel with a parameter that controls the size of the support of J. We show that this double limit exhibits some interesting features. We also study a nonlocal Dirichlet problem f (x) =∫RNJɛ (x - y) (uɛ (y) -uɛ (x)) dy, x ∈ Ω, with uɛ (x) ≡ 0, x ∈RN ∖ Ω, and deal with similar issues. In this case the limit as ɛ → 0 is u0 = 0 and the double limit problem commutes and also gives v ≡ 0 at the end.

  20. Characterization of the Blue-Light-Activated Adenylyl Cyclase mPAC by Flash Photolysis and FTIR Spectroscopy.

    PubMed

    Kerruth, Silke; Langner, Pit; Raffelberg, Sarah; Gärtner, Wolfgang; Heberle, Joachim

    2017-05-01

    The recently discovered photo-activated adenylyl cyclase (mPAC from Microcoleus chthonoplastes) is the first PAC that owes a light-, oxygen- and voltage-sensitive (LOV) domain for blue-light sensing. The photoreaction of the mPAC receptor was studied by time-resolved UV/vis and light-induced Fourier transform infrared (FTIR) absorption difference spectroscopy. The photocycle comprises of the typical triplet state LOV715 and the thio-adduct state LOV390 . While the adduct state decays with a time constant of 8 s, the lifetime of the triplet state is with 656 ns significantly shorter than in all other reported LOV domains. The light-induced FTIR difference spectrum shows the typical bands of the LOV390 and LOV450 intermediates. The negative S-H stretching vibration at 2573 cm(-1) is asymmetric suggesting two rotamer configurations of the protonated side chain of C194. A positive band at 3632 cm(-1) is observed, which is assigned to an internal water molecule. In contrast to other LOV domains, mPAC exhibits a second positive feature at 3674 cm(-1) which is due to the O-H stretch of a second intrinsic water molecule and the side chain of Y476. We conclude that the latter might be involved in the dimerization of the cyclase domain which is crucial for ATP binding. © 2017 The American Society of Photobiology.

  1. Domain Adaptation with Conditional Transferable Components

    PubMed Central

    Gong, Mingming; Zhang, Kun; Liu, Tongliang; Tao, Dacheng; Glymour, Clark; Schölkopf, Bernhard

    2017-01-01

    Domain adaptation arises in supervised learning when the training (source domain) and test (target domain) data have different distributions. Let X and Y denote the features and target, respectively, previous work on domain adaptation mainly considers the covariate shift situation where the distribution of the features P(X) changes across domains while the conditional distribution P(Y∣X) stays the same. To reduce domain discrepancy, recent methods try to find invariant components T(X) that have similar P(T(X)) on different domains by explicitly minimizing a distribution discrepancy measure. However, it is not clear if P(Y∣T(X)) in different domains is also similar when P(Y∣X) changes. Furthermore, transferable components do not necessarily have to be invariant. If the change in some components is identifiable, we can make use of such components for prediction in the target domain. In this paper, we focus on the case where P(X∣Y) and P(Y) both change in a causal system in which Y is the cause for X. Under appropriate assumptions, we aim to extract conditional transferable components whose conditional distribution P(T(X)∣Y) is invariant after proper location-scale (LS) transformations, and identify how P(Y) changes between domains simultaneously. We provide theoretical analysis and empirical evaluation on both synthetic and real-world data to show the effectiveness of our method. PMID:28239433

  2. Domain Adaptation with Conditional Transferable Components.

    PubMed

    Gong, Mingming; Zhang, Kun; Liu, Tongliang; Tao, Dacheng; Glymour, Clark; Schölkopf, Bernhard

    2016-06-01

    Domain adaptation arises in supervised learning when the training (source domain) and test (target domain) data have different distributions. Let X and Y denote the features and target, respectively, previous work on domain adaptation mainly considers the covariate shift situation where the distribution of the features P(X) changes across domains while the conditional distribution P(Y∣X) stays the same. To reduce domain discrepancy, recent methods try to find invariant components [Formula: see text] that have similar [Formula: see text] on different domains by explicitly minimizing a distribution discrepancy measure. However, it is not clear if [Formula: see text] in different domains is also similar when P(Y∣X) changes. Furthermore, transferable components do not necessarily have to be invariant. If the change in some components is identifiable, we can make use of such components for prediction in the target domain. In this paper, we focus on the case where P(X∣Y) and P(Y) both change in a causal system in which Y is the cause for X. Under appropriate assumptions, we aim to extract conditional transferable components whose conditional distribution [Formula: see text] is invariant after proper location-scale (LS) transformations, and identify how P(Y) changes between domains simultaneously. We provide theoretical analysis and empirical evaluation on both synthetic and real-world data to show the effectiveness of our method.

  3. Electron-beam-induced ferroelectric domain behavior in the transmission electron microscope: Toward deterministic domain patterning

    NASA Astrophysics Data System (ADS)

    Hart, James L.; Liu, Shi; Lang, Andrew C.; Hubert, Alexander; Zukauskas, Andrius; Canalias, Carlota; Beanland, Richard; Rappe, Andrew M.; Arredondo, Miryam; Taheri, Mitra L.

    2016-11-01

    We report on transmission electron microscope beam-induced ferroelectric domain nucleation and motion. While previous observations of this phenomenon have been reported, a consistent theory explaining induced domain response is lacking, and little control over domain behavior has been demonstrated. We identify positive sample charging, a result of Auger and secondary electron emission, as the underlying mechanism driving domain behavior. By converging the electron beam to a focused probe, we demonstrate controlled nucleation of nanoscale domains. Molecular dynamics simulations performed are consistent with experimental results, confirming positive sample charging and reproducing the result of controlled domain nucleation. Furthermore, we discuss the effects of sample geometry and electron irradiation conditions on induced domain response. These findings elucidate past reports of electron beam-induced domain behavior in the transmission electron microscope and provide a path towards more predictive, deterministic domain patterning through electron irradiation.

  4. Spread spectrum time domain reflectometry

    NASA Astrophysics Data System (ADS)

    Smith, Paul Samuel

    For many years, wiring has been treated as a system that could be installed and expected to work for the life of the aircraft. As aircraft age far beyond their original expected life span, this attitude is rapidly changing. Wiring problems have recently been identified as the cause of several tragic mishaps and hundreds of thousands of lost mission hours. Intermittent wiring faults have been and continue to be difficult to resolve. Test methods that pinpoint faults on the ground can miss intermittent failures. New test methods involving spread spectrum signals are investigated that could be used in flight to locate intermittent failures, including open circuits, short circuits, and arcs. Spread spectrum time domain reflectometry (SSTDR) and sequence time domain reflectometry (STDR) are analyzed in light of the signals commonly present on aircraft wiring. Pseudo noise codes used for the generation of STDR and SSTDR signals are analyzed for application in a STDR/SSTDR test system in the presence of noise. The effects of Mil-Std 1553 and white noise on the STDR and SSTDR signals are discussed analytically, through simulations, and with the use of test hardware. A test system using STDR and SSTDR is designed, built, and used to collect STDR and SSTDR test data. The data collected with the STDR/SSTDR test hardware is analyzed and compared to the theoretical results. Experimental data for open and short circuits collected using SSTDR and a curve fitting algorithm shows a maximum range estimation error of +/-0.2 ft for 75O coaxial cable up to 100ft, and +/-0.6ft for a sample 32.5ft non-controlled impedance aircraft cable. Mil-Std 1553 is specified to operate reliably with a signal-to-noise ratio of 17.5dB, and the SSTDR test system was able to locate an open circuit on a cable also carrying simulated Mil-Std 1553 data where the SSTDR signal was 50dB below the Mil-Std 1553 signal. STDR and SSTDR are shown to be effective in detecting and locating dry and wet arcs on wires.

  5. Targeting Discoidin Domain Receptors in Prostate Cancer

    DTIC Science & Technology

    2016-08-01

    Agency: DOD-BCRP Grant #: Breakthrough Award L1 BC150621P Title: “Discoidin Domain Receptors: Novel Targets in Breast Cancer Bone Metastasis...1 AWARD NUMBER: W81XWH-15-1-0226 TITLE: Targeting Discoidin Domain Receptors in Prostate Cancer PRINCIPAL INVESTIGATOR: Dr. Rafael Fridman...4. TITLE AND SUBTITLE 5a. CONTRACT NUMBER W81XWH-15-1-0226 Targeting Discoidin Domain Receptors in Prostate Cancer 5b. GRANT NUMBER W81XWH-15

  6. Domain decomposition for the SPN solver MINOS

    SciTech Connect

    Jamelot, Erell; Baudron, Anne-Marie; Lautard, Jean-Jacques

    2012-07-01

    In this article we present a domain decomposition method for the mixed SPN equations, discretized with Raviart-Thomas-Nedelec finite elements. This domain decomposition is based on the iterative Schwarz algorithm with Robin interface conditions to handle communications. After having described this method, we give details on how to optimize the convergence. Finally, we give some numerical results computed in a realistic 3D domain. The computations are done with the MINOS solver of the APOLLO3 (R) code. (authors)

  7. Domain Transfer Learning for MCI Conversion Prediction

    PubMed Central

    Cheng, Bo; Liu, Mingxia; Zhang, Daoqiang; Munsell, Brent C.; Shen, Dinggang

    2015-01-01

    Machine learning methods have been increasingly used to predict the conversion of mild cognitive impairment (MCI) to Alzheimer's disease (AD), by classifying MCI converters (MCI-C) from MCI non-converters (MCI-NC). However, most of existing methods construct classifiers using only data from one particular target domain (e.g., MCI), and ignore data in the other related domains (e.g., AD and normal control (NC)) that could provide valuable information to promote the performance of MCI conversion prediction. To this end, we develop a novel domain transfer learning method for MCI conversion prediction, which can use data from both the target domain (i.e., MCI) and the auxiliary domains (i.e., AD and NC). Specifically, the proposed method consists of three key components: 1) a domain transfer feature selection (DTFS) component that selects the most informative feature-subset from both target domain and auxiliary domains with different imaging modalities, 2) a domain transfer sample selection (DTSS) component that selects the most informative sample-subset from the same target and auxiliary domains with different data modalities, and 3) a domain transfer support vector machine (DTSVM) classification component that fuses the selected features and samples to separate MCI-C and MCI-NC patients. We evaluate our method on 202 subjects from the Alzheimer’s Disease Neuroimaging Initiative (ADNI) with MRI, FDG-PET and CSF data. The experimental results show that the proposed method can classify MCI-C patients from MCI-NC patients with an accuracy of 79.4%, with the aid of additional domain knowledge learned from AD and NC. PMID:25751861

  8. Optical Theory Improvements to Space Domain Awareness

    DTIC Science & Technology

    2016-09-15

    OPTICAL THEORY IMPROVEMENTS TO SPACE DOMAIN AWARENESS DISSERTATION Tyler J. Hardy, Captain, USAF AFIT-ENG-DS-16-S-011 DEPARTMENT OF THE AIR FORCE AIR...copyright protection in the United States. AFIT-ENG-DS-16-S-011 OPTICAL THEORY IMPROVEMENTS TO SPACE DOMAIN AWARENESS DISSERTATION Presented to the...APPROVED FOR PUBLIC RELEASE; DISTRIBUTION UNLIMITED AFIT-ENG-DS-16-S-011 OPTICAL THEORY IMPROVEMENTS TO SPACE DOMAIN AWARENESS Tyler J. Hardy, BSEE

  9. Domain Decomposition for the SPN Solver MINOS

    NASA Astrophysics Data System (ADS)

    Jamelot, Erell; Baudron, Anne-Marie; Lautard, Jean-Jacques

    2012-12-01

    In this article we present a domain decomposition method for the mixed SPN equations, discretized with Raviart-Thomas-Nédélec finite elements. This domain decomposition is based on the iterative Schwarz algorithm with Robin interface conditions to handle communications. After having described this method, we give details on how to optimize the convergence. Finally, we give some numerical results computed in a realistic 3D domain. The computations are done with the MINOS solver of the APOLLO3® code.

  10. Domain-specific control of selective attention.

    PubMed

    Lin, Szu-Hung; Yeh, Yei-Yu

    2014-01-01

    Previous research has shown that loading information on working memory affects selective attention. However, whether the load effect on selective attention is domain-general or domain-specific remains unresolved. The domain-general effect refers to the findings that load in one content (e.g. phonological) domain in working memory influences processing in another content (e.g., visuospatial) domain. Attentional control supervises selection regardless of information domain. The domain-specific effect refers to the constraint of influence only when maintenance and processing operate in the same domain. Selective attention operates in a specific content domain. This study is designed to resolve this controversy. Across three experiments, we manipulated the type of representation maintained in working memory and the type of representation upon which the participants must exert control to resolve conflict and select a target into the focus of attention. In Experiments 1a and 1b, participants maintained digits and nonverbalized objects, respectively, in working memory while selecting a target in a letter array. In Experiment 2, we presented auditory digits with a letter flanker task to exclude the involvement of resource competition within the same input modality. In Experiments 3a and 3b, we replaced the letter flanker task with an object flanker task while manipulating the memory load on object and digit representation, respectively. The results consistently showed that memory load modulated distractibility only when the stimuli of the two tasks were represented in the same domain. The magnitude of distractor interference was larger under high load than under low load, reflecting a lower efficacy of information prioritization. When the stimuli of the two tasks were represented in different domains, memory load did not modulate distractibility. Control of processing priority in selective attention demands domain-specific resources.

  11. Domain Transfer Learning for MCI Conversion Prediction.

    PubMed

    Cheng, Bo; Liu, Mingxia; Zhang, Daoqiang; Munsell, Brent C; Shen, Dinggang

    2015-07-01

    Machine learning methods have successfully been used to predict the conversion of mild cognitive impairment (MCI) to Alzheimer's disease (AD), by classifying MCI converters (MCI-C) from MCI nonconverters (MCI-NC). However, most existing methods construct classifiers using data from one particular target domain (e.g., MCI), and ignore data in other related domains (e.g., AD and normal control (NC)) that may provide valuable information to improve MCI conversion prediction performance. To address is limitation, we develop a novel domain transfer learning method for MCI conversion prediction, which can use data from both the target domain (i.e., MCI) and auxiliary domains (i.e., AD and NC). Specifically, the proposed method consists of three key components: 1) a domain transfer feature selection component that selects the most informative feature-subset from both target domain and auxiliary domains from different imaging modalities; 2) a domain transfer sample selection component that selects the most informative sample-subset from the same target and auxiliary domains from different data modalities; and 3) a domain transfer support vector machine classification component that fuses the selected features and samples to separate MCI-C and MCI-NC patients. We evaluate our method on 202 subjects from the Alzheimer's Disease Neuroimaging Initiative (ADNI) that have MRI, FDG-PET, and CSF data. The experimental results show the proposed method can classify MCI-C patients from MCI-NC patients with an accuracy of 79.4%, with the aid of additional domain knowledge learned from AD and NC.

  12. Definition and identification of homology domains.

    PubMed

    Lawrence, C B; Goldman, D A

    1988-03-01

    A method is described for identifying and evaluating regions of significant similarity between two sequences. The notion of a 'homology domain' is employed which defines the boundaries of a region of sequence homology containing no insertions or deletions. The relative significance of different potential homology domains is evaluated using a non-linear similarity score related to the probability of finding the observed level of similarity in the region by chance. The sensitivity of the method is demonstrated by simulating the evolution of homology domains and applying the method to their detection. Several examples of the use of homology domain identification are given.

  13. Transform domain steganography with blind source separation

    NASA Astrophysics Data System (ADS)

    Jouny, Ismail

    2015-05-01

    This paper applies blind source separation or independent component analysis for images that may contain mixtures of text, audio, or other images for steganography purposes. The paper focuses on separating mixtures in the transform domain such as Fourier domain or the Wavelet domain. The study addresses the effectiveness of steganography when using linear mixtures of multimedia components and the ability of standard blind sources separation techniques to discern hidden multimedia messages. Mixing in the space, frequency, and wavelet (scale) domains is compared. Effectiveness is measured using mean square error rate between original and recovered images.

  14. Frequency domain FIR and IIR adaptive filters

    NASA Technical Reports Server (NTRS)

    Lynn, D. W.

    1990-01-01

    A discussion of the LMS adaptive filter relating to its convergence characteristics and the problems associated with disparate eigenvalues is presented. This is used to introduce the concept of proportional convergence. An approach is used to analyze the convergence characteristics of block frequency-domain adaptive filters. This leads to a development showing how the frequency-domain FIR adaptive filter is easily modified to provide proportional convergence. These ideas are extended to a block frequency-domain IIR adaptive filter and the idea of proportional convergence is applied. Experimental results illustrating proportional convergence in both FIR and IIR frequency-domain block adaptive filters is presented.

  15. Multiple graph regularized protein domain ranking

    PubMed Central

    2012-01-01

    Background Protein domain ranking is a fundamental task in structural biology. Most protein domain ranking methods rely on the pairwise comparison of protein domains while neglecting the global manifold structure of the protein domain database. Recently, graph regularized ranking that exploits the global structure of the graph defined by the pairwise similarities has been proposed. However, the existing graph regularized ranking methods are very sensitive to the choice of the graph model and parameters, and this remains a difficult problem for most of the protein domain ranking methods. Results To tackle this problem, we have developed the Multiple Graph regularized Ranking algorithm, MultiG-Rank. Instead of using a single graph to regularize the ranking scores, MultiG-Rank approximates the intrinsic manifold of protein domain distribution by combining multiple initial graphs for the regularization. Graph weights are learned with ranking scores jointly and automatically, by alternately minimizing an objective function in an iterative algorithm. Experimental results on a subset of the ASTRAL SCOP protein domain database demonstrate that MultiG-Rank achieves a better ranking performance than single graph regularized ranking methods and pairwise similarity based ranking methods. Conclusion The problem of graph model and parameter selection in graph regularized protein domain ranking can be solved effectively by combining multiple graphs. This aspect of generalization introduces a new frontier in applying multiple graphs to solving protein domain ranking applications. PMID:23157331

  16. Domain walls and defects in ferroelectric materials

    NASA Astrophysics Data System (ADS)

    Rojac, Tadej; Damjanovic, Dragan

    2017-10-01

    The results of recent studies of domain walls and their interaction with defects in BaTiO3, Pb(Zr,Ti)O3, and BiFeO3 are discussed. The studies reveal why donor- and acceptor-doped Pb(Zr,Ti)O3 behave differently, what is the role of stationary charged domain walls in enhanced properties of domain engineered BaTiO3 crystals, and give evidence of a large concentration of specific charged point defects within domain walls in BiFeO3 ceramics.

  17. Stability on Time-Dependent Domains

    NASA Astrophysics Data System (ADS)

    Knobloch, E.; Krechetnikov, R.

    2014-06-01

    We explore the key differences in the stability picture between extended systems on time-fixed and time-dependent spatial domains. As a paradigm, we take the complex Swift-Hohenberg equation, which is the simplest nonlinear model with a finite critical wavenumber, and use it to study dynamic pattern formation and evolution on time-dependent spatial domains in translationally invariant systems, i.e., when dilution effects are absent. In particular, we discuss the effects of a time-dependent domain on the stability of spatially homogeneous and spatially periodic base states, and explore its effects on the Eckhaus instability of periodic states. New equations describing the nonlinear evolution of the pattern wavenumber on time-dependent domains are derived, and the results compared with those on fixed domains. Pattern coarsening on time-dependent domains is contrasted with that on fixed domains with the help of the Cahn-Hilliard equation extended here to time-dependent domains. Parallel results for the evolution of the Benjamin-Feir instability on time-dependent domains are also given.

  18. Domain walls in antiferromagnetically coupled multilayer films.

    PubMed

    Hellwig, Olav; Berger, Andreas; Fullerton, Eric E

    2003-11-07

    We report experimentally observed magnetic domain-wall structures in antiferromagnetically coupled multilayer films with perpendicular anisotropy. Our studies reveal a first-order phase transition from domain walls with no net moment to domain walls with ferromagnetic cores. The transition originates from the competition between dipolar and exchange energies, which we tune by means of layer thickness. Although observed in a synthetic antiferromagnetic system, such domain-wall structures may be expected to occur in A-type antiferromagnets with anisotropic exchange coupling.

  19. Domain Tuning of Bilingual Lexicons for MT

    DTIC Science & Technology

    2003-02-01

    SUBTITLE Domain Tuning of Bilingual Lexicons for MT 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d. PROJECT NUMBER...Standard Form 298 (Rev. 8-98) Prescribed by ANSI Std Z39-18 Domain Tuning of Bilingual Lexicons for MT Necip Fazıl Ayan, Bonnie J. Dorr, Okan Kolak...umiacs.umd.edu Domain Tuning of Bilingual Lexicons for MT Abstract Our overall objective is to translate a domain-specific document in a for- eign language (in

  20. Cooperative interactions between paired domain and homeodomain.

    PubMed

    Jun, S; Desplan, C

    1996-09-01

    The Pax proteins are a family of transcriptional regulators involved in many developmental processes in all higher eukaryotes. They are characterized by the presence of a paired domain (PD), a bipartite DNA binding domain composed of two helix-turn-helix (HTH) motifs,the PAI and RED domains. The PD is also often associated with a homeodomain (HD) which is itself able to form homo- and hetero-dimers on DNA. Many of these proteins therefore contain three HTH motifs each able to recognize DNA. However, all PDs recognize highly related DNA sequences, and most HDs also recognize almost identical sites. We show here that different Pax proteins use multiple combinations of their HTHs to recognize several types of target sites. For instance, the Drosophila Paired protein can bind, in vitro, exclusively through its PAI domain, or through a dimer of its HD, or through cooperative interaction between PAI domain and HD. However, prd function in vivo requires the synergistic action of both the PAI domain and the HD. Pax proteins with only a PD appear to require both PAI and RED domains, while a Pax-6 isoform and a new Pax protein, Lune, may rely on the RED domain and HD. We propose a model by which Pax proteins recognize different target genes in vivo through various combinations of their DNA binding domains, thus expanding their recognition repertoire.

  1. Optical coherence domain reflectometry guidewire

    DOEpatents

    Colston, Billy W.; Everett, Matthew; Da Silva, Luiz B.; Matthews, Dennis

    2001-01-01

    A guidewire with optical sensing capabilities is based on a multiplexed optical coherence domain reflectometer (OCDR), which allows it to sense location, thickness, and structure of the arterial walls or other intra-cavity regions as it travels through the body during minimally invasive medical procedures. This information will be used both to direct the guidewire through the body by detecting vascular junctions and to evaluate the nearby tissue. The guidewire contains multiple optical fibers which couple light from the proximal to distal end. Light from the fibers at the distal end of the guidewire is directed onto interior cavity walls via small diameter optics such as gradient index lenses and mirrored corner cubes. Both forward viewing and side viewing fibers can be included. The light reflected or scattered from the cavity walls is then collected by the fibers, which are multiplexed at the proximal end to the sample arm of an optical low coherence reflectometer. The guidewire can also be used in nonmedical applications.

  2. Frequency domain convolution for SCANSAR

    NASA Astrophysics Data System (ADS)

    Cantraine, Guy; Dendal, Didier

    1994-12-01

    Starting from basic signals expressions, the rigorous formulation of frequency domain convolution is demonstrated, in general and impulse terms, including antenna patterns and squint angle. The major differences with conventional algorithms are discussed and theoretical concepts clarified. In a second part, the philosophy of advanced SAR algorithms is compared with that of a SCANSAR observation (several subswaths). It is proved that a general impulse response can always be written as the product of three factors, i.e., a phasor, an antenna coefficient, and a migration expression, and that the details of antenna effects can be ignored in the usual SAR system, but not the range migration (the situation is reversed in a SCANSAR reconstruction scheme). In a next step, some possible inverse filter kernels (the matched filter, the true inverse filter, ...) for general SAR or SCANSAR mode reconstructions, are compared. By adopting a noise corrupted model of data, we get the corresponding Wiener filter, the major interest of which is to avoid all divergence risk. Afterwards, the vocable `a class of filter' is introduced and summarized by a parametric formulation. Lastly, the homogeneity of the reconstruction, with a noncyclic fast Fourier transform deconvolution is studied by comparing peak responses according to the burst location. The more homogeneous sensitivity of the Wiener filter, with a stepper fall when the target begins to go outside the antenna pattern, is confirmed. A linear optimal merging of adjacent looks (in azimuth) minimizing the rms noise is also presented, as well as consideration about squint ambiguity.

  3. Bioconvection in spatially extended domains

    NASA Astrophysics Data System (ADS)

    Karimi, A.; Paul, M. R.

    2013-05-01

    We numerically explore gyrotactic bioconvection in large spatially extended domains of finite depth using parameter values from available experiments with the unicellular alga Chlamydomonas nivalis. We numerically integrate the three-dimensional, time-dependent continuum model of Pedley [J. Fluid Mech.10.1017/S0022112088002393 195, 223 (1988)] using a high-order, parallel, spectral-element approach. We explore the long-time nonlinear patterns and dynamics found for layers with an aspect ratio of 10 over a range of Rayleigh numbers. Our results yield the pattern wavelength and pattern dynamics which we compare with available theory and experimental measurement. There is good agreement for the pattern wavelength at short times between numerics, experiment, and a linear stability analysis. At long times we find that the general sequence of patterns given by the nonlinear evolution of the governing equations correspond qualitatively to what has been described experimentally. However, at long times the patterns in numerics grow to larger wavelengths, in contrast to what is observed in experiment where the wavelength is found to decrease with time.

  4. Acidic domains around nucleic acids.

    PubMed Central

    Lamm, G; Pack, G R

    1990-01-01

    The hydrogen ion concentration in the vicinity of DNA was mapped out within the Poisson-Boltzmann approximation. Experimental conditions were modeled by assuming Na-DNA to be solvated in a buffer solution containing 45 mM Tris and 3 mM Mg cations at pH 7.5. Three regions of high H+ concentration (greater than 10 microM) are predicted: one throughout the minor groove of DNA and two localized in the major groove near N7 of guanine and C5 of cytosine for a G.C base pair. These acidic domains correlate well with the observed covalent binding sites of benzo[a]pyrene epoxide (N2 of guanine) and of aflatoxin B1 epoxide (N7 of guanine), chemical carcinogens that presumably undergo acid catalysis to form highly reactive carbocations that ultimately bind to DNA. It is suggested that these regions of high H+ concentration may also be of concern in understanding interactions involving proteins and noncarcinogenic molecules with or near nucleic acids. PMID:2123348

  5. Light responses in Photoperiodism in Arabidopsis thaliana

    SciTech Connect

    Anthony R. Cashmore

    2006-08-01

    ADO1: An Arabidopsis blue light photoreceptor We have reported the characterization of an Arabidopsis gene encoding the ADAGIO 1 (ADO1) protein (Jarillo et al., 2001a). ADO1 contains a LOV domain, similar to WHITE COLLAR 1 (WC1), a photoreceptor for entrainment of Neurospora circadian rhythms (Froehlich et al., 2002), as well as PHOT1 and PHOT2, the blue light photoreceptors for phototropism (Briggs et al., 2001; Christie et al., 1998; Jarillo et al., 2001b; Kinoshita et al., 2001). Loss of function ado1 mutants show an unusually long periodicity for their free running circadian rhythm (Jarillo et al., 2001a). This observation holds for plants grown under white light as well as blue light and surprisingly, plants grown under red light also show altered circadian properties. The similarity of the LOV domain of ADO1 to those of PHOT1, PHOT2 and WC1 (known flavoprotein photoreceptors) as well as the genetic and molecular properties of ADO1, indicate that ADO1 is likely a new class of blue light photoreceptor. Indeed, the LOV domain of the related FKF1/ADO3 has been shown to bind FMN, and exhibit the in vitro photochemistry characteristic of PHOT1 (Imaizumi et al., 2003). Furthermore, ZTL/ADO1 has been shown to participate in the circadian and proteasome mediated degradation of the Arabidopsis clock protein, TOC1 (Mas et al., 2003). We also showed that the ado1 mutation selectively confers hypersensitivity to red light — when grown under red light (but not blue light) the ado1 mutant possesses an unusually short hypocotyl. This red light hypersensivity is even more severe in a triple ado1 ado2 ado3 mutant — ADO2 and ADO3 being the two other members of this ADAGIO gene family. This finding of a mutant phenotype under red light is somewhat unexpected for a protein thought to function as a photoreceptor for blue light. We have pursued our studies of ADO1 by preparing a mutant gene for which we have altered the codon for the cysteine residue conserved in all LOV

  6. Fuzzy domains: new way of describing flexibility and interdependence of the protein domains.

    PubMed

    Yesylevskyy, Semen O; Kharkyanen, Valery N

    2009-03-01

    We proposed the innovative method of domain identification based on the concept of the fuzzy domains. In this method each residue of the protein can belong to several domains simultaneously with certain weights, which reflect to what extent this residue shares the motion pattern of the given domain. Our method allows describing the fuzzy boundaries between the domains and the gradual changes of the motion pattern from one domain to the other. It provides the reasonable compromise between the continuous change of the protein dynamics from one residue to the other and the discrete description of the structure in terms of small number of domains. We suggested quantitative criterion, which shows the overall degree of domain flexibility in the protein. The concept of the fuzzy domains provides an innovative way of visualization of domain flexibility, which makes the gradual transitions between the domains clearly visible and comparable to available experimental and structural data. In the future, the concept of the fuzzy domains can be used in the coarse-grained simulations of the domain dynamics in order to account for internal protein flexibility.

  7. Molecular dynamics study of ferroelectric domain nucleation and domain switching dynamics.

    PubMed

    Boddu, Vishal; Endres, Florian; Steinmann, Paul

    2017-04-11

    Ferroelectric materials contain domains of ordered electric dipoles, separated by domain walls, that can undergo polarisation switching under externally applied electric fields. The domain switching dynamics in ferroelectric materials plays an essential role in their application to electronic and electro-optic de- vices. Previous studies suggest that the switching occurs largely through domain wall motion which is explained from the viewpoint of statistical physics on surface growth as the behaviour of a pinned elas- tic interface. We perform molecular dynamics simulations to investigate the domain switching process and quantitatively estimate the switching speed of anti-parallel 180° domains in ferroelectric, tetragonal BaTiO3 perfect single crystals at room temperature using the core-shell model. We observe an unprece- dented, non-linear increase in the domain switching speed caused by the nucleation of new domains within the switching domain. We determine the strength of the electric field to evoke nucleation of new domains and show that the nucleated domains diffuse into nearby favourable domains when the electric field is removed. Furthermore, we discuss the prominence of domain nucleations during ferroelectric switching.

  8. 41 CFR 102-173.35 - Who authorizes domain names?

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... DOMAIN Registration § 102-173.35 Who authorizes domain names? Domain names must be authorized by the... selected domain names, but reserves the right to not assign domain names on a case-by-case basis. Non-Federal government domain names must follow the naming conventions described in §§ 102-173.50 through 102...

  9. Waveform inversion in the shifted Laplace domain

    NASA Astrophysics Data System (ADS)

    Kwon, Jungmin; Jun, Hyunggu; Song, Hyeonjun; Jang, U. Geun; Shin, Changsoo

    2017-07-01

    Laplace domain waveform inversion (WI) is one of the most effective algorithms to generate an initial velocity model. Because of its bandwidth independence with respect to the source wavelet, this method can yield reasonable initial models without low-frequency components in the seismic data. However, the conventional Laplace domain WI algorithm has an accuracy problem from its simultaneous consideration of the first arrival traveltime and apparent amplitude in the Laplace domain wavefield. This simultaneous consideration creates undesirable cross-correlation terms between the residual of the traveltime and the partial derivatives of the apparent amplitude in the gradient directions and between the residual of the apparent amplitude and the partial derivatives of the traveltime in the gradient directions. In this paper, we introduce a new objective function that uses a shifted Laplace domain wavefield to solve the problem of Laplace domain WI. Information that is associated with the traveltime and apparent amplitude can be separately inverted by using this shifted Laplace domain WI. This separation of the information can suppress the undesirable cross-correlation terms between the residual of the traveltime and the partial derivatives of apparent amplitude and between the residual of the apparent amplitude and the partial derivatives of the traveltime in the gradient directions. We can effectively perform shifted Laplace domain modelling by using the damped monochromatic wave equation. We verify the accuracy of this shifted Laplace domain modelling scheme by comparing the shifted Laplace-transformed result from a synthetic seismogram to a wavefield that is modelled in the shifted Laplace domain. We perform a contribution analysis to demonstrate that the shifted Laplace domain wavefield is essential to improve the accuracy of the inverted results. Finally, we confirm the robustness of the shifted Laplace domain WI algorithm by testing it against a BP model.

  10. Public domain optical character recognition

    NASA Astrophysics Data System (ADS)

    Garris, Michael D.; Blue, James L.; Candela, Gerald T.; Dimmick, Darrin L.; Geist, Jon C.; Grother, Patrick J.; Janet, Stanley A.; Wilson, Charles L.

    1995-03-01

    A public domain document processing system has been developed by the National Institute of Standards and Technology (NIST). The system is a standard reference form-based handprint recognition system for evaluating optical character recognition (OCR), and it is intended to provide a baseline of performance on an open application. The system's source code, training data, performance assessment tools, and type of forms processed are all publicly available. The system recognizes the handprint entered on handwriting sample forms like the ones distributed with NIST Special Database 1. From these forms, the system reads hand-printed numeric fields, upper and lowercase alphabetic fields, and unconstrained text paragraphs comprised of words from a limited-size dictionary. The modular design of the system makes it useful for component evaluation and comparison, training and testing set validation, and multiple system voting schemes. The system contains a number of significant contributions to OCR technology, including an optimized probabilistic neural network (PNN) classifier that operates a factor of 20 times faster than traditional software implementations of the algorithm. The source code for the recognition system is written in C and is organized into 11 libraries. In all, there are approximately 19,000 lines of code supporting more than 550 subroutines. Source code is provided for form registration, form removal, field isolation, field segmentation, character normalization, feature extraction, character classification, and dictionary-based postprocessing. The recognition system has been successfully compiled and tested on a host of UNIX workstations. This paper gives an overview of the recognition system's software architecture, including descriptions of the various system components along with timing and accuracy statistics.

  11. RPT2/NCH1 subfamily of NPH3-like proteins is essential for the chloroplast accumulation response in land plants

    PubMed Central

    Takemiya, Atsushi; Kong, Sam-Geun; Higa, Takeshi; Komatsu, Aino; Shimazaki, Ken-ichiro; Kohchi, Takayuki; Wada, Masamitsu

    2016-01-01

    In green plants, the blue light receptor kinase phototropin mediates various photomovements and developmental responses, such as phototropism, chloroplast photorelocation movements (accumulation and avoidance), stomatal opening, and leaf flattening, which facilitate photosynthesis. In Arabidopsis, two phototropins (phot1 and phot2) redundantly mediate these responses. Two phototropin-interacting proteins, NONPHOTOTROPIC HYPOCOTYL 3 (NPH3) and ROOT PHOTOTROPISM 2 (RPT2), which belong to the NPH3/RPT2-like (NRL) family of BTB (broad complex, tramtrack, and bric à brac) domain proteins, mediate phototropism and leaf flattening. However, the roles of NRL proteins in chloroplast photorelocation movement remain to be determined. Here, we show that another phototropin-interacting NRL protein, NRL PROTEIN FOR CHLOROPLAST MOVEMENT 1 (NCH1), and RPT2 redundantly mediate the chloroplast accumulation response but not the avoidance response. NPH3, RPT2, and NCH1 are not involved in the chloroplast avoidance response or stomatal opening. In the liverwort Marchantia polymorpha, the NCH1 ortholog, MpNCH1, is essential for the chloroplast accumulation response but not the avoidance response, indicating that the regulation of the phototropin-mediated chloroplast accumulation response by RPT2/NCH1 is conserved in land plants. Thus, the NRL protein combination could determine the specificity of diverse phototropin-mediated responses. PMID:27578868

  12. The Domain Specificity of Academic Emotional Experiences

    ERIC Educational Resources Information Center

    Goetz, Thomas; Frenzel, Anne C.; Pekrun, Reinhard; Hall, Nathan C.

    2006-01-01

    The authors analyzed the domain specificity of emotions and focused on experiences of enjoyment, anxiety, and boredom in the domains of mathematics, Latin, German, and English. On the basis of assumptions in R. Pekrun's (2000; in press) control-value theory and findings of pilot studies, the authors hypothesized the existence of a largely…

  13. Domain 2: Sport Safety and Injury Prevention

    ERIC Educational Resources Information Center

    Gurchiek, Larry; Mokha, Monique Butcher

    2004-01-01

    Most coaches recognize the importance of creating a safe environment and preventing injuries of their athletes. Domain 2 is dedicated to this important aspect of coaching, and outlines specific areas within safety and injury prevention that coaches should address. Domain 2 sets the standards for facility, equipment, and environmental safety…

  14. XML Based Markup Languages for Specific Domains

    NASA Astrophysics Data System (ADS)

    Varde, Aparna; Rundensteiner, Elke; Fahrenholz, Sally

    A challenging area in web based support systems is the study of human activities in connection with the web, especially with reference to certain domains. This includes capturing human reasoning in information retrieval, facilitating the exchange of domain-specific knowledge through a common platform and developing tools for the analysis of data on the web from a domain expert's angle. Among the techniques and standards related to such work, we have XML, the eXtensible Markup Language. This serves as a medium of communication for storing and publishing textual, numeric and other forms of data seamlessly. XML tag sets are such that they preserve semantics and simplify the understanding of stored information by users. Often domain-specific markup languages are designed using XML, with a user-centric perspective. Standardization bodies and research communities may extend these to include additional semantics of areas within and related to the domain. This chapter outlines the issues to be considered in developing domain-specific markup languages: the motivation for development, the semantic considerations, the syntactic constraints and other relevant aspects, especially taking into account human factors. Illustrating examples are provided from domains such as Medicine, Finance and Materials Science. Particular emphasis in these examples is on the Materials Markup Language MatML and the semantics of one of its areas, namely, the Heat Treating of Materials. The focus of this chapter, however, is not the design of one particular language but rather the generic issues concerning the development of domain-specific markup languages.

  15. Time Domain Switched Accelerometer Design and Fabrication

    DTIC Science & Technology

    2014-09-01

    TECHNICAL REPORT 2052 September 2014 Time -Domain Switched Accelerometer Design and Fabrication Paul Swanson Andrew Wang...Approved for public release. SSC Pacific San Diego, CA 92152-5001 TECHNICAL REPORT 2052 September 2014 Time ...objective of this report is to record the decision-making process for developing the device design and fabrication workflow for the time -domain switched

  16. Domain transfer learning for MCI conversion prediction.

    PubMed

    Cheng, Bo; Zhang, Daoqiang; Shen, Dinggang

    2012-01-01

    In recent studies of Alzheimer's disease (AD), it has increasing attentions in identifying mild cognitive impairment (MCI) converters (MCI-C) from MCI non-converters (MCI-NC). Note that MCI is a prodromal stage of AD, with possibility to convert to AD. Most traditional methods for MCI conversion prediction learn information only from MCI subjects (including MCI-C and MCI-NC), not from other related subjects, e.g., AD and normal controls (NC), which can actually aid the classification between MCI-C and MCI-NC. In this paper, we propose a novel domain-transfer learning method for MCI conversion prediction. Different from most existing methods, we classify MCI-C and MCI-NC with aid from the domain knowledge learned with AD and NC subjects as auxiliary domain to further improve the classification performance. Our method contains two key components: (1) the cross-domain kernel learning for transferring auxiliary domain knowledge, and (2) the adapted support vector machine (SVM) decision function construction for cross-domain and auxiliary domain knowledge fusion. Experimental results on the Alzheimer's Disease neuroimaging initiative (ADNI) database show that the proposed method can significantly improve the classification performance between MCI-C and MCI-NC, with aid of domain knowledge learned from AD and NC subjects.

  17. Domains of the Florida Performance Measurement System.

    ERIC Educational Resources Information Center

    Florida State Dept. of Education, Tallahassee.

    This monograph sets forth in detail the concepts included in the five domains of teaching as identified by the Florida Coalition for the Development of a Performance Evaluation System. The first domain, planning, includes the concepts: (1) content coverage; (2) utilization of instructional materials; (3) activity structure; (4) goal focusing; and…

  18. Multiple hypothesis tracking for the cyber domain

    NASA Astrophysics Data System (ADS)

    Schwoegler, Stefan; Blackman, Sam; Holsopple, Jared; Hirsch, Michael J.

    2011-09-01

    This paper discusses how methods used for conventional multiple hypothesis tracking (MHT) can be extended to domain-agnostic tracking of entities from non-kinematic constraints such as those imposed by cyber attacks in a potentially dense false alarm background. MHT is widely recognized as the premier method to avoid corrupting tracks with spurious data in the kinematic domain but it has not been extensively applied to other problem domains. The traditional approach is to tightly couple track maintenance (prediction, gating, filtering, probabilistic pruning, and target confirmation) with hypothesis management (clustering, incompatibility maintenance, hypothesis formation, and Nassociation pruning). However, by separating the domain specific track maintenance portion from the domain agnostic hypothesis management piece, we can begin to apply the wealth of knowledge gained from ground and air tracking solutions to the cyber (and other) domains. These realizations led to the creation of Raytheon's Multiple Hypothesis Extensible Tracking Architecture (MHETA). In this paper, we showcase MHETA for the cyber domain, plugging in a well established method, CUBRC's INFormation Engine for Real-time Decision making, (INFERD), for the association portion of the MHT. The result is a CyberMHT. We demonstrate the power of MHETA-INFERD using simulated data. Using metrics from both the tracking and cyber domains, we show that while no tracker is perfect, by applying MHETA-INFERD, advanced nonkinematic tracks can be captured in an automated way, perform better than non-MHT approaches, and decrease analyst response time to cyber threats.

  19. Thermodynamics of heme-induced conformational changes in hemopexin: role of domain-domain interactions.

    PubMed Central

    Wu, M. L.; Morgan, W. T.

    1995-01-01

    Hemopexin is a serum glycoprotein that binds heme with high affinity and delivers heme to the liver cells via receptor-mediated endocytosis. A hinge region connects the two non-disulfide-linked domains of hemopexin, a 35-kDa N-terminal domain (domain I) that binds heme, and a 25-kDa C-terminal domain (domain II). Although domain II does not bind heme, it assumes one structural state in apo-hemopexin and another in heme-hemopexin, and this change is important in facilitating the association of heme-hemopexin with its receptor. In order to elucidate the structure and function of hemopexin, it is important to understand how structural information is transmitted to domain II when domain I binds heme. Here we report a study of the protein-protein interactions between domain I and domain II using analytical ultracentrifugation and isothermal titration calorimetry. Sedimentation equilibrium analysis showed that domain I associates with domain II both in the presence and absence of heme with Kd values of 0.8 microM and 55 microM, respectively. The interaction between heme-domain I and domain II has a calorimetric enthalpy of +11 kcal/mol, a heat capacity (delta Cp) of -720 cal/mol.K, and a calculated entropy of +65 cal/mol.K. By varying the temperature of the centrifugation equilibrium runs, a van't Hoff plot with an apparent change in enthalpy (delta H) of -3.6 kcal/mol and change in entropy (delta S) of +8.1 cal/mol.K for the association of apo-domain I with domain II was obtained.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:7773173

  20. Novel blue light-sensitive proteins from a metagenomic approach.

    PubMed

    Pathak, G P; Ehrenreich, A; Losi, A; Streit, W R; Gärtner, W

    2009-09-01

    A microarray-based approach was used to screen a soil metagenome for the presence of blue light (BL) photoreceptor-encoding genes. The microarray carried 149 different 54-mer oligonucleotides, derived from consensus sequences of light, oxygen and voltage (LOV) domain BL photoreceptor genes. Calibration of the microarrays allowed the detection of minimally 50 ng of genomic DNA against a background of 2-5 microg of genomic DNA. Identification of a positive cosmid clone was still possible for an amount of 0.25 ng against a background of 10 microg of labelled DNA clones. The array could readily identify targets carrying 4% sequence mismatch. Using the LOV microarray, up to 1200 library clones in concentrations of c. 20 ng each with a c. 40 kb insert size could be screened in a single batch. After calibration and reliability controls, the microarray was probed with cosmid-cloned DNA from the thermophilic fraction of a soil sample. From this approach, a novel gene was isolated that encodes a protein consisting of several Per-Arnt-Sim domains, a LOV domain associated to a histidine kinase and a response regulator domain. The novel gene showed highest similarity to a known sequence from Kineococcus radiotolerans SRS30216 (58% identity for the LOV domain only) and to a gene from Methylibium petroleiphilum PM1 (57% identity). The gene, designated as ht-met1 (Hamburg Thermophile Metagenome 1), was isolated and fully sequenced (3615 bp). ht-met1 is followed by a second open reading frame encoding a Fe-chelatase, an arrangement quite frequent for BL photoreceptors. The LOV domain region of ht-met1 was subcloned and expressed yielding a fully functional, flavin-containing LOV domain. Irradiation generated the typical LOV photochemistry, with the transient formation of a flavin-protein photoadduct. The dark recovery lifetime was found as tau(REC) = 120 s (20 degrees C) and is among the fastest ones determined so far for bacterial LOV domains.

  1. Requirements analysis, domain knowledge, and design

    NASA Technical Reports Server (NTRS)

    Potts, Colin

    1988-01-01

    Two improvements to current requirements analysis practices are suggested: domain modeling, and the systematic application of analysis heuristics. Domain modeling is the representation of relevant application knowledge prior to requirements specification. Artificial intelligence techniques may eventually be applicable for domain modeling. In the short term, however, restricted domain modeling techniques, such as that in JSD, will still be of practical benefit. Analysis heuristics are standard patterns of reasoning about the requirements. They usually generate questions of clarification or issues relating to completeness. Analysis heuristics can be represented and therefore systematically applied in an issue-based framework. This is illustrated by an issue-based analysis of JSD's domain modeling and functional specification heuristics. They are discussed in the context of the preliminary design of simple embedded systems.

  2. Time-Domain Stability Margin Assessment

    NASA Technical Reports Server (NTRS)

    Clements, Keith

    2016-01-01

    The baseline stability margins for NASA's Space Launch System (SLS) launch vehicle were generated via the classical approach of linearizing the system equations of motion and determining the gain and phase margins from the resulting frequency domain model. To improve the fidelity of the classical methods, the linear frequency domain approach can be extended by replacing static, memoryless nonlinearities with describing functions. This technique, however, does not address the time varying nature of the dynamics of a launch vehicle in flight. An alternative technique for the evaluation of the stability of the nonlinear launch vehicle dynamics along its trajectory is to incrementally adjust the gain and/or time delay in the time domain simulation until the system exhibits unstable behavior. This technique has the added benefit of providing a direct comparison between the time domain and frequency domain tools in support of simulation validation.

  3. Time Domain Stability Margin Assessment Method

    NASA Technical Reports Server (NTRS)

    Clements, Keith

    2017-01-01

    The baseline stability margins for NASA's Space Launch System (SLS) launch vehicle were generated via the classical approach of linearizing the system equations of motion and determining the gain and phase margins from the resulting frequency domain model. To improve the fidelity of the classical methods, the linear frequency domain approach can be extended by replacing static, memoryless nonlinearities with describing functions. This technique, however, does not address the time varying nature of the dynamics of a launch vehicle in flight. An alternative technique for the evaluation of the stability of the nonlinear launch vehicle dynamics along its trajectory is to incrementally adjust the gain and/or time delay in the time domain simulation until the system exhibits unstable behavior. This technique has the added benefit of providing a direct comparison between the time domain and frequency domain tools in support of simulation validation.

  4. FERM Domain Interaction Promotes FAK Signaling

    PubMed Central

    Dunty, Jill M.; Gabarra-Niecko, Veronica; King, Michelle L.; Ceccarelli, Derek F. J.; Eck, Michael J.; Schaller, Michael D.

    2004-01-01

    From the results of deletion analyses, the FERM domain of FAK has been proposed to inhibit enzymatic activity and repress FAK signaling. We have identified a sequence in the FERM domain that is important for FAK signaling in vivo. Point mutations in this sequence had little effect upon catalytic activity in vitro. However, the mutant exhibits reduced tyrosine phosphorylation and dramatically reduced Src family kinase binding. Further, the abilities of the mutant to transduce biochemical signals and to promote cell migration were severely impaired. The results implicate a FERM domain interaction in cell adhesion-dependent activation of FAK and downstream signaling. We also show that the purified FERM domain of FAK interacts with full-length FAK in vitro, and mutation of this sequence disrupts the interaction. These findings are discussed in the context of models of FAK regulation by its FERM domain. PMID:15169899

  5. The SH2 domain interaction landscape

    PubMed Central

    Tinti, Michele; Kiemer, Lars; Costa, Stefano; Miller, Martin; Sacco, Francesca; Olsen, Jesper V.; Carducci, Martina; Paoluzi, Serena; Langone, Francesca; Workman, Christopher T.; Blom, Nikolaj; Machida, Kazuya; Thompson, Christopher M.; Schutkowski, Mike; Brunak, Søren; Mann, Matthias; Mayer, Bruce J.; Castagnoli, Luisa; Cesareni, Gianni

    2014-01-01

    Summary Members of the SH2 domain family modulate signal transduction by binding to short peptides containing phosphorylated tyrosines. Each domain displays a distinct preference for the sequence context of the phosphorylated residue. We have developed a new high-density peptide chip technology that allows probing the affinity of most SH2 domains for a large fraction of the entire complement of tyrosine phosphopeptides in the human proteome. Using this technique we have experimentally identified thousands of putative SH2- peptide interactions for more than 70 different SH2 domains. By integrating this rich data set with orthogonal context-specific information, we have assembled an SH2 mediated probabilistic interaction network, which we make available as a community resource in the PepSpotDB database. A new predicted dynamic interaction between the SH2 domains of the tyrosine phosphatase SHP2 and the phosphorylated tyrosine in the ERK activation loop was validated by experiments in living cells. PMID:23545499

  6. Discoidin Domains as Emerging Therapeutic Targets.

    PubMed

    Villoutreix, Bruno O; Miteva, Maria A

    2016-08-01

    Discoidin (DS) domains are found in eukaryotic and prokaryotic extracellular and transmembrane multidomain proteins. These small domains play different functional roles and can interact with phospholipids, glycans, and proteins, including collagens. DS domain-containing proteins are often involved in cellular adhesion, migration, proliferation, and matrix-remodeling events, while some play a major role in blood coagulation. Mutations in DS domains have been associated with various disease conditions. This review provides an update on the structure, function, and modulation of the DS domains, with a special emphasis on two circulating blood coagulation cofactors, factor V and factor VIII, and the transmembrane neuropilin receptors that have been targeted for inhibition by biologics and small chemical compounds.

  7. Automotion of domain walls for spintronic interconnects

    SciTech Connect

    Nikonov, Dmitri E.; Manipatruni, Sasikanth; Young, Ian A.

    2014-06-07

    We simulate “automotion,” the transport of a magnetic domain wall under the influence of demagnetization and magnetic anisotropy, in nanoscale spintronic interconnects. In contrast to spin transfer driven magnetic domain wall motion, the proposed interconnects operate without longitudinal charge current transfer, with only a transient current pulse at domain wall creation and have favorable scaling down to the 20 nm dimension. Cases of both in-plane and out-of-plane magnetization are considered. Analytical dependence of the velocity of domain walls on the angle of magnetization are compared with full micromagnetic simulations. Deceleration, attenuation and disappearance, and reflection of domain walls are demonstrated through simulation. Dependences of the magnetization angle on the current pulse parameters are studied. The energy and delay analysis suggests that automotion is an attractive option for spintronic logic interconnects.

  8. Investigation of multilayer magnetic domain lattice file

    NASA Technical Reports Server (NTRS)

    Torok, E. J.; Kamin, M.; Tolman, C. H.

    1980-01-01

    The feasibility of the self structured multilayered bubble domain memory as a mass memory medium for satellite applications is examined. Theoretical considerations of multilayer bubble supporting materials are presented, in addition to the experimental evaluation of current accessed circuitry for various memory functions. The design, fabrication, and test of four device designs is described, and a recommended memory storage area configuration is presented. Memory functions which were demonstrated include the current accessed propagation of bubble domains and stripe domains, pinning of stripe domain ends, generation of single and double bubbles, generation of arrays of coexisting strip and bubble domains in a single garnet layer, and demonstration of different values of the strip out field for single and double bubbles indicating adequate margins for data detection. All functions necessary to develop a multilayer self structured bubble memory device were demonstrated in individual experiments.

  9. Field tuning of ferromagnetic domain walls on elastically coupled ferroelectric domain boundaries

    NASA Astrophysics Data System (ADS)

    Franke, Kévin J. A.; Lahtinen, Tuomas H. E.; van Dijken, Sebastiaan

    2012-03-01

    We report on the evolution of ferromagnetic domain walls during magnetization reversal in elastically coupled ferromagnetic-ferroelectric heterostructures. Using optical polarization microscopy and micromagnetic simulations, we demonstrate that the spin rotation and width of ferromagnetic domain walls can be accurately controlled by the strength of the applied magnetic field if the ferromagnetic walls are pinned onto 90∘ ferroelectric domain boundaries. Moreover, reversible switching between magnetically charged and uncharged domain walls is initiated by magnetic field rotation. Switching between both wall types reverses the wall chirality and abruptly changes the width of the ferromagnetic domain walls by up to 1000%.

  10. J domain independent functions of J proteins.

    PubMed

    Ajit Tamadaddi, Chetana; Sahi, Chandan

    2016-07-01

    Heat shock proteins of 40 kDa (Hsp40s), also called J proteins, are obligate partners of Hsp70s. Via their highly conserved and functionally critical J domain, J proteins interact and modulate the activity of their Hsp70 partners. Mutations in the critical residues in the J domain often result in the null phenotype for the J protein in question. However, as more J proteins have been characterized, it is becoming increasingly clear that a significant number of J proteins do not "completely" rely on their J domains to carry out their cellular functions, as previously thought. In some cases, regions outside the highly conserved J domain have become more important making the J domain dispensable for some, if not for all functions of a J protein. This has profound effects on the evolution of such J proteins. Here we present selected examples of J proteins that perform J domain independent functions and discuss this in the context of evolution of J proteins with dispensable J domains and J-like proteins in eukaryotes.

  11. Structural organization of human replication timing domains.

    PubMed

    Boulos, Rasha E; Drillon, Guénola; Argoul, Françoise; Arneodo, Alain; Audit, Benjamin

    2015-10-07

    Recent analysis of genome-wide epigenetic modification data, mean replication timing (MRT) profiles and chromosome conformation data in mammals have provided increasing evidence that flexibility in replication origin usage is regulated locally by the epigenetic landscape and over larger genomic distances by the 3D chromatin architecture. Here, we review the recent results establishing some link between replication domains and chromatin structural domains in pluripotent and various differentiated cell types in human. We reconcile the originally proposed dichotomic picture of early and late constant timing regions that replicate by multiple rather synchronous origins in separated nuclear compartments of open and closed chromatins, with the U-shaped MRT domains bordered by "master" replication origins specified by a localized (∼200-300 kb) zone of open and transcriptionally active chromatin from which a replication wave likely initiates and propagates toward the domain center via a cascade of origin firing. We discuss the relationships between these MRT domains, topologically associated domains and lamina-associated domains. This review sheds a new light on the epigenetically regulated global chromatin reorganization that underlies the loss of pluripotency and the determination of differentiation properties.

  12. Benchmark Generation using Domain Specific Modeling

    SciTech Connect

    Bui, Ngoc B.; Zhu, Liming; Gorton, Ian; Liu, Yan

    2007-08-01

    Performance benchmarks are domain specific applications that are specialized to a certain set of technologies and platforms. The development of a benchmark application requires mapping the performance specific domain concepts to an implementation and producing complex technology and platform specific code. Domain Specific Modeling (DSM) promises to bridge the gap between application domains and implementations by allowing designers to specify solutions in domain-specific abstractions and semantics through Domain Specific Languages (DSL). This allows generation of a final implementation automatically from high level models. The modeling and task automation benefits obtained from this approach usually justify the upfront cost involved. This paper employs a DSM based approach to invent a new DSL, DSLBench, for benchmark generation. DSLBench and its associated code generation facilities allow the design and generation of a completely deployable benchmark application for performance testing from a high level model. DSLBench is implemented using Microsoft Domain Specific Language toolkit. It is integrated with the Visual Studio 2005 Team Suite as a plug-in to provide extra modeling capabilities for performance testing. We illustrate the approach using a case study based on .Net and C#.

  13. Chiral spin torque at magnetic domain walls.

    PubMed

    Ryu, Kwang-Su; Thomas, Luc; Yang, See-Hun; Parkin, Stuart

    2013-07-01

    Spin-polarized currents provide a powerful means of manipulating the magnetization of nanodevices, and give rise to spin transfer torques that can drive magnetic domain walls along nanowires. In ultrathin magnetic wires, domain walls are found to move in the opposite direction to that expected from bulk spin transfer torques, and also at much higher speeds. Here we show that this is due to two intertwined phenomena, both derived from spin-orbit interactions. By measuring the influence of magnetic fields on current-driven domain-wall motion in perpendicularly magnetized Co/Ni/Co trilayers, we find an internal effective magnetic field acting on each domain wall, the direction of which alternates between successive domain walls. This chiral effective field arises from a Dzyaloshinskii-Moriya interaction at the Co/Pt interfaces and, in concert with spin Hall currents, drives the domain walls in lock-step along the nanowire. Elucidating the mechanism for the manipulation of domain walls in ultrathin magnetic films will enable the development of new families of spintronic devices.

  14. MIT domain of Vps4 is a Ca2+-dependent phosphoinositide-binding domain.

    PubMed

    Iwaya, Naoko; Takasu, Hirotoshi; Goda, Natsuko; Shirakawa, Masahiro; Tanaka, Toshiki; Hamada, Daizo; Hiroaki, Hidekazu

    2013-05-01

    The microtubule interacting and trafficking (MIT) domain is a small protein module that is conserved in proteins of diverged function, such as Vps4, spastin and sorting nexin 15 (SNX15). The molecular function of the MIT domain is protein-protein interaction, in which the domain recognizes peptides containing MIT-interacting motifs. Recently, we identified an evolutionarily related domain, 'variant' MIT domain at the N-terminal region of the microtubule severing enzyme katanin p60. We found that the domain was responsible for binding to microtubules and Ca(2+). Here, we have examined whether the authentic MIT domains also bind Ca(2+). We found that the loop between the first and second α-helices of the MIT domain binds a Ca(2+) ion. Furthermore, the MIT domains derived from Vps4b and SNX15a showed phosphoinositide-binding activities in a Ca(2+)-dependent manner. We propose that the MIT domain is a novel membrane-associating domain involved in endosomal trafficking.

  15. A new principle technic for the transformation from frequency domain to time domain

    NASA Astrophysics Data System (ADS)

    Gao, Ben-Qing

    2017-03-01

    A principle technic for the transformation from frequency domain to time domain is presented. Firstly, a special type of frequency domain transcendental equation is obtained for an expected frequency domain parameter which is a rational or irrational fraction expression. Secondly, the inverse Laplace transformation is performed. When the two time-domain factors corresponding to the two frequency domain factors at two sides of frequency domain transcendental equation are known quantities, a time domain transcendental equation is reached. At last, the expected time domain parameter corresponding to the expected frequency domain parameter can be solved by the inverse convolution process. Proceeding from rational or irrational fraction expression, all solving process is provided. In the meantime, the property of time domain sequence is analyzed and the strategy for choosing the parameter values is described. Numerical examples are presented to verify the proposed theory and technic. Except for rational or irrational fraction expressions, examples of complex relative permittivity of water and plasma are used as verification method. The principle method proposed in the paper can easily solve problems which are difficult to be solved by Laplace transformation.

  16. Structural conservation of the PIN domain active site across all domains of life.

    PubMed

    Senissar, M; Manav, M C; Brodersen, D E

    2017-08-01

    The PIN (PilT N-terminus) domain is a compact RNA-binding protein domain present in all domains of life. This 120-residue domain consists of a central and parallel β sheet surrounded by α helices, which together organize 4-5 acidic residues in an active site that binds one or more divalent metal ions and in many cases has endoribonuclease activity. In bacteria and archaea, the PIN domain is primarily associated with toxin-antitoxin loci, consisting of a toxin (the PIN domain nuclease) and an antitoxin that inhibits the function of the toxin under normal growth conditions. During nutritional or antibiotic stress, the antitoxin is proteolytically degraded causing activation of the PIN domain toxin leading to a dramatic reprogramming of cellular metabolism to cope with the new situation. In eukaryotes, PIN domains are commonly found as parts of larger proteins and are involved in a range of processes involving RNA cleavage, including ribosomal RNA biogenesis and nonsense-mediated mRNA decay. In this review, we provide a comprehensive overview of the structural characteristics of the PIN domain and compare PIN domains from all domains of life in terms of structure, active site architecture, and activity. © 2017 The Protein Society.

  17. Thermal variations of domain wall thickness and number of domains in magnetic rectangular grains

    NASA Astrophysics Data System (ADS)

    Xu, Song; Merrill, Ronald T.

    1990-12-01

    Equilibrium domain wall thickness and number of domains in rectangular magnetic grains are determined by using a modified Amar model. It is shown that domain structure, particularly domain wall thickness, in a magnetized grain depends strongly on grain shape and orientation. These dependencies are attributed to the existence of two competing self-magnetostatic interactions, one from the ends of the grain and the other from the sides. One of the consequences of this is that the thermal variation of domain wall thickness in an elongated grain is greater (smaller) than predicted by classical theory when the grain is magnetized along the shortest (longest) dimension. For magnetite, classical theory provides a good approximation in predicting both domain wall thickness and number of domains in equal-dimensional grains larger than about 4 μm.

  18. The domain-specific and domain-general relationships of visuospatial working memory to reasoning ability.

    PubMed

    Shipstead, Zach; Yonehiro, Jade

    2016-10-01

    The degree to which visuospatial working memory (VSWM) is separable from working memory in general is an open question. On one hand, the construct is often researched as a unitary, domain-specific system. On the other, there is evidence that VWSM shares a common processing component with verbal memory. One might interpret this shared component as domain-general attention. We used confirmatory factor analysis to demonstrate that VSWM shares a domain-general component with verbal memory tasks and has a domain-specific component that is independent of verbal memory. Furthermore, the domain-general component was found to correlate with reasoning ability in both the visuospatial and verbal domains. The domain-specific component only correlated with reasoning ability when the tests had a strong visuospatial component. We argue that theories of VSWM need to place greater emphasis on its multiply determined nature.

  19. LOVely enzymes – towards engineering light‐controllable biocatalysts

    PubMed Central

    Krauss, Ulrich; Lee, Jeeyeon; Benkovic, Stephen J.; Jaeger, Karl‐Erich

    2010-01-01

    Summary Light control over enzyme function represents a novel and exciting field of biocatalysis research. Blue‐light photoreceptors of the Light, Oxygen, Voltage (LOV) family have recently been investigated for their applicability as photoactive switches. We discuss here the primary photochemical events leading to light activation of LOV domains as well as the proposed signal propagation mechanism to the respective effector domain. Furthermore, we describe the construction of LOV fusions to different effector domains, namely a dihydrofolate reductase from Escherichia coli and a lipase from Bacillus subtilis. Both fusion partners retained functionality, and alteration of enzyme activity by light was also demonstrated. Hence, it appears that fusion of LOV photoreceptors to functional enzyme target sites via appropriate linker structures may represent a straightforward strategy to design light controllable biocatalysts. PMID:21255302

  20. Structural domain walls in polar hexagonal manganites

    NASA Astrophysics Data System (ADS)

    Kumagai, Yu

    2014-03-01

    The domain structure in the multiferroic hexagonal manganites is currently intensely investigated, motivated by the observation of intriguing sixfold topological defects at their meeting points [Choi, T. et al,. Nature Mater. 9, 253 (2010).] and nanoscale electrical conductivity at the domain walls [Wu, W. et al., Phys. Rev. Lett. 108, 077203 (2012).; Meier, D. et al., Nature Mater. 11, 284 (2012).], as well as reports of coupling between ferroelectricity, magnetism and structural antiphase domains [Geng, Y. et al., Nano Lett. 12, 6055 (2012).]. The detailed structure of the domain walls, as well as the origin of such couplings, however, was previously not fully understood. In the present study, we have used first-principles density functional theory to calculate the structure and properties of the low-energy structural domain walls in the hexagonal manganites [Kumagai, Y. and Spaldin, N. A., Nature Commun. 4, 1540 (2013).]. We find that the lowest energy domain walls are atomically sharp, with {210}orientation, explaining the orientation of recently observed stripe domains and suggesting their topological protection [Chae, S. C. et al., Phys. Rev. Lett. 108, 167603 (2012).]. We also explain why ferroelectric domain walls are always simultaneously antiphase walls, propose a mechanism for ferroelectric switching through domain-wall motion, and suggest an atomistic structure for the cores of the sixfold topological defects. This work was supported by ETH Zurich, the European Research Council FP7 Advanced Grants program me (grant number 291151), the JSPS Postdoctoral Fellowships for Research Abroad, and the MEXT Elements Strategy Initiative to Form Core Research Center TIES.

  1. A thermodynamic definition of protein domains

    PubMed Central

    Porter, Lauren L.; Rose, George D.

    2012-01-01

    Protein domains are conspicuous structural units in globular proteins, and their identification has been a topic of intense biochemical interest dating back to the earliest crystal structures. Numerous disparate domain identification algorithms have been proposed, all involving some combination of visual intuition and/or structure-based decomposition. Instead, we present a rigorous, thermodynamically-based approach that redefines domains as cooperative chain segments. In greater detail, most small proteins fold with high cooperativity, meaning that the equilibrium population is dominated by completely folded and completely unfolded molecules, with a negligible subpopulation of partially folded intermediates. Here, we redefine structural domains in thermodynamic terms as cooperative folding units, based on m-values, which measure the cooperativity of a protein or its substructures. In our analysis, a domain is equated to a contiguous segment of the folded protein whose m-value is largely unaffected when that segment is excised from its parent structure. Defined in this way, a domain is a self-contained cooperative unit; i.e., its cooperativity depends primarily upon intrasegment interactions, not intersegment interactions. Implementing this concept computationally, the domains in a large representative set of proteins were identified; all exhibit consistency with experimental findings. Specifically, our domain divisions correspond to the experimentally determined equilibrium folding intermediates in a set of nine proteins. The approach was also proofed against a representative set of 71 additional proteins, again with confirmatory results. Our reframed interpretation of a protein domain transforms an indeterminate structural phenomenon into a quantifiable molecular property grounded in solution thermodynamics. PMID:22635268

  2. A thermodynamic definition of protein domains.

    PubMed

    Porter, Lauren L; Rose, George D

    2012-06-12

    Protein domains are conspicuous structural units in globular proteins, and their identification has been a topic of intense biochemical interest dating back to the earliest crystal structures. Numerous disparate domain identification algorithms have been proposed, all involving some combination of visual intuition and/or structure-based decomposition. Instead, we present a rigorous, thermodynamically-based approach that redefines domains as cooperative chain segments. In greater detail, most small proteins fold with high cooperativity, meaning that the equilibrium population is dominated by completely folded and completely unfolded molecules, with a negligible subpopulation of partially folded intermediates. Here, we redefine structural domains in thermodynamic terms as cooperative folding units, based on m-values, which measure the cooperativity of a protein or its substructures. In our analysis, a domain is equated to a contiguous segment of the folded protein whose m-value is largely unaffected when that segment is excised from its parent structure. Defined in this way, a domain is a self-contained cooperative unit; i.e., its cooperativity depends primarily upon intrasegment interactions, not intersegment interactions. Implementing this concept computationally, the domains in a large representative set of proteins were identified; all exhibit consistency with experimental findings. Specifically, our domain divisions correspond to the experimentally determined equilibrium folding intermediates in a set of nine proteins. The approach was also proofed against a representative set of 71 additional proteins, again with confirmatory results. Our reframed interpretation of a protein domain transforms an indeterminate structural phenomenon into a quantifiable molecular property grounded in solution thermodynamics.

  3. Compositional Dictionaries for Domain Adaptive Face Recognition.

    PubMed

    Qiang Qiu; Chellappa, Rama

    2015-12-01

    We present a dictionary learning approach to compensate for the transformation of faces due to the changes in view point, illumination, resolution, and so on. The key idea of our approach is to force domain-invariant sparse coding, i.e., designing a consistent sparse representation of the same face in different domains. In this way, the classifiers trained on the sparse codes in the source domain consisting of frontal faces can be applied to the target domain (consisting of faces in different poses, illumination conditions, and so on) without much loss in recognition accuracy. The approach is to first learn a domain base dictionary, and then describe each domain shift (identity, pose, and illumination) using a sparse representation over the base dictionary. The dictionary adapted to each domain is expressed as the sparse linear combinations of the base dictionary. In the context of face recognition, with the proposed compositional dictionary approach, a face image can be decomposed into sparse representations for a given subject, pose, and illumination. This approach has three advantages. First, the extracted sparse representation for a subject is consistent across domains, and enables pose and illumination insensitive face recognition. Second, sparse representations for pose and illumination can be subsequently used to estimate the pose and illumination condition of a face image. Last, by composing sparse representations for the subject and the different domains, we can also perform pose alignment and illumination normalization. Extensive experiments using two public face data sets are presented to demonstrate the effectiveness of the proposed approach for face recognition.

  4. Cross domains Arabic named entity recognition system

    NASA Astrophysics Data System (ADS)

    Al-Ahmari, S. Saad; Abdullatif Al-Johar, B.

    2016-07-01

    Named Entity Recognition (NER) plays an important role in many Natural Language Processing (NLP) applications such as; Information Extraction (IE), Question Answering (QA), Text Clustering, Text Summarization and Word Sense Disambiguation. This paper presents the development and implementation of domain independent system to recognize three types of Arabic named entities. The system works based on a set of domain independent grammar-rules along with Arabic part of speech tagger in addition to gazetteers and lists of trigger words. The experimental results shown, that the system performed as good as other systems with better results in some cases of cross-domains corpora.

  5. Domain-decomposed preconditionings for transport operators

    NASA Technical Reports Server (NTRS)

    Chan, Tony F.; Gropp, William D.; Keyes, David E.

    1991-01-01

    The performance was tested of five different interface preconditionings for domain decomposed convection diffusion problems, including a novel one known as the spectral probe, while varying mesh parameters, Reynolds number, ratio of subdomain diffusion coefficients, and domain aspect ratio. The preconditioners are representative of the range of practically computable possibilities that have appeared in the domain decomposition literature for the treatment of nonoverlapping subdomains. It is shown that through a large number of numerical examples that no single preconditioner can be considered uniformly superior or uniformly inferior to the rest, but that knowledge of particulars, including the shape and strength of the convection, is important in selecting among them in a given problem.

  6. Asymmetric counter propagation of domain walls

    NASA Astrophysics Data System (ADS)

    Andrade-Silva, I.; Clerc, M. G.; Odent, V.

    2016-07-01

    Far from equilibrium systems show different states and domain walls between them. These walls, depending on the type of connected equilibria, exhibit a rich spatiotemporal dynamics. Here, we investigate the asymmetrical counter propagation of domain walls in an in-plane-switching cell filled with a nematic liquid crystal. Experimentally, we characterize the shape and speed of the domain walls. Based on the molecular orientation, we infer that the counter propagative walls have different elastic deformations. These deformations are responsible of the asymmetric counter propagating fronts. Theoretically, based on symmetry arguments, we propose a simple bistable model under the influence of a nonlinear gradient, which qualitatively describes the observed dynamics.

  7. Domain decomposition algorithms and computational fluid dynamics

    NASA Technical Reports Server (NTRS)

    Chan, Tony F.

    1988-01-01

    Some of the new domain decomposition algorithms are applied to two model problems in computational fluid dynamics: the two-dimensional convection-diffusion problem and the incompressible driven cavity flow problem. First, a brief introduction to the various approaches of domain decomposition is given, and a survey of domain decomposition preconditioners for the operator on the interface separating the subdomains is then presented. For the convection-diffusion problem, the effect of the convection term and its discretization on the performance of some of the preconditioners is discussed. For the driven cavity problem, the effectiveness of a class of boundary probe preconditioners is examined.

  8. Skyrmions from Instantons inside Domain Walls

    NASA Astrophysics Data System (ADS)

    Eto, Minoru; Nitta, Muneto; Ohashi, Keisuke; Tong, David

    2005-12-01

    Some years ago, Atiyah and Manton described a method to construct approximate Skyrmion solutions from Yang-Mills instantons. Here we present a dynamical realization of this construction using domain walls in a five-dimensional gauge theory. The non-Abelian gauge symmetry is broken in each vacuum but restored in the core of the domain wall, allowing instantons to nestle inside the wall. We show that the world volume dynamics of the wall is given by the Skyrme model, including the four-derivative term, and the instantons appear as domain wall Skyrmions.

  9. Inferring Evolutionary Scenarios for Protein Domain Compositions

    NASA Astrophysics Data System (ADS)

    Wiedenhoeft, John; Krause, Roland; Eulenstein, Oliver

    Essential cellular processes are controlled by functional interactions of protein domains, which can be inferred from their evolutionary histories. Methods to reconstruct these histories are challenged by the complexity of reconstructing macroevolutionary events. In this work we model these events using a novel network-like structure that represents the evolution of domain combinations, called plexus. We describe an algorithm to find a plexus that represents the evolution of a given collection of domain histories as phylogenetic trees with the minimum number of macroevolutionary events, and demonstrate its effectiveness in practice.

  10. Domain landscapes of somatic mutations in cancer

    PubMed Central

    2012-01-01

    Background Large-scale tumor sequencing projects are now underway to identify genetic mutations that drive tumor initiation and development. Most studies take a gene-based approach to identifying driver mutations, highlighting genes mutated in a large percentage of tumor samples as those likely to contain driver mutations. However, this gene-based approach usually does not consider the position of the mutation within the gene or the functional context the position of the mutation provides. Here we introduce a novel method for mapping mutations to distinct protein domains, not just individual genes, in which they occur, thus providing the functional context for how the mutation contributes to disease. Furthermore, aggregating mutations from all genes containing a specific protein domain enables the identification of mutations that are rare at the gene level, but that occur frequently within the specified domain. These highly mutated domains potentially reveal disruptions of protein function necessary for cancer development. Results We mapped somatic mutations from the protein coding regions of 100 colon adenocarcinoma tumor samples to the genes and protein domains in which they occurred, and constructed topographical maps to depict the “mutational landscapes” of gene and domain mutation frequencies. We found significant mutation frequency in a number of genes previously known to be somatically mutated in colon cancer patients including APC, TP53 and KRAS. In addition, we found significant mutation frequency within specific domains located in these genes, as well as within other domains contained in genes having low mutation frequencies. These domain “peaks” were enriched with functions important to cancer development including kinase activity, DNA binding and repair, and signal transduction. Conclusions Using our method to create the domain landscapes of mutations in colon cancer, we were able to identify somatic mutations with high potential to drive cancer

  11. An introduction to recognizing functional domains.

    PubMed

    Stormo, Gary D

    2006-10-01

    This unit provides an overview of issues involved in domain recognition in protein and DNA sequences. It opens with a discussion of the two primary methods of domain representation, namely consensus sequences and alignment matrices (e.g., the log-odds matrix). The unit continues with a brief overview of some of the resources available for identifying functional domains in nucleotide sequences (e.g., TRANSFAC). In addition, it reviews databases such as Pfam, InterPro and Blocks, which are available for protein analysis.

  12. Domain decomposition algorithms and computational fluid dynamics

    NASA Technical Reports Server (NTRS)

    Chan, Tony F.

    1988-01-01

    Some of the new domain decomposition algorithms are applied to two model problems in computational fluid dynamics: the two-dimensional convection-diffusion problem and the incompressible driven cavity flow problem. First, a brief introduction to the various approaches of domain decomposition is given, and a survey of domain decomposition preconditioners for the operator on the interface separating the subdomains is then presented. For the convection-diffusion problem, the effect of the convection term and its discretization on the performance of some of the preconditioners is discussed. For the driven cavity problem, the effectiveness of a class of boundary probe preconditioners is examined.

  13. Time-domain flicker measurement technique

    NASA Astrophysics Data System (ADS)

    Miseli, Joseph

    1999-04-01

    The visibility of flicker on a display depends upon many factors, including the observer's sensitivity to flicker. Whenever flicker is observed, it is probably undesirable and often unacceptable. Much has been written about flicker, its perception, and its variability. Methods have been presented to the industry that use frequency domain analysis of measured flicker response. Here we prose an alternate method to quantify flicker in the time domain, just as people see it, and we will try to understand how the measurements relate to what people see. Both the frequency domain and time domain flicker measurements can be found in the Video Electronics Standards Association Flat Panel Display Measurements Standard. An attempt is made to compare the two methods and show how the simpler measurement can be employed for many display technologies.

  14. Dynamical depinning of chiral domain walls

    NASA Astrophysics Data System (ADS)

    Moretti, Simone; Voto, Michele; Martinez, Eduardo

    2017-08-01

    The domain wall depinning field represents the minimum magnetic field needed to move a domain wall, typically pinned by samples' disorder or patterned constrictions. Conventionally, such a field is considered independent on the Gilbert damping since it is assumed to be the field at which the Zeeman energy equals the pinning energy barrier (both damping independent). Here we analyze numerically the domain wall depinning field as a function of the Gilbert damping in a system with perpendicular magnetic anisotropy and Dzyaloshinskii-Moriya interaction. Contrary to expectations, we find that the depinning field depends on the Gilbert damping and that it strongly decreases for small damping parameters. We explain this dependence with a simple one-dimensional model and we show that the reduction of the depinning field is related to the finite size of the pinning barriers and to the domain wall internal dynamics, connected to the Dzyaloshinskii-Moriya interaction and the shape anisotropy.

  15. Visualizing ferromagnetic domains in magnetic topological insulators

    DOE PAGES

    Wang, Wenbo; Gu, G. D.; Yang, Fang; ...

    2015-05-13

    We report a systematic study of ferromagnetic domains in both single-crystal and thin-film specimens of magnetic topological insulators Cr doped (Bi0.1Sb0.9)2Te3 using magnetic force microscopy (MFM). The temperature and field dependences of MFM and in situ resistance data are consistent with previous bulk transport and magnetic characterization. Bubble-like ferromagnetic domains were observed in both single crystals and thin films. Significantly, smaller domain size (~500 nm) with narrower domain wall (~150 – 300 nm) was observed in thin films of magnetic topological insulators, likely due to vertical confinement effect. As a result, these results suggest that thin films are more promisingmore » for visualization of chiral edge states.« less

  16. Resistance domain in type II superconductors

    SciTech Connect

    Gurevich, A.V.; Mints, R.G.

    1980-01-05

    We show that traveling domains with a finite resistance can exist in type II superconductors in the presence of a transport current. An experiment in which this effect generates an alternating electric field and current is proposed.

  17. Domain wall magneto-Seebeck effect

    NASA Astrophysics Data System (ADS)

    Krzysteczko, Patryk; Hu, Xiukun; Liebing, Niklas; Sievers, Sibylle; Schumacher, Hans W.

    2015-10-01

    The interplay between charge, spin, and heat currents in magnetic nanostructures subjected to a temperature gradient has led to a variety of novel effects and promising applications studied in the fast-growing field of spin caloritronics. Here, we explore the magnetothermoelectrical properties of an individual magnetic domain wall in a permalloy nanowire. In thermal gradients of the order of few K /μ m along the long wire axis, we find a clear magneto-Seebeck signature due to the presence of a single domain wall. The observed domain wall magneto-Seebeck effect can be explained by the magnetization-dependent Seebeck coefficient of permalloy in combination with the local spin configuration of the domain wall.

  18. FHA domains: Phosphopeptide binding and beyond.

    PubMed

    Almawi, Ahmad W; Matthews, Lindsay A; Guarné, Alba

    2016-12-08

    Forkhead-associated (FHA) domains are small phosphopeptide recognition modules found in eubacterial and eukaryotic, but not archeal, genomes. Although they were originally found in forkhead-type transcription factors, they have now been identified in many other signaling proteins. FHA domains share a remarkably conserved fold despite very low sequence conservation. They only have five conserved amino acids that are important for binding to phosphorylated epitopes. Recent work from several laboratories has demonstrated that FHA domains can mediate many interactions that do not depend on their ability to recognize a phosphorylated threonine. In this review, we present structural and biochemical work that has unveiled novel interaction interfaces on FHA domains. We discuss how these non-canonical interactions modulate the recognition of phosphorylated and non-phosphorylated substrates, as well as protein oligomerization - events that collectively determine FHA function.

  19. Magnified time-domain ghost imaging

    NASA Astrophysics Data System (ADS)

    Ryczkowski, Piotr; Barbier, Margaux; Friberg, Ari T.; Dudley, John M.; Genty, Goëry

    2017-04-01

    Ghost imaging allows the imaging of an object without directly seeing this object. Originally demonstrated in the spatial domain, it was recently shown that ghost imaging can be transposed into the time domain to detect ultrafast signals, even in the presence of distortion. We propose and experimentally demonstrate a temporal ghost imaging scheme which generates a 5× magnified ghost image of an ultrafast waveform. Inspired by shadow imaging in the spatial domain and building on the dispersive Fourier transform of an incoherent supercontinuum in an optical fiber, the approach overcomes the resolution limit of standard time-domain ghost imaging generally imposed by the detectors speed. The method can be scaled up to higher magnification factors using longer fiber lengths and light source with shorter duration.

  20. Investigations on polarimetric terahertz frequency domain spectroscopy

    NASA Astrophysics Data System (ADS)

    Gong, Yandong; Zhang, Banghong; Notake, Takashi; Minamide, Hiroaki; Olivo, Malini; Sugii, Shigeki

    2014-04-01

    A polarimetric Terahertz frequency-domain spectroscopy system is presented which has an additional polarization measurement function at the Terahertz band. The achromatic Terahertz waveplate, which acts as the key device in the system, is also presented.

  1. Substructure coupling in the frequency domain

    NASA Technical Reports Server (NTRS)

    1985-01-01

    Frequency domain analysis was found to be a suitable method for determining the transient response of systems subjected to a wide variety of loads. However, since a large number of calculations are performed within the discrete frequency loop, the method loses it computational efficiency if the loads must be represented by a large number of discrete frequencies. It was also discovered that substructure coupling in the frequency domain work particularly well for analyzing structural system with a small number of interface and loaded degrees of freedom. It was discovered that substructure coupling in the frequency domain can lead to an efficient method of obtaining natural frequencies of undamped structures. It was also found that the damped natural frequencies of a system may be determined using frequency domain techniques.

  2. Epistemic Analysis of Interrogative Domains using Cuboids

    NASA Astrophysics Data System (ADS)

    Hughes, Cameron; Hughes, Tracey

    We are interested in analyzing the propositional knowledge extracted by an epistemic agent from interrogative domains. The interrogative domains that have our current focus are taken from transcripts of legal trials, congressional hearings, or law enforcement interrogations. These transcripts have be encoded in XML or HTML formats. The agent uses these transcripts as a primary knowledge source. The complexity, size, scope and potentially conflicting nature of transcripts from interrogative domains bring into question the quality of propositional knowledge that can be garnered by the agent. Epistemic Cuboids or Cubes are used as a knowledge analysis technique that helps determine the quality and quantity of the propositional knowledge extracted by an epistemic agent from an interrogative domain. In this paper we explore how 'Epistemic Cubes' can be used to evaluate the nature of the agent's propositional knowledge.

  3. De novo design of synthetic prion domains.

    PubMed

    Toombs, James A; Petri, Michelina; Paul, Kacy R; Kan, Grace Y; Ben-Hur, Asa; Ross, Eric D

    2012-04-24

    Prions are important disease agents and epigenetic regulatory elements. Prion formation involves the structural conversion of proteins from a soluble form into an insoluble amyloid form. In many cases, this structural conversion is driven by a glutamine/asparagine (Q/N)-rich prion-forming domain. However, our understanding of the sequence requirements for prion formation and propagation by Q/N-rich domains has been insufficient for accurate prion propensity prediction or prion domain design. By focusing exclusively on amino acid composition, we have developed a prion aggregation prediction algorithm (PAPA), specifically designed to predict prion propensity of Q/N-rich proteins. Here, we show not only that this algorithm is far more effective than traditional amyloid prediction algorithms at predicting prion propensity of Q/N-rich proteins, but remarkably, also that PAPA is capable of rationally designing protein domains that function as prions in vivo.

  4. Electric fingerprint of voltage sensor domains.

    PubMed

    Souza, Caio S; Amaral, Cristiano; Treptow, Werner

    2014-12-09

    A dynamic transmembrane voltage field has been suggested as an intrinsic element in voltage sensor (VS) domains. Here, the dynamic field contribution to the VS energetics was analyzed via electrostatic calculations applied to a number of atomistic structures made available recently. We find that the field is largely static along with the molecular motions of the domain, and more importantly, it is minimally modified across VS variants. This finding implies that sensor domains transfer approximately the same amount of gating charges when moving the electrically charged S4 helix between fixed microscopic configurations. Remarkably, the result means that the observed operational diversity of the domain, including the extension, rate, and voltage dependence of the S4 motion, as dictated by the free energy landscape theory, must be rationalized in terms of dominant variations of its chemical free energy.

  5. Supporting multiple domains in a single reuse repository

    NASA Technical Reports Server (NTRS)

    Eichmann, David A.

    1992-01-01

    Domain analysis typically results in the construction of a domain-specific repository. Such a repository imposes artificial boundaries on the sharing of similar assets between related domains. A lattice-based approach to repository modeling can preserve a reuser's domain specific view of the repository, while avoiding replication of commonly used assets and supporting a more general perspective on domain interrelationships.

  6. Separating Cognitive and Content Domains in Mathematical Competence

    ERIC Educational Resources Information Center

    Harks, Birgit; Klieme, Eckhard; Hartig, Johannes; Leiss, Dominik

    2014-01-01

    The present study investigates the empirical separability of mathematical (a) content domains, (b) cognitive domains, and (c) content-specific cognitive domains. There were 122 items representing two content domains (linear equations vs. theorem of Pythagoras) combined with two cognitive domains (modeling competence vs. technical competence)…

  7. Supporting multiple domains in a single reuse repository

    NASA Technical Reports Server (NTRS)

    Eichmann, David

    1992-01-01

    Domain analysis typically results in the construction of a domain-specific repository. Such a repository imposes artificial boundaries on the sharing of similar assets between related domains. A lattice-based approach to repository modeling can preserve a reuser's domain specific view of the repository, while avoiding replication of commonly used assets and supporting a more general perspective on domain interrelationships.

  8. Between-domain relations of students' academic emotions and their judgments of school domain similarity

    PubMed Central

    Goetz, Thomas; Haag, Ludwig; Lipnevich, Anastasiya A.; Keller, Melanie M.; Frenzel, Anne C.; Collier, Antonie P. M.

    2014-01-01

    With the aim to deepen our understanding of the between-domain relations of academic emotions, a series of three studies was conducted. We theorized that between-domain relations of trait (i.e., habitual) emotions reflected students' judgments of domain similarities, whereas between-domain relations of state (i.e., momentary) emotions did not. This supposition was based on the accessibility model of emotional self-report, according to which individuals' beliefs tend to strongly impact trait, but not state emotions. The aim of Study 1 (interviews; N = 40; 8th and 11th graders) was to gather salient characteristics of academic domains from students' perspective. In Study 2 (N = 1709; 8th and 11th graders) the 13 characteristics identified in Study 1 were assessed along with academic emotions in four different domains (mathematics, physics, German, and English) using a questionnaire-based trait assessment. With respect to the same domains, state emotions were assessed in Study 3 (N = 121; 8th and 11th graders) by employing an experience sampling approach. In line with our initial assumptions, between-domain relations of trait but not state academic emotions reflected between-domain relations of domain characteristics. Implications for research and practice are discussed. PMID:25374547

  9. The BAH domain of Rsc2 is a histone H3 binding domain

    PubMed Central

    Chambers, Anna L.; Pearl, Laurence H.; Oliver, Antony W.; Downs, Jessica A.

    2013-01-01

    Bromo-adjacent homology (BAH) domains are commonly found in chromatin-associated proteins and fall into two classes; Remodels the Structure of Chromatin (RSC)-like or Sir3-like. Although Sir3-like BAH domains bind nucleosomes, the binding partners of RSC-like BAH domains are currently unknown. The Rsc2 subunit of the RSC chromatin remodeling complex contains an RSC-like BAH domain and, like the Sir3-like BAH domains, we find Rsc2 BAH also interacts with nucleosomes. However, unlike Sir3-like BAH domains, we find that Rsc2 BAH can bind to recombinant purified H3 in vitro, suggesting that the mechanism of nucleosome binding is not conserved. To gain insight into the Rsc2 BAH domain, we determined its crystal structure at 2.4 Å resolution. We find that it differs substantially from Sir3-like BAH domains and lacks the motifs in these domains known to be critical for making contacts with histones. We then go on to identify a novel motif in Rsc2 BAH that is critical for efficient H3 binding in vitro and show that mutation of this motif results in defective Rsc2 function in vivo. Moreover, we find this interaction is conserved across Rsc2-related proteins. These data uncover a binding target of the Rsc2 family of BAH domains and identify a novel motif that mediates this interaction. PMID:23907388

  10. Time-Domain vs. Frequency-Domain CSEM: Implications for Marine Exploration

    NASA Astrophysics Data System (ADS)

    Connell, D. M.; Key, K. W.

    2010-12-01

    The frequency-domain marine controlled source electromagnetic (CSEM) method is now routinely applied to map resistive hydrocarbons buried beneath the seabed in deepwater. Alternatively, it has been suggested that time-domain CSEM methods may offer improved resolution of difficult targets such as deeply buried reservoirs. Furthermore, time-domain methods may overcome a sensitivity limitation imposed by the airwave saturation that is experienced for shallow-water frequency-domain CSEM. In order to examine and test these claims, we have developed a modeling code for computing time-domain responses for layered 1D models with arbitrarily located and oriented transmitters and receivers. Our code extends the open-source frequency domain code Dipole1D by efficiently computing the time-domain step-on and impulse responses by Fourier transformation of the frequency-domain kernels. By applying a realistic noise model to synthetic data generated from this code, we systematically examine the sensitivity and resolution of time-domain and frequency-domain CSEM to representative targets of interest for offshore hydrocarbon exploration and exploration surveys of seafloor volcanic and hydrothermal systems. These studies have practical implications for marine EM survey systems that use either towed or stationary transmitters and receivers.

  11. Forum domain in Drosophila melanogaster cut locus possesses looped domains inside.

    PubMed

    Tchurikov, N A; Krasnov, A N; Ponomarenko, N A; Golova, Y B; Chernov, B K

    1998-07-01

    We have studied the relationship between chromosomal forum domains and looped domains in the cut locus of Drosophila melanogaster . Forum domains were earlier detected by separation in pulsed-field gels of 50-150 kb chromosomal DNA fragments obtained after spontaneous non-random degradation of chromosomes. We have localized the boundary region where cleavage sites are scattered between two forum domains in the regulatory region of the cut locus. We have sequenced a 13 kb region spanning few kilobases from distal domain, the boundary region and part of the proximal forum domain where several scaffold associated regions (SARs) were observed. We conclude that forum domains and looped domains are physically different types of domains and belong to different levels of organization in eukaryotic chromosomes. The boundary region between the neighboring forum domains in the cut locus possesses the Doc element insertion and a micro-satellite stretch and thus might remind a small island of heterochromatin and correspond to so-called intercalary heterochromatin that is known to be located in the 7B1-2 band where the major part of the cut locus is reside.

  12. VISAR Analysis in the Frequency Domain

    DOE PAGES

    Dolan, D. H.; Specht, P.

    2017-05-18

    VISAR measurements are typically analyzed in the time domain, where velocity is approximately proportional to fringe shift. Moving to the frequency domain clarifies the limitations of this approximation and suggests several improvements. For example, optical dispersion preserves high-frequency information, so a zero-dispersion (air delay) interferometer does not provide optimal time resolution. Combined VISAR measurements can also improve time resolution. With adequate bandwidth and reasonable noise levels, it is quite possible to achieve better resolution than the VISAR approximation allows.

  13. Moving Towards Domain Wall Devices in Ferroics

    NASA Astrophysics Data System (ADS)

    Gregg, Marty

    Domain walls in ferroelectric, ferroelastic and multiferroic oxides are distinct functional materials in their own right. They can be conducting, or even superconducting, when surrounding domains are insulating; they can demonstrate magnetism when the surrounding bulk is non-magnetic and they can contain ordered electrical dipoles when the matrix containing them is non-polar. Since domain walls can also be created, destroyed, and controllably moved from place to place, there is an amazing opportunity for us to design new forms of devices in which functionality is actively and dynamically deployed (now you see it; now you don't). This is the essence of the emerging field known as ``domain wall nanoelectronics''. In time, this arena of research could change the way we think of nanoscale functional devices, moving increasingly towards agile circuitry and neuromorphic device architectures. While the control of domain wall injection, movement and annihilation has been developed rather well in the nanomagnetics community (in race-track and domain wall logic research), similar research has not been widely performed in nanoscale ferroelectrics, ferroelastics and multiferroics. This talk will discuss progress that has been made to date and the way in which nanomagnetics research can be used as a source of inspiration. Site-specific domain wall injection and motion control in both proper and improper ferroelectrics using inhomogeneous electric and elastic fields, as well as dielectric patterning in uniaxial ferroelectrics, will be specifically considered. As will be shown, sufficient control has been developed to allow the creation of a diode for domain wall motion in ferroelectrics, for example. The author acknowledges support from the Engineering and Physical Sciences Research Council (EPSRC).

  14. Frequency domain fluorometry: theory and application.

    PubMed

    Vetromile, Carissa M; Jameson, David M

    2014-01-01

    Frequency domain fluorometry is a widely utilized tool in the physical, chemical, and biological sciences. This chapter focuses on the theory of the method and the practical aspects required to carry out intensity decay, i.e., lifetime measurements on a modern frequency domain fluorometer. Several chemical/biological systems are utilized to illustrate data acquisition protocols. Data analysis procedures and methodologies are also discussed.

  15. Multi-domain training enhances attentional control.

    PubMed

    Binder, Julia C; Martin, Mike; Zöllig, Jacqueline; Röcke, Christina; Mérillat, Susan; Eschen, Anne; Jäncke, Lutz; Shing, Yee Lee

    2016-06-01

    Multi-domain training potentially increases the likelihood of overlap in processing components with transfer tasks and everyday life, and hence is a promising training approach for older adults. To empirically test this, 84 healthy older adults aged 64 to 75 years were randomly assigned to one of three single-domain training conditions (inhibition, visuomotor function, spatial navigation) or to the simultaneous training of all three cognitive functions (multi-domain training condition). All participants trained on an iPad at home for 50 training sessions. Before and after the training, and at a 6-month follow-up measurement, cognitive functioning and training transfer were assessed with a neuropsychological test battery including tests targeting the trained functions (near transfer) and transfer to executive functions (far transfer: attentional control, working memory, speed). Participants in all four training groups showed a linear increase in training performance over the 50 training sessions. Using a latent difference score model, the multi-domain training group, compared with the single-domain training groups, showed more improvement on the far transfer attentional control composite. Individuals with initially lower baseline performance showed higher training-related improvements, indicating that training compensated for lower initial cognitive performance. At the 6-month follow-up, performance on the cognitive test battery remained stable. This is one of the first studies to investigate systematically multi-domain training including comparable single-domain training conditions. Our findings suggest that multi-domain training enhances attentional control involved in handling several different tasks at the same time, an aspect in everyday life that is particularly challenging for older people. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

  16. Impact of Domain Analysis on Reuse Methods

    DTIC Science & Technology

    1989-11-06

    reusable. The resultant model is called a system archetype . The archetype is then adapted to build a new system according to the needs of each...Domain modelhig, archetypes , DARTS software generation system. o GTE Laboratories - Domain analysis process, component classification, tools for...called an archetype . Altematively, if a working system already exists in this problem class, then this system can be modified to be an archetype . Once

  17. Work Domain Analysis: Theoretical Concepts and Methodology

    DTIC Science & Technology

    2005-02-01

    method to elicit expert knowledge: A case study in the methodology of cognitive task analysis. Human Factors, 40, 254-276. Itoh, J., Sakuma, A...Work Domain Analysis: Theoretical Concepts and Methodology Neelam Naikar, Robyn Hopcroft, and Anna Moylan Air Operations...theoretical and methodological approach for work domain analysis (WDA), the first phase of cognitive work analysis. The report: (1) addresses a number of

  18. A time domain technique for mechanism extraction

    NASA Technical Reports Server (NTRS)

    Dominek, Allen K.; Peters, Leon, Jr.; Burnside, Walter D.

    1987-01-01

    The properties of scattered fields from a structure can be better evaluated from the characteristics of the individual scatterers. Decomposition techniques can be classified either as a matrix or an integral formulation. With either formulation, aspect pattern of frequency information of a scattering center can be obtained. Emphasis is placed on an integral (time domain) isolation extraction technique to obtain the frequency characteristics of scattering mechanisms. This technique has its origins in the time domain interpretation of scattered fields.

  19. Planning with Continuous Resources in Stochastic Domains

    NASA Technical Reports Server (NTRS)

    Mausam, Mausau; Benazera, Emmanuel; Brafman, Roneu; Hansen, Eric

    2005-01-01

    We consider the problem of optimal planning in stochastic domains with metric resource constraints. Our goal is to generate a policy whose expected sum of rewards is maximized for a given initial state. We consider a general formulation motivated by our application domain--planetary exploration--in which the choice of an action at each step may depend on the current resource levels. We adapt the forward search algorithm AO* to handle our continuous state space efficiently.

  20. Time domain wave separation using multiple microphones.

    PubMed

    Kemp, Jonathan A; van Walstijn, Maarten; Campbell, D Murray; Chick, John P; Smith, Richard A

    2010-07-01

    Methods of measuring the acoustic behavior of tubular systems can be broadly characterized as steady state measurements, where the measured signals are analyzed in terms of infinite duration sinusoids, and reflectometry measurements which exploit causality to separate the forward and backward going waves in a duct. This paper sets out a multiple microphone reflectometry technique which performs wave separation by using time domain convolution to track the forward and backward going waves in a cylindrical source tube. The current work uses two calibration runs (one for forward going waves and one for backward going waves) to measure the time domain transfer functions for each pair of microphones. These time domain transfer functions encode the time delay, frequency dependent losses and microphone gain ratios for travel between microphones. This approach is applied to the measurement of wave separation, bore profile and input impedance. The work differs from existing frequency domain methods in that it combines the information of multiple microphones within a time domain algorithm, and differs from existing time domain methods in its inclusion of the effect of losses and gain ratios in intermicrophone transfer functions.

  1. Joining RDC data from flexible protein domains

    NASA Astrophysics Data System (ADS)

    Sgheri, Luca

    2010-11-01

    We study the inverse problem of determining the conformational freedom of two protein domains from residual dipolar coupling (RDC) measurements. For each paramagnetic ion attached to one of the domains we obtain a magnetic susceptibility tensor χ from the RDC of couples of atoms of that domain, and a mean paramagnetic susceptibility tensor {\\bar{\\chi }} from the RDC of couples of atoms of the other domain. The latter is an integral average of rotations of χ which depends on the conformational freedom of the two domains. In this paper we consider the case when we have data from paramagnetic ions attached separately to each of the domains. We prove that in this case not all the elements of χ and {\\bar{\\chi }} are independent. We derive the mathematical equations for the compatibility of the measurements and show how these relations can be used in the presence of noisy data to determine a compatible set of χ and {\\bar{\\chi }} with an unconstrained minimization. If available, information about the shape of the noise can be included in the target function. We show that in this case the compatible set obtained has a reduced error with respect to the noisy data.

  2. Functional domains of the poliovirus receptor

    SciTech Connect

    Koike, Satoshi; Ise, Iku; Nomoto, Akio )

    1991-05-15

    A number of mutant cDNAs of the human poliovirus receptor were constructed to identify essential regions of the molecule as the receptor. All mutant cDNAs carrying the sequence coding for the entire N-terminal immunoglobulin-like domain (domain I) confer permissiveness for poliovirus to mouse L cells, but a mutant cDNA lacking the sequence for domain I does not. The transformants permissive for poliovirus were able to bind the virus and were also recognized by monoclonal antibody D171, which competes with poliovirus for the cellular receptor. These results strongly suggest that the poliovirus binding site resides in domain I of the receptor. Mutant cDNAs for the sequence encoding the intracellular peptide were also constructed and expressed in mouse L cells. Susceptibility of these cells to poliovirus revealed that the entire putative cytoplasmic domain is not essential for virus infection. Thus, the cytoplasmic domain of the molecule appears not to play a role in the penetration of poliovirus.

  3. Robust ferromagnetism carried by antiferromagnetic domain walls

    NASA Astrophysics Data System (ADS)

    Hirose, Hishiro T.; Yamaura, Jun-Ichi; Hiroi, Zenji

    2017-02-01

    Ferroic materials, such as ferromagnetic or ferroelectric materials, have been utilized as recording media for memory devices. A recent trend for downsizing, however, requires an alternative, because ferroic orders tend to become unstable for miniaturization. The domain wall nanoelectronics is a new developing direction for next-generation devices, in which atomic domain walls, rather than conventional, large domains themselves, are the active elements. Here we show that atomically thin magnetic domain walls generated in the antiferromagnetic insulator Cd2Os2O7 carry unusual ferromagnetic moments perpendicular to the wall as well as electron conductivity: the ferromagnetic moments are easily polarized even by a tiny field of 1 mT at high temperature, while, once cooled down, they are surprisingly robust even in an inverse magnetic field of 7 T. Thus, the magnetic domain walls could serve as a new-type of microscopic, switchable and electrically readable magnetic medium which is potentially important for future applications in the domain wall nanoelectronics.

  4. Robust ferromagnetism carried by antiferromagnetic domain walls

    PubMed Central

    Hirose, Hishiro T.; Yamaura, Jun-ichi; Hiroi, Zenji

    2017-01-01

    Ferroic materials, such as ferromagnetic or ferroelectric materials, have been utilized as recording media for memory devices. A recent trend for downsizing, however, requires an alternative, because ferroic orders tend to become unstable for miniaturization. The domain wall nanoelectronics is a new developing direction for next-generation devices, in which atomic domain walls, rather than conventional, large domains themselves, are the active elements. Here we show that atomically thin magnetic domain walls generated in the antiferromagnetic insulator Cd2Os2O7 carry unusual ferromagnetic moments perpendicular to the wall as well as electron conductivity: the ferromagnetic moments are easily polarized even by a tiny field of 1 mT at high temperature, while, once cooled down, they are surprisingly robust even in an inverse magnetic field of 7 T. Thus, the magnetic domain walls could serve as a new-type of microscopic, switchable and electrically readable magnetic medium which is potentially important for future applications in the domain wall nanoelectronics. PMID:28195565

  5. Stable charged antiparallel domain walls in hyperferroelectrics

    NASA Astrophysics Data System (ADS)

    Liu, S.; Cohen, R. E.

    2017-06-01

    Charge-neutral 180° domain walls that separate domains of antiparallel polarization directions are common structural topological defects in ferroelectrics. In normal ferroelectrics, charged 180° domain walls running perpendicular to the polarization directions are highly energetically unfavorable because of the depolarization field and are difficult to stabilize. We explore both neutral and charged 180° domain walls in hyperferroelectrics, a class of proper ferroelectrics with persistent polarization in the presence of a depolarization field, using density functional theory. We obtain zero temperature equilibrium structures of head-to-head and tail-to-tail walls in recently discovered ABC-type hexagonal hyperferroelectrics. Charged domain walls can also be stabilized in canonical ferroelectrics represented by LiNbO3 without any dopants, defects or mechanical clamping. First-principles electronic structure calculations show that charged domain walls can reduce and even close the band gap of host materials and support quasi-two-dimensional electron(hole) gas with enhanced electrical conductivity.

  6. Constant domain-regulated antibody catalysis.

    PubMed

    Sapparapu, Gopal; Planque, Stephanie; Mitsuda, Yukie; McLean, Gary; Nishiyama, Yasuhiro; Paul, Sudhir

    2012-10-19

    Some antibodies contain variable (V) domain catalytic sites. We report the superior amide and peptide bond-hydrolyzing activity of the same heavy and light chain V domains expressed in the IgM constant domain scaffold compared with the IgG scaffold. The superior catalytic activity of recombinant IgM was evident using two substrates, a small model peptide that is hydrolyzed without involvement of high affinity epitope binding, and HIV gp120, which is recognized specifically by noncovalent means prior to the hydrolytic reaction. The catalytic activity was inhibited by an electrophilic phosphonate diester, consistent with a nucleophilic catalytic mechanism. All 13 monoclonal IgMs tested displayed robust hydrolytic activities varying over a 91-fold range, consistent with expression of the catalytic functions at distinct levels by different V domains. The catalytic activity of polyclonal IgM was superior to polyclonal IgG from the same sera, indicating that on average IgMs express the catalytic function at levels greater than IgGs. The findings indicate a favorable effect of the remote IgM constant domain scaffold on the integrity of the V-domain catalytic site and provide a structural basis for conceiving antibody catalysis as a first line immune function expressed at high levels prior to development of mature IgG class antibodies.

  7. Incubational domain characterization in lightly doped ceria

    SciTech Connect

    Li Zhipeng; Mori, Toshiyuki; John Auchterlonie, Graeme; Zou Jin; Drennan, John

    2012-08-15

    Microstructures of both Gd- and Y-doped ceria with different doping level (i.e., 10 at% and 25 at%) have been comprehensively characterized by means of high resolution transmission electron microscopy and selected area electron diffraction. Coherent nano-sized domains can be widely observed in heavily doped ceria. Nevertheless, it was found that a large amount of dislocations actually exist in lightly doped ceria instead of heavily doped ones. Furthermore, incubational domains can be detected in lightly doped ceria, with dislocations located at the interfaces. The interactions between such linear dislocations and dopant defects have been simulated accordingly. As a consequence, the formation mechanism of incubational domains is rationalized in terms of the interaction between intrinsic dislocations of doped ceria and dopant defects. This study offers the insights into the initial state and related mechanism of the formation of nano-sized domains, which have been widely observed in heavily rare-earth-doped ceria in recent years. - Graphical abstract: Interactions between dislocations and dopants lead to incubational domain formation in lightly doped ceria. Highlights: Black-Right-Pointing-Pointer Microstructures were characterized in both heavily and light Gd-/Y-doped ceria. Black-Right-Pointing-Pointer Dislocations are existed in lightly doped ceria rather than heavily doped one. Black-Right-Pointing-Pointer Interactions between dislocations and dopant defects were simulated. Black-Right-Pointing-Pointer Formation of dislocation associated incubational domain is rationalized.

  8. Robust ferromagnetism carried by antiferromagnetic domain walls.

    PubMed

    Hirose, Hishiro T; Yamaura, Jun-Ichi; Hiroi, Zenji

    2017-02-14

    Ferroic materials, such as ferromagnetic or ferroelectric materials, have been utilized as recording media for memory devices. A recent trend for downsizing, however, requires an alternative, because ferroic orders tend to become unstable for miniaturization. The domain wall nanoelectronics is a new developing direction for next-generation devices, in which atomic domain walls, rather than conventional, large domains themselves, are the active elements. Here we show that atomically thin magnetic domain walls generated in the antiferromagnetic insulator Cd2Os2O7 carry unusual ferromagnetic moments perpendicular to the wall as well as electron conductivity: the ferromagnetic moments are easily polarized even by a tiny field of 1 mT at high temperature, while, once cooled down, they are surprisingly robust even in an inverse magnetic field of 7 T. Thus, the magnetic domain walls could serve as a new-type of microscopic, switchable and electrically readable magnetic medium which is potentially important for future applications in the domain wall nanoelectronics.

  9. Mechanical Properties of Nanoscopic Lipid Domains

    SciTech Connect

    Nickels, Jonathan D.; Cheng, Xiaolin; Mostofian, Barmak; Stanley, Christopher; Lindner, Benjamin; Heberle, Frederick A.; Perticaroli, Stefania; Feygenson, Mikhail; Egami, Takeshi; Standaert, Robert F.; Smith, Jeremy C.; Myles, Dean A. A.; Ohl, Michael; Katsaras, John

    2015-09-28

    We found that the lipid raft hypothesis presents insight into how the cell membrane organizes proteins and lipids to accomplish its many vital functions. Yet basic questions remain about the physical mechanisms that lead to the formation, stability, and size of lipid rafts. Thus, much interest has been generated in the study of systems that contain similar lateral heterogeneities, or domains. In the current work we present an experimental approach that is capable of isolating the bending moduli of lipid domains. This is accomplished using neutron scattering and its unique sensitivity to the isotopes of hydrogen. Combining contrast matching approaches with inelastic neutron scattering, we isolate the bending modulus of ~13 nm diameter domains residing in 60 nm unilamellar vesicles, whose lipid composition mimics the mammalian plasma membrane outer leaflet. Importantly, the bending modulus of the nanoscopic domains differs from the modulus of the continuous phase surrounding them. Moreover, from additional structural measurements and all-atom simulations, we also determine that nanoscopic domains are in-register across the bilayer leaflets. Taken together, these results inform a number of theoretical models of domain/raft formation and highlight the fact that mismatches in bending modulus must be accounted for when explaining the emergence of lateral heterogeneities in lipid systems and biological membranes.

  10. Mechanical Properties of Nanoscopic Lipid Domains

    DOE PAGES

    Nickels, Jonathan D.; Cheng, Xiaolin; Mostofian, Barmak; ...

    2015-09-28

    We found that the lipid raft hypothesis presents insight into how the cell membrane organizes proteins and lipids to accomplish its many vital functions. Yet basic questions remain about the physical mechanisms that lead to the formation, stability, and size of lipid rafts. Thus, much interest has been generated in the study of systems that contain similar lateral heterogeneities, or domains. In the current work we present an experimental approach that is capable of isolating the bending moduli of lipid domains. This is accomplished using neutron scattering and its unique sensitivity to the isotopes of hydrogen. Combining contrast matching approachesmore » with inelastic neutron scattering, we isolate the bending modulus of ~13 nm diameter domains residing in 60 nm unilamellar vesicles, whose lipid composition mimics the mammalian plasma membrane outer leaflet. Importantly, the bending modulus of the nanoscopic domains differs from the modulus of the continuous phase surrounding them. Moreover, from additional structural measurements and all-atom simulations, we also determine that nanoscopic domains are in-register across the bilayer leaflets. Taken together, these results inform a number of theoretical models of domain/raft formation and highlight the fact that mismatches in bending modulus must be accounted for when explaining the emergence of lateral heterogeneities in lipid systems and biological membranes.« less

  11. Structured hints : extracting and abstracting domain expertise.

    SciTech Connect

    Hereld, M.; Stevens, R.; Sterling, T.; Gao, G. R.; Mathematics and Computer Science; California Inst. of Tech.; Louisiana State Univ.; Univ. of Delaware

    2009-03-16

    We propose a new framework for providing information to help optimize domain-specific application codes. Its design addresses problems that derive from the widening gap between the domain problem statement by domain experts and the architectural details of new and future high-end computing systems. The design is particularly well suited to program execution models that incorporate dynamic adaptive methodologies for live tuning of program performance and resource utilization. This new framework, which we call 'structured hints', couples a vocabulary of annotations to a suite of performance metrics. The immediate target is development of a process by which a domain expert describes characteristics of objects and methods in the application code that would not be readily apparent to the compiler; the domain expert provides further information about what quantities might provide the best indications of desirable effect; and the interactive preprocessor identifies potential opportunities for the domain expert to evaluate. Our development of these ideas is progressing in stages from case study, through manual implementation, to automatic or semi-automatic implementation. In this paper we discuss results from our case study, an examination of a large simulation of a neural network modeled after the neocortex.

  12. Domain-specific and domain-general processes in social perception--A complementary approach.

    PubMed

    Michael, John; D'Ausilio, Alessandro

    2015-11-01

    In this brief discussion, we explicate and evaluate Heyes and colleagues' deflationary approach to interpreting apparent evidence of domain-specific processes for social perception. We argue that the deflationary approach sheds important light on how functionally specific processes in social perception can be subserved at least in part by domain-general processes. On the other hand, we also argue that the fruitfulness of this approach has been unnecessarily hampered by a contrastive conception of the relationship between domain-general and domain-specific processes. As an alternative, we propose a complementary conception: the identification of domain-general processes that are engaged in instances of social perception can play a positive, structuring role by adding additional constraints to be accounted for in modelling the domain-specific processes that are also involved in such instances. Copyright © 2014 Elsevier Inc. All rights reserved.

  13. Controllability of vortex domain structure in ferroelectric nanodot: fruitful domain patterns and transformation paths.

    PubMed

    Wu, C M; Chen, W J; Zheng, Yue; Ma, D C; Wang, B; Liu, J Y; Woo, C H

    2014-02-04

    Ferroelectric vortex domain structure which exists in low-dimensional ferroelectrics is being intensively researched for future applications in functional nanodevices. Here we demonstrate that adjusting surface charge screening in combination with temperature can provide an efficient way to gain control of vortex domain structure in ferroelectric nanodot. Systematical simulating experiments have been conducted to reveal the stability and evolution mechanisms of domain structure in ferroelectric nanodot under various conditions, including processes of cooling-down/heating-up under different surface charge screening conditions, and increasing/decreasing surface charge screening at different temperatures. Fruitful phase diagrams as functions of surface screening and temperature are presented, together with evolution paths of various domain patterns. Calculations discover up to 25 different kinds of domain patterns and 22 typical evolution paths of phase transitions. The fruitful controllability of vortex domain structure by surface charge screening in combination with temperature should shed light on prospective nanodevice applications of low-dimensional ferroelectric nanostructures.

  14. Controllability of Vortex Domain Structure in Ferroelectric Nanodot: Fruitful Domain Patterns and Transformation Paths

    PubMed Central

    Wu, C. M.; Chen, W. J.; Zheng, Yue; Ma, D. C.; Wang, B.; Liu, J. Y.; Woo, C. H.

    2014-01-01

    Ferroelectric vortex domain structure which exists in low-dimensional ferroelectrics is being intensively researched for future applications in functional nanodevices. Here we demonstrate that adjusting surface charge screening in combination with temperature can provide an efficient way to gain control of vortex domain structure in ferroelectric nanodot. Systematical simulating experiments have been conducted to reveal the stability and evolution mechanisms of domain structure in ferroelectric nanodot under various conditions, including processes of cooling-down/heating-up under different surface charge screening conditions, and increasing/decreasing surface charge screening at different temperatures. Fruitful phase diagrams as functions of surface screening and temperature are presented, together with evolution paths of various domain patterns. Calculations discover up to 25 different kinds of domain patterns and 22 typical evolution paths of phase transitions. The fruitful controllability of vortex domain structure by surface charge screening in combination with temperature should shed light on prospective nanodevice applications of low-dimensional ferroelectric nanostructures. PMID:24492764

  15. Human-computer interface incorporating personal and application domains

    DOEpatents

    Anderson, Thomas G [Albuquerque, NM

    2011-03-29

    The present invention provides a human-computer interface. The interface includes provision of an application domain, for example corresponding to a three-dimensional application. The user is allowed to navigate and interact with the application domain. The interface also includes a personal domain, offering the user controls and interaction distinct from the application domain. The separation into two domains allows the most suitable interface methods in each: for example, three-dimensional navigation in the application domain, and two- or three-dimensional controls in the personal domain. Transitions between the application domain and the personal domain are under control of the user, and the transition method is substantially independent of the navigation in the application domain. For example, the user can fly through a three-dimensional application domain, and always move to the personal domain by moving a cursor near one extreme of the display.

  16. Human-computer interface incorporating personal and application domains

    DOEpatents

    Anderson, Thomas G.

    2004-04-20

    The present invention provides a human-computer interface. The interface includes provision of an application domain, for example corresponding to a three-dimensional application. The user is allowed to navigate and interact with the application domain. The interface also includes a personal domain, offering the user controls and interaction distinct from the application domain. The separation into two domains allows the most suitable interface methods in each: for example, three-dimensional navigation in the application domain, and two- or three-dimensional controls in the personal domain. Transitions between the application domain and the personal domain are under control of the user, and the transition method is substantially independent of the navigation in the application domain. For example, the user can fly through a three-dimensional application domain, and always move to the personal domain by moving a cursor near one extreme of the display.

  17. A simple method for converting frequency domain aerodynamics to the time domain

    NASA Technical Reports Server (NTRS)

    Dowell, E. H.

    1980-01-01

    A simple, direct procedure was developed for converting frequency domain aerodynamics into indicial aerodynamics. The data required for aerodynamic forces in the frequency domain may be obtained from any available (linear) theory. The method retains flexibility for the analyst and is based upon the particular character of the frequency domain results. An evaluation of the method was made for incompressible, subsonic, and transonic two dimensional flows.

  18. Putative Domain-Domain Interactions in the Vesicular Stomatitis Virus L Polymerase Protein Appendage Region

    PubMed Central

    Ruedas, John B.

    2014-01-01

    ABSTRACT The multidomain polymerase protein (L) of nonsegmented negative-strand (NNS) RNA viruses catalyzes transcription and replication of the virus genome. The N-terminal half of the protein forms a ring-like polymerase structure, while the C-terminal half encoding viral mRNA transcript modifications consists of a flexible appendage with three distinct globular domains. To gain insight into putative transient interactions between L domains during viral RNA synthesis, we exchanged each of the four distinct regions encompassing the appendage region of vesicular stomatitis virus (VSV) Indiana serotype L protein with their counterparts from VSV New Jersey and analyzed effects on virus polymerase activity in a minigenome system. The methyltransferase domain exchange yielded a fully active polymerase protein, which functioned as well as wild-type L in the context of a recombinant virus. Exchange of the downstream C-terminal nonconserved region abolished activity, but coexchanging it with the methyltransferase domain generated a polymerase favoring replicase over transcriptase activity, providing strong evidence of interaction between these two regions. Exchange of the capping enzyme domain or the adjacent nonconserved region thought to function as an “unstructured” linker also abrogated polymerase activity even when either domain was coexchanged with other appendage domains. Further probing of the putative linker segment using in-frame enhanced green fluorescent protein (EGFP) insertions similarly abrogated activity. We discuss the implications of these findings with regard to L protein appendage domain structure and putative domain-domain interactions required for polymerase function. IMPORTANCE NNS viruses include many well-known human pathogens (e.g., rabies, measles, and Ebola viruses), as well as emerging viral threats (e.g., Nipah and Hendra viruses). These viruses all encode a large L polymerase protein similarly organized into multiple domains that work in

  19. Low energy electron imaging of domains and domain walls in magnesium-doped lithium niobate

    PubMed Central

    Nataf, G. F.; Grysan, P.; Guennou, M.; Kreisel, J.; Martinotti, D.; Rountree, C. L.; Mathieu, C.; Barrett, N.

    2016-01-01

    The understanding of domain structures, specifically domain walls, currently attracts a significant attention in the field of (multi)-ferroic materials. In this article, we analyze contrast formation in full field electron microscopy applied to domains and domain walls in the uniaxial ferroelectric lithium niobate, which presents a large 3.8 eV band gap and for which conductive domain walls have been reported. We show that the transition from Mirror Electron Microscopy (MEM – electrons reflected) to Low Energy Electron Microscopy (LEEM – electrons backscattered) gives rise to a robust contrast between domains with upwards (Pup) and downwards (Pdown) polarization, and provides a measure of the difference in surface potential between the domains. We demonstrate that out-of-focus conditions of imaging produce contrast inversion, due to image distortion induced by charged surfaces, and also carry information on the polarization direction in the domains. Finally, we show that the intensity profile at domain walls provides experimental evidence for a local stray, lateral electric field. PMID:27608605

  20. Identification of domains and domain interface residues in multidomain proteins from graph spectral method.

    PubMed

    Sistla, Ramesh K; K V, Brinda; Vishveshwara, Saraswathi

    2005-05-15

    We present a novel method for the identification of structural domains and domain interface residues in proteins by graph spectral method. This method converts the three-dimensional structure of the protein into a graph by using atomic coordinates from the PDB file. Domain definitions are obtained by constructing either a protein backbone graph or a protein side-chain graph. The graph is constructed based on the interactions between amino acid residues in the three-dimensional structure of the proteins. The spectral parameters of such a graph contain information regarding the domains and subdomains in the protein structure. This is based on the fact that the interactions among amino acids are higher within a domain than across domains. This is evident in the spectra of the protein backbone and the side-chain graphs, thus differentiating the structural domains from one another. Further, residues that occur at the interface of two domains can also be easily identified from the spectra. This method is simple, elegant, and robust. Moreover, a single numeric computation yields both the domain definitions and the interface residues. Copyright 2005 Wiley-Liss, Inc.

  1. Low energy electron imaging of domains and domain walls in magnesium-doped lithium niobate

    NASA Astrophysics Data System (ADS)

    Nataf, G. F.; Grysan, P.; Guennou, M.; Kreisel, J.; Martinotti, D.; Rountree, C. L.; Mathieu, C.; Barrett, N.

    2016-09-01

    The understanding of domain structures, specifically domain walls, currently attracts a significant attention in the field of (multi)-ferroic materials. In this article, we analyze contrast formation in full field electron microscopy applied to domains and domain walls in the uniaxial ferroelectric lithium niobate, which presents a large 3.8 eV band gap and for which conductive domain walls have been reported. We show that the transition from Mirror Electron Microscopy (MEM - electrons reflected) to Low Energy Electron Microscopy (LEEM - electrons backscattered) gives rise to a robust contrast between domains with upwards (Pup) and downwards (Pdown) polarization, and provides a measure of the difference in surface potential between the domains. We demonstrate that out-of-focus conditions of imaging produce contrast inversion, due to image distortion induced by charged surfaces, and also carry information on the polarization direction in the domains. Finally, we show that the intensity profile at domain walls provides experimental evidence for a local stray, lateral electric field.

  2. DomainRBF: a Bayesian regression approach to the prioritization of candidate domains for complex diseases

    PubMed Central

    2011-01-01

    Background Domains are basic units of proteins, and thus exploring associations between protein domains and human inherited diseases will greatly improve our understanding of the pathogenesis of human complex diseases and further benefit the medical prevention, diagnosis and treatment of these diseases. Within a given domain-domain interaction network, we make the assumption that similarities of disease phenotypes can be explained using proximities of domains associated with such diseases. Based on this assumption, we propose a Bayesian regression approach named "domainRBF" (domain Rank with Bayes Factor) to prioritize candidate domains for human complex diseases. Results Using a compiled dataset containing 1,614 associations between 671 domains and 1,145 disease phenotypes, we demonstrate the effectiveness of the proposed approach through three large-scale leave-one-out cross-validation experiments (random control, simulated linkage interval, and genome-wide scan), and we do so in terms of three criteria (precision, mean rank ratio, and AUC score). We further show that the proposed approach is robust to the parameters involved and the underlying domain-domain interaction network through a series of permutation tests. Once having assessed the validity of this approach, we show the possibility of ab initio inference of domain-disease associations and gene-disease associations, and we illustrate the strong agreement between our inferences and the evidences from genome-wide association studies for four common diseases (type 1 diabetes, type 2 diabetes, Crohn's disease, and breast cancer). Finally, we provide a pre-calculated genome-wide landscape of associations between 5,490 protein domains and 5,080 human diseases and offer free access to this resource. Conclusions The proposed approach effectively ranks susceptible domains among the top of the candidates, and it is robust to the parameters involved. The ab initio inference of domain-disease associations shows

  3. Dual-domain point diffraction interferometer

    DOEpatents

    Naulleau, Patrick P.; Goldberg, Kenneth Alan

    2000-01-01

    A hybrid spatial/temporal-domain point diffraction interferometer (referred to as the dual-domain PS/PDI) that is capable of suppressing the scattered-reference-light noise that hinders the conventional PS/PDI is provided. The dual-domain PS/PDI combines the separate noise-suppression capabilities of the widely-used phase-shifting and Fourier-transform fringe pattern analysis methods. The dual-domain PS/PDI relies on both a more restrictive implementation of the image plane PS/PDI mask and a new analysis method to be applied to the interferograms generated and recorded by the modified PS/PDI. The more restrictive PS/PDI mask guarantees the elimination of spatial-frequency crosstalk between the signal and the scattered-light noise arising from scattered-reference-light interfering with the test beam. The new dual-domain analysis method is then used to eliminate scattered-light noise arising from both the scattered-reference-light interfering with the test beam and the scattered-reference-light interfering with the "true" pinhole-diffracted reference light. The dual-domain analysis method has also been demonstrated to provide performance enhancement when using the non-optimized standard PS/PDI design. The dual-domain PS/PDI is essentially a three-tiered filtering system composed of lowpass spatial-filtering the test-beam electric field using the more restrictive PS/PDI mask, bandpass spatial-filtering the individual interferogram irradiance frames making up the phase-shifting series, and bandpass temporal-filtering the phase-shifting series as a whole.

  4. Domain structure of Lassa virus L protein.

    PubMed

    Brunotte, Linda; Lelke, Michaela; Hass, Meike; Kleinsteuber, Katja; Becker-Ziaja, Beate; Günther, Stephan

    2011-01-01

    The 200-kDa L protein of arenaviruses plays a central role in viral genome replication and transcription. This study aimed at providing evidence for the domain structure of L protein by combining bioinformatics with a stepwise mutagenesis approach using the Lassa virus minireplicon system. Potential interdomain linkers were predicted using various algorithms. The prediction was challenged by insertion of flexible sequences into the predicted linkers. Insertion of 5 or 10 amino acid residues was tolerated at seven sites (S407, G446, G467, G774, G939, S1952, and V2074 in Lassa virus AV). At two of these sites, G467 and G939, L protein could be split into an N-terminal and a C-terminal part, which were able to trans-complement each other and reconstitute a functional complex upon coexpression. Coimmunoprecipitation studies revealed physical interaction between the N- and C-terminal domains, irrespective of whether L protein was split at G467 or G939. In confocal immunofluorescence microscopy, the N-terminal domains showed a dot-like, sometimes perinuclear, cytoplasmic distribution similar to that of full-length L protein, while the C-terminal domains were homogenously distributed in cytoplasm. The latter were redistributed into the dot-like structures upon coexpression with the corresponding N-terminal domain. In conclusion, this study demonstrates two interdomain linkers in Lassa virus L protein, at G467 and G939, suggesting that L protein is composed of at least three structural domains spanning residues 1 to 467, 467 to 939, and 939 to 2220. The first domain seems to mediate accumulation of L protein into cytoplasmic dot-like structures.

  5. Identifying structural domains of proteins using clustering

    PubMed Central

    2012-01-01

    Background Protein structures are comprised of modular elements known as domains. These units are used and re-used over and over in nature, and usually serve some particular function in the structure. Thus it is useful to be able to break up a protein of interest into its component domains, prior to similarity searching for example. Numerous computational methods exist for doing so, but most operate only on a single protein chain and many are limited to making a series of cuts to the sequence, while domains can and do span multiple chains. Results This study presents a novel clustering-based approach to domain identification, which works equally well on individual chains or entire complexes. The method is simple and fast, taking only a few milliseconds to run, and works by clustering either vectors representing secondary structure elements, or buried alpha-carbon positions, using average-linkage clustering. Each resulting cluster corresponds to a domain of the structure. The method is competitive with others, achieving 70% agreement with SCOP on a large non-redundant data set, and 80% on a set more heavily weighted in multi-domain proteins on which both SCOP and CATH agree. Conclusions It is encouraging that a basic method such as this performs nearly as well or better than some far more complex approaches. This suggests that protein domains are indeed for the most part simply compact regions of structure with a higher density of buried contacts within themselves than between each other. By representing the structure as a set of points or vectors in space, it allows us to break free of any artificial limitations that other approaches may depend upon. PMID:23116496

  6. Algorithms for propagating uncertainty across heterogeneous domains

    SciTech Connect

    Cho, Heyrim; Yang, Xiu; Venturi, D.; Karniadakis, George E.

    2015-12-30

    We address an important research area in stochastic multi-scale modeling, namely the propagation of uncertainty across heterogeneous domains characterized by partially correlated processes with vastly different correlation lengths. This class of problems arise very often when computing stochastic PDEs and particle models with stochastic/stochastic domain interaction but also with stochastic/deterministic coupling. The domains may be fully embedded, adjacent or partially overlapping. The fundamental open question we address is the construction of proper transmission boundary conditions that preserve global statistical properties of the solution across different subdomains. Often, the codes that model different parts of the domains are black-box and hence a domain decomposition technique is required. No rigorous theory or even effective empirical algorithms have yet been developed for this purpose, although interfaces defined in terms of functionals of random fields (e.g., multi-point cumulants) can overcome the computationally prohibitive problem of preserving sample-path continuity across domains. The key idea of the different methods we propose relies on combining local reduced-order representations of random fields with multi-level domain decomposition. Specifically, we propose two new algorithms: The first one enforces the continuity of the conditional mean and variance of the solution across adjacent subdomains by using Schwarz iterations. The second algorithm is based on PDE-constrained multi-objective optimization, and it allows us to set more general interface conditions. The effectiveness of these new algorithms is demonstrated in numerical examples involving elliptic problems with random diffusion coefficients, stochastically advected scalar fields, and nonlinear advection-reaction problems with random reaction rates.

  7. Competition between LIM-binding domains.

    PubMed

    Matthews, Jacqueline M; Bhati, Mugdha; Craig, Vanessa J; Deane, Janet E; Jeffries, Cy; Lee, Christopher; Nancarrow, Amy L; Ryan, Daniel P; Sunde, Margaret

    2008-12-01

    LMO (LIM-only) and LIM-HD (LIM-homeodomain) proteins form a family of proteins that is required for myriad developmental processes and which can contribute to diseases such as T-cell leukaemia and breast cancer. The four LMO and 12 LIM-HD proteins in mammals are expressed in a combinatorial manner in many cell types, forming a transcriptional 'LIM code'. The proteins all contain a pair of closely spaced LIM domains near their N-termini that mediate protein-protein interactions, including binding to the approximately 30-residue LID (LIM interaction domain) of the essential co-factor protein Ldb1 (LIM domain-binding protein 1). In an attempt to understand the molecular mechanisms behind the LIM code, we have determined the molecular basis of binding of LMO and LIM-HD proteins for Ldb1(LID) through a series of structural, mutagenic and biophysical studies. These studies provide an explanation for why Ldb1 binds the LIM domains of the LMO/LIM-HD family, but not LIM domains from other proteins. The LMO/LIM-HD family exhibit a range of affinities for Ldb1, which influences the formation of specific functional complexes within cells. We have also identified an additional LIM interaction domain in one of the LIM-HD proteins, Isl1. Despite low sequence similarity to Ldb1(LID), this domain binds another LIM-HD protein, Lhx3, in an identical manner to Ldb1(LID). Through our and other studies, it is emerging that the multiple layers of competitive binding involving LMO and LIM-HD proteins and their partner proteins contribute significantly to cell fate specification and development.

  8. Cellular Domain Patterns in Magnetic Garnet Films.

    NASA Astrophysics Data System (ADS)

    Babcock, Kenneth Lawrence

    This thesis presents the first experimental study of two-dimensional cellular patterns of magnetic domains in garnet films. Room-temperature observations focused on a Bismuth-substituted film designed for magneto-optic device applications. Measurements of energies and statistical quantities were aided by computer analysis of digitized pattern images. An external bias field H_ B induces pattern evolution that is shown to be governed by three elemental domain structures: (i) Stripe segments that form the cell boundaries. Magnetic field and domain wall energies produce effective tension in the stripe segments that drives the domain motion. (ii) 3 -fold vertices that join the stripe segments. Cellular patterns saturate when the vertices are destroyed at the bias value H_{V} (= 0.79 times 4pi M = 150 Oe), the largest saturation field of all domain pattern topologies. (iii) Pentagonal bubble traps, 5-fold symmetric structures containing trapped magnetic bubble domains. Isolated bubble traps collapse at a critical bias field H_5 (= 0.54 times 4pi M = 103 Oe). A simple geometric model illustrates the energetic mechanism of bubble trap collapse. An analytic pattern model accounts for domain interactions so as to elucidate the bias and configuration dependence of the stripe tension and outline the energetic bias regimes. All stripe segments are under tension in the nonequilibrium regime H _{RI}domains. Cellular patterns in this regime are supported by the robust pentagonal bubble traps acting as 5-fold vertices, an unusual topology among experimental cellular systems. An ac field component is shown to mitigate coercive effects that can hinder the pattern evolution, and criteria are developed for the ac amplitude. Characterized for the first time are several collective phenomena relevant to condense matter systems, including: (i) Coarsening of the cellular patterns in an increasing bias

  9. Direct measurement of antiferromagnetic domain fluctuations.

    PubMed

    Shpyrko, O G; Isaacs, E D; Logan, J M; Feng, Yejun; Aeppli, G; Jaramillo, R; Kim, H C; Rosenbaum, T F; Zschack, P; Sprung, M; Narayanan, S; Sandy, A R

    2007-05-03

    Measurements of magnetic noise emanating from ferromagnets owing to domain motion were first carried out nearly 100 years ago, and have underpinned much science and technology. Antiferromagnets, which carry no net external magnetic dipole moment, yet have a periodic arrangement of the electron spins extending over macroscopic distances, should also display magnetic noise. However, this must be sampled at spatial wavelengths of the order of several interatomic spacings, rather than the macroscopic scales characteristic of ferromagnets. Here we present a direct measurement of the fluctuations in the nanometre-scale superstructure of spin- and charge-density waves associated with antiferromagnetism in elemental chromium. The technique used is X-ray photon correlation spectroscopy, where coherent X-ray diffraction produces a speckle pattern that serves as a 'fingerprint' of a particular magnetic domain configuration. The temporal evolution of the patterns corresponds to domain walls advancing and retreating over micrometre distances. This work demonstrates a useful measurement tool for antiferromagnetic domain wall engineering, but also reveals a fundamental finding about spin dynamics in the simplest antiferromagnet: although the domain wall motion is thermally activated at temperatures above 100 K, it is not so at lower temperatures, and indeed has a rate that saturates at a finite value-consistent with quantum fluctuations-on cooling below 40 K.

  10. The architecture of the protein domain universe.

    PubMed

    Dokholyan, Nikolay V

    2005-03-14

    Understanding the design of the universe of protein structures may provide insights into protein evolution. We study the architecture of the protein domain universe, which has been found to poses peculiar scale-free properties. We examine the origin of these scale-free properties of the graph of protein domain structures (PDUG) and determine that that the PDUG is not modular, i.e. it does not consist of modules with uniform properties. Instead, we find the PDUG to be self-similar at all scales. We further characterize the PDUG architecture by studying the properties of the hub nodes that are responsible for the scale-free connectivity of the PDUG. We introduce a measure of the betweenness centrality of protein domains in the PDUG and find a power-law distribution of the betweenness centrality values. The scale-free distribution of hubs in the protein universe suggests that a set of specific statistical mechanics models, such as the self-organized criticality model, can potentially identify the principal driving forces of protein evolution. We also find a gatekeeper protein domain, removal of which partitions the largest cluster into two large sub-clusters. We suggest that the loss of such gatekeeper protein domains in the course of evolution is responsible for the creation of new fold families.

  11. Tunable inertia of chiral magnetic domain walls

    NASA Astrophysics Data System (ADS)

    Torrejon, Jacob; Martinez, Eduardo; Hayashi, Masamitsu

    2016-11-01

    The time it takes to accelerate an object from zero to a given velocity depends on the applied force and the environment. If the force ceases, it takes exactly the same time to completely decelerate. A magnetic domain wall is a topological object that has been observed to follow this behaviour. Here we show that acceleration and deceleration times of chiral Neel walls driven by current are different in a system with low damping and moderate Dzyaloshinskii-Moriya exchange constant. The time needed to accelerate a domain wall with current via the spin Hall torque is much faster than the time it needs to decelerate once the current is turned off. The deceleration time is defined by the Dzyaloshinskii-Moriya exchange constant whereas the acceleration time depends on the spin Hall torque, enabling tunable inertia of chiral domain walls. Such unique feature of chiral domain walls can be utilized to move and position domain walls with lower current, key to the development of storage class memory devices.

  12. Tunable inertia of chiral magnetic domain walls.

    PubMed

    Torrejon, Jacob; Martinez, Eduardo; Hayashi, Masamitsu

    2016-11-24

    The time it takes to accelerate an object from zero to a given velocity depends on the applied force and the environment. If the force ceases, it takes exactly the same time to completely decelerate. A magnetic domain wall is a topological object that has been observed to follow this behaviour. Here we show that acceleration and deceleration times of chiral Neel walls driven by current are different in a system with low damping and moderate Dzyaloshinskii-Moriya exchange constant. The time needed to accelerate a domain wall with current via the spin Hall torque is much faster than the time it needs to decelerate once the current is turned off. The deceleration time is defined by the Dzyaloshinskii-Moriya exchange constant whereas the acceleration time depends on the spin Hall torque, enabling tunable inertia of chiral domain walls. Such unique feature of chiral domain walls can be utilized to move and position domain walls with lower current, key to the development of storage class memory devices.

  13. Almost isometric mesh parameterization through abstract domains.

    PubMed

    Pietroni, Nico; Tarini, Marco; Cignoni, Paolo

    2010-01-01

    In this paper, we propose a robust, automatic technique to build a global hi-quality parameterization of a two-manifold triangular mesh. An adaptively chosen 2D domain of the parameterization is built as part of the process. The produced parameterization exhibits very low isometric distortion, because it is globally optimized to preserve both areas and angles. The domain is a collection of equilateral triangular 2D regions enriched with explicit adjacency relationships (it is abstract in the sense that no 3D embedding is necessary). It is tailored to minimize isometric distortion, resulting in excellent parameterization qualities, even when meshes with complex shape and topology are mapped into domains composed of a small number of large continuous regions. Moreover, this domain is, in turn, remapped into a collection of 2D square regions, unlocking many advantages found in quad-based domains (e.g., ease of packing). The technique is tested on a variety of cases, including challenging ones, and compares very favorably with known approaches. An open-source implementation is made available.

  14. Tunable inertia of chiral magnetic domain walls

    PubMed Central

    Torrejon, Jacob; Martinez, Eduardo; Hayashi, Masamitsu

    2016-01-01

    The time it takes to accelerate an object from zero to a given velocity depends on the applied force and the environment. If the force ceases, it takes exactly the same time to completely decelerate. A magnetic domain wall is a topological object that has been observed to follow this behaviour. Here we show that acceleration and deceleration times of chiral Neel walls driven by current are different in a system with low damping and moderate Dzyaloshinskii–Moriya exchange constant. The time needed to accelerate a domain wall with current via the spin Hall torque is much faster than the time it needs to decelerate once the current is turned off. The deceleration time is defined by the Dzyaloshinskii–Moriya exchange constant whereas the acceleration time depends on the spin Hall torque, enabling tunable inertia of chiral domain walls. Such unique feature of chiral domain walls can be utilized to move and position domain walls with lower current, key to the development of storage class memory devices. PMID:27882932

  15. Generalized vector calculus on convex domain

    NASA Astrophysics Data System (ADS)

    Agrawal, Om P.; Xu, Yufeng

    2015-06-01

    In this paper, we apply recently proposed generalized integral and differential operators to develop generalized vector calculus and generalized variational calculus for problems defined over a convex domain. In particular, we present some generalization of Green's and Gauss divergence theorems involving some new operators, and apply these theorems to generalized variational calculus. For fractional power kernels, the formulation leads to fractional vector calculus and fractional variational calculus for problems defined over a convex domain. In special cases, when certain parameters take integer values, we obtain formulations for integer order problems. Two examples are presented to demonstrate applications of the generalized variational calculus which utilize the generalized vector calculus developed in the paper. The first example leads to a generalized partial differential equation and the second example leads to a generalized eigenvalue problem, both in two dimensional convex domains. We solve the generalized partial differential equation by using polynomial approximation. A special case of the second example is a generalized isoperimetric problem. We find an approximate solution to this problem. Many physical problems containing integer order integrals and derivatives are defined over arbitrary domains. We speculate that future problems containing fractional and generalized integrals and derivatives in fractional mechanics will be defined over arbitrary domains, and therefore, a general variational calculus incorporating a general vector calculus will be needed for these problems. This research is our first attempt in that direction.

  16. Lipid membrane domains in the brain.

    PubMed

    Aureli, Massimo; Grassi, Sara; Prioni, Simona; Sonnino, Sandro; Prinetti, Alessandro

    2015-08-01

    The brain is characterized by the presence of cell types with very different functional specialization, but with the common trait of a very high complexity of structures originated by their plasma membranes. Brain cells bear evident membrane polarization with the creation of different morphological and functional subcompartments, whose formation, stabilization and function require a very high level of lateral order within the membrane. In other words, the membrane specialization of brain cells implies the presence of distinct membrane domains. The brain is the organ with the highest enrichment in lipids like cholesterol, glycosphingolipids, and the most recently discovered brain membrane lipid, phosphatidylglucoside, whose collective behavior strongly favors segregation within the membrane leading to the formation of lipid-driven membrane domains. Lipid-driven membrane domains function as dynamic platforms for signal transduction, protein processing, and membrane turnover. Essential events involved in the development and in the maintenance of the functional integrity of the brain depend on the organization of lipid-driven membrane domains, and alterations in lipid homeostasis, leading to deranged lipid-driven membrane organization, are common in several major brain diseases. In this review, we summarize the forces behind the formation of lipid membrane domains and their biological roles in different brain cells. This article is part of a Special Issue entitled Brain Lipids.

  17. Time-Resolved X-Ray Solution Scattering Reveals the Structural Photoactivation of a Light-Oxygen-Voltage Photoreceptor.

    PubMed

    Berntsson, Oskar; Diensthuber, Ralph P; Panman, Matthijs R; Björling, Alexander; Hughes, Ashley J; Henry, Léocadie; Niebling, Stephan; Newby, Gemma; Liebi, Marianne; Menzel, Andreas; Henning, Robert; Kosheleva, Irina; Möglich, Andreas; Westenhoff, Sebastian

    2017-06-06

    Light-oxygen-voltage (LOV) receptors are sensory proteins controlling a wide range of organismal adaptations in multiple kingdoms of life. Because of their modular nature, LOV domains are also attractive for use as optogenetic actuators. A flavin chromophore absorbs blue light, forms a bond with a proximal cysteine residue, and induces changes in the surroundings. There is a gap of knowledge on how this initial signal is relayed further through the sensor to the effector module. To characterize these conformational changes, we apply time-resolved X-ray scattering to the homodimeric LOV domain from Bacillus subtilis YtvA. We observe a global structural change in the LOV dimer synchronous with the formation of the chromophore photoproduct state. Using molecular modeling, this change is identified as splaying apart and relative rotation of the two monomers, which leads to an increased separation at the anchoring site of the effector modules. Copyright © 2017 Elsevier Ltd. All rights reserved.

  18. Evolution of magnetic domain structures from Pseudo-Single-Domain to Multidomain.

    NASA Astrophysics Data System (ADS)

    Williams, Wyn; Nagy, Lesleis; Fabian, Karl; Muxworthy, Adrian

    2016-04-01

    Palaeomagnetic observations over the last 60 years have made a significant contribution to our understanding of the geological structure of the Earth. The interpretation of these recordings is almost entirely based on the assumption that the remanence is held in uniformly magnetised (single-domain) particles. However it has long been recognised that the upper limit for SD magnetite is at about 80nm (for equidimensional grains of magnetite) and it is likely that many palaeomagnetic samples will contain a much broader range of grain sizes, which may be dominated by non-uniformly magnetised pseudo-single-domain (PSD) grains. Recent progress in determining energy barriers between the different possible domain states in a grain (to be discussed in this session by Nagy et al.) shows that the thermal stability of PSD grains are dominated by energy barriers and domain transitions whose characteristics are SD-like. The magnetic structures in PSD grains undergo a form of domain rotation rather than the domain wall motions observed in multidomain (MD) grains. Thus transition in stability and fidelity of palaeomagentic recorders from the more reliable PSD to less reliable MD structures can be mapped to the evolution of domain walls from the vortex cores of PSD grains. In this talk we will discuss our preliminary results for very large scale micromagnetic models using a new parallel numerical model called DUNLOP. We will outline the magnetic properties and structures of what we classify as PSD grains and how these types of domains evolve from vortex-dominated to MD structures for easy-axis aligned domains. Such domains are separated by narrow Bloch and Néel - type walls and we discuss the likely impact on the classification of reliable palaeomagentic domain structures.

  19. The Evolutionary History of Protein Domains Viewed by Species Phylogeny

    PubMed Central

    Yang, Song; Bourne, Philip E.

    2009-01-01

    Background Protein structural domains are evolutionary units whose relationships can be detected over long evolutionary distances. The evolutionary history of protein domains, including the origin of protein domains, the identification of domain loss, transfer, duplication and combination with other domains to form new proteins, and the formation of the entire protein domain repertoire, are of great interest. Methodology/Principal Findings A methodology is presented for providing a parsimonious domain history based on gain, loss, vertical and horizontal transfer derived from the complete genomic domain assignments of 1015 organisms across the tree of life. When mapped to species trees the evolutionary history of domains and domain combinations is revealed, and the general evolutionary trend of domain and combination is analyzed. Conclusions/Significance We show that this approach provides a powerful tool to study how new proteins and functions emerged and to study such processes as horizontal gene transfer among more distant species. PMID:20041107

  20. Structure and function of WD40 domain proteins.

    PubMed

    Xu, Chao; Min, Jinrong

    2011-03-01

    The WD40 domain exhibits a β-propeller architecture, often comprising seven blades. The WD40 domain is one of the most abundant domains and also among the top interacting domains in eukaryotic genomes. In this review, we will discuss the identification, definition and architecture of the WD40 domains. WD40 domain proteins are involved in a large variety of cellular processes, in which WD40 domains function as a protein-protein or protein-DNA interaction platform. WD40 domain mediates molecular recognition events mainly through the smaller top surface, but also through the bottom surface and sides. So far, no WD40 domain has been found to display enzymatic activity. We will also discuss the different binding modes exhibited by the large versatile family of WD40 domain proteins. In the last part of this review, we will discuss how post-translational modifications are recognized by WD40 domain proteins.

  1. Adaptive corrector operating in frequency domain

    NASA Astrophysics Data System (ADS)

    Radikaynen, Y. M.

    1984-11-01

    An interference-immune corrector for a signal converter with automatic regulation of adaptation speed is described which operates in the frequency domain with fast convergence and high signal-to-noise ratio. It contains an analog-to-digital converter, a demodulator, and a filter array with equidistant spacing of center frequencies, three multipliers and two summators, as well as a reference signal generator, a frequency divider, a counter, and a noise meter. Filtering is done by a n-point Fourier transformation or bunching with a memory at the filter input followed by inverse Fourier transformation or debunching, respectively. The algorithm of corrector operation in the frequency domain can be constructed heuristically by an analog to the complex algorithm of minimizing the mean-square error in the time domain. Each weight factor can be processed independently and only once per Fourier transformation cycle, which ensures fast convergence without preliminary phase correction even with large distortions in the communication channel.

  2. Transactions in domain-specific information systems

    NASA Astrophysics Data System (ADS)

    Zacek, Jaroslav

    2017-07-01

    Substantial number of the current information system (IS) implementations is based on transaction approach. In addition, most of the implementations are domain-specific (e.g. accounting IS, resource planning IS). Therefore, we have to have a generic transaction model to build and verify domain-specific IS. The paper proposes a new transaction model for domain-specific ontologies. This model is based on value oriented business process modelling technique. The transaction model is formalized by the Petri Net theory. First part of the paper presents common business processes and analyses related to business process modeling. Second part defines the transactional model delimited by REA enterprise ontology paradigm and introduces states of the generic transaction model. The generic model proposal is defined and visualized by the Petri Net modelling tool. Third part shows application of the generic transaction model. Last part of the paper concludes results and discusses a practical usability of the generic transaction model.

  3. Photo sorting and compression in frequency domain

    NASA Astrophysics Data System (ADS)

    Lu, Yang; Wong, Tien-Tsin; Heng, Pheng-Ann

    2004-10-01

    With the increasing popularity of digital camera, organizing and managing the large collection of digital photos effectively are therefore required. In this paper, we study the photo album sorting, clustering and compression techniques in DCT frequency domain without having to decompress JPEG photos into spatial domain firstly. We utilize the first several non-zero DCT coefficients to build our feature set and calculate the energy histograms in frequency domain directly. We then calculate the similarity distance of every two photos, and perform photo album sorting and adaptive clustering algorithms to group the most similar photos together. We further compress those clustered photos by a MPEG-like algorithm with variable IBP frames and adaptive search windows. Our methods provide a compact and reasonable format for people to store and transmit their large number of digital photos. Experiments prove that our algorithm is efficient and effective for digital photo processing.

  4. On automating domain connectivity for overset grids

    NASA Technical Reports Server (NTRS)

    Chiu, Ing-Tsau; Meakin, Robert L.

    1995-01-01

    An alternative method for domain connectivity among systems of overset grids is presented. Reference uniform Cartesian systems of points are used to achieve highly efficient domain connectivity, and form the basis for a future fully automated system. The Cartesian systems are used to approximate body surfaces and to map the computational space of component grids. By exploiting the characteristics of Cartesian systems, Chimera type hole-cutting and identification of donor elements for intergrid boundary points can be carried out very efficiently. The method is tested for a range of geometrically complex multiple-body overset grid systems. A dynamic hole expansion/contraction algorithm is also implemented to obtain optimum domain connectivity; however, it is tested only for geometry of generic shapes.

  5. Time domain reflectometry in time variant plasmas

    NASA Technical Reports Server (NTRS)

    Scherner, Michael J.

    1992-01-01

    The effects of time-dependent electron density fluctuations on a synthesized time domain reflectometry response of a one-dimensional cold plasma sheath are considered. Numerical solutions of the Helmholtz wave equation, which describes the electric field of a normally incident plane wave in a specified static electron density profile, are used. A study of the effects of Doppler shifts resulting from moving density fluctuations in the electron density profile of the sheath is included. Varying electron density levels corrupt time domain and distance measurements. Reducing or modulating the electron density levels of a given electron density profile affects the time domain response of a plasma and results in motion of the turning point, and the effective motion has a significant effect on measuring electron density locations.

  6. Bragg projection ptychography on niobium phase domains

    NASA Astrophysics Data System (ADS)

    Burdet, Nicolas; Shi, Xiaowen; Clark, Jesse N.; Huang, Xiaojing; Harder, Ross; Robinson, Ian

    2017-07-01

    Bragg projection ptychography (BPP) is a coherent x-ray diffraction imaging technique which combines the strengths of scanning microscopy with the phase contrast of x-ray ptychography. Here we apply it for high resolution imaging of the phase-shifted crystalline domains associated with epitaxial growth. The advantages of BPP are that the spatial extent of the sample is arbitrary, it is nondestructive, and it gives potentially diffraction limited spatial resolution. Here we demonstrate the application of BPP for revealing the domain structure caused by epitaxial misfit in a nanostructured metallic thin film. Experimental coherent diffraction data were collected from a niobium thin film, epitaxially grown on a sapphire substrate as the beam was scanned across the sample. The data were analyzed by BPP using a carefully selected combination of refinement procedures. The resulting image shows a close packed array of epitaxial domains, shifted with respect to each other due to misfit between the film and its substrate.

  7. Dispersive Stiffness of Dzyaloshinskii Domain Walls

    NASA Astrophysics Data System (ADS)

    Pellegren, J. P.; Lau, D.; Sokalski, V.

    2017-07-01

    It is well documented that subjecting perpendicular magnetic films that exhibit the interfacial Dzyaloshinskii-Moriya interaction to an in-plane magnetic field results in a domain wall (DW) energy σ , which is highly anisotropic with respect to the orientation of the DW in the film plane Θ . We demonstrate that this anisotropy has a profound impact on the elastic response of the DW as characterized by the surface stiffness σ ˜ (Θ )=σ (Θ )+σ''(Θ ) and evaluate its dependence on the length scale of deformation. The influence of stiffness on DW mobility in the creep regime is assessed, with analytic and numerical calculations showing trends in σ ˜ that better represent experimental measurements of domain wall velocity in magnetic thin films compared to σ alone. Our treatment provides experimental support for theoretical models of the mobility of anisotropic elastic manifolds and makes progress toward a more complete understanding of magnetic domain wall creep.

  8. Moment domain representation of nonblind image deblurring.

    PubMed

    Kumar, Ahlad; Paramesran, Raveendran; Shakibaei, Barmak Honarvar

    2014-04-01

    In this paper, we propose the use of geometric moments to the field of nonblind image deblurring. Using the developed relationship of geometric moments for original and blurred images, a mathematical formulation based on the Euler-Lagrange identity and variational techniques is proposed. It uses an iterative procedure to deblur the image in moment domain. The theoretical framework is validated by a set of experiments. A comparative analysis of the results obtained using the spatial and moment domains are evaluated using a quality assessment method known as the Blind/Reference-less Image Spatial Quality Evaluator (BRISQUE). The results show that the proposed method yields a higher quality score when compared with the spatial domain method for the same number of iterations.

  9. On thick domain walls in general relativity

    NASA Technical Reports Server (NTRS)

    Goetz, Guenter; Noetzold, Dirk

    1989-01-01

    Planar scalar field configurations in general relativity differ considerably from those in flat space. It is shown that static domain walls of finite thickness in curved space-time do not possess a reflection symmetry. At infinity, the space-time tends to the Taub vacuum on one side of the wall and to the Minkowski vacuum (Rindler space-time) on the other. Massive test particles are always accelerated towards the Minkowski side, i.e., domain walls are attractive on the Taub side, but repulsive on the Minkowski side (Taub-vacuum cleaner). It is also proved that the pressure in all directions is always negative. Finally, a brief comment is made concerning the possibility of infinite, i.e., bigger than horizon size, domain walls in our universe. All of the results are independent of the form of the potential V(phi) greater than or equal to 0 of the scalar field phi.

  10. Moving Object Completion on the Compressed Domain

    NASA Astrophysics Data System (ADS)

    Yiwei, Jiang; de, Xu; Na, Liu; Congyan, Lang

    Moving object completion is a process of completing moving object's missing information based on local structures. Over the past few years, a number of computable algorithms of video completion have been developed, however most of these algorithms are based on the pixel domain. Little theoretical and computational work in video completion is based on the compressed domain. In this paper, a moving object completion method on the compressed domain is proposed. It is composed of three steps: motion field transferring, thin plate spline interpolation and combination. Missing space-time blocks will be completed by placing new motion vectors on them so that the resulting video sequence will have as much global visual coherence with the video portions outside the hole. The experimental results are presented to demonstrate the efficiency and accuracy of the proposed algorithm.

  11. A Domain Description Language for Data Processing

    NASA Technical Reports Server (NTRS)

    Golden, Keith

    2003-01-01

    We discuss an application of planning to data processing, a planning problem which poses unique challenges for domain description languages. We discuss these challenges and why the current PDDL standard does not meet them. We discuss DPADL (Data Processing Action Description Language), a language for describing planning domains that involve data processing. DPADL is a declarative, object-oriented language that supports constraints and embedded Java code, object creation and copying, explicit inputs and outputs for actions, and metadata descriptions of existing and desired data. DPADL is supported by the IMAGEbot system, which we are using to provide automation for an ecological forecasting application. We compare DPADL to PDDL and discuss changes that could be made to PDDL to make it more suitable for representing planning domains that involve data processing actions.

  12. Anomalous feedback and negative domain wall resistance

    NASA Astrophysics Data System (ADS)

    Cheng, Ran; Zhu, Jian-Gang; Xiao, Di

    2016-11-01

    Magnetic induction can be regarded as a negative feedback effect, where the motive-force opposes the change of magnetic flux that generates the motive-force. In artificial electromagnetics emerging from spintronics, however, this is not necessarily the case. By studying the current-induced domain wall dynamics in a cylindrical nanowire, we show that the spin motive-force exerting on electrons can either oppose or support the applied current that drives the domain wall. The switching into the anomalous feedback regime occurs when the strength of the dissipative torque β is about twice the value of the Gilbert damping constant α. The anomalous feedback manifests as a negative domain wall resistance, which has an analogy with the water turbine.

  13. Targeting SH2 domains in breast cancer.

    PubMed

    Morlacchi, Pietro; Robertson, Fredika M; Klostergaard, Jim; McMurray, John S

    2014-01-01

    Breast cancer is among the most commonly diagnosed cancer types in women worldwide and is the second leading cause of cancer-related disease in the USA. SH2 domains recruit signaling proteins to phosphotyrosine residues on aberrantly activated growth factor and cytokine receptors and contribute to cancer cell cycling, metastasis, angiogenesis and so on. Herein we review phosphopeptide mimetic and small-molecule approaches targeting the SH2 domains of Grb2, Grb7 and STAT3 that inhibit their targets and reduce proliferation in in vitro breast cancer models. Only STAT3 inhibitors have been evaluated in in vivo models and have led to tumor reduction. Taken together, these studies suggest that targeting SH2 domains is an important approach to the treatment of breast cancer.

  14. Multilevel domain decomposition for electronic structure calculations

    SciTech Connect

    Barrault, M. . E-mail: maxime.barrault@edf.fr; Cances, E. . E-mail: cances@cermics.enpc.fr; Hager, W.W. . E-mail: hager@math.ufl.edu; Le Bris, C. . E-mail: lebris@cermics.enpc.fr

    2007-03-01

    We introduce a new multilevel domain decomposition method (MDD) for electronic structure calculations within semi-empirical and density functional theory (DFT) frameworks. This method iterates between local fine solvers and global coarse solvers, in the spirit of domain decomposition methods. Using this approach, calculations have been successfully performed on several linear polymer chains containing up to 40,000 atoms and 200,000 atomic orbitals. Both the computational cost and the memory requirement scale linearly with the number of atoms. Additional speed-up can easily be obtained by parallelization. We show that this domain decomposition method outperforms the density matrix minimization (DMM) method for poor initial guesses. Our method provides an efficient preconditioner for DMM and other linear scaling methods, variational in nature, such as the orbital minimization (OM) procedure.

  15. Domain walls as probes of gravity

    SciTech Connect

    Dvali, Gia; Gabadadze, Gregory; Pujolas, Oriol; Rahman, Rakibur

    2007-06-15

    We show that domain walls are probes that enable one to distinguish large-distance modified gravity from general relativity (GR) at short distances. For example, low-tension domain walls are stealth in modified gravity, while they do produce global gravitational effects in GR. We demonstrate this by finding exact solutions for various domain walls in the DGP model. A wall with tension lower than the fundamental Planck scale does not inflate and has no gravitational effects on a 4D observer, since its 4D tension is completely screened by gravity itself. We argue that this feature remains valid in a generic class of models of infrared modified gravity. As a byproduct, we obtain exact solutions for supermassive codimension-2 branes.

  16. Domain switching of fatigued ferroelectric thin films

    SciTech Connect

    Tak Lim, Yun; Yeog Son, Jong E-mail: hoponpop@ulsan.ac.kr; Shin, Young-Han E-mail: hoponpop@ulsan.ac.kr

    2014-05-12

    We investigate the domain wall speed of a ferroelectric PbZr{sub 0.48}Ti{sub 0.52}O{sub 3} (PZT) thin film using an atomic force microscope incorporated with a mercury-probe system to control the degree of electrical fatigue. The depolarization field in the PZT thin film decreases with increasing the degree of electrical fatigue. We find that the wide-range activation field previously reported in ferroelectric domains result from the change of the depolarization field caused by the electrical fatigue. Domain wall speed exhibits universal behavior to the effective electric field (defined by an applied electric field minus the depolarization field), regardless of the degree of the electrical fatigue.

  17. Intellectual Growth in Children as a Function of Domain Specific and Domain General Working Memory Subgroups

    ERIC Educational Resources Information Center

    Swanson, H. Lee

    2011-01-01

    This study examined whether children's growth on measures of fluid (Raven Colored Progressive Matrices) and crystallized (reading and math achievement) intelligence was attributable to domain-specific or domain-general functions of working memory (WM). A sample of 290 elementary school children was tested on measures of intelligence across three…

  18. Electric-field-driven dynamics of magnetic domain walls in magnetic nanowires patterned on ferroelectric domains

    NASA Astrophysics Data System (ADS)

    Van de Wiele, Ben; Leliaert, Jonathan; Franke, Kévin J. A.; van Dijken, Sebastiaan

    2016-03-01

    Strong coupling of magnetic domain walls onto straight ferroelastic boundaries of a ferroelectric layer enables full and reversible electric-field control of magnetic domain wall motion. In this paper, the dynamics of this new driving mechanism is analyzed using micromagnetic simulations. We show that transverse domain walls with a near-180° spin structure are stabilized in magnetic nanowires and that electric fields can move these walls with high velocities. Above a critical velocity, which depends on material parameters, nanowire geometry and the direction of domain wall motion, the magnetic domain walls depin abruptly from the ferroelastic boundaries. Depinning evolves either smoothly or via the emission and annihilation of a vortex or antivortex core (Walker breakdown). In both cases, the magnetic domain wall slows down after depinning in an oscillatory fashion and eventually comes to a halt. The simulations provide design rules for hybrid ferromagnetic-ferroelectric domain-wall-based devices and indicate that material disorder and structural imperfections only influence Walker-breakdown-like depinning at high domain wall velocities.

  19. Quantum Oscillations of Interacting Nanoscale Structural Inhomogeneities in a Domain Wall of Magnetic Stripe Domain

    NASA Astrophysics Data System (ADS)

    Shevchenko, Andriy; Barabash, Maksym

    2016-10-01

    It was established that at low temperatures, quantum oscillations of a pair of interacting nanoscale structural inhomogeneities (vertical Bloch lines) occur in a domain wall of stripe domain in uniaxial ferromagnetic film. The effective mass of vertical Bloch line and conditions for this effect were determined. The effect can be used in the hybrid storage devices bit + q-bit.

  20. SH3 Domains Differentially Stimulate Distinct Dynamin I Assembly Modes and G Domain Activity

    PubMed Central

    Krishnan, Sai; Collett, Michael; Robinson, Phillip J.

    2015-01-01

    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. PMID:26659814

  1. Conducting Ferroelectric Walls, Domain Topology, and Domain Switching Kinetics in a Hybrid Improper Ferroelectric

    NASA Astrophysics Data System (ADS)

    Cheong, Sang-Wook; Rutgers CenterEmergent Materials Team

    Charged polar interfaces such as charged ferroelectric domain walls or heterostructured interfaces of ZnO/(Zn,Mg)O and LaAlO 3 /SrTiO 3 , across which the normal component of electric polarization changes suddenly, can host large two-dimensional conduction. Charged ferroelectric domain walls can be highly conducting but energetically unfavored; however, they were found to be mysteriously abundant in hybrid improper ferroelectric (Ca,Sr) 3 Ti 2 O 7 single crystals. From the exploration of antiphase domain boundaries, which are hidden in piezoresponse force microscopy, using dark-field electron microscopy, we have explored the macroscopic topology of polarization domains and antiphase domains. We found that the macroscopic domain topology is directly responsible for the presence of charged domain walls, and is closely related with the polarization domain switching mechanism in (Ca,Sr) 3 Ti 2 O 7 . Rutgers Center for Emergent Materials and Department of Physics and Astronomy, Rutgers University, Piscataway, New Jersey 08854, USA.

  2. Continuous and discontinuous domains: an algorithm for the automatic generation of reliable protein domain definitions.

    PubMed Central

    Siddiqui, A. S.; Barton, G. J.

    1995-01-01

    An algorithm is presented for the fast and accurate definition of protein structural domains from coordinate data without prior knowledge of the number or type of domains. The algorithm explicitly locates domains that comprise one or two continuous segments of protein chain. Domains that include more than two segments are also located. The algorithm was applied to a nonredundant database of 230 protein structures and the results compared to domain definitions obtained from the literature, or by inspection of the coordinates on molecular graphics. For 70% of the proteins, the derived domains agree with the reference definitions, 18% show minor differences and only 12% (28 proteins) show very different definitions. Three screens were applied to identify the derived domains least likely to agree with the subjective definition set. These screens revealed a set of 173 proteins, 97% of which agree well with the subjective definitions. The algorithm represents a practical domain identification tool that can be run routinely on the entire structural database. Adjustment of parameters also allows smaller compact units to be identified in proteins. PMID:7663343

  3. Ultrastructure and function of the fractalkine mucin domain in CX(3)C chemokine domain presentation.

    PubMed

    Fong, A M; Erickson, H P; Zachariah, J P; Poon, S; Schamberg, N J; Imai, T; Patel, D D

    2000-02-11

    Fractalkine (FKN), a CX(3)C chemokine/mucin hybrid molecule on endothelium, functions as an adhesion molecule to capture and induce firm adhesion of a subset of leukocytes in a selectin- and integrin-independent manner. We hypothesized that the FKN mucin domain may be important for its function in adhesion, and tested the ability of secreted alkaline phosphatase (SEAP) fusion proteins containing the entire extracellular region (FKN-SEAP), the chemokine domain (CX3C-SEAP), or the mucin domain (mucin-SEAP) to support firm adhesion under flow. CX3C-SEAP induced suboptimal firm adhesion of resting peripheral blood mononuclear cells, compared with FKN-SEAP, and mucin-SEAP induced no firm adhesion. CX3C-SEAP and FKN-SEAP bound to CX(3)CR1 with similar affinities. By electron microscopy, fractalkine was 29 nm in length with a long stalk (mucin domain), and a globular head (CX(3)C). To test the function of the mucin domain, a chimeric protein replacing the mucin domain with a rod-like segment of E-selectin was constructed. This chimeric protein gave the same adhesion of peripheral blood mononuclear cells as intact FKN, both when immobilized on glass and when expressed on the cell surface. This implies that the function of the mucin domain is to provide a stalk, extending the chemokine domain away from the endothelial cell surface to present it to flowing leukocytes.

  4. Design PID controllers for desired time-domain or frequency-domain response.

    PubMed

    Zhang, Weidong; Xi, Yugeng; Yang, Genke; Xu, Xiaoming

    2002-10-01

    Practical requirements on the design of control systems, especially process control systems, are usually specified in terms of time-domain response, such as overshoot and rise time, or frequency-domain response, such as resonance peak and stability margin. Although numerous methods have been developed for the design of the proportional-integral-derivative (PID) controller, little work has been done in relation to the quantitative time-domain and frequency-domain responses. In this paper, we study the following problem: Given a nominal stable process with time delay, we design a suboptimal PID controller to achieve the required time-domain response or frequency-domain response for the nominal system or the uncertain system. An H(infinity) PID controller is developed based on optimal control theory and the parameters are derived analytically. Its properties are investigated and compared with that of two developed suboptimal controllers: an H2 PID controller and a Maclaurin PID controller. It is shown that all three controllers can provide the quantitative time-domain and frequency-domain responses.

  5. Matter antimatter domains: A possible solution to the CP domain wall problem in the early universe

    NASA Technical Reports Server (NTRS)

    Mohanty, A. K.; Stecker, F. W.

    1984-01-01

    An SU(5) grand unified theory model is used to show how the degeneracy between vacua with different spontaneously broken charge parity can be dynamically lifted by a condensate of heavy fermion pairs. This drives a phase transition to a unique vacuum state with definite charge parity. The transition eliminates the domain walls in a matter antimatter symmetric domain cosmology.

  6. An inhibitor domain in Sp3 regulates its glutamine-rich activation domains.

    PubMed Central

    Dennig, J; Beato, M; Suske, G

    1996-01-01

    Sp3 is a ubiquitously expressed human transcription factor closely related to Sp1 and Sp4. All three proteins contain a highly conserved DNA binding domain and two glutamine-rich regions, suggesting that they possess similar activation functions. In our previous experiments, however, Sp3 failed to activate transcription. Instead, it repressed Sp1-mediated transcriptional activation, suggesting that it is an inhibitory member of this family of regulatory factors. Here we show that Sp3 can also act as a positive regulator of transcription. The glutamine-rich domains on their own have a strong activation function and interact with the TATA box binding protein (TBP)-associated factor dTAFII110. However, in full-length Sp3 as well as in Gal4-Sp3 fusion proteins, both activation domains are silenced by an inhibitory domain located between the second glutamine-rich region and the DNA binding domain. The inhibitory domain completely suppressed transcriptional activation when fused to a heterologous glutamine-rich domain but only moderately suppressed transcription when linked to an acidic activation domain. Site-directed mutagenesis identified a stretch of highly charged amino acid residues essential for inhibitor function. Substitution of the amino acid triplet KEE by alanine residues within this region changed the almost transcriptionally inactive Sp3 into a strong activator. Our results suggest that the transcriptional activity of Sp3 might be regulated in vivo by relief of inhibition. Images PMID:8896459

  7. Evolutionary cross-domain discriminative Hessian Eigenmaps.

    PubMed

    Si, Si; Tao, Dacheng; Chan, Kwok-Ping

    2010-04-01

    Is it possible to train a learning model to separate tigers from elks when we have 1) labeled samples of leopard and zebra and 2) unlabelled samples of tiger and elk at hand? Cross-domain learning algorithms can be used to solve the above problem. However, existing cross-domain algorithms cannot be applied for dimension reduction, which plays a key role in computer vision tasks, e.g., face recognition and web image annotation. This paper envisions the cross-domain discriminative dimension reduction to provide an effective solution for cross-domain dimension reduction. In particular, we propose the cross-domain discriminative Hessian Eigenmaps or CDHE for short. CDHE connects training and test samples by minimizing the quadratic distance between the distribution of the training set and that of the test set. Therefore, a common subspace for data representation can be well preserved. Furthermore, we basically expect the discriminative information used to separate leopards and zebra can be shared to separate tigers and elks, and thus we have a chance to duly address the above question. Margin maximization principle is adopted in CDHE so the discriminative information for separating different classes (e.g., leopard and zebra here) can be well preserved. Finally, CDHE encodes the local geometry of each training class (e.g., leopard and zebra here) in the local tangent space which is locally isometric to the data manifold and thus CDHE preserves the intraclass local geometry. The objective function of CDHE is not convex, so the gradient descent strategy can only find a local optimal solution. In this paper, we carefully design an evolutionary search strategy to find a better solution of CDHE. Experimental evidence on both synthetic and real word image datasets demonstrates the effectiveness of CDHE for cross-domain web image annotation and face recognition.

  8. Proteins and cholesterol-rich domains.

    PubMed

    Epand, Richard M

    2008-01-01

    Biological membranes are composed of many molecular species of lipids and proteins. These molecules do not mix ideally. In the plane of the membrane components are segregated into domains that are enriched in certain lipids and proteins. Cholesterol is a membrane lipid that is not uniformly distributed in the membrane. Proteins play an important role in determining cholesterol distribution. Certain types of protein lipidation are known to cause the lipoprotein to sequester with cholesterol and to stabilize cholesterol-rich domains. However, proteins that are excluded from such domains also contribute to the redistribution of cholesterol. One of the motifs that favor interaction with cholesterol is the CRAC motif. The role of the CRAC motif of the gp41 fusogenic protein of HIV is discussed. The distribution of the multianionic lipid, phosphatidylinositol(4,5)bis-phosphate (PtnIns(4,5)P2), is also not uniform in cell membranes. This lipid has several functions in the cell, including a morphological role in determining the sites of attachment of the actin cytoskeleton to the plasma membrane. PtnIns(4,5)P2 is sequestered by proteins having clusters of cationic residues in their sequence. Certain proteins containing cationic clusters also contain moieties such as myristoylation or a CRAC segment that would also endow them with the ability to sequester to a cholesterol-rich domain. These proteins interact with PtnIns(4,5)P2 in a cholesterol-dependent manner forming domains that are enriched in both cholesterol and in PtnIns(4,5)P2 but can also be distinct from liquid-ordered raft-like domains.

  9. Identification and characterization of structural domains of human ERp57: association with calreticulin requires several domains.

    PubMed

    Silvennoinen, Laura; Myllyharju, Johanna; Ruoppolo, Margherita; Orrù, Stefania; Caterino, Marianna; Kivirikko, Kari I; Koivunen, Peppi

    2004-04-02

    The amino acid sequence of ERp57, which functions in the endoplasmic reticulum together with the lectins calreticulin and calnexin to achieve folding of newly synthesized glycoproteins, is highly similar to that of protein disulfide isomerase (PDI), but they have their own distinct roles in protein folding. We have characterized the domain structure of ERp57 by limited proteolysis and N-terminal sequencing and have found it to be similar but not identical to that of PDI. ERp57 had three major protease-sensitive regions, the first of which was located between residues 120 and 150, the second between 201 and 215, and the third between 313 and 341, the data thus being consistent with a four-domain structure abb'a'. Recombinant expression in Escherichia coli was used to verify the domain boundaries. Each single domain and a b'a' double domain could be produced in the form of soluble, folded polypeptides, as verified by circular dichroism spectra and urea gradient gel electrophoresis. When the ability of ERp57 and its a and a' domains to fold denatured RNase A was studied by electrospray mass analyses, ERp57 markedly enhanced the folding rate at early time points, although less effectively than PDI, but was an ineffective catalyst of the overall process. The a and a' domains produced only minor, if any, increases in the folding rate at the early stages and no increase at the late stages. Interaction of the soluble ERp57 domains with the P domain of calreticulin was studied by chemical cross-linking in vitro. None of the single ERp57 domains nor the b'a' double domain could be cross-linked to the P domain, whereas cross-linking was obtained with a hybrid ERpabb'PDIa'c polypeptide but not with ERpabPDIb'a'c, indicating that multiple domains are involved in this protein-protein interaction and that the b' domain of ERp57 cannot be replaced by that of PDI.

  10. Differential ghost imaging in time domain

    NASA Astrophysics Data System (ADS)

    O-oka, Yoshiki; Fukatsu, Susumu

    2017-08-01

    Differential ghost imaging is attempted in time domain, i.e., temporal differential ghost imaging (TDGI), using pseudo-randomized light pulses and a temporal object consisting of no-return-to-zero bit patterns of varying duty. Evaluation of the signal-to-noise characteristics by taking into account errors due to false cross-correlation between the reference and the bucket detector readings indicates that the TDGI outperforms its non-differential counterpart, i.e., time-domain GI, in terms of consistently high and even duty-independent signal-to-noise ratios that are achieved.

  11. Standing gravitational waves from domain walls

    SciTech Connect

    Gogberashvili, Merab; Myrzakul, Shynaray; Singleton, Douglas

    2009-07-15

    We construct a plane symmetric, standing gravitational wave for a domain wall plus a massless scalar field. The scalar field can be associated with a fluid which has the properties of 'stiff' matter, i.e., matter in which the speed of sound equals the speed of light. Although domain walls are observationally ruled out in the present era, the solution has interesting features which might shed light on the character of exact nonlinear wave solutions to Einstein's equations. Additionally this solution may act as a template for higher dimensional 'brane-world' model standing waves.

  12. On automating domain connectivity for overset grids

    NASA Technical Reports Server (NTRS)

    Chiu, Ing-Tsau

    1994-01-01

    An alternative method for domain connectivity among systems of overset grids is presented. Reference uniform Cartesian systems of points are used to achieve highly efficient domain connectivity, and form the basis for a future fully automated system. The Cartesian systems are used to approximated body surfaces and to map the computational space of component grids. By exploiting the characteristics of Cartesian Systems, Chimera type hole-cutting and identification of donor elements for intergrid boundary points can be carried out very efficiently. The method is tested for a range of geometrically complex multiple-body overset grid systems.

  13. Models for Gapped Boundaries and Domain Walls

    NASA Astrophysics Data System (ADS)

    Kitaev, Alexei; Kong, Liang

    2012-07-01

    We define a class of lattice models for two-dimensional topological phases with boundary such that both the bulk and the boundary excitations are gapped. The bulk part is constructed using a unitary tensor category {C} as in the Levin-Wen model, whereas the boundary is associated with a module category over {C} . We also consider domain walls (or defect lines) between different bulk phases. A domain wall is transparent to bulk excitations if the corresponding unitary tensor categories are Morita equivalent. Defects of higher codimension will also be studied. In summary, we give a dictionary between physical ingredients of lattice models and tensor-categorical notions.

  14. [Development of domain specific search engines].

    PubMed

    Takai, T; Tokunaga, M; Maeda, K; Kaminuma, T

    2000-01-01

    As cyber space exploding in a pace that nobody has ever imagined, it becomes very important to search cyber space efficiently and effectively. One solution to this problem is search engines. Already a lot of commercial search engines have been put on the market. However these search engines respond with such cumbersome results that domain specific experts can not tolerate. Using a dedicate hardware and a commercial software called OpenText, we have tried to develop several domain specific search engines. These engines are for our institute's Web contents, drugs, chemical safety, endocrine disruptors, and emergent response for chemical hazard. These engines have been on our Web site for testing.

  15. Casimir forces in the time domain: Theory

    SciTech Connect

    Rodriguez, Alejandro W.; McCauley, Alexander P.; Joannopoulos, John D.; Johnson, Steven G.

    2009-07-15

    We present a method to compute Casimir forces in arbitrary geometries and for arbitrary materials based on the finite-difference time-domain (FDTD) scheme. The method involves the time evolution of electric and magnetic fields in response to a set of current sources, in a modified medium with frequency-independent conductivity. The advantage of this approach is that it allows one to exploit existing FDTD software, without modification, to compute Casimir forces. In this paper, we focus on the derivation, implementation choices, and essential properties of the time-domain algorithm, both considered analytically and illustrated in the simplest parallel-plate geometry.

  16. Anderson localization in the time domain

    NASA Astrophysics Data System (ADS)

    Sacha, Krzysztof; Delande, Dominique

    2016-08-01

    In analogy with the usual Anderson localization taking place in time-independent disordered quantum systems where the disorder acts in configuration space, systems exposed to temporally disordered potentials can display Anderson localization in the time domain. We demonstrate this phenomenon with one-dimensional examples where a temporally disordered potential induces localization during the quantum evolution of wave packets, in contrast with a fully delocalized classical dynamics. This is an example of a time crystal phenomenon, i.e., a crystalline behavior in the time domain.

  17. Small domain-size multiblock copolymer electrolytes

    DOEpatents

    Pistorino, Jonathan; Eitouni, Hany Basam

    2016-09-20

    New block polymer electrolytes have been developed which have higher conductivities than previously reported for other block copolymer electrolytes. The new materials are constructed of multiple blocks (>5) of relatively low domain size. The small domain size provides greater protection against formation of dendrites during cycling against lithium in an electrochemical cell, while the large total molecular weight insures poor long range alignment, which leads to higher conductivity. In addition to higher conductivity, these materials can be more easily synthesized because of reduced requirements on the purity level of the reagents.

  18. Training Humans for the Human Domain

    DTIC Science & Technology

    2015-11-01

    TRAINING HUMANS FOR THE HUMAN DOMAIN Dr. Steve Tatham Mr. Keir Giles U.S. ARMY WAR COLLEGE ~~~ ~O.L STRATEGIC STUDIES INSTITUTE Report...REPORT TYPE 3. DATES COVERED 00-00-2015 to 00-00-2015 4. TITLE AND SUBTITLE Training Humans for the Human Domain 5a. CONTRACT NUMBER 5b. GRANT...NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d. PROJECT NUMBER 5e. TASK NUMBER 5f. WORK UNIT NUMBER 7. PERFORMING ORGANIZATION NAME(S) AND

  19. Convergence Analysis of a Domain Decomposition Paradigm

    SciTech Connect

    Bank, R E; Vassilevski, P S

    2006-06-12

    We describe a domain decomposition algorithm for use in several variants of the parallel adaptive meshing paradigm of Bank and Holst. This algorithm has low communication, makes extensive use of existing sequential solvers, and exploits in several important ways data generated as part of the adaptive meshing paradigm. We show that for an idealized version of the algorithm, the rate of convergence is independent of both the global problem size N and the number of subdomains p used in the domain decomposition partition. Numerical examples illustrate the effectiveness of the procedure.

  20. Angular Dependence of Domain Wall Resistivity in Artificial Magnetic Domain Structures

    NASA Astrophysics Data System (ADS)

    Aziz, A.; Bending, S. J.; Roberts, H. G.; Crampin, S.; Heard, P. J.; Marrows, C. H.

    2006-11-01

    We exploit the ability to precisely control the magnetic domain structure of perpendicularly magnetized Pt/Co/Pt trilayers to fabricate artificial domain wall arrays and study their transport properties. The scaling behavior of this model system confirms the intrinsic domain wall origin of the magnetoresistance, and systematic studies using domains patterned at various angles to the current flow are excellently described by an angular-dependent resistivity tensor containing perpendicular and parallel domain wall resistivities. We find that the latter are fully consistent with Levy-Zhang theory, which allows us to estimate the ratio of minority to majority spin carrier resistivities, ρ↓/ρ↑˜5.5, in good agreement with thin film band structure calculations.