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Sample records for phytochrome gaf domain

  1. Bright blue-shifted fluorescent proteins with Cys in the GAF domain engineered from bacterial phytochromes: fluorescence mechanisms and excited-state dynamics

    PubMed Central

    Hontani, Yusaku; Shcherbakova, Daria M.; Baloban, Mikhail; Zhu, Jingyi; Verkhusha, Vladislav V.; Kennis, John T. M.

    2016-01-01

    Near-infrared fluorescent proteins (NIR FPs) engineered from bacterial phytochromes (BphPs) are of great interest for in vivo imaging. They utilize biliverdin (BV) as a chromophore, which is a heme degradation product, and therefore they are straightforward to use in mammalian tissues. Here, we report on fluorescence properties of NIR FPs with key alterations in their BV binding sites. BphP1-FP, iRFP670 and iRFP682 have Cys residues in both PAS and GAF domains, rather than in the PAS domain alone as in wild-type BphPs. We found that NIR FP variants with Cys in the GAF or with Cys in both PAS and GAF show blue-shifted emission with long fluorescence lifetimes. In contrast, mutants with Cys in the PAS only or no Cys residues at all exhibit red-shifted emission with shorter lifetimes. Combining these results with previous biochemical and BphP1-FP structural data, we conclude that BV adducts bound to Cys in the GAF are the origin of bright blue-shifted fluorescence. We propose that the long fluorescence lifetime follows from (i) a sterically more constrained thioether linkage, leaving less mobility for ring A than in canonical BphPs, and (ii) that π-electron conjugation does not extend on ring A, making excited-state deactivation less sensitive to ring A mobility. PMID:27857208

  2. Bright blue-shifted fluorescent proteins with Cys in the GAF domain engineered from bacterial phytochromes: fluorescence mechanisms and excited-state dynamics

    NASA Astrophysics Data System (ADS)

    Hontani, Yusaku; Shcherbakova, Daria M.; Baloban, Mikhail; Zhu, Jingyi; Verkhusha, Vladislav V.; Kennis, John T. M.

    2016-11-01

    Near-infrared fluorescent proteins (NIR FPs) engineered from bacterial phytochromes (BphPs) are of great interest for in vivo imaging. They utilize biliverdin (BV) as a chromophore, which is a heme degradation product, and therefore they are straightforward to use in mammalian tissues. Here, we report on fluorescence properties of NIR FPs with key alterations in their BV binding sites. BphP1-FP, iRFP670 and iRFP682 have Cys residues in both PAS and GAF domains, rather than in the PAS domain alone as in wild-type BphPs. We found that NIR FP variants with Cys in the GAF or with Cys in both PAS and GAF show blue-shifted emission with long fluorescence lifetimes. In contrast, mutants with Cys in the PAS only or no Cys residues at all exhibit red-shifted emission with shorter lifetimes. Combining these results with previous biochemical and BphP1-FP structural data, we conclude that BV adducts bound to Cys in the GAF are the origin of bright blue-shifted fluorescence. We propose that the long fluorescence lifetime follows from (i) a sterically more constrained thioether linkage, leaving less mobility for ring A than in canonical BphPs, and (ii) that π-electron conjugation does not extend on ring A, making excited-state deactivation less sensitive to ring A mobility.

  3. Minimal domain of bacterial phytochrome required for chromophore binding and fluorescence

    NASA Astrophysics Data System (ADS)

    Rumyantsev, Konstantin A.; Shcherbakova, Daria M.; Zakharova, Natalia I.; Emelyanov, Alexander V.; Turoverov, Konstantin K.; Verkhusha, Vladislav V.

    2015-12-01

    Fluorescent proteins (FP) are used to study various biological processes. Recently, a series of near-infrared (NIR) FPs based on bacterial phytochromes was developed. Finding ways to improve NIR FPs is becoming progressively important. By applying rational design and molecular evolution we have engineered R. palustris bacterial phytochrome into a single-domain NIR FP of 19.6 kDa, termed GAF-FP, which is 2-fold and 1.4-fold smaller than bacterial phytochrome-based NIR FPs and GFP-like proteins, respectively. Engineering of GAF-FP involved a substitution of 15% of its amino acids and a deletion of the knot structure. GAF-FP covalently binds two tetrapyrrole chromophores, biliverdin (BV) and phycocyanobilin (PCB). With the BV chromophore GAF-FP absorbs at 635 nm and fluoresces at 670 nm. With the PCB chromophore GAF-FP becomes blue-shifted and absorbs at 625 nm and fluoresces at 657 nm. The GAF-FP structure has a high tolerance to small peptide insertions. The small size of GAF-FP and its additional absorbance band in the violet range has allowed for designing a chimeric protein with Renilla luciferase. The chimera exhibits efficient non-radiative energy transfer from luciferase to GAF-FP, resulting in NIR bioluminescence. This study opens the way for engineering of small NIR FPs and NIR luciferases from bacterial phytochromes.

  4. Minimal domain of bacterial phytochrome required for chromophore binding and fluorescence

    PubMed Central

    Rumyantsev, Konstantin A.; Shcherbakova, Daria M.; Zakharova, Natalia I.; Emelyanov, Alexander V.; Turoverov, Konstantin K.; Verkhusha, Vladislav V.

    2015-01-01

    Fluorescent proteins (FP) are used to study various biological processes. Recently, a series of near-infrared (NIR) FPs based on bacterial phytochromes was developed. Finding ways to improve NIR FPs is becoming progressively important. By applying rational design and molecular evolution we have engineered R. palustris bacterial phytochrome into a single-domain NIR FP of 19.6 kDa, termed GAF-FP, which is 2-fold and 1.4-fold smaller than bacterial phytochrome-based NIR FPs and GFP-like proteins, respectively. Engineering of GAF-FP involved a substitution of 15% of its amino acids and a deletion of the knot structure. GAF-FP covalently binds two tetrapyrrole chromophores, biliverdin (BV) and phycocyanobilin (PCB). With the BV chromophore GAF-FP absorbs at 635 nm and fluoresces at 670 nm. With the PCB chromophore GAF-FP becomes blue-shifted and absorbs at 625 nm and fluoresces at 657 nm. The GAF-FP structure has a high tolerance to small peptide insertions. The small size of GAF-FP and its additional absorbance band in the violet range has allowed for designing a chimeric protein with Renilla luciferase. The chimera exhibits efficient non-radiative energy transfer from luciferase to GAF-FP, resulting in NIR bioluminescence. This study opens the way for engineering of small NIR FPs and NIR luciferases from bacterial phytochromes. PMID:26679720

  5. Multiple Roles of a Conserved GAF Domain Tyrosine Residue in Cyanobacterial and Plant Phytochromes†

    PubMed Central

    Fischer, Amanda J.; Rockwell, Nathan C.; Jang, Abigail Y.; Ernst, Lauren A.; Waggoner, Alan S.; Duan, Yong; Lei, Hongxing; Lagarias, J. Clark

    2005-01-01

    The phytochrome family of red/far-red photoreceptors has been optimized to support photochemical isomerization of a bound bilin chromophore, a process that triggers a conformational change and modulates biochemical output from the surrounding protein scaffold. Recent studies have established that the efficiency of this photochemical process is profoundly altered by mutation of a conserved tyrosine residue (Tyr176) within the bilin-binding GAF domain of the cyanobacterial phytochrome Cph1 [Fischer, A. J., and Lagarias, J. C. (2004) Harnessing phytochrome’s glowing potential, Proc. Natl. Acad. Sci. U.S.A. 101, 17334–17339]. Here, we show that the equivalent mutation in plant phytochromes behaves similarly, indicating that the function of this tyrosine in the primary photochemical mechanism is conserved. Saturation mutagenesis of Tyr176 in Cph1 establishes that no other residue can support comparably efficient photoisomerization. The spectroscopic consequences of Tyr176 mutations also reveal that Tyr176 regulates the conversion of the porphyrin-like conformation of the bilin precursor to a more extended conformation. The porphyrin-binding ability of the Tyr176Arg mutant protein indicates that Tyr176 also regulates the ligand-binding specificity of apophytochrome. On the basis of the hydrogen-bonding ability of Tyr176 substitutions that support the nonphotochemical C15-Z,syn to C15-Z,anti interconversion, we propose that Tyr176 orients the carboxyl side chain of a conserved acidic residue to stabilize protonation of the bilin chromophore. A homology model of the GAF domain of Cph1 predicts a C5-Z,syn, C10-Z,syn, C15-Z,anti configuration for the chromophore and implicates Glu189 as the proposed acidic residue stabilizing the extended conformation, an interpretation consistent with site-directed mutagenesis of this conserved acidic residue. PMID:16285723

  6. A second conserved GAF domain cysteine is required for the blue/green photoreversibility of cyanobacteriochrome Tlr0924 from Thermosynechococcus elongatus.

    PubMed Central

    Rockwell, Nathan C.; Njuguna, Stephanie Lane; Roberts, Laurel; Castillo, Elenor; Parson, Victoria L.; Dwojak, Sunshine; Lagarias, J. Clark; Spiller, Susan C.

    2008-01-01

    Phytochromes are widely occurring red/far-red photoreceptors that utilize a linear tetrapyrrole (bilin) chromophore covalently bound within a knotted PAS-GAF domain pair. Cyanobacteria also contain more distant relatives of phytochromes that lack this knot, such as the phytochrome-related cyanobacteriochromes implicated to function as blue/green switchable photoreceptors. In this study, we characterize the cyanobacteriochrome Tlr0924 from the thermophilic cyanobacterium Thermosynechococcus elongatus. Full-length Tlr0924 exhibits blue/green photoconversion across a broad range of temperatures, including physiologically relevant temperatures for this organism. Spectroscopic characterization of Tlr0924 demonstrates that its green-absorbing state is in equilibrium with a labile, spectrally distinct blue-absorbing species. The photochemically generated blue-absorbing state is in equilibrium with another species absorbing at longer wavelengths, giving a total of 4 states. Cys499 is essential for this behavior, because mutagenesis of this residue results in red-absorbing mutant biliproteins. Characterization of the C499D mutant protein by absorbance and CD spectroscopy supports the conclusion that its bilin chromophore adopts a similar conformation to the red-light-absorbing Pr form of phytochrome. We propose a model photocycle in which Z/E photoisomerization of the 15/16 bond modulates formation of a reversible thioether linkage between Cys499 and C10 of the chromophore, providing the basis for the blue/green switching of cyanobacteriochromes. PMID:18549244

  7. Conformation Changes N-terminal Involvement and cGMP Signal Relay in the Phosphodiesterase-5 GAF Domain

    SciTech Connect

    H Wang; H Robinson; H Ke

    2011-12-31

    The activity of phosphodiesterase-5 (PDE5) is specific for cGMP and is regulated by cGMP binding to GAF-A in its regulatory domain. To better understand the regulatory mechanism, x-ray crystallographic and biochemical studies were performed on constructs of human PDE5A1 containing the N-terminal phosphorylation segment, GAF-A, and GAF-B. Superposition of this unliganded GAF-A with the previously reported NMR structure of cGMP-bound PDE5 revealed dramatic conformational differences and suggested that helix H4 and strand B3 probably serve as two lids to gate the cGMP-binding pocket in GAF-A. The structure also identified an interfacial region among GAF-A, GAF-B, and the N-terminal loop, which may serve as a relay of the cGMP signal from GAF-A to GAF-B. N-terminal loop 98-147 was physically associated with GAF-B domains of the dimer. Biochemical analyses showed an inhibitory effect of this loop on cGMP binding and its involvement in the cGMP-induced conformation changes.

  8. Conformation changes, N-terminal involvement and cGMP signal relay in phosphodiesterase-5 GAF domain

    SciTech Connect

    Wang, H.; Robinson, H.; Ke, H.

    2010-12-03

    The activity of phosphodiesterase-5 (PDE5) is specific for cGMP and is regulated by cGMP binding to GAF-A in its regulatory domain. To better understand the regulatory mechanism, x-ray crystallographic and biochemical studies were performed on constructs of human PDE5A1 containing the N-terminal phosphorylation segment, GAF-A, and GAF-B. Superposition of this unliganded GAF-A with the previously reported NMR structure of cGMP-bound PDE5 revealed dramatic conformational differences and suggested that helix H4 and strand B3 probably serve as two lids to gate the cGMP-binding pocket in GAF-A. The structure also identified an interfacial region among GAF-A, GAF-B, and the N-terminal loop, which may serve as a relay of the cGMP signal from GAF-A to GAF-B. N-terminal loop 98-147 was physically associated with GAF-B domains of the dimer. Biochemical analyses showed an inhibitory effect of this loop on cGMP binding and its involvement in the cGMP-induced conformation changes.

  9. Structural rearrangement accompanying ligand binding in the GAF domain of CodY from Bacillus subtilis

    PubMed Central

    Levdikov, Vladimir M.; Blagova, Elena; Colledge, Vicki L.; Lebedev, Andrey A.; Williamson, David C.; Sonenshein, Abraham L.; Wilkinson, Anthony J

    2011-01-01

    The GAF domain is a simple module widespread in proteins of diverse function including cell signalling proteins and transcription factors. Its structure, typically spanning 150 residues, has three tiers; a basal layer of two or more α-helices, a middle layer of β-pleated sheet and a top layer formed by segments of the polypeptide that connect strands of the β-sheet. In structures of GAF domains in complex with their effectors, these polypeptide segments envelop the ligand enclosing it in a cavity whose base is formed by the β-sheet, so that ligand binding and release must be accompanied by conformational rearrangements of the distal portion of the structure. Descriptions of binding are presently limited by the absence of a GAF domain for which both liganded and unliganded structures are known. Earlier, we solved the crystal structure of the GAF domain of CodY, a branched chain amino acid and GTP responsive regulator of the transcription of stationary phase and virulence genes in Bacillus, in complexes with isoleucine and valine. Here, we report the structure of this domain in its unliganded form, allowing definition of the structural changes accompanying ligand binding. The core of the protein and its dimerisation interface are essentially unchanged in agreement with circular dichroism spectroscopy experiments that show that the secondary structure composition is unperturbed by ligand binding. There is however, extensive refolding of the binding site loops, with up to 15 Å movements of the coiled segment linking β3 and β4, such that in the absence of the ligand, the binding pocket is not formed. The implications of these structural rearrangements for ligand affinity and specificity are discussed. Finally, saturation transfer difference NMR spectroscopy showed binding of isoleucine, but not GTP, to the GAF domain suggesting that the two cofactors do not have a common binding site. PMID:19500589

  10. Structure of the GAF domain, a ubiquitous signaling motif and a new class of cyclic GMP receptor

    PubMed Central

    Ho, Yew-Seng J.; Burden, Lisa M.; Hurley, James H.

    2000-01-01

    GAF domains are ubiquitous motifs present in cyclic GMP (cGMP)-regulated cyclic nucleotide phosphodiesterases, certain adenylyl cyclases, the bacterial transcription factor FhlA, and hundreds of other signaling and sensory proteins from all three kingdoms of life. The crystal structure of the Saccharomyces cerevisiae YKG9 protein was determined at 1.9 Å resolution. The structure revealed a fold that resembles the PAS domain, another ubiquitous signaling and sensory transducer. YKG9 does not bind cGMP, but the isolated first GAF domain of phosphodiesterase 5 binds with Kd = 650 nM. The cGMP binding site of the phosphodiesterase GAF domain was identified by homology modeling and site-directed mutagenesis, and consists of conserved Arg, Asn, Lys and Asp residues. The structural and binding studies taken together show that the cGMP binding GAF domains form a new class of cyclic nucleotide receptors distinct from the regulatory domains of cyclic nucleotide-regulated protein kinases and ion channels. PMID:11032796

  11. Solution Structure of the cGMP Binding GAF Domain from Phosphodiesterase 5: Insights into Nucleotide Specificity, Dimerization, and cGMP-Dependent Conformational Change

    SciTech Connect

    Heikaus, Clemens C.; Stout, Joseph R.; Sekharan, Monica R.; Eakin, Catherine M.; Rajagopal, Ponni; Brzovic, Peter S.; Beavo, Joseph A.; Klevit, Rachel E.

    2008-08-15

    Phosphodiesterase 5 (PDE5) controls intracellular levels of cGMP through its regulation of cGMP hydrolysis. Hydrolytic activity of the C-terminal catalytic domain is increased by cGMP binding to the N-terminal GAF A domain. We present the NMR solution structure of the cGMP-bound PDE5A GAF A domain. The cGMP orientation in the buried binding pocket was defined through 37 intermolecular NOEs.

  12. Redox-dependent Ligand Switching in a Sensory Heme-binding GAF Domain of the Cyanobacterium Nostoc sp. PCC7120.

    PubMed

    Tang, Kun; Knipp, Markus; Liu, Bing-Bing; Cox, Nicholas; Stabel, Robert; He, Qi; Zhou, Ming; Scheer, Hugo; Zhao, Kai-Hong; Gärtner, Wolfgang

    2015-07-31

    The genome of the cyanobacterium Nostoc sp. PCC7120 carries three genes (all4978, all7016, and alr7522) encoding putative heme-binding GAF (cGMP-specific phosphodiesterases, adenylyl cyclases, and FhlA) proteins that were annotated as transcriptional regulators. They are composed of an N-terminal cofactor domain and a C-terminal helix-turn-helix motif. All4978 showed the highest affinity for protoheme binding. The heme binding capability of All7016 was moderate, and Alr7522 did not bind heme at all. The "as isolated" form of All4978, identified by Soret band (λmax = 427 nm), was assigned by electronic absorption, EPR, and resonance Raman spectroscopy as a hexa-coordinated low spin Fe(III) heme with a distal cysteine ligand (absorption of δ-band around 360 nm). The protoheme cofactor is noncovalently incorporated. Reduction of the heme could be accomplished by chemically using sodium dithionite and electrospectrochemically; this latter method yielded remarkably low midpoint potentials of -445 and -453 mV (following Soret and α-band absorption changes, respectively). The reduced form of the heme (Fe(II) state) binds both NO and CO. Cysteine coordination of the as isolated Fe(III) protein is unambiguous, but interestingly, the reduced heme instead displays spectral features indicative of histidine coordination. Cys-His ligand switches have been reported as putative signaling mechanisms in other heme-binding proteins; however, these novel cyanobacterial proteins are the first where such a ligand-switch mechanism has been observed in a GAF domain. DNA binding of the helix-turn-helix domain was investigated using a DNA sequence motif from its own promoter region. Formation of a protein-DNA complex preferentially formed in ferric state of the protein.

  13. Redox-dependent Ligand Switching in a Sensory Heme-binding GAF Domain of the Cyanobacterium Nostoc sp. PCC7120*

    PubMed Central

    Tang, Kun; Knipp, Markus; Liu, Bing-Bing; Cox, Nicholas; Stabel, Robert; He, Qi; Zhou, Ming; Scheer, Hugo; Zhao, Kai-Hong; Gärtner, Wolfgang

    2015-01-01

    The genome of the cyanobacterium Nostoc sp. PCC7120 carries three genes (all4978, all7016, and alr7522) encoding putative heme-binding GAF (cGMP-specific phosphodiesterases, adenylyl cyclases, and FhlA) proteins that were annotated as transcriptional regulators. They are composed of an N-terminal cofactor domain and a C-terminal helix-turn-helix motif. All4978 showed the highest affinity for protoheme binding. The heme binding capability of All7016 was moderate, and Alr7522 did not bind heme at all. The “as isolated” form of All4978, identified by Soret band (λmax = 427 nm), was assigned by electronic absorption, EPR, and resonance Raman spectroscopy as a hexa-coordinated low spin FeIII heme with a distal cysteine ligand (absorption of δ-band around 360 nm). The protoheme cofactor is noncovalently incorporated. Reduction of the heme could be accomplished by chemically using sodium dithionite and electrospectrochemically; this latter method yielded remarkably low midpoint potentials of −445 and −453 mV (following Soret and α-band absorption changes, respectively). The reduced form of the heme (FeII state) binds both NO and CO. Cysteine coordination of the as isolated FeIII protein is unambiguous, but interestingly, the reduced heme instead displays spectral features indicative of histidine coordination. Cys-His ligand switches have been reported as putative signaling mechanisms in other heme-binding proteins; however, these novel cyanobacterial proteins are the first where such a ligand-switch mechanism has been observed in a GAF domain. DNA binding of the helix-turn-helix domain was investigated using a DNA sequence motif from its own promoter region. Formation of a protein-DNA complex preferentially formed in ferric state of the protein. PMID:26063806

  14. Effect of ATP and 2-oxoglutarate on the in vitro interaction between the NifA GAF domain and the GlnB protein of Azospirillum brasilense

    PubMed Central

    Sotomaior, P.; Araújo, L.M.; Nishikawa, C.Y.; Huergo, L.F.; Monteiro, R.A.; Pedrosa, F.O.; Chubatsu, L.S.; Souza, E.M.

    2012-01-01

    Azospirillum brasilense is a diazotroph that associates with important agricultural crops and thus has potential to be a nitrogen biofertilizer. The A. brasilense transcription regulator NifA, which seems to be constitutively expressed, activates the transcription of nitrogen fixation genes. It has been suggested that the nitrogen status-signaling protein GlnB regulates NifA activity by direct interaction with the NifA N-terminal GAF domain, preventing the inhibitory effect of this domain under conditions of nitrogen fixation. In the present study, we show that an N-terminal truncated form of NifA no longer required GlnB for activity and lost regulation by ammonium. On the other hand, in trans co-expression of the N-terminal GAF domain inhibited the N-truncated protein in response to fixed nitrogen levels. We also used pull-down assays to show in vitro interaction between the purified N-terminal GAF domain of NifA and the GlnB protein. The results showed that A. brasilense GlnB interacts directly with the NifA N-terminal domain and this interaction is dependent on the presence of ATP and 2-oxoglutarate. PMID:22983183

  15. Characterization of tobacco expressing functional oat phytochrome. Domains responsible for the rapid degradation of Pfr are conserved between monocots and dicots

    SciTech Connect

    Cherry, J.R.; Vierstra, R.D. ); Hershey, H.P. )

    1991-07-01

    Constitutive expression of a chimeric oat phytochrome gene in tobacco (Nicotiana tabacum) results in the accumulation of a functional 124-kilodalton photoreceptor that markedly alters the phenotype of light-grown tobacco. Here, we provide a detailed phenotypic and biochemical characterization of homozygous tobacco expressing high levels of oat phytochrome. Phenotypic changes include a substantial inhibition of stem elongation, decreased apical dominance, increased leaf chlorophyll content, and delayed leaf senescence. Oat phytochrome synthesized in tobacco is indistinguishable from that present in etiolated oats, having photoreversible difference spectrum maxima at 665 and 730 nanometers, exhibiting negligible dark reversion of phytochrome - far red-absorbing from (Pfr) to phytochrome - red-absorbing form (Pr), and existing as a dimer with an apparent size of approximately 300 kilodaltons. Heterodimers between the oat and tobacco chromoproteins were detected. Endogenous tobacco phytochrome and transgenically expressed oat phytochrome are rapidly degraded in vivo upon photoconversion of Pr to Pfr. Breakdown of both oat and tobacco Pfr is associated with the accumulation of ubiquitin-phytochrome conjugates, suggesting that degradation occurs via the ubiquitin-dependent proteolytic pathway. This result indicates that the factors responsible for selective recognition of Pfr by the ubiquitin pathway are conserved between monocot and dicot phytochromes. More broadly, it demonstrates that the domains(s) within a plant protein responsible for its selective breakdown can be recognized by the degradation machinery of heterologous species.

  16. 2.3 Å X-ray Structure of the Heme-Bound GAF Domain of Sensory Histidine Kinase DosT of Mycobacterium tuberculosis†

    PubMed Central

    Podust, Larissa M.; Ioanoviciu, Alexandra; Ortiz de Montellano, Paul R.

    2009-01-01

    Mycobacterium tuberculosis responds to the changes in environmental conditions through a two-component signaling system that detects reduced O2 tension and NO and CO exposures via the heme-binding GAF domains of two sensory histidine kinases, DosT and DevS, and the transcriptional regulator DosR. We report the first x-ray structure of the DosT heme-bound GAF domain (GAFDosT) in both oxy and deoxy forms determined to a resolution of 2.3 Å. In GAFDosT, heme binds in an orientation orthogonal to that in the PAS domains via a highly conserved motif including invariant H147 as a proximal heme axial ligand. On the distal side, invariant Y169 is in stacking interactions with the heme with its long axis parallel and the plane of the ring orthogonal to the heme plane. In one of the two protein monomers in an asymmetric unit, O2 binds as a second axial ligand to the heme iron, and is stabilized via an H-bond to the OH-group of Y169. The structure reveals two small tunnel-connected cavities and a pore on the protein surface that suggest a potential route for O2 access to the sensing pocket. The limited conformational differences observed between differently heme iron-ligated GAFDosT monomers in the asymmetric unit may result from crystal lattice limitations since atmospheric oxygen binding likely occurs in the crystal as a result of x-ray induced Fe3+ photoreduction during diffraction data collection. Determination of the GAFDosT structure sets up a framework in which to address ligand-recognition, discrimination, and signal propagation schemes in the heme-based GAF domains of biological sensors. PMID:18980385

  17. Diverse two-cysteine photocycles in phytochromes and cyanobacteriochromes.

    PubMed

    Rockwell, Nathan C; Martin, Shelley S; Feoktistova, Kateryna; Lagarias, J Clark

    2011-07-19

    Phytochromes are well-known as photoactive red- and near IR-absorbing chromoproteins with cysteine-linked linear tetrapyrrole (bilin) prosthetic groups. Phytochrome photoswitching regulates adaptive responses to light in both photosynthetic and nonphotosynthetic organisms. Exclusively found in cyanobacteria, the related cyanobacteriochrome (CBCR) sensors extend the photosensory range of the phytochrome superfamily to shorter wavelengths of visible light. Blue/green light sensing by a well-studied subfamily of CBCRs proceeds via a photolabile thioether linkage to a second cysteine fully conserved in this subfamily. In the present study, we show that dual-cysteine photosensors have repeatedly evolved in cyanobacteria via insertion of a second cysteine at different positions within the bilin-binding GAF domain (cGMP-specific phosphodiesterases, cyanobacterial adenylate cyclases, and formate hydrogen lyase transcription activator FhlA) shared by CBCRs and phytochromes. Such sensors exhibit a diverse range of photocycles, yet all share ground-state absorbance of near-UV to blue light and a common mechanism of light perception: reversible photoisomerization of the bilin 15,16 double bond. Using site-directed mutagenesis, chemical modification and spectroscopy to characterize novel dual-cysteine photosensors from the cyanobacterium Nostoc punctiforme ATCC 29133, we establish that this spectral diversity can be tuned by varying the light-dependent stability of the second thioether linkage. We also show that such behavior can be engineered into the conventional phytochrome Cph1 from Synechocystis sp. PCC6803. Dual-cysteine photosensors thus allow the phytochrome superfamily in cyanobacteria to sense the full solar spectrum at the earth surface from near infrared to near ultraviolet.

  18. Discrete and essential roles of the multiple domains of Arabidopsis FHY3 in mediating phytochrome A signal transduction.

    PubMed

    Lin, Rongcheng; Teng, Yibo; Park, Hee-Jin; Ding, Lei; Black, Christopher; Fang, Ping; Wang, Haiyang

    2008-10-01

    Phytochrome A is the primary photoreceptor for mediating various far-red light-induced responses in higher plants. We recently showed that Arabidopsis (Arabidopsis thaliana) FAR-RED ELONGATED HYPOCOTYL3 (FHY3) and FAR-RED-IMPAIRED RESPONSE1 (FAR1), a pair of homologous proteins sharing significant sequence homology to Mutator-like transposases, act as novel transcription factors essential for activating the expression of FHY1 and FHL (for FHY1-like), whose products are required for light-induced phytochrome A nuclear accumulation and subsequent light responses. FHY3, FAR1, and Mutator-like transposases also share a similar domain structure, including an N-terminal C2H2 zinc finger domain, a central putative core transposase domain, and a C-terminal SWIM motif (named after SWI2/SNF and MuDR transposases). In this study, we performed a promoter-swapping analysis of FHY3 and FAR1. Our results suggest that the partially overlapping functions of FHY3 and FAR1 entail divergence of their promoter activities and protein subfunctionalization. To gain a better understanding of the molecular mode of FHY3 function, we performed a structure-function analysis, using site-directed mutagenesis and transgenic approaches. We show that the conserved N-terminal C2H2 zinc finger domain is essential for direct DNA binding and biological function of FHY3 in mediating light signaling, whereas the central core transposase domain and C-terminal SWIM domain are essential for the transcriptional regulatory activity of FHY3 and its homodimerization or heterodimerization with FAR1. Furthermore, the ability to form homodimers or heterodimers largely correlates with the transcriptional regulatory activity of FHY3 in plant cells. Together, our results reveal discrete roles of the multiple domains of FHY3 and provide functional support for the proposition that FHY3 and FAR1 represent transcription factors derived from a Mutator-like transposase(s).

  19. Ultrafast ligand dynamics in the heme-based GAF sensor domains of the histidine kinases DosS and DosT from Mycobacterium tuberculosis†

    PubMed Central

    Vos, Marten H.; Bouzhir-Sima, Latifa; Lambry, Jean-Christophe; Luo, Hao; Eaton-Rye, Julian J.; Ioanoviciu, Alexandra; Ortiz de Montellano, Paul R.; Liebl, Ursula

    2011-01-01

    The transcriptional regulator DosR from M. tuberculosis plays a crucial role in the virulence to dormancy transition of the pathogen. DosR can be activated by DosT and DosS, two histidine kinases with heme-containing sensor GAF domains, capable of diatomic ligand binding, To investigate the initial processes occurring upon ligand dissociation, we performed ultrafast time-resolved absorption spectroscopy of the isolated sensor domains ligated with O2, NO and CO. The results reveal a relatively closed heme pocket for both proteins. For DosT the yield of O2 escape from the heme pocket on the picoseconds timescale upon photodissociation was found to be very low (1.5%), similar to other heme-based oxygen sensor proteins, implying that this sensor acts as an effective O2 trap. Remarkably, this yield is an order of magnitude higher in DosS (18%). For CO, by contrast, the fraction of CO rebinding within the heme pocket is higher in DosS. Experiments with mutant DosT sensor domains and molecular dynamics simulations indicate an important role in ligand discrimination of the distal tyrosine, present in both proteins, which forms a hydrogen bond with heme-bound O2. We conclude that despite their similarity, DosT and DosS display ligand-specific different primary dynamics during the initial phases of intra-protein signaling. The distal tyrosine, present in both proteins, plays an important role in these processes. PMID:22142262

  20. Marine algae and land plants share conserved phytochrome signaling systems

    DOE PAGES

    Duanmu, Deqiang; Bachy, Charles; Sudek, Sebastian; ...

    2014-09-29

    Phytochrome photosensors control a vast gene network in streptophyte plants, acting as master regulators of diverse growth and developmental processes throughout the life cycle. In contrast with their absence in known chlorophyte algal genomes and most sequenced prasinophyte algal genomes, a phytochrome is found in Micromonas pusilla, a widely distributed marine picoprasinophyte (<2 µm cell diameter). Together with phytochromes identified from other prasinophyte lineages, we establish that prasinophyte and streptophyte phytochromes share core light-input and signaling-output domain architectures except for the loss of C-terminal response regulator receiver domains in the streptophyte phytochrome lineage. Phylogenetic reconstructions robustly support the presence ofmore » phytochrome in the common progenitor of green algae and land plants. These analyses reveal a monophyletic clade containing streptophyte, prasinophyte, cryptophyte, and glaucophyte phytochromes implying an origin in the eukaryotic ancestor of the Archaeplastida. Transcriptomic measurements reveal diurnal regulation of phytochrome and bilin chromophore biosynthetic genes in Micromonas. The expression of these genes precedes both light-mediated phytochrome redistribution from the cytoplasm to the nucleus and increased expression of photosynthesis-associated genes. Prasinophyte phytochromes perceive wavelengths of light transmitted farther through seawater than the red/far-red light sensed by land plant phytochromes. Prasinophyte phytochromes also retain light-regulated histidine kinase activity lost in the streptophyte phytochrome lineage. Our studies demonstrate that light-mediated nuclear translocation of phytochrome predates the emergence of land plants and likely represents a widespread signaling mechanism in unicellular algae.« less

  1. Marine algae and land plants share conserved phytochrome signaling systems

    SciTech Connect

    Duanmu, Deqiang; Bachy, Charles; Sudek, Sebastian; Wong, Chee -Hong; Jimenez, Valeria; Rockwell, Nathan C.; Martin, Shelley S.; Ngan, Chew Yee; Reistetter, Emily N.; van Baren, Marijke J.; Price, Dana C.; Wei, Chia -Lin; Reyes-Prieto, Adrian; Lagarias, J. Clark; Worden, Alexandra Z.

    2014-09-29

    Phytochrome photosensors control a vast gene network in streptophyte plants, acting as master regulators of diverse growth and developmental processes throughout the life cycle. In contrast with their absence in known chlorophyte algal genomes and most sequenced prasinophyte algal genomes, a phytochrome is found in Micromonas pusilla, a widely distributed marine picoprasinophyte (<2 µm cell diameter). Together with phytochromes identified from other prasinophyte lineages, we establish that prasinophyte and streptophyte phytochromes share core light-input and signaling-output domain architectures except for the loss of C-terminal response regulator receiver domains in the streptophyte phytochrome lineage. Phylogenetic reconstructions robustly support the presence of phytochrome in the common progenitor of green algae and land plants. These analyses reveal a monophyletic clade containing streptophyte, prasinophyte, cryptophyte, and glaucophyte phytochromes implying an origin in the eukaryotic ancestor of the Archaeplastida. Transcriptomic measurements reveal diurnal regulation of phytochrome and bilin chromophore biosynthetic genes in Micromonas. The expression of these genes precedes both light-mediated phytochrome redistribution from the cytoplasm to the nucleus and increased expression of photosynthesis-associated genes. Prasinophyte phytochromes perceive wavelengths of light transmitted farther through seawater than the red/far-red light sensed by land plant phytochromes. Prasinophyte phytochromes also retain light-regulated histidine kinase activity lost in the streptophyte phytochrome lineage. Our studies demonstrate that light-mediated nuclear translocation of phytochrome predates the emergence of land plants and likely represents a widespread signaling mechanism in unicellular algae.

  2. Marine algae and land plants share conserved phytochrome signaling systems.

    PubMed

    Duanmu, Deqiang; Bachy, Charles; Sudek, Sebastian; Wong, Chee-Hong; Jiménez, Valeria; Rockwell, Nathan C; Martin, Shelley S; Ngan, Chew Yee; Reistetter, Emily N; van Baren, Marijke J; Price, Dana C; Wei, Chia-Lin; Reyes-Prieto, Adrian; Lagarias, J Clark; Worden, Alexandra Z

    2014-11-04

    Phytochrome photosensors control a vast gene network in streptophyte plants, acting as master regulators of diverse growth and developmental processes throughout the life cycle. In contrast with their absence in known chlorophyte algal genomes and most sequenced prasinophyte algal genomes, a phytochrome is found in Micromonas pusilla, a widely distributed marine picoprasinophyte (<2 µm cell diameter). Together with phytochromes identified from other prasinophyte lineages, we establish that prasinophyte and streptophyte phytochromes share core light-input and signaling-output domain architectures except for the loss of C-terminal response regulator receiver domains in the streptophyte phytochrome lineage. Phylogenetic reconstructions robustly support the presence of phytochrome in the common progenitor of green algae and land plants. These analyses reveal a monophyletic clade containing streptophyte, prasinophyte, cryptophyte, and glaucophyte phytochromes implying an origin in the eukaryotic ancestor of the Archaeplastida. Transcriptomic measurements reveal diurnal regulation of phytochrome and bilin chromophore biosynthetic genes in Micromonas. Expression of these genes precedes both light-mediated phytochrome redistribution from the cytoplasm to the nucleus and increased expression of photosynthesis-associated genes. Prasinophyte phytochromes perceive wavelengths of light transmitted farther through seawater than the red/far-red light sensed by land plant phytochromes. Prasinophyte phytochromes also retain light-regulated histidine kinase activity lost in the streptophyte phytochrome lineage. Our studies demonstrate that light-mediated nuclear translocation of phytochrome predates the emergence of land plants and likely represents a widespread signaling mechanism in unicellular algae.

  3. A Modified Reverse One-Hybrid Screen Identifies Transcriptional Activation Domains in PHYTOCHROME-INTERACTING FACTOR 3

    PubMed Central

    Dalton, Jutta C.; Bätz, Ulrike; Liu, Jason; Curie, Gemma L.; Quail, Peter H.

    2016-01-01

    Transcriptional activation domains (TADs) are difficult to predict and identify, since they are not conserved and have little consensus. Here, we describe a yeast-based screening method that is able to identify individual amino acid residues involved in transcriptional activation in a high throughput manner. A plant transcriptional activator, PIF3 (phytochrome interacting factor 3), was fused to the yeast GAL4-DNA-binding Domain (BD), driving expression of the URA3 (Orotidine 5′-phosphate decarboxylase) reporter, and used for negative selection on 5-fluroorotic acid (5FOA). Randomly mutagenized variants of PIF3 were then selected for a loss or reduction in transcriptional activation activity by survival on FOA. In the process, we developed a strategy to eliminate false positives from negative selection that can be used for both reverse-1- and 2-hybrid screens. With this method we were able to identify two distinct regions in PIF3 with transcriptional activation activity, both of which are functionally conserved in PIF1, PIF4, and PIF5. Both are collectively necessary for full PIF3 transcriptional activity, but neither is sufficient to induce transcription autonomously. We also found that the TAD appear to overlap physically with other PIF3 functions, such as phyB binding activity and consequent phosphorylation. Our protocol should provide a valuable tool for identifying, analyzing and characterizing novel TADs in eukaryotic transcription factors, and thus potentially contribute to the unraveling of the mechanism underlying transcriptional activation. PMID:27379152

  4. Mapping-by-Sequencing Identifies HvPHYTOCHROME C as a Candidate Gene for the early maturity 5 Locus Modulating the Circadian Clock and Photoperiodic Flowering in Barley

    PubMed Central

    Pankin, Artem; Campoli, Chiara; Dong, Xue; Kilian, Benjamin; Sharma, Rajiv; Himmelbach, Axel; Saini, Reena; Davis, Seth J; Stein, Nils; Schneeberger, Korbinian; von Korff, Maria

    2014-01-01

    Phytochromes play an important role in light signaling and photoperiodic control of flowering time in plants. Here we propose that the red/far-red light photoreceptor HvPHYTOCHROME C (HvPHYC), carrying a mutation in a conserved region of the GAF domain, is a candidate underlying the early maturity 5 locus in barley (Hordeum vulgare L.). We fine mapped the gene using a mapping-by-sequencing approach applied on the whole-exome capture data from bulked early flowering segregants derived from a backcross of the Bowman(eam5) introgression line. We demonstrate that eam5 disrupts circadian expression of clock genes. Moreover, it interacts with the major photoperiod response gene Ppd-H1 to accelerate flowering under noninductive short days. Our results suggest that HvPHYC participates in transmission of light signals to the circadian clock and thus modulates light-dependent processes such as photoperiodic regulation of flowering. PMID:24996910

  5. The Crystal Structures of the N-terminal Photosensory Core Module of Agrobacterium Phytochrome Agp1 as Parallel and Anti-parallel Dimers.

    PubMed

    Nagano, Soshichiro; Scheerer, Patrick; Zubow, Kristina; Michael, Norbert; Inomata, Katsuhiko; Lamparter, Tilman; Krauß, Norbert

    2016-09-23

    Agp1 is a canonical biliverdin-binding bacteriophytochrome from the soil bacterium Agrobacterium fabrum that acts as a light-regulated histidine kinase. Crystal structures of the photosensory core modules (PCMs) of homologous phytochromes have provided a consistent picture of the structural changes that these proteins undergo during photoconversion between the parent red light-absorbing state (Pr) and the far-red light-absorbing state (Pfr). These changes include secondary structure rearrangements in the so-called tongue of the phytochrome-specific (PHY) domain and structural rearrangements within the long α-helix that connects the cGMP-specific phosphodiesterase, adenylyl cyclase, and FhlA (GAF) and the PHY domains. We present the crystal structures of the PCM of Agp1 at 2.70 Å resolution and of a surface-engineered mutant of this PCM at 1.85 Å resolution in the dark-adapted Pr states. Whereas in the mutant structure the dimer subunits are in anti-parallel orientation, the wild-type structure contains parallel subunits. The relative orientations between the PAS-GAF bidomain and the PHY domain are different in the two structures, due to movement involving two hinge regions in the GAF-PHY connecting α-helix and the tongue, indicating pronounced structural flexibility that may give rise to a dynamic Pr state. The resolution of the mutant structure enabled us to detect a sterically strained conformation of the chromophore at ring A that we attribute to the tight interaction with Pro-461 of the conserved PRXSF motif in the tongue. Based on this observation and on data from mutants where residues in the tongue region were replaced by alanine, we discuss the crucial roles of those residues in Pr-to-Pfr photoconversion.

  6. Genomewide analysis of phytochrome proteins in the phylum Basidiomycota.

    PubMed

    Lavín, José L; Ramírez, Lucía; Pisabarro, Antonio G; Oguiza, José A

    2015-09-01

    Phytochromes are photoreceptor proteins involved in the detection of the red and far-red regions of the visible light spectrum. Fungal phytochromes are hybrid histidine kinases with a conserved domain architecture composed of an N-terminal photosensory module and a C-terminal regulatory output module that includes the histidine kinase and response regulator receiver domains. In this study, we have analyzed the distribution, domain architecture, and phylogenetic analysis of phytochrome proteins in 47 published genome sequences among the phylum Basidiomycota. Genome analysis revealed that almost every genome of basidiomycetes contained at least one gene encoding a phytochrome protein. Domain architecture of fungal phytochromes was completely conserved in the identified phytochromes of basidiomycetes, and phylogenetic analysis clustered these proteins into clades related with the phylogenetic classification of this fungal phylum.

  7. Phytochrome a overexpression inhibits hypocotyl elongation in transgenic Arabidopsis.

    PubMed Central

    Boylan, M T; Quail, P H

    1991-01-01

    To develop a model plant system for efficient functional analysis of mutagenized phytochrome polypeptides, we have overexpressed oat phytochrome A in Arabidopsis thaliana. R1 seedlings from selfed primary transformants segregated for hypocotyl length, when grown in the light, with a ratio of 3 short to 1 of normal length. When homozygous lines were established from these two size classes, accumulation of immunologically detectable oat phytochrome cosegregated with the short-hypocotyl trait. The short-hypocotyl seedlings contained substantially more spectrally active phytochrome than their normal-sized siblings, indicating that the introduced oat protein was photoreversible. The short-hypocotyl phenotype was strictly light-dependent, since no morphological effects of phytochrome overexpression could be seen in etiolated seedlings. Overexpression of only the chromophore-bearing, N-terminal domain of phytochrome A did not induce short hypocotyls in light-grown seedlings, indicating that additional sequence is essential for photoreceptor function. Similarly, overexpression of a full-length sequence mutated at the chromophore attachment site had no effect on phenotype, indicating the absence of any detectable dominant negative effect of the chromophoreless polypeptide on the activity of endogenous Arabidopsis phytochrome. Thus, the readily scorable short-hypocotyl phenotype of Arabidopsis seedlings overexpressing phytochrome A provides a simple visual assay for rapidly monitoring the biological activity of mutagenized phytochrome A polypeptides. Images PMID:11607244

  8. Infrared emission spectrum of GaF

    NASA Astrophysics Data System (ADS)

    Uehara, Hiromichi; Horiai, Koui; Nakagawa, Kuniaki; Suguro, Hiroshi

    1991-04-01

    The infrared emission spectrum of Δ v=1 bands of GaF has been observed at 1000°C with a resolution of 0.1 cm -1. The v=1-0 to 5-4 vibration-rotation bands of 69GaF and the v=1-0 to 4-3 bands of 71GaF were assigned in the wavenumber range between 500 and 645 cm -1. The analysis has led to a set of values of eight Dunham coefficients, Y10, Y20, Y30, Y01, Y11, Y21, Y02 and Y12 of 69GaF, Y10 and Y20 were determined to be 622.367(11) and -3.3049(42) cm -1, respectively, with twice the standard errors in parentheses. The infrared diode-laser spectrum of GaF has also been observed and the assignment of some spectral lines is shown.

  9. Phytochrome in photosynthetically competent plants: characterization by monoclonal antibodies. Progress report

    SciTech Connect

    Pratt, L.H.

    1985-01-01

    New monoclonal antibodies have been prepared to 124-kdalton phytochrome from etiolated oats, to phytochrome from etiolated peas, and to alkaline phosphatase. Simultaneously, progress has been made in improving methodologies for purification of phytochrome from green oats. Mice have been immunized with phytochrome electrophoretically purified from green oats. Methodologies needed to perform immunizations in vitro have been adapted to our purposes and screening protocols needed to identify antibodies to phytochrome from green oats are being refined. Forty-two rabbit antisera to phytochrome have been screened for their ability to immunoprecipitate phytochrome from green oats. The data are consistent with the hypothesis that green-oat phytochrome may be a minor component of the phytochrome isolated from etiolated oats. In addition, our panel of monoclonal antibodies has been screened for their ability to bind to phytochrome from green oats. Two that do so (oat-9 and oat-16) have been identified and characterized. A third (pea-25) has only recently been identified and is presently under intense investigation. Oat-9 and oat-16 apparently bind to the same domain on phytochrome, which is located near the site of chromophore attachment. They bind by ELISA to Pfr with greater affinity than to Pr. Pea-25 binds to phytochrome on immunoblots of sodium dodecyl sulfate, polyacrylamide gels. With this antibody it has been possible to determine that phytochrome from green oats appears to be identical in size to that obtained from etiolated oats. Data have also been obtained to indicate that a relatively small, but highly significant, proportion of the phytochrome obtained from green peas is immunochemically distinct from that obtained from etiolated peas. It thus appears that the observations made with green versus etiolated oats might represent a general phenomenon.

  10. Phytochromes in photosynthetically competent plants

    SciTech Connect

    Pratt, L.H.

    1991-01-01

    Major improvements have been made in the purification of green-oat phytochrome. An effective protease inhibitor has been incorporated, the scale of preparations has been increased greatly, an immunodominant contaminant has been eliminated, and the extent of purification has been increased by at least a factor of ten. Five new MAbs and rabbit PAbs to green-oat phytochrome, as well as rabbit PAbs to a synthetic, putative green-oat phytochrome peptide, have been produced and characterized, together with two MAbs to green-oat phytochrome that had been identified previously. Our earlier hypothesis that green-oat phytochrome itself consists of two types was found to be true. One type of green-oat phytochrome has an apparent monomer size of 125 kDa while the other is 123 kDa. The latter undergoes a Zn[sup 2+]-induced mobility shift during SDS PAGE and the two phytochromes are immunochemically distinct from one another. Affinity columns prepared with MAbs to green-oat phytochrome have been used to purify 125-kDa green-oat phytochrome to near homogeneity. A proteolytically derived peptide has been isolated from immunopurified green-oat phytochrome and 19 residues have been determined by microsequencing. The results verify that in monocotyledons as well as dicotyledons green- and etiolated-oat phytochromes derive from different genes.

  11. Phytochrome in photosynthetically competent plants characterization by monoclonal antibodies: Progress report

    SciTech Connect

    Pratt, L.H.

    1987-03-01

    It is evident that phytochrome in green oats differs more markedly from that in etiolated oats than could have been anticipated. More effort has gone into characterization of green-oat phytochrome, including elimination of likely artifacts that might have been responsible for the observed differences with etiolated-oat phytochrome, and into the generation of new probes for green-oat phytochrome. The liability of green-oat phytochrome has increased the difficulty of this work. Immunochemical differences between etiolated- and green-oat phytochrome have been elucidated. A domain on green-oat phytochrome that undergoes a change upon phototransformation of at least etiolated-oat phytochrome has been discovered. A lambda gt11 cDNA library has been prepared from size-enriched poly(A)/sup +/-mRNA isolated from green oat shoots and has been screened immunochemically. An amplified ELISA protocol suitable for screening hybridoma supernatants against crude green-oat phytochrome preparations has been developed. Monoclonal antibodies directed to green-oat phytochrome have been identified. 5 refs.

  12. Ultrafast red light activation of Synechocystis phytochrome Cph1 triggers major structural change to form the Pfr signalling-competent state.

    PubMed

    Heyes, Derren J; Khara, Basile; Sakuma, Michiyo; Hardman, Samantha J O; O'Cualain, Ronan; Rigby, Stephen E J; Scrutton, Nigel S

    2012-01-01

    Phytochromes are dimeric photoreceptors that regulate a range of responses in plants and microorganisms through interconversion of red light-absorbing (Pr) and far-red light-absorbing (Pfr) states. Photoconversion between these states is initiated by light-driven isomerization of a bilin cofactor, which triggers protein structural change. The extent of this change, and how light-driven structural changes in the N-terminal photosensory region are transmitted to the C-terminal regulatory domain to initiate the signalling cascade, is unknown. We have used pulsed electron-electron double resonance (PELDOR) spectroscopy to identify multiple structural transitions in a phytochrome from Synechocystis sp. PCC6803 (Cph1) by measuring distances between nitroxide labels introduced into the protein. We show that monomers in the Cph1 dimer are aligned in a parallel 'head-to-head' arrangement and that photoconversion between the Pr and Pfr forms involves conformational change in both the N- and C-terminal domains of the protein. Cryo-trapping and kinetic measurements were used to probe the extent and temporal properties of protein motions for individual steps during photoconversion of Cph1. Formation of the primary photoproduct Lumi-R is not affected by changes in solvent viscosity and dielectric constant. Lumi-R formation occurs at cryogenic temperatures, consistent with their being no major structural reorganization of Cph1 during primary photoproduct formation. All remaining steps in the formation of the Pfr state are affected by solvent viscosity and dielectric constant and occur only at elevated temperatures, implying involvement of a series of long-range solvent-coupled conformational changes in Cph1. We show that signalling is achieved through ultrafast photoisomerization where localized structural change in the GAF domain is transmitted and amplified to cause larger-scale and slower conformational change in the PHY and histidine kinase domains. This hierarchy of

  13. Arabidopsis thaliana life without phytochromes

    PubMed Central

    Strasser, Bárbara; Sánchez-Lamas, Maximiliano; Yanovsky, Marcelo J.; Casal, Jorge J.; Cerdán, Pablo D.

    2010-01-01

    Plants use light as a source of energy for photosynthesis and as a source of environmental information perceived by photoreceptors. Testing whether plants can complete their cycle if light provides energy but no information about the environment requires a plant devoid of phytochromes because all photosynthetically active wavelengths activate phytochromes. Producing such a quintuple mutant of Arabidopsis thaliana has been challenging, but we were able to obtain it in the flowering locus T (ft) mutant background. The quintuple phytochrome mutant does not germinate in the FT background, but it germinates to some extent in the ft background. If germination problems are bypassed by the addition of gibberellins, the seedlings of the quintuple phytochrome mutant exposed to red light produce chlorophyll, indicating that phytochromes are not the sole red-light photoreceptors, but they become developmentally arrested shortly after the cotyledon stage. Blue light bypasses this blockage, rejecting the long-standing idea that the blue-light receptors cryptochromes cannot operate without phytochromes. After growth under white light, returning the quintuple phytochrome mutant to red light resulted in rapid senescence of already expanded leaves and severely impaired expansion of new leaves. We conclude that Arabidopsis development is stalled at several points in the presence of light suitable for photosynthesis but providing no photomorphogenic signal. PMID:20176939

  14. Phytochrome C is a key factor controlling long-day flowering in barley.

    PubMed

    Nishida, Hidetaka; Ishihara, Daisuke; Ishii, Makoto; Kaneko, Takuma; Kawahigashi, Hiroyuki; Akashi, Yukari; Saisho, Daisuke; Tanaka, Katsunori; Handa, Hirokazu; Takeda, Kazuyoshi; Kato, Kenji

    2013-10-01

    The spring-type near isogenic line (NIL) of the winter-type barley (Hordeum vulgare ssp. vulgare) var. Hayakiso 2 (HK2) was developed by introducing VERNALIZATION-H1 (Vrn-H1) for spring growth habit from the spring-type var. Indo Omugi. Contrary to expectations, the spring-type NIL flowered later than winter-type HK2. This phenotypic difference was controlled by a single gene, which cosegregated only with phytochrome C (HvPhyC) among three candidates around the Vrn-H1 region (Vrn-H1, HvPhyC, and CASEIN KINASE IIα), indicating that HvPhyC was the most likely candidate gene. Compared with the late-flowering allele HvPhyC-l from the NIL, the early-flowering allele HvPhyC-e from HK2 had a single nucleotide polymorphism T1139C in exon 1, which caused a nonsynonymous amino acid substitution of phenylalanine at position 380 by serine in the functionally essential GAF (3', 5'-cyclic-GMP phosphodiesterase, adenylate cyclase, formate hydrogen lyase activator protein) domain. Functional assay using a rice (Oryza sativa) phyA phyC double mutant line showed that both of the HvPhyC alleles are functional, but HvPhyC-e may have a hyperfunction. Expression analysis using NILs carrying HvPhyC-e and HvPhyC-l (NIL [HvPhyC-e] and NIL [HvPhyC-l], respectively) showed that HvPhyC-e up-regulated only the flowering promoter FLOWERING LOCUS T1 by bypassing the circadian clock genes and flowering integrator CONSTANS1 under a long photoperiod. Consistent with the up-regulation, NIL (HvPhyC-e) flowered earlier than NIL (HvPhyC-l) under long photoperiods. These results implied that HvPhyC is a key factor to control long-day flowering directly.

  15. Phytochrome diversity in green plants and the origin of canonical plant phytochromes.

    PubMed

    Li, Fay-Wei; Melkonian, Michael; Rothfels, Carl J; Villarreal, Juan Carlos; Stevenson, Dennis W; Graham, Sean W; Wong, Gane Ka-Shu; Pryer, Kathleen M; Mathews, Sarah

    2015-07-28

    Phytochromes are red/far-red photoreceptors that play essential roles in diverse plant morphogenetic and physiological responses to light. Despite their functional significance, phytochrome diversity and evolution across photosynthetic eukaryotes remain poorly understood. Using newly available transcriptomic and genomic data we show that canonical plant phytochromes originated in a common ancestor of streptophytes (charophyte algae and land plants). Phytochromes in charophyte algae are structurally diverse, including canonical and non-canonical forms, whereas in land plants, phytochrome structure is highly conserved. Liverworts, hornworts and Selaginella apparently possess a single phytochrome, whereas independent gene duplications occurred within mosses, lycopods, ferns and seed plants, leading to diverse phytochrome families in these clades. Surprisingly, the phytochrome portions of algal and land plant neochromes, a chimera of phytochrome and phototropin, appear to share a common origin. Our results reveal novel phytochrome clades and establish the basis for understanding phytochrome functional evolution in land plants and their algal relatives.

  16. Phytochrome diversity in green plants and the origin of canonical plant phytochromes

    PubMed Central

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

    2015-01-01

    Phytochromes are red/far-red photoreceptors that play essential roles in diverse plant morphogenetic and physiological responses to light. Despite their functional significance, phytochrome diversity and evolution across photosynthetic eukaryotes remain poorly understood. Using newly available transcriptomic and genomic data we show that canonical plant phytochromes originated in a common ancestor of streptophytes (charophyte algae and land plants). Phytochromes in charophyte algae are structurally diverse, including canonical and non-canonical forms, whereas in land plants, phytochrome structure is highly conserved. Liverworts, hornworts and Selaginella apparently possess a single phytochrome, whereas independent gene duplications occurred within mosses, lycopods, ferns and seed plants, leading to diverse phytochrome families in these clades. Surprisingly, the phytochrome portions of algal and land plant neochromes, a chimera of phytochrome and phototropin, appear to share a common origin. Our results reveal novel phytochrome clades and establish the basis for understanding phytochrome functional evolution in land plants and their algal relatives. PMID:26215968

  17. Phytochromes in photosynthetically competent plants

    SciTech Connect

    Pratt, L.H.

    1990-07-01

    Plants utilize light as a source of information in photomorphogenesis and of free energy in photosynthesis, two processes that are interrelated in that the former serves to increase the efficiency with which plants can perform the latter. Only one pigment involved in photomorphogenesis has been identified unequivocally, namely phytochrome. The thrust of this proposal is to investigate this pigment and its mode(s) of action in photosynthetically competent plants. Our long term objective is to characterize phytochrome and its functions in photosynthetically competent plants from molecular, biochemical and cellular perspectives. It is anticipated that others will continue to contribute indirectly to these efforts at the physiological level. The ultimate goal will be to develop this information from a comparative perspective in order to learn whether the different phytochromes have significantly different physicochemical properties, whether they fulfill independent functions and if so what these different functions are, and how each of the different phytochromes acts at primary molecular and cellular levels.

  18. Phytochromes in photosynthetically competent plants. Final report

    SciTech Connect

    Pratt, L.H.

    1991-12-31

    Major improvements have been made in the purification of green-oat phytochrome. An effective protease inhibitor has been incorporated, the scale of preparations has been increased greatly, an immunodominant contaminant has been eliminated, and the extent of purification has been increased by at least a factor of ten. Five new MAbs and rabbit PAbs to green-oat phytochrome, as well as rabbit PAbs to a synthetic, putative green-oat phytochrome peptide, have been produced and characterized, together with two MAbs to green-oat phytochrome that had been identified previously. Our earlier hypothesis that green-oat phytochrome itself consists of two types was found to be true. One type of green-oat phytochrome has an apparent monomer size of 125 kDa while the other is 123 kDa. The latter undergoes a Zn{sup 2+}-induced mobility shift during SDS PAGE and the two phytochromes are immunochemically distinct from one another. Affinity columns prepared with MAbs to green-oat phytochrome have been used to purify 125-kDa green-oat phytochrome to near homogeneity. A proteolytically derived peptide has been isolated from immunopurified green-oat phytochrome and 19 residues have been determined by microsequencing. The results verify that in monocotyledons as well as dicotyledons green- and etiolated-oat phytochromes derive from different genes.

  19. Synthetic Studies in Phytochrome Chemistry

    PubMed Central

    Jacobi, Peter A.; Adel Odeh, Imad M.; Buddhu, Subhas C.; Cai, Guolin; Rajeswari, Sundaramoorthi; Fry, Douglas; Zheng, Wanjun; DeSimone, Robert W.; Guo, Jiasheng; Coutts, Lisa D.; Hauck, Sheila I.; Leung, Sam H.; Ghosh, Indranath; Pippin., Douglas

    2008-01-01

    An account is given of the author’s several approaches to the synthesis of the parent chromophore of phytochrome (1), a protein-bound linear tetrapyrrole derivative that controls photomorphogenesis in higher plants. These studies culminated in enantioselective syntheses of both 2R- and 2S-phytochromobilin (4), as well as several 13C-labeled derivatives designed to probe the site of Z,E-isomerization during photoexcitation. When reacted in vitro, synthetic 2R-4 and recombinant-derived phytochrome apoprotein N-C produced a protein-bound chromophore with identical difference spectra to naturally occurring 1. PMID:18633455

  20. Ultrafast Red Light Activation of Synechocystis Phytochrome Cph1 Triggers Major Structural Change to Form the Pfr Signalling-Competent State

    PubMed Central

    Heyes, Derren J.; Khara, Basile; Sakuma, Michiyo; Hardman, Samantha J. O.; O'Cualain, Ronan; Rigby, Stephen E. J.; Scrutton, Nigel S.

    2012-01-01

    Phytochromes are dimeric photoreceptors that regulate a range of responses in plants and microorganisms through interconversion of red light-absorbing (Pr) and far-red light-absorbing (Pfr) states. Photoconversion between these states is initiated by light-driven isomerization of a bilin cofactor, which triggers protein structural change. The extent of this change, and how light-driven structural changes in the N-terminal photosensory region are transmitted to the C-terminal regulatory domain to initiate the signalling cascade, is unknown. We have used pulsed electron-electron double resonance (PELDOR) spectroscopy to identify multiple structural transitions in a phytochrome from Synechocystis sp. PCC6803 (Cph1) by measuring distances between nitroxide labels introduced into the protein. We show that monomers in the Cph1 dimer are aligned in a parallel ‘head-to-head’ arrangement and that photoconversion between the Pr and Pfr forms involves conformational change in both the N- and C-terminal domains of the protein. Cryo-trapping and kinetic measurements were used to probe the extent and temporal properties of protein motions for individual steps during photoconversion of Cph1. Formation of the primary photoproduct Lumi-R is not affected by changes in solvent viscosity and dielectric constant. Lumi-R formation occurs at cryogenic temperatures, consistent with their being no major structural reorganization of Cph1 during primary photoproduct formation. All remaining steps in the formation of the Pfr state are affected by solvent viscosity and dielectric constant and occur only at elevated temperatures, implying involvement of a series of long-range solvent-coupled conformational changes in Cph1. We show that signalling is achieved through ultrafast photoisomerization where localized structural change in the GAF domain is transmitted and amplified to cause larger-scale and slower conformational change in the PHY and histidine kinase domains. This hierarchy of

  1. Structural photoactivation of a full-length bacterial phytochrome

    PubMed Central

    Björling, Alexander; Berntsson, Oskar; Lehtivuori, Heli; Takala, Heikki; Hughes, Ashley J.; Panman, Matthijs; Hoernke, Maria; Niebling, Stephan; Henry, Léocadie; Henning, Robert; Kosheleva, Irina; Chukharev, Vladimir; Tkachenko, Nikolai V.; Menzel, Andreas; Newby, Gemma; Khakhulin, Dmitry; Wulff, Michael; Ihalainen, Janne A.; Westenhoff, Sebastian

    2016-01-01

    Phytochromes are light sensor proteins found in plants, bacteria, and fungi. They function by converting a photon absorption event into a conformational signal that propagates from the chromophore through the entire protein. However, the structure of the photoactivated state and the conformational changes that lead to it are not known. We report time-resolved x-ray scattering of the full-length phytochrome from Deinococcus radiodurans on micro- and millisecond time scales. We identify a twist of the histidine kinase output domains with respect to the chromophore-binding domains as the dominant change between the photoactivated and resting states. The time-resolved data further show that the structural changes up to the microsecond time scales are small and localized in the chromophore-binding domains. The global structural change occurs within a few milliseconds, coinciding with the formation of the spectroscopic meta-Rc state. Our findings establish key elements of the signaling mechanism of full-length bacterial phytochromes. PMID:27536728

  2. Eukaryotic algal phytochromes span the visible spectrum

    PubMed Central

    Rockwell, Nathan C.; Duanmu, Deqiang; Martin, Shelley S.; Bachy, Charles; Price, Dana C.; Bhattacharya, Debashish; Worden, Alexandra Z.; Lagarias, J. Clark

    2014-01-01

    Plant phytochromes are photoswitchable red/far-red photoreceptors that allow competition with neighboring plants for photosynthetically active red light. In aquatic environments, red and far-red light are rapidly attenuated with depth; therefore, photosynthetic species must use shorter wavelengths of light. Nevertheless, phytochrome-related proteins are found in recently sequenced genomes of many eukaryotic algae from aquatic environments. We examined the photosensory properties of seven phytochromes from diverse algae: four prasinophyte (green algal) species, the heterokont (brown algal) Ectocarpus siliculosus, and two glaucophyte species. We demonstrate that algal phytochromes are not limited to red and far-red responses. Instead, different algal phytochromes can sense orange, green, and even blue light. Characterization of these previously undescribed photosensors using CD spectroscopy supports a structurally heterogeneous chromophore in the far-red–absorbing photostate. Our study thus demonstrates that extensive spectral tuning of phytochromes has evolved in phylogenetically distinct lineages of aquatic photosynthetic eukaryotes. PMID:24567382

  3. Phytochrome C Is A Key Factor Controlling Long-Day Flowering in Barley1[W

    PubMed Central

    Nishida, Hidetaka; Ishihara, Daisuke; Ishii, Makoto; Kaneko, Takuma; Kawahigashi, Hiroyuki; Akashi, Yukari; Saisho, Daisuke; Tanaka, Katsunori; Handa, Hirokazu; Takeda, Kazuyoshi; Kato, Kenji

    2013-01-01

    The spring-type near isogenic line (NIL) of the winter-type barley (Hordeum vulgare ssp. vulgare) var. Hayakiso 2 (HK2) was developed by introducing VERNALIZATION-H1 (Vrn-H1) for spring growth habit from the spring-type var. Indo Omugi. Contrary to expectations, the spring-type NIL flowered later than winter-type HK2. This phenotypic difference was controlled by a single gene, which cosegregated only with phytochrome C (HvPhyC) among three candidates around the Vrn-H1 region (Vrn-H1, HvPhyC, and CASEIN KINASE IIα), indicating that HvPhyC was the most likely candidate gene. Compared with the late-flowering allele HvPhyC-l from the NIL, the early-flowering allele HvPhyC-e from HK2 had a single nucleotide polymorphism T1139C in exon 1, which caused a nonsynonymous amino acid substitution of phenylalanine at position 380 by serine in the functionally essential GAF (3′, 5′-cyclic-GMP phosphodiesterase, adenylate cyclase, formate hydrogen lyase activator protein) domain. Functional assay using a rice (Oryza sativa) phyA phyC double mutant line showed that both of the HvPhyC alleles are functional, but HvPhyC-e may have a hyperfunction. Expression analysis using NILs carrying HvPhyC-e and HvPhyC-l (NIL [HvPhyC-e] and NIL [HvPhyC-l], respectively) showed that HvPhyC-e up-regulated only the flowering promoter FLOWERING LOCUS T1 by bypassing the circadian clock genes and flowering integrator CONSTANS1 under a long photoperiod. Consistent with the up-regulation, NIL (HvPhyC-e) flowered earlier than NIL (HvPhyC-l) under long photoperiods. These results implied that HvPhyC is a key factor to control long-day flowering directly. PMID:24014575

  4. 42 CFR 414.26 - Determining the GAF.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 42 Public Health 3 2010-10-01 2010-10-01 false Determining the GAF. 414.26 Section 414.26 Public Health CENTERS FOR MEDICARE & MEDICAID SERVICES, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICARE PROGRAM PAYMENT FOR PART B MEDICAL AND OTHER HEALTH SERVICES Physicians and Other...

  5. 42 CFR 414.26 - Determining the GAF.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 42 Public Health 3 2012-10-01 2012-10-01 false Determining the GAF. 414.26 Section 414.26 Public Health CENTERS FOR MEDICARE & MEDICAID SERVICES, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICARE PROGRAM (CONTINUED) PAYMENT FOR PART B MEDICAL AND OTHER HEALTH SERVICES Physicians and...

  6. Intramolecular co-action of two independent photosensory modules in the fern phytochrome 3.

    PubMed

    Kanegae, Takeshi

    2015-01-01

    Fern phytochrome3/neochrome1 (phy3/neo1) is a chimeric photoreceptor composed of a phytochrome-chromophore binding domain and an almost full-length phototropin. phy3 thus contains two different light-sensing modules; a red/far-red light receptor phytochrome and a blue light receptor phototropin. phy3 induces both red light- and blue light-dependent phototropism in phototropin-deficient Arabidopsis thaliana (phot1 phot2) seedlings. The red-light response is dependent on the phytochrome module of phy3, and the blue-light response is dependent on the phototropin module. We recently showed that both the phototropin-sensing module and the phytochrome-sensing module mediate the blue light-dependent phototropic response. Particularly under low-light conditions, these two light-sensing modules cooperate to induce the blue light-dependent phototropic response. This intramolecular co-action of two independent light-sensing modules in phy3 enhances light sensitivity, and perhaps allowed ferns to adapt to the low-light canopy conditions present in angiosperm forests.

  7. Bottom-up Assembly of the Phytochrome Network

    PubMed Central

    Sánchez-Lamas, Maximiliano; Lorenzo, Christian D.; Cerdán, Pablo D.

    2016-01-01

    Plants have developed sophisticated systems to monitor and rapidly acclimate to environmental fluctuations. Light is an essential source of environmental information throughout the plant’s life cycle. The model plant Arabidopsis thaliana possesses five phytochromes (phyA-phyE) with important roles in germination, seedling establishment, shade avoidance, and flowering. However, our understanding of the phytochrome signaling network is incomplete, and little is known about the individual roles of phytochromes and how they function cooperatively to mediate light responses. Here, we used a bottom-up approach to study the phytochrome network. We added each of the five phytochromes to a phytochrome-less background to study their individual roles and then added the phytochromes by pairs to study their interactions. By analyzing the 16 resulting genotypes, we revealed unique roles for each phytochrome and identified novel phytochrome interactions that regulate germination and the onset of flowering. Furthermore, we found that ambient temperature has both phytochrome-dependent and -independent effects, suggesting that multiple pathways integrate temperature and light signaling. Surprisingly, none of the phytochromes alone conferred a photoperiodic response. Although phyE and phyB were the strongest repressors of flowering, both phyB and phyC were needed to confer a flowering response to photoperiod. Thus, a specific combination of phytochromes is required to detect changes in photoperiod, whereas single phytochromes are sufficient to respond to light quality, indicating how phytochromes signal different light cues. PMID:27820825

  8. A phytochrome from the fern Adiantum with features of the putative photoreceptor NPH1

    PubMed Central

    Nozue, Kazunari; Kanegae, Takeshi; Imaizumi, Takato; Fukuda, Shunsuke; Okamoto, Haruko; Yeh, Kuo-Chen; Lagarias, J. Clark; Wada, Masamitsu

    1998-01-01

    In plant photomorphogenesis, it is well accepted that the perception of red/far-red and blue light is mediated by distinct photoreceptor families, i.e., the phytochromes and blue-light photoreceptors, respectively. Here we describe the discovery of a photoreceptor gene from the fern Adiantum that encodes a protein with features of both phytochrome and NPH1, the putative blue-light receptor for second-positive phototropism in seed plants. The fusion of a functional photosensory domain of phytochrome with a nearly full-length NPH1 homolog suggests that this polypeptide could mediate both red/far-red and blue-light responses in Adiantum normally ascribed to distinct photoreceptors. PMID:9861055

  9. Kinetically Distinguishable Populations of Phytochrome 1

    PubMed Central

    Purves, William K.; Briggs, Winslow R.

    1968-01-01

    Two or more kinetically distinguishable populations of phytochrome molecules were observed in living tissues of oat, pea, maize, and cauliflower, as well as in extracts of oat. At least 3 different populations occurred in cauliflower florets, while 2 were observed in each of the other species. In extracted oat phytochrome, the relative proportions of the 2 forms remained constant during successive stages of purification. The physiological significance of this multiplicity of forms remains unclear. PMID:16656909

  10. Phytochrome regulation of branching in Arabidopsis.

    PubMed

    Finlayson, Scott A; Krishnareddy, Srirama R; Kebrom, Tesfamichael H; Casal, Jorge J

    2010-04-01

    The red light:far-red light ratio perceived by phytochromes controls plastic traits of plant architecture, including branching. Despite the significance of branching for plant fitness and productivity, there is little quantitative and mechanistic information concerning phytochrome control of branching responses in Arabidopsis (Arabidopsis thaliana). Here, we show that in Arabidopsis, the negative effects of the phytochrome B mutation and of low red light:far-red light ratio on branching were largely due to reduced bud outgrowth capacity and an increased degree of correlative inhibition acting on the buds rather than due to a reduced number of leaves and buds available for branching. Phytochrome effects on the degree of correlative inhibition required functional BRANCHED1 (BRC1), BRC2, AXR1, MORE AXILLARY GROWTH2 (MAX2), and MAX4. The analysis of gene expression in selected buds indicated that BRC1 and BRC2 are part of different gene networks. The BRC1 network is linked to the growth capacity of specific buds, while the BRC2 network is associated with coordination of growth among branches. We conclude that the branching integrators BRC1 and BRC2 are necessary for responses to phytochrome, but they contribute differentially to these responses, likely acting through divergent pathways.

  11. Functional analyses of the Physcomitrella patens phytochromes in regulating chloroplast avoidance movement.

    PubMed

    Uenaka, Hidetoshi; Kadota, Akeo

    2007-09-01

    Red light-induced chloroplast movement in Physcomitrella patens (Pp) is mediated by dichroic phytochrome in the cytoplasm. To analyze the molecular function of the photoreceptor in the cytoplasm, we developed a protoplast system in which chloroplast photomovement was exclusively dependent on the expression of phytochrome cDNA constructs introduced by polyethylene glycol (PEG) transformation. YFP was fused to the phytochrome constructs and their expression was detected by fluorescence. The chloroplast avoidance response was induced in the protoplasts expressing a YFP fusion of PHY1-PHY3, but not of PHY4 or YFP alone. Phy::yfp fluorescence was detected in the cytoplasm. No change in the location of phy1::yfp or phy2::yfp was revealed before and after photomovement. When phy1::yfp and phy2::yfp were targeted to the nucleus by fusing a nuclear localization signal to the constructs, red light avoidance was not induced. To determine the domains of PHY2 essential for avoidance response, various partially-deleted PHY2::YFP constructs were tested. The N-terminal extension domain (NTE) was found to be necessary but the C-terminal histidine kinase-related domain (HKRD) was dispensable. An avoidance response was not induced under expression of phytochrome N-terminal half domain [deleting both the PAS (Per, Arnt, Sim)-related domain (PRD) and HKRD]. GUS fusion of this N-terminal half domain, reported to be fully functional in Arabidopsis for several phyA- and phyB-regulated responses was not effective in chloroplast avoidance movement. Domain requirement and GUS fusion effect were also confirmed in PHY1. These results indicate that Pp phy1-Pp phy3 in the cytoplasm mediate chloroplast avoidance movement, and that NTE and PRD, but not HKRD, are required for their function.

  12. Light-induced import of the chromoprotein, phytochrome, into mitochondria

    NASA Technical Reports Server (NTRS)

    Serlin, B. S.; Roux, S. J.

    1986-01-01

    Mitochondria extracted from plants that were irradiated with actinic light in vivo have associated with them the chromoprotein, phytochrome. This phytochrome retains its native subunit size of 124 kDa after proteolytic treatment of the mitochondria with trypsin and chymotrypsin. This result suggests that phytochrome is not exposed on the outer surface of the outer mitochondrial membrane. Phytochrome, so protected, is not found to be associated with mitochondria derived from unirradiated plants. The possibility that the photoactivation of phytochrome induces a conformational change in its structure which facilitates its transport into the mitochondrion is discussed.

  13. Phytochrome, plant growth and flowering

    NASA Technical Reports Server (NTRS)

    King, R. W.; Bagnall, D. J.

    1994-01-01

    Attempts to use artificially lit cabinets to grow plants identical to those growing in sunlight have provided compelling evidence of the importance of light quality for plant growth. Changing the balance of red (R) to far-red (FR) radiation, but with a fixed photosynthetic input can shift the phytochrome photoequilibrium in a plant and generate large differences in plant growth. With FR enrichment the plants elongate, and may produce more leaf area and dry matter. Similar morphogenic responses are also obtained when light quality is altered only briefly (15-30 min) at the end-of-the-day. Conversely, for plants grown in natural conditions the response of plant form to selective spectral filtering has again shown that red and far-red wavebands are important as found by Kasperbauer and coworkers. Also, where photosynthetic photon flux densities (PPFD) of sunlight have been held constant, the removal of far-red alone alters plant growth. With FR depletion plants grown in sunlight are small, more branched and darker green. Here we examine the implications for plant growth and flowering when the far-red composition of incident radiation in plant growth chambers is manipulated.

  14. Pr-specific phytochrome phosphorylation in vitro by a protein kinase present in anti-phytochrome maize immunoprecipitates

    NASA Technical Reports Server (NTRS)

    Biermann, B. J.; Pao, L. I.; Feldman, L. J.

    1994-01-01

    Protein kinase activity has repeatedly been found to co-purify with the plant photoreceptor phytochrome, suggesting that light signals received by phytochrome may be transduced or modulated through protein phosphorylation. In this study immunoprecipitation techniques were used to characterize protein kinase activity associated with phytochrome from maize (Zea mays L.). A protein kinase that specifically phosphorylated phytochrome was present in washed anti-phytochrome immunoprecipitates of etiolated coleoptile proteins. No other substrate tested was phosphorylated by this kinase. Adding salts or detergents to disrupt low-affinity protein interactions reduced background phosphorylation in immunoprecipitates without affecting phytochrome phosphorylation, indicating that the protein kinase catalytic activity is either intrinsic to the phytochrome molecule or associated with it by high-affinity interactions. Red irradiation (of coleoptiles or extracts) sufficient to approach photoconversion saturation reduced phosphorylation of immunoprecipitated phytochrome. Subsequent far-red irradiation reversed the red-light effect. Phytochrome phosphorylation was stimulated about 10-fold by a co-immunoprecipitated factor. The stimulatory factor was highest in immunoprecipitates when Mg2+ was present in immunoprecipitation reactions but remained in the supernatant in the absence of Mg2+. These observations provide strong support for the hypothesis that phytochrome-associated protein kinase modulates light responses in vivo. Since only phytochrome was found to be phosphorylated, the co-immunoprecipitated protein kinase may function to regulate receptor activity.

  15. Characterization of Phytochrome Interacting Factors from the Moss Physcomitrella patens Illustrates Conservation of Phytochrome Signaling Modules in Land Plants.

    PubMed

    Possart, Anja; Xu, Tengfei; Paik, Inyup; Hanke, Sebastian; Keim, Sarah; Hermann, Helen-Maria; Wolf, Luise; Hiß, Manuel; Becker, Claude; Huq, Enamul; Rensing, Stefan A; Hiltbrunner, Andreas

    2017-02-01

    Across the plant kingdom, phytochrome (PHY) photoreceptors play an important role during adaptive and developmental responses to light. In Arabidopsis thaliana, light-activated PHYs accumulate in the nucleus, where they regulate downstream signaling components, such as phytochrome interacting factors (PIFs). PIFs are transcription factors that act as repressors of photomorphogenesis; their inhibition by PHYs leads to substantial changes in gene expression. The nuclear function of PHYs, however, has so far been investigated in only a few non-seed plants. Here, we identified putative target genes of PHY signaling in the moss Physcomitrella patens and found light-regulated genes that are putative orthologs of PIF-controlled genes in Arabidopsis. Phylogenetic analyses revealed that an ancestral PIF-like gene was already present in streptophyte algae, i.e., before the water-to-land transition of plants. The PIF homologs in the genome of P. patens resemble Arabidopsis PIFs in their protein domain structure, molecular properties, and physiological effects, albeit with notable differences in the motif-dependent PHY interaction. Our results suggest that P. patens PIFs are involved in PHY signaling. The PHY-PIF signaling node that relays light signals to target genes has been largely conserved during land plant evolution, with evidence of lineage-specific diversification.

  16. Evolutionary origin of phytochrome responses and signaling in land plants.

    PubMed

    Inoue, Keisuke; Nishihama, Ryuichi; Kohchi, Takayuki

    2017-01-18

    Phytochromes comprise one of the major photoreceptor families in plants, and they regulate many aspects of plant growth and development throughout the plant life cycle. A canonical land plant phytochrome originated in the common ancestor of streptophytes. Phytochromes have diversified in seed plants and some basal land plants because of lineage-specific gene duplications that occurred during the course of land plant evolution. Molecular genetic analyses using Arabidopsis thaliana suggested that there are two types of phytochromes in angiosperms, light-labile type I and light-stable type II, which have different signaling mechanisms and which regulate distinct responses. In basal land plants, little is known about molecular mechanisms of phytochrome signaling, although red light/far-red photoreversible physiological responses and the distribution of phytochrome genes are relatively well documented. Recent advances in molecular genetics using the moss Physcomitrella patens and the liverwort Marchantia polymorpha revealed that basal land plants show far-red-induced responses and that the establishment of phytochrome-mediated transcriptional regulation dates back to at least the common ancestor of land plants. In this review, we summarize our knowledge concerning functions of land plant phytochromes, especially in basal land plants, and discuss subfunctionalization/neofunctionalization of phytochrome signaling during the course of land plant evolution.

  17. Phytochrome from green plants: assay, purification, and characterization

    SciTech Connect

    Quail, P.H.

    1983-01-01

    Phytochrome from the chlorophyllous cells of light-grown higher plants and green algae has been isolated and characterized. We have developed a simple procedure that separates chlorophyll from phytochrome in crude extracts from green tissue thus permitting spectral measurement of the phytochrome in such extracts for the first time. Spectral and immunochemical analysis of phytochrome from green oat tissue indicates the presence of two distinct species of the molecule: a minority species (approx. 20%) that is recognized by antibodies directed against phytochrome from etiolated tissue and that has an apparent molecular mass of 124 kilodaltons (kD), the same as that of the native molecule from etiolated tissue; and a majority species (approx. 80%) that is not recognized by anti-etiolated tissue phytochrome Ig and has a Pr absorbance maximum some 14 nm shorter than its etiolated tissue counterpart. Mixing experiments have established that these different molecular species preexist in the green cell and are not the results of posthomogenization modifications. Attempts to purify the phytochrome from green tissue by immunoaffinity chromatography have been thwarted by the lack of immunological cross-reactivity referred to. We have begun to identify monoclonal antibodies specific for antigenic sites distributed throughout the length of the etiolated-tissue phytochrome polypeptide. Axenic cultures of the alga Mesotaenium have been established and preliminary spectral analysis of phytochrome isolated from these cells has been carried out.

  18. Role of calcium ions in phytochrome responses: an update

    NASA Technical Reports Server (NTRS)

    Roux, S. J.; Wayne, R. O.; Datta, N.

    1986-01-01

    Recent findings related to the role of calcium ions in phytochrome responses are reviewed and summarized. Hypotheses tested are the activation of calmodulin by light-regulated Ca2+ transport in cells and the photoinduction of calmodulin-activated enzyme activities. Discussion focuses on evidence that Ca2+ helps to regulate phytochrome responses, calcium requirements for photoinduced spore germination in the fern Onoclea, Ca2+ fluxes and phytochrome function in the alga Mougeotia, calmodulin antagonist blocking of red-light stimulated chloroplast rotation, the role of phosphorylation in calmodulin-regulated responses, and phytochrome regulation of nuclear protein phosphorylation.

  19. The room temperature crystal structure of a bacterial phytochrome determined by serial femtosecond crystallography

    SciTech Connect

    Edlund, Petra; Takala, Heikki; Claesson, Elin; Henry, Léocadie; Dods, Robert; Lehtivuori, Heli; Panman, Matthijs; Pande, Kanupriya; White, Thomas; Nakane, Takanori; Berntsson, Oskar; Gustavsson, Emil; Båth, Petra; Modi, Vaibhav; Roy-Chowdhury, Shatabdi; Zook, James; Berntsen, Peter; Pandey, Suraj; Poudyal, Ishwor; Tenboer, Jason; Kupitz, Christopher; Barty, Anton; Fromme, Petra; Koralek, Jake D.; Tanaka, Tomoyuki; Spence, John; Liang, Mengning; Hunter, Mark S.; Boutet, Sebastien; Nango, Eriko; Moffat, Keith; Groenhof, Gerrit; Ihalainen, Janne; Stojković, Emina A.; Schmidt, Marius; Westenhoff, Sebastian

    2016-10-19

    Phytochromes are a family of photoreceptors that control light responses of plants, fungi and bacteria. A sequence of structural changes, which is not yet fully understood, leads to activation of an output domain. Time-resolved serial femtosecond crystallography (SFX) can potentially shine light on these conformational changes. Here we report the room temperature crystal structure of the chromophore-binding domains of the Deinococcus radiodurans phytochrome at 2.1 Å resolution. The structure was obtained by serial femtosecond X-ray crystallography from microcrystals at an X-ray free electron laser. We find overall good agreement compared to a crystal structure at 1.35 Å resolution derived from conventional crystallography at cryogenic temperatures, which we also report here. The thioether linkage between chromophore and protein is subject to positional ambiguity at the synchrotron, but is fully resolved with SFX. As a result, the study paves the way for time-resolved structural investigations of the phytochrome photocycle with time-resolved SFX.

  20. The room temperature crystal structure of a bacterial phytochrome determined by serial femtosecond crystallography

    DOE PAGES

    Edlund, Petra; Takala, Heikki; Claesson, Elin; ...

    2016-10-19

    Phytochromes are a family of photoreceptors that control light responses of plants, fungi and bacteria. A sequence of structural changes, which is not yet fully understood, leads to activation of an output domain. Time-resolved serial femtosecond crystallography (SFX) can potentially shine light on these conformational changes. Here we report the room temperature crystal structure of the chromophore-binding domains of the Deinococcus radiodurans phytochrome at 2.1 Å resolution. The structure was obtained by serial femtosecond X-ray crystallography from microcrystals at an X-ray free electron laser. We find overall good agreement compared to a crystal structure at 1.35 Å resolution derived frommore » conventional crystallography at cryogenic temperatures, which we also report here. The thioether linkage between chromophore and protein is subject to positional ambiguity at the synchrotron, but is fully resolved with SFX. As a result, the study paves the way for time-resolved structural investigations of the phytochrome photocycle with time-resolved SFX.« less

  1. The room temperature crystal structure of a bacterial phytochrome determined by serial femtosecond crystallography

    PubMed Central

    Edlund, Petra; Takala, Heikki; Claesson, Elin; Henry, Léocadie; Dods, Robert; Lehtivuori, Heli; Panman, Matthijs; Pande, Kanupriya; White, Thomas; Nakane, Takanori; Berntsson, Oskar; Gustavsson, Emil; Båth, Petra; Modi, Vaibhav; Roy-Chowdhury, Shatabdi; Zook, James; Berntsen, Peter; Pandey, Suraj; Poudyal, Ishwor; Tenboer, Jason; Kupitz, Christopher; Barty, Anton; Fromme, Petra; Koralek, Jake D.; Tanaka, Tomoyuki; Spence, John; Liang, Mengning; Hunter, Mark S.; Boutet, Sebastien; Nango, Eriko; Moffat, Keith; Groenhof, Gerrit; Ihalainen, Janne; Stojković, Emina A.; Schmidt, Marius; Westenhoff, Sebastian

    2016-01-01

    Phytochromes are a family of photoreceptors that control light responses of plants, fungi and bacteria. A sequence of structural changes, which is not yet fully understood, leads to activation of an output domain. Time-resolved serial femtosecond crystallography (SFX) can potentially shine light on these conformational changes. Here we report the room temperature crystal structure of the chromophore-binding domains of the Deinococcus radiodurans phytochrome at 2.1 Å resolution. The structure was obtained by serial femtosecond X-ray crystallography from microcrystals at an X-ray free electron laser. We find overall good agreement compared to a crystal structure at 1.35 Å resolution derived from conventional crystallography at cryogenic temperatures, which we also report here. The thioether linkage between chromophore and protein is subject to positional ambiguity at the synchrotron, but is fully resolved with SFX. The study paves the way for time-resolved structural investigations of the phytochrome photocycle with time-resolved SFX. PMID:27756898

  2. The room temperature crystal structure of a bacterial phytochrome determined by serial femtosecond crystallography

    NASA Astrophysics Data System (ADS)

    Edlund, Petra; Takala, Heikki; Claesson, Elin; Henry, Léocadie; Dods, Robert; Lehtivuori, Heli; Panman, Matthijs; Pande, Kanupriya; White, Thomas; Nakane, Takanori; Berntsson, Oskar; Gustavsson, Emil; Båth, Petra; Modi, Vaibhav; Roy-Chowdhury, Shatabdi; Zook, James; Berntsen, Peter; Pandey, Suraj; Poudyal, Ishwor; Tenboer, Jason; Kupitz, Christopher; Barty, Anton; Fromme, Petra; Koralek, Jake D.; Tanaka, Tomoyuki; Spence, John; Liang, Mengning; Hunter, Mark S.; Boutet, Sebastien; Nango, Eriko; Moffat, Keith; Groenhof, Gerrit; Ihalainen, Janne; Stojković, Emina A.; Schmidt, Marius; Westenhoff, Sebastian

    2016-10-01

    Phytochromes are a family of photoreceptors that control light responses of plants, fungi and bacteria. A sequence of structural changes, which is not yet fully understood, leads to activation of an output domain. Time-resolved serial femtosecond crystallography (SFX) can potentially shine light on these conformational changes. Here we report the room temperature crystal structure of the chromophore-binding domains of the Deinococcus radiodurans phytochrome at 2.1 Å resolution. The structure was obtained by serial femtosecond X-ray crystallography from microcrystals at an X-ray free electron laser. We find overall good agreement compared to a crystal structure at 1.35 Å resolution derived from conventional crystallography at cryogenic temperatures, which we also report here. The thioether linkage between chromophore and protein is subject to positional ambiguity at the synchrotron, but is fully resolved with SFX. The study paves the way for time-resolved structural investigations of the phytochrome photocycle with time-resolved SFX.

  3. Chromopeptides from phytochrome. The structure and linkage of the PR form of the phytochrome chromophore

    SciTech Connect

    Lagarias, J. Clark; Rapoport, Henry

    1980-07-01

    The isolation and chromatographic purification of chromophore-containing peptides from the PR form of phytochrome treated with pepsin and thermolysin are described. From the amino acid sequence and 1H NMR spectral analysis of phytochromobiliundeca peptide (2), the structure of the PR phytochrome chromophore and the nature of the thioether linkage joining pigment to peptide have been established. Furthermore, confirmatory evidence was obtained from similar analysis of phytochromobilioctapeptide (3). The implications of this structural assignment with respect to the mechanism of the PR to PFR phototransformation are considered.

  4. Mechanism for the selective conjugation of ubiquitin to phytochrome

    SciTech Connect

    Vierstra, R.D.

    1990-01-01

    The goal of this project is to understand at the molecular level how phytochrome functions and how intracellular proteins are degraded. Phytochrome is marked for degradation by covalent attachment of ubiquitin. Ubiquitin-phytochrome conjugates (UbP) were characterized with respect to formation kinetics, subcellular localization and site of ubiquitin attachment. UbP appears to be a general phenomenon during phytochrome degradation in a variety of species. UbP was isolated from oat seedlings and characterized. Residues 747-830 of phytochrome have been identified as a possible attachment site for ubiquitin. By placing the gene for etiolated phytochrome in tobacco we have created a transgenic system for over expressing phytochrome. The effects of this over expression are described, and it appears that tobacco degrades this foreign protein through formation of UbP. We have created a series of site-directed mutants of the oat phytochrome gene, and are in the process of characterizing them to determine sequence requirements for ubiquination. 8 refs., 1 fig. (MHB)

  5. Mechanistic duality of transcription factor function in phytochrome signaling

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The phytochrome (phy) family of sensory photoreceptors (phyA–E in Arabidopsis) elicit changes in gene expression after light-induced migration to the nucleus, where they interact with basic helix–loop–helix transcription factors, such as phytochrome-interacting factor 3 (PIF3). The mechanism by whic...

  6. Phytochrome A-specific signaling in Arabidopsis thaliana.

    PubMed

    Kircher, Stefan; Terecskei, Kata; Wolf, Iris; Sipos, Mark; Adam, Eva

    2011-11-01

    Among the five phytochromes in Arabidopsis thaliana, phytochrome A (phyA) plays a major role in seedling de-etiolation. Until now more then ten positive and some negative components acting downstream of phyA have been identified. However, their site of action and hierarchical relationships are not completely understood yet.

  7. In vivo measurement of phytochrome in tomato fruit.

    PubMed

    Jen, J J

    1977-04-01

    Presence of phytochrome in two kinds of tomatoes (Lycopersicon esculentum Mill.), the yellow lutescent strain and cherry tomatoes (L. esculentum Mill. var. cerasiformecv. Red Cherry), was established by measuring the absorption difference spectra of the whole fruit after irradiation with red and with far red light. Phytochrome content was determined in yellow lutescent tomatoes and decreased gradually during the ripening period.

  8. Overexpression of Arabidopsis phytochrome B inhibits phytochrome A function in the presence of sucrose.

    PubMed

    Short, T W

    1999-04-01

    Overexpression of phytochrome B (phyB) in Arabidopsis has previously been demonstrated to result in dominant negative interference of phytochrome A (phyA)-mediated hypocotyl growth inhibition in far-red (FR) light. This phenomenon has been examined further in this study and has been found to be dependent on the FR fluence rate and on the availability of metabolizable sugars in the growth medium. Poorly metabolized sugars capable of activating the putative hexokinase sensory function were not effective in eliciting the phytochrome interference response. Overexpressed phyB lacking the chromophore-binding site was also effective at inhibiting the phyA response, especially at higher fluence rates of FR. Overexpressed phyB produces the dominant negative phenotype without any apparent effect on phyA abundance or degradation. It is possible that phyA and phyB interact with a common reaction partner but that either the energy state of the cell or a separate sugar-signaling mechanism modulates the phytochrome-signaling interactions.

  9. Phytochrome in photosynthetically competent plants characterization by monoclonal antibodies. Progress report

    SciTech Connect

    Pratt, L.H.

    1986-01-01

    Detailed information concerning the physicochemical properties of phytochrome is sought, but since only trace quantities are present in plant tissues, it is extremely labile to modification in crude plant extracts, efficient and sensitive methods for its purification and characterization will be required. Towards this end immune serums directed towards oat phytochrome have been prepared. Unfortunately the phytochrome in green oats is immunochemically distinct from phytochrome in etiolated oats. Consequently, effort has been directed at preparation of monoclonal antibodies for green-oat phytochrome.

  10. Vibrational-rotational spectra of GaF and global multi-isotopologue analysis

    NASA Astrophysics Data System (ADS)

    Uehara, Hiromichi; Horiai, Koui; Katsuie, Shunsuke

    2016-07-01

    In total, 521 vibrational-rotational spectral lines of the Δv = 1 transitions of 69GaF and 71GaF up to bands v = 5-4 and 4-3, respectively, were recorded in emission with a Fourier-transform spectrometer at unapodized resolution 0.010 cm-1 in range 625-660 cm-1. The response of a HgCdTe detector enforced the lower limit, 625 cm-1. To calibrate accurately the spectral lines, the absorption spectrum of CO2 was simultaneously recorded, using dual sample cells, to serve as wavenumber standards. A set of 782 spectral lines comprising all present vibrational-rotational spectra of 69GaF and 71GaF, the reported laser-diode measurements of the Δv = 1 band sequence and the reported rotational spectra was subjected to a global multi-isotopologue analysis through fitting with 11 isotopically invariant, irreducible molecular parameters in a single set. Normalized standard deviation 1.093 indicates a satisfactory fit. For the effects of the breakdown of the Born-Oppenheimer approximation on GaF, the values of non-Born-Oppenheimer parameters ΔBGa, ΔωGa and r1qGa(=r1qF) are experimentally determined for the first time. To facilitate the calculations or predictions of spectral frequencies, the values of the Dunham coefficients of 24 Yij and 81 band parameters for both 69GaF and 71GaF were back-calculated with uncertainties using the 11 evaluated molecular parameters. To date, various types of effective Be, re, ωe, and k have been reported for GaF. Because, in the present work, Dunham coefficients Yij are algebraically expressed with the genuine Be, ωe, ai (i = 1, …) and the non-Born-Oppenheimer correction parameters, the exact expressions for the physical significance of effective quantities are derivable. The various effective quantities of Be, re, ωe and k calculated with these expressions for the physical significance and the determined values of the fitted parameters of GaF agree satisfactorily with the reported values. The physical significance of the conventional

  11. Oat Phytochrome Is Biologically Active in Transgenic Tomatoes.

    PubMed

    Boylan, M. T.; Quail, P. H.

    1989-08-01

    To determine the functional homology between phytochromes from evolutionarily divergent species, we used the cauliflower mosaic virus 35S promoter to express a monocot (oat) phytochrome cDNA in a dicot plant (tomato). Immunoblot analysis shows that more than 50% of the transgenic tomato plants synthesize the full-length oat phytochrome polypeptide. Moreover, leaves of light-grown transgenic plants contain appreciably less oat phytochrome than leaves from dark-adapted plants, and etiolated R1 transgenic seedlings have higher levels of spectrally active phytochrome than wild-type tomato seedlings in direct proportion to the level of immunochemically detectable oat polypeptide present. These data suggest that the heterologous oat polypeptide carries a functional chromophore, allowing reversible photoconversion between the two forms of the molecule, and that the far-red absorbing form (Pfr) is recognized and selectively degraded by the Pfr-specific degradative machinery in the dicot cell. The overexpression of oat phytochrome has pleiotropic, phenotypic consequences at all major phases of the life cycle. Adult transgenic tomato plants expressing high levels of the oat protein tend to be dwarfed, with dark green foliage and fruits. R1 transgenic seedlings have short hypocotyls with elevated anthocyanin contents. We conclude that a monocot phytochrome can be synthesized and correctly processed to a biologically active form in a dicot cell, and that the transduction pathway components that interact with the photoreceptor are evolutionarily conserved.

  12. The Arabidopsis Phytochrome-Interacting Factor PIF7, Together with PIF3 and PIF4, Regulates Responses to Prolonged Red Light by Modulating phyB Levels

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We show that a previously uncharacterized Arabidopsis thaliana basic helix-loop-helix (bHLH) phytochrome interacting factor (PIF), designated PIF7, interacts specifically with the far-red light–absorbing Pfr form of phyB through a conserved domain called the active phyB binding motif. Similar to PIF...

  13. Selective inhibition of Erwinia amylovora by the herbicidally-active Germination-Arrest Factor (GAF) produced by Pseudomonas bacteria

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Aims: The Germination-Arrest Factor (GAF) produced by Pseudomonas fluorescens WH6, and identified as 4-formylaminooxyvinylglycine, specifically inhibits the germination of a wide range of grassy weeds. The present study was undertaken to determine if GAF has antimicrobial activity in addition to it...

  14. Structure-guided Engineering Enhances a Phytochrome-based Infrared Fluorescent Protein*

    PubMed Central

    Auldridge, Michele E.; Satyshur, Kenneth A.; Anstrom, David M.; Forest, Katrina T.

    2012-01-01

    Phytochrome is a multidomain dimeric red light photoreceptor that utilizes a chromophore-binding domain (CBD), a PHY domain, and an output module to induce cellular changes in response to light. A promising biotechnology tool emerged when a structure-based substitution at Asp-207 was shown to be an infrared fluorophore that uses a biologically available tetrapyrrole chromophore. We report multiple crystal structures of this D207H variant of the Deinococcus radiodurans CBD, in which His-207 is observed to form a hydrogen bond with either the tetrapyrrole A-ring oxygen or the Tyr-263 hydroxyl. Based on the implications of this duality for fluorescence properties, Y263F was introduced and shown to have stronger fluorescence than the original D207H template. Our structures are consistent with the model that the Y263F change prevents a red light-induced far-red light absorbing phytochrome chromophore configuration. With the goal of decreasing size and thereby facilitating use as a fluorescent tag in vivo, we also engineered a monomeric form of the CBD. Unexpectedly, photoconversion was observed in the monomer despite the lack of a PHY domain. This observation underscores an interplay between dimerization and the photochemical properties of phytochrome and suggests that the monomeric CBD could be used for further studies of the photocycle. The D207H substitution on its own in the monomer did not result in fluorescence, whereas Y263F did. Combined, the D207H and Y263F substitutions in the monomeric CBD lead to the brightest of our variants, designated Wisconsin infrared phytofluor (Wi-Phy). PMID:22210774

  15. Surface-enhanced resonance Raman scattering spectroscopy applied to phytochrome and its model compounds. 2. Phytochrome and phycocyanin chromophores

    SciTech Connect

    Farrens, D.L.; Holt, R.E.; Rospendowski, B.N.; Song, Pillsoon; Cotton, T.M. )

    1989-12-20

    Surface-enhanced resonance Raman scattering (SERRS) spectra of phytochrome at 77 K are reported. The spectra reveal significant differences between Pr and Pfr forms of phytochrome. SERRS spectra of C-phycocyanin Z,Z,Z- and Z,Z,E-chromopeptide isomers at 77 K are also reported. The phycocyanin chromopeptide studies are used to provide a basis for interpreting the phytochrome SERRS spectra. The spectra indicate that photoisomerization of chromophores from C-phycocyanin chromopeptides (from a Z,Z,Z to a Z,Z,E configuration) is detectable with SERRS.

  16. Phytochrome B inhibits binding of Phytochrome-Interacting Factors to their target promoters

    PubMed Central

    Park, Eunae; Park, Jeongmoo; Kim, Junghyun; Nagatani, Akira; Lagarias, J. Clark; Choi, Giltsu

    2012-01-01

    Summary Phytochromes are red and far-red light receptors in plants that mediate critical responses to light throughout the life cycle. They achieve this in part by targeting negatively acting bHLH transcription factors called phytochrome-interacting factors (PIFs) for degradation within the nucleus. It is not known, however, if protein degradation is the primary mechanism by which phytochromes inhibit these repressors of photomorphogenesis. Here, we use ChIP analysis to show that phyB inhibits the regulatory activity of PIF1 and PIF3 by releasing them from their DNA targets. The N-terminal fragment of phyB (NG-GUS-NLS; NGB) also inhibits the binding of PIF3 to its target promoters. Unlike the full-length phyB, however, NGB does not promote PIF3 degradation, establishing the activity of NGB reflects its ability to inhibit PIFs’ binding to DNA. We further show that Pfr forms of both full-length phyB and NGB inhibit the DNA binding of PIF1 and PIF3 in vitro. Taken together, our results indicate that phyB inhibition of PIF function involves two separate processes, sequestration and protein degradation. PMID:22849408

  17. An Analysis of Phytochrome-mediated Anthocyanin Synthesis

    PubMed Central

    Lange, H.; Shropshire, W.; Mohr, H.

    1971-01-01

    Phytochrome (far red form) alone can mediate anthocyanin synthesis in the mustard seedling (Sinapis alba L.). Complete photoreversibility and reciprocity, for both red and far red light exposures over a period of at least 5 minutes, demonstrate this phytochrome involvement. The duration of the initial lag-phase is constant (about 3 hours at 25 C) for seedlings more than 30 hours old and is specific for the system, being independent of the dose or quality of light. Since a complete reversal by far red of a red light induction is possible only during a 5 minute period, phytochrome (far red form) obviously mediates anthocyanin synthesis during the lag-phase although the actual synthesis of pigment can proceed only after the lag-phase is overcome. We suggest that phytochrome (far red form) exerts a double function during the initial lag-phase. It mediates both the build up of a biosynthetic potential (“capacity”) and anthocyanin synthesis. However, the sequence of events leading to anthocyanin is arrested at some intermediate stage until this “capacity” is built up after 3 hours. Once “capacity” is achieved it does not decay readily. Therefore, no significant “secondary lag-phase” occurs if the seedling, under appropriate conditions, is reirradiated after an intervening dark period. The rate or extent of synthesis for both anthocyanin and lipoxygenase, previously reported (32), are functions of the amount of phytochrome (far red form). No “phytochrome paradoxes,” i.e., nonrational relationships between the amount of phytochrome (far red form) and rate or extent of response, were detected. This fact suggests that the mustard seedling is especially well suited for investigating the biophysical and molecular mechanisms of phytochrome action. PMID:16657678

  18. Phytochrome from green plants: Assay, purification, and characterization

    SciTech Connect

    Quail, P.H. . Dept. of Plant and Soil Biology Agricultural Research Service, Albany, CA . Plant Gene Expression Center)

    1991-06-10

    This funding period was directed at developing an in-depth molecular analysis of the low-abundance, 118,000 M{sub r} green-tissue phytochrome that had at that time been relatively recently identified as being distinct from the better characterized 124,000 M{sub r} phytochrome abundant in etiolated tissue. The specific objectives as stated in the original proposal were: (1) To generate monoclonal antibodies specific to the 118,000 M{sub r} green-tissue phytochrome. (2) To develop additional and improved procedures to permit progress toward the ultimate goal of purifying green-tissue phytochrome to homogeneity. (3) To initiate an alternative approach to determining the structural properties of green-tissue phytochrome by isolating and sequencing cDNA cones representing the 118,000 M{sub r} green-tissue polypeptide in Avena. This approach is based on and will test hypothesis that the 118,000 M{sub r} polypeptide is encoded by a gene(s) distinct from those encoding etiolated-tissue 124,000 M{sub r} phytochrome. (4) To utilize any such 118,000 M{sub r} phytochrome specific cDNA clones as hybridization probes to begin to investigate the structure, organization, and regulation of the corresponding gene(s) in Avena. (5) To begin to investigate the possible presence in other higher plant and algal species of sequences homologous to the 118,000 M{sub r} Avena polypeptide using the Avena clones at hybridization probes. Most of these objectives have been accomplished, at least in principle, although the major breakthrough establishing that phytochrome is encoded by a multigene family came from the use of Arabidopsis rather than Avena. Similarly, much of the characterization subsequent to this discovery has been performed in Arabidopsis and rise as model dicot and monocot systems, respectively, rather than Avena. 13 refs., 9 figs.

  19. Phytochromes: An Atomic Perspective on Photoactivation and Signaling

    PubMed Central

    Burgie, E. Sethe

    2014-01-01

    The superfamily of phytochrome (Phy) photoreceptors regulates a wide array of light responses in plants and microorganisms through their unique ability to reversibly switch between stable dark-adapted and photoactivated end states. Whereas the downstream signaling cascades and biological consequences have been described, the initial events that underpin photochemistry of the coupled bilin chromophore and the ensuing conformational changes needed to propagate the light signal are only now being understood. Especially informative has been the rapidly expanding collection of 3D models developed by x-ray crystallographic, NMR, and single-particle electron microscopic methods from a remarkably diverse array of bacterial Phys. These structures have revealed how the modular architecture of these dimeric photoreceptors engages the buried chromophore through distinctive knot, hairpin, and helical spine features. When collectively viewed, these 3D structures reveal complex structural alterations whereby photoisomerization of the bilin drives nanometer-scale movements within the Phy dimer through bilin sliding, hairpin reconfiguration, and spine deformation that ultimately impinge upon the paired signal output domains. When integrated with the recently described structure of the photosensory module from Arabidopsis thaliana PhyB, new opportunities emerge for the rational redesign of plant Phys with novel photochemistries and signaling properties potentially beneficial to agriculture and their exploitation as optogenetic reagents. PMID:25480369

  20. Spectrophotometric phytochrome measurements in light-grown Avena sativa L.

    PubMed

    Jabben, M; Deitzer, G F

    1978-01-01

    Phytochrome was studied spectrophotometrically in Avena sativa L. seedlings that had been grown for 6 d in continous white fluorescent light from lamps. Greening was prevented through the use of the herbicide San 9789. When placed in the light, phytochrome (Ptot) decreased with first order kinetics (τ1/2 ≈ 2 h) but reached a stable low level (≈2.5% of the dark level) after 36 h. This concentration of phytochrome remained constant in the light and during the initial hours of a subsequent dark period, but increased significantly after a prolonged dark period. Evidence suggests that the constant pool of phytochrome in the light is achieved through an equilibrium between synthesis of the red absorbing (Pr) and destruction of the far-red absorbing form (Pfr) of phytochrome. It is concluded that the phytochrome system in light-grown oat seedlings is qualitatively the same as that known from etiolated monocotyledonous seedlings, but different than that described for cauliflower florets.

  1. Structure and expression of maize phytochrome family homeologs.

    PubMed Central

    Sheehan, Moira J; Farmer, Phyllis R; Brutnell, Thomas P

    2004-01-01

    To begin the study of phytochrome signaling in maize, we have cloned and characterized the phytochrome gene family from the inbred B73. Through DNA gel blot analysis of maize genomic DNA and BAC library screens, we show that the PhyA, PhyB, and PhyC genes are each duplicated once in the genome of maize. Each gene pair was positioned to homeologous regions of the genome using recombinant inbred mapping populations. These results strongly suggest that the duplication of the phytochrome gene family in maize arose as a consequence of an ancient tetraploidization in the maize ancestral lineage. Furthermore, sequencing of Phy genes directly from BAC clones indicates that there are six functional phytochrome genes in maize. Through Northern gel blot analysis and a semiquantitative reverse transcriptase polymerase chain reaction assay, we determined that all six phytochrome genes are transcribed in several seedling tissues. However, expression from PhyA1, PhyB1, and PhyC1 predominate in all seedling tissues examined. Dark-grown seedlings express higher levels of PhyA and PhyB than do light-grown plants but PhyC genes are expressed at similar levels under light and dark growth conditions. These results are discussed in relation to phytochrome gene regulation in model eudicots and monocots and in light of current genome sequencing efforts in maize. PMID:15280251

  2. Phytochromes inhibit hypocotyl negative gravitropism by regulating the development of endodermal amyloplasts through phytochrome-interacting factors.

    PubMed

    Kim, Keunhwa; Shin, Jieun; Lee, Sang-Hee; Kweon, Hee-Seok; Maloof, Julin N; Choi, Giltsu

    2011-01-25

    Phytochromes are red and far-red light photoreceptors that regulate various aspects of plant development. One of the less-understood roles of phytochromes is the inhibition of hypocotyl negative gravitropism, which refers to the loss of hypocotyl gravitropism and resulting random growth direction in red or far-red light. This light response allows seedlings to curve toward blue light after emergence from the soil and enhances seedling establishment in the presence of mulch. Phytochromes inhibit hypocotyl negative gravitropism by inhibiting four phytochrome-interacting factors (PIF1, PIF3, PIF4, PIF5), as shown by hypocotyl agravitropism of dark-grown pif1 pif3 pif4 pif5 quadruple mutants. We show that phytochromes inhibit negative gravitropism by converting starch-filled gravity-sensing endodermal amyloplasts to other plastids with chloroplastic or etioplastic features in red or far-red light, whereas PIFs promote negative gravitropism by inhibiting the conversion of endodermal amyloplasts to etioplasts in the dark. By analyzing transgenic plants expressing PIF1 with an endodermis-specific SCARECROW promoter, we further show that endodermal PIF1 is sufficient to inhibit the conversion of endodermal amyloplasts to etioplasts and hypocotyl negative gravitropism of the pif quadruple mutant in the dark. Although the functions of phytochromes in gravitropism and chloroplast development are normally considered distinct, our results indicate that these two functions are closely related.

  3. Collecting Information for Rating Global Assessment of Functioning (GAF): Sources of Information and Methods for Information Collection

    PubMed Central

    Aas, I. H. Monrad

    2014-01-01

    Introduction: Global Assessment of Functioning (GAF) is an assessment instrument that is known worldwide. It is widely used for rating the severity of illness. Results from evaluations in psychiatry should characterize the patients. Rating of GAF is based on collected information. The aim of the study is to identify the factors involved in collecting information that is relevant for rating GAF, and gaps in knowledge where it is likely that further development would play a role for improved scoring. Methods: A literature search was conducted with a combination of thorough hand search and search in the bibliographic databases PubMed, PsycINFO, Google Scholar, and Campbell Collaboration Library of Systematic Reviews. Results: Collection of information for rating GAF depends on two fundamental factors: the sources of information and the methods for information collection. Sources of information are patients, informants, health personnel, medical records, letters of referral and police records about violence and substance abuse. Methods for information collection include the many different types of interview – unstructured, semi-structured, structured, interviews for Axis I and II disorders, semistructured interviews for rating GAF, and interviews of informants – as well as instruments for rating symptoms and functioning, and observation. The different sources of information, and methods for collection, frequently result in inconsistencies in the information collected. The variation in collected information, and lack of a generally accepted algorithm for combining collected information, is likely to be important for rated GAF values, but there is a fundamental lack of knowledge about the degree of importance. Conclusions: Research to improve GAF has not reached a high level. Rated GAF values are likely to be influenced by both the sources of information used and the methods employed for information collection, but the lack of research-based information about these

  4. Calcium requirement of phytochrome-mediated fern-spore germination: no direct phytochrome-calcium interaction in the phytochrome-initiated transduction chain

    NASA Technical Reports Server (NTRS)

    Scheuerlein, R.; Wayne, R.; Roux, S. J.

    1989-01-01

    Phytochrome-mediated germination of fern spores of Dryopteris paleacea Sw. was initiated by a saturating red-light (R) irradiation after 20 h of imbibition. For its realization external Ca2+ was required, with a threshold at a submicromolar concentration, and an optimum was reached around 10(-4) M. At concentrations > or = 10(-1) M only a reduced response was obtained, based probably on an unspecific osmotic or ionic effect. The germination response was inhibited by La3+, an antagonist of Ca2+. From these results it is concluded that Ca2+ influx from the medium into the spores may be an important event in phytochrome-mediated germination. In the absence of Ca2+ the R-stimulated system remained capable of responding to Ca2+, added as late as 40 h after R. Moreover, Ca2+ was effective even if added after the active form of phytochrome, Pfr, had been abolished by far-red (FR) 24 h after R. Thus, the primary effect of Pfr, that initiates the transduction chain, does not require calcium. "Coupling" of Pfr to subsequent dark reactions has been investigated by R-FR irradiations with various dark intervals. The resulting "escape kinetics" were characterized by a lag phase (6 h) and half-maximal escape from FR reversibility (19 h). These kinetics were not significantly changed by the presence or absence of calcium. Thus, direct interaction of Pfr and calcium is not a step in the transduction chain initiated by the active form of phytochrome.

  5. Phytochrome-mediated regulation of plant respiration and photorespiration.

    PubMed

    Igamberdiev, Abir U; Eprintsev, Alexander T; Fedorin, Dmitry N; Popov, Vasily N

    2014-02-01

    The expression of genes encoding various enzymes participating in photosynthetic and respiratory metabolism is regulated by light via the phytochrome system. While many photosynthetic, photorespiratory and some respiratory enzymes, such as the rotenone-insensitive NADH and NADPH dehydrogenases and the alternative oxidase, are stimulated by light, succinate dehydrogenase, subunits of the pyruvate dehydrogenase complex, cytochrome oxidase and fumarase are inhibited via the phytochrome mechanism. The effect of light, therefore, imposes limitations on the tricarboxylic acid cycle and on the mitochondrial electron transport coupled to ATP synthesis, while the non-coupled pathways become activated. Phytochrome-mediated regulation of gene expression also creates characteristic distribution patterns of photosynthetic, photorespiratory and respiratory enzymes across the leaf generating different populations of mitochondria, either enriched by glycine decarboxylase (in the upper part) or by succinate dehydrogenase (in the bottom part of the leaf).

  6. Photophysical diversity of two novel cyanobacteriochromes with phycocyanobilin chromophores: photochemistry and dark reversion kinetics.

    PubMed

    Chen, Yu; Zhang, Juan; Luo, Juan; Tu, Jun-Ming; Zeng, Xiao-Li; Xie, Jie; Zhou, Ming; Zhao, Jing-Quan; Scheer, Hugo; Zhao, Kai-Hong

    2012-01-01

    Cyanobacteriochromes are phytochrome homologues in cyanobacteria that act as sensory photoreceptors. We compare two cyanobacteriochromes, RGS (coded by slr1393) from Synechocystis sp. PCC 6803 and AphC (coded by all2699) from Nostoc sp. PCC 7120. Both contain three GAF (cGMP phosphodiesterase, adenylyl cyclase and FhlA protein) domains (GAF1, GAF2 and GAF3). The respective full-length, truncated and cysteine point-mutated genes were expressed in Escherichia coli together with genes for chromophore biosynthesis. The resulting chromoproteins were analyzed by UV-visible absorption, fluorescence and circular dichroism spectroscopy as well as by mass spectrometry. RGS shows a red-green photochromism (λ(max) = 650 and 535 nm) that is assigned to the reversible 15Z/E isomerization of a single phycocyanobilin-chromophore (PCB) binding to Cys528 of GAF3. Of the three GAF domains, only GAF3 binds a chromophore and the binding is autocatalytic. RGS autophosphorylates in vitro; this reaction is photoregulated: the 535 nm state containing E-PCB was more active than the 650 nm state containing Z-PCB. AphC from Nostoc could be chromophorylated at two GAF domains, namely GAF1 and GAF3. PCB-GAF1 is photochromic, with the proposed 15E state (λ(max) = 685 nm) reverting slowly thermally to the thermostable 15Z state (λ(max)  = 635 nm). PCB-GAF3 showed a novel red-orange photochromism; the unstable state (putative 15E, λ(max) = 595 nm) reverts very rapidly (τ ~ 20 s) back to the thermostable Z state (λ(max) = 645 nm). The photochemistry of doubly chromophorylated AphC is accordingly complex, as is the autophosphorylation: E-GAF1/E-GAF3 shows the highest rate of autophosphorylation activity, while E-GAF1/Z-GAF3 has intermediate activity, and Z-GAF1/Z-GAF3 is the least active state.

  7. Mechanism for the selective conjugation of ubiquitin to phytochrome

    SciTech Connect

    Vierstra, R.D.

    1989-01-01

    The long term goal of this project is to understand at the molecular level how intracellular proteins are degraded. The purpose of this research is to characterize the form-dependent degradation of phytochrome as a model system for the study of selective protein breakdown. Phytochrome exists in two photo-interconveretible forms, a red-absorbing Pr form and a far-red absorbing Pfr form. Recent evidence indicates that selective breakdown of phytochrome in etiolated oat seedlings occurs by a ubiquitin-dependent proteolytic pathway. Ubiquitin is a 76 amino acid eukaryotic protein that is covalently ligated to proteins destined for catabolism and serves as recognition signal for proteases specific for ubiquitin-protein conjugates. In an attempt to understand why Pfr and not Pr is recognized by the ubiquitin pathway, we have characterized ubiquitin-phytochrome conjugates (Ub-P) with respect to their kinetics of accumulation, localization within the cell, and sites of ubiquitin attachment. We also examined Pfr degradation in etiolated seedlings from a variety of other plant species (corn, rye, pea and zucchini squash) for their ability to form Ub-P during Pfr degradation. 4 refs.

  8. Phytochrome-mediated Carotenoids Biosynthesis in Ripening Tomatoes.

    PubMed

    Thomas, R L; Jen, J J

    1975-09-01

    Red light induced and far red light inhibited carotenoid biosynthesis in ripening tomatoes (Lycopersicon esculentum Mill.) when compared to controls kept in the dark. Red illumination following far red illumination reversed the inhibitory action of far red light on carotenoid biosynthesis, suggesting a phytochrome-mediated process. Quantitation of individual carotenoids favored the hypothesis of two separate carotenoid biosynthetic pathways in tomatoes.

  9. Characterization by enzyme-linked immunosorbent assay of monoclonal antibodies to Pisum and Avena phytochrome

    SciTech Connect

    Cordonnier, M.M.; Greppin, H.; Pratt, L.H.

    1984-01-01

    Nine monoclonal antibodies to pea (Pisum sativum L.) and 16 to oat (Avena sativa L.) phytochrome are characterized by enzyme-linked immunosorbent assay against phytochrome from six different sources: pea, zucchini (Cucurbita pepo L.), lettuce (Lactuca sativa L.), oat, rye (Secale cereale L.), and barley (Hordeum vulgare L.). All antibodies were raised against phytochrome with a monomer size near 120,000 daltons. Nevertheless, none of them discriminated qualitatively between 118/114-kilodalton oat phytochrome and a photoreversible, 60-kilodalton proteolytic degradation product derived from it. In addition, none of the 23 antibodies tested discriminated substantially between phytochrome - red-absorbing form and phytochrome - far red-absorbing form. Two antibodies to pea and six to oat phytochrome also bound strongly to phytochrome from the other species, even though these two plants are evolutionarily widely divergent. Of these eight antibodies, two bound significantly to all of the six phytochrome preparations tested, indicating that these two may recognize highly conserved regions of the chromoprotein. Since the molecular function of phytochrome is unknown, these two antibodies may serve as unique probes for regions of this pigment that are important to its mode of action. 27 references, 3 figures, 1 table.

  10. Rapid transcriptional regulation by phytochrome of the genes for phytochrome and chlorophyll a/b-binding protein in Avena sativa.

    PubMed Central

    Lissemore, J L; Quail, P H

    1988-01-01

    We have examined phytochrome-regulated transcription of phytochrome (phy) and chlorophyll a/b binding protein (cab) genes in dark-grown Avena seedlings by using run-on transcription in isolated nuclei. Kinetic analysis of phy transcription following pulse-light treatments to produce various amounts of Pfr, the active form of phytochrome, leads to these conclusions. (i) Transcription decreases rapidly (discernible within 5 min) after Pfr formation, reaching an essentially undetectable level by 1 h. (ii) The response is very sensitive; less than 1% Pfr is sufficient to produce maximum feedback repression over the first 30 min. (iii) The duration of transcriptional repression is proportional to the Pfr concentration; derepression begins once the concentration falls below some saturation level because of degradation of Pfr. Concurrent analysis of cab transcription leads to these conclusions. (i) After Pfr formation, transcription increases approximately 10-fold by 3 h, but this response is not detectable until after a 30-min lag. (ii) Detectable induction of cab requires a greater than 30-fold-higher Pfr level than is needed to repress phy expression. (iii) Transcription returns to the preirradiation level considerably sooner than does phy transcription (less than 12 h versus greater than 24 h respectively), indicating that a high level of Pfr is needed to sustain the increased transcription of cab. Taken together, these results suggest that differences in the phytochrome signal transduction pathway are responsible for the distinct patterns of regulation of these genes. Full repression of phy occurs even when protein synthesis is inhibited greater than 90% by cycloheximide and chloramphenicol. In conjunction with the rapidity of the response to Pfr, this result provides evidence that feedback repression of phy gene transcription does not require expression of an intervening regulatory gene(s). Thus, phy is the first gene for which there is evidence for direct control

  11. Negative regulation of Germination-Arrest Factor (GAF) production in Pseudomonas fluorescens WH6 by a putative extracytoplasmic function sigma factor

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Pseudomonas fluorescens WH6 secretes a Germination-Arrest Factor (GAF) that we have previously identified as 4-formylaminooxyvinylglycine. GAF irreversibly inhibits germination of the seeds of numerous grassy weed species and selectively inhibits growth of the bacterial plant pathogen Erwinia amylo...

  12. Drosophila BTB/POZ domains of "ttk group" can form multimers and selectively interact with each other.

    PubMed

    Bonchuk, Artem; Denisov, Stepan; Georgiev, Pavel; Maksimenko, Oksana

    2011-09-23

    The BTB (bric-a-brac, tramtrack and broad complex)/POZ (poxvirus and zinc finger) domain is a conserved protein-protein interaction motif contained in a variety of transcription factors involved in development, chromatin remodeling, insulator activity, and carcinogenesis. All well-studied mammalian BTB domains form obligate homodimers and, rarely, tetramers. Only the BTB domain of the Drosophila GAGA factor (GAF) has been shown to exist as higher-order multimers. The BTB domain of GAF belongs to the "ttk group" that contains several highly conserved sequences not found in other BTB domains. Here, we have shown by size-exclusion chromatography, chemical cross-linking, and nondenaturing PAGE that four additional BTB domains of the ttk group-Batman, Mod(mdg4), Pipsqueak, and Tramtrack-can form multimers, like GAF. Interestingly, the BTB domains of GAF and Batman have formed a wide range of complexes and interacted in the yeast two-hybrid assay with other BTB domains tested. In contrast, the BTB domains of Mod(mdg4), Pipsqueak, and Tramtrack have formed stable high-order multimer complexes and failed to interact with each other. The BTB domain of Drosophila CP190 protein does not belong to the ttk group. This BTB domain has formed stable dimers and has not interacted with domains of the ttk group. Previously, it was suggested that GAF oligomerization into higher-order complexes facilitates long-range activation by providing a protein bridge between an enhancer and a promoter. Unexpectedly, experiments in the Drosophila model system have not supported the role of GAF in organization of long-distance interaction between the yeast GAL4 activator and the white promoter.

  13. Picosecond time-resolved fluorescence spectroscopy of phytochrome and stentorin

    NASA Astrophysics Data System (ADS)

    Song, Pill-Soon

    1991-05-01

    Phytochrome is a tetrapyrrole chromoprotein. It serves as a sensitive photosensor for red lightmediated gene expression and other developmental/morphological responses in plants. In this paper photochemical dynamics of the phytochrome molecule have been described in terms of photoisomerization of the tetrapyrrole chromophore in its singlet excited state and subsequent thermal processes in the Pr Pfr phototransformation of phytochrome. Stentorin acts as the photosensor molecule in the ciliate Stentor coeruleus. This unicellular protozoan is most sensitive to red light (610-620 urn). Stentor also senses the direction of light propagation as evidenced by their light-avoiding and negative phototactic swimming behaviors. This aneural photosensory phenomenon is triggered by the photoreceptor stentorin. The possible involvement of a light-induced transient proton release from the photoreceptor as the primary mechanism of light-signal processing has been discussed on the basis of picosecond fluorescence decays and time-resolved fluorescence spectra of stentorin in solution. An initial sensory signal generated by the primary photoprocess of stentorin then triggers subsequent transduction steps that include calcium ion influx from the extracellular medium. Calcium ion influx from the extracellular medium to the cytosol causes the Stentor cell to reverse its ciliary beating and subsequently steer away from the light trap. II.

  14. Use of GafChromic film to diagnose laser generated proton beams

    SciTech Connect

    Hey, D. S.; Key, M. H.; Mackinnon, A. J.; MacPhee, A. G.; Patel, P. K.; Freeman, R. R.; Van Woerkom, L. D.; Castaneda, C. M.

    2008-05-15

    A calibration of three types of GafChromic radiochromic film (HS, MD-55, and HD-810) was carried out on the Crocker Nuclear Laboratory's 76 in. cyclotron at UC Davis over doses ranging from 0.001 to 15 kGy. The film was digitized with a scanning microdensitometer with which it was scanned twice with two different filters to increase the film's effective dynamic range. We demonstrate how this calibrated film can be used to measure the spectrum and total energy of a laser generated proton beam. This technique was applied to an experiment on the 10 J, 100 fs Callisto laser at Lawrence Livermore National Laboratory. The resulting proton spectrum was compared to that obtained by simultaneous measurement of Ti nuclear activation; the two methods give the same proton beam slope temperature and agree in number of protons to within 27%.

  15. Phytochromes are the sole photoreceptors for perceiving red/far-red light in rice

    PubMed Central

    Takano, Makoto; Inagaki, Noritoshi; Xie, Xianzhi; Kiyota, Seiichiro; Baba-Kasai, Akiko; Tanabata, Takanari; Shinomura, Tomoko

    2009-01-01

    Phytochromes are believed to be solely responsible for red and far-red light perception, but this has never been definitively tested. To directly address this hypothesis, a phytochrome triple mutant (phyAphyBphyC) was generated in rice (Oryza sativa L. cv. Nipponbare) and its responses to red and far-red light were monitored. Since rice only has three phytochrome genes (PHYA, PHYB and PHYC), this mutant is completely lacking any phytochrome. Rice seedlings grown in the dark develop long coleoptiles while undergoing regular circumnutation. The phytochrome triple mutants also show this characteristic skotomorphogenesis, even under continuous red or far-red light. The morphology of the triple mutant seedlings grown under red or far-red light appears completely the same as etiolated seedlings, and they show no expression of the light-induced genes. This is direct evidence demonstrating that phytochromes are the sole photoreceptors for perceiving red and far-red light, at least during rice seedling establishment. Furthermore, the shape of the triple mutant plants was dramatically altered. Most remarkably, triple mutants extend their internodes even during the vegetative growth stage, which is a time during which wild-type rice plants never elongate their internodes. The triple mutants also flowered very early under long day conditions and set very few seeds due to incomplete male sterility. These data indicate that phytochromes play an important role in maximizing photosynthetic abilities during the vegetative growth stage in rice. PMID:19706555

  16. A Constitutively Active Allele of Phytochrome B Maintains Circadian Robustness in the Absence of Light.

    PubMed

    Jones, Matthew Alan; Hu, Wei; Litthauer, Suzanne; Lagarias, J Clark; Harmer, Stacey Lynn

    2015-09-01

    The sensitivity of the circadian system to light allows entrainment of the clock, permitting coordination of plant metabolic function and flowering time across seasons. Light affects the circadian system via both photoreceptors, such as phytochromes and cryptochromes, and sugar production by photosynthesis. In the present study, we introduce a constitutively active version of phytochrome B-Y276H (YHB) into both wild-type and phytochrome null backgrounds of Arabidopsis (Arabidopsis thaliana) to distinguish the effects of photoreceptor signaling on clock function from those of photosynthesis. We find that the YHB mutation is sufficient to phenocopy red light input into the circadian mechanism and to sustain robust rhythms in steady-state mRNA levels even in plants grown without light or exogenous sugars. The pace of the clock is insensitive to light intensity in YHB plants, indicating that light input to the clock is constitutively activated by this allele. Mutation of YHB so that it is retained in the cytoplasm abrogates its effects on clock function, indicating that nuclear localization of phytochrome is necessary for its clock regulatory activity. We also demonstrate a role for phytochrome C as part of the red light sensing network that modulates phytochrome B signaling input into the circadian system. Our findings indicate that phytochrome signaling in the nucleus plays a critical role in sustaining robust clock function under red light, even in the absence of photosynthesis or exogenous sources of energy.

  17. The aurea mutant of tomato is deficient in spectrophotometrically and immunochemically detectable phytochrome.

    PubMed

    Parks, B M; Jones, A M; Adamse, P; Koornneef, M; Kendrick, R E; Quail, P H

    1987-03-01

    The aurea locus mutant (au (w)) of tomato contains less than 5% of the level of phytochrome in wild-type tissue as measured by in vivo difference spectroscopy. Immunoblot analysis using antibodies directed against etiolated-oat phytochrome demonstrates that crude extracts of etiolated mutant tissue are deficient in a major immunodetectable protein (116 kDa) normally present in the parent wild type. Analyses of wild-type tissue extracts strongly indicate that the 116-kDa protein is phytochrome by showing that this protein: a) is degraded more rapidly in vitro after a brief far-red irradiation than after a brief red irradiation (Vierstra RD, Quail PH, Planta 156: 158-165, 1982); b) contains a covalently bound chromophore as detected by Zn-chromophore fluorescence on nitrocellulose blots; and c) has an apparent molecular mass comparable to phytochrome from other species on size exclusion chromatography under non-denaturing conditions. The demonstration that the aurea mutant is deficient in this 116-kDa phytochrome indicates that the lack of spectrally detectable phytochrome in this mutant is the result of a lesion which affects the abundance of the phytochrome molecule as opposed to its spectral integrity.

  18. An assessment of GafChromic film for measuring 50 kV and 100 kV percentage depth dose curves.

    PubMed

    Fletcher, Claire Lesley; Mills, John A

    2008-06-07

    Percentage depth dose (PDD) curves were obtained for 50 kV and 100 kV x-rays on a Gulmay Medical D3000 DXR unit. Different dosimetry systems were compared including a Scanditronix Wellhofer small volume cylindrical ion chamber, a Wellhofer photon PFD diode, a PTW soft x-ray parallel plate chamber (N23342) and two types of radiochromic film: GafChromic EBT and GafChromic MD55. The PDD curves were also compared to BEAMnrc Monte Carlo predictions. GafChromic film was found to be a valid choice of dosimeter for measuring percentage depth dose curves at 100 kV and 50 kV. All the dosimeters showed agreement with predictions at depths greater than 10 mm, while near the surface GafChromic film and PFD diodes give the best agreement to Monte Carlo values.

  19. Genetic Evidence That the Red-Absorbing Form of Phytochrome B Modulates Gravitropism in Arabidopsis thaliana.

    PubMed Central

    Liscum, E.; Hangarter, R. P.

    1993-01-01

    Hypocotyls of dark-grown Arabidopsis seedlings exhibit strong negative gravitropism, whereas in red light, gravitropism is strongly reduced. Red/far-red light-pulse experiments and analysis of specific phytochrome-deficient mutants indicate that the red-absorbing (Pr) form of phytochrome B regulates normal hypocotyl gravitropism in darkness, and depletion of Pr by photoconversion to the far-red-absorbing form attenuates hypocotyl gravitropism. These studies provide genetic evidence that the Pr form of phytochrome has an active function in plant development. PMID:12231913

  20. Nuclear phytochrome A signaling promotes phototropism in Arabidopsis.

    PubMed

    Kami, Chitose; Hersch, Micha; Trevisan, Martine; Genoud, Thierry; Hiltbrunner, Andreas; Bergmann, Sven; Fankhauser, Christian

    2012-02-01

    Phototropin photoreceptors (phot1 and phot2 in Arabidopsis thaliana) enable responses to directional light cues (e.g., positive phototropism in the hypocotyl). In Arabidopsis, phot1 is essential for phototropism in response to low light, a response that is also modulated by phytochrome A (phyA), representing a classical example of photoreceptor coaction. The molecular mechanisms underlying promotion of phototropism by phyA remain unclear. Most phyA responses require nuclear accumulation of the photoreceptor, but interestingly, it has been proposed that cytosolic phyA promotes phototropism. By comparing the kinetics of phototropism in seedlings with different subcellular localizations of phyA, we show that nuclear phyA accelerates the phototropic response, whereas in the fhy1 fhl mutant, in which phyA remains in the cytosol, phototropic bending is slower than in the wild type. Consistent with this data, we find that transcription factors needed for full phyA responses are needed for normal phototropism. Moreover, we show that phyA is the primary photoreceptor promoting the expression of phototropism regulators in low light (e.g., PHYTOCHROME KINASE SUBSTRATE1 [PKS1] and ROOT PHOTO TROPISM2 [RPT2]). Although phyA remains cytosolic in fhy1 fhl, induction of PKS1 and RPT2 expression still occurs in fhy1 fhl, indicating that a low level of nuclear phyA signaling is still present in fhy1 fhl.

  1. Characterization of GafChromic XR-RV2 film and comparator strip using a flatbed scanner in reflection mode

    SciTech Connect

    Mendoza-Moctezuma, A. I.

    2010-12-07

    Interventional cardiology procedures are an effective alternative for the reestablishment of correct sanguineous circulation in the heart. However, this kind of procedures exposes to the patients to a relatively high radiation doses. Usually, the surface peak skin dose is evaluated using a visual scale with a comparator strip, nevertheless, even if the comparator strip provides a simple and quick method for estimating the dose it has an uncertainty of {+-}25%. For this reason, a better evaluation method is needed. The objective of our project is to determine the surface peak skin dose of interventional cardiology procedures using GafChromic XR-RV2 film together with a commercial flatbed scanner in reflection mode. Here we report a protocol to handle GafChromic XR-RV2 film using a commercial flat bed scanner in reflection mode aiming at an uncertainty of {+-}3%.

  2. A spectroscopic study of the chromatic properties of GafChromic™EBT3 films

    SciTech Connect

    Callens, M. Van Den Abeele, K.; Crijns, W.; Depuydt, T.; Haustermans, K.; Simons, V.; De Wolf, I.; Maes, F.; D’Agostino, E.; Wevers, M.; Pfeiffer, H.

    2016-03-15

    Purpose: This work provides an interpretation of the chromatic properties of GafChromic™EBT3 films based on the chemical nature of the polydiacetylene (PDA) molecules formed upon interaction with ionizing radiation. The EBT3 films become optically less transparent with increasing radiation dose as a result of the radiation-induced polymerization of diacetylene monomers. In contrast to empirical quantification of the chromatic properties, less attention has been given to the underlying molecular mechanism that induces the strong decrease in transparency. Methods: Unlaminated GafChromic™EBT3 films were irradiated with a 6 MV photon beam to dose levels up to 20 Gy. The optical absorption properties of the films were investigated using visible (vis) spectroscopy. The presence of PDA molecules in the active layer of the EBT3 films was investigated using Raman spectroscopy, which probes the vibrational modes of the molecules in the layer. The vibrational modes assigned to PDA’s were used in a theoretical vis-absorption model to fit our experimental vis-absorption spectra. From the fit parameters, one can assess the relative contribution of different PDA conformations and the length distribution of PDA’s in the film. Results: Vis-spectroscopy shows that the optical density increases with dose in the full region of the visible spectrum. The Raman spectrum is dominated by two vibrational modes, most notably by the ν(C≡C) and the ν(C=C) stretching modes of the PDA backbone. By fitting the vis-absorption model to experimental spectra, it is found that the active layer contains two distinct PDA conformations with different absorption properties and reaction kinetics. Furthermore, the mean PDA conjugation length is found to be 2–3 orders of magnitude smaller than the crystals PDA’s are embedded in. Conclusions: Vis- and Raman spectroscopy provided more insight into the molecular nature of the radiochromic properties of EBT3 films through the identification of

  3. Transcription factors GAF and HSF act at distinct regulatory steps to modulate stress-induced gene activation.

    PubMed

    Duarte, Fabiana M; Fuda, Nicholas J; Mahat, Dig B; Core, Leighton J; Guertin, Michael J; Lis, John T

    2016-08-01

    The coordinated regulation of gene expression at the transcriptional level is fundamental to development and homeostasis. Inducible systems are invaluable when studying transcription because the regulatory process can be triggered instantaneously, allowing the tracking of ordered mechanistic events. Here, we use precision run-on sequencing (PRO-seq) to examine the genome-wide heat shock (HS) response in Drosophila and the function of two key transcription factors on the immediate transcription activation or repression of all genes regulated by HS. We identify the primary HS response genes and the rate-limiting steps in the transcription cycle that GAGA-associated factor (GAF) and HS factor (HSF) regulate. We demonstrate that GAF acts upstream of promoter-proximally paused RNA polymerase II (Pol II) formation (likely at the step of chromatin opening) and that GAF-facilitated Pol II pausing is critical for HS activation. In contrast, HSF is dispensable for establishing or maintaining Pol II pausing but is critical for the release of paused Pol II into the gene body at a subset of highly activated genes. Additionally, HSF has no detectable role in the rapid HS repression of thousands of genes.

  4. X-ray derived experimental charge density distribution in GaF3 and VF3 solid systems

    NASA Astrophysics Data System (ADS)

    Sujatha, K.; Israel, S.; Anzline, C.; Niranjana Devi, R.; Sheeba, R. A. J. R.

    2016-09-01

    The electronic structure and bonding features of metal and transition metal fluorides in low oxidation states, GaF3 and VF3, have been studied from precise single crystal X-ray diffraction data using multipole and maximum entropy methods. The topology of the charge density is analyzed and the (3,-1) bond critical points are determined. Existences of ionic nature of bonding in low valent fluorine compounds are clearly evident. The spherical core of metal atom and aspherical or twisted core of transition metal atom reveal the fact that GaF3 is much more rigid than VF3. Aspherical cores of the polarized ligand atoms are also visible in the two-dimensional density distribution pictures. The true valence charge density surfaces with encapsulating the atomic basins maps are elucidated. An elongated saddle with mid-bond density of 0.6191 e/Å3, observed in the compound VF3, shows that its lattice is less rigid and has more ionic character than GaF3.

  5. Phytochrome and retrograde signalling pathways coverage to antogonistically regulate a light-induced transcription network

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Plastid-to-nucleus retrograde signals emitted by dysfunctional chloroplasts impact photomorphogenic development, but the molecular link between retrograde and photosensory-receptor signaling has remained undefined. Here, we show that the phytochrome (phy) and retrograde signaling pathways converge a...

  6. Effects of gibberellins on seed germination of phytochrome-deficient mutants of Arabidopsis thaliana.

    PubMed

    Yang, Y Y; Nagatani, A; Zhao, Y J; Kang, B J; Kendrick, R E; Kamiya, Y

    1995-10-01

    Experiments were carried out to explore the involvement of gibberellins (GAs) in the light-induced germination of Arabidopsis thaliana (L.) Heynh, using wild type (WT) and phytochrome-deficient mutants (phyA, phyB and phyAphyB deficient in phytochrome A, B and A plus B, respectively). Seed germination of WT and phytochrome-deficient mutants was inhibited by uniconazole (an inhibitor of an early step in biosynthesis of GA, the oxidation of ent-kaurene) and prohexadione (an inhibitor of late steps, namely, 2 beta- and 3 beta-hydroxylation). This inhibition was overcome by simultaneous application of 10(-5) M GA4. The relative activity of GAs for promoting germination of uniconazole-treated seeds was GA4 > GA1 = GA9 > GA20. The wild type and the phyA and phyB mutants had an increased response to a red light pulse in the presence of GA1, GA4, GA9, GA20 and GA24 but there were no significant differences in activity of each GA between the mutants. Therefore, neither phytochrome A nor hytochrome B appears to regulate GA biosynthesis from GA12 to GA4 during seed germination, since the conversion of GA12 to GA9 is regulated by one enzyme (GA 20-oxidase). However, GA responsiveness appears to be regulated by phytochromes other than phytochromes A and B, since the phyAphyB double mutant retains the photoreversible increased response to GAs after a red light pulse.

  7. Light-regulated nuclear import and degradation of Arabidopsis phytochrome-A N-terminal fragments.

    PubMed

    Wolf, Iris; Kircher, Stefan; Fejes, Erzsébet; Kozma-Bognár, László; Schäfer, Eberhard; Nagy, Ferenc; Adám, Eva

    2011-02-01

    The photoreceptor phytochrome-A (phyA) regulates germination and seedling establishment by mediating very low fluence (VLFR) and far-red high irradiance (FR-HIR) responses in Arabidopsis thaliana. In darkness, phyA homodimers exist in the biologically inactive Pr form and are localized in the cytoplasm. Light induces formation of the biologically active Pfr form and subsequent rapid nuclear import. PhyA Pfr, in contrast to the Pr form, is labile and has a half-life of ∼30 min. We produced transgenic plants in a phyA-201 null background that express the PHYA-yellow fluorescent protein (YFP) or the PHYA686-YFP-dimerization domain (DD) and PHYA686-YFP-DD-nuclear localization signal (NLS) or PHYA686-YFP-DD-nuclear exclusion signal (NES) fusion proteins. The PHYA686-YFP fusion proteins contained the N-terminal domain of phyA (686 amino acid residues), a short DD and the YFP. Here we report that (i) PHYA686-YFP-DD fusion protein is imported into the nucleus in a light-dependent fashion; (ii) neither of the PHYA686 fusion proteins is functional in FR-HIR and nuclear VLFR; and (iii) the phyA-dependent, blue light-induced inhibition of hypocotyl growth is mediated by the PHYA686-YFP-DD-NES but not by the PHYA686-YFP-DD-NLS and PHYA686-YFP-DD fusion proteins. We demonstrate that (i) light induces degradation of all PHYA N-terminal-containing fusion proteins and (ii) these N-terminal domain-containing fusion proteins including the constitutively nuclear PHYA686-YFP-DD-NLS and predominantly cytoplasmic PHYA686-YFP-DD-NES degrade at comparable rates but markedly more slowly than PHYA-YFP, whereas (iii) light-induced degradation of the native phyA is faster compared with PHYA-YFP.

  8. Phytochrome B promotes branching in Arabidopsis by suppressing auxin signaling.

    PubMed

    Krishna Reddy, Srirama; Finlayson, Scott A

    2014-03-01

    Many plants respond to competition signals generated by neighbors by evoking the shade avoidance syndrome, including increased main stem elongation and reduced branching. Vegetation-induced reduction in the red light:far-red light ratio provides a competition signal sensed by phytochromes. Plants deficient in phytochrome B (phyB) exhibit a constitutive shade avoidance syndrome including reduced branching. Because auxin in the polar auxin transport stream (PATS) inhibits axillary bud outgrowth, its role in regulating the phyB branching phenotype was tested. Removing the main shoot PATS auxin source by decapitation or chemically inhibiting the PATS strongly stimulated branching in Arabidopsis (Arabidopsis thaliana) deficient in phyB, but had a modest effect in the wild type. Whereas indole-3-acetic acid (IAA) levels were elevated in young phyB seedlings, there was less IAA in mature stems compared with the wild type. A split plate assay of bud outgrowth kinetics indicated that low auxin levels inhibited phyB buds more than the wild type. Because the auxin response could be a result of either the auxin signaling status or the bud's ability to export auxin into the main shoot PATS, both parameters were assessed. Main shoots of phyB had less absolute auxin transport capacity compared with the wild type, but equal or greater capacity when based on the relative amounts of native IAA in the stems. Thus, auxin transport capacity was unlikely to restrict branching. Both shoots of young phyB seedlings and mature stem segments showed elevated expression of auxin-responsive genes and expression was further increased by auxin treatment, suggesting that phyB suppresses auxin signaling to promote branching.

  9. Detection of phytochrome-like genes from Rhazya stricta (Apocynaceae) using de novo genome assembly.

    PubMed

    Sabir, Jamal S M; Baeshen, Nabih A; Shokry, Ahmed M; Gadalla, Nour O; Edris, Sherif; Mutwakil, Mohammed H; Ramadan, Ahmed M; Atef, Ahmed; Al-Kordy, Magdy A; Abuzinadah, Osama A; El-Domyati, Fotouh M; Jansen, Robert K; Bahieldin, Ahmed

    2013-01-01

    Phytochrome-like genes in the wild plant species Rhazya stricta Decne were characterized using a de novo genome assembly of next generation sequence data. Rhazya stricta contains more than 100 alkaloids with multiple pharmacological properties, and leaf extracts have been used to cure chronic rheumatism, to treat tumors, and in the treatment of several other diseases. Phytochromes are known to be involved in the light-regulated biosynthesis of some alkaloids. Phytochromes are soluble chromoproteins that function in the absorption of red and far-red light and the transduction of intracellular signals during light-regulated plant development. De novo assembly of the nuclear genome of R. stricta recovered 45,641 contigs greater than 1000bp long, which were used in constructing a local database. Five sequences belonging to Arabidopsis thaliana phytochrome gene family (i.e., AtphyABCDE) were used to identify R. stricta contigs with phytochrome-like sequences using BLAST. This led to the identification of three contigs with phytochrome-like sequences covering AtphyA-, AtphyC- and AtphyE-like full-length genes. Annotation of the three sequences showed that each contig consists of one phytochrome-like gene with three exons and two introns. BLASTn and BLASTp results indicated that RsphyA mRNA and protein sequences had homologues in Wrightia coccinea and and Solanum tuberosum, respectively. RsphyC-like mRNA and protein sequence were homologous to Vitis vinifera and Vitis riparia. RsphyE-like mRNA coding and protein sequences were homologous to Ipomoea nil. Multiple-sequence alignment of phytochrome proteins indicated a homology with 30 sequences from 23 different species of flowering plants. Phylogenetic analysis confirmed that each R. stricta phytochrome gene is related to the same phytochrome gene of other flowering plants. It is proposed that the absence of phyB gene in R. stricta is due to RsphyA gene taking over the role of phyB.

  10. Does a web-based feedback training program result in improved reliability in clinicians' ratings of the Global Assessment of Functioning (GAF) Scale?

    PubMed

    Støre-Valen, Jakob; Ryum, Truls; Pedersen, Geir A F; Pripp, Are H; Jose, Paul E; Karterud, Sigmund

    2015-09-01

    The Global Assessment of Functioning (GAF) Scale is used in routine clinical practice and research to estimate symptom and functional severity and longitudinal change. Concerns about poor interrater reliability have been raised, and the present study evaluated the effect of a Web-based GAF training program designed to improve interrater reliability in routine clinical practice. Clinicians rated up to 20 vignettes online, and received deviation scores as immediate feedback (i.e., own scores compared with expert raters) after each rating. Growth curves of absolute SD scores across the vignettes were modeled. A linear mixed effects model, using the clinician's deviation scores from expert raters as the dependent variable, indicated an improvement in reliability during training. Moderation by content of scale (symptoms; functioning), scale range (average; extreme), previous experience with GAF rating, profession, and postgraduate training were assessed. Training reduced deviation scores for inexperienced GAF raters, for individuals in clinical professions other than nursing and medicine, and for individuals with no postgraduate specialization. In addition, training was most beneficial for cases with average severity of symptoms compared with cases with extreme severity. The results support the use of Web-based training with feedback routines as a means to improve the reliability of GAF ratings performed by clinicians in mental health practice. These results especially pertain to clinicians in mental health practice who do not have a masters or doctoral degree.

  11. Distinct phytochrome actions in nonvascular plants revealed by targeted inactivation of phytobilin biosynthesis

    PubMed Central

    Chen, Yu-Rong; Su, Yi-shin; Tu, Shih-Long

    2012-01-01

    The red/far-red light photoreceptor phytochrome mediates photomorphological responses in plants. For light sensing and signaling, phytochromes need to associate with open-chain tetrapyrrole molecules as the chromophore. Biosynthesis of tetrapyrrole chromophores requires members of ferredoxin-dependent bilin reductases (FDBRs). It was shown that LONG HYPOCOTYL 2 (HY2) is the only FDBR in flowering plants producing the phytochromobilin (PΦB) for phytochromes. However, in the moss Physcomitrella patens, we found a second FDBR that catalyzes the formation of phycourobilin (PUB), a tetrapyrrole pigment usually found as the protein-bound form in cyanobacteria and red algae. Thus, we named the enzyme PUB synthase (PUBS). Severe photomorphogenic phenotypes, including the defect of phytochrome-mediated phototropism, were observed in Physcomitrella patens when both HY2 and PUBS were disrupted by gene targeting. This indicates HY2 and PUBS function redundantly in phytochrome-mediated responses of nonvascular plants. Our studies also show that functional PUBS orthologs are found in selected lycopod and chlorophyte genomes. Using mRNA sequencing for transcriptome profiling, we demonstrate that expression of the majority of red-light-responsive genes are misregulated in the pubs hy2 double mutant. These studies showed that moss phytochromes rapidly repress expression of genes involved in cell wall organization, transcription, hormone responses, and protein phosphorylation but activate genes involved in photosynthesis and stress signaling during deetiolation. We propose that, in nonvascular plants, HY2 and PUBS produce structurally different but functionally similar chromophore precursors for phytochromes. Holophytochromes regulate biological processes through light signaling to efficiently reprogram gene expression for vegetative growth in the light. PMID:22566621

  12. Near-Infrared Fluorescent Proteins, Biosensors, and Optogenetic Tools Engineered from Phytochromes.

    PubMed

    Chernov, Konstantin G; Redchuk, Taras A; Omelina, Evgeniya S; Verkhusha, Vladislav V

    2017-04-12

    Phytochrome photoreceptors absorb far-red and near-infrared (NIR) light and regulate light responses in plants, fungi, and bacteria. Their multidomain structure and autocatalytic incorporation of linear tetrapyrrole chromophores make phytochromes attractive molecular templates for the development of light-sensing probes. A subclass of bacterial phytochromes (BphPs) utilizes heme-derived biliverdin tetrapyrrole, which is ubiquitous in mammalian tissues, as a chromophore. Because biliverdin possesses the largest electron-conjugated chromophore system among linear tetrapyrroles, BphPs exhibit the most NIR-shifted spectra that reside within the NIR tissue transparency window. Here we analyze phytochrome structure and photochemistry to describe the molecular mechanisms by which they function. We then present strategies to engineer BphP-based NIR fluorescent proteins and review their properties and applications in modern imaging technologies. We next summarize designs of reporters and biosensors and describe their use in the detection of protein-protein interactions, proteolytic activities, and posttranslational modifications. Finally, we provide an overview of optogenetic tools developed from phytochromes and describe their use in light-controlled cell signaling, gene expression, and protein localization. Our review provides guidelines for the selection of NIR probes and tools for noninvasive imaging, sensing, and light-manipulation applications, specifically focusing on probes developed for use in mammalian cells and in vivo.

  13. Morphological responses of wheat to changes in phytochrome photoequilibrium

    NASA Technical Reports Server (NTRS)

    Barnes, C.; Bugbee, B.

    1991-01-01

    Wheat plants (Triticum aestivum L.) were grown at the same photosynthetic photon flux (PPF), 200 micromoles per square meter per second, but with phytochrome photoequilibrium (phi) values of 0.81, 0.55, and 0.33. Plants grown at phi values of 0.55 and 0.33 tillered 43 and 56%, less compared with plants grown at phi of 0.81. Main culm development (Haun stage) was slightly more advanced at lower values of phi, and leaf sheaths, but not leaf lamina, were longer at lower phi. Dry-mass accumulation was not affected by different levels of phi. Three levels of PPF (100, 200, and 400 micromoles per square meter per second) and two lamp types, metal halide and high pressure sodium, were also tested. Higher levels of PPF resulted in more dry mass, more tillering, and a more advanced Haun stage. There was no difference in plant dry mass or development under metal halide versus high pressure sodium lamps, except for total leaf length, which was greater under high pressure sodium lamps (49.5 versus 44.9 centimeters, P < 0.01).

  14. Evidence for involvement of phytochrome in tumor development on plants

    NASA Technical Reports Server (NTRS)

    Morrow, R. C.; Tibbitts, T. W.

    1988-01-01

    The regulation of nonpathogenic tumorous growths on tomato plants by red and far-red radiation was studied using leaf discs floated on water and irradiated from beneath. It was found that red light (600-700 nanometers) was required for the induction of tumors on tomato (Lycopersicon hirsutum Humb. & Bonpl. Plant Introduction LA 1625), while both blue (400-500 nanometers) and green (500-600 nanometers) light had little effect on tumor development. Detailed studies with red light demonstrated that tumor development increased with increasing photon flux and duration, though duration was the more significant factor. It was observed that tumor development could be prevented by the addition of far-red irradiance to red irradiance or by providing far-red irradiance immediately following red irradiance. The effectiveness of red and far-red irradiance in the regulation of tumor development indicates phytochrome involvement in this response. These findings should provide additional insight into the multiplicity of physiological factors regulating the development of nonpathogenic tumorous growths in plants.

  15. Phytochrome A increases tolerance to high evaporative demand.

    PubMed

    Auge, Gabriela Alejandra; Rugnone, Matías Leandro; Cortés, Leandro Emanuel; González, Carina Verónica; Zarlavsky, Gabriela; Boccalandro, Hernán Esteban; Sánchez, Rodolfo Augusto

    2012-10-01

    Stresses resulting from high transpiration demand induce adjustments in plants that lead to reductions of water loss. These adjustments, including changes in water absorption, transport and/or loss by transpiration, are crucial to normal plant development. Tomato wild type (WT) and phytochrome A (phyA)-mutant plants, fri1-1, were exposed to conditions of either low or high transpiration demand and several morphological and physiological changes were measured during stress conditions. Mutant plants rapidly wilted compared to WT plants after exposure to high evaporative demand. Root size and hydraulic conductivity did not show significant differences between genotypes, suggesting that water absorption and transport through this organ could not explain the observed phenotype. Moreover, stomatal density was similar between genotypes, whereas transpiration and stomatal conductance were both lower in mutant than in WT plants. This was accompanied by a lower stem-specific hydraulic conductivity in mutant plants, which was associated to lower xylem vessel number and transversal area in fri1-1 plants, producing a reduction in water supply to the leaves, which rapidly wilted under high evaporative demand. PhyA signaling might facilitate the adjustment to environments differing widely in water evaporative demand in part through the modulation of xylem dimensions.

  16. Morphological Responses of Wheat to Changes in Phytochrome Photoequilibrium 1

    PubMed Central

    Barnes, Charles; Bugbee, Bruce

    1991-01-01

    Wheat plants (Triticum aestivum L.) were grown at the same photosynthetic photon flux (PPF), 200 micromoles per square meter per second, but with phytochrome photoequilibrium ([unk]) values of 0.81, 0.55, and 0.33. Plants grown at [unk] values of 0.55 and 0.33 tillered 43 and 56%, less compared with plants grown at [unk] of 0.81. Main culm development (Haun stage) was slightly more advanced at lower values of [unk], and leaf sheaths, but not leaf lamina, were longer at lower [unk]. Dry-mass accumulation was not affected by different levels of [unk]. Three levels of PPF (100, 200, and 400 micromoles per square meter per second) and two lamp types, metal halide and high pressure sodium, were also tested. Higher levels of PPF resulted in more dry mass, more tillering, and a more advanced Haun stage. There was no difference in plant dry mass or development under metal halide versus high pressure sodium lamps, except for total leaf length, which was greater under high pressure sodium lamps (49.5 versus 44.9 centimeters, P < 0.01). PMID:11538375

  17. Evidence for involvement of phytochrome in tumor development on plants.

    PubMed

    Morrow, R C; Tibbitts, T W

    1988-01-01

    The regulation of nonpathogenic tumorous growths on tomato plants by red and far-red radiation was studied using leaf discs floated on water and irradiated from beneath. It was found that red light (600-700 nanometers) was required for the induction of tumors on tomato (Lycopersicon hirsutum Humb. & Bonpl. Plant Introduction LA 1625), while both blue (400-500 nanometers) and green (500-600 nanometers) light had little effect on tumor development. Detailed studies with red light demonstrated that tumor development increased with increasing photon flux and duration, though duration was the more significant factor. It was observed that tumor development could be prevented by the addition of far-red irradiance to red irradiance or by providing far-red irradiance immediately following red irradiance. The effectiveness of red and far-red irradiance in the regulation of tumor development indicates phytochrome involvement in this response. These findings should provide additional insight into the multiplicity of physiological factors regulating the development of nonpathogenic tumorous growths in plants.

  18. Genetic analysis of the roles of phytochromes A and B1 in the reversed gravitropic response of the lz-2 tomato mutant.

    PubMed

    Behringer, F J; Lomax, T L

    1999-05-01

    The lz-2 mutation in tomato (Lycopersicon esculentum) causes conditional reversal of shoot gravitropism by light. This response is mediated by phytochrome. To further elicit the mechanism by which phytochrome regulates the lz-2 phenotype, phytochrome-deficient lz-2 plants were generated. Introduction of au alleles, which severely block chromophore biosynthesis, eliminated the reversal of hypocotyl gravitropism in continuous red and far-red light. The fri1 and tri1 alleles were introduced to specifically deplete phytochromes A and B1, respectively. In dark-grown seedlings, phytochrome A was necessary for response to high-irradiance far-red light, a complete response to low fluence red light, and also mediated the effects of blue light in a far-red reversible manner. Loss of phytochrome B1 alone did not significantly affect the behaviour of lz-2 plants under any light treatment tested. However, dark-grown lz-2 plants lacking both phytochrome A and B1 exhibited reduced responses to continuous red and were less responsive to low fluence red light and high fluence blue light than plants that were deficient for phytochrome A alone. In high light, full spectrum greenhouse conditions, lz-2 plants grew downward regardless of the phytochrome deficiency. These results indicate that phytochromes A and B1 play significant roles in mediating the lz-2 phenotype and that at least one additional phytochrome is involved in reversing shoot gravitropism in this mutant.

  19. Genetic analysis of the roles of phytochromes A and B1 in the reversed gravitropic response of the lz-2 tomato mutant

    NASA Technical Reports Server (NTRS)

    Behringer, F. J.; Lomax, T. L.

    1999-01-01

    The lz-2 mutation in tomato (Lycopersicon esculentum) causes conditional reversal of shoot gravitropism by light. This response is mediated by phytochrome. To further elicit the mechanism by which phytochrome regulates the lz-2 phenotype, phytochrome-deficient lz-2 plants were generated. Introduction of au alleles, which severely block chromophore biosynthesis, eliminated the reversal of hypocotyl gravitropism in continuous red and far-red light. The fri1 and tri1 alleles were introduced to specifically deplete phytochromes A and B1, respectively. In dark-grown seedlings, phytochrome A was necessary for response to high-irradiance far-red light, a complete response to low fluence red light, and also mediated the effects of blue light in a far-red reversible manner. Loss of phytochrome B1 alone did not significantly affect the behaviour of lz-2 plants under any light treatment tested. However, dark-grown lz-2 plants lacking both phytochrome A and B1 exhibited reduced responses to continuous red and were less responsive to low fluence red light and high fluence blue light than plants that were deficient for phytochrome A alone. In high light, full spectrum greenhouse conditions, lz-2 plants grew downward regardless of the phytochrome deficiency. These results indicate that phytochromes A and B1 play significant roles in mediating the lz-2 phenotype and that at least one additional phytochrome is involved in reversing shoot gravitropism in this mutant.

  20. Demonstration of transcriptional regulation of specific genes by phytochrome action

    PubMed Central

    Silverthorne, Jane; Tobin, Elaine M.

    1984-01-01

    We have developed an in vitro transcription system that uses nuclei isolated from Lemna gibba G-3. The in vitro transcripts include sequences homologous to hybridization probes for the small subunit of ribulose-1,5-bisphosphate carboxylase [3-phospho-D-glycerate carboxy-lyase (dimerizing), EC 4.1.1.39], the light-harvesting chlorophyll a/b-protein, and rRNA. Light-harvesting chlorophyll a/b-protein sequences are transcribed to a greater extent in nuclei isolated from plants grown in darkness with 2 min of red light every 8 hr than in nuclei isolated from dark-treated plants. Furthermore, the amount of these transcripts measured in plants given a single minute of red light after dark treatment is increased over the amount measured in dark-treated plants. The effect of red light is at least partially reversible by 10 min of far-red light given immediately after the red light pulse. Transcription of both rRNA and small subunit sequences is also stimulated by a single minute of red light as compared to dark-treated tissue. However, the relative magnitudes of the increases compared to the dark levels are smaller than the increase seen for the chlorophyll a/b-protein, possibly because of the higher level of transcription of these sequences in the dark. The effect of red light on the transcription of small subunit and rRNA sequences is also reversible by immediate treatment with 10 min of far-red light. Pulse chase studies of dark-treated nuclei for up to 110 min do not show substantial turnover of in vitro labeled small subunit and chlorophyll a/b-protein transcripts. We therefore conclude that phytochrome action has induced specific changes in transcription of these genes. Images PMID:16593420

  1. Identification of photo-inactive phytochrome A in etiolated seedlings and photo-active phytochrome B in green leaves of the aurea mutant of tomato.

    PubMed

    Sharma, R; López-Juez, E; Nagatani, A; Furuya, M

    1993-12-01

    The contents of spectrophotometrically measurable phytochrome A (PhyA) and phytochrome B (PhyB) and the corresponding immunochemically detectable apoproteins (PHYA and PHYB) were examined in dark- and light-grown tissues of the aurea mutant of tomato and its wild-type (WT). The amount of PHYA in etiolated aurea seedlings was found to be about 20% of that in the WT; this PHYA showed no photo-reversible changes in absorbance, no downregulation of the level of PHYA in light-grown seedlings, and no differential proteolysis of Pr and Pfr species in vitro which was seen in the case of the WT. By contrast, the amount of PHYB in aurea seedlings was not significantly different from that in WT seedlings. Phytochrome isolated from green leaves of the aurea mutant and purified by ion-exchange chromatography showed a red/far-red reversible spectral change, and its elution profile during chromatography was essentially similar to that of PHYB. The results indicate that aurea is a mutant that is deficient in photoactive PhyA at the etiolated stage, when it contains a spectrally inactive PHYA. However, the mutant contains spectrally active PhyB in its green tissue as does the WT.

  2. Phytochrome Induces Rapid PIF5 Phosphorylation and Degradation in Response to Red-Light Activation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The phytochrome (phy) family of sensory photoreceptors (phyA–phyE in Arabidopsis thaliana) induces changes in target-gene expression upon light-induced translocation to the nucleus, where certain members interact with selected members of the constitutively nuclear basic helix-loop-helix transcriptio...

  3. [Role of phytochrome in organ formation processes in Cucumis sativus L].

    PubMed

    Sysoeva, M I; Marovskaia, E F

    2013-01-01

    The role of phytochrome B in the organogenesis process in the apical and axillary shoot meristems during early ontogenesis stages in cucumber Cucumis sativus L. at photoperiods (day/night) 10/14, 16/8 h, and continuous light in comparison with wild type plants and phytochrome B-deficient mutant (lh-mutant) was investigated. In mutant phytochrome B, deficiency caused inhibition of initiation of leaves both in the leading shoot and off-shoots and increased the number of flower buds (IV stage of organogenesis). With continuous light, the number of off-shoots and flowers during stage IV of organogenesis in wild-type plants increased twofold in comparison with the mutant. Short-term temperature drops did not induce floral ontogenesis in mutants but increased the number of off-shoots in both experimental variants during a long photoperiod and continuous light situations. We propose that phytochrome B, by increasing the compactness of chromatin, may facilitate coordination of ontogenesis processes with changing environmental conditions.

  4. Ca2+ transport in plant cells and mechanisms of transformation of phytochrome-induced photosignals

    NASA Astrophysics Data System (ADS)

    Volotovski, Igor D.

    1995-01-01

    The recent data on the influence of phytochrome on the efficiency of Ca2+ translocation across the membranes of oat protoplasts are given. Ca2+ uptake in the protoplasts was shown to be influenced by the red light (R) illumination. This effect was reverted by the following far-red light (FR) illumination. To elucidate the sensitivity to phytochrome-controlling action the screening between the mechanisms of Ca2+ transport across the plasma membranes of oat protoplasts, Na+/Ca2+ and Ca2+/H+ exchangers, Ca2+-pump and Ca2+-channel was done. It was established that phytochrome modulated the activity of Na+/Ca2+-exchanger and Ca2+-pump. The light-mediated oscillations of cytoplasmic Ca2+ concentration in the oat protoplasts were demonstrated using fluorescence probe quin2 loaded into the cells and laser monitoring of fluorescence signal. The evidences were obtained that the oscillations were not the result of the elevation of cytoplasmic Ca2+ concentration and had no connection with Ca2+ pool of mitochondria. The possibility of the relation between the Ca2+ oscillations and phosphoinositide metabolism in plant cell membranes is analyzed. The mechanisms of transformation of primary phytochrome signal into biological effects were discussed.

  5. The discovery of phytochrome: unlocking the secrets of plants and their connection to light

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The US Department of Agriculture (USDA), Beltsville Agricultural Research Center in Beltsville, Maryland USA was recently designated an American Chemical Society National Historic Chemical Landmark for the seminal work of USDA scientists in the discovery of phytochrome, the ubiquitous plant pigment ...

  6. Light-Stimulated Cotyledon Expansion in Arabidopsis Seedlings (The Role of Phytochrome B).

    PubMed Central

    Neff, M. M.; Van Volkenburgh, E.

    1994-01-01

    Leaf and cotyledon expansion in dicotyledonous plants is a light-dependent developmental process. The unique role of phytochrome B has been tested by investigating expansion of cotyledons in wild-type and phytochrome-deficient mutants of Arabidopsis thaliana (L.) Heynh. A relatively rapid method for measuring cotyledon area was developed to quantify growth in large populations (average n [greater than or equal to] 100) of wild-type or mutant seedlings under different light and chemical treatments. Three-day-old wild-type (La-er) Arabidopsis seedlings, grown in saturating, low-fluence red light (2-4 [mu]mol m-2 s-1), showed a >250% increase in cotyledon area after 48 h of bright-red light when compared with the phytochrome mutants hy1, hy2, and hy3. An increase in epidermal cell area was observed in wild-type cotyledons but not in hy3, indicating that light-stimulated growth is due in part to cell expansion. The mutant phenotype was rescued by feeding the chromophore precursor biliverdin to the chromophore biosynthesis mutants hy1 and hy6. This treatment did not rescue the hy3 mutant. Since the hy3 lesion is specific to phytochrome B, we conclude that this pigment is involved in the enhancement of cotyledon cell expansion in bright-red light. PMID:12232145

  7. Spatiotemporal Phytochrome Signaling during Photomorphogenesis: From Physiology to Molecular Mechanisms and Back.

    PubMed

    Montgomery, Beronda L

    2016-01-01

    Light exposure results in distinct responses in specific seedling tissues during photomorphogenesis. Light promotes growth of cotyledons and leaves, as well as development and elongation of roots, whereas light inhibits elongation of hypocotyls. For distinct plant responses such as shade avoidance, far-red light or shifts in spectral light quality similarly have disparate impacts on distinct plant tissues, resulting in elongation of stems or petioles and a reduction in growth of leaf blades for many species. The physiological bases of such tissue- and organ-specific light responses were initially studied using localized irradiation of specific tissues and organs, or irradiation of dissected plant parts. These historical approaches were used to identify spatial-specific pools of photoreceptors responsible for regulating local, i.e., tissue- or organ-specific, or distal, i.e., interorgan, plant responses. The red/far-red responsive phytochromes have been the most widely studied among photoreceptors in this regard. Whereas, the spatial localization of photoreceptors regulating many tissue- or organ-specific light responses were identified, the underlying signaling networks responsible for mediating the observed responses have not been well defined. Recent approaches used to investigate the molecular bases of spatiotemporal light responses include selective irradiation of plants harboring mutations in specific photoreceptors, tissue-specific expression of photoreceptors, primarily in photoreceptor mutant backgrounds, or tissue-specific biochemical ablation of photoreceptor accumulation. Progressive integration of such approaches for regulating the availability of localized pools of phytochromes with the use of transcriptomic or proteomic analyses for assessing the genes or proteins which these spatially discrete pools of phytochrome regulate is yielding emergent insight into the molecular bases of spatiotemporal phytochrome signaling pathways responsible for regulating

  8. Spatiotemporal Phytochrome Signaling during Photomorphogenesis: From Physiology to Molecular Mechanisms and Back

    PubMed Central

    Montgomery, Beronda L.

    2016-01-01

    Light exposure results in distinct responses in specific seedling tissues during photomorphogenesis. Light promotes growth of cotyledons and leaves, as well as development and elongation of roots, whereas light inhibits elongation of hypocotyls. For distinct plant responses such as shade avoidance, far-red light or shifts in spectral light quality similarly have disparate impacts on distinct plant tissues, resulting in elongation of stems or petioles and a reduction in growth of leaf blades for many species. The physiological bases of such tissue- and organ-specific light responses were initially studied using localized irradiation of specific tissues and organs, or irradiation of dissected plant parts. These historical approaches were used to identify spatial-specific pools of photoreceptors responsible for regulating local, i.e., tissue- or organ-specific, or distal, i.e., interorgan, plant responses. The red/far-red responsive phytochromes have been the most widely studied among photoreceptors in this regard. Whereas, the spatial localization of photoreceptors regulating many tissue- or organ-specific light responses were identified, the underlying signaling networks responsible for mediating the observed responses have not been well defined. Recent approaches used to investigate the molecular bases of spatiotemporal light responses include selective irradiation of plants harboring mutations in specific photoreceptors, tissue-specific expression of photoreceptors, primarily in photoreceptor mutant backgrounds, or tissue-specific biochemical ablation of photoreceptor accumulation. Progressive integration of such approaches for regulating the availability of localized pools of phytochromes with the use of transcriptomic or proteomic analyses for assessing the genes or proteins which these spatially discrete pools of phytochrome regulate is yielding emergent insight into the molecular bases of spatiotemporal phytochrome signaling pathways responsible for regulating

  9. Overexpression of homologous phytochrome genes in tomato: exploring the limits in photoperception.

    PubMed

    Husaineid, Said S H; Kok, Rosan A; Schreuder, Marielle E L; Hanumappa, Mamatha; Cordonnier-Pratt, Marie-Michèle; Pratt, Lee H; van der Plas, Linus H W; van der Krol, Alexander R

    2007-01-01

    Transgenic tomato [Lycopersicon esculentum (=Solanum lycopersicum)] lines overexpressing tomato PHYA, PHYB1, or PHYB2, under control of the constitutive double-35S promoter from cauliflower mosaic virus (CaMV) have been generated to test the level of saturation in individual phytochrome-signalling pathways in tomato. Western blot analysis confirmed the elevated phytochrome protein levels in dark-grown seedlings of the respective PHY overexpressing (PHYOE) lines. Exposure to 4 h of red light resulted in a decrease in phytochrome A protein level in the PHYAOE lines, indicating that the chromophore availability is not limiting for assembly into holoprotein and that the excess of phytochrome A protein is also targeted for light-regulated destruction. The elongation and anthocyanin accumulation responses of plants grown under white light, red light, far-red light, and end-of-day far-red light were used for characterization of selected PHYOE lines. In addition, the anthocyanin accumulation response to different fluence rates of red light of 4-d-old dark-grown seedlings was studied. The elevated levels of phyA in the PHYAOE lines had little effect on seedling and adult plant phenotype. Both PHYAOE in the phyA mutant background and PHYB2OE in the double-mutant background rescued the mutant phenotype, proving that expression of the transgene results in biologically active phytochrome. The PHYB1OE lines showed mild effects on the inhibition of stem elongation and anthocyanin accumulation and little or no effect on the red light high irradiance response. By contrast, the PHYB2OE lines showed a strong inhibition of elongation, enhancement of anthocyanin accumulation, and a strong amplification of the red light high irradiance response.

  10. Time courses for phytochrome-induced enzyme levels in phenylpropanoid metabolism (phenylalanine ammonia-lyase, naringenin-chalcone synthase) compared with time courses for phytochrome-mediated end-product accumulation (anthocyanin, quercetin).

    PubMed

    Brödenfeldt, R; Mohr, H

    1988-12-01

    Time course for changes in the levels of enzymes characteristic of general phenylpropanoid metabolism (phenylalanine ammonia-lyase, PAL; EC 4.3.1.5) and of the flavonoid-glycoside branch pathway (naringenin-chalcone synthase, CHS; EC 2.3.1.74) were measured in the cotyledons of mustard (Sinapis alba L.) seedlings and compared with the rates of accumulation of related end products (anthocyanin and quercetin). Induction of enzyme levels and of end-product accumulation was carried out with red and far-red (FR) light, operating via phytochrome. The data are compatible with the concept that the phytochrome-mediated appearance of enzymes such as PAL and CHS is indeed a prerequisite for the appearance of anthocyanins and flavonols. However, there is no close correlation between enzyme levels and the rates of synthesis of end products which could justify the identification of specific rate-limiting enzymes. Rather, the data indicate that there is a second phytochrome-dependent step, beyond enzyme induction, where the actual rate of flavonoid accumulation is determined. Anthocyanin and quercetin accumulation respond differently to light. However, the relative action of continuous FR, red light pulses and 'stored phytochrome signal' is the same in both cases. This indicates that the mode of operation of phytochrome is the same in both cases. The two syntheses differ only in the degree of responsiveness towards phytochrome. The time course for changes in CHS levels in continuous FR, i.e. under conditions of phytochrome photosteady state, is similar to the time course for PAL levels whereas the time courses in darkness, following transfer from FR to darkness, are totally different. In the case of CHS, a transient rise is observed whereas, with PAL, an instantaneous drop in enzyme level occurs after transfer from FR to darkness. It is concluded that the 'stored phytochrome signal' operates in darkness in the case of CHS but not in the case of PAL.

  11. Phytochrome-mediated induction of phenylalanine ammonia-lyase in the cotyledons of tomato (Lycopersicon esculentum Mill.) plants.

    PubMed

    Lercari, B; Sodi, F; Fastami, C

    1982-01-01

    Phenylalanine ammonia-lyase (PAL; EC 4.3.1.5.) induction in cotyledons from 96-h dark-grown Lycopersicon esculentum Mill. was studied in response to continuous light and hourly light pulses (blue, red, far red). The increases of PAL promoted by blue and red pulses are reversed completely by immediately following 758 nm irradiations. The response to continuous red light could be substituted for by hourly 6-min red light pulses. The effect of continuous red treatments is mainly due to a multiple induction effect of phytochrome. In contrast to red light, hourly light pulses with far red and blue, light can only partially substitute for continuous irradiation. The continuous blue response could be due to a combination of a multiple induction response and of a high irradiance response of phytochrome. The continuous far red response, could represent a high irradiance response of phytochrome. Dichromatic irradiations indicate that phytochrome is the photoreceptor controlling the light response (PAL) in tomato seedlings.

  12. Dynamic Structural Changes Underpin Photoconversion of a Blue/Green Cyanobacteriochrome between Its Dark and Photoactivated States*

    PubMed Central

    Cornilescu, Claudia C.; Cornilescu, Gabriel; Burgie, E. Sethe; Markley, John L.; Ulijasz, Andrew T.; Vierstra, Richard D.

    2014-01-01

    The phytochrome superfamily of photoreceptors exploits reversible light-driven changes in the bilin chromophore to initiate a variety of signaling cascades. The nature of these alterations and how they impact the protein moiety remain poorly resolved and might include several species-specific routes. Here, we provide a detailed picture of photoconversion for the photosensing cGMP phosphodiesterase/adenylyl cyclase/FhlA (GAF) domain from Thermosynechococcus elongatus (Te) PixJ, a member of the cyanobacteriochrome clade. Solution NMR structures of the blue light-absorbing dark state Pb and green light-absorbing photoactivated state Pg, combined with paired crystallographic models, revealed that the bilin and GAF domain dynamically transition via breakage of the C10/Cys-494 thioether bond, opposite rotations of the A and D pyrrole rings, sliding of the bilin in the GAF pocket, and the appearance of an extended region of disorder that includes Cys-494. Changes in GAF domain backbone dynamics were also observed that are likely important for inter-domain signal propagation. Taken together, photoconversion of T. elongatus PixJ from Pb to Pg involves complex structural changes within the GAF domain pocket that transduce light into a mechanical signal, many aspects of which should be relevant to others within the extended phytochrome superfamily. PMID:24337572

  13. Ethylene Is Not Responsible for Phytochrome-Mediated Apical Hook Exaggeration in Tomato

    PubMed Central

    Takahashi-Asami, Miki; Shichijo, Chizuko; Tsurumi, Seiji; Hashimoto, Tohru

    2016-01-01

    The apical hook of tomato seedlings is exaggerated by phytochrome actions, while in other species such as bean, pea and Arabidopsis, the hook is exaggerated by ethylene and opens by phytochrome actions. The present study was aimed to clarify mainly whether ethylene is responsible for the phytochrome-mediated hook exaggeration of tomato seedlings. Dark-grown 5-day-old seedlings were subjected to various ways of ethylene application in the dark as well as under the actions of red (R) or far-red light (FR). The ethylene emitted by seedlings was also quantified relative to hook exaggeration. The results show: Ambient ethylene, up-to about 1.0 μL L-1, suppressed (opened) the hooks formed in the dark as well as the ones exaggerated by R or FR, while at 3.0–10 μL L-1 it enhanced (closed) the hook only slightly as compared with the most-suppressed level at about 1.0 μL L-1. Treatment with 1-aminocyclopropane-1-carboxylic acid (ACC), the immediate precursor of ethylene biosynthesis, did not enhance the hook, only mimicking the suppressive effects of ambient ethylene. The biosynthesis inhibitor, CoCl2 or aminoethoxyvinylglycine, enhanced hook curvature, and the enhancement was canceled by supplement of ethylene below 1.0 μL L-1. Auxin transport inhibitor, N-1-naphthylphthalamic acid, by contrast, suppressed curvature markedly without altering ethylene emission. The effects of the above-stated treatments did not differentiate qualitatively among the R-, FR-irradiated seedlings and dark control so as to explain phytochrome-mediated hook exaggeration. In addition, ethylene emission by seedlings was affected neither by R nor FR at such fluences as to cause hook exaggeration. In conclusion, (1) ethylene suppresses not only the light-exaggerated hook, but also the dark-formed one; (2) ethylene emission is not affected by R or FR, and also not correlated with the hook exaggerations; thus ethylene is not responsible for the hook exaggeration in tomato; and (3) auxin is

  14. SU-E-T-286: Dose Verification of Spot-Scanning Proton Beam Using GafChromic EBT3 Film

    SciTech Connect

    Chen, C; Tang, S; Mah, D; Chan, M

    2015-06-15

    Purpose: Dose verification of spot-scanning proton pencil beam is performed via planar dose measurements at several depths using an ionization-chamber array, requiring repeat irradiations of each field for each depth. Here we investigate film dosimetry which has two advantages: higher resolution and efficiency from one-shot irradiation for multiple depths. Methods: Film calibration was performed using an EBT3 film at 20-cm depth of Plastic Water (CIRS, Norfolk, VA) exposed by a 10-level step wedge on a Proteus Plus proton system (IBA, Belgium). The calibration doses ranged from 25–250 cGy(RBE) for proton energies of 170–200 MeV. A uniform 1000 cm{sup 3} dose cube and a clinical prostate combined with seminal-vesicle and pelvic-nodes plan were used for this study. All treatment plans were generated in the RayStation (RaySearch Lab, Sweden). The planar doses at different depths for both cases were measured with film using triple-channel dosimetry and the MatriXX PT (IBA Dosimetry, Germany). The Gamma passing rates, dose-difference maps, and profiles of 2D planar doses measured with EBT3 film and MatriXX, versus treatment planning system (TPS) calculations were analyzed and compared using the FilmQA Pro (Ashland Inc., Bridgewater, NJ). Results: The EBT3 film measurement results matched well with the TPS calculation data with an average passing rate >95% for 2%/2mm and are comparable with the MatriXX measurements (0.7%, 1.8%, 3.8% mean differences corresponding to 3%/3mm, 3%/2mm, 2%/2mm, respectively). Overall passing rates for EBT3 films appear higher than those with MatriXX detectors. Conclusion: The energy dependence of the film response could be minimized by calibration using proton beam with mixed energies. The greater efficiency of the dose verification using GafChromic EBT3 results in a potential cost trade-off between room capacity and film cost. EBT3 film may offer distinct advantages in highly intensity-modulated fields due to its higher resolution

  15. Phytochrome from Green Plants: Properties and biological Function

    SciTech Connect

    Quail, Peter H.

    2014-07-25

    Plants constantly monitor the light environment for informational light signals used to direct adaptational responses to the prevailing conditions. One major such response, the Shade-Avaoidance Response (SAR), triggered when plants sense the presence of competing neighbors, results in enhanced channeling of photosynthetically-fixed carbon into stem elongation at the expense of deposition in reproductive tissues. This response has been selected against in many modern food crops to ensure maximum edible yield (e.g. seeds). Converse enhancement of the SAR, with consequent increased carbon channeling into vegetative cellulose, could contribute to the generation of crops with improved yield of tissues suitable for cellulosic biofuel production. The signal for this response is light enriched in far-red wavelengths. This signal is produced by sunlight filtered through, or reflected from, neighboring vegetation, as a result of preferential depletion of red photons through chlorophyll absorption. The plant phytochrome (phy) photoreceptor system (predominantly phyB) senses this signal through its capacity to switch reversibly, in milliseconds, between two molecular states: the biologically inactive Pr (red-light-absorbing) and biologically active Pfr (far-red-light-absorbing) conformers. The photoequilibrium established between these two conformers in light-grown plants is determined by the ratio of red-to-far-red wavelengths in the incoming signal. The levels of Pfr then dictate the recipient plant’s growth response: high levels suppress elongation growth; low levels promote elongation growth. Studies on seedling deetiolation have advanced our understanding considerably in recent years, of the mechanism by which the photoactivated phy molecule transduces its signal into cellular growth responses. The data show that a subfamily of phy-interacting bHLH transcription factors (PIFs) promote skotomorphogenic seedling development in post-germinative darkness, but that the phy

  16. Quantification of the fluorine containing drug 5-fluorouracil in cancer cells by GaF molecular absorption via high-resolution continuum source molecular absorption spectrometry

    NASA Astrophysics Data System (ADS)

    Krüger, Magnus; Huang, Mao-Dong; Becker-Roß, Helmut; Florek, Stefan; Ott, Ingo; Gust, Ronald

    The development of high-resolution continuum source molecular absorption spectrometry made the quantification of fluorine feasible by measuring the molecular absorption as gallium monofluoride (GaF). Using this new technique, we developed on the example of 5-fluorouracil (5-FU) a graphite furnace method to quantify fluorine in organic molecules. The effect of 5-FU on the generation of the diatomic GaF molecule was investigated. The experimental conditions such as gallium nitrate amount, temperature program, interfering anions (represented as corresponding acids) and calibration for the determination of 5-FU in standard solution and in cellular matrix samples were investigated and optimized. The sample matrix showed no effect on the sensitivity of GaF molecular absorption. A simple calibration curve using an inorganic sodium fluoride solution can conveniently be used for the calibration. The described method is sensitive and the achievable limit of detection is 0.23 ng of 5-FU. In order to establish the concept of "fluorine as a probe in medicinal chemistry" an exemplary application was selected, in which the developed method was successfully demonstrated by performing cellular uptake studies of the 5-FU in human colon carcinoma cells.

  17. Heterologous expression of Arabidopsis phytochrome B in transgenic potato influences photosynthetic performance and tuber development

    SciTech Connect

    Thiele, A.; Herold, M.; Lenk, I.; Gatz, C. . Albrecht von Haller Inst. fuer Pflanzenwissenschaften); Quail, P.H. )

    1999-05-01

    Transgenic potato (Solanum tuberosum) plants expressing Arabidopsis phytochrome B were characterized morphologically and physiologically under white light in a greenhouse to explore their potential for improved photosynthesis and higher tuber yields. As expected, overexpression of functional phytochrome B caused pleiotropic effects such as semidwarfism, decreased apical dominance, a higher number of smaller but thicker leaves, and increased pigmentation. Because of increased numbers of chloroplasts in elongated palisade cells, photosynthesis per leaf area and in each individual plant increased. In addition, photosynthesis was less sensitive to photoinactivation under prolonged light stress. The beginning of senescence was not delayed, but deceleration of chlorophyll degradation extended the lifetime of photosynthetically active plants. Both the higher photosynthetic performance and the longer lifespan of the transgenic plants allowed greater biomass production, resulting in extended underground organs with increased tuber yields.

  18. Localization of phytochrome in etioplasts and its regulation in vitro of gibberellin levels

    PubMed Central

    Evans, A.; Smith, H.

    1976-01-01

    Etioplasts isolated from barley leaves and purified on a Sephadex G-50 (coarse) column were characterized by electron microscopy and nucleic acid analysis. The majority of etioplasts retained an intact outer envelope, and contamination by other fragments was extremely low. The level of gibberellin-like substances extractable from intact etioplast suspensions was enhanced within 5 min of the termination of a saturating red irradiation, and the response was far-red reversible. Ultra-sonication caused a 3-fold increase in extractable activity both in dark control suspension and suspensions treated with red light. It is concluded that phytochrome, as a function of its interconversions, probably causes the transport of gibberellin from inside the etioplast into the surrounding medium. This leads to increased production of active gibberellins, possibly by release of feedback control of late steps of the biosynthetic pathway. Dual wavelength difference spectrophotometry has demonstrated the presence of a proportion of total cellular phytochrome within the etioplast. Images PMID:16592300

  19. Calcium-regulated nuclear enzymes: potential mediators of phytochrome-induced changes in nuclear metabolism?

    NASA Technical Reports Server (NTRS)

    Roux, S. J.

    1992-01-01

    Calcium ions have been proposed to serve as important regulatory elements in stimulus-response coupling for phytochrome responses. An important test of this hypothesis will be to identify specific targets of calcium action that are required for some growth or development process induced by the photoactivated form of phytochrome (Pfr). Initial studies have revealed that there are at least two enzymes in pea nuclei that are stimulated by Pfr in a Ca(2+)-dependent fashion, a calmodulin-regulated nucleoside triphosphatase and a calmodulin-independent but Ca(2+)-dependent protein kinase. The nucleoside triphosphatase appears to be associated with the nuclear envelope, while the protein kinase co-purifies with a nuclear fraction highly enriched for chromatin. This short review summarizes the latest findings on these enzymes and relates them to what is known about Pfr-regulated nuclear metabolism.

  20. Mapping light-driven conformational changes within the photosensory module of plant phytochrome B

    PubMed Central

    von Horsten, Silke; Straß, Simon; Hellwig, Nils; Gruth, Verena; Klasen, Ramona; Mielcarek, Andreas; Linne, Uwe; Morgner, Nina; Essen, Lars-Oliver

    2016-01-01

    Organisms developed different photoreceptors to be able to adapt to changing environmental light conditions. Phytochromes are red/far-red (r/fr) photochromic photoreceptors that belong to the classical photoreceptors along with cryptochromes and phototropins. They convert absorbed light into a biological signal by switching between two states in a light-dependent manner therefore enabling the light control downstream signalling. Their Pfr conformation is the biological active form in plants, but until now only a structure of the ground state (Pr) was solved. Here, the authors provide information about structural changes occurring during photoconversion within phytochrome B and identify possible interaction sites for its N-terminal extension (NTE) utilising hydrogen/deuterium exchange rate analyses of its amide backbone. Especially, the newly identified light-dependency of two regions in the NTE are of particular interest for understanding the involvement of the phytochrome’s NTE in the regulation of its downstream signalling. PMID:27694986

  1. Ecological modulation of plant defense via phytochrome control of jasmonate sensitivity

    PubMed Central

    Moreno, Javier E.; Tao, Yi; Chory, Joanne; Ballaré, Carlos L.

    2009-01-01

    For plants, the tradeoff between resource investment in defense and increased growth to out-compete neighbors creates an allocation dilemma. How plants resolve this dilemma, at the mechanistic level, is unclear. We found that Arabidopsis plants produced an attenuated defense phenotype under conditions of crowding and when exposed to far-red (FR) radiation, a light signal that plants use to detect the proximity of neighbors via the photoreceptor phytochrome. This phenotype was detectable through standard bioassays that measured the growth of Spodoptera frugiperda caterpillars. Two possible explanations for the effect of FR are: (i) a simple by-product of the diversion of resources to competition, and (ii) a specific effect of phytochrome on defense signaling. The first possibility was ruled out by the fact that the auxin-deficient sav3 mutant, which fails to induce growth responses to FR, still responded to FR with an attenuated defense phenotype. In support of the second hypothesis, we found that phytochrome inactivation by FR caused a strong reduction of plant sensitivity to jasmonates, which are key regulators of plant immunity. The effects of FR on jasmonate sensitivity were restricted to certain elements of the pathway. Supporting the idea that the FR effects on jasmonate signaling are functionally significant, we found that FR failed to increase tissue quality in jar1, a mutant impaired in jasmonate response. We conclude that the plant modulates its investment in defense as a function of the perceived risk of competition, and that this modulation is effected by phytochrome via selective desensitization to jasmonates. PMID:19251652

  2. Ultraviolet B Radiation Enhances a Phytochrome-B-Mediated Photomorphogenic Response in Arabidopsis1

    PubMed Central

    Boccalandro, Hernán E.; Mazza, Carlos A.; Mazzella, M. Agustina; Casal, Jorge J.; Ballaré, Carlos L.

    2001-01-01

    Ultraviolet B radiation (UV-B, 290–315 nm) can cause damage and induce photomorphogenic responses in plants. The mechanisms that mediate the photomorphogenic effects of UV-B are unclear. In etiolated Arabidopsis seedlings, a daily exposure to 2.5 h of UV-B enhanced the cotyledon opening response induced by a subsequent red light (R) pulse. An R pulse alone, 2.5 h of UV-B terminated with a far-red pulse, or 2.5 h of continuous R caused very little cotyledon opening. The enhancing effect of UV-B increased with fluence rate up to approximately 7.58 μmol m−2 s−1; at higher fluence rates the response to UV-B was greatly reduced. The phyA, phyA cry1, and cry1 cry2 mutants behaved like the wild type when exposed to UV-B followed by an R pulse. In contrast, phyB, phyB cry1, and phyB phyA mutants failed to open the cotyledons. Thus, phytochrome B was required for the cotyledon opening response to UV-B → R treatments, whereas phytochrome A and cryptochromes 1 and 2 were not necessary under the conditions of our experiments. The enhancing effect of low doses of UV-B on cotyledon opening in uvr1 uvr2 and uvr1 uvr3 mutants, deficient in DNA repair, was similar to that found in the wild type, suggesting that this effect of UV-B was not elicited by signals derived from UV-B-induced DNA lesions (cyclobutane pyrimidine dimers and 6-4 photoproducts). We conclude that low doses of UV-B, perceived by a receptor system different from phytochromes, cryptochromes, or DNA, enhance a de-etiolation response that is induced by active phytochrome B. PMID:11402206

  3. Reversibly switchable photoacoustic tomography using a genetically encoded near-infrared phytochrome

    NASA Astrophysics Data System (ADS)

    Yao, Junjie; Kaberniuk, Andrii A.; Li, Lei; Shcherbakova, Daria M.; Zhang, Ruiying; Wang, Lidai; Li, Guo; Verkhusha, Vladislav V.; Wang, Lihong V.

    2016-03-01

    Optical imaging of genetically encoded probes has revolutionized biomedical studies by providing valuable information about targeted biological processes. Here, we report a novel imaging technique, termed reversibly switchable photoacoustic tomography (RS-PAT), which exhibits large penetration depth, high detection sensitivity, and super-resolution. RS-PAT combines advanced photoacoustic imaging techniques with, for the first time, a nonfluorescent photoswitchable bacterial phytochrome. This bacterial phytochrome is the most near-infrared shifted genetically encoded probe reported so far. Moreover, this bacterial phytochrome is reversibly photoconvertible between its far-red and near-infrared light absorption states. Taking maximum advantage of the powerful imaging capability of PAT and the unique photochemical properties of the phytochrome, RS-PAT has broken through both the optical diffusion limit for deep-tissue imaging and the optical diffraction limit for super-resolution photoacoustic microscopy. Specifically, with RS-PAT we have achieved an unprecedented detection sensitivity of ~2 μM, or as few as ~20 tumor cells, at a centimeter depth. Such high sensitivity is fully demonstrated in our study by monitoring tumor growth and metastasis at whole-body level with ~100 μm resolution. Moreover, our microscopic implementation of RS-PAT is capable of imaging mammalian cells with a sub-diffraction lateral resolution of ~140 nm and axial resolution of ~400 nm, which are respectively ~2-fold and ~75-fold finer than those of our conventional photoacoustic microscopy. Overall, RS-PAT is a new and promising imaging technology for studying biological processes at different length scales.

  4. Ultrafast dynamics of phytochrome from the cyanobacterium synechocystis, reconstituted with phycocyanobilin and phycoerythrobilin.

    PubMed Central

    Heyne, Karsten; Herbst, Johannes; Stehlik, Dietmar; Esteban, Berta; Lamparter, Tilman; Hughes, Jon; Diller, Rolf

    2002-01-01

    Femtosecond time-resolved transient absorption spectroscopy was employed to characterize for the first time the primary photoisomerization dynamics of a bacterial phytochrome system in the two thermally stable states of the photocycle. The 85-kDa phytochrome Cph1 from the cyanobacterium Synechocystis PCC 6803 expressed in Escherichia coli was reconstituted with phycocyanobilin (Cph1-PCB) and phycoerythrobilin (Cph1-PEB). The red-light-absorbing form Pr of Cph1-PCB shows an approximately 150 fs relaxation in the S(1) state after photoexcitation at 650 nm. The subsequent Z-E isomerization between rings C and D of the linear tetrapyrrole-chromophore is best described by a distribution of rate constants with the first moment at (16 ps)(-1). Excitation at 615 nm leads to a slightly broadened distribution. The reverse E-Z isomerization, starting from the far-red-absorbing form Pfr, is characterized by two shorter time constants of 0.54 and 3.2 ps. In the case of Cph1-PEB, double-bond isomerization does not take place, and the excited-state lifetime extends into the nanosecond regime. Besides a stimulated emission rise time between 40 and 150 fs, no fast relaxation processes are observed. This suggests that the chromophore-protein interaction along rings A, B, and C does not contribute much to the picosecond dynamics observed in Cph1-PCB but rather the region around ring D near the isomerizing C(15) [double bond] C(16) double bond. The primary reaction dynamics of Cph1-PCB at ambient temperature is found to exhibit very similar features as those described for plant type A phytochrome, i.e., a relatively slow Pr, and a fast Pfr, photoreaction. This suggests that the initial reactions were established already before evolution of plant phytochromes began. PMID:11806940

  5. Altered Phytochrome Regulation of Greening in an aurea Mutant of Tomato.

    PubMed

    Ken-Dror, S; Horwitz, B A

    1990-04-01

    A brief pulse of red light accelerates chlorophyll accumulation upon subsequent transfer of dark-grown tomato (Lycopersicon esculentum) seedlings to continuous white light. Such potentiation of greening was compared in wild type and an aurea mutant W616. This mutant has been the subject of recent studies of phytochrome phototransduction; its dark-grown seedlings are deficient in phytochrome, and light-grown plants have yellow-green leaves. The rate of greening was slower in the mutant, but the extent (relative to the dark control) of potentiation by the red pulse was similar to that in the wild type. In the wild type, the fluence-response curve for potentiation of greening indicates substantial components in the VLF (very low fluence) and LF (low fluence) ranges. Far-red light could only partially reverse the effect of red. In the aurea mutant, only red light in the LF range was effective, and the effect of red was completely reversed by far-red light. When grown in total darkness, aurea seedlings are also deficient in photoconvertible PChl(ide). Upon transfer to white light, the aurea mutant was defective in both the abundance and light regulation of the light-harvesting chlorophyll a/b binding polypeptide(s) [LHC(II)]. The results are consistent with the VLF response in greening being mediated by phytochrome. Furthermore, the data support the hypothesis that light modulates LHC(II) levels through its control of the synthesis of both chlorophyll and its LHC(II) apoproteins. Some, but not all, aspects of the aurea phenotype can be accounted for by the deficiency in photoreception by phytochrome.

  6. Far-red light-insensitive, phytochrome A-deficient mutants of tomato.

    PubMed

    van Tuinen, A; Kerckhoffs, L H; Nagatani, A; Kendrick, R E; Koornneef, M

    1995-01-20

    We have selected two recessive mutants of tomato with slightly longer hypocotyls than the wild type, one under low fluence rate (3 mumol/m2/s) red light (R) and the other under low fluence rate blue light. These two mutants were shown to be allelic and further analysis revealed that hypocotyl growth was totally insensitive to far-red light (FR). We propose the gene symbol fri (far-red light insensitive) for this locus and have mapped it on chromosome 10. Immunochemically detectable phytochrome A polypeptide is essentially absent in the fri mutants as is the bulk spectrophotometrically detectable labile phytochrome pool in etiolated seedlings. A phytochrome B-like polypeptide is present in normal amounts and a small stable phytochrome pool can be readily detected by spectrophotometry in the fri mutants. Inhibition of hypocotyl growth by a R pulse given every 4 h is quantitatively similar in the fri mutants and wild type and the effect is to a large extent reversible if R pulses are followed immediately by a FR pulse. After 7 days in darkness, both fri mutants and the wild type become green on transfer to white light, but after 7 days in FR, the wild-type seedlings that have expanded their cotyledons lose their capacity to green in white light, while the fri mutants de-etiolate. Adult plants of the fri mutants show retarded growth and are prone to wilting, but exhibit a normal elongation response to FR given at the end of the daily photoperiod. The inhibition of seed germination by continuous FR exhibited by the wild type is normal in the fri mutants.(ABSTRACT TRUNCATED AT 250 WORDS)

  7. SU-E-T-32: An Application of GafChromic RTQA2 Film to the Patient Specified Quality Assurance

    SciTech Connect

    Peng, J; Hu, W

    2014-06-01

    Purpose: GafChromic RTQA2 film is known as a quality assurance (QA) tool for light field and radiation field verification. This study is attempted to apply the RTQA2 film to the patient specified quality assurance. Methods: Pre-irradiated and post-irradiated RTQA2 films were scanned in a reflection mode using a flatbed scanner. A plan-based dose calibration method utilized the mapping information of calculated dose image and measured film image to create a dose vs. pixel value calibration model. This model was used to calibrate the measured film image from the pixel value (gray value) image to the dose image. The dose agreement between calculated and measured dose images were analyzed using the gamma analysis. To evaluate the feasibility of this method, three clinical approved RapidArc cases (one abdomen cancer and two head-and-neck cancer patients) were tested. The tolerance of 3% dose difference and 3 mm distance to agreement (DTA) and gamma index ≤ 1 were set for the analysis. Results: The calibrated film dose image from measurement was successfully compared to the predicted dose image from the commercial treatment planning. The gamma analysis results showed good consistency. Gamma passing rates were 99.02%, 94.84%, and 98.33% for the three patients, respectively. Conclusion: The plan based calibration method has the feasibility for dose verification without shortages of film batch and development time variation.

  8. The adaptive evolution of plasticity: phytochrome-mediated shade avoidance responses.

    PubMed

    Schmitt, Johanna; Stinchcombe, John R; Heschel, M Shane; Huber, Heidrun

    2003-07-01

    Many plants display a characteristic suite of developmental "shade avoidance" responses, such as stem elongation and accelerated reproduction, to the low ratio of red to far-red wavelengths (R:FR) reflected or transmitted from green vegetation. This R:FR cue of crowding and vegetation shade is perceived by the phytochrome family of photoreceptors. Phytochrome-mediated responses provide an ideal system for investigating the adaptive evolution of phenotypic plasticity in natural environments. The molecular and developmental mechanisms underlying shade avoidance responses are well studied, and testable ecological hypotheses exist for their adaptive significance. Experimental manipulation of phenotypes demonstrates that shade avoidance responses may be adaptive, resulting in phenotypes with high relative fitness in the environments that induce those phenotypes. The adaptive value of shade avoidance depends upon the competitive environment, resource availability, and the reliability of the R:FR cue for predicting the selective environment experienced by an induced phenotype. Comparative studies and a reciprocal transplant experiment with Impatiens capensis provide evidence of adaptive divergence in shade avoidance responses between woodland and clearing habitats, which may result from population differences in the frequency of selection on shade avoidance traits, as well as differences in the reliability of the R:FR cue. Recent rapid progress in elucidating phytochrome signaling pathways in the genetic model Arabidopsis thaliana and other species now provides the opportunity for studying how selection on shade avoidance traits in natural environments acts upon the molecular mechanisms underlying natural phenotypic variation.

  9. Diatom Phytochromes Reveal the Existence of Far-Red-Light-Based Sensing in the Ocean.

    PubMed

    Fortunato, Antonio Emidio; Jaubert, Marianne; Enomoto, Gen; Bouly, Jean-Pierre; Raniello, Raffaella; Thaler, Michael; Malviya, Shruti; Bernardes, Juliana Silva; Rappaport, Fabrice; Gentili, Bernard; Huysman, Marie J J; Carbone, Alessandra; Bowler, Chris; d'Alcalà, Maurizio Ribera; Ikeuchi, Masahiko; Falciatore, Angela

    2016-03-01

    The absorption of visible light in aquatic environments has led to the common assumption that aquatic organisms sense and adapt to penetrative blue/green light wavelengths but show little or no response to the more attenuated red/far-red wavelengths. Here, we show that two marine diatom species, Phaeodactylum tricornutum and Thalassiosira pseudonana, possess a bona fide red/far-red light sensing phytochrome (DPH) that uses biliverdin as a chromophore and displays accentuated red-shifted absorbance peaks compared with other characterized plant and algal phytochromes. Exposure to both red and far-red light causes changes in gene expression in P. tricornutum, and the responses to far-red light disappear in DPH knockout cells, demonstrating that P. tricornutum DPH mediates far-red light signaling. The identification of DPH genes in diverse diatom species widely distributed along the water column further emphasizes the ecological significance of far-red light sensing, raising questions about the sources of far-red light. Our analyses indicate that, although far-red wavelengths from sunlight are only detectable at the ocean surface, chlorophyll fluorescence and Raman scattering can generate red/far-red photons in deeper layers. This study opens up novel perspectives on phytochrome-mediated far-red light signaling in the ocean and on the light sensing and adaptive capabilities of marine phototrophs.

  10. Phytochrome and retrograde signalling pathways converge to antagonistically regulate a light-induced transcriptional network.

    PubMed

    Martín, Guiomar; Leivar, Pablo; Ludevid, Dolores; Tepperman, James M; Quail, Peter H; Monte, Elena

    2016-05-06

    Plastid-to-nucleus retrograde signals emitted by dysfunctional chloroplasts impact photomorphogenic development, but the molecular link between retrograde- and photosensory-receptor signalling has remained unclear. Here, we show that the phytochrome and retrograde signalling (RS) pathways converge antagonistically to regulate the expression of the nuclear-encoded transcription factor GLK1, a key regulator of a light-induced transcriptional network central to photomorphogenesis. GLK1 gene transcription is directly repressed by PHYTOCHROME-INTERACTING FACTOR (PIF)-class bHLH transcription factors in darkness, but light-activated phytochrome reverses this activity, thereby inducing expression. Conversely, we show that retrograde signals repress this induction by a mechanism independent of PIF mediation. Collectively, our data indicate that light at moderate levels acts through the plant's nuclear-localized sensory-photoreceptor system to induce appropriate photomorphogenic development, but at excessive levels, sensed through the separate plastid-localized RS system, acts to suppress such development, thus providing a mechanism for protection against photo-oxidative damage by minimizing the tissue exposure to deleterious radiation.

  11. Phytochrome and retrograde signalling pathways converge to antagonistically regulate a light-induced transcriptional network

    PubMed Central

    Martín, Guiomar; Leivar, Pablo; Ludevid, Dolores; Tepperman, James M.; Quail, Peter H.; Monte, Elena

    2016-01-01

    Plastid-to-nucleus retrograde signals emitted by dysfunctional chloroplasts impact photomorphogenic development, but the molecular link between retrograde- and photosensory-receptor signalling has remained unclear. Here, we show that the phytochrome and retrograde signalling (RS) pathways converge antagonistically to regulate the expression of the nuclear-encoded transcription factor GLK1, a key regulator of a light-induced transcriptional network central to photomorphogenesis. GLK1 gene transcription is directly repressed by PHYTOCHROME-INTERACTING FACTOR (PIF)-class bHLH transcription factors in darkness, but light-activated phytochrome reverses this activity, thereby inducing expression. Conversely, we show that retrograde signals repress this induction by a mechanism independent of PIF mediation. Collectively, our data indicate that light at moderate levels acts through the plant's nuclear-localized sensory-photoreceptor system to induce appropriate photomorphogenic development, but at excessive levels, sensed through the separate plastid-localized RS system, acts to suppress such development, thus providing a mechanism for protection against photo-oxidative damage by minimizing the tissue exposure to deleterious radiation. PMID:27150909

  12. HYPERSENSITIVE TO RED AND BLUE 1, a ZZ-type zinc finger protein, regulates phytochrome B-mediated red and cryptochrome-mediated blue light responses.

    PubMed

    Kang, Xiaojun; Chong, Jason; Ni, Min

    2005-03-01

    Plant photoreceptors that regulate photomorphogenic development include red/far-red-light-absorbing phytochromes and blue/UV-A-light-absorbing cryptochromes. We have undertaken a genetic screen to identify additional components downstream of the photoreceptors in Arabidopsis thaliana. We identified a short hypocotyl mutant under red and blue light, hypersensitive to red and blue 1 (hrb1). Mutation in HRB1 also enhances the end-of-day far-red light response, inhibits leaf expansion and petiole elongation, and attenuates the expression of CAB3 and CHS. Double mutant analysis indicates that phyB is epistatic to hrb1 under red light, and cry1 cry2 is epistatic to hrb1 under blue light for both hypocotyl growth and light-regulated gene expression responses. HRB1 localizes to the nucleus and belongs to a protein family of Drought induced 19 (Di19). HRB1 and all other family members contain a ZZ-type zinc finger domain, which in other organisms is implicated in protein-protein interactions between dystrophin and calmodulin and between transcriptional adaptors and activators. HRB1 activity is also required for red and blue light-induced expression of PHYTOCHROME INTERACTING FACTOR 4 (PIF4). pif4 shows a very similar hypersensitive response as hrb1 to both red light and blue light and is epistatic to hrb1 in control of light-regulated gene expression responses. Thus, the roles of HRB1 and PIF4 together in regulating both red and blue light responses may represent points where red light signaling and blue light signaling intersect.

  13. Analysis of cloned cDNA and genomic sequences for phytochrome: complete amino acid sequences for two gene products expressed in etiolated Avena.

    PubMed Central

    Hershey, H P; Barker, R F; Idler, K B; Lissemore, J L; Quail, P H

    1985-01-01

    Cloned cDNA and genomic sequences have been analyzed to deduce the amino acid sequence of phytochrome from etiolated Avena. Restriction endonuclease site polymorphism between clones indicates that at least four phytochrome genes are expressed in this tissue. Sequence analysis of two complete and one partial coding region shows approximately 98% homology at both the nucleotide and amino acid levels, with the majority of amino acid changes being conservative. High sequence homology is also found in the 5'-untranslated region but significant divergence occurs in the 3'-untranslated region. The phytochrome polypeptides are 1128 amino acid residues long corresponding to a molecular mass of 125 kdaltons. The known protein sequence at the chromophore attachment site occurs only once in the polypeptide, establishing that phytochrome has a single chromophore per monomer covalently linked to Cys-321. Computer analyses of the amino acid sequences have provided predictions regarding a number of structural features of the phytochrome molecule. PMID:3001642

  14. [An in vivo study of detectable phytochrome in seeds of Cucurbita pepo L. in the course of different phases of germination].

    PubMed

    Zouaghi, M; Malcoste, R; Rollin, P

    1972-03-01

    In dry gourd seeds all the phytochrome is in the Pfr form. The increase of phytochrome content from the beginning of hydration involves two phases, A and B, in the embryonic axis as well as in the cotyledons. Cycloheximide does not prevent the appearance of Pr during phase A. We assume that Pr is gradually released from an inactive complex. On the other hand phase B is inhibited by cycloheximide; this could mean that a de novo synthesis of Pr occurs.Some experiments indicate that the phytochrome which is localized in the embryonic axis may be involved only in the germinating process.The phytochrome which is synthesized during phase B disappears when the seeds are irradiated with red light, while the original phytochrome does not.According to our data it seems necessary to lay down a new and precise definition of the germination process.

  15. Accurate dosimetry with GafChromic EBT film of a 6 MV photon beam in water: What level is achievable?

    SciTech Connect

    Battum, L. J. van; Hoffmans, D.; Piersma, H.; Heukelom, S.

    2008-02-15

    This paper focuses on the accuracy, in absolute dose measurements, with GafChromic EBT film achievable in water for a 6 MV photon beam up to a dose of 2.3 Gy. Motivation is to get an absolute dose detection system to measure up dose distributions in a (water) phantom, to check dose calculations. An Epson 1680 color (red green blue) transmission flatbed scanner has been used as film scanning system, where the response in the red color channel has been extracted and used for the analyses. The influence of the flatbed film scanner on the film based dose detection process was investigated. The scan procedure has been optimized; i.e. for instance a lateral correction curve was derived to correct the scan value, up to 10%, as a function of optical density and lateral position. Sensitometric curves of different film batches were evaluated in portrait and landscape scan mode. Between various batches important variations in sensitometric curve were observed. Energy dependence of the film is negligible, while a slight variation in dose response is observed for very large angles between film surface and incident photon beam. Improved accuracy in absolute dose detection can be obtained by repetition of a film measurement to tackle at least the inherent presence of film inhomogeneous construction. We state that the overall uncertainty is random in absolute EBT film dose detection and of the order of 1.3% (1 SD) under the condition that the film is scanned in a limited centered area on the scanner and at least two films have been applied. At last we advise to check a new film batch on its characteristics compared to available information, before using that batch for absolute dose measurements.

  16. Crystal Structure of Deinococcus Phytochrome in the Photoactivated State Reveals a Cascade of Structural Rearrangements during Photoconversion.

    PubMed

    Burgie, E Sethe; Zhang, Junrui; Vierstra, Richard D

    2016-03-01

    Phytochromes are photochromic photoreceptors responsible for a myriad of red/far-red light-dependent processes in plants and microorganisms. Interconversion is initially driven by photoreversible isomerization of bilin, but how this alteration directs the photostate-dependent changes within the protein to actuate signaling is poorly understood. Here, we describe the structure of the Deinococcus phytochrome photosensory module in its near complete far-red light-absorbing Pfr state. In addition to confirming the 180° rotation of the D-pyrrole ring, the dimeric structure clearly identifies downstream rearrangements that trigger large-scale conformational differences between the dark-adapted and photoactivated states. Mutational analyses verified the importance of residues surrounding the bilin in Pfr stabilization, and protease sensitivity assays corroborated photostate alterations that propagate along the dimeric interface. Collectively, these data support a cooperative "toggle" model for phytochrome photoconversion and advance our understanding of the allosteric connection between the photosensory and output modules.

  17. Phylogenetic utility of the nuclear genes AGAMOUS 1 and PHYTOCHROME B in palms (Arecaceae): an example within Bactridinae

    PubMed Central

    Ludeña, Bertha; Chabrillange, Nathalie; Aberlenc-Bertossi, Frédérique; Adam, Hélène; Tregear, James W.; Pintaud, Jean-Christophe

    2011-01-01

    Background and Aims Molecular phylogenetic studies of palms (Arecaceae) have not yet provided a fully resolved phylogeny of the family. There is a need to increase the current set of markers to resolve difficult groups such as the Neotropical subtribe Bactridinae (Arecoideae: Cocoseae). We propose the use of two single-copy nuclear genes as valuable tools for palm phylogenetics. Methods New primers were developed for the amplification of the AGAMOUS 1 (AG1) and PHYTOCHROME B (PHYB) genes. For the AGAMOUS gene, the paralogue 1 of Elaeis guineensis (EgAG1) was targeted. The region amplified contained coding sequences between the MIKC K and C MADS-box domains. For the PHYB gene, exon 1 (partial sequence) was first amplified in palm species using published degenerate primers for Poaceae, and then specific palm primers were designed. The two gene portions were sequenced in 22 species of palms representing all genera of Bactridinae, with emphasis on Astrocaryum and Hexopetion, the status of the latter genus still being debated. Key Results The new primers designed allow consistent amplification and high-quality sequencing within the palm family. The two loci studied produced more variability than chloroplast loci and equally or less variability than PRK, RPBII and ITS nuclear markers. The phylogenetic structure obtained with AG1 and PHYB genes provides new insights into intergeneric relationships within the Bactridinae and the intrageneric structure of Astrocaryum. The Hexopetion clade was recovered as monophyletic with both markers and was weakly supported as sister to Astrocaryum sensu stricto in the combined analysis. The rare Astrocaryum minus formed a species complex with Astrocaryum gynacanthum. Moreover, both AG1 and PHYB contain a microsatellite that could have further uses in species delimitation and population genetics. Conclusions AG1 and PHYB provide additional phylogenetic information within the palm family, and should prove useful in combination with other

  18. SU-E-T-526: Irradiation of Human Cell Lines Using Carbon Ions: Real Time Dosimetry Using Gaf-Chromic Film

    SciTech Connect

    Lin, Y; Held, K; La Tessa, C; Rusek, A

    2015-06-15

    Purpose: The purpose of this study is to investigate and quantify several factors affecting biological effects of carbon ions such as cell type, dose, energy and position where the cells are irradiated along the pristine Bragg curve. Methods: Experiments to quantify clonogenic cell survival in three human lung cancer cell lines and a fibroblast cell line were performed at the NASA Space Radiation Laboratory, BNL, Upton, USA. A system of water or media-filled T25 flasks lined up along the beam axis was designed so that the cell-containing surfaces of the flasks were placed at specific depths along the Bragg curve. Gaf-chromic films were placed between the flasks to monitor the dose distribution in the sample as soon as the irradiation was finished. Additional studies were conducted at four selected depths along the Bragg curve to obtain full cell survival dose response curves for the four cell lines. Results: The percent depth dose of the beams was determined using an ionization chamber and showed that the physical Bragg peak is at 22.5 cm water depth. However, the clonogenic cell survival data indicated that the maximum cell killing occurred at 21.5 cm. Gaf-chromic films revealed some inhomogeneity in the dose distribution on the flasks near the peak, presumably due to lack of scattering from the sides of the flasks, which might account for the differences. Depending on the cell line and radiation dose, the maximum cell killing (i.e., the greatest RBE) is at the 21.5 (the peak) or 24 cm (distal fall off) depth. Conclusion: There is a difference in biological effect along the Bragg curve of a carbon ion beam, indicating an elevated RBE at or beyond the end of the range. Gaf-chromic films are proven to be effective in monitoring the 2D irradiation pattern to the flasks. Research supported by NIH/NCI through grant no. R21 CA182259.

  19. In vivo surface dose measurement using GafChromic film dosimetry in breast cancer radiotherapy: comparison of 7-field IMRT, tangential IMRT and tangential 3D-CRT

    PubMed Central

    2014-01-01

    Purpose The purpose of this study was to compare the surface dose of 7-field IMRT (7 F-IMRT), tangential beam IMRT (TB-IMRT), and tangential beam 3D-CRT (3D-CRT) of breast cancer patients receiving adjuvant radiotherapy by means of in vivo GafChromic film dosimetry. Material and methods Breast cancer patients receiving adjuvant radiotherapy of the whole breast or the chest wall were eligible for the study. Study patients were treated with a treatment plan using two different radiotherapy techniques (first patient series, 3D-CRT followed by TB-IMRT; second patient series, TB-IMRT followed by 7 F-IMRT). The surface dose was evaluated on three consecutive treatment fractions per radiotherapy technique using in vivo GafChromic film dosimetry. The paired t-test was used to assess the difference of in vivo GafChromic film readings or calculated plan parameters of the compared pairs of radiation techniques for statistical significance. Results Forty-five unselected breast cancer patients were analysed in this study. 7 F-IMRT significantly reduced the surface dose compared to TB-IMRT. Differences were greatest in the central and lateral breast or chest wall region and amounted to a dose reduction of -11.8% to -18.8%. No significant difference of the surface dose was observed between TB-IMRT and 3D-CRT. A corresponding observation was obtained for the calculated skin dose derived from dose-volume histograms. Conclusions In adjuvant breast cancer radiotherapy, 7 F-IMRT offers a significantly reduced surface dose compared to TB-IMRT or 3D-CRT. PMID:25022449

  20. Use of phytochrome-dependent reaction in evaluating the effect of space flight factors on the plant organism

    NASA Technical Reports Server (NTRS)

    Shteyne, B. A.; Nevzgodina, L. V.; Miller, A. T.

    1982-01-01

    The effects of space flight factors on lettuce seeds aboard the Kosmos-936 and Kosmos-1129 satellites for 20 days were studied. The phytochrome dependent (PD) reaction of light sensitive seeds was a sensitive criterion for evaluating the biological effects of space flight factors. The PD reaction of air dry lettuce seeds was suppressed after space flight, especially if the seeds were exposed to open space during the flight. Space flight affects the physiological activity of both phytochrome forms, and both the phi sub 730 dependent reactions of lettuce seeds were suppressed.

  1. Phytochrome B Negatively Affects Cold Tolerance by Regulating OsDREB1 Gene Expression through Phytochrome Interacting Factor-Like Protein OsPIL16 in Rice

    PubMed Central

    He, Yanan; Li, Yaping; Cui, Lixin; Xie, Lixia; Zheng, Chongke; Zhou, Guanhua; Zhou, Jinjun; Xie, Xianzhi

    2016-01-01

    Cross talk between light signaling and cold signaling has been elucidated in the model plant Arabidopsis and tomato, but little is known about their relationship in rice. Here, we report that phytochrome B (phyB) mutants exhibit improved cold tolerance compared with wild type (WT) rice (Oryza sativa L. cv. Nipponbare). The phyB mutants had a lower electrolyte leakage index and malondialdehyde concentration than the WT, suggesting that they had greater cell membrane integrity and less lipid peroxidation. Real-time PCR analysis revealed that the expression levels of dehydration-responsive element binding protein 1 (OsDREB1) family genes, which functions in the cold stress response in rice, were increased in the phyB mutant under normal and cold stress conditions. PIFs are central players in phytochrome-mediated light signaling networks. To explore the relationship between rice PIFs and OsDREB1 gene expression, we produced overexpression lines of rice PIF genes. OsDREB1 family genes were up-regulated in OsPIL16-overexpression lines, which had improved cold tolerance relative to the WT. Chromatin immunoprecipitation (ChIP)-qPCR assay revealed that OsPIL16 can bind to the N-box region of OsDREB1B promoter. Expression pattern analyses revealed that OsPIL16 transcripts were induced by cold stress and was significantly higher in the phyB mutant than in the WT. Moreover, yeast two-hybrid assay showed that OsPIL16 can bind to rice PHYB. Based on these results, we propose that phyB deficiency positively regulates OsDREB1 expression through OsPIL16 to enhance cell membrane integrity and to reduce the malondialdehyde concentration, resulting in the improved cold tolerance of the phyB mutants. PMID:28083003

  2. SUMOylation of phytochrome-B negatively regulates light-induced signaling in Arabidopsis thaliana

    PubMed Central

    Sadanandom, Ari; Ádám, Éva; Orosa, Beatriz; Viczián, András; Klose, Cornelia; Zhang, Cunjin; Josse, Eve-Marie; Kozma-Bognár, László; Nagy, Ferenc

    2015-01-01

    The red/far red light absorbing photoreceptor phytochrome-B (phyB) cycles between the biologically inactive (Pr, λmax, 660 nm) and active (Pfr; λmax, 730 nm) forms and functions as a light quality and quantity controlled switch to regulate photomorphogenesis in Arabidopsis. At the molecular level, phyB interacts in a conformation-dependent fashion with a battery of downstream regulatory proteins, including PHYTOCHROME INTERACTING FACTOR transcription factors, and by modulating their activity/abundance, it alters expression patterns of genes underlying photomorphogenesis. Here we report that the small ubiquitin-like modifier (SUMO) is conjugated (SUMOylation) to the C terminus of phyB; the accumulation of SUMOylated phyB is enhanced by red light and displays a diurnal pattern in plants grown under light/dark cycles. Our data demonstrate that (i) transgenic plants expressing the mutant phyBLys996Arg-YFP photoreceptor are hypersensitive to red light, (ii) light-induced SUMOylation of the mutant phyB is drastically decreased compared with phyB-YFP, and (iii) SUMOylation of phyB inhibits binding of PHYTOCHROME INTERACTING FACTOR 5 to phyB Pfr. In addition, we show that OVERLY TOLERANT TO SALT 1 (OTS1) de-SUMOylates phyB in vitro, it interacts with phyB in vivo, and the ots1/ots2 mutant is hyposensitive to red light. Taken together, we conclude that SUMOylation of phyB negatively regulates light signaling and it is mediated, at least partly, by the action of OTS SUMO proteases. PMID:26283376

  3. Modulation of phytochrome signaling networks for improved biomass accumulation using a bioenergy crop model

    SciTech Connect

    Mockler, Todd C.

    2016-11-07

    Plant growth and development, including stem elongation, flowering time, and shade-avoidance habits, are affected by wavelength composition (i.e., light quality) of the light environment. the molecular mechanisms underlying light perception and signaling pathways in plants have been best characterized in Arabidopsis thaliana where dozens of genes have been implicated in converging, complementary, and antagonistic pathways communicating light quality cues perceived by the phytochrome (red/far-red) cryptochrome (blue) and phototropin (blue) photorecptors. Light perception and signaling have been studied in grasses, including rice and sorghum but in much less detail than in Arabidopsis. During the course of the Mocker lab's DOE-funded wrok generating a gene expression atlas in Brachypodium distachyon we observed that Brachypodium plants grown in continuous monochromatic red light or continuous white light enriched in far-red light accumulated significantly more biomass and exhibited significantly greater seed yield than plants grown in monochromatic blue light or white light. This phenomenon was also observed in two other grasses, switchgrass and rice. We will systematically manipulate the expression of genes predicted to function in Brachypodium phytochrome signaling and assess the phenotypic consequences in transgenic Brachypodium plants in terms of morphology, stature, biomass accumulation, and cell wall composition. We will also interrogate direct interactions between candidate phytochrome signaling transcription factors and target promoters using a high-throughput yeast one-hybrid system. Brachypodium distachyon has emerged as a model grass species and is closely related to candidate feedstock crops for bioethanol production. Identification of genes capable of modifying growth characteristics of Brachypodium, when misexpressed, in particular increasing biomass accumulation, by modulating photoreceptor signaling will provide valuable candidates for manipulation in

  4. Phytochromes A and B mediate red-light-induced positive phototropism in roots

    NASA Technical Reports Server (NTRS)

    Kiss, John Z.; Mullen, Jack L.; Correll, Melanie J.; Hangarter, Roger P.

    2003-01-01

    The interaction of tropisms is important in determining the final growth form of the plant body. In roots, gravitropism is the predominant tropistic response, but phototropism also plays a role in the oriented growth of roots in flowering plants. In blue or white light, roots exhibit negative phototropism that is mediated by the phototropin family of photoreceptors. In contrast, red light induces a positive phototropism in Arabidopsis roots. Because this red-light-induced response is weak relative to both gravitropism and negative phototropism, we used a novel device to study phototropism without the complications of a counteracting gravitational stimulus. This device is based on a computer-controlled system using real-time image analysis of root growth and a feedback-regulated rotatable stage. Our data show that this system is useful to study root phototropism in response to red light, because in wild-type roots, the maximal curvature detected with this apparatus is 30 degrees to 40 degrees, compared with 5 degrees to 10 degrees without the feedback system. In positive root phototropism, sensing of red light occurs in the root itself and is not dependent on shoot-derived signals resulting from light perception. Phytochrome (Phy)A and phyB were severely impaired in red-light-induced phototropism, whereas the phyD and phyE mutants were normal in this response. Thus, PHYA and PHYB play a key role in mediating red-light-dependent positive phototropism in roots. Although phytochrome has been shown to mediate phototropism in some lower plant groups, this is one of the few reports indicating a phytochrome-dependent phototropism in flowering plants.

  5. A Tightly Regulated Genetic Selection System with Signaling-Active Alleles of Phytochrome B.

    PubMed

    Hu, Wei; Lagarias, J Clark

    2017-01-01

    Selectable markers derived from plant genes circumvent the potential risk of antibiotic/herbicide-resistance gene transfer into neighboring plant species, endophytic bacteria, and mycorrhizal fungi. Toward this goal, we have engineered and validated signaling-active alleles of phytochrome B (eYHB) as plant-derived selection marker genes in the model plant Arabidopsis (Arabidopsis thaliana). By probing the relationship of construct size and induction conditions to optimal phenotypic selection, we show that eYHB-based alleles are robust substitutes for antibiotic/herbicide-dependent marker genes as well as surprisingly sensitive reporters of off-target transgene expression.

  6. A Tightly Regulated Genetic Selection System with Signaling-Active Alleles of Phytochrome B1[OPEN

    PubMed Central

    2017-01-01

    Selectable markers derived from plant genes circumvent the potential risk of antibiotic/herbicide-resistance gene transfer into neighboring plant species, endophytic bacteria, and mycorrhizal fungi. Toward this goal, we have engineered and validated signaling-active alleles of phytochrome B (eYHB) as plant-derived selection marker genes in the model plant Arabidopsis (Arabidopsis thaliana). By probing the relationship of construct size and induction conditions to optimal phenotypic selection, we show that eYHB-based alleles are robust substitutes for antibiotic/herbicide-dependent marker genes as well as surprisingly sensitive reporters of off-target transgene expression. PMID:27881727

  7. Rice phytochrome-interacting factor protein OsPIFff14 represses OsDREB1B gene expression through an extended N-box and interacts preferentially with the active form of phytochrome B

    Technology Transfer Automated Retrieval System (TEKTRAN)

    DREB1/CBF genes, known as major regulators of plant stress responses, are rapidly and transiently induced by low temperatures. Using a Yeast one Hybrid screening, we identified a putative Phytochrome-Interacting bHLH Factor (OsPIF14), as binding to the OsDREB1B promoter. bHLH proteins are able to bi...

  8. Phytochrome and Seed Germination. I. Temperature Dependence and Relative P(FR) Levels in the Germination of Dark-germinating Tomato Seeds.

    PubMed

    Mancinelli, A L; Yaniv, Z; Smith, P

    1967-03-01

    Germination of the dark-germinating seeds of 3 varieties of tomato is controlled by the phytochrome system. Germination is inhibited by far red radiation and repromoted by red applied after far red. At low temperatures, 17 to 20 degrees , a single, low energy far red irradiation is sufficient to inhibit germination in all 3 varieties. At higher temperatures far red is less effective in the inhibition of the germination of the tomato seeds. The phytochrome fraction present as P(FR) in the dark-germinating seeds of the Ace variety is about 40% of the total phytochrome present.

  9. The Basic Helix-Loop-Helix Transcription Factor PIF5 Acts on Ethylene Biosynthesis and Phytochrome Signaling by Distinct Mechanisms

    Technology Transfer Automated Retrieval System (TEKTRAN)

    HYTOCHROME-INTERACTING FACTOR5 (PIF5), a basic helix-loop-helix transcription factor, interacts specifically with the photoactivated form of phytochrome B (phyB). Here, we report that dark-grown Arabidopsis thaliana seedlings overexpressing PIF5 (PIF5-OX) exhibit exaggerated apical hooks and short h...

  10. The effects of phytochrome-mediated light signals on the developmental acquisition of photoperiod sensitivity in rice.

    PubMed

    Yoshitake, Yoshihiro; Yokoo, Takayuki; Saito, Hiroki; Tsukiyama, Takuji; Quan, Xu; Zikihara, Kazunori; Katsura, Hitomi; Tokutomi, Satoru; Aboshi, Takako; Mori, Naoki; Inoue, Hiromo; Nishida, Hidetaka; Kohchi, Takayuki; Teraishi, Masayoshi; Okumoto, Yutaka; Tanisaka, Takatoshi

    2015-01-09

    Plants commonly rely on photoperiodism to control flowering time. Rice development before floral initiation is divided into two successive phases: the basic vegetative growth phase (BVP, photoperiod-insensitive phase) and the photoperiod-sensitive phase (PSP). The mechanism responsible for the transition of rice plants into their photoperiod-sensitive state remains elusive. Here, we show that se13, a mutation detected in the extremely early flowering mutant X61 is a nonsense mutant gene of OsHY2, which encodes phytochromobilin (PΦB) synthase, as evidenced by spectrometric and photomorphogenic analyses. We demonstrated that some flowering time and circadian clock genes harbor different expression profiles in BVP as opposed to PSP, and that this phenomenon is chiefly caused by different phytochrome-mediated light signal requirements: in BVP, phytochrome-mediated light signals directly suppress Ehd2, while in PSP, phytochrome-mediated light signals activate Hd1 and Ghd7 expression through the circadian clock genes' expression. These findings indicate that light receptivity through the phytochromes is different between two distinct developmental phases corresponding to the BVP and PSP in the rice flowering process. Our results suggest that these differences might be involved in the acquisition of photoperiod sensitivity in rice.

  11. [Control of chlorophyll a synthesis by phytochrome and cryptochrome in the red alga Corallina elongata Ellis et Soland].

    PubMed

    López-Figueroa, F; Niell, F X

    1988-09-01

    Chlorophyll a synthesis in the red alga Corallina elongata is controlled by phytochrome and by a specific blue light photoreceptor. Although the estimated photoequilibrium of phytochrome is similar in blue and red light, the amount of chlorophyll accumulated is greater in blue light, which implies the action of cryptochrome, according to the criteria for the specific blue light photoreceptor involvement. The amount of chlorophyll synthesized is greater when the level of photoequilibrium approaches 65% (in blue and red light) than with higher levels (72.7% in white light and 70.8% in green light). The action of phytochrome is demonstrated by the induction of chlorophyll synthesis after red pulses and the reversion after far red pulses. The reversion is not complete but the percentage of reversibility is high (85-90%). The amount of chlorophyll accumulated is greater in darkness after the application of red light pulses than in white light after the same light pulses. The induction of chlorophyll synthesis is greater after red pulses than after continuous red light. The existence of a fast destruction of chlorophyll in continuous light is observed. This destruction is greater in the high photoequilibrium of phytochrome (70-72%). The turnover times and the induction mechanism of chlorophyll synthesis must be very fast. This indicates the existence of a possible rapid adaptation to the change in light quality and intensity in the marine system.

  12. The effects of phytochrome-mediated light signals on the developmental acquisition of photoperiod sensitivity in rice

    PubMed Central

    Yoshitake, Yoshihiro; Yokoo, Takayuki; Saito, Hiroki; Tsukiyama, Takuji; Quan, Xu; Zikihara, Kazunori; Katsura, Hitomi; Tokutomi, Satoru; Aboshi, Takako; Mori, Naoki; Inoue, Hiromo; Nishida, Hidetaka; Kohchi, Takayuki; Teraishi, Masayoshi; Okumoto, Yutaka; Tanisaka, Takatoshi

    2015-01-01

    Plants commonly rely on photoperiodism to control flowering time. Rice development before floral initiation is divided into two successive phases: the basic vegetative growth phase (BVP, photoperiod-insensitive phase) and the photoperiod-sensitive phase (PSP). The mechanism responsible for the transition of rice plants into their photoperiod-sensitive state remains elusive. Here, we show that se13, a mutation detected in the extremely early flowering mutant X61 is a nonsense mutant gene of OsHY2, which encodes phytochromobilin (PΦB) synthase, as evidenced by spectrometric and photomorphogenic analyses. We demonstrated that some flowering time and circadian clock genes harbor different expression profiles in BVP as opposed to PSP, and that this phenomenon is chiefly caused by different phytochrome-mediated light signal requirements: in BVP, phytochrome-mediated light signals directly suppress Ehd2, while in PSP, phytochrome-mediated light signals activate Hd1 and Ghd7 expression through the circadian clock genes' expression. These findings indicate that light receptivity through the phytochromes is different between two distinct developmental phases corresponding to the BVP and PSP in the rice flowering process. Our results suggest that these differences might be involved in the acquisition of photoperiod sensitivity in rice. PMID:25573482

  13. Phytochrome C plays a major role in the acceleration of wheat flowering under long-day photoperiod.

    PubMed

    Chen, Andrew; Li, Chengxia; Hu, Wei; Lau, Mei Yee; Lin, Huiqiong; Rockwell, Nathan C; Martin, Shelley S; Jernstedt, Judith A; Lagarias, J Clark; Dubcovsky, Jorge

    2014-07-15

    Phytochromes are dimeric proteins that function as red and far-red light sensors influencing nearly every phase of the plant life cycle. Of the three major phytochrome families found in flowering plants, phytochrome C (PHYC) is the least understood. In Arabidopsis and rice, PHYC is unstable and functionally inactive unless it heterodimerizes with another phytochrome. However, when expressed in an Arabidopsis phy-null mutant, wheat PHYC forms signaling active homodimers that translocate into the nucleus in red light to mediate photomorphogenic responses. Tetraploid wheat plants homozygous for loss-of-function mutations in all PHYC copies (phyC(AB)) flower on average 108 d later than wild-type plants under long days but only 19 d later under short days, indicating a strong interaction between PHYC and photoperiod. This interaction is further supported by the drastic down-regulation in the phyC(AB) mutant of the central photoperiod gene photoperiod 1 (PPD1) and its downstream target flowering locus T1, which are required for the promotion of flowering under long days. These results implicate light-dependent, PHYC-mediated activation of PPD1 expression in the acceleration of wheat flowering under inductive long days. Plants homozygous for the phyC(AB) mutations also show altered profiles of circadian clock and clock-output genes, which may also contribute to the observed differences in heading time. Our results highlight important differences in the photoperiod pathways of the temperate grasses with those of well-studied model plant species.

  14. Sequential and coordinated action of phytochromes A and B during Arabidopsis stem growth revealed by kinetic analysis

    NASA Technical Reports Server (NTRS)

    Parks, B. M.; Spalding, E. P.; Evans, M. L. (Principal Investigator)

    1999-01-01

    Photoreceptor proteins of the phytochrome family mediate light-induced inhibition of stem (hypocotyl) elongation during the development of photoautotrophy in seedlings. Analyses of overt mutant phenotypes have established the importance of phytochromes A and B (phyA and phyB) in this developmental process, but kinetic information that would augment emerging molecular models of phytochrome signal transduction is absent. We have addressed this deficiency by genetically dissecting phytochrome-response kinetics, after having solved the technical issues that previously limited growth studies of small Arabidopsis seedlings. We show here, with resolution on the order of minutes, that phyA initiated hypocotyl growth inhibition upon the onset of continuous red light. This primary contribution of phyA began to decrease after 3 hr of irradiation, the same time at which immunochemically detectable phyA disappeared and an exclusively phyB-dependent phase of inhibition began. The sequential and coordinated actions of phyA and phyB in red light were not observed in far-red light, which inhibited growth persistently through an exclusively phyA-mediated pathway.

  15. Holophytochrome-Interacting Proteins in Physcomitrella: Putative Actors in Phytochrome Cytoplasmic Signaling

    PubMed Central

    Ermert, Anna Lena; Mailliet, Katharina; Hughes, Jon

    2016-01-01

    Phytochromes are the principle photoreceptors in light-regulated plant development, primarily acting via translocation of the light-activated photoreceptor into the nucleus and subsequent gene regulation. However, several independent lines of evidence indicate unambiguously that an additional cytoplasmic signaling mechanism must exist. Directional responses in filament tip cells of the moss Physcomitrella patens are steered by phy4 which has been shown to interact physically with the blue light receptor phototropin at the plasma membrane. This complex might perceive and transduce vectorial information leading to cytoskeleton reorganization and finally a directional growth response. We developed yeast two-hybrid procedures using photochemically functional, full-length phy4 as bait in Physcomitrella cDNA library screens and growth assays under different light conditions, revealing Pfr-dependent interactions possibly associated with phytochrome cytoplasmic signaling. Candidate proteins were then expressed in planta with fluorescent protein tags to determine their intracellular localization in darkness and red light. Of 14 candidates, 12 were confirmed to interact with phy4 in planta using bimolecular fluorescence complementation. We also used database information to study their expression patterns relative to those of phy4. We discuss the likely functional characteristics of these holophytochrome-interacting proteins (HIP’s) and their possible roles in signaling. PMID:27242820

  16. Bell-like homeodomain selectively regulates the high-irradiance response of phytochrome A.

    PubMed

    Staneloni, Roberto J; Rodriguez-Batiller, María José; Legisa, Danilo; Scarpin, María R; Agalou, Adamantia; Cerdán, Pablo D; Meijer, Annemarie H; Ouwerkerk, Pieter B F; Casal, Jorge J

    2009-08-11

    Plant responses mediated by phytochrome A display a first phase saturated by transient light signals and a second phase requiring sustained excitation with far-red light (FR). These discrete outcomes, respectively so-called very-low-fluence response (VLFR) and high-irradiance response (HIR), are appropriate in different environmental and developmental contexts but the mechanisms that regulate the switch remain unexplored. Promoter analysis of a light-responsive target gene revealed a motif necessary for HIR but not for VLFR. This motif is required for binding of the Bell-like homeodomain 1 (BLH1) to the promoter in in vitro and in yeast 1-hybrid experiments. Promoter substitutions that increased BLH1 binding also enhanced HIR. blh1 mutants showed reduced responses to continuous FR and to deep canopy shadelight, but they retained normal responses to pulsed FR or red light and unfiltered sunlight. BLH1 enhanced BLH1 expression and its promotion by FR. We conclude that BLH1 specifically regulates HIR and not VLFR of phytochrome A.

  17. Phytochrome B and REVEILLE1/2-mediated signalling controls seed dormancy and germination in Arabidopsis

    PubMed Central

    Jiang, Zhimin; Xu, Gang; Jing, Yanjun; Tang, Weijiang; Lin, Rongcheng

    2016-01-01

    Seeds maintain a dormant state to withstand adverse conditions and germinate when conditions become favourable to give rise to a new generation of flowering plants. Seed dormancy and germination are tightly controlled by internal and external signals. Although phytochrome photoreceptors are proposed to regulate primary seed dormancy, the underlying molecular mechanism remains elusive. Here we show that the REVEILLE1 (RVE1) and RVE2 transcription factors promote primary seed dormancy and repress red/far-red-light-reversible germination downstream of phytochrome B (phyB) in Arabidopsis thaliana. RVE1 and RVE2 expression is downregulated after imbibition and by phyB. RVE1 directly binds to the promoter of GIBBERELLIN 3-OXIDASE 2, inhibits its transcription and thus suppresses the biosynthesis of bioactive gibberellins. In addition, DELAY OF GERMINATION 1 also acts downstream of phyB. This study identifies a signalling pathway that integrates environmental light input with internal factors to control both seed dormancy and germination. PMID:27506149

  18. Circadian Clock-Regulated Expression of Phytochrome and Cryptochrome Genes in Arabidopsis1

    PubMed Central

    Tóth, Réka; Kevei, Éva; Hall, Anthony; Millar, Andrew J.; Nagy, Ferenc; Kozma-Bognár, László

    2001-01-01

    Many physiological and biochemical processes in plants exhibit endogenous rhythms with a period of about 24 h. Endogenous oscillators called circadian clocks regulate these rhythms. The circadian clocks are synchronized to the periodic environmental changes (e.g. day/night cycles) by specific stimuli; among these, the most important is the light. Photoreceptors, phytochromes, and cryptochromes are involved in setting the clock by transducing the light signal to the central oscillator. In this work, we analyzed the spatial, temporal, and long-term light-regulated expression patterns of the Arabidopsis phytochrome (PHYA to PHYE) and cryptochrome (CRY1 and CRY2) promoters fused to the luciferase (LUC+) reporter gene. The results revealed new details of the tissue-specific expression and light regulation of the PHYC and CRY1 and 2 promoters. More importantly, the data obtained demonstrate that the activities of the promoter::LUC+ constructs, with the exception of PHYC::LUC+, display circadian oscillations under constant conditions. In addition, it is shown by measuring the mRNA abundance of PHY and CRY genes under constant light conditions that the circadian control is also maintained at the level of mRNA accumulation. These observations indicate that the plant circadian clock controls the expression of these photoreceptors, revealing the formation of a new regulatory loop that could modulate gating and resetting of the circadian clock. PMID:11743105

  19. Water content and the conversion of phytochrome regulation of lettuce dormancy

    NASA Technical Reports Server (NTRS)

    Vertucci, C. W.; Vertucci, F. A.; Leopold, A. C.

    1987-01-01

    In an effort to determine which biological reactions can occur in relation to the water content of seeds, the regulation of lettuce seed dormancy by red and far red light was determined at various hydration levels. Far red light had an inhibiting effect on germination for seeds at all moisture contents from 4 to 32% water. Germination was progressively stimulated by red light as seed hydration increased from 8 to 15%, and reached a maximum at moisture contents above 18%. Red light was ineffective at moisture contents below 8%. Seeds that had been stimulated by red light and subsequently dried lost the enhanced germinability if stored at moisture contents above 8%. The contrast between the presumed photoconversion of phytochrome far red-absorbing (Pfr) to (Pr) occurring at any moisture content and the reverse reaction occurring only if the seed moisture content is greater than 8% may be explained on the basis of the existence of unstable intermediates in the Pr to Pfr conversion. Our results suggest that the initial photoreaction involved in phytochrome conversion is relatively independent of water content, while the subsequent partial reactions become increasingly facilitated as water content increases from 8 to 18%.

  20. Phytochromes play a role in phototropism and gravitropism in Arabidopsis roots

    NASA Astrophysics Data System (ADS)

    Correll, Melanie J.; Coveney, Katrina M.; Raines, Steven V.; Mullen, Jack L.; Hangarter, Roger P.; Kiss, John Z.

    2003-05-01

    Phototropism as well as gravitropism plays a role in the oriented growth of roots in flowering plants. In blue or white light, roots exhibit negative phototropism, but red light induces positive phototropism in Arabidopsis roots. Phytochrome A (phyA) and phyB mediate the positive red-light-based photoresponse in roots since single mutants (and the double phyAB mutant) were severely impaired in this response. In blue-light-based negative phototropism, phyA and phyAB (but not phyB) were inhibited in the response relative to the WT. In root gravitropism, phyB and phyAB (but not phyA) were inhibited in the response compared to the WT. The differences observed in tropistic responses were not due to growth limitations since the growth rates among all the mutants tested were not significantly different from that of the WT. Thus, our study shows that the blue-light and red-light systems interact in roots and that phytochrome plays a key role in plant development by integrating multiple environmental stimuli.

  1. Phytochromes play a role in phototropism and gravitropism in Arabidopsis roots

    NASA Technical Reports Server (NTRS)

    Correll, Melanie J.; Coveney, Katrina M.; Raines, Steven V.; Mullen, Jack L.; Hangarter, Roger P.; Kiss, John Z.

    2003-01-01

    Phototropism as well as gravitropism plays a role in the oriented growth of roots in flowering plants. In blue or white light, roots exhibit negative phototropism, but red light induces positive phototropism in Arabidopsis roots. Phytochrome A (phyA) and phyB mediate the positive red-light-based photoresponse in roots since single mutants (and the double phyAB mutant) were severely impaired in this response. In blue-light-based negative phototropism, phyA and phyAB (but not phyB) were inhibited in the response relative to the WT. In root gravitropism, phyB and phyAB (but not phyA) were inhibited in the response compared to the WT. The differences observed in tropistic responses were not due to growth limitations since the growth rates among all the mutants tested were not significantly different from that of the WT. Thus, our study shows that the blue-light and red-light systems interact in roots and that phytochrome plays a key role in plant development by integrating multiple environmental stimuli. c2003 COSPAR. Published by Elsevier Ltd. All rights reserved.

  2. Bell-like homeodomain selectively regulates the high-irradiance response of phytochrome A

    PubMed Central

    Staneloni, Roberto J.; Rodriguez-Batiller, María José; Legisa, Danilo; Scarpin, María R.; Agalou, Adamantia; Cerdán, Pablo D.; Meijer, Annemarie H.; Ouwerkerk, Pieter B. F.; Casal, Jorge J.

    2009-01-01

    Plant responses mediated by phytochrome A display a first phase saturated by transient light signals and a second phase requiring sustained excitation with far-red light (FR). These discrete outcomes, respectively so-called very-low-fluence response (VLFR) and high-irradiance response (HIR), are appropriate in different environmental and developmental contexts but the mechanisms that regulate the switch remain unexplored. Promoter analysis of a light-responsive target gene revealed a motif necessary for HIR but not for VLFR. This motif is required for binding of the Bell-like homeodomain 1 (BLH1) to the promoter in in vitro and in yeast 1-hybrid experiments. Promoter substitutions that increased BLH1 binding also enhanced HIR. blh1 mutants showed reduced responses to continuous FR and to deep canopy shadelight, but they retained normal responses to pulsed FR or red light and unfiltered sunlight. BLH1 enhanced BLH1 expression and its promotion by FR. We conclude that BLH1 specifically regulates HIR and not VLFR of phytochrome A. PMID:19666535

  3. The altered gravitropic response of the lazy-2 mutant of tomato is phytochrome regulated.

    PubMed

    Gaiser, J C; Lomax, T L

    1993-06-01

    Shoots of the lazy-2 (lz-2) gravitropic mutant of tomato (Lycopersicon esculentum Mill.) have a normal gravitropic response when grown in the dark, but grow downward in response to gravity when grown in the light. Experiments were undertaken to investigate the nature of the light induction of the downward growth of lz-2 shoots. Red light was effective at causing downward growth of hypocotyls of lz-2 seedlings, whereas treatment with blue light did not alter the dark-grown (wild-type) gravity response. Downward growth of lz-2 seedlings is greatest 16 h after a 1-h red light irradiation, after which the seedlings begin to revert to the dark-grown phenotype. lz-2 seedlings irradiated with a far-red light pulse immediately after a red light pulse exhibited no downward growth. However, continuous red or far-red light both resulted in downward growth of lz-2 seedlings. Thus, the light induction of downward growth of lz-2 appears to involve the photoreceptor phytochrome. Fluence-response experiments indicate that the induction of downward growth of lz-2 by red light is a low-fluence phytochrome response, with a possible high-irradiance response component.

  4. PHYTOCHROME C Is an Essential Light Receptor for Photoperiodic Flowering in the Temperate Grass, Brachypodium distachyon

    PubMed Central

    Woods, Daniel P.; Ream, Thomas S.; Minevich, Gregory; Hobert, Oliver; Amasino, Richard M.

    2014-01-01

    We show that in the temperate grass, Brachypodium distachyon, PHYTOCHROME C (PHYC), is necessary for photoperiodic flowering. In loss-of-function phyC mutants, flowering is extremely delayed in inductive photoperiods. PHYC was identified as the causative locus by utilizing a mapping by sequencing pipeline (Cloudmap) optimized for identification of induced mutations in Brachypodium. In phyC mutants the expression of Brachypodium homologs of key flowering time genes in the photoperiod pathway such as GIGANTEA (GI), PHOTOPERIOD 1 (PPD1/PRR37), CONSTANS (CO), and florigen/FT are greatly attenuated. PHYC also controls the day-length dependence of leaf size as the effect of day length on leaf size is abolished in phyC mutants. The control of genes upstream of florigen production by PHYC was likely to have been a key feature of the evolution of a long-day flowering response in temperate pooid grasses. PMID:25023399

  5. Phytochrome regulates GTP-binding protein activity in the envelope of pea nuclei

    NASA Technical Reports Server (NTRS)

    Clark, G. B.; Memon, A. R.; Thompson, G. A. Jr; Roux, S. J.

    1993-01-01

    Three GTP-binding proteins with apparent molecular masses of 27, 28 and 30 kDa have been detected in isolated nuclei of etiolated pea plumules. After LDS-PAGE and transfer to nitrocellulose these proteins bind [32P]GTP in the presence of excess ATP, suggesting that they are monomeric G proteins. When nuclei are disrupted, three proteins co-purify with the nuclear envelope fraction and are highly enriched in this fraction. The level of [32P]GTP-binding for all three protein bands is significantly increased when harvested pea plumules are irradiated by red light, and this effect is reversed by far-red light. The results indicate that GTP-binding activity associated with the nuclear envelope of plant cells is photoreversibly regulated by the pigment phytochrome.

  6. Ultrafast E to Z photoisomerization dynamics of the Cph1 phytochrome

    NASA Astrophysics Data System (ADS)

    Kim, Peter W.; Pan, Jie; Rockwell, Nathan C.; Chang, Che-Wei; Taylor, Keenan C.; Clark Lagarias, J.; Larsen, Delmar S.

    2012-10-01

    Femtosecond photodynamics of the reverse (15EPfr → 15ZPr) reaction of the red/far-red phytochrome Cph1 from Synechocystis were resolved with visible broadband transient absorption spectroscopy. Multi-phasic dynamics were resolved and separated via global target analysis into a fast-decaying (260 fs) excited-state population that bifurcates to generate the isomerized Lumi-F primary photoproduct and a non-isomerizing vibrationally excited ground state that relaxes back into the 15EPfr ground state on a 2.8-ps time scale. Relaxation on a 1-ms timescale results in the loss of red absorbing region, but not blue region, of Lumi-F, which indicates that formation of 15ZPr occurs on slower timescales.

  7. Function of phytochrome A in potato plants as revealed through the study of transgenic plants.

    PubMed Central

    Heyer, A G; Mozley, D; Landschütze, V; Thomas, B; Gatz, C

    1995-01-01

    We have generated transgenic potato plants (Solanum tuberosum) containing the potato phytochrome protein encoded by the PHYA gene cDNA (phyA) in sense or antisense orientation under the control of the 35S cauliflower mosaic virus promoter. Plants with increased and decreased phyA levels were analyzed. When grown under white light, development and growth of sprouts and plants were barely distinguishable from wild type. Under continuous far-red light, stem extension, leaf expansion, and hook opening of sprouts were accelerated in phyA overexpressors and delayed in antisense plants. Sprouts with reduced phyA levels were less sensitive to red light with regard to stem extension and expression of the small subunit genes for ribulose bisphosphate carboxylase. Under low red light:far-red light ratios, increased phyA levels reduced the stem extension component of the shade-avoidance response, whereas decreased levels led to an increase in the response. PMID:7480332

  8. The PHYTOCHROME C photoreceptor gene mediates natural variation in flowering and growth responses of Arabidopsis thaliana

    PubMed Central

    Balasubramanian, Sureshkumar; Sureshkumar, Sridevi; Agrawal, Mitesh; Michael, Todd P.; Wessinger, Carrie; Maloof, Julin N.; Clark, Richard; Warthmann, Norman; Chory, Joanne; Weigel, Detlef

    2006-01-01

    Light plays an important role in modulating seedling growth and flowering time1. We show that allelic variation at the PHYTOCHROME C (PHYC) photoreceptor locus affects both traits in natural populations of A. thaliana. Two functionally distinct PHYC haplotype groups are distributed in a FRIGIDA-dependent latitudinal cline that is stronger than the one reported for FLOWERING LOCUS C, which together with FRIGIDA explains a large portion of the variation in A. thaliana flowering time2. In a genome-wide scan for association of 65 loci with latitude, there was an excess of significant p-values, indicative of population structure. Nevertheless, PHYC was the most strongly associated locus across 163 strains, suggesting that PHYC alleles are under diversifying selection in A. thaliana. Our work, together with previous findings3–6, suggests that photoreceptor genes are major agents of natural variation in plant flowering and growth response. PMID:16732287

  9. PHYTOCHROME C is an essential light receptor for photoperiodic flowering in the temperate grass, Brachypodium distachyon.

    PubMed

    Woods, Daniel P; Ream, Thomas S; Minevich, Gregory; Hobert, Oliver; Amasino, Richard M

    2014-09-01

    We show that in the temperate grass, Brachypodium distachyon, PHYTOCHROME C (PHYC), is necessary for photoperiodic flowering. In loss-of-function phyC mutants, flowering is extremely delayed in inductive photoperiods. PHYC was identified as the causative locus by utilizing a mapping by sequencing pipeline (Cloudmap) optimized for identification of induced mutations in Brachypodium. In phyC mutants the expression of Brachypodium homologs of key flowering time genes in the photoperiod pathway such as GIGANTEA (GI), PHOTOPERIOD 1 (PPD1/PRR37), CONSTANS (CO), and florigen/FT are greatly attenuated. PHYC also controls the day-length dependence of leaf size as the effect of day length on leaf size is abolished in phyC mutants. The control of genes upstream of florigen production by PHYC was likely to have been a key feature of the evolution of a long-day flowering response in temperate pooid grasses.

  10. Rice Phytochrome B (OsPhyB) Negatively Regulates Dark- and Starvation-Induced Leaf Senescence

    PubMed Central

    Piao, Weilan; Kim, Eun-Young; Han, Su-Hyun; Sakuraba, Yasuhito; Paek, Nam-Chon

    2015-01-01

    Light regulates leaf senescence and light deprivation causes large-scale transcriptional reprogramming to dismantle cellular components and remobilize nutrients to sink organs, such as seeds and storage tissue. We recently reported that in Arabidopsis (Arabidopsis thaliana), Phytochrome-Interacting Factor4 (PIF4) and PIF5 promote dark-induced senescence and natural senescence by directly activating the expression of typical senescence-associated genes (SAGs), including ORESARA1 (ORE1) and ETHYLENE INSENSITIVE3 (EIN3). In contrast, phytochrome B (PhyB) inhibits leaf senescence by repressing PIF4 and PIF5 at the post-translational level. Although we found how red light signaling represses leaf senescence in Arabidopsis, it remains unknown whether PhyB and/or PhyA are involved in leaf senescence in rice (Oryza sativa). Here we show that rice phyB knockout mutants (osphyB-1, -2, and -3) exhibited an early senescence phenotype during dark-induced senescence, but an osphyA knockout mutant (osphyA-3) senesced normally. The RT-qPCR analysis revealed that several senescence-associated genes, including OsORE1 and OsEIN3, were significantly up-regulated in osphyB-2 mutants, indicating that OsPhyB also inhibits leaf senescence, like Arabidopsis PhyB. We also found that leaf segments of osphyB-2 senesced faster even under light conditions. Supplementation with nitrogen compounds, such as KNO3 and NH4NO3, rescued the early senescence phenotype of osphyB-2, indicating that starvation is one of the major signaling factors in the OsPhyB-dependent leaf senescence pathway. PMID:27135344

  11. cis-acting elements involved in photoregulation of an oat phytochrome promoter in rice.

    PubMed Central

    Bruce, W B; Quail, P H

    1990-01-01

    Phytochrome negatively regulates the transcription of its own phyA genes. High levels of Pfr, the active, far-red-light absorbing form of phytochrome, repress phyA transcription; low Pfr levels result in derepression. We have utilized microprojectile-mediated gene transfer to identify regions of an oat phyA3 gene involved in this autoregulation. Chimeric constructs containing various deletion and sequence substitution mutants of the oat phyA3 gene fused to a chloramphenicol acetyltransferase reporter (phyA3/CAT) have been introduced into etiolated rice seedlings by particle bombardment. Low Pfr concentrations induce high phyA3/CAT expression, whereas high Pfr represses activity to near basal levels. Removal of phyA3 sequences 3' to the transcription start site reduces expression about fivefold, suggesting that intron 1 of the phyA3 gene may be required for high activity. The degree of high-Pfr-imposed repression is unaffected by any of a series of deletions or sequence substitutions in the phyA3 promoter, thus providing no evidence of any Pfr-activated negative elements. In contrast, 5' and internal deletions identify a minimum of three major positive promoter elements, designated PE1 [-381 base pairs (bp) to -348 bp], PE2 (-635 bp to -489 bp), and PE3 (-110 bp to -76 bp) that are necessary for high-level expression in low-Pfr cells. The data indicate that PE1 and PE2 are functionally redundant, but that PE3 is required in conjunction with either PE1 or PE2 for activity. PE3 contains a sequence element that is highly conserved between monocot phyA promoters, indicative of a critical role in phyA expression. PMID:2152109

  12. High-level expression and phosphorylation of phytochrome B modulates flowering time in Arabidopsis.

    PubMed

    Hajdu, Anita; Ádám, Éva; Sheerin, David J; Dobos, Orsolya; Bernula, Péter; Hiltbrunner, Andreas; Kozma-Bognár, László; Nagy, Ferenc

    2015-09-01

    Optimal timing of flowering in higher plants is crucial for successful reproduction and is coordinated by external and internal factors, including light and the circadian clock. In Arabidopsis, light-dependent stabilization of the rhythmically expressed CONSTANS (CO) is required for the activation of FLOWERING LOCUS T (FT), resulting in the initiation of flowering. Phytochrome A and cryptochrome photoreceptors stabilize CO in the evening by attenuating the activity of the CONSTITUTIVE PHOTOMORPHOGENIC 1-SUPPRESSOR OF PHYA-105 1 (COP1-SPA1) ubiquitin ligase complex, which promotes turnover of CO. In contrast, phytochrome B (phyB) facilitates degradation of CO in the morning and delays flowering. Accordingly, flowering is accelerated in phyB mutants. Paradoxically, plants overexpressing phyB also show early flowering, which may arise from an early phase of rhythmic CO expression. Here we demonstrate that overexpression of phyB induces FT transcription at dusk and in the night without affecting the phase or level of CO transcription. This response depends on the light-activated Pfr form of phyB that inhibits the function of the COP1-SPA1 complex by direct interactions. Our data suggest that attenuation of COP1 activity results in the accumulation of CO protein and subsequent induction of FT. We show that phosphorylation of Ser-86 inhibits this function of phyB by accelerating dark reversion and thus depletion of Pfr forms in the night. Our results explain the early flowering phenotype of phyB overexpression and reveal additional features of the molecular machinery by which photoreceptors mediate photoperiodism.

  13. Structural communication between the chromophore binding pocket and the N-terminal extension in plant phytochrome phyB.

    PubMed

    Velázquez Escobar, Francisco; Buhrke, David; Fernandez Lopez, Maria; Shenkutie, Sintayehu Manaye; von Horsten, Silke; Essen, Lars-Oliver; Hughes, Jon; Hildebrandt, Peter

    2017-04-04

    The N-terminal extension (NTE) of plant phytochromes has been suggested to play a functional role in signaling photoinduced structural changes. Here, we use resonance Raman spectroscopy to study the effect of the NTE on the chromophore structure of B-type phytochromes from two evolutionarily distant plants. NTE deletion seems to have no effect on the chromophore in the inactive Pr state, but alters the torsion of the C-D ring methine bridge and the surrounding hydrogen bonding network in the physiologically active Pfr state. These changes are accompanied by a shift of the conformational equilibrium between two Pfr sub-states, which might affect the thermal isomerization rate of the C-D double bond and, thus, account for the effect of the NTE on the dark reversion kinetics. This article is protected by copyright. All rights reserved.

  14. A Temporarily Red Light-Insensitive Mutant of Tomato Lacks a Light-Stable, B-Like Phytochrome.

    PubMed Central

    Van Tuinen, A.; Kerckhoffs, LHJ.; Nagatani, A.; Kendrick, R. E.; Koornneef, M.

    1995-01-01

    We have selected four recessive mutants in tomato (Lycopersicon esculentum Mill.) that, under continuous red light (R), have long hypocotyls and small cotyledons compared to wild type (WT), a phenotype typical of phytochrome B (phyB) mutants of other species. These mutants, which are allelic, are only insensitive to R during the first 2 days upon transition from darkness to R, and therefore we propose the gene symbol tri (temporarily red light insensitive). White light-grown mutant plants have a more elongated growth habit than that of the WT. An immunochemically and spectrophotometrically detectable phyB-like polypeptide detectable in the WT is absent or below detection limits in the tri1 mutant. In contrast to the absence of an elongation growth response to far-red light (FR) given at the end of the daily photoperiod (EODFR) in all phyB-deficient mutants so far characterized, the tri1 mutant responds to EODFR treatment. The tri1 mutant also shows a strong response to supplementary daytime far-red light. We propose that the phyB-like phytochrome deficient in the tri mutants plays a major role during de-etiolation and that other light-stable phytochromes can regulate the EODFR and shade-avoidance responses in tomato. PMID:12228517

  15. Phytochrome induces changes in the immunodetectable level of a wall peroxidase that precede growth changes in maize seedlings

    NASA Technical Reports Server (NTRS)

    Kim, S. H.; Shinkle, J. R.; Roux, S. J.

    1989-01-01

    The regulatory pigment phytochrome induces rapid and opposite growth changes in different regions of etiolated maize seedlings: it stimulates the elongation rate of coleoptiles and inhibits that of mesocotyls. As measured by a quantitative immunoassay, phytochrome also promotes rapid and opposite changes in the extractable content of a Mr 98,000 anionic isoperoxidase in the cell walls of these same organs: it induces a decrease of this peroxidase in coleoptiles and an increase in mesocotyls. The peroxidase changes precede the growth changes. As measured by video stereomicroscopy or a position transducer, red light (R), which photoactivates phytochrome, stimulates coleoptile elongation with a lag of about 15-20 min and suppresses mesocotyl growth with a lag of 45-50 min. R also induces a 50% reduction in the extractable level of the anionic peroxidase in coleoptile walls in less than 10 min and a 40% increase in the level of this peroxidase in mesocotyl walls within 30 min. Ascorbic acid, an inhibitor of peroxidase activity, blocks the effects of R on mesocotyl section growth. These results are relevant to hypotheses that postulate that certain wall peroxidases can participate in light-induced changes in growth rate by their effects on wall extensibility.

  16. Diatom Phytochromes Reveal the Existence of Far-Red-Light-Based Sensing in the Ocean[OPEN

    PubMed Central

    Enomoto, Gen; Bouly, Jean-Pierre; Thaler, Michael; Malviya, Shruti; Bernardes, Juliana Silva; Rappaport, Fabrice; Gentili, Bernard; Huysman, Marie J.J.; Carbone, Alessandra; Bowler, Chris; Ikeuchi, Masahiko; Falciatore, Angela

    2016-01-01

    The absorption of visible light in aquatic environments has led to the common assumption that aquatic organisms sense and adapt to penetrative blue/green light wavelengths but show little or no response to the more attenuated red/far-red wavelengths. Here, we show that two marine diatom species, Phaeodactylum tricornutum and Thalassiosira pseudonana, possess a bona fide red/far-red light sensing phytochrome (DPH) that uses biliverdin as a chromophore and displays accentuated red-shifted absorbance peaks compared with other characterized plant and algal phytochromes. Exposure to both red and far-red light causes changes in gene expression in P. tricornutum, and the responses to far-red light disappear in DPH knockout cells, demonstrating that P. tricornutum DPH mediates far-red light signaling. The identification of DPH genes in diverse diatom species widely distributed along the water column further emphasizes the ecological significance of far-red light sensing, raising questions about the sources of far-red light. Our analyses indicate that, although far-red wavelengths from sunlight are only detectable at the ocean surface, chlorophyll fluorescence and Raman scattering can generate red/far-red photons in deeper layers. This study opens up novel perspectives on phytochrome-mediated far-red light signaling in the ocean and on the light sensing and adaptive capabilities of marine phototrophs. PMID:26941092

  17. A Temporarily Red Light-Insensitive Mutant of Tomato Lacks a Light-Stable, B-Like Phytochrome.

    PubMed

    Van Tuinen, A.; Kerckhoffs, LHJ.; Nagatani, A.; Kendrick, R. E.; Koornneef, M.

    1995-07-01

    We have selected four recessive mutants in tomato (Lycopersicon esculentum Mill.) that, under continuous red light (R), have long hypocotyls and small cotyledons compared to wild type (WT), a phenotype typical of phytochrome B (phyB) mutants of other species. These mutants, which are allelic, are only insensitive to R during the first 2 days upon transition from darkness to R, and therefore we propose the gene symbol tri (temporarily red light insensitive). White light-grown mutant plants have a more elongated growth habit than that of the WT. An immunochemically and spectrophotometrically detectable phyB-like polypeptide detectable in the WT is absent or below detection limits in the tri1 mutant. In contrast to the absence of an elongation growth response to far-red light (FR) given at the end of the daily photoperiod (EODFR) in all phyB-deficient mutants so far characterized, the tri1 mutant responds to EODFR treatment. The tri1 mutant also shows a strong response to supplementary daytime far-red light. We propose that the phyB-like phytochrome deficient in the tri mutants plays a major role during de-etiolation and that other light-stable phytochromes can regulate the EODFR and shade-avoidance responses in tomato.

  18. Dynamic Antagonism between Phytochromes and PIF Family Basic Helix-Loop-Helix Factors Induces Selective Reciprocal Responses to Light and Shade in a Rapidly Responsive Transcriptional Network in Arabidopsis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Plants respond to shade-modulated light signals via phytochrome (phy)-induced adaptive changes, termed shade avoidance. To examine the roles of Phytochrome-Interacting basic helix-loop-helix Factors, PIF1, 3, 4, and 5, in relaying such signals to the transcriptional network, we compared the shade-re...

  19. Blue light is required for survival of the tomato phytochrome-deficient aurea mutant and the expression of four nuclear genes coding for plastidic proteins.

    PubMed

    Oelmüller, R; Kendrick, R E

    1991-02-01

    When dark-grown aurea mutant tomato seedlings which lack more than 95% of the phytochrome present in isogenic wild-type seedlings are kept in white or blue light, four nuclear-encoded transcripts coding for plastidic proteins (the light-harvesting chlorophyll a/b-binding protein of photosystem I and II [cab-PSII], plastocyanin and subunit 2 of photosystem I) are present in comparable amounts. These transcript levels in red light are strongly reduced in aurea seedlings when compared with those of wild type. Thus, blue light is required for normal expression of these genes in the mutant, while red light alone is not sufficient. Red light-grown aurea seedlings are very sensitive to blue light, even 10 minutes of blue light every day suffices to cause a measurable increase in cab-PSII transcript level. The action of blue light on the expression of cab-PSII in the mutant is under phytochrome control. After 8 days of blue light, phytochrome is almost as effective in inducing cab-PSII mRNA as in the isogenic wild type, whereas after 8 days of red light, only a small phytochrome response was observed in the mutant. It is concluded that blue light sensitizes the mutant to the residual phytochrome which allows normal gene expression and survival of the mutant under daylight conditions.

  20. NMR chemical shift pattern changed by ammonium sulfate precipitation in cyanobacterial phytochrome Cph1

    PubMed Central

    Song, Chen; Lang, Christina; Kopycki, Jakub; Hughes, Jon; Matysik, Jörg

    2015-01-01

    Phytochromes are dimeric biliprotein photoreceptors exhibiting characteristic red/far-red photocycles. Full-length cyanobacterial phytochrome Cph1 from Synechocystis 6803 is soluble initially but tends to aggregate in a concentration-dependent manner, hampering attempts to solve the structure using NMR and crystallization methods. Otherwise, the Cph1 sensory module (Cph1Δ2), photochemically indistinguishable from the native protein and used extensively in structural and other studies, can be purified to homogeneity in >10 mg amounts at mM concentrations quite easily. Bulk precipitation of full-length Cph1 by ammonium sulfate (AmS) was expected to allow us to produce samples for solid-state magic-angle spinning (MAS) NMR from dilute solutions before significant aggregation began. It was not clear, however, what effects the process of partial dehydration might have on the molecular structure. Here we test this by running solid-state MAS NMR experiments on AmS-precipitated Cph1Δ2 in its red-absorbing Pr state carrying uniformly 13C/15N-labeled phycocyanobilin (PCB) chromophore. 2D 13C–13C correlation experiments allowed a complete assignment of 13C responses of the chromophore. Upon precipitation, 13C chemical shifts for most of PCB carbons move upfield, in which we found major changes for C4 and C6 atoms associated with the A-ring positioning. Further, the broad spectral lines seen in the AmS 13C spectrum reflect primarily the extensive inhomogeneous broadening presumably due to an increase in the distribution of conformational states in the protein, in which less free water is available to partake in the hydration shells. Our data suggest that the effect of dehydration process indeed leads to changes of electronic structure of the bilin chromophore and a decrease in its mobility within the binding pocket, but not restricted to the protein surface. The extent of the changes induced differs from the freezing process of the solution samples routinely used in

  1. Phytochrome RNAi enhances major fibre quality and agronomic traits of the cotton Gossypium hirsutum L.

    PubMed

    Abdurakhmonov, Ibrokhim Y; Buriev, Zabardast T; Saha, Sukumar; Jenkins, Johnie N; Abdukarimov, Abdusattor; Pepper, Alan E

    2014-01-01

    Simultaneous improvement of fibre quality, early-flowering, early-maturity and productivity in Upland cotton (G. hirsutum) is a challenging task for conventional breeding. The influence of red/far-red light ratio on the fibre length prompted us to examine the phenotypic effects of RNA interference (RNAi) of the cotton PHYA1 gene. Here we show a suppression of up to ~70% for the PHYA1 transcript, and compensatory overexpression of up to ~20-fold in the remaining phytochromes in somatically regenerated PHYA1 RNAi cotton plants. Two independent transformants of three generations exhibited vigorous root and vegetative growth, early-flowering, significantly improved upper half mean fibre length and an improvement in other major fibre characteristics. Small decreases in lint traits were observed but seed cotton yield was increased an average 10-17% compared with controls. RNAi-associated phenotypes were heritable and transferable via sexual hybridization. These results should aid in the development of early-maturing and productive Upland cultivars with superior fibre quality.

  2. Phytochrome B control of total leaf area and stomatal density affects drought tolerance in rice.

    PubMed

    Liu, Jing; Zhang, Fang; Zhou, Jinjun; Chen, Fan; Wang, Baoshan; Xie, Xianzhi

    2012-02-01

    We report that phytochrome B (phyB) mutants exhibit improved drought tolerance compared to wild type (WT) rice (Oryza sativa L. cv. Nipponbare). To understand the underlying mechanism by which phyB regulates drought tolerance, we analyzed root growth and water loss from the leaves of phyB mutants. The root system showed no significant difference between the phyB mutants and WT, suggesting that improved drought tolerance has little relation to root growth. However, phyB mutants exhibited reduced total leaf area per plant, which was probably due to a reduction in the total number of cells per leaf caused by enhanced expression of Orysa;KRP1 and Orysa;KRP4 (encoding inhibitors of cyclin-dependent kinase complex activity) in the phyB mutants. In addition, the developed leaves of phyB mutants displayed larger epidermal cells than WT leaves, resulting in reduced stomatal density. phyB deficiency promoted the expression of both putative ERECTA family genes and EXPANSIN family genes involved in cell expansion in leaves, thus causing greater epidermal cell expansion in the phyB mutants. Reduced stomatal density resulted in reduced transpiration per unit leaf area in the phyB mutants. Considering all these findings, we propose that phyB deficiency causes both reduced total leaf area and reduced transpiration per unit leaf area, which explains the reduced water loss and improved drought tolerance of phyB mutants.

  3. Phytochrome B enhances photosynthesis at the expense of water-use efficiency in Arabidopsis.

    PubMed

    Boccalandro, Hernán E; Rugnone, Matías L; Moreno, Javier E; Ploschuk, Edmundo L; Serna, Laura; Yanovsky, Marcelo J; Casal, Jorge J

    2009-06-01

    In open places, plants are exposed to higher fluence rates of photosynthetically active radiation and to higher red to far-red ratios than under the shade of neighbor plants. High fluence rates are known to increase stomata density. Here we show that high, compared to low, red to far-red ratios also increase stomata density in Arabidopsis (Arabidopsis thaliana). High red to far-red ratios increase the proportion of phytochrome B (phyB) in its active form and the phyB mutant exhibited a constitutively low stomata density. phyB increased the stomata index (the ratio between stomata and epidermal cells number) and the level of anphistomy (by increasing stomata density more intensively in the adaxial than in the abaxial face). phyB promoted the expression of FAMA and TOO MANY MOUTHS genes involved in the regulation of stomata development in young leaves. Increased stomata density resulted in increased transpiration per unit leaf area. However, phyB promoted photosynthesis rates only at high fluence rates of photosynthetically active radiation. In accordance to these observations, phyB reduced long-term water-use efficiency estimated by the analysis of isotopic discrimination against (13)CO(2). We propose a model where active phyB promotes stomata differentiation in open places, allowing plants to take advantage of the higher irradiances at the expense of a reduction of water-use efficiency, which is compensated by a reduced leaf area.

  4. The Tissue-Specific Expression of a Tobacco Phytochrome B Gene.

    PubMed Central

    Adam, E.; Kozma-Bognar, L.; Kolar, C.; Schafer, E.; Nagy, F.

    1996-01-01

    We have isolated a genomic clone from Nicotiana tabacum, designated Nt-PHYB-1, encoding a type-II, "green tissue" phytochrome apoprotein. Recombinant genes, consisting of the 3319-bp promoter of the Nt-PHYB-1 gene (including the entire 5[prime] untranslated sequence but not the ATG) or its deletion derivatives and the bacterial [beta]-glucuronidase reporter gene, were constructed and transferred into tobacco. The expression patterns and levels of the endogenous Nt-PHYB-1, as well as those of the transgenes, were determined by RNase protection assays and by [beta]-glucuronidase histochemical staining. We show that (a) the PHYB-1 gene has three transcription start sites, (b) the abundance of the three PHYB-1-specific mRNAs is different, and that (c) it is not regulated by light. However, we do demonstrate that transcription of the endogenous PHYB-1 gene and that of the recombinant genes exhibit a well-defined organ and tissue specificity. This tobacco PHYB gene is relatively highly expressed in leaf, stem, and different floral organs but not in root. Deletion analysis of the Nt-PHYB-1 promoter indicates that a 382-bp region, located between -1472 and -1089, is required for high-level expression of this gene. PMID:12226242

  5. An optogenetic system based on bacterial phytochrome controllable with near-infrared light

    PubMed Central

    Kaberniuk, Andrii A.; Shemetov, Anton A.; Verkhusha, Vladislav V.

    2016-01-01

    Light-mediated control of protein-protein interactions to regulate metabolic pathways is an important approach of optogenetics. Here, we report the first optogenetic system based on a reversible light-induced binding between a bacterial phytochrome BphP1 and its natural partner PpsR2 from Rhodopseudomonas palustris bacteria. We extensively characterized the BphP1–PpsR2 interaction both in vitro and in mammalian cells, and then used it to translocate target proteins to specific cellular compartments, such as plasma membrane and nucleus. Applying this approach we achieved a light-control of cell morphology resulting in the substantial increase of cell area. We next demonstrated the light-induced gene expression with the 40-fold contrast in cultured cells, 32-fold subcutaneously and 5.7-fold in deep tissues in mice. The unique characteristics of the BphP1–PpsR2 optogenetic system are its sensitivity to 740–780 nm near-infrared light, ability to utilize an endogenous biliverdin chromophore in eukaryotes including mammals, and spectral compatibility with blue-light optogenetic systems. PMID:27159085

  6. Far-red light photoactivatable near-infrared fluorescent proteins engineered from a bacterial phytochrome

    PubMed Central

    Piatkevich, Kiryl D.; Subach, Fedor V.; Verkhusha, Vladislav V.

    2013-01-01

    Ability to modulate fluorescence of optical probes can be used to enhance signal-to-noise ratio for imaging within highly autofluorescent environments, such as intact tissues and living organisms. Here we report two phytochrome-based photoactivatable near-infrared fluorescent proteins, named PAiRFP1 and PAiRFP2. PAiRFPs utilize heme-derived biliverdin, ubiquitous in mammalian tissues, as the chromophore. Initially weakly fluorescent PAiRFPs undergo photoconversion into a highly fluorescent state with excitation/emission at 690 nm/717 nm following a brief irradiation with far-red light. After photoactivation, PAiRFPs slowly revert back to initial state, enabling multiple photoactivation-relaxation cycles. Low-temperature optical spectroscopy reveals several intermediates involved in PAiRFP photocycles, which all differ from that of the bacteriophytochrome precursor. PAiRFPs can be photoactivated in a spatially selective manner in mouse tissues, and optical modulation of their fluorescence allows for substantial contrast enhancement, making PAiRFPs advantageous over permanently fluorescent probes for in vivo imaging conditions of high autofluorescence and low signal levels. PMID:23842578

  7. Rice phytochrome-interacting factor protein OsPIF14 represses OsDREB1B gene expression through an extended N-box and interacts preferentially with the active form of Phytochrome B

    PubMed Central

    Cordeiro, André M.; Figueiredo, Duarte D.; Tepperman, James; Borba, Ana Rita; Lourenço, Tiago; Abreu, Isabel A.; Ouwerkerk, Pieter B.F.; Quail, Peter H.; Oliveira, M. Margarida; Saibo, Nelson J. M.

    2016-01-01

    DREB1/CBF genes, known as major regulators of plant stress responses, are rapidly and transiently induced by low temperatures. Using a Yeast one Hybrid screening, we identified a putative Phytochrome-Interacting bHLH Factor (OsPIF14), as binding to the OsDREB1B promoter. bHLH proteins are able to bind to hexameric E-box (CANNTG) or N-box (CACG(A/C)G) motifs, depending on transcriptional activity. We have shown that OsPIF14 binds to the OsDREB1B promoter through two N-boxes and that the flanking regions of the hexameric core are essential for protein-DNA interaction and stability. We also showed that OsPIF14 down-regulates OsDREB1B gene expression in rice protoplasts, corroborating the OsPIF14 repressor activity observed in the transactivation assays using Arabidopsis protoplasts. In addition, we showed that OsPIF14 is indeed a Phytochrome Interacting Factor, which preferentially binds to the active form (Pfr) of rice phytochrome B. This raises the possibility that OsPIF14 activity might be modulated by light. However, we did not observe any regulation of the OsDREB1B gene expression by light under control conditions. Moreover, OsPIF14 gene expression was shown to be modulated by different treatments, such as drought, salt, cold and ABA. Interestingly, OsPIF14 showed also a specific cold-induced alternative splicing. All together, these results suggest the possibility that OsPIF14 is involved in cross-talk between light and stress signaling through interaction with the OsDREB1B promoter. Although in the absence of stress, OsDREB1B gene expression was not regulated by light, given previous reports, it remains possible that OsPIF14 has a role in light modulation of stress responses. PMID:26732823

  8. Rice phytochrome-interacting factor protein OsPIF14 represses OsDREB1B gene expression through an extended N-box and interacts preferentially with the active form of phytochrome B

    DOE PAGES

    Cordeiro, André M.; Figueiredo, Duarte D.; Tepperman, James; ...

    2015-12-28

    DREB1/CBF genes, known as major regulators of plant stress responses, are rapidly and transiently induced by low temperatures. Using a yeast one-hybrid screening, we identified a putative Phytochrome-Interacting bHLH Factor (OsPIF14), as binding to the OsDREB1B promoter. bHLH proteins are able to bind to hexameric E-box (CANNTG) or N-box (CACG(A/C)G) motifs, depending on transcriptional activity. We have shown that OsPIF14 binds to the OsDREB1B promoter through two N-boxes and that the flanking regions of the hexameric core are essential for protein–DNA interaction and stability. We also showed that OsPIF14 down-regulates OsDREB1B gene expression in rice protoplasts, corroborating the OsPIF14 repressormore » activity observed in the transactivation assays using Arabidopsis protoplasts. Additionally, we showed that OsPIF14 is indeed a phytochrome interacting factor, which preferentially binds to the active form (Pfr) of rice phytochrome B. This raises the possibility that OsPIF14 activity might be modulated by light. However, we did not observe any regulation of the OsDREB1B gene expression by light under control conditions. Moreover, OsPIF14 gene expression was shown to be modulated by different treatments, such as drought, salt, cold and ABA. Interestingly, OsPIF14 showed also a specific cold-induced alternative splicing. Our results suggest the possibility that OsPIF14 is involved in cross-talk between light and stress signaling through interaction with the OsDREB1B promoter. Finally, although in the absence of stress, OsDREB1B gene expression was not regulated by light, given previous reports, it remains possible that OsPIF14 has a role in light modulation of stress responses.« less

  9. Rice phytochrome-interacting factor protein OsPIF14 represses OsDREB1B gene expression through an extended N-box and interacts preferentially with the active form of phytochrome B.

    PubMed

    Cordeiro, André M; Figueiredo, Duarte D; Tepperman, James; Borba, Ana Rita; Lourenço, Tiago; Abreu, Isabel A; Ouwerkerk, Pieter B F; Quail, Peter H; Margarida Oliveira, M; Saibo, Nelson J M

    2016-02-01

    DREB1/CBF genes, known as major regulators of plant stress responses, are rapidly and transiently induced by low temperatures. Using a yeast one-hybrid screening, we identified a putative Phytochrome-Interacting bHLH Factor (OsPIF14), as binding to the OsDREB1B promoter. bHLH proteins are able to bind to hexameric E-box (CANNTG) or N-box (CACG(A/C)G) motifs, depending on transcriptional activity. We have shown that OsPIF14 binds to the OsDREB1B promoter through two N-boxes and that the flanking regions of the hexameric core are essential for protein-DNA interaction and stability. We also showed that OsPIF14 down-regulates OsDREB1B gene expression in rice protoplasts, corroborating the OsPIF14 repressor activity observed in the transactivation assays using Arabidopsis protoplasts. In addition, we showed that OsPIF14 is indeed a phytochrome interacting factor, which preferentially binds to the active form (Pfr) of rice phytochrome B. This raises the possibility that OsPIF14 activity might be modulated by light. However, we did not observe any regulation of the OsDREB1B gene expression by light under control conditions. Moreover, OsPIF14 gene expression was shown to be modulated by different treatments, such as drought, salt, cold and ABA. Interestingly, OsPIF14 showed also a specific cold-induced alternative splicing. All together, these results suggest the possibility that OsPIF14 is involved in cross-talk between light and stress signaling through interaction with the OsDREB1B promoter. Although in the absence of stress, OsDREB1B gene expression was not regulated by light, given previous reports, it remains possible that OsPIF14 has a role in light modulation of stress responses.

  10. Rice phytochrome-interacting factor protein OsPIF14 represses OsDREB1B gene expression through an extended N-box and interacts preferentially with the active form of phytochrome B

    SciTech Connect

    Cordeiro, André M.; Figueiredo, Duarte D.; Tepperman, James; Borba, Ana Rita; Lourenço, Tiago; Abreu, Isabel A.; Ouwerkerk, Pieter B. F.; Quail, Peter H.; Margarida Oliveira, M.; Saibo, Nelson J. M.

    2015-12-28

    DREB1/CBF genes, known as major regulators of plant stress responses, are rapidly and transiently induced by low temperatures. Using a yeast one-hybrid screening, we identified a putative Phytochrome-Interacting bHLH Factor (OsPIF14), as binding to the OsDREB1B promoter. bHLH proteins are able to bind to hexameric E-box (CANNTG) or N-box (CACG(A/C)G) motifs, depending on transcriptional activity. We have shown that OsPIF14 binds to the OsDREB1B promoter through two N-boxes and that the flanking regions of the hexameric core are essential for protein–DNA interaction and stability. We also showed that OsPIF14 down-regulates OsDREB1B gene expression in rice protoplasts, corroborating the OsPIF14 repressor activity observed in the transactivation assays using Arabidopsis protoplasts. Additionally, we showed that OsPIF14 is indeed a phytochrome interacting factor, which preferentially binds to the active form (Pfr) of rice phytochrome B. This raises the possibility that OsPIF14 activity might be modulated by light. However, we did not observe any regulation of the OsDREB1B gene expression by light under control conditions. Moreover, OsPIF14 gene expression was shown to be modulated by different treatments, such as drought, salt, cold and ABA. Interestingly, OsPIF14 showed also a specific cold-induced alternative splicing. Our results suggest the possibility that OsPIF14 is involved in cross-talk between light and stress signaling through interaction with the OsDREB1B promoter. Finally, although in the absence of stress, OsDREB1B gene expression was not regulated by light, given previous reports, it remains possible that OsPIF14 has a role in light modulation of stress responses.

  11. Recombinant phytochrome of the moss Ceratodon purpureus (CP2): fluorescence spectroscopy and photochemistry.

    PubMed

    Sineshchekov, V; Koppel, L; Hughes, J; Lamparter, T; Zeidler, M

    2000-07-01

    The recombinant phytochrome of the moss Ceratodon purpureus (CP2) expressed in Saccharomyces cerevisiae and reconstituted with phycocyanobilin (PCB) was investigated using fluorescence spectroscopy. The pigment had an emission maximum at 670 nm at low temperature (85 K) and at 667 nm at room temperature (RT) and an excitation maximum at 650-652 nm at 85 K (excitation spectra could not be measured at RT). Both spectra had a half-band width of approx. 30-35 nm at 85 K. The fluorescence intensity revealed a steep temperature dependence with an activation energy of fluorescence decay (Ea) of 5.9-6.4 and 12.6-14.7 kJ mol(-1) in the interval from 85 to 210 K and from 210 to 275 K, respectively. The photochemical properties of CP2/PCB were characterised by the extent of the red-induced (lambda(a) = 639 nm) Pr conversion into the first photoproduct lumi-R at 85 K (gamma1) of approximately 0.07 and into Pfr at RT (gamma2) of approximately 0.7. From these characteristics, CP2/PCB can be attributed to the Pr" photochemical type with gamma1 < or = 0.05, which comprises the minor phyA fraction (phyA"), phyB, Adiantum phy1 and Synechocystis Cph1 in contrast to the major phyA' fraction (Pr' type with gamma1 = 0.5). Within the Pr" type, it is closer to phyA" than to phyB and Cph1.

  12. PF1: an A-T hook-containing DNA binding protein from rice that interacts with a functionally defined d(AT)-rich element in the oat phytochrome A3 gene promoter.

    PubMed Central

    Nieto-Sotelo, J; Ichida, A; Quail, P H

    1994-01-01

    Phytochrome-imposed down-regulation of the expression of its own phytochrome A gene (PHYA) is one of the fastest light-induced effects on transcription reported in plants to date. Functional analysis of the oat PHYA3 promoter in a transfection assay has revealed two positive elements, PE1 and PE3, that function synergistically to support high levels of transcription in the absence of light. We have isolated a rice cDNA clone (pR4) encoding a DNA binding protein that binds to the AT-rich PE1 element. We tested the selectivity of the pR4-encoded DNA binding activity using linker substitution mutations of PE1 that are known to disrupt positive expression supported by the PHYA3 promoter in vivo. Binding to these linker substitution mutants was one to two orders of magnitude less than to the native PE1 element. Because this is the behavior expected of positive factor 1 (PF1), the presumptive nuclear transcription factor that acts in trans at the PE1 element in vivo, the data support the conclusion that the protein encoded by pR4 is in fact rice PF1. The PF1 polypeptide encoded by pR4 is 213 amino acids long and contains four repeats of the A-T hook DNA binding motif found in high-mobility group I-Y (HMGI-Y) proteins. In addition, PF1 contains an 11-amino acid-long hydrophobic region characteristic of HMG I proteins, its N-terminal region shows strong similarities to a pea H1 histone sequence and a short peptide sequence from wheat HMGa, and it shows a high degree of similarity along its entire length to the HMG Y-like protein encoded by a soybean cDNA, SB16. In vitro footprinting and quantitative gel shift analyses showed that PF1 binds preferentially to the PE1 element but also at lower affinity to two other AT-rich regions upstream of PE1. This feature is consistent with the binding characteristics of HMG I-Y proteins that are known to bind to most runs of six or more AT base pairs. Taken together, the properties of PF1 suggest that it belongs to a newly described

  13. Characterization of XR-RV3 GafChromic{sup ®} films in standard laboratory and in clinical conditions and means to evaluate uncertainties and reduce errors

    SciTech Connect

    Farah, J. Clairand, I.; Huet, C.; Trianni, A.; Ciraj-Bjelac, O.; De Angelis, C.; Delle Canne, S.; Hadid, L.; Waryn, M. J.; Jarvinen, H.; Siiskonen, T.; Negri, A.; Novák, L.; Pinto, M.; Knežević, Ž.

    2015-07-15

    Purpose: To investigate the optimal use of XR-RV3 GafChromic{sup ®} films to assess patient skin dose in interventional radiology while addressing the means to reduce uncertainties in dose assessment. Methods: XR-Type R GafChromic films have been shown to represent the most efficient and suitable solution to determine patient skin dose in interventional procedures. As film dosimetry can be associated with high uncertainty, this paper presents the EURADOS WG 12 initiative to carry out a comprehensive study of film characteristics with a multisite approach. The considered sources of uncertainties include scanner, film, and fitting-related errors. The work focused on studying film behavior with clinical high-dose-rate pulsed beams (previously unavailable in the literature) together with reference standard laboratory beams. Results: First, the performance analysis of six different scanner models has shown that scan uniformity perpendicular to the lamp motion axis and that long term stability are the main sources of scanner-related uncertainties. These could induce errors of up to 7% on the film readings unless regularly checked and corrected. Typically, scan uniformity correction matrices and reading normalization to the scanner-specific and daily background reading should be done. In addition, the analysis on multiple film batches has shown that XR-RV3 films have generally good uniformity within one batch (<1.5%), require 24 h to stabilize after the irradiation and their response is roughly independent of dose rate (<5%). However, XR-RV3 films showed large variations (up to 15%) with radiation quality both in standard laboratory and in clinical conditions. As such, and prior to conducting patient skin dose measurements, it is mandatory to choose the appropriate calibration beam quality depending on the characteristics of the x-ray systems that will be used clinically. In addition, yellow side film irradiations should be preferentially used since they showed a lower

  14. Calibration of GafChromic EBT3 for absorbed dose measurements in 5 MeV proton beam and {sup 60}Co γ-rays

    SciTech Connect

    Vadrucci, M. Ronsivalle, C.; Marracino, F.; Montereali, R. M.; Picardi, L.; Piccinini, M.; Vincenti, M. A.; Esposito, G.; De Angelis, C.; Cherubini, R.; Pimpinella, M.

    2015-08-15

    Purpose: To study EBT3 GafChromic film in low-energy protons, and for comparison purposes, in a reference {sup 60}Co beam in order to use it as a calibrated dosimetry system in the proton irradiation facility under construction within the framework of the Oncological Therapy with Protons (TOP)-Intensity Modulated Proton Linear Accelerator for RadioTherapy (IMPLART) Project at ENEA-Frascati, Italy. Methods: EBT3 film samples were irradiated at the Istituto Nazionale di Fisica Nucleare—Laboratori Nazionali di Legnaro, Italy, with a 5 MeV proton beam generated by a 7 MV Van de Graaff CN accelerator. The nominal dose rates used were 2.1 Gy/min and 40 Gy/min. The delivered dose was determined by measuring the particle fluence and the energy spectrum in air with silicon surface barrier detector monitors. A preliminary study of the EBT3 film beam quality dependence in low-energy protons was conducted by passively degrading the beam energy. EBT3 films were also irradiated at ENEA-National Institute of Ionizing Radiation Metrology with gamma radiation produced by a {sup 60}Co source characterized by an absorbed dose to water rate of 0.26 Gy/min as measured by a calibrated Farmer type ionization chamber. EBT3 film calibration curves were determined by means of a set of 40 film pieces irradiated to various doses ranging from 0.5 Gy to 30 Gy absorbed dose to water. An EPSON Expression 11000XL color scanner in transmission mode was used for film analysis. Scanner response stability, intrafilm uniformity, and interfilm reproducibility were verified. Optical absorption spectra measurements were performed on unirradiated and irradiated EBT3 films to choose the most sensitive color channel to the dose range used. Results: EBT3 GafChromic films show an under response up to about 33% for low-energy protons with respect to {sup 60}Co gamma radiation, which is consistent with the linear energy transfer dependence already observed with higher energy protons, and a negligible dose

  15. Choice of tracks, microtubules and/or actin filaments for chloroplast photo-movement is differentially controlled by phytochrome and a blue light receptor.

    PubMed

    Sato, Y; Wada, M; Kadota, A

    2001-01-01

    Light induced chloroplast movement has been studied as a model system for photoreception and actin microfilament (MF)-based intracellular motilities in plants. Chloroplast photo-accumulation and -avoidance movement is mediated by phytochrome as well as blue light (BL) receptor in the moss Physcomitrella patens. Here we report the discovery of an involvement of a microtubule (MT)-based system in addition to an MF-based system in photorelocation of chloroplasts in this moss. In the dark, MTs provided tracks for rapid movement of chloroplasts in a longitudinal direction and MFs contributed the tracks for slow movement in any direction. We found that phytochrome responses utilized only the MT-based system, while BL responses had an alternative way of moving, either along MTs or MFs. MT-based systems were mediated by both photoreceptors, but chloroplasts showed movements with different velocity and pattern between them. No apparent difference in the behavior of chloroplast movement between the accumulation and avoidance movement was detected in phytochrome responses or BL responses, except for the direction of the movement. The results presented here demonstrate that chloroplasts use both MTs and MFs for motility and that phytochrome and a BL receptor control directional photo-movement of chloroplasts through the differential regulation of these motile systems.

  16. A Negative Feedback Loop between PHYTOCHROME INTERACTING FACTORs and HECATE Proteins Fine-Tunes Photomorphogenesis in Arabidopsis

    PubMed Central

    Zhu, Ling; Bu, Qingyun; Shen, Hui; Dang, Jonathan

    2016-01-01

    The phytochrome interacting factors (PIFs), a small group of basic helix-loop-helix transcription factors, repress photomorphogenesis both in the dark and light. Light signals perceived by the phytochrome family of photoreceptors induce rapid degradation of PIFs to promote photomorphogenesis. Here, we show that HECATE (HEC) proteins, another small group of HLH proteins, antagonistically regulate PIFs to promote photomorphogenesis. HEC1 and HEC2 heterodimerize with PIF family members. PIF1, HEC1, and HEC2 genes are spatially and temporally coexpressed, and HEC2 is localized in the nucleus. hec1, hec2, and hec3 single mutants and the hec1 hec2 double mutant showed hyposensitivity to light-induced seed germination and accumulation of chlorophyll and carotenoids, hallmark processes oppositely regulated by PIF1. HEC2 inhibits PIF1 target gene expression by directly heterodimerizing with PIF1 and preventing DNA binding and transcriptional activation activity of PIF1. Conversely, PIFs directly activate the expression of HEC1 and HEC2 in the dark, and light reduces the expression of these HECs possibly by degrading PIFs. HEC2 is partially degraded in the dark through the ubiquitin/26S-proteasome pathway and is stabilized by light. HEC2 overexpression also reduces the light-induced degradation of PIF1. Taken together, these data suggest that PIFs and HECs constitute a negative feedback loop to fine-tune photomorphogenesis in Arabidopsis thaliana. PMID:27073231

  17. In Vivo Assessment of Cold Tolerance through Chlorophyll-a Fluorescence in Transgenic Zoysiagrass Expressing Mutant Phytochrome A

    PubMed Central

    Gururani, Mayank Anand; Venkatesh, Jelli; Ganesan, Markkandan; Strasser, Reto Jörg; Han, Yunjeong; Kim, Jeong-Il; Lee, Hyo-Yeon; Song, Pill-Soon

    2015-01-01

    Chlorophyll-a fluorescence analysis provides relevant information about the physiology of plants growing under abiotic stress. In this study, we evaluated the influence of cold stress on the photosynthetic machinery of transgenic turfgrass, Zoysia japonica, expressing oat phytochrome A (PhyA) or a hyperactive mutant phytochrome A (S599A) with post-translational phosphorylation blocked. Biochemical analysis of zoysiagrass subjected to cold stress revealed reduced levels of hydrogen peroxide, increased proline accumulation, and enhanced specific activities of antioxidant enzymes compared to those of control plants. Detailed analyses of the chlorophyll-a fluorescence data through the so-called OJIP test exhibited a marked difference in the physiological status among transgenic and control plants. Overall, these findings suggest an enhanced level of cold tolerance in S599A zoysiagrass cultivars as reflected in the biochemical and physiological analyses. Further, we propose that chlorophyll-a fluorescence analysis using OJIP test is an efficient tool in determining the physiological status of plants under cold stress conditions. PMID:26010864

  18. Phytochrome Interacting Factors (PIFs) in Solanum lycopersicum: Diversity, Evolutionary History and Expression Profiling during Different Developmental Processes

    PubMed Central

    Rosado, Daniele; Gramegna, Giovanna; Cruz, Aline; Lira, Bruno Silvestre; Freschi, Luciano; de Setta, Nathalia

    2016-01-01

    Although the importance of light for tomato plant yield and edible fruit quality is well known, the PHYTOCHROME INTERACTING FACTORS (PIFs), main components of phytochrome-mediated light signal transduction, have been studied almost exclusively in Arabidopsis thaliana. Here, the diversity, evolution and expression profile of PIF gene subfamily in Solanum lycopersicum was characterized. Eight tomato PIF loci were identified, named SlPIF1a, SlPIF1b, SlPIF3, SlPIF4, SlPIF7a, SlPIF7b, SlPIF8a and SlPIF8b. The duplication of SlPIF1, SlPIF7 and SlPIF8 genes were dated and temporally coincided with the whole-genome triplication event that preceded tomato and potato divergence. Different patterns of mRNA accumulation in response to light treatments were observed during seedling deetiolation, dark-induced senescence, diel cycle and fruit ripening. SlPIF4 showed similar expression profile as that reported for A. thaliana homologs, indicating an evolutionary conserved function of PIF4 clade. A comprehensive analysis of the evolutionary and transcriptional data allowed proposing that duplicated SlPIFs have undergone sub- and neofunctionalization at mRNA level, pinpointing the importance of transcriptional regulation for the maintenance of duplicated genes. Altogether, the results indicate that genome polyploidization and functional divergence have played a major role in diversification of the Solanum PIF gene subfamily. PMID:27802334

  19. The phytochrome-interacting vascular plant one-zinc finger1 and VOZ2 redundantly regulate flowering in Arabidopsis.

    PubMed

    Yasui, Yukiko; Mukougawa, Keiko; Uemoto, Mitsuhiro; Yokofuji, Akira; Suzuri, Ryota; Nishitani, Aiko; Kohchi, Takayuki

    2012-08-01

    The timing of the transition to flowering in plants is regulated by various environmental factors, including daylength and light quality. Although the red/far-red photoreceptor phytochrome B (phyB) represses flowering by indirectly regulating the expression of a key flowering regulator, FLOWERING LOCUS T (FT), the mechanism of phyB signaling for flowering is largely unknown. Here, we identified two Arabidopsis thaliana genes, VASCULAR PLANT ONE-ZINC FINGER1 (VOZ1) and VOZ2, which are highly conserved throughout land plant evolution, as phyB-interacting factors. voz1 voz2 double mutants, but neither single mutant, showed a late-flowering phenotype under long-day conditions, which indicated that VOZ1 and VOZ2 redundantly promote flowering. voz1 voz2 mutations suppressed the early-flowering phenotype of the phyB mutant, and FT expression was repressed in the voz1 voz2 mutant. Green fluorescent protein-VOZ2 signal was observed in the cytoplasm, and interaction of VOZ proteins with phyB was indicated to occur in the cytoplasm under far-red light. However, VOZ2 protein modified to localize constitutively in the nucleus promoted flowering. In addition, the stability of VOZ2 proteins in the nucleus was modulated by light quality in a phytochrome-dependent manner. We propose that partial translocation of VOZ proteins from the cytoplasm to the nucleus mediates the initial step of the phyB signal transduction pathway that regulates flowering.

  20. Structural model of the cytosolic domain of the plant ethylene receptor 1 (ETR1).

    PubMed

    Mayerhofer, Hubert; Panneerselvam, Saravanan; Kaljunen, Heidi; Tuukkanen, Anne; Mertens, Haydyn D T; Mueller-Dieckmann, Jochen

    2015-01-30

    Ethylene initiates important aspects of plant growth and development through disulfide-linked receptor dimers located in the endoplasmic reticulum. The receptors feature a small transmembrane, ethylene binding domain followed by a large cytosolic domain, which serves as a scaffold for the assembly of large molecular weight complexes of different ethylene receptors and other cellular participants of the ethylene signaling pathway. Here we report the crystallographic structures of the ethylene receptor 1 (ETR1) catalytic ATP-binding and the ethylene response sensor 1 dimerization histidine phosphotransfer (DHp) domains and the solution structure of the entire cytosolic domain of ETR1, all from Arabidopsis thaliana. The isolated dimeric ethylene response sensor 1 DHp domain is asymmetric, the result of different helical bending angles close to the conserved His residue. The structures of the catalytic ATP-binding, DHp, and receiver domains of ethylene receptors and of a homologous, but dissimilar, GAF domain were refined against experimental small angle x-ray scattering data, leading to a structural model of the entire cytosolic domain of the ethylene receptor 1. The model illustrates that the cytosolic domain is shaped like a dumbbell and that the receiver domain is flexible and assumes a position different from those observed in prokaryotic histidine kinases. Furthermore the cytosolic domain of ETR1 plays a key role, interacting with all other receptors and several participants of the ethylene signaling pathway. Our model, therefore, provides the first step toward a detailed understanding of the molecular mechanics of this important signal transduction process in plants.

  1. Phytochrome-controlled phototropism of protonemata of the moss ceratodon purpureus: physiology of the wild type and class 2 ptr-mutants

    PubMed

    Esch; Hartmann; Cove; Wada; Lamparter

    1999-09-01

    Phototropism and polarotropism in protonemata of the moss Ceratodon purpureus are controlled by the photoreceptor phytochrome. One class of phototropism mutants is characterised by growing randomly when kept for a prolonged time (5 d or longer) in unilateral red light. It was found that a subclass of these mutants grows faster than the wild type, the rate of cell division and the length of the cells being increased. This difference is found for light-grown and dark-grown filaments. It is therefore suggested that the mutant phenotype neither results from a defect in phytochrome photoconversion nor from a defect in phytochrome-gradient formation. Instead, it is possible that a factor which is involved in both signal transduction of phototropism and regulation of cell size and cell division is deregulated. If dark-grown mutant filaments are phototropically stimulated for 24 h, they show a weak phototropic response. Phototropism and polarotropism fluence-rate effect curves for mutants were flattened and shifted to higher fluence rates compared with those for the wild type. With wild-type filaments, a previously unreported response was observed. At a low fluence rate, half of the filaments grew positively phototropically, while the other half grew negatively phototropically. It seems that under these conditions, a phytochrome gradient with two maxima for the far-red-absorbing form of phytochrome (Pfr) within the cross-section of the cell is displayed by the response of the filaments. At higher fluence rates, all filaments of the wild type grew towards the light. These data and results from microbeam irradiation experiments and from phototropism studies with filaments growing within agar, indicate that light refraction plays an important role in the formation of the Pfr gradient in phototropism of Ceratodon.

  2. A Photo-Labile Thioether Linkage to Phycoviolobilin Provides the Foundation for the Blue/Green Photocycles in DXCF-Cyanobacteriochromes

    SciTech Connect

    Burgie, E. Sethe; Walker, Joseph M.; George N. Phillips Jr.; Vierstra, Richard D.

    2013-01-08

    The phytochrome superfamily encompasses a diverse collection of photochromic photoreceptors in plants and microorganisms that employ a covalently linked bilin cradled in a cGMP-phosphodiesterase/adenylyl-cyclase/FhlA (GAF) domain to detect light. Whereas most interconvert between red- and far-red-light-absorbing states, cyanobacteria also express variants called cyanobacteriochromes (CBCRs) that modify bilin absorption to collectively perceive the entire visible spectrum. Here, we present two X-ray crystallographic structures of the GAF domain from the blue/green photochromic CBCR PixJ from Thermosynechococcus elongatus. Moreover, these structures confirm the hypothesis that CBCRs variably manipulate the chromophore π-conjugation system through isomerization and a second thioether linkage, in this case involving the bilin C10 carbon and Cys494 within a DXCF sequence characteristic of blue/green CBCRs. Biochemical studies support a mechanism for photoconversion whereby the second linkage ruptures on route to the green-light-absorbing state. All together, theTePixJ(GAF) models illustrate the remarkable structural and photochemical versatility among phytochromes and CBCRs in driving light perception.

  3. Crystal structure of Pseudomonas aeruginosa bacteriophytochrome: Photoconversion and signal transduction

    PubMed Central

    Yang, Xiaojing; Kuk, Jane; Moffat, Keith

    2008-01-01

    Phytochromes are red-light photoreceptors that regulate light responses in plants, fungi, and bacteria via reversible photoconversion between red (Pr) and far-red (Pfr) light-absorbing states. Here we report the crystal structure at 2.9 Å resolution of a bacteriophytochrome from Pseudomonas aeruginosa with an intact, fully photoactive photosensory core domain in its dark-adapted Pfr state. This structure reveals how unusual interdomain interactions, including a knot and an “arm” structure near the chromophore site, bring together the PAS (Per-ARNT-Sim), GAF (cGMP phosphodiesterase/adenyl cyclase/FhlA), and PHY (phytochrome) domains to achieve Pr/Pfr photoconversion. The PAS, GAF, and PHY domains have topologic elements in common and may have a single evolutionary origin. We identify key interactions that stabilize the chromophore in the Pfr state and provide structural and mutational evidence to support the essential role of the PHY domain in efficient Pr/Pfr photoconversion. We also identify a pair of conserved residues that may undergo concerted conformational changes during photoconversion. Modeling of the full-length bacteriophytochrome structure, including its output histidine kinase domain, suggests how local structural changes originating in the photosensory domain modulate interactions between long, cross-domain signaling helices at the dimer interface and are transmitted to the spatially distant effector domain, thereby regulating its histidine kinase activity. PMID:18799746

  4. Developing new extension of GafChromic RTQA2 film to patient quality assurance field using a plan-based calibration method

    NASA Astrophysics Data System (ADS)

    Peng, Jiayuan; Zhang, Zhen; Wang, Jiazhou; Xie, Jiang; Chen, Junchao; Hu, Weigang

    2015-10-01

    GafChromic RTQA2 film is a type of radiochromic film designed for light field and radiation field alignment. The aim of this study is to extend the application of RTQA2 film to the measurement of patient specific quality assurance (QA) fields as a 2D relative dosimeter. Pre-irradiated and post-irradiated RTQA2 films were scanned in reflection mode using a flatbed scanner. A plan-based calibration (PBC) method utilized the mapping information of the calculated dose image and film grayscale image to create a dose versus pixel value calibration model. This model was used to calibrate the film grayscale image to the film relative dose image. The dose agreement between calculated and film dose images were analyzed by gamma analysis. To evaluate the feasibility of this method, eight clinically approved RapidArc cases (one abdomen cancer and seven head-and-neck cancer patients) were tested using this method. Moreover, three MLC gap errors and two MLC transmission errors were introduced to eight Rapidarc cases respectively to test the robustness of this method. The PBC method could overcome the film lot and post-exposure time variations of RTQA2 film to get a good 2D relative dose calibration result. The mean gamma passing rate of eight patients was 97.90%  ±  1.7%, which showed good dose consistency between calculated and film dose images. In the error test, the PBC method could over-calibrate the film, which means some dose error in the film would be falsely corrected to keep the dose in film consistent with the dose in the calculated dose image. This would then lead to a false negative result in the gamma analysis. In these cases, the derivative curve of the dose calibration curve would be non-monotonic which would expose the dose abnormality. By using the PBC method, we extended the application of more economical RTQA2 film to patient specific QA. The robustness of the PBC method has been improved by analyzing the monotonicity of the derivative of the

  5. Calibration of GafChromic XR-RV3 radiochromic film for skin dose measurement using standardized x-ray spectra and a commercial flatbed scanner

    PubMed Central

    McCabe, Bradley P.; Speidel, Michael A.; Pike, Tina L.; Van Lysel, Michael S.

    2011-01-01

    Purpose: In this study, newly formulated XR-RV3 GafChromic® film was calibrated with National Institute of Standards and Technology (NIST) traceability for measurement of patient skin dose during fluoroscopically guided interventional procedures. Methods: The film was calibrated free-in-air to air kerma levels between 15 and 1100 cGy using four moderately filtered x-ray beam qualities (60, 80, 100, and 120 kVp). The calibration films were scanned with a commercial flatbed document scanner. Film reflective density-to-air kerma calibration curves were constructed for each beam quality, with both the orange and white sides facing the x-ray source. A method to correct for nonuniformity in scanner response (up to 25% depending on position) was developed to enable dose measurement with large films. The response of XR-RV3 film under patient backscattering conditions was examined using on-phantom film exposures and Monte Carlo simulations. Results: The response of XR-RV3 film to a given air kerma depended on kVp and film orientation. For a 200 cGy air kerma exposure with the orange side of the film facing the source, the film response increased by 20% from 60 to 120 kVp. At 500 cGy, the increase was 12%. When 500 cGy exposures were performed with the white side facing the x-ray source, the film response increased by 4.0% (60 kVp) to 9.9% (120 kVp) compared to the orange-facing orientation. On-phantom film measurements and Monte Carlo simulations show that using a NIST-traceable free-in-air calibration curve to determine air kerma in the presence of backscatter results in an error from 2% up to 8% depending on beam quality. The combined uncertainty in the air kerma measurement from the calibration curves and scanner nonuniformity correction was ±7.1% (95% C.I.). The film showed notable stability. Calibrations of film and scanner separated by 1 yr differed by 1.0%. Conclusions: XR-RV3 radiochromic film response to a given air kerma shows dependence on beam quality and film

  6. Calibration of GafChromic XR-RV3 radiochromic film for skin dose measurement using standardized x-ray spectra and a commercial flatbed scanner

    SciTech Connect

    McCabe, Bradley P.; Speidel, Michael A.; Pike, Tina L.; Van Lysel, Michael S.

    2011-04-15

    Purpose: In this study, newly formulated XR-RV3 GafChromic film was calibrated with National Institute of Standards and Technology (NIST) traceability for measurement of patient skin dose during fluoroscopically guided interventional procedures. Methods: The film was calibrated free-in-air to air kerma levels between 15 and 1100 cGy using four moderately filtered x-ray beam qualities (60, 80, 100, and 120 kVp). The calibration films were scanned with a commercial flatbed document scanner. Film reflective density-to-air kerma calibration curves were constructed for each beam quality, with both the orange and white sides facing the x-ray source. A method to correct for nonuniformity in scanner response (up to 25% depending on position) was developed to enable dose measurement with large films. The response of XR-RV3 film under patient backscattering conditions was examined using on-phantom film exposures and Monte Carlo simulations. Results: The response of XR-RV3 film to a given air kerma depended on kVp and film orientation. For a 200 cGy air kerma exposure with the orange side of the film facing the source, the film response increased by 20% from 60 to 120 kVp. At 500 cGy, the increase was 12%. When 500 cGy exposures were performed with the white side facing the x-ray source, the film response increased by 4.0% (60 kVp) to 9.9% (120 kVp) compared to the orange-facing orientation. On-phantom film measurements and Monte Carlo simulations show that using a NIST-traceable free-in-air calibration curve to determine air kerma in the presence of backscatter results in an error from 2% up to 8% depending on beam quality. The combined uncertainty in the air kerma measurement from the calibration curves and scanner nonuniformity correction was {+-}7.1% (95% C.I.). The film showed notable stability. Calibrations of film and scanner separated by 1 yr differed by 1.0%. Conclusions: XR-RV3 radiochromic film response to a given air kerma shows dependence on beam quality and film

  7. Regulation of hormone metabolism in Arabidopsis seeds: phytochrome regulation of abscisic acid metabolism and abscisic acid regulation of gibberellin metabolism.

    PubMed

    Seo, Mitsunori; Hanada, Atsushi; Kuwahara, Ayuko; Endo, Akira; Okamoto, Masanori; Yamauchi, Yukika; North, Helen; Marion-Poll, Annie; Sun, Tai-Ping; Koshiba, Tomokazu; Kamiya, Yuji; Yamaguchi, Shinjiro; Nambara, Eiji

    2006-11-01

    In a wide range of plant species, seed germination is regulated antagonistically by two plant hormones, abscisic acid (ABA) and gibberellin (GA). In the present study, we have revealed that ABA metabolism (both biosynthesis and inactivation) was phytochrome-regulated in an opposite fashion to GA metabolism during photoreversible seed germination in Arabidopsis. Endogenous ABA levels were decreased by irradiation with a red (R) light pulse in dark-imbibed seeds pre-treated with a far-red (FR) light pulse, and the reduction in ABA levels in response to R light was inhibited in a phytochrome B (PHYB)-deficient mutant. Expression of an ABA biosynthesis gene, AtNCED6, and the inactivation gene, CYP707A2, was regulated in a photoreversible manner, suggesting a key role for the genes in PHYB-mediated regulation of ABA metabolism. Abscisic acid-deficient mutants such as nced6-1, aba2-2 and aao3-4 exhibited an enhanced ability to germinate relative to wild type when imbibed in the dark after irradiation with an FR light pulse. In addition, the ability to synthesize GA was improved in the aba2-2 mutant compared with wild type during dark-imbibition after an FR light pulse. Activation of GA biosynthesis in the aba2-2 mutant was also observed during seed development. These data indicate that ABA is involved in the suppression of GA biosynthesis in both imbibed and developing seeds. Spatial expression patterns of the AtABA2 and AAO3 genes, responsible for last two steps of ABA biosynthesis, were distinct from that of the GA biosynthesis gene, AtGA3ox2, in both imbibed and developing seeds, suggesting that biosynthesis of ABA and GA in seeds occurs in different cell types.

  8. Cryptochrome 1 and phytochrome B control shade-avoidance responses in Arabidopsis via partially independent hormonal cascades

    PubMed Central

    Keller, Mercedes M; Jaillais, Yvon; Pedmale, Ullas V; Moreno, Javier E; Chory, Joanne; Ballaré, Carlos L

    2011-01-01

    Plants respond to a reduction in the red/far-red ratio (R:FR) of light, caused by the proximity of other plants, by initiating morphological changes that improve light capture. In Arabidopsis, this response (shade avoidance syndrome, SAS) is controlled by phytochromes (particularly phyB), and is dependent on the TAA1 pathway of auxin biosynthesis. However, when grown in real canopies, we found that phyB mutants and mutants deficient in TAAI (sav3) still display robust SAS responses to increased planting density and leaf shading. The SAS morphology (leaf hyponasty and reduced lamina/petiole ratio) could be phenocopied by exposing plants to blue light attenuation. These responses to blue light attenuation required the UV-A/blue light photoreceptor cry1. Moreover, they were mediated through mechanisms that showed only limited overlap with the pathways recruited by phyB inactivation. In particular, pathways for polar auxin transport, auxin biosynthesis and gibberellin signaling that are involved in SAS responses to low R:FR were not required for the SAS responses to blue light depletion. By contrast, the brassinosteroid response appeared to be required for the full expression of the SAS phenotype under low blue light. The phyB and cry1 inactivation pathways appeared to converge in their requirement for the basic/helix-loop-helix (bHLH) transcription factors PHYTOCHROME INTERACTING FACTORs 4 and 5 (PIF4 and PIF5) to elicit the SAS phenotype. Our results suggest that blue light is an important control of SAS responses, and that PIF4 and PIF5 are critical hubs for a diverse array of signaling routes that control plant architecture in canopies. PMID:21457375

  9. Genomic Survey and Biochemical Analysis of Recombinant Candidate Cyanobacteriochromes Reveals Enrichment for Near UV/Violet Sensors in the Halotolerant and Alkaliphilic Cyanobacterium Microcoleus IPPAS B353*

    PubMed Central

    Cho, Sung Mi; Jeoung, Sae Chae; Song, Ji-Young; Kupriyanova, Elena V.; Pronina, Natalia A.; Lee, Bong-Woo; Jo, Seong-Whan; Park, Beom-Seok; Choi, Sang-Bong; Song, Ji-Joon; Park, Youn-Il

    2015-01-01

    Cyanobacteriochromes (CBCRs), which are exclusive to and widespread among cyanobacteria, are photoproteins that sense the entire range of near-UV and visible light. CBCRs are related to the red/far-red phytochromes that utilize linear tetrapyrrole (bilin) chromophores. Best characterized from the unicellular cyanobacterium Synechocystis sp. PCC 6803 and the multicellular heterocyst forming filamentous cyanobacteria Nostoc punctiforme ATCC 29133 and Anabaena sp. PCC 7120, CBCRs have been poorly investigated in mat-forming, nonheterocystous cyanobacteria. In this study, we sequenced the genome of one of such species, Microcoleus IPPAS B353 (Microcoleus B353), and identified two phytochromes and seven CBCRs with one or more bilin-binding cGMP-specific phosphodiesterase, adenylyl cyclase and FhlA (GAF) domains. Biochemical and spectroscopic measurements of 23 purified GAF proteins from phycocyanobilin (PCB) producing recombinant Escherichia coli indicated that 13 of these proteins formed near-UV and visible light-absorbing covalent adducts: 10 GAFs contained PCB chromophores, whereas three contained the PCB isomer, phycoviolobilin (PVB). Furthermore, the complement of Microcoleus B353 CBCRs is enriched in near-UV and violet sensors, but lacks red/green and green/red CBCRs that are widely distributed in other cyanobacteria. We hypothesize that enrichment in short wavelength-absorbing CBCRs is critical for acclimation to high-light environments where this organism is found. PMID:26405033

  10. Non-Bonded Interactions Drive the Sub-Picosecond Bilin Photoisomerization in the P(fr) State of Phytochrome Cph1.

    PubMed

    Yang, Yang; Heyne, Karsten; Mathies, Richard A; Dasgupta, Jyotishman

    2016-02-03

    Phytochromes are protein-based photoreceptors harboring a bilin-based photoswitch in the active site. The timescale of photosignaling via C15 =C16 E-to-Z photoisomerization has been ambiguous in the far-red-absorbing Pfr state. Here we present a unified view of the structural events in phytochrome Cph1 post excitation with femtosecond precision, obtained via stimulated Raman and polarization-resolved transient IR spectroscopy. We demonstrate that photoproduct formation occurs within 700 fs, determined by a two-step partitioning process initiated by a planarization on the electronic excited state with a 300 fs time scale. The ultrafast isomerization timescale for Pfr -to-Pr conversion highlights the active role of the nonbonding methyl-methyl clash initiating the reaction in the excited state. We envision that our results will motivate the synthesis of new artificial photoswitches with precisely tuned non-bonded interactions for ultrafast response.

  11. PIF1 promotes phytochrome-regulated growth under photoperiodic conditions in Arabidopsis together with PIF3, PIF4, and PIF5

    PubMed Central

    Soy, Judit; Leivar, Pablo; Monte, Elena

    2014-01-01

    Seedlings growing under diurnal conditions display maximal growth at the end of the night in short-day (SD) photoperiods. Current evidence indicates that this behaviour involves the action of PHYTOCHROME-INTERACTING FACTOR 3 (PIF3) together with PIF4 and PIF5, through direct regulation of growth-related genes at dawn coinciding with a PIF3 accumulation peak generated by phytochrome-imposed oscillations in protein abundance. Here, to assess how alterations in PIF3 levels impact seedling growth, the night-specific accumulation of PIF3 was modulated by releasing SD-grown seedlings into continuous light, or by exposing them to a phytochrome-inactivating end-of-day far-red pulse (EOD-FRp). The data show a strong direct correlation between PIF3 accumulation, PIF3-regulated induction of growth-related genes, and hypocotyl elongation, and suggest that growth promotion in SD conditions involves factors other than PIF3, PIF4, and PIF5. Using a pif1 mutant, evidence is provided that PIF1 also contributes to inducing hypocotyl elongation during the dark period under diurnal conditions. PIF1 displayed constitutive transcript levels in SD conditions, suggesting that phytochrome-imposed oscillations in PIF1 protein abundance determine its accumulation and action during the night, similar to PIF3 and in contrast to PIF4 and PIF5, which oscillate diurnally due to a combination of circadian clock-regulated transcription and light control of protein accumulation. Furthermore, using single and higher order pif mutants, the relative contribution of each member of the PIF quartet to the regulation of morphogenesis and the expression of selected growth marker genes under SD conditions, or under SD conditions supplemented with an EOD-FRp, is defined. Collectively, the data indicate that PIF1, PIF3, PIF4, and PIF5 act together to promote and optimize growth under photoperiodic conditions. PMID:24420574

  12. Novel near-infrared BiFC systems from a bacterial phytochrome for imaging protein interactions and drug evaluation under physiological conditions.

    PubMed

    Chen, Minghai; Li, Wei; Zhang, Zhiping; Liu, Sanying; Zhang, Xiaowei; Zhang, Xian-En; Cui, Zongqiang

    2015-04-01

    Monitoring protein-protein interactions (PPIs) in live subjects is critical for understanding these fundamental biological processes. Bimolecular fluorescence complementation (BiFC) provides a good technique for imaging PPIs; however, a BiFC system with a long wavelength remains to be pursued for in vivo imaging. Here, we conducted systematic screening of split reporters from a bacterial phytochrome-based, near-infrared fluorescent protein (iRFP). Several new near-infrared phytochrome BiFC systems were built based on selected split sites including the amino acids residues 97/98, 99/100, 122/123, and 123/124. These new near-infrared BiFC systems from a bacterial phytochrome were verified as powerful tools for imaging PPIs under physiological conditions in live cells and in live mice. The interaction between HIV-1 integrase (IN) and cellular cofactor protein Lens epithelium-derived growth factor (LEDGF/p75) was visualized in live cells using the newly constructed iRFP BiFC system because of its important roles in HIV-1 integration and replication. Because the HIV IN-LEDGF/p75 interaction is an attractive anti-HIV target, drug evaluation assays to inhibit the HIV IN-LEDGF/p75 interaction were also performed using the newly constructed BiFC system. The results showed that compound 6 and carbidopa inhibit the HIV IN-LEDGF/p75 interaction in a dose-dependent manner under physiological conditions in the BiFC assays. This study provides novel near-infrared BiFC systems for imaging protein interactions under physiological conditions and provides guidance for splitting other bacterial phytochrome-like proteins to construct BiFC systems. The study also provides a new method for drug evaluation in live cells based on iRFP BiFC systems and supplies some new information regarding candidate drugs for anti-HIV therapies.

  13. Improving the energy response of external beam therapy (EBT) GafChromic{sup TM} dosimetry films at low energies (≤100 keV)

    SciTech Connect

    Bekerat, H. Devic, S.; DeBlois, F.; Singh, K.; Sarfehnia, A.; Seuntjens, J.; Shih, Shelley; Yu, Xiang; Lewis, D.

    2014-02-15

    Purpose: Purpose of this work is to investigate the effects of varying the active layer composition of external beam therapy (EBT) GafChromic{sup TM} films on the energy dependence of the film, as well as try to develop a new prototype with more uniform energy response at low photon energies (⩽100 keV). Methods: First, the overall energy response (S{sub AD,} {sub W}(Q)) of different commercial EBT type film models that represent the three different generations produced to date, i.e., EBT, EBT2, and EBT3, was investigated. Pieces of each film model were irradiated to a fixed dose of 2 Gy to water for a wide range of beam qualities and the corresponding S{sub AD,} {sub W}(Q) was measured using a flatbed document scanner. Furthermore, the DOSRZnrc Monte Carlo code was used to determine the absorbed dose to water energy dependence of the film, f(Q). Moreover, the intrinsic energy dependence, k{sub bq}(Q), for each film model was evaluated using the corresponding S{sub AD,} {sub W}(Q) and f(Q). In the second part of this study, the authors investigated the effects of changing the chemical composition of the active layer on S{sub AD,} {sub W}(Q). Finally, based on these results, the film manufacturer fabricated several film prototypes and the authors evaluated their S{sub AD,} {sub W}(Q). Results: The commercial EBT film model shows an under response at all energies below 100 keV reaching 39% ± 4% at about 20 keV. The commercial EBT2 and EBT3 film models show an under response of about 27% ± 4% at 20 keV and an over response of about 16% ± 4% at 40 keV.S{sub AD,} {sub W}(Q) of the three commercial film models at low energies show strong correlation with the corresponding f{sup −1}(Q) curves. The commercial EBT3 model with 4% Cl in the active layer shows under response of 22% ± 4% at 20 keV and 6% ± 4% at about 40 keV. However, increasing the mass percent of chlorine makes the film more hygroscopic which may affect the stability of the film's readout. The

  14. Role of phytochromes A and B in the regulation of cell death and acclimatory responses to UV stress in Arabidopsis thaliana

    PubMed Central

    Rusaczonek, Anna; Czarnocka, Weronika; Kacprzak, Sylwia; Witoń, Damian; Ślesak, Ireneusz; Szechyńska-Hebda, Magdalena; Gawroński, Piotr; Karpiński, Stanisław

    2015-01-01

    Plants coordinate their responses to various biotic and abiotic stresses in order to optimize their developmental and acclimatory programmes. The ultimate response to an excessive amount of stress is local induction of cell death mechanisms. The death of certain cells can help to maintain tissue homeostasis and enable nutrient remobilization, thus increasing the survival chances of the whole organism in unfavourable environmental conditions. UV radiation is one of the environmental factors that negatively affects the photosynthetic process and triggers cell death. The aim of this work was to evaluate a possible role of the red/far-red light photoreceptors phytochrome A (phyA) and phytochrome B (phyB) and their interrelations during acclimatory responses to UV stress. We showed that UV-C treatment caused a disturbance in photosystem II and a deregulation of photosynthetic pigment content and antioxidant enzymes activities, followed by increased cell mortality rate in phyB and phyAB null mutants. We also propose a regulatory role of phyA and phyB in CO2 assimilation, non-photochemical quenching, reactive oxygen species accumulation and salicylic acid content. Taken together, our results suggest a novel role of phytochromes as putative regulators of cell death and acclimatory responses to UV. PMID:26385378

  15. Blue-light mediated accumulation of nuclear-encoded transcripts coding for proteins of the thylakoid membrane is absent in the phytochrome-deficient aurea mutant of tomato.

    PubMed

    Oelmüller, R; Kendrick, R E; Briggs, W R

    1989-08-01

    Polyclonal antibodies against pea phytochrome detect 2 protein bands (about 116 and 120 kDa) on blots of crude protein extracts and protein of microsomal preparations of dark-grown tomato seedlings. Both protein bands are undetectable in Western blots of the aurea mutant extracts. Neither protein band is detectable after isogenic wild-type seedlings are illuminated with 3 h of red light, either in the crude extract or in the membrane fraction of the irradiated seedlings; this result is consistent with the hypothesis that both bands are phytochrome. When dark-grown wild-type seedlings are illuminated with 3 h of red light or blue light against a red light background, the transcript levels for chlorophyll a/b-binding proteins of photosystem I and II, plastocyanin, and the subunit II of photosystem I increase. In all cases, the same fluence rate of blue light is much more effective than red light alone, a result that indicates the involvement of a blue/UV-A light photoreceptor in addition to the involvement of the far-red-absorbing form of phytochrome, Pfr. The aurea mutant responds neither to red light nor to blue light. Thus, no Pfr-independent induction of the four transcripts by a blue/UV-A light photoreceptor can be measured in the aurea mutant.

  16. Resistance of Arabidopsis thaliana L. photosynthetic apparatus to UV-B is reduced by deficit of phytochromes B and A.

    PubMed

    Khudyakova, Aleksandra Yu; Kreslavski, Vladimir D; Shirshikova, Galina N; Zharmukhamedov, Sergey K; Kosobryukhov, Anatoly A; Allakhverdiev, Suleyman I

    2017-03-01

    The photosynthetic responses of 25-day-old Arabidopsis phyA phyB double mutant (DM) compared with the wild type (WT) to UV-B radiation (1Wm(-2), 30min) were investigated. UV-B irradiation led to reduction of photosystem 2 (PS-2) activity and the photosynthetic rate. In plants grown under both white and red light (λm - 660nm) the reduction was greater in DM plants compared to the WT. Without UV-B irradiation a decrease in PS-2 activity was observed in DM grown under RL only. It is assumed that the lower content of UV-absorbing pigments and carotenoids observed in DM may be one of the reasons of reduced PS-2 resistance to UV-B. Higher decrease in activities under UV in DM plants grown under RL compared to DM plants grown under white light is likely due to the lack of activity of cryptochromes in plants grown under red light. Rates of post-stress recovery of photosynthetic activity of DM compared with WT plants under white and red light of low intensity were studied. Almost complete recovery of the activity was found which was not observed under dark conditions and in the presence of a protein synthesis inhibitor, chloramphenicol. It is assumed that phytochrome system participates in stress-protective mechanisms of the photosynthetic apparatus to UV-radiation.

  17. Functional properties and regulatory complexity of a minimal RBCS light-responsive unit activated by phytochrome, cryptochrome, and plastid signals.

    PubMed

    Martínez-Hernández, Aída; López-Ochoa, Luisa; Argüello-Astorga, Gerardo; Herrera-Estrella, Luis

    2002-04-01

    Light-inducible promoters are able to respond to a wide spectrum of light through multiple photoreceptor systems. Several cis-acting elements have been identified as components of light-responsive promoter elements; however, none of these regulatory elements by itself appears to be sufficient to confer light responsiveness; rather, the combination of at least two elements seems to be required. Using phylogenetic structural analysis, we have identified conserved DNA modular arrays (CMAs) associated with light-responsive promoter regions that have been conserved throughout the evolutionary radiation of angiosperms. Here, we report the functional characterization of CMA5, a native 52-bp fragment of the Nicotiana plumbaginifolia rbcS 8B promoter, which contains an I- and a G-box cis-element. CMA5 behaves as a light-responsive minimal unit capable of activating a heterologous minimal promoter in a phytochrome-, cryptochrome-, and plastid-dependent manner. We also show that CMA5 light induction requires HY5 and that downstream negative regulators COP (constitutive photomorphogenic)/DET (de-etiolated) regulate its activity. Our results show that the simplest light-responsive promoter element from photosynthesis-associated genes described to date is the common target for different signals involved in light regulation. The possible mechanism involved in light-transcriptional regulation and tissue specificity of combinatorial elements units is discussed.

  18. Phytochrome-interacting factors PIF4 and PIF5 negatively regulate anthocyanin biosynthesis under red light in Arabidopsis seedlings.

    PubMed

    Liu, Zhongjuan; Zhang, Yongqiang; Wang, Jianfeng; Li, Ping; Zhao, Chengzhou; Chen, Yadi; Bi, Yurong

    2015-09-01

    Light is an important environmental factor inducing anthocyanin accumulation in plants. Phytochrome-interacting factors (PIFs) have been shown to be a family of bHLH transcription factors involved in light signaling in Arabidopsis. Red light effectively increased anthocyanin accumulation in wild-type Col-0, whereas the effects were enhanced in pif4 and pif5 mutants but impaired in overexpression lines PIF4OX and PIF5OX, indicating that PIF4 and PIF5 are both negative regulators for red light-induced anthocyanin accumulation. Consistently, transcript levels of several genes involved in anthocyanin biosynthesis and regulatory pathway, including CHS, F3'H, DFR, LDOX, PAP1 and TT8, were significantly enhanced in mutants pif4 and pif5 but decreased in PIF4OX and PIF5OX compared to in Col-0, indicating that PIF4 and PIF5 are transcriptional repressor of these gene. Transient expression assays revealed that PIF4 and PIF5 could repress red light-induced promoter activities of F3'H and DFR in Arabidopsis protoplasts. Furthermore, chromatin immunoprecipitation-quantitative PCR (ChIP-qPCR) test and electrophoretic mobility shift assay (EMSA) showed that PIF5 could directly bind to G-box motifs present in the promoter of DFR. Taken together, these results suggest that PIF4 and PIF5 negatively regulate red light-induced anthocyanin accumulation through transcriptional repression of the anthocyanin biosynthetic genes in Arabidopsis.

  19. PHYTOCHROME-INTERACTING FACTOR 5 (PIF5) positively regulates dark-induced senescence and chlorophyll degradation in Arabidopsis.

    PubMed

    Zhang, Yongqiang; Liu, Zhongjuan; Chen, Yadi; He, Jun-Xian; Bi, Yurong

    2015-08-01

    Darkness is a known environmental factor that induces plant senescence. Here, Phytochrome-Interacting Factors (PIFs), several bHLH transcription factors involved in plant skotomorphogenesis, were examined for their roles in the regulation of dark-induced senescence and chlorophyll breakdown in Arabidopsis thaliana. After light-grown seedlings were transferred to darkness, green leaves turned yellow, and chlorophyll contents decreased, but membrane lipid peroxidation and cell death increased in wild-type Col-0. These responses were enhanced in overexpression line PIF5OX but decreased in mutant pif5-3. Darkness significantly induced expression of several genes involved in chlorophyll breakdown, including SGR, NYC1, NOL, and PAO, as well as genes encoding for transcription factors that have been shown to be required for dark-induced senescence, including WRKY22, NAP, EIN3, EIL1, and ORE1. These effects on gene expression were also enhanced in PIF5OX but decreased in pif5-3 relative to Col-0. Further analyses using ChIP-qPCR, EMSA, and protoplast transient assays indicated that PIF5 binds to the G-box motifs in the promoters of SGR, NYC1, and ORE1 genes and stimulate their expression. Collectively, our data indicate that PIF5 is a key factor that positively regulates dark-induced senescence upstream of ORE1 and regulates chlorophyll breakdown upstream of SGR and NYC1.

  20. Structure-Guided Engineering of Plant Phytochrome B with Altered Photochemistry and Light Signaling1[W][OA

    PubMed Central

    Zhang, Junrui; Stankey, Robert J.; Vierstra, Richard D.

    2013-01-01

    Phytochromes (phys) encompass a diverse collection of biliproteins that enable cellular light perception by photoconverting between a red-light-absorbing ground state (Pr) and a far-red light-absorbing active state (Pfr). Based on the central role of plant phys in controlling numerous agriculturally important processes, their rational redesign offers great promise toward accelerating crop improvement. Employing as templates the available three-dimensional models of the photosensory module within bacterial phys, we report here our initial attempt to apply structure-guided mutagenesis to phy engineering using Arabidopsis (Arabidopsis thaliana) phyB, the dominant isoform in light-grown plants, as the example. A collection of phyB mutants was generated affecting the bilin-binding pocket that altered photochemistry, thermal stability, and/or nuclear localization patterns, some of which also impacted phenotypic outputs. Of particular interest are the Y361F substitution, which created Arabidopsis plants with greatly enhanced light sensitivity, mutants variably altered in Pfr-to-Pr thermal reversion and nuclear aggregation, and the D307A substitution, which failed to photoconvert from Pr to Pfr and display light-induced nuclear aggregation but retained some biological activity and accelerated turnover in red light. Taken together, this collection provides variants potentially useful to agriculture as well as new tools to better understand the molecular mechanisms underpinning phy signaling. PMID:23321421

  1. Arabidopsis DE-ETIOLATED1 represses photomorphogenesis by positively regulating phytochrome-interacting factors in the dark.

    PubMed

    Dong, Jie; Tang, Dafang; Gao, Zhaoxu; Yu, Renbo; Li, Kunlun; He, Hang; Terzaghi, William; Deng, Xing Wang; Chen, Haodong

    2014-09-01

    Arabidopsis thaliana seedlings undergo photomorphogenic development even in darkness when the function of DE-ETIOLATED1 (DET1), a repressor of photomorphogenesis, is disrupted. However, the mechanism by which DET1 represses photomorphogenesis remains unclear. Our results indicate that DET1 directly interacts with a group of transcription factors known as the phytochrome-interacting factors (PIFs). Furthermore, our results suggest that DET1 positively regulates PIF protein levels primarily by stabilizing PIF proteins in the dark. Genetic analysis showed that each pif single mutant could enhance the det1-1 phenotype, and ectopic expression of each PIF in det1-1 partially suppressed the det1-1 phenotype, based on hypocotyl elongation and cotyledon opening angles observed in darkness. Genomic analysis also revealed that DET1 may modulate the expression of light-regulated genes to mediate photomorphogenesis partially through PIFs. The observed interaction and regulation between DET1 and PIFs not only reveal how DET1 represses photomorphogenesis, but also suggest a possible mechanism by which two groups of photomorphogenic repressors, CONSTITUTIVE PHOTOMORPHOGENESIS/DET/FUSCA and PIFs, work in concert to repress photomorphogenesis in darkness.

  2. Multi-scale photoacoustic tomography using reversibly switchable bacterial phytochrome as a near-infrared photochromic probe

    PubMed Central

    Yao, Junjie; Kaberniuk, Andrii A.; Li, Lei; Shcherbakova, Daria M.; Zhang, Ruiying; Wang, Lidai; Li, Guo; Verkhusha, Vladislav V.; Wang, Lihong V.

    2015-01-01

    Photoacoustic tomography (PAT) of genetically encoded probes allows imaging of targeted biological processes with high spatial resolution at depths. Here, we combined multi-scale photoacoustic imaging with, for the first time, a reversibly switchable non-fluorescent bacterial phytochrome BphP1. With a heme-derived biliverdin chromophore, BphP1 has the most red-shifted absorption among reported genetically encoded probes, and is reversibly photoconvertible between its red and near-infrared light absorption states. We combined single-wavelength PAT with efficient BphP1 photoswitching, enabling differential imaging that substantially removed background signals, enhanced detection sensitivity, increased penetration depth, and improved spatial resolution. In doing so, we monitored tumor growth and metastasis with a ~100 µm resolution at depths approaching 10 mm using photoacoustic computed tomography, and imaged individual cancer cells with a sub-optical-diffraction resolution of ~140 nm using photoacoustic microscopy. This technology is promising for biomedical studies at different length scales. PMID:26550774

  3. Contribution of calcium ions and hydrogen ions to the signal transduction chain in phytochrome-mediated spore germination. [Onoclea sensibilis L

    SciTech Connect

    Wayne, R.

    1985-01-01

    Red light stimulates germination in the spores of Onoclea sensibilis L. Phytochrome is confirmed to be the photoreceptor pigment in the germination response by demonstrating red-far-red photoreversibility. External Ca/sup 2 +/ is required for this response with a threshold at a submicromolar concentration. Red light stimulates an increase in the total concentration of intracellular calcium in the spores as determined by atomic absorption spectroscopy. Subsequent exposure to far-red light inhibits the red light-induced increase in intracellular calcium. The majority of the increase occurs 5 minutes after the onset of irradiation. The calcium-antagonist, La/sup 3 +/ inhibits both germination and the red light-induced increase in intracellular calcium. Using /sup 31/P-nuclear magnetic resonance spectroscopy, the author tested the hypothesis that a sustained increase in intracellular pH contributes to the signal transduction chain. He never detected a red light-induced increase in intracellular pH or a change in portion efflux. An artificially induced change in intracellular pH of greater than 1 pH unit (5.8-7.2) has no effect on germination. Although the intracellular pH can be varied in magnitude greater than it would be expected to change if it were acting as an intracellular signal, germination of Onoclea spores is independent of intracellular pH in this range. These data indicate that a sustained increase in intracellular pH does not contribute to the single transduction chain phytochrome-mediated fern spore germination. Therefore, Ca/sup 2 +/, but not pH, contributes to the signal transduction chain in phytochrome-mediated fern spore germination.

  4. Light-regulated expression of the nitrate-reductase and nitrite-reductase genes in tomato and in the phytochrome-deficient aurea mutant of tomato.

    PubMed

    Becker, T W; Foyer, C; Caboche, M

    1992-08-01

    The phytochrome-deficient aurea mutant of tomato (Lycopersicon esculentum (L.) Mill) was used to investigate if phytochrome plays a role in the regulation of nitrate-reductase (NR, EC 1.6.6.1) and nitrite-reductase (NiR, EC 1.7.7.1) gene expression. We show that the expression of the tomato NR and NiR genes is stimulated by light and that this light response is mediated by the photoreceptor phytochrome. The red-light response of the NR and NiR genes was reduced in etiolated aurea seedlings when compared to isogenic wild-type cotyledons. The relative levels of NR mRNA and NiR transcripts and their diurnal fluctuations were identical in mature white-light-grown leaves of the wild-type and of the aurea mutant. The transcript levels for cab and RbcS (genes for the chlorophyll-a/b-binding protein of PSII and the small subunit of the enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase, respectively) in aurea leaves grown in white light were indistinguishable from the respective transcript levels in the leaves of the wildtype grown under the same conditions. Despite a severe reduction in the chlorophyll content, the rate of net CO2 uptake by leaves of the aurea mutant was only slightly reduced when compared to the rate of net photosynthesis of wild-type leaves. This difference in the photosynthetic performances of wild-type and aurea mutant plants disappeared during aging of the plants. The increase in zeaxanthin and the concomitant decrease in violaxanthin in leaves of the aurea mutant compared with the same pigment levels in leaves of the wild-type indicate that the activity of the xanthophyll cycle is increased in aurea leaves as a consequence of the reduced CO2-fixation capacity of the mutant leaves.

  5. Chromophore Structure in the Photocycle of the Cyanobacterial Phytochrome Cph1

    PubMed Central

    van Thor, Jasper J.; Mackeen, Mukram; Kuprov, Ilya; Dwek, Raymond A.; Wormald, Mark R.

    2006-01-01

    The chromophore conformations of the red and far red light induced product states “Pfr” and “Pr” of the N-terminal photoreceptor domain Cph1-N515 from Synechocystis 6803 have been investigated by NMR spectroscopy, using specific 13C isotope substitutions in the chromophore. 13C-NMR spectroscopy in the Pfr and Pr states indicated reversible chemical shift differences predominantly of the C4 carbon in ring A of the phycocyanobilin chromophore, in contrast to differences of C15 and C5, which were much less pronounced. Ab initio calculations of the isotropic shielding and optical transition energies identify a region for C4-C5-C6-N2 dihedral angle changes where deshielding of C4 is correlated with red-shifted absorption. These could occur during thermal reactions on microsecond and millisecond timescales after excitation of Pr which are associated with red-shifted absorption. A reaction pathway involving a hula-twist at C5 could satisfy the observed NMR and visible absorption changes. Alternatively, C15 Z-E photoisomerization, although expected to lead to a small change of the chemical shift of C15, in addition to changes of the C4-C5-C6-N2 dihedral angle could be consistent with visible absorption changes and the chemical shift difference at C4. NMR spectroscopy of a 13C-labeled chromopeptide provided indication for broadening due to conformational exchange reactions in the intact photoreceptor domain, which is more pronounced for the C- and D-rings of the chromophore. This broadening was also evident in the F2 hydrogen dimension from heteronuclear 1H-13C HSQC spectroscopy, which did not detect resonances for the 13C5-H, 13C10-H, and 13C15-H hydrogen atoms whereas strong signals were detected for the 13C-labeled chromopeptide. The most pronounced 13C-chemical shift difference between chromopeptide and intact receptor domain was that of the 13C4-resonance, which could be consistent with an increased conformational energy of the C4-C5-C6-N2 dihedral angle in the

  6. A role for ABCB19-mediated polar auxin transport in seedling photomorphogenesis mediated by cryptochrome 1 and phytochrome B.

    PubMed

    Wu, Guosheng; Cameron, John N; Ljung, Karin; Spalding, Edgar P

    2010-04-01

    During seedling establishment, blue and red light suppress hypocotyl growth through the cryptochrome 1 (cry1) and phytochrome B (phyB) photosensory pathways, respectively. How these photosensory pathways integrate with growth control mechanisms to achieve the appropriate degree of stem elongation was investigated by combining cry1 and phyB photoreceptor mutations with genetic manipulations of a multidrug resistance-like membrane protein known as ABCB19 that influenced auxin distribution within the plant, as evidenced by a combination of reporter gene assays and direct auxin measurements. Auxin signaling and ABCB19 protein levels, hypocotyl growth rates, and apical hook opening were measured in mutant and wild-type seedlings exposed to a range of red and blue light conditions. Ectopic/overexpression of ABCB19 (B19OE) greatly increased auxin in the hypocotyl, which reduced the sensitivity of hypocotyl growth specifically to blue light in long-term assays and red light in high-resolution, short-term assays. Loss of ABCB19 partially suppressed the cry1 hypocotyl growth phenotype in blue light. Hypocotyl growth of B19OE seedlings in red light was very similar to phyB mutants. Altered auxin distribution in B19OE seedlings also affected the opening of the apical hook. The cry1 and phyB photoreceptor mutations both increased ABCB19 protein levels at the plasma membrane, as measured by confocal microscopy. The B19OE plant proved to be a useful tool for determining aspects of the mechanism by which light, acting through cry1 or phyB, influences the auxin transport process to control hypocotyl growth during de-etiolation.

  7. Overexpression of phytochrome A and its hyperactive mutant improves shade tolerance and turf quality in creeping bentgrass and zoysiagrass.

    PubMed

    Ganesan, Markkandan; Han, Yun-Jeong; Bae, Tae-Woong; Hwang, Ok-Jin; Chandrasekhar, Thummala; Chandrasekkhar, Thummala; Shin, Ah-Young; Goh, Chang-Hyo; Nishiguchi, Satoshi; Song, In-Ja; Lee, Hyo-Yeon; Kim, Jeong-Il; Song, Pill-Soon

    2012-10-01

    Phytochrome A (phyA) in higher plants is known to function as a far-red/shade light-sensing photoreceptor in suppressing shade avoidance responses (SARs) to shade stress. In this paper, the Avena PHYA gene was introduced into creeping bentgrass (Agrostis stolonifera L.) and zoysiagrass (Zoysia japonica Steud.) to improve turf quality by suppressing the SARs. In addition to wild-type PHYA, a hyperactive mutant gene (S599A-PHYA), in which a phosphorylation site involved in light-signal attenuation was removed, was also transformed into the turfgrasses. Phenotypic traits of the transgenic plants were compared to assess the suppression of SARs under a simulated shade condition and outdoor field conditions after three growth seasons. Under the shade condition, the S599A-PhyA transgenic creeping bentgrass plants showed shade avoidance-suppressing phenotypes with a 45 % shorter leaf lengths, 24 % shorter internode lengths, and twofold increases in chlorophyll concentrations when compared with control plants. Transgenic zoysiagrass plants overexpressing S599A-PHYA also showed shade-tolerant phenotypes under the shade condition with reductions in leaf length (15 %), internode length (30 %), leaf length/width ratio (19 %) and leaf area (22 %), as well as increases in chlorophyll contents (19 %) and runner lengths (30 %) compared to control plants. The phenotypes of transgenic zoysiagrass were also investigated in dense field habitats, and the transgenic turfgrass exhibited shade-tolerant phenotypes similar to those observed under laboratory shade conditions. Therefore, the present study suggests that the hyperactive phyA is effective for the development of shade-tolerant plants, and that the shade tolerance nature is sustained under field conditions.

  8. SUPPRESSOR OF PHYTOCHROME B4-#3 Represses Genes Associated with Auxin Signaling to Modulate Hypocotyl Growth1[OPEN

    PubMed Central

    Iwase, Akira

    2016-01-01

    Developing seedlings are well equipped to alter their growth in response to external factors in order to maximize their chances of survival. SUPPRESSOR OF PHYTOCHROME B4-#3 (SOB3) and other members of the AT-HOOK MOTIF CONTAINING NUCLEAR LOCALIZED (AHL) family of transcription factors modulate the development of Arabidopsis (Arabidopsis thaliana) by repressing hypocotyl elongation in young seedlings growing in light. However, the molecular mechanism behind how AHLs influence seedling development is largely unknown. We have identified genes associated with auxin-mediated hypocotyl elongation as downstream targets of SOB3. We found that YUCCA8 (YUC8) as well as members of the SMALL AUXIN UP-REGULATED RNA19 (SAUR19) subfamily were down-regulated in the short-hypocotyl, gain-of-function SOB3-D mutant and up-regulated in the dominant-negative, tall-hypocotyl sob3-6 mutant. SOB3-D and sob3-6 hypocotyls also exhibited altered sensitivity to the polar auxin transport inhibitor N-1-napthylphthalamic acid, suggesting a critical connection between auxin and the modulation of seedling elongation by SOB3. Finally, we found that overexpression of GREEN FLUORESCENT PROTEIN-SAUR19 in the SOB3-D line partially rescued defects in hypocotyl elongation, and SOB3 bound directly to the promoters of YUC8 and SAUR19 subfamily members. Taken together, these data indicate that SOB3 modulates hypocotyl elongation in young seedlings by directly repressing the transcription of genes associated with auxin signaling. PMID:27342309

  9. PHYTOCHROME AND FLOWERING TIME1/MEDIATOR25 Regulates Lateral Root Formation via Auxin Signaling in Arabidopsis1[C][W

    PubMed Central

    Raya-González, Javier; Ortiz-Castro, Randy; Ruíz-Herrera, León Francisco; Kazan, Kemal; López-Bucio, José

    2014-01-01

    Root system architecture is a major determinant of water and nutrient acquisition as well as stress tolerance in plants. The Mediator complex is a conserved multiprotein complex that acts as a universal adaptor between transcription factors and the RNA polymerase II. In this article, we characterize possible roles of the MEDIATOR8 (MED8) and MED25 subunits of the plant Mediator complex in the regulation of root system architecture in Arabidopsis (Arabidopsis thaliana). We found that loss-of-function mutations in PHYTOCHROME AND FLOWERING TIME1 (PFT1)/MED25 increase primary and lateral root growth as well as lateral and adventitious root formation. In contrast, PFT1/MED25 overexpression reduces these responses, suggesting that PFT1/MED25 is an important element of meristematic cell proliferation and cell size control in both lateral and primary roots. PFT1/MED25 negatively regulates auxin transport and response gene expression in most parts of the plant, as evidenced by increased and decreased expression of the auxin-related reporters PIN-FORMED1 (PIN1)::PIN1::GFP (for green fluorescent protein), DR5:GFP, DR5:uidA, and BA3:uidA in pft1-2 mutants and in 35S:PFT1 seedlings, respectively. No alterations in endogenous auxin levels could be found in pft1-2 mutants or in 35S:PFT1-overexpressing seedlings. However, detailed analyses of DR5:GFP and DR5:uidA activity in wild-type, pft1-2, and 35S:PFT1 seedlings in response to indole-3-acetic acid, naphthaleneacetic acid, and the polar auxin transport inhibitor 1-N-naphthylphthalamic acid indicated that PFT1/MED25 principally regulates auxin transport and response. These results provide compelling evidence for a new role for PFT1/MED25 as an important transcriptional regulator of root system architecture through auxin-related mechanisms in Arabidopsis. PMID:24784134

  10. Thermoperiodic control of hypocotyl elongation depends on auxin-induced ethylene signaling that controls downstream PHYTOCHROME INTERACTING FACTOR3 activity.

    PubMed

    Bours, Ralph; Kohlen, Wouter; Bouwmeester, Harro J; van der Krol, Alexander

    2015-02-01

    We show that antiphase light-temperature cycles (negative day-night temperature difference [-DIF]) inhibit hypocotyl growth in Arabidopsis (Arabidopsis thaliana). This is caused by reduced cell elongation during the cold photoperiod. Cell elongation in the basal part of the hypocotyl under -DIF was restored by both 1-aminocyclopropane-1-carboxylic acid (ACC; ethylene precursor) and auxin, indicating limited auxin and ethylene signaling under -DIF. Both auxin biosynthesis and auxin signaling were reduced during -DIF. In addition, expression of several ACC Synthase was reduced under -DIF but could be restored by auxin application. In contrast, the reduced hypocotyl elongation of ethylene biosynthesis and signaling mutants could not be complemented by auxin, indicating that auxin functions upstream of ethylene. The PHYTOCHROME INTERACTING FACTORS (PIFs) PIF3, PIF4, and PIF5 were previously shown to be important regulators of hypocotyl elongation. We now show that, in contrast to pif4 and pif5 mutants, the reduced hypocotyl length in pif3 cannot be rescued by either ACC or auxin. In line with this, treatment with ethylene or auxin inhibitors reduced hypocotyl elongation in PIF4 overexpressor (PIF4ox) and PIF5ox but not PIF3ox plants. PIF3 promoter activity was strongly reduced under -DIF but could be restored by auxin application in an ACC Synthase-dependent manner. Combined, these results show that PIF3 regulates hypocotyl length downstream, whereas PIF4 and PIF5 regulate hypocotyl length upstream of an auxin and ethylene cascade. We show that, under -DIF, lower auxin biosynthesis activity limits the signaling in this pathway, resulting in low activity of PIF3 and short hypocotyls.

  11. I-125 ROPES eye plaque dosimetry: Validation of a commercial 3D ophthalmic brachytherapy treatment planning system and independent dose calculation software with GafChromic{sup ®} EBT3 films

    SciTech Connect

    Poder, Joel; Corde, Stéphanie

    2013-12-15

    Purpose: The purpose of this study was to measure the dose distributions for different Radiation Oncology Physics and Engineering Services, Australia (ROPES) type eye plaques loaded with I-125 (model 6711) seeds using GafChromic{sup ®} EBT3 films, in order to verify the dose distributions in the Plaque Simulator™ (PS) ophthalmic 3D treatment planning system. The brachytherapy module of RADCALC{sup ®} was used to independently check the dose distributions calculated by PS. Correction factors were derived from the measured data to be used in PS to account for the effect of the stainless steel ROPES plaque backing on the 3D dose distribution.Methods: Using GafChromic{sup ®} EBT3 films inserted in a specially designed Solid Water™ eye ball phantom, dose distributions were measured three-dimensionally both along and perpendicular to I-125 (model 6711) loaded ROPES eye plaque's central axis (CAX) with 2 mm depth increments. Each measurement was performed in full scatter conditions both with and without the stainless steel plaque backing attached to the eye plaque, to assess its effect on the dose distributions. Results were compared to the dose distributions calculated by Plaque Simulator™ and checked independently with RADCALC{sup ®}.Results: The EBT3 film measurements without the stainless steel backing were found to agree with PS and RADCALC{sup ®} to within 2% and 4%, respectively, on the plaque CAX. Also, RADCALC{sup ®} was found to agree with PS to within 2%. The CAX depth doses measured using EBT3 film with the stainless steel backing were observed to result in a 4% decrease relative to when the backing was not present. Within experimental uncertainty, the 4% decrease was found to be constant with depth and independent of plaque size. Using a constant dose correction factor of T= 0.96 in PS, where the calculated dose for the full water scattering medium is reduced by 4% in every voxel in the dose grid, the effect of the plaque backing was accurately

  12. Long-Term Operation and Maintenance of Engine Monitoring Systems - Recommendations Derived from 15 Years of OLMOS Use by the GAF

    DTIC Science & Technology

    2003-02-01

    vieillissants et le controle] [Symposium Partie A - Developpements dans le domaine de l’aeroacoustique et I’hydroacoustique numeriques ] [Symposium Partie B...derivatives is illustrated in Figure 2 (Source: [A100]). Strategies are known how to mitigate both hardware and Paper presented at the RTO A VTSymposium...8-11 October 2001. and published in RTO-MP-079(I). (SYB) 3-2 software related obsolescence problems [CT98, NRCOI]. Implementing these strategies

  13. Mechanism of Dual Targeting of the Phytochrome Signaling Component HEMERA/pTAC12 to Plastids and the Nucleus1[OPEN

    PubMed Central

    2017-01-01

    HEMERA (HMR) is a nuclear and plastidial dual-targeted protein. While it functions in the nucleus as a transcriptional coactivator in phytochrome signaling to regulate a distinct set of light-responsive, growth-relevant genes, in plastids it is known as pTAC12, which associates with the plastid-encoded RNA polymerase, and is essential for inducing the plastomic photosynthetic genes and initiating chloroplast biogenesis. However, the mechanism of targeting HMR to the nucleus and plastids is still poorly understood. Here, we show that HMR can be directly imported into chloroplasts through a transit peptide residing in the N-terminal 50 amino acids. Upon cleavage of the transit peptide and additional proteolytic processing, mature HMR, which begins from Lys-58, retains its biochemical properties in phytochrome signaling. Unexpectedly, expression of mature HMR failed to rescue not only the plastidial but also the nuclear defects of the hmr mutant. This is because the predicted nuclear localization signals of HMR are nonfunctional, and therefore mature HMR is unable to accumulate in either plastids or the nucleus. Surprisingly, fusing the transit peptide of the small subunit of Rubisco with mature HMR rescues both its plastidial and nuclear localization and functions. These results, combined with the observation that the nuclear form of HMR has the same reduced molecular mass as plastidial HMR, support a retrograde protein translocation mechanism in which HMR is targeted first to plastids, processed to the mature form, and then relocated to the nucleus. PMID:28232584

  14. Rewiring of jasmonate and phytochrome B signalling uncouples plant growth-defense tradeoffs

    PubMed Central

    Campos, Marcelo L.; Yoshida, Yuki; Major, Ian T.; de Oliveira Ferreira, Dalton; Weraduwage, Sarathi M.; Froehlich, John E.; Johnson, Brendan F.; Kramer, David M.; Jander, Georg; Sharkey, Thomas D.; Howe, Gregg A.

    2016-01-01

    Plants resist infection and herbivory with innate immune responses that are often associated with reduced growth. Despite the importance of growth-defense tradeoffs in shaping plant productivity in natural and agricultural ecosystems, the molecular mechanisms that link growth and immunity are poorly understood. Here, we demonstrate that growth-defense tradeoffs mediated by the hormone jasmonate are uncoupled in an Arabidopsis mutant (jazQ phyB) lacking a quintet of Jasmonate ZIM-domain transcriptional repressors and the photoreceptor phyB. Analysis of epistatic interactions between jazQ and phyB reveal that growth inhibition associated with enhanced anti-insect resistance is likely not caused by diversion of photoassimilates from growth to defense but rather by a conserved transcriptional network that is hardwired to attenuate growth upon activation of jasmonate signalling. The ability to unlock growth-defense tradeoffs through relief of transcription repression provides an approach to assemble functional plant traits in new and potentially useful ways. PMID:27573094

  15. Photobody Localization of Phytochrome B Is Tightly Correlated with Prolonged and Light-Dependent Inhibition of Hypocotyl Elongation in the Dark.

    PubMed

    Van Buskirk, Elise K; Reddy, Amit K; Nagatani, Akira; Chen, Meng

    2014-06-01

    Photobody localization of Arabidopsis (Arabidopsis thaliana) phytochrome B (phyB) fused to green fluorescent protein (PBG) correlates closely with the photoinhibition of hypocotyl elongation. However, the amino-terminal half of phyB fused to green fluorescent protein (NGB) is hypersensitive to light despite its inability to localize to photobodies. Therefore, the significance of photobodies in regulating hypocotyl growth remains debatable. Accumulating evidence indicates that under diurnal conditions, photoactivated phyB persists into darkness to inhibit hypocotyl elongation. Here, we examine whether photobodies are involved in inhibiting hypocotyl growth in darkness by comparing the PBG and NGB lines after the red light-to-dark transition. Surprisingly, after the transition from 10 μmol m(-2) s(-1) red light to darkness, PBG inhibits hypocotyl elongation three times longer than NGB. The disassembly of photobodies in PBG hypocotyl nuclei correlates tightly with the accumulation of the growth-promoting transcription factor PHYTOCHROME-INTERACTING FACTOR3 (PIF3). Destabilizing photobodies by either decreasing the light intensity or adding monochromatic far-red light treatment before the light-to-dark transition leads to faster PIF3 accumulation and a dramatic reduction in the capacity for hypocotyl growth inhibition in PBG. In contrast, NGB is defective in PIF3 degradation, and its hypocotyl growth in the dark is nearly unresponsive to changes in light conditions. Together, our results support the model that photobodies are required for the prolonged, light-dependent inhibition of hypocotyl elongation in the dark by repressing PIF3 accumulation and by stabilizing the far-red light-absorbing form of phyB. Our study suggests that photobody localization patterns of phyB could serve as instructive cues that control light-dependent photomorphogenetic responses in the dark.

  16. In response to partial plant shading, the lack of phytochrome A does not directly induce leaf senescence but alters the fine-tuning of chlorophyll biosynthesis.

    PubMed

    Brouwer, Bastiaan; Gardeström, Per; Keech, Olivier

    2014-07-01

    Phytochrome is thought to control the induction of leaf senescence directly, however, the signalling and molecular mechanisms remain unclear. In the present study, an ecophysiological approach was used to establish a functional connection between phytochrome signalling and the physiological processes underlying the induction of leaf senescence in response to shade. With shade it is important to distinguish between complete and partial shading, during which either the whole or only a part of the plant is shaded, respectively. It is first shown here that, while PHYB is required to maintain chlorophyll content in a completely shaded plant, only PHYA is involved in maintaining the leaf chlorophyll content in response to partial plant shading. Second, it is shown that leaf yellowing associated with strong partial shading in phyA-mutant plants actually correlates to a decreased biosynthesis of chlorophyll rather than to an increase of its degradation. Third, it is shown that the physiological impact of this decreased biosynthesis of chlorophyll in strongly shaded phyA-mutant leaves is accompanied by a decreased capacity to adjust the Light Compensation Point. However, the increased leaf yellowing in phyA-mutant plants is not accompanied by an increase of senescence-specific molecular markers, which argues against a direct role of PHYA in inducing leaf senescence in response to partial shade. In conclusion, it is proposed that PHYA, but not PHYB, is essential for fine-tuning the chlorophyll biosynthetic pathway in response to partial shading. In turn, this mechanism allows the shaded leaf to adjust its photosynthetic machinery to very low irradiances, thus maintaining a positive carbon balance and repressing the induction of leaf senescence, which can occur under prolonged periods of shade.

  17. Both PHYTOCHROME RAPIDLY REGULATED1 (PAR1) and PAR2 Promote Seedling Photomorphogenesis in Multiple Light Signaling Pathways1[C][W][OPEN

    PubMed Central

    Zhou, Peng; Song, Meifang; Yang, Qinghua; Su, Liang; Hou, Pei; Guo, Lin; Zheng, Xu; Xi, Yulin; Meng, Fanhua; Xiao, Yang; Yang, Li; Yang, Jianping

    2014-01-01

    Arabidopsis (Arabidopsis thaliana) seedlings undergo photomorphogenesis in the light and etiolation in the dark. Light-activated photoreceptors transduce the light signals through a series of photomorphogenesis promoting or repressing factors to modulate many developmental processes in plants, such as photomorphogenesis and shade avoidance. CONSTITUTIVE PHOTOMORPHOGENIC1 (COP1) is a conserved RING finger E3 ubiquitin ligase, which mediates degradation of several photomorphogenesis promoting factors, including ELONGATED HYPOCOTYL5 (HY5) and LONG HYPOCOTYL IN FAR-RED1 (HFR1), through a 26S proteasome-dependent pathway. PHYTOCHROME RAPIDLY REGULATED1 (PAR1) was first detected as an early repressed gene in both phytochrome A (phyA)-mediated far-red and phyB-mediated red signaling pathways, and subsequent studies showed that both PAR1 and PAR2 are negative factors of shade avoidance in Arabidopsis. However, the role of PAR1 and PAR2 in seedling deetiolation, and their relationships with other photomorphogenesis promoting and repressing factors are largely unknown. Here, we confirmed that both PAR1 and PAR2 redundantly enhance seedling deetiolation in multiple photoreceptor signaling pathways. Their transcript abundances are repressed by phyA, phyB, and cryptochrome1 under far-red, red, and blue light conditions, respectively. Both PAR1 and PAR2 act downstream of COP1, and COP1 mediates the degradation of PAR1 and PAR2 through the 26S proteasome pathway. Both PAR1 and PAR2 act in a separate pathway from HY5 and HFR1 under different light conditions, except for sharing in the same pathway with HFR1 under far-red light. Together, our results substantiate that PAR1 and PAR2 are positive factors functioning in multiple photoreceptor signaling pathways during seedling deetiolation. PMID:24335334

  18. Comparative functional analysis of full-length and N-terminal fragments of phytochrome C, D and E in red light-induced signaling.

    PubMed

    Ádám, Éva; Kircher, Stefan; Liu, Peng; Mérai, Zsuzsanna; González-Schain, Nahuel; Hörner, Maximilian; Viczián, András; Monte, Elena; Sharrock, Robert A; Schäfer, Eberhard; Nagy, Ferenc

    2013-10-01

    Phytochromes (phy) C, D and E are involved in the regulation of red/far-red light-induced photomorphogenesis of Arabidopsis thaliana, but only limited data are available on the mode of action and biological function of these lesser studied phytochrome species. We fused N-terminal fragments or full-length PHYC, D and E to YELLOW FLUORESCENT PROTEIN (YFP), and analyzed the function, stability and intracellular distribution of these fusion proteins in planta. The activity of the constitutively nuclear-localized homodimers of N-terminal fragments was comparable with that of full-length PHYC, D, E-YFP, and resulted in the regulation of various red light-induced photomorphogenic responses in the studied genetic backgrounds. PHYE-YFP was active in the absence of phyB and phyD, and PHYE-YFP controlled responses, as well as accumulation, of the fusion protein in the nuclei, was saturated at low fluence rates of red light and did not require functional FAR-RED ELONGATED HYPOCOTYL1 (FHY-1) and FHY-1-like proteins. Our data suggest that PHYC-YFP, PHYD-YFP and PHYE-YFP fusion proteins, as well as their truncated N-terminal derivatives, are biologically active in the modulation of red light-regulated photomorphogenesis. We propose that PHYE-YFP can function as a homodimer and that low-fluence red light-induced translocation of phyE and phyA into the nuclei is mediated by different molecular mechanisms.

  19. Phytochrome-like responses in Euglena: A low fluence response that reorganizes the spectral dependence of the high irradiance response in long-day photoperiodic induction of cell division.

    PubMed

    Bolige, Aoen; Goto, Ken

    2007-02-01

    Irradiance spectra change spatiotemporally, and angiosperms adapt accordingly, mainly through phytochromes. This study challenges the long-held belief that the flagellated alga Euglena gracilis lacks phytochromes and is therefore unaffected by spectral changes. We photoautotrophically cultured the alga under continuous light (LL), then transferred it to darkness. After about 26h in darkness, different irradiations for 3h enabled cell division in dark-arrested G2 cells evoking a high-irradiance response (HIR). The spectral characteristics of the irradiation during the LL period (pre-irradiation) defined the spectral sensitivity in the subsequent dark period. LL with light rich in the red spectrum led to a HIR to the red spectrum (R-HIR), whereas light rich in the far-red spectrum (FR) led to a FR-HIR. Finishing the period of pre-irradiation consisting of continuous cool-white fluorescent light (rich in R) by a FR pulse enhanced the characteristics of the FR-HIR 26h later. By contrast, a R pulse given at the end of the pre-irradiation rich in FR potentiated the R-HIR. The effects were completely photoreversible between R and FR with critical fluences of about 2mmolm(-2), satisfying the classic diagnostic feature of phytochromes. The action spectrum of the FR effect at the end of pre-irradiation consisting of continuous cool-white fluorescent light (rich in R) had a main peak at 740nm and a minor peak at 380nm, whereas antagonization of the FR effect had a main peak at 640nm and a minor peak at 480nm. Wavelengths of 610 and 670nm appeared in both spectra. We also demonstrated the photoreversibility of 380/640, 480/740, and (610 and 670)/(640 and 740) nm. We conclude that Euglena displays phytochrome-like responses similar to the 'shade avoidance' and 'end-of-day FR' effects reported in angiosperms.

  20. Solution-state (15)N NMR spectroscopic study of alpha-C-phycocyanin: implications for the structure of the chromophore-binding pocket of the cyanobacterial phytochrome Cph1.

    PubMed

    Hahn, Janina; Kühne, Ronald; Schmieder, Peter

    2007-12-17

    The detailed structure of the chromophore-binding pocket in phytochrome proteins and the structural changes associated with its photocycle are still matters of debate. Insight into the structure and dynamics of the binding pocket has been gained through the comparison of a (15)N NMR spectrum of alpha-C-phycocyanin, which is often used as a model system for the study of phytochromes, with the previously described (15)N NMR spectrum of the cyanobacterial phytochrome Cph1. The former spectrum supports the hypothesis that all four nitrogen atoms of the alpha-C-phycocyanin chromophore are protonated, in analogy with the proposed protonation state for the P(r) and P(fr) forms of Cph1. The spectra show that the chromophores in both proteins exhibit a distinct dynamic behavior, as also indicated by a NOESY spectrum of Cph1. Finally, stereochemical arguments and a Cph1 homology model support the hypothesis that the chromophore in Cph1 is most likely in the ZZZssa conformation in the P(r) form of the protein.

  1. SU-E-T-44: A Micro-Raman Spectroscopy Study of the Dose-Dependence of EBT3 GafChromicTM Films for Quantifying the Degree of Molecular Polymerization

    SciTech Connect

    Callens, M; Van Den Abeele, K; Crijns, W; Depuydt, T; Maes, F; Haustermans, K; Simons, V; De Wolf, I; D’hooge, J; D’Agostino, E; Pfeiffer, H

    2015-06-15

    Purpose: Radiochromic films, such as the poly-diacetylene-based EBT3 GafChromic{sup TM} films (Ashland Specialty Ingredients, Wayne, NY, USA), are widely used for dosimetry applications because of their clear energy independence, high spatial resolution, near tissue equivalence and easy handling. The films undergo a slight color change by radiation-induced polymerization of diacetylene monomers. But more importantly, the film becomes optically less transparent with increasing radiation dose, with a saturation starting between 10 and 20 Gy, i.e. a common SBRT dose level. In contrast to the chromatic properties, less attention has been given to the underlying molecular mechanism that induces this partial color change and strongly reduces the transparency. Therefore, the current work investigates the variation of the molecular composition of the active layer of EBT3 films for an SBRT dose range. Method: Uncoated EBT3 films were irradiated with a 6 MV photon beam using dose levels between 0 and 20 Gy. The relative variation of the polymer content as a function of the applied radiation dose was studied using micro-Raman spectroscopy. Raman spectroscopy with a 633 nm probe laser incident on the active layer allowed to identify the film constituents and to estimate the amount of poly-diacetylenes from the intensities of the unique molecular vibrations of the molecule. Results: The normalized intensity of all polymeric vibrations, and most notably the polymeric triple and double carbon-carbon bonds at 2058 cm{sup −1} and 1446 cm{sup −1} respectively, increase with increasing dose up to a saturation level starting at about 10 Gy, indicating a corresponding increase and saturation of the amount of polymers. This molecular saturation process is the main cause of the non-linear dose response (i.e. a transparency reduction) and of the limited dose range of the studied films. Conclusion: Raman spectroscopy provides new and more fundamental insights in the mechanism of the

  2. Status of the GAF Tornado reconnaissance system

    NASA Astrophysics Data System (ADS)

    Siegert, Eva; Hochenbleicher, Gerhard

    1996-11-01

    The development of the new reconnaissance pod for the German Air Force is continuing according to schedule. A first flight is planned for the end of 1996. Carried on the centerline station of the IDS Tornado, the pod contains two daylight film cameras and one infra-red linescanner system. The infra-red image is recorded on a digital tape recorder and will also be displayed on the TV-Tabs. The modular structure of the pod exhibits a high flexibility for incorporation of various sensor systems on other payloads.

  3. Phytochrome-mediated germination and early development in spores of Dryopteris filix-mas L.: phase-specific and non phase-specific inhibition by staurosporine

    NASA Technical Reports Server (NTRS)

    Haas, C. J.; Scheuerlein, R.; Roux, S. J.

    1991-01-01

    The alkaloid staurosporine, currently known as the most potent inhibitor of protein kinase C, PKC, was tested for its ability to inhibit phytochrome-mediated spore germination in Dryopteris filix-mas L., evaluated by the induction of chlorophyll synthesis. Approximately half-maximal inhibition was obtained at a concentration of 10(-5) M. This effect of staurosporine was phase-specific and was found during the same period in which the presence of extracellular calcium is necessary for realization of the light signal. Furthermore, the ability of staurosporine to prevent progression of a germinated spore into early gametophyte development, evaluated by the accumulation of chlorophyll, was examined. Again, staurosporine (10(-5) M) significantly diminished chlorophyll accumulation, determined quantitatively in vivo by single-cell measurements, in a non-phase specific way. The fact that the phase-specific inhibitory effect of staurosporine in preventing germination was coincident with the phase-specific requirement of Ca2+ suggests that both Ca2+ and staurosporine affect the same step in the signal-transduction chain. A phosphorylation event catalysed by PKC or any Ca2+ -dependent protein kinase is proposed as the target of staurosporine and Ca2+.

  4. The GATA-type transcription factors GNC and GNL/CGA1 repress gibberellin signaling downstream from DELLA proteins and PHYTOCHROME-INTERACTING FACTORS.

    PubMed

    Richter, René; Behringer, Carina; Müller, Isabel Karin; Schwechheimer, Claus

    2010-09-15

    The phytohormone gibberellin (GA) regulates various developmental processes in plants such as germination, greening, elongation growth, and flowering time. DELLA proteins, which are degraded in response to GA, repress GA signaling by inhibitory interactions with PHYTOCHROME-INTERACTING FACTOR (PIF) family transcription factors. How GA signaling is controlled downstream from the DELLA and PIF regulators is, at present, unclear. Here, we characterize GNC (GATA, NITRATE-INDUCIBLE, CARBON-METABOLISM INVOLVED) and GNL/CGA1 (GNC-LIKE/CYTOKININ-RESPONSIVE GATA FACTOR1), two homologous GATA-type transcription factors from Arabidopsis thaliana that we initially identified as GA-regulated genes. Our genetic analyses of loss-of-function mutants and overexpression lines establish that GNC and GNL are functionally redundant regulators of germination, greening, elongation growth and flowering time. We further show by chromatin immunoprecipitation that both genes are potentially direct transcription targets of PIF transcription factors, and that their expression is up-regulated in pif mutant backgrounds. In line with a key role of GNC or GNL downstream from DELLA and PIF signaling, we find that their overexpression leads to gene expression changes that largely resemble those observed in a ga1 biosynthesis mutant or a pif quadruple mutant. These findings, together with the fact that gnc and gnl loss-of-function mutations suppress ga1 phenotypes, support the hypothesis that GNC and GNL are important repressors of GA signaling downstream from the DELLA and PIF regulators.

  5. A knot in the protein structure - probing the near-infrared fluorescent protein iRFP designed from a bacterial phytochrome.

    PubMed

    Stepanenko, Olesya V; Bublikov, Grigory S; Stepanenko, Olga V; Shcherbakova, Daria M; Verkhusha, Vladislav V; Turoverov, Konstantin K; Kuznetsova, Irina M

    2014-05-01

    The possibility of engineering near-infrared fluorescent proteins and biosensors from bacterial phytochrome photoreceptors (BphPs) has led to substantial interest in this family of proteins. The near-infrared fluorescent proteins have allowed non-invasive bio-imaging of deep tissues and whole organs in living animals. BphPs and derived near-infrared fluorescent proteins contain a structural element, called a knot, in their polypeptide chains. The formation of knot structures in proteins was refuted for a long time. Here, we studied the denaturation and renaturation processes of the near-infrared fluorescent probe iRFP, engineered from RpBphP2, which utilizes a heme-derived tetrapyrrole compound biliverdin as a chromophore. iRFP contains a unique figure-of-eight knot. The denaturation and renaturation curves of the iRFP apoform coincided well, suggesting efficient refolding. However, the iRFP holoform exhibited irreversible unfolding and aggregation associated with the bound chromophore. The knot structure in the apoform did not prevent subsequent binding of biliverdin, resulting in the functional iRFP holoform. We suggest that the irreversibility of protein unfolding is caused by post-translational protein modifications, such as chromophore binding, rather than the presence of the knot. These results are essential for future design of BphP-based near-infrared probes, and add important features to our knowledge of protein folding.

  6. LEAFY COTYLEDON1-CASEIN KINASE I-TCP15-PHYTOCHROME INTERACTING FACTOR4 Network Regulates Somatic Embryogenesis by Regulating Auxin Homeostasis1[OPEN

    PubMed Central

    Min, Ling; Hu, Qin; Li, Yaoyao; Xu, Jiao; Ma, Yizan; Zhu, Longfu; Yang, Xiyan; Zhang, Xianlong

    2015-01-01

    Somatic embryogenesis (SE) is an efficient tool for the propagation of plant species and also, a useful model for studying the regulatory networks in embryo development. However, the regulatory networks underlying the transition from nonembryogenic callus to somatic embryos during SE remain poorly understood. Here, we describe an upland cotton (Gossypium hirsutum) CASEIN KINASE I gene, GhCKI, which is a unique key regulatory factor that strongly affects SE. Overexpressing GhCKI halted the formation of embryoids and plant regeneration because of a block in the transition from nonembryogenic callus to somatic embryos. In contrast, defective GhCKI in plants facilitated SE. To better understand the mechanism by which GhCKI regulates SE, the regulatory network was analyzed. A direct upstream negative regulator protein, cotton LEAFY COTYLEDON1, was identified to be targeted to a cis-element, CTTTTC, in the promoter of GhCKI. Moreover, GhCKI interacted with and phosphorylated cotton CINCINNATA-like TEOSINTE BRANCHED1-CYCLOIDEA-PCF transcription factor15 by coordinately regulating the expression of cotton PHYTOCHROME INTERACTING FACTOR4, finally disrupting auxin homeostasis, which led to increased cell proliferation and aborted somatic embryo formation in GhCKI-overexpressing somatic cells. Our results show a complex process of SE that is negatively regulated by GhCKI through a complex regulatory network. PMID:26491146

  7. LEAFY COTYLEDON1-CASEIN KINASE I-TCP15-PHYTOCHROME INTERACTING FACTOR4 Network Regulates Somatic Embryogenesis by Regulating Auxin Homeostasis.

    PubMed

    Min, Ling; Hu, Qin; Li, Yaoyao; Xu, Jiao; Ma, Yizan; Zhu, Longfu; Yang, Xiyan; Zhang, Xianlong

    2015-12-01

    Somatic embryogenesis (SE) is an efficient tool for the propagation of plant species and also, a useful model for studying the regulatory networks in embryo development. However, the regulatory networks underlying the transition from nonembryogenic callus to somatic embryos during SE remain poorly understood. Here, we describe an upland cotton (Gossypium hirsutum) CASEIN KINASE I gene, GhCKI, which is a unique key regulatory factor that strongly affects SE. Overexpressing GhCKI halted the formation of embryoids and plant regeneration because of a block in the transition from nonembryogenic callus to somatic embryos. In contrast, defective GhCKI in plants facilitated SE. To better understand the mechanism by which GhCKI regulates SE, the regulatory network was analyzed. A direct upstream negative regulator protein, cotton LEAFY COTYLEDON1, was identified to be targeted to a cis-element, CTTTTC, in the promoter of GhCKI. Moreover, GhCKI interacted with and phosphorylated cotton CINCINNATA-like TEOSINTE BRANCHED1-CYCLOIDEA-PCF transcription factor15 by coordinately regulating the expression of cotton PHYTOCHROME INTERACTING FACTOR4, finally disrupting auxin homeostasis, which led to increased cell proliferation and aborted somatic embryo formation in GhCKI-overexpressing somatic cells. Our results show a complex process of SE that is negatively regulated by GhCKI through a complex regulatory network.

  8. LLM-Domain B-GATA Transcription Factors Promote Stomatal Development Downstream of Light Signaling Pathways in Arabidopsis thaliana Hypocotyls.

    PubMed

    Klermund, Carina; Ranftl, Quirin L; Diener, Julia; Bastakis, Emmanouil; Richter, René; Schwechheimer, Claus

    2016-03-01

    Stomata are pores that regulate the gas and water exchange between the environment and aboveground plant tissues, including hypocotyls, leaves, and stems. Here, we show that mutants of Arabidopsis thaliana LLM-domain B-GATA genes are defective in stomata formation in hypocotyls. Conversely, stomata formation is strongly promoted by overexpression of various LLM-domain B-class GATA genes, most strikingly in hypocotyls but also in cotyledons. Genetic analyses indicate that these B-GATAs act upstream of the stomata formation regulators SPEECHLESS(SPCH), MUTE, and SCREAM/SCREAM2 and downstream or independent of the patterning regulators TOO MANY MOUTHS and STOMATAL DENSITY AND DISTRIBUTION1 The effects of the GATAs on stomata formation are light dependent but can be induced in dark-grown seedlings by red, far-red, or blue light treatments. PHYTOCHROME INTERACTING FACTOR(PIF) mutants form stomata in the dark, and in this genetic background, GATA expression is sufficient to induce stomata formation in the dark. Since the expression of the LLM-domain B-GATAs GNC(GATA, NITRATE-INDUCIBLE, CARBON METABOLISM-INVOLVED) and GNC-LIKE/CYTOKININ-RESPONSIVE GATA FACTOR1 as well as that of SPCH is red light induced but the induction of SPCH is compromised in a GATA gene mutant background, we hypothesize that PIF- and light-regulated stomata formation in hypocotyls is critically dependent on LLM-domain B-GATA genes.

  9. 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…

  10. Light signalling mediated by phytochrome plays an important role in cold-induced gene expression through the C-repeat/dehydration responsive element (C/DRE) in Arabidopsis thaliana.

    PubMed

    Kim, Hyoun-Joung; Kim, Yun-Kyoung; Park, Jin-Young; Kim, Jungmook

    2002-03-01

    Low temperature induces a number of genes that encode the proteins promoting tolerance to freezing, mediated by ABA-dependent and ABA-independent pathways in plants. The cis-acting element called C/DRE is known to respond to low temperature independently of ABA action. To investigate the signalling and network of ABA-independent pathways, the transgenic Arabidopsis plants were generated containing several copies of the C/DRE derived from cor15a gene with a minimal promoter fused to a GUS reporter gene. The transgenic plants containing four copies of the C/DRE (4C/DRE-GUS) showed responsiveness to cold and drought treatments and were used for characterization of cold signalling and cross-talk. Cold-induced GUS expression was inhibited by okadaic acid at 1 nM, indicating that protein phosphatase 2A might act as a positive regulator. Light was shown to activate cold- and drought-induced GUS expression. Photo-reversibility of the GUS mRNA by red and far-red light with concomitant cold treatment suggests a role of phytochrome as a photoreceptor in mediating light signalling to activate the cold-induced gene expression through the C/DRE. Furthermore, GUS expression analysis in phyA or phyB or phyAphyB mutant backgrounds showed that phytochrome B is a primary photoreceptor responsible for the activation of cold-stress signalling in response to light. Light enhanced the induction kinetics of CBF1, 2, and 3 encoding the cognate transcription factors, and cor15a, in a consecutive manner compared to the dark condition in the cold, suggesting that the connection point between cold and light signalling mediated by phytochrome is at a higher step than the expression of CBF genes.

  11. Polar distribution of annexin-like proteins during phytochrome-mediated initiation and growth of rhizoids in the ferns Dryopteris and Anemia

    NASA Technical Reports Server (NTRS)

    Clark, G. B.; Turnwald, S.; Tirlapur, U. K.; Haas, C. J.; von der Mark, K.; Roux, S. J.; Scheuerlein, R.

    1995-01-01

    Although the calcium requirement of phytochrome-mediated fern spore germination and early rhizoid growth is well established, the calcium-binding proteins that serve as transducers for these responses are not known. Here we report the presence of annexin-like proteins in germinating spores of Dryopteris filix-mas (L.) Schott and Anemia phyllitidis (L.) Sw. and evidence that they may be important participants in early photomorphogenic changes in gametophytes. Immunolocalization and immunoblot assays of these proteins were carried out using polyclonal antibodies raised either against a 35-kDa annexin-like protein from pea or against anchorin CII from chicken. Western-blot analysis showed that crude protein extracts obtained from both species after red-light treatment contained two cross-reactive protein bands with molecular weights around 70 kDa. These proteins were annexin-like in that they bound to a phosphatidylserine affinity column in a calcium-dependent fashion. Using this column, two protein bands around 70 kDa, i.e. 67 and 73 kDa, were partially purified together with proteins at 36 kDa and a doublet at 54 kDa. Proteins of these latter molecular weights are suggested to be members of the annexin family, but no cross-reactivity could be found between these and the two antibodies used in our investigations. Immunodetectable levels of these proteins were observed only after light-mediated induction of spore germination. Imaging of the immuno-localization patterns observed with both antibodies showed that the annexin-like proteins are concentrated at the extreme tips of the rhizoids in D. filix-mas and A. phyllitidis during rhizoid initiation and all stages of elongation. We suggest that these proteins may play a major role in the tip-oriented exocytosis events that are critical for the initiation and growth of fern rhizoids.

  12. Leaf development and phytochrome modulate the activation ofpsbD-psbC transcription by high-fluence blue light in barley chloroplasts.

    PubMed

    Christopher, D A

    1996-03-01

    Activation ofpsbD transcription by light assists in maintaining the synthesis of the PS II reaction center protein, D2, which is photodamaged in plants exposed to high light. In this study, the photosensory pathways and mechanisms that regulate the expression of thepsbD-psbC light-responsive promoter, LRP, were investigated during barley (Hordeum vulgare L.) seedling development. Accumulation ofpsbD-psbC mRNAs in response to light was observed in apical sections of primary leaves with little or no increase in mRNAs in basal sections. In both 4.5- and 7.5-day-old etiolated seedlings, blue light was most effective for activating mRNA accumulation from thepsbD-psbC LRP. However, the response of the LRP to red light increased 7-fold in 7.5-day relative to 4.5-day-old seedlings. Blue light preferentially activatedpsbD-psbC transcription, while red light was most effective for activating total plastid transcription and the expression of genes encoding the small (RbcS) and large (rbcL) subunits of ribulose-1,5-bisphosphate carboxylase/oxygenase and Chl-a/b-binding protein (Lhcb). The stimulatory effects of red light onpsbD-psbC expression were partially reversed, and of blue light were not reversed, by subsequent pulses of far-red light. In contrast, continuous far-red light given together with blue light enhancedpsbD-psbC transcription in a synergistic manner. These observations indicate that phytochrome modulates the effects of high-fluence blue light onpsbD-psbC transcription by affecting total plastid transcription.

  13. GT-2: in vivo transcriptional activation activity and definition of novel twin DNA binding domains with reciprocal target sequence selectivity.

    PubMed

    Ni, M; Dehesh, K; Tepperman, J M; Quail, P H

    1996-06-01

    GT-2 is a novel DNA binding protein that interacts with a triplet functionally defined, positively acting GT-box motifs (GT1-bx, GT2-bx, and GT3-bx) in the rice phytochrome A gene (PHYA) promoter. Data from a transient transfection assay used here show that recombinant GT-2 enhanced transcription from both homologous and heterologous GT-box-containing promoters, thereby indicating that this protein can function as a transcriptional activator in vivo. Previously, we have shown that GT-2 contains separate DNA binding determinants in its N- and C-terminal halves, with binding site preferences for the GT3-bx and GT2-bx promoter motifs, respectively. Here, we demonstrate that the minimal DNA binding domains reside within dual 90-amino acid polypeptide segments encompassing duplicated sequences, termed trihelix regions, in each half of the molecule, plus 15 additional immediately adjacent amino acids downstream. These minimal binding domains retained considerable target sequence selectivity for the different GT-box motifs, but this selectivity was enhanced by a separate polypeptide segment farther downstream on the C-terminal side of each trihelix region. Therefore, the data indicate that the twin DNA binding domains of GT-2 each consist of a general GT-box recognition core with intrinsic differential binding activity toward closely related target motifs and a modified sequence conferring higher resolution reciprocal selectivity between these motifs.

  14. Phytochrome B Mediates the Regulation of Chlorophyll Biosynthesis through Transcriptional Regulation of ChlH and GUN4 in Rice Seedlings.

    PubMed

    Inagaki, Noritoshi; Kinoshita, Keisuke; Kagawa, Takatoshi; Tanaka, Ayumi; Ueno, Osamu; Shimada, Hiroaki; Takano, Makoto

    2015-01-01

    Accurate regulation of chlorophyll synthesis is crucial for chloroplast formation during the greening process in angiosperms. In this study, we examined the role of phytochrome B (phyB) in the regulation of chlorophyll synthesis in rice seedlings (Oryza sativa L.) through the characterization of a pale-green phenotype observed in the phyB mutant grown under continuous red light (Rc) irradiation. Our results show that the Rc-induced chlorophyll accumulation can be divided into two components--a phyB-dependent and a phyB-independent component, and that the pale-green phenotype is caused by the absence of the phyB-dependent component. To elucidate the role of the missing component we established an Rc-induced greening experiment, the results of which revealed that several genes encoding proteins on the chlorophyll branch were repressed in the phyB mutant. Notable among them were ChlH and GUN4 genes, which encode subunit H and an activating factor of magnesium chelatase (Mg-chelatase), respectively, that were largely repressed in the mutant. Moreover, the kinetic profiles of chlorophyll precursors suggested that Mg-chelatase activity simultaneously decreased with the reduction in the transcript levels of ChlH and GUN4. These results suggest that phyB mediates the regulation of chlorophyll synthesis through transcriptional regulation of these two genes, whose products exert their action at the branching point of the chlorophyll biosynthesis pathway. Reduction of 5-aminolevulinic acid (5-ALA) synthesis could be detected in the mutant, but the kinetic profiles of chlorophyll precursors indicated that it was an event posterior to the reduction of the Mg-chelatase activity. It means that the repression of 5-ALA synthesis should not be a triggering event for the appearance of the pale-green phenotype. Instead, the repression of 5-ALA synthesis might be important for the subsequent stabilization of the pale-green phenotype for preventing excessive accumulation of hazardous

  15. Phytochrome B Mediates the Regulation of Chlorophyll Biosynthesis through Transcriptional Regulation of ChlH and GUN4 in Rice Seedlings

    PubMed Central

    Kagawa, Takatoshi; Tanaka, Ayumi; Ueno, Osamu; Shimada, Hiroaki; Takano, Makoto

    2015-01-01

    Accurate regulation of chlorophyll synthesis is crucial for chloroplast formation during the greening process in angiosperms. In this study, we examined the role of phytochrome B (phyB) in the regulation of chlorophyll synthesis in rice seedlings (Oryza sativa L.) through the characterization of a pale-green phenotype observed in the phyB mutant grown under continuous red light (Rc) irradiation. Our results show that the Rc-induced chlorophyll accumulation can be divided into two components—a phyB-dependent and a phyB-independent component, and that the pale-green phenotype is caused by the absence of the phyB-dependent component. To elucidate the role of the missing component we established an Rc-induced greening experiment, the results of which revealed that several genes encoding proteins on the chlorophyll branch were repressed in the phyB mutant. Notable among them were ChlH and GUN4 genes, which encode subunit H and an activating factor of magnesium chelatase (Mg-chelatase), respectively, that were largely repressed in the mutant. Moreover, the kinetic profiles of chlorophyll precursors suggested that Mg-chelatase activity simultaneously decreased with the reduction in the transcript levels of ChlH and GUN4. These results suggest that phyB mediates the regulation of chlorophyll synthesis through transcriptional regulation of these two genes, whose products exert their action at the branching point of the chlorophyll biosynthesis pathway. Reduction of 5-aminolevulinic acid (5-ALA) synthesis could be detected in the mutant, but the kinetic profiles of chlorophyll precursors indicated that it was an event posterior to the reduction of the Mg-chelatase activity. It means that the repression of 5-ALA synthesis should not be a triggering event for the appearance of the pale-green phenotype. Instead, the repression of 5-ALA synthesis might be important for the subsequent stabilization of the pale-green phenotype for preventing excessive accumulation of hazardous

  16. Chromophore Structure of Cyanobacterial Phytochrome Cph1 in the Pr State: Reconciling Structural and Spectroscopic Data by QM/MM Calculations

    PubMed Central

    Mroginski, Maria Andrea; von Stetten, David; Escobar, Francisco Velazquez; Strauss, Holger M.; Kaminski, Steve; Scheerer, Patrick; Günther, Mina; Murgida, Daniel H.; Schmieder, Peter; Bongards, Christian; Gärtner, Wolfgang; Mailliet, Jo; Hughes, Jon; Essen, Lars-Oliver; Hildebrandt, Peter

    2009-01-01

    A quantum mechanics (QM)/molecular mechanics (MM) hybrid method was applied to the Pr state of the cyanobacterial phytochrome Cph1 to calculate the Raman spectra of the bound PCB cofactor. Two QM/MM models were derived from the atomic coordinates of the crystal structure. The models differed in the protonation site of His260 in the chromophore-binding pocket such that either the δ-nitrogen (M-HSD) or the ɛ-nitrogen (M-HSE) carried a hydrogen. The optimized structures of the two models display small differences specifically in the orientation of His260 with respect to the PCB cofactor and the hydrogen bond network at the cofactor-binding site. For both models, the calculated Raman spectra of the cofactor reveal a good overall agreement with the experimental resonance Raman (RR) spectra obtained from Cph1 in the crystalline state and in solution, including Cph1 adducts with isotopically labeled PCB. However, a distinctly better reproduction of important details in the experimental spectra is provided by the M-HSD model, which therefore may represent an improved structure of the cofactor site. Thus, QM/MM calculations of chromoproteins may allow for refining crystal structure models in the chromophore-binding pocket guided by the comparison with experimental RR spectra. Analysis of the calculated and experimental spectra also allowed us to identify and assign the modes that sensitively respond to chromophore-protein interactions. The most pronounced effect was noted for the stretching mode of the methine bridge A-B adjacent to the covalent attachment site of PCB. Due a distinct narrowing of the A-B methine bridge bond angle, this mode undergoes a large frequency upshift as compared with the spectrum obtained by QM calculations for the chromophore in vacuo. This protein-induced distortion of the PCB geometry is the main origin of a previous erroneous interpretation of the RR spectra based on QM calculations of the isolated cofactor. PMID:19450486

  17. Crystallization and preliminary X-ray characterization of the full-length bacteriophytochrome from the plant pathogen Xanthomonas campestris pv. campestris.

    PubMed

    Klinke, Sebastián; Otero, Lisandro H; Rinaldi, Jimena; Sosa, Santiago; Guimarães, Beatriz G; Shepard, William E; Goldbaum, Fernando A; Bonomi, Hernán R

    2014-12-01

    Phytochromes give rise to the largest photosensor family known to date. However, they are underrepresented in the Protein Data Bank. Plant, cyanobacterial, fungal and bacterial phytochromes share a canonical architecture consisting of an N-terminal photosensory module (PAS2-GAF-PHY domains) and a C-terminal variable output module. The bacterium Xanthomonas campestris pv. campestris, a worldwide agricultural pathogen, codes for a single bacteriophytochrome (XccBphP) that has this canonical architecture, bearing a C-terminal PAS9 domain as the output module. Full-length XccBphP was cloned, expressed and purified to homogeneity by nickel-NTA affinity and size-exclusion chromatography and was then crystallized at room temperature bound to its cofactor biliverdin. A complete native X-ray diffraction data set was collected to a maximum resolution of 3.25 Å. The crystals belonged to space group P43212, with unit-cell parameters a = b = 103.94, c = 344.57 Å and a dimer in the asymmetric unit. Refinement is underway after solving the structure by molecular replacement.

  18. 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.

  19. 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

  20. 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.

  1. 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…

  2. 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…

  3. 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

  4. 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

  5. Light Signaling Mechanism of Two Tandem Bacteriophytochromes

    PubMed Central

    Yang, Xiaojing; Stojković, Emina A.; Ozarowski, Wesley B.; Kuk, Jane; Davydova, Erna; Moffat, Keith

    2015-01-01

    RpBphP2 and RpBphP3, two tandem bacteriophytochromes from the photosynthetic bacterium R. palustris, share high sequence identity but exhibit distinct photoconversion behavior. Unlike the canonical RpBphP2, RpBphP3 photoconverts to an unusual nearred-absorbing (Pnr) state; both are required for synthesis of light harvesting complexes under low-light conditions. Here we report the crystal structures of the photosensory core modules of RpBphP2 and RpBphP3. Despite different quaternary structures, RpBphP2 and RpBphP3 adopt nearly identical tertiary structures. The RpBphP3 structure reveals “tongue-and-groove” interactions at the interface between the GAF and PHY domains. A single mutation in the PRxSF motif at the GAF-PHY interface abolishes light-induced formation of the Pnr state in RpBphP3, possibly due to altered structural rigidity of the chromophore-binding pocket. Structural comparisons suggest that long-range signaling involves structural rearrangement of the helical spine at the dimer interface. These structures together with mutational studies provide insights into photoconversion and long-range signaling mechanism in phytochromes. PMID:26095026

  6. Dynamic antagonism between phytochromes and PIF family basic helix-loop-helix factors induces selective reciprocal responses to light and shade in a rapidly responsive transcriptional network in Arabidopsis.

    PubMed

    Leivar, Pablo; Tepperman, James M; Cohn, Megan M; Monte, Elena; Al-Sady, Bassem; Erickson, Erika; Quail, Peter H

    2012-04-01

    Plants respond to shade-modulated light signals via phytochrome (phy)-induced adaptive changes, termed shade avoidance. To examine the roles of Phytochrome-Interacting basic helix-loop-helix Factors, PIF1, 3, 4, and 5, in relaying such signals to the transcriptional network, we compared the shade-responsive transcriptome profiles of wild-type and quadruple pif (pifq) mutants. We identify a subset of genes, enriched in transcription factor-encoding loci, that respond rapidly to shade, in a PIF-dependent manner, and contain promoter G-box motifs, known to bind PIFs. These genes are potential direct targets of phy-PIF signaling that regulate the primary downstream transcriptional circuitry. A second subset of PIF-dependent, early response genes, lacking G-box motifs, are enriched for auxin-responsive loci, and are thus potentially indirect targets of phy-PIF signaling, mediating the rapid cell expansion induced by shade. Comparing deetiolation- and shade-responsive transcriptomes identifies another subset of G-box-containing genes that reciprocally display rapid repression and induction in response to light and shade signals. These data define a core set of transcriptional and hormonal processes that appear to be dynamically poised to react rapidly to light-environment changes via perturbations in the mutually antagonistic actions of the phys and PIFs. Comparing the responsiveness of the pifq and triple pif mutants to light and shade confirms that the PIFs act with overlapping redundancy on seedling morphogenesis and transcriptional regulation but that each PIF contributes differentially to these responses.

  7. Structure of the Full-Length Bacteriophytochrome from the Plant Pathogen Xanthomonas campestris Provides Clues to its Long-Range Signaling Mechanism.

    PubMed

    Otero, Lisandro Horacio; Klinke, Sebastián; Rinaldi, Jimena; Velázquez-Escobar, Francisco; Mroginski, María Andrea; Fernández López, María; Malamud, Florencia; Vojnov, Adrián Alberto; Hildebrandt, Peter; Goldbaum, Fernando Alberto; Bonomi, Hernán Ruy

    2016-09-25

    Phytochromes constitute a major superfamily of light-sensing proteins that are reversibly photoconverted between a red-absorbing (Pr) and a far-red-absorbing (Pfr) state. Bacteriophytochromes (BphPs) are found among photosynthetic and non-photosynthetic bacteria, including pathogens. To date, several BphPs have been biophysically characterized. However, it is still not fully understood how structural changes are propagated from the photosensory module to the output module during the signal transduction event. Most phytochromes share a common architecture consisting of an N-terminal photosensor that includes the PAS2-GAF-PHY domain triad and a C-terminal variable output module. Here we present the crystal structure of the full-length BphP from the plant pathogen Xanthomonas campestris pv. campestris (XccBphP) bearing its photosensor and its complete output module, a PAS9 domain. In the crystals, the protein was found to be in the Pr state, whereas diffraction data together with resonance Raman spectroscopic and theoretical results indicate a ZZZssa and a ZZEssa chromophore configuration corresponding to a mixture of Pr and Meta-R state, the precursor of Pfr. The XccBphP quaternary assembly reveals a head-to-head dimer in which the output module contributes to the helical dimer interface. The photosensor, which is shown to be a bathy-like BphP, is influenced in its dark reactions by the output module. Our structural analyses suggest that the photoconversion between the Pr and Pfr states in the full-length XccBphP may involve changes in the relative positioning of the output module. This work contributes to understand the light-induced structural changes propagated from the photosensor to the output modules in phytochrome signaling.

  8. 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;…

  9. 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).

  10. 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

  11. 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.

  12. 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.

  13. 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.

  14. 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…

  15. 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.

  16. 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…

  17. 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.

  18. Ectopic expression of a phytochrome B gene from Chinese cabbage (Brassica rapa L. ssp. pekinensis) in Arabidopsis thaliana promotes seedling de-etiolation, dwarfing in mature plants, and delayed flowering.

    PubMed

    Song, Mei-Fang; Zhang, Shu; Hou, Pei; Shang, Hong-Zhong; Gu, Hai-Ke; Li, Jing-Juan; Xiao, Yang; Guo, Lin; Su, Liang; Gao, Jian-Wei; Yang, Jian-Ping

    2015-04-01

    Phytochrome B (phyB) is an essential red light receptor that predominantly mediates seedling de-etiolation, shade-avoidance response, and flowering time. In this study, we isolate a full-length cDNA of PHYB, designated BrPHYB, from Chinese cabbage (Brassica rapa L. ssp. pekinensis), and we find that BrphyB protein has high amino acid sequence similarity and the closest evolutionary relationship to Arabidopsis thaliana phyB (i.e., AtphyB). Quantitative reverse transcription (RT)-PCR results indicate that the BrPHYB gene is ubiquitously expressed in different tissues under all light conditions. Constitutive expression of the BrPHYB gene in A. thaliana significantly enhances seedling de-etiolation under red- and white-light conditions, and causes dwarf stature in mature plants. Unexpectedly, overexpression of BrPHYB in transgenic A. thaliana resulted in reduced expression of gibberellins biosynthesis genes and delayed flowering under short-day conditions, whereas AtPHYB overexpression caused enhanced expression of FLOWERING LOCUS T and earlier flowering. Our results suggest that BrphyB might play an important role in regulating the development of Chinese cabbage. BrphyB and AtphyB have conserved functions during de-etiolation and vegetative plant growth and divergent functions in the regulation of flowering time.

  19. Frequency domain nonlinear optics

    NASA Astrophysics Data System (ADS)

    Legare, Francois

    2016-05-01

    The universal dilemma of gain narrowing occurring in fs amplifiers prevents ultra-high power lasers from delivering few-cycle pulses. This problem is overcome by a new amplification concept: Frequency domain Optical Parametric Amplification - FOPA. It enables simultaneous up-scaling of peak power and amplified spectral bandwidth and can be performed at any wavelength range of conventional amplification schemes, however, with the capability to amplify single cycles of light. The key idea for amplification of octave-spanning spectra without loss of spectral bandwidth is to amplify the broad spectrum ``slice by slice'' in the frequency domain, i.e. in the Fourier plane of a 4f-setup. The striking advantages of this scheme, are its capability to amplify (more than) one octave of bandwidth without shorting the corresponding pulse duration. This is because ultrabroadband phase matching is not defined by the properties of the nonlinear crystal employed but the number of crystals employed. In the same manner, to increase the output energy one simply has to increase the spectral extension in the Fourier plane and to add one more crystal. Thus, increasing pulse energy and shortening its duration accompany each other. A proof of principle experiment was carried out at ALLS on the sub-two cycle IR beam line and yielded record breaking performance in the field of few-cycle IR lasers. 100 μJ two-cycle pulses from a hollow core fibre compression setup were amplified to 1.43mJ without distorting spatial or temporal properties. Pulse duration at the input of FOPA and after FOPA remains the same. Recently, we have started upgrading this system to be pumped by 250 mJ to reach 40 mJ two-cycle IR few-cycle pulses and latest results will be presented at the conference. Furthermore, the extension of the concept of FOPA to other nonlinear optical processes will be discussed. Frequency domain nonlinear optics.

  20. 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.

  1. Space Domain Awareness

    DTIC Science & Technology

    2012-09-01

    information required to characterize a space object. Another key parameter to be considered is the frequency of observation. This sampling rate varies...useful to define the values of these parameters that approximate the current and future state of the space domain. The current catalog and network... Parameters used in estimating data needs for SDA Current Threshold Objective βmo , βimg 0.1, 10Kb 0.1, 10Kb 0.1, 10Kb Number of Objects (Na , Np

  2. 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).

  3. 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

  4. 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.

  5. 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.

  6. High Speed Aerodynamic Characteristics of the GAF0PH Aerofoil

    DTIC Science & Technology

    1980-09-01

    upper surface of the aerofoil for angles of incidence greater than 210. POSTAL ADDRESS: Chief Superintendent, Aeronautical Research Laboratories, Box...kCLAERO-.NOTE3 98 -AR-002-223 -LEVEL m DEPARTMENT OF DEFENCE 00 DEFENCE SCIENCE AND TECHNOLOGY ORGANISATION AERONAUTICAL RESEARCH LABORATORIES...MELBOURNE, VICTORIA AERODYNAMICS NOTE 398 ’,\\ HIGH SPEED AERODYNAMIC CHARACTERISTICS OF THE GAFPH AEROFOIL by ~B D :, . , .IR-© Approved for Public Release

  7. 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

  8. 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

  9. 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

  10. 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.

  11. 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

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. The very-low-fluence and high-irradiance responses of the phytochromes have antagonistic effects on germination, mannan-degrading activities, and DfGA3ox transcript levels in Datura ferox seeds.

    PubMed

    Arana, María Verónica; Burgin, María José; de Miguel, Lucila C; Sánchez, Rodolfo A

    2007-01-01

    Seed germination can be promoted by the modes of action of two of the phytochromes: the low-fluence response (LFR), which is the classical red (R)-far-red (FR) reversible response and the very-low-fluence response (VLFR) that can be saturated by extremely low levels of Pfr, which can be elicited by a saturating FR pulse. The Datura ferox seed population used in this work had acquired the capacity to germinate through a VLFR after pretreatment in a water-saturated atmosphere (WSA) at constant 25 degrees C. After 12 d in WSA germination after a FR pulse was 82%, while it was less than 10% in darkness. It was found that the VLFR of germination is associated with increments in the embryo growth potential (EGP) and in the activity of two enzymes related to the weakening of the micropylar region of the endosperm (ME); endo-beta-mannanase and beta-mannosidase. The FR pulse also significantly stimulated the expression of DfGA3ox, a GA 3beta-hydroxylase, suggesting that the promotion of germination by the VLFR is associated with an increase in the synthesis of active gibberellins. The promotive action of the VLFR on germination is reduced when the FR pulse is immediately followed by a continuous FR treatment for 24 h (FRc). The effect of FRc cannot be reproduced by hourly FR pulses during the same period, showing that the antagonistic effect of FRc is a high-irradiance response (HIR). The action of the HIR in germination is associated with a decrease of both the mannan-degrading enzyme activity and the expression of DfMan in the ME, whereas no changes in the EGP were observed. The HIR also inhibits the accumulation of DfGA3ox in embryos, indicating that its action on germination is mediated, at least in part, through the modulation of active GA contents in seeds. This is the first report of a gene that participates in the VLFR-HIR antagonism in seeds.

  2. 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

  3. 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.

  4. 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.

  5. Xanthomonas campestris attenuates virulence by sensing light through a bacteriophytochrome photoreceptor.

    PubMed

    Bonomi, Hernán R; Toum, Laila; Sycz, Gabriela; Sieira, Rodrigo; Toscani, Andrés M; Gudesblat, Gustavo E; Leskow, Federico C; Goldbaum, Fernando A; Vojnov, Adrián A; Malamud, Florencia

    2016-11-01

    Phytochromes constitute a major photoreceptor family found in plants, algae, fungi, and prokaryotes, including pathogens. Here, we report that Xanthomonas campestris pv. campestris (Xcc), the causal agent of black rot disease which affects cruciferous crops worldwide, codes for a functional bacteriophytochrome (XccBphP). XccBphP possesses an N-terminal PAS2-GAF-PHY photosensory domain triad and a C-terminal PAS9 domain as its output module. Our results show that illumination of Xcc, prior to plant infection, attenuates its virulence in an XccBphP-dependent manner. Moreover, in response to light, XccBphP downregulates xanthan exopolysaccharide production and biofilm formation, two known Xcc virulence factors. Furthermore, the XccbphP null mutant shows enhanced virulence, similar to that of dark-adapted Xcc cultures. Stomatal aperture regulation and callose deposition, both well-established plant defense mechanisms against bacterial pathogens, are overridden by the XccbphP strain. Additionally, an RNA-Seq analysis reveals that far-red light or XccBphP overexpression produces genomewide transcriptional changes, including the inhibition of several Xcc virulence systems. Our findings indicate that Xcc senses light through XccBphP, eliciting bacterial virulence attenuation via downregulation of bacterial virulence factors. The capacity of XccBphP to respond to light both in vitro and in vivo was abolished by a mutation on the conserved Cys13 residue. These results provide evidence for a novel bacteriophytochrome function affecting an infectious process.

  6. 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.

  7. 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.

  8. 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.

  9. 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…

  10. 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.

  11. 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…

  12. 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.

  13. Impact of Domain Analysis on Reuse Methods

    DTIC Science & Technology

    1989-11-06

    libraries with very different domain models . The semantic network knowledge representation system (differing in this respect from object-oriented approaches...2.1.4 Organizational Strategies ...... ............. 10 2.1.5 Role of Existing Systems ..... .............. ..11 2.2 Process Models for Domain Analysis...Acquire Domain Analysis Resources. ... 15 2.2.4 Develop the Domain Model ..... .............. .16 2.2.4.1 Identification of Domain Objects

  14. 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

  15. 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

  16. 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.

  17. 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.

  18. 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

  19. 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.

  20. 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.

  1. 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

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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...

  8. 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...

  9. 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...

  10. Pectin Homogalacturonans: Nanostructural Characterization of Methylesterified Domains

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  11. 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

  12. 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

  13. 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.

  14. 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.

  15. 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

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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)

  10. 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.

  11. 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.

  12. 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.

  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. 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.

  15. PHYTOCHOME STRUCTURE AND SIGNALING MECHANISMS

    PubMed Central

    Rockwell, Nathan C.; Su, Yi-Shin; Lagarias, J. Clark

    2009-01-01

    Phytochromes are a widespread family of red/far-red responsive photoreceptors first discovered in plants, where they constitute one of the three main classes of photomorphogenesis regulators. All phytochromes utilize covalently attached bilin chromophores that enable photoconversion between red-absorbing (Pr) and far-red-absorbing (Pfr) forms. Phytochromes are thus photoswitchable photosensors; canonical phytochromes have a conserved N-terminal photosensory core and a C-terminal regulatory region which typically includes a histidine-kinase-related domain. The discovery of new bacterial and cyanobacterial members of the phytochrome family within the last decade has greatly aided biochemical and structural characterization of this family, with the first crystal structure of a bacteriophytochrome photosensory core appearing in 2005. This structure and other recent biochemical studies have provided exciting new insights into the structure of phytochrome, the photoconversion process that is central to light sensing, and the mechanism of signal transfer by this important family of photoreceptors. PMID:16669784

  16. 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.

  17. 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.

  18. Discoidin Domain Receptors in Disease

    PubMed Central

    Borza, Corina M; Pozzi, Ambra

    2014-01-01

    Discoidin domain receptors, DDR1 and DDR2, lie at the intersection of two large receptor families, namely the extracellular matrix and tyrosine kinase receptors. As such, DDRs are uniquely positioned to function as sensors for extracellular matrix and to regulate a wide range of cell functions from migration and proliferation to cytokine secretion and extracellular matrix homeostasis/remodeling. While activation of DDRs by extracellular matrix collagens is required for normal development and tissue homeostasis, aberrant activation of these receptors following injury or in disease is detrimental. The availability of mice lacking DDRs has enabled us to identify key roles played by these receptors in disease initiation and progression. DDR1 promotes inflammation in atherosclerosis, lung fibrosis and kidney injury, while DDR2 contributes to osteoarthritis. Furthermore, both DDRs have been implicated in cancer progression. Yet the mechanisms whereby DDRs contribute to diseases progression are poorly understood. In this review we highlight the mechanisms whereby DDRs regulate two important processes, namely inflammation and tissue fibrosis. In addition, we discuss the challenges of targeting DDRs in disease. Selective targeting of these receptors requires understanding of how they interact with and are activated by extracellular matrix, and whether their cellular function is dependent on or independent of receptor kinase activity. PMID:24361528

  19. 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

  20. 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.

  1. 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.

  2. 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

  3. 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…

  4. 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…

  5. 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.

  6. 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.

  7. 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

  8. 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

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. Light-induced structural changes in a monomeric bacteriophytochrome

    PubMed Central

    Takala, Heikki; Niebling, Stephan; Berntsson, Oskar; Björling, Alexander; Lehtivuori, Heli; Häkkänen, Heikki; Panman, Matthijs; Gustavsson, Emil; Hoernke, Maria; Newby, Gemma; Zontone, Federico; Wulff, Michael; Menzel, Andreas; Ihalainen, Janne A.; Westenhoff, Sebastian

    2016-01-01

    Phytochromes sense red light in plants and various microorganism. Light absorption causes structural changes within the protein, which alter its biochemical activity. Bacterial phytochromes are dimeric proteins, but the functional relevance of this arrangement remains unclear. Here, we use time-resolved X-ray scattering to reveal the solution structural change of a monomeric variant of the photosensory core module of the phytochrome from Deinococcus radiodurans. The data reveal two motions, a bend and a twist of the PHY domain with respect to the chromophore-binding domains. Infrared spectroscopy shows the refolding of the PHY tongue. We conclude that a monomer of the phytochrome photosensory core is sufficient to perform the light-induced structural changes. This implies that allosteric cooperation with the other monomer is not needed for structural activation. The dimeric arrangement may instead be intrinsic to the biochemical output domains of bacterial phytochromes. PMID:27679804

  15. Cyanochrome fluorophores

    DOEpatents

    Ulijasz, Andrew T.; Vierstra, Richard D.

    2016-06-14

    Genetically-engineered cyanochrome fluorophore molecules (fluorophores) with increased fluorescence and with absorbing fluorescence in the blue and green (blue/green) portion of the light spectrum are provided. These fluorophores are derived from the domains of phytochromes, and in particular cyanobacterial phytochromes. Methods for generating these fluorophores and various applications of these fluorophores are also provided.

  16. 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%.

  17. Energy transfer between fusion biliproteins co-expressed with phycobiliprotein in Escherichia coli.

    PubMed

    Ma, Qiong; Zhou, Nan; Zhou, Ming

    2016-10-01

    In cyanobacteria, phycobiliproteins (PBS) show excellent energy transfer among the chromophores absorbing over most of the visible. The energy transfers are used to study phycobilisome assembly and bioimaging. Using All4261GAF2(C81L) as energy donor, ApcE(1-240/Δ87-130) as energy acceptor, we co-expressed fusion protein ApcE(1-240/Δ87-130)::All4261GAF2(C81L) with phycobiliprotein in Escherichia Coli and studied the energy transfer between two protein domains. With N-terminal His6 tag, ApcE(1-240/Δ87-130)::All4261GAF2(C81L) cannot be purified by nickel-affinity column. We added six histidines in the C-terminal of ApcE(1-240/Δ87-130)::All4261GAF2(C81L) and co-expressed it with phycobiliprotein. ApcE(1-240/Δ87-130)::PCB-All4261GAF2(C81L)His6 was purified successfully and only singly chromophorylated at All4261GAF2(C81L)His6 domain. The singly chromophorylate ApcE(1-240/Δ87-130)::PCB-All4261GAF2(C81L)His6 was incubated with fresh PCB and the doubly chromophorylated PCB-ApcE(1-240/Δ87-130)::PCB-All4261GAF2(C81L)His6 was obtained. The double chromophored fusion protein absorbed light in the range of 615-660 nm, and fluoresced only at 668 nm. Photochemistry analysis showed that excitation energy transfer from the short-wavelength absorbing at All4261GAF2(C81L) domain was achieved successfully to the long-wavelength absorbing at the ApcE(1-240/Δ87-130) domain.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  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. 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.

  7. 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.

  8. 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.

  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. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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

  2. 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.

  3. Targeting Discoidin Domain Receptors in Prostate Cancer

    DTIC Science & Technology

    2016-08-01

    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...DDRs in prostate cancer . During the first funding period, we conducted immunohistochemical studies by staining a 200 case Grade/Stage tissue

  4. 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

  5. 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.

  6. 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

  7. 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).

  8. 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.

  9. 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.

  10. 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.

  11. 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

  12. 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.

  13. 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.

  14. 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

  15. 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.

  16. Protein function prediction using domain families

    PubMed Central

    2013-01-01

    Here we assessed the use of domain families for predicting the functions of whole proteins. These 'functional families' (FunFams) were derived using a protocol that combines sequence clustering with supervised cluster evaluation, relying on available high-quality Gene Ontology (GO) annotation data in the latter step. In essence, the protocol groups domain sequences belonging to the same superfamily into families based on the GO annotations of their parent proteins. An initial test based on enzyme sequences confirmed that the FunFams resemble enzyme (domain) families much better than do families produced by sequence clustering alone. For the CAFA 2011 experiment, we further associated the FunFams with GO terms probabilistically. All target proteins were first submitted to domain superfamily assignment, followed by FunFam assignment and, eventually, function assignment. The latter included an integration step for multi-domain target proteins. The CAFA results put our domain-based approach among the top ten of 31 competing groups and 56 prediction methods, confirming that it outperforms simple pairwise whole-protein sequence comparisons. PMID:23514456

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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

  2. A new and unexpected domain-domain interaction in the AraC protein.

    PubMed

    Cole, Stephanie Dirla; Schleif, Robert

    2012-05-01

    An interaction between the dimerization domains and DNA binding domains of the dimeric AraC protein has previously been shown to facilitate repression of the Escherichia coli araBAD operon by AraC in the absence of arabinose. A new interaction between the domains of AraC in the presence of arabinose is reported here, the regulatory consequences of which are unknown. Evidence for the interaction is the following: the dissociation rate of arabinose-bound AraC from half-site DNA is considerably faster than that of free DNA binding domain, and the affinity of the dimerization domains for arabinose is increased when half-site DNA is bound. In addition, an increase in the fluorescence intensity of tryptophan residues located in the arabinose-bound dimerization domain is observed upon binding of half-site DNA to the DNA binding domains. Direct physical evidence of the new domain-domain interaction is demonstrated by chemical crosslinking and NMR experiments.

  3. 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.

  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. 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.

  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. 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

  8. 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.

  9. 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.

  10. 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.

  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. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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

  7. 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.

  8. 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

  9. 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.

  10. 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.

  11. 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.

  12. 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

  13. 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.

  14. 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.

  15. Reconstituting Protein Interaction Networks Using Parameter-Dependent Domain-Domain Interactions

    DTIC Science & Technology

    2013-05-07

    Superfamily ( SF ) [33], and SMART [34,35]. PFAM domains: FH2, Drf_FH3, and two Drf_GBD domains; SF domains: Formin homology 2 domain (FH2 domain) and ARM...annotation data from six commonly used annotation databases: PFAM-A (release 25.0) [32], Superfamily ( SF ) [33], SMART [34,35], PRODOM [36], TIGRFAM [37... SF 3,651 62.1 962,602 33.0 1,355 1,307 0.79 SMART 3,023 51.4 455,523 15.6 392 379 0.66 PRODOM 146 2.5 19,760 0.7 111 111 0.02 TIGRFAM 3,019 51.3

  16. 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.

  17. [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.

  18. 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.

  19. 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.

  20. A PH domain in ACAP1 possesses key features of the BAR domain in promoting membrane curvature

    PubMed Central

    Pang, Xiaoyun; Fan, Jun; Zhang, Yan; Zhang, Kai; Gao, Bingquan; Ma, Jun; Li, Jian; Deng, Yuchen; Zhou, Qiangjun; Egelman, Edward H.; Hsu, Victor W.; Sun, Fei

    2014-01-01

    SUMMARY The BAR (Bin-Amphiphysin-Rvs) domain undergoes dimerization to produce a curved protein structure, which superimposes onto membrane through electrostatic interactions to sense and impart membrane curvature. In some cases, a BAR domain also possesses an amphipathic helix that inserts into the membrane to induce curvature. ACAP1 (Arfgap with Coil coil, Ankyrin repeat and PH domain protein 1) contains a BAR domain. Here, we show that this BAR domain can neither bind membrane nor impart curvature, but instead, requires a neighboring PH (Pleckstrin Homology) domain to achieve these functions. Specific residues within the PH domain are responsible for both membrane binding and curvature generation. The BAR domain adjacent to the PH domain instead interacts with the BAR domains of neighboring ACAP1 proteins to enable clustering at the membrane. Thus, we have uncovered the molecular basis for an unexpected and unconventional collaboration between PH and BAR domains in membrane bending. PMID:25284369

  1. Effects of sub-domain structure on initial magnetization curve and domain size distribution of stacked media

    NASA Astrophysics Data System (ADS)

    Sato, S.; Kumagai, S.; Sugita, R.

    2015-03-01

    In this paper, in order to confirm the sub-domain structure in stacked media demagnetized with in-plane field, initial magnetization curves and magnetic domain size distribution were investigated. Both experimental and simulation results showed that an initial magnetization curve for the medium demagnetized with in-plane field (MDI) initially rose faster than that for the medium demagnetized with perpendicular field (MDP). It is inferred that this is because the MDI has a larger number of domain walls than the MDP due to the existence of the sub-domains, resulting in an increase in the probability of domain wall motion. Dispersion of domain size for the MDI was larger than that for the MDP. This is because sub-domains are formed not only inside the domain but also at the domain boundary region, and they change the position of the domain boundary to affect the domain size.

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

    PubMed

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

    2016-02-27

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

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

  4. Rsp5 WW domains interact directly with the carboxyl-terminal domain of RNA polymerase II.

    PubMed

    Chang, A; Cheang, S; Espanel, X; Sudol, M

    2000-07-07

    RSP5 is an essential gene in Saccharomyces cerevisiae and was recently shown to form a physical and functional complex with RNA polymerase II (RNA pol II). The amino-terminal half of Rsp5 consists of four domains: a C2 domain, which binds membrane phospholipids; and three WW domains, which are protein interaction modules that bind proline-rich ligands. The carboxyl-terminal half of Rsp5 contains a HECT (homologous to E6-AP carboxyl terminus) domain that catalytically ligates ubiquitin to proteins and functionally classifies Rsp5 as an E3 ubiquitin-protein ligase. The C2 and WW domains are presumed to act as membrane localization and substrate recognition modules, respectively. We report that the second (and possibly third) Rsp5 WW domain mediates binding to the carboxyl-terminal domain (CTD) of the RNA pol II large subunit. The CTD comprises a heptamer (YSPTSPS) repeated 26 times and a PXY core that is critical for interaction with a specific group of WW domains. An analysis of synthetic peptides revealed a minimal CTD sequence that is sufficient to bind to the second Rsp5 WW domain (Rsp5 WW2) in vitro and in yeast two-hybrid assays. Furthermore, we found that specific "imperfect" CTD repeats can form a complex with Rsp5 WW2. In addition, we have shown that phosphorylation of this minimal CTD sequence on serine, threonine and tyrosine residues acts as a negative regulator of the Rsp5 WW2-CTD interaction. In view of the recent data pertaining to phosphorylation-driven interactions between the RNA pol II CTD and the WW domain of Ess1/Pin1, we suggest that CTD dephosphorylation may be a prerequisite for targeted RNA pol II degradation.

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

    PubMed Central

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

    2016-01-01

    The use of Fourier domain model observer is challenged by iterative reconstruction (IR), because IR algorithms are nonlinear and IR images have noise texture different from that of FBP. A modified Fourier domain model observer, which incorporates nonlinear noise and resolution properties, has been proposed for IR and needs to be validated with human detection performance. On the other hand, the spatial domain model observer is theoretically applicable to IR, but more computationally intensive than the Fourier domain method. The purpose of this study is to compare the modified Fourier domain model observer to the spatial domain model observer with both FBP and IR images, using human detection performance as the gold standard. A phantom with inserts of various low contrast levels and sizes was repeatedly scanned 100 times on a third-generation, dual-source CT scanner at 5 dose levels and reconstructed using FBP and IR algorithms. The human detection performance of the inserts was measured via a 2-alternative-forced-choice (2AFC) test. In addition, two model observer performances were calculated, including a Fourier domain non-prewhitening model observer and a spatial domain channelized Hotelling observer. The performance of these two mode observers was compared in terms of how well they correlated with human observer performance. Our results demonstrated that the spatial domain model observer correlated well with human observers across various dose levels, object contrast levels, and object sizes. The Fourier domain observer correlated well with human observers using FBP images, but overestimated the detection performance using IR images. PMID:27239086

  6. Folding mechanism of a multiple independently-folding domain protein: double B domain of protein A.

    PubMed

    Arora, Pooja; Hammes, Gordon G; Oas, Terrence G

    2006-10-10

    The antibody binding properties of staphylococcal protein A (SpA) can be attributed to the presence of five highly homologous domains (E, D, A, B, and C). Although the folding of the B domain of protein A (BdpA) is well-characterized, the folding behavior of this domain in the context of full-length SpA in the cell remains unexplored. The sequence of the B domain is 89 and 91% identical to those of domains A and C, respectively. We have fused B domain sequences (BBdpA) as a close approximation of the A-B or B-C portion of SpA. Circular dichroism and fluorescence-detected denaturation curves of BBdpA are experimentally indistinguishable from those of BdpA. The rate constants for folding and unfolding from NMR line shape analysis for the single- and double-domain proteins are the same within experimental uncertainties (+/-20%). These results support the designation of SpA as a multiple independently-folding domain (MIFD) protein. We develop a mathematical model that describes the folding thermodynamics and kinetics of MIFD proteins. The model depicts MIFD protein folding and unfolding as a parallel network and explicitly calculates the flux through all parallel pathways. These fluxes are combined to give a complete description of the global thermodynamics and kinetics of the folding and unfolding of MIFD proteins. The global rates for complete folding and unfolding of a MIFD protein and those of the individual domains depend on the stability of the protein. We show that the global unfolding rate of a MIFD protein may be many orders of magnitude slower than that of the constituent domains.

  7. Critical role of domain crystallinity, domain purity and domain interface sharpness for reduced bimolecular recombination in polymer solar cells

    DOE PAGES

    Venkatesan, Swaminathan; Chen, Jihua; Ngo, Evan C.; ...

    2014-12-31

    In this study, inverted bulk heterojunction solar cells were fabricated using poly(3-hexylthiophene) (P3HT) blended with two different fullerene derivatives namely phenyl-C61-butyric acid methyl ester (PC60BM) and indene-C60 bis-adduct (IC60BA). The effects of annealing temperatures on the morphology, optical and structural properties were studied and correlated to differences in photovoltaic device performance. It was observed that annealing temperature significantly improved the performance of P3HT:IC60BA solar cells while P3HT:PC60BM cells showed relatively less improvement. The performance improvement is attributed to the extent of fullerene mixing with polymer domains. Energy filtered transmission electron microscopy (EFTEM) and x-ray diffraction (XRD) results showed that ICBAmore » mixes with disordered P3HT much more readily than PC60BM which leads to lower short circuit current density and fill factor for P3HT:IC60BA cells annealed below 120°C. Annealing above 120°C improves the crystallinity of P3HT in case of P3HT:IC60BA whereas in P3HT:PC60BM films, annealing above 80°C leads to negligible change in crystallinity. Crystallization of P3HT also leads to higher domain purity as seen EFTEM. Further it is seen that cells processed with additive nitrobenzene (NB) showed enhanced short circuit current density and power conversion efficiency regardless of the fullerene derivative used. Addition of NB led to nanoscale phase separation between purer polymer and fullerene domains. Kelvin probe force microscopy (KPFM) images showed that enhanced domain purity in additive casted films led to a sharper interface between polymer and fullerene. Lastly, enhanced domain purity and interfacial sharpness led to lower bimolecular recombination and higher mobility and charge carrier lifetime in NB modified devices.« less

  8. Regional Climate Model Sensitivity to Domain Size

    NASA Astrophysics Data System (ADS)

    Leduc, M.; Laprise, R.

    2006-05-01

    Regional Climate Models are increasingly used to add small-scale features that are not present in their lateral boundary conditions (LBCs). It is well known that the limited area over which a model integrates must be large enough to allow the full development of small scales features (Jones et al., 1995). On the other hand, integrations on very large domains have shown important departures from the driving data, unless large-scale nudging is applied (e.g., Castro and Pielke, 2005). Here the effects of domain size on the development of small-scales are examined using the "Big-Brother" approach developed by Denis et al. (2002). This method consists of generating a high-resolution simulation over a large domain (the Big-Brother). The next step is to degrade this dataset with a low-pass filter based on discrete cosine transform (DCT; Denis et al., 2002) to emulate coarse-resolution LBCs that are usually taken from GCMs or reanalyses. A second simulation (the Little-Brother) is driven by the coarse-resolution LBCs and generates its own small-scale features inside the new smaller domain. Nested and added scales of the Little- Brother can then be compared with the Big-Brother (unfiltered) ones by using the DCT-filter again. Three February months (1990,1991 and 1992) were integrated over a continental grid (Big-Brother: 196x196 gridpoints) with a spatial resolution of 45 km covering almost the entire North-America. After filtering, this dataset is used to drive five simulations with varying domain size (48x48, 72x72, 96x96, 120x120 and 144x144) centred on the same geographic location; all other parameters are kept constant. Monthly statistics of the five Little-Brothers are compared with the virtual reference (Big-Brother) over the common domain (28x28) corresponding to the smallest Little-Brother but without its sponge zone. Results show that temporal correlation of large-scale events increases when the domain size is reduced from 144x144 to 48x48. For the same domain

  9. Extra domains in secondary transport carriers and channel proteins.

    PubMed

    Barabote, Ravi D; Tamang, Dorjee G; Abeywardena, Shannon N; Fallah, Neda S; Fu, Jeffrey Yu Chung; Lio, Jeffrey K; Mirhosseini, Pegah; Pezeshk, Ronnie; Podell, Sheila; Salampessy, Marnae L; Thever, Mark D; Saier, Milton H

    2006-10-01

    "Extra" domains in members of the families of secondary transport carrier and channel proteins provide secondary functions that expand, amplify or restrict the functional nature of these proteins. Domains in secondary carriers include TrkA and SPX domains in DASS family members, DedA domains in TRAP-T family members (both of the IT superfamily), Kazal-2 and PDZ domains in OAT family members (of the MF superfamily), USP, IIA(Fru) and TrkA domains in ABT family members (of the APC superfamily), ricin domains in OST family members, and TrkA domains in AAE family members. Some transporters contain highly hydrophilic domains consisting of multiple repeat units that can also be found in proteins of dissimilar function. Similarly, transmembrane alpha-helical channel-forming proteins contain unique, conserved, hydrophilic domains, most of which are not found in carriers. In some cases the functions of these domains are known. They may be ligand binding domains, phosphorylation domains, signal transduction domains, protein/protein interaction domains or complex carbohydrate-binding domains. These domains mediate regulation, subunit interactions, or subcellular targeting. Phylogenetic analyses show that while some of these domains are restricted to closely related proteins derived from specific organismal types, others are nearly ubiquitous within a particular family of transporters and occur in a tremendous diversity of organisms. The former probably became associated with the transporters late in the evolutionary process; the latter probably became associated with the carriers much earlier. These domains can be located at either end of the transporter or in a central region, depending on the domain and transporter family. These studies provide useful information about the evolution of extra domains in channels and secondary carriers and provide novel clues concerning function.

  10. The Loyal Opposition Comments on Plan Domain Description Languages

    NASA Technical Reports Server (NTRS)

    Frank, Jeremy; Golden, Keith; Jonsson, Ari

    2003-01-01

    In this paper we take a critical look at PDDL 2.1 as designers and users of plan domain description languages. We describe planning domains that have features which are hard to model using PDDL 2.1. We then offer some suggestions on domain description language design, and describe how these suggestions make modeling our chosen domains easier.

  11. GAGA factor binding to DNA via a single trinucleotide sequence element.

    PubMed Central

    Wilkins, R C; Lis, J T

    1998-01-01

    GAGA transcription factor (GAF) is an essential protein in Drosophila , important for the transcriptional regulation of numerous genes. GAF binds to GA repeats in the promoters of these genes via a DNA-binding domain containing a single zinc finger. While GAF binding sites are typically composed of 3.5 GA repeats, the Drosophila hsp70 gene contains much smaller elements, some of which are as little as three bases (GAG) in length. Interestingly, the binding of GAF to more distant trinucleotide elements is relatively strong and not appreciably affected by the removal of larger GA arrays in the promoter. Moreover, a simple synthetic GAG sequence is sufficient to bind GAF in vitro . Here we directly compare the affinity of GAF for different sequence elements by immunoprecipitation and gel mobility shift analysis. Furthermore, our measures of the concentration of GAF in vivo indicate that it is a highly abundant nuclear protein, prevalent enough to occupy a sizable fraction of correspondingly abundant trinucleotide sites. PMID:9592153

  12. Flares In Time-Domain Surveys

    NASA Astrophysics Data System (ADS)

    Kowalski, Adam; Hawley, Suzanne; Davenport, James; Berlicki, Arkadiusz; Cauzzi, Gianna; Fletcher, Lyndsay; Heinzel, Petr; Notsu, Yuta; Loyd, Parke; Martinez Oliveros, Juan Carlos; Pugh, Chloe; Schmidt, Sarah Jane; Karmakar, Subhajeet; Pye, John; Flaccomio, Ettore

    2016-07-01

    Proceedings for the splinter session "Flares in Time-Domain Surveys" convened at Cool Stars 19 on June 07, 2016 in Uppsala, Sweden. Contains a two page summary of the splinter session, links to YouTube talks, and a PDF copy of the slides from the presenters.

  13. Developing Domain Ontologies for Course Content

    ERIC Educational Resources Information Center

    Boyce, Sinead; Pahl, Claus

    2007-01-01

    Ontologies have the potential to play an important role in instructional design and the development of course content. They can be used to represent knowledge about content, supporting instructors in creating content or learners in accessing content in a knowledge-guided way. While ontologies exist for many subject domains, their quality and…

  14. Factor Score Reliabilities and Domain Validities.

    ERIC Educational Resources Information Center

    Gorsuch, Richard L.

    1980-01-01

    Kaiser and Michael reported a formula for factor scores giving an internal consistency reliability and its square root, the domain validity. Using this formula is inappropriate if variables are included which have trival weights rather than salient weights for the factor for which the score is being computed. (Author/RL)

  15. Public Domain Microcomputer Software for Forestry.

    ERIC Educational Resources Information Center

    Martin, Les

    A project was conducted to develop a computer forestry/forest products bibliography applicable to high school and community college vocational/technical programs. The project director contacted curriculum clearinghouses, computer companies, and high school and community college instructors in order to obtain listings of public domain programs for…

  16. An English language interface for constrained domains

    NASA Technical Reports Server (NTRS)

    Page, Brenda J.

    1989-01-01

    The Multi-Satellite Operations Control Center (MSOCC) Jargon Interpreter (MJI) demonstrates an English language interface for a constrained domain. A constrained domain is defined as one with a small and well delineated set of actions and objects. The set of actions chosen for the MJI is from the domain of MSOCC Applications Executive (MAE) Systems Test and Operations Language (STOL) directives and contains directives for signing a cathode ray tube (CRT) on or off, calling up or clearing a display page, starting or stopping a procedure, and controlling history recording. The set of objects chosen consists of CRTs, display pages, STOL procedures, and history files. Translation from English sentences to STOL directives is done in two phases. In the first phase, an augmented transition net (ATN) parser and dictionary are used for determining grammatically correct parsings of input sentences. In the second phase, grammatically typed sentences are submitted to a forward-chaining rule-based system for interpretation and translation into equivalent MAE STOL directives. Tests of the MJI show that it is able to translate individual clearly stated sentences into the subset of directives selected for the prototype. This approach to an English language interface may be used for similarly constrained situations by modifying the MJI's dictionary and rules to reflect the change of domain.

  17. Nucleic acids encoding a cellulose binding domain

    DOEpatents

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

    1996-01-01

    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.

  18. Nucleic acids encoding a cellulose binding domain

    DOEpatents

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

    1996-03-05

    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. 15 figs.

  19. Solving the Cross-Domain Conundrum

    DTIC Science & Technology

    2013-03-01

    synchronous or asynchronous, depending on mission requirements and data pedigree . The cross-domain enterprise will also provide information discovery...context of Eisenhower’s Executive Order 10290. Today’s networks inherit their genetic disposition to the 1958 ARPA scheme of physical data segregation

  20. Scalable Domain Decomposed Monte Carlo Particle Transport

    SciTech Connect

    O'Brien, Matthew Joseph

    2013-12-05

    In this dissertation, we present the parallel algorithms necessary to run domain decomposed Monte Carlo particle transport on large numbers of processors (millions of processors). Previous algorithms were not scalable, and the parallel overhead became more computationally costly than the numerical simulation.