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Sample records for control light-induced chromatin

  1. Combinatorial Control of Light Induced Chromatin Remodeling and Gene Activation in Neurospora

    PubMed Central

    Sancar, Cigdem; Ha, Nati; Yilmaz, Rüstem; Tesorero, Rafael; Fisher, Tamas; Brunner, Michael; Sancar, Gencer

    2015-01-01

    Light is an important environmental cue that affects physiology and development of Neurospora crassa. The light-sensing transcription factor (TF) WCC, which consists of the GATA-family TFs WC1 and WC2, is required for light-dependent transcription. SUB1, another GATA-family TF, is not a photoreceptor but has also been implicated in light-inducible gene expression. To assess regulation and organization of the network of light-inducible genes, we analyzed the roles of WCC and SUB1 in light-induced transcription and nucleosome remodeling. We show that SUB1 co-regulates a fraction of light-inducible genes together with the WCC. WCC induces nucleosome eviction at its binding sites. Chromatin remodeling is facilitated by SUB1 but SUB1 cannot activate light-inducible genes in the absence of WCC. We identified FF7, a TF with a putative O-acetyl transferase domain, as an interaction partner of SUB1 and show their cooperation in regulation of a fraction of light-inducible and a much larger number of non light-inducible genes. Our data suggest that WCC acts as a general switch for light-induced chromatin remodeling and gene expression. SUB1 and FF7 synergistically determine the extent of light-induction of target genes in common with WCC but have in addition a role in transcription regulation beyond light-induced gene expression. PMID:25822411

  2. DNA-protein interactions in nucleosomes and in chromatin. Structural studies of chromatin stabilized by ultraviolet-light induced crosslinking.

    PubMed

    Mandel, R; Kolomijtseva, G; Brahms, J G

    1979-05-15

    Crosslinking induced by ultraviolet light irradiation at 254 nm has been utilized to investigate the structure of chromatin and isolated nucleosomes. The results presented here imply that the four core histones, as well as histone H1, have reactive groups within a bond length of the DNA bases. In nucleosomes depleted of H1, all of the core histones react similarly with the DNA and form crosslinks. In chromatin, the rate of crosslinking of all histones to DNA is essentially similar. Comparison of mononucleosomes, dinucleosomes and whole chromatin shows that the rate of crosslinking increases significantly with increasing number of connected nucleosomes. These differences in the rate of crosslinking are interpreted in terms of interactions between neighbouring nucleosomes on the chromatin fiber, which are absent in an isolated mononucleosome.

  3. Relationship of ultraviolet light-induced DNA-protein cross-linkage to chromatin structure.

    PubMed

    Bianchi, N O; Morgan, W F; Cleaver, J E

    1985-02-01

    The production of banding patterns in metaphase chromosomes by restriction enzymes is inhibited by ultraviolet (UV) irradiation. Irradiation of fixed chromatin produces a 15-fold decrease in DNA extraction by restriction enzymes in comparison with that observed by irradiation before fixation. Alcohol-acid fixation of chromatin produces two major changes, the extraction of histones and dehydration. The effect of UV light is probably the result of a net increase in the yield of DNA-protein cross-links at comparable fluences of UV light and of the stabilization of the structural changes in the fixed chromatin fibril induced by the photoadducts. The X-irradiation of cells before fixation, as well as the rehydration of fixed chromatin, increases the extraction of DNA from fixed chromatin irradiated with UV light to levels similar to or even higher than those obtained with living cells. The effect of UV light before and after fixation on the extraction of DNA by restriction enzymes and proteinase K can be related to changes in chromatin structure and DNA conformation.

  4. UV light-induced DNA lesions cause dissociation of yeast RNA polymerases-I and establishment of a specialized chromatin structure at rRNA genes

    PubMed Central

    Tremblay, Maxime; Charton, Romain; Wittner, Manuel; Levasseur, Geneviève; Griesenbeck, Joachim; Conconi, Antonio

    2014-01-01

    The cytotoxicity of UV light-induced DNA lesions results from their interference with transcription and replication. DNA lesions arrest elongating RNA polymerases, an event that triggers transcription-coupled nucleotide excision repair. Since arrested RNA polymerases reduce the accessibility of repair factors to DNA lesions, they might be displaced. The fate of arrested RNA polymerases-II at DNA lesions has been extensively studied, yielding partially contradictory results. Considerably less is known about RNA polymerases-I that transcribe nucleosomes-depleted rRNA genes at very high rate. To investigate the fate of arrested RNA polymerases-I at DNA lesions, chromatin-immunoprecipitation, electron microscopy, transcription run-on, psoralen-cross-linking and chromatin-endogenous cleavage were employed. We found that RNA polymerases-I density increased at the 5′-end of the gene, likely due to continued transcription initiation followed by elongation and pausing/release at the first DNA lesion. Most RNA polymerases-I dissociated downstream of the first DNA lesion, concomitant with chromatin closing that resulted from deposition of nucleosomes. Although nucleosomes were deposited, the high mobility group-box Hmo1 (component of actively transcribed rRNA genes) remained associated. After repair of DNA lesions, Hmo1 containing chromatin might help to restore transcription elongation and reopening of rRNA genes chromatin. PMID:24097442

  5. Arabidopsis Pol II-Dependent in Vitro Transcription System Reveals Role of Chromatin for Light-Inducible rbcS Gene Transcription.

    PubMed

    Ido, Ayaka; Iwata, Shinya; Iwata, Yuka; Igarashi, Hisako; Hamada, Takahiro; Sonobe, Seiji; Sugiura, Masahiro; Yukawa, Yasushi

    2016-02-01

    In vitro transcription is an essential tool to study the molecular mechanisms of transcription. For over a decade, we have developed an in vitro transcription system from tobacco (Nicotiana tabacum)-cultured cells (BY-2), and this system supported the basic activities of the three RNA polymerases (Pol I, Pol II, and Pol III). However, it was not suitable to study photosynthetic genes, because BY-2 cells have lost their photosynthetic activity. Therefore, Arabidopsis (Arabidopsis thaliana) in vitro transcription systems were developed from green and etiolated suspension cells. Sufficient in vitro Pol II activity was detected after the minor modification of the nuclear soluble extracts preparation method; removal of vacuoles from protoplasts and L-ascorbic acid supplementation in the extraction buffer were particularly effective. Surprisingly, all four Arabidopsis Rubisco small subunit (rbcS-1A, rbcS-1B, rbcS-2B, and rbcS-3B) gene members were in vitro transcribed from the naked DNA templates without any light-dependent manner. However, clear light-inducible transcriptions were observed using chromatin template of rbcS-1A gene, which was prepared with a human nucleosome assembly protein 1 (hNAP1) and HeLa histones. This suggested that a key determinant of light-dependency through the rbcS gene transcription was a higher order of DNA structure (i.e. chromatin). PMID:26662274

  6. Chromatin Control of Developmental Dynamics and Plasticity.

    PubMed

    Perino, Matteo; Veenstra, Gert Jan C

    2016-09-26

    Chromatin structure is intimately connected with gene expression and cell identity. Here we review recent advances in the field and discuss how establishment of cell identity during development is accompanied by large-scale remodeling of the epigenetic landscape and how this remodeling drives and supports lineage specification and maintenance. We discuss maternal control of the early embryonic epigenetic landscape, selective usage of enhancer clusters via 3D chromatin contacts leading to activation of transcription factor networks, and conserved regulation of developmental pathways by specific DNA demethylation of key regulatory regions. Together, these processes establish an epigenetic framework regulating different phases of embryonic development. PMID:27676434

  7. A light-inducible CRISPR/Cas9 system for control of endogenous gene activation

    PubMed Central

    Polstein, Lauren R.; Gersbach, Charles A.

    2015-01-01

    Optogenetic systems enable precise spatial and temporal control of cell behavior. We engineered a light-activated CRISPR/Cas9 effector (LACE) system that induces transcription of endogenous genes in the presence of blue light. This was accomplished by fusing the light-inducible heterodimerizing proteins CRY2 and CIB1 to a transactivation domain and the catalytically inactive dCas9, respectively. The versatile LACE system can be easily directed to new DNA sequences for the dynamic regulation of endogenous genes. PMID:25664691

  8. Non-photochemical light-induced nucleation and control of polymorphism through polarization-switching

    NASA Astrophysics Data System (ADS)

    Matic, Jelena

    This dissertation examines the effect of polarization, intensity and wavelength on crystallization from supersaturated solutions using non-photochemical light-induced nucleation (NPLIN). Using NPLIN crystal structure can be controlled. Intense pulses of linearly-polarized laser light induce the nucleation of the gamma-glycine polymorph, which otherwise does not form under the same conditions. Moreover, intense pulses of circularly-polarized light induce the alpha-glycine polymorph to crystallize from solutions prepared using the same procedure. The observation that polymorphism could be controlled by changing between linear and circular polarization was named polarization-switching. It represents the strongest evidence to date that the mechanism involved in NPLIN is indeed non-photochemical. The interaction of light and matter responsible for the phenomenon is discussed, as well as the implication of the results of NPLIN experiments on the current understanding of the structure of supersaturated solutions and nucleation. The success rate of NPLIN shows a non-linear dependence on intensity, with a threshold value of 0.02--0.03 GW/cm2. Nucleation could successfully be induced at two different wavelengths, lending further support to the non-photochemical mechanism hypothesis. Green light was shown to be more effective than near-IR light at inducing nucleation. The difference was attributed to the lower absorption of water at the visible wavelength. The potential for use of NPLIN in fundamental studies of nucleation through pump-probe experiments is explored. In addition, evidence is presented that NPLIN has the potential to create unknown polymorphs. The powder x-ray diffraction pattern of a new polymorph of L-alanine is presented and discussed.

  9. Control of RNA synthesis by chromatin proteins.

    PubMed Central

    Cedar, H; Solage, A; Zurucki, F

    1976-01-01

    The effect of chromatin proteins on template activity has been studied. Using both E. coli RNA polymerase and calf thymmus polymerase B we have measured the number of initiation sites on chromatin and various histone-DNA complexes. Chromatin can be reconstituted with histone proteins alone and this complex is still a restricted template for RNA synthesis. The removal of histone f1 causes a large increase in the template activity. Chromatin is then treated with Micrococcal nuclease and the DNA fragments protected from nuclease attack ("covered DNA") are isolated. Alternatively, the chromatin is titrated with poly-D-lysine, and by successive treatment with Pronase and nuclease, the DNA regions accessible to polylysine are isolated ("open DNA"). Both fractions were tested for template activity. It was found that RNA polymerase initiation sites are distributed equally in open and covered region DNA. PMID:787926

  10. A repressor-antirepressor pair links two loci controlling light-induced carotenogenesis in Myxococcus xanthus.

    PubMed

    López-Rubio, José Juan; Elías-Arnanz, Montserrat; Padmanabhan, S; Murillo, Francisco José

    2002-03-01

    The light-inducible carB operon encodes all but one of the structural genes for carotenogenesis in Myxococcus xanthus. It is transcriptionally controlled by two proteins expressed from two unlinked genetic loci: CarS from the light-inducible carQRS operon, and CarA from the light-independent carA operon. CarA represses transcription from the carB promoter (P(B)) in the dark, and CarS counteracts this on illumination. The CarA sequence revealed a helix-turn-helix DNA-binding motif of the type found in bacterial MerR transcriptional factors, whereas CarS contains no known DNA-binding motif. Here, we examine the molecular interplay between CarA and CarS. We demonstrate the following. (i) Whereas CarS exhibits no DNA binding in vitro, CarA binds specifically to a region encompassing P(B) to form at least two distinct complexes. (ii) A palindrome located between positions -46 and -63 relative to the transcription start point is essential but not sufficient for the formation of the two CarA-DNA complexes observed. (iii) CarS abrogates the specific DNA binding of CarA. CarA is therefore a repressor and CarS an antirepressor. (iv) CarS physically interacts with CarA; thus, the functional interaction between them is mediated by protein-protein interactions.

  11. Protein phosphatase PHLPP1 controls the light-induced resetting of the circadian clock

    PubMed Central

    Masubuchi, Satoru; Gao, Tianyan; O'Neill, Audrey; Eckel-Mahan, Kristin; Newton, Alexandra C.; Sassone-Corsi, Paolo

    2010-01-01

    The pleckstrin homology domain leucine-rich repeat protein phosphatase 1 (PHLPP1) differentially attenuates Akt, PKC, and ERK1/2 signaling, thereby controlling the duration and amplitude of responses evoked by these kinases. PHLPP1 is expressed in the mammalian central clock, the suprachiasmatic nucleus, where it oscillates in a circadian fashion. To explore the role of PHLPP1 in vivo, we have generated mice with a targeted deletion of the PHLPP1 gene. Here we show that PHLPP1-null mice, although displaying normal circadian rhythmicity, have a drastically impaired capacity to stabilize the circadian period after light-induced resetting, producing a large phase shift after light resetting. Our findings reveal that PHLPP1 exerts a previously unappreciated role in circadian control, governing the consolidation of circadian periodicity after resetting. PMID:20080691

  12. A SWI/SNF Chromatin Remodelling Protein Controls Cytokinin Production through the Regulation of Chromatin Architecture

    PubMed Central

    Jégu, Teddy; Domenichini, Séverine; Blein, Thomas; Ariel, Federico; Christ, Aurélie; Kim, Soon-Kap; Crespi, Martin; Boutet-Mercey, Stéphanie; Mouille, Grégory; Bourge, Mickaël; Hirt, Heribert; Bergounioux, Catherine; Raynaud, Cécile; Benhamed, Moussa

    2015-01-01

    Chromatin architecture determines transcriptional accessibility to DNA and consequently gene expression levels in response to developmental and environmental stimuli. Recently, chromatin remodelers such as SWI/SNF complexes have been recognized as key regulators of chromatin architecture. To gain insight into the function of these complexes during root development, we have analyzed Arabidopsis knock-down lines for one sub-unit of SWI/SNF complexes: BAF60. Here, we show that BAF60 is a positive regulator of root development and cell cycle progression in the root meristem via its ability to down-regulate cytokinin production. By opposing both the deposition of active histone marks and the formation of a chromatin regulatory loop, BAF60 negatively regulates two crucial target genes for cytokinin biosynthesis (IPT3 and IPT7) and one cell cycle inhibitor (KRP7). Our results demonstrate that SWI/SNF complexes containing BAF60 are key factors governing the equilibrium between formation and dissociation of a chromatin loop controlling phytohormone production and cell cycle progression. PMID:26457678

  13. A SWI/SNF Chromatin Remodelling Protein Controls Cytokinin Production through the Regulation of Chromatin Architecture.

    PubMed

    Jégu, Teddy; Domenichini, Séverine; Blein, Thomas; Ariel, Federico; Christ, Aurélie; Kim, Soon-Kap; Crespi, Martin; Boutet-Mercey, Stéphanie; Mouille, Grégory; Bourge, Mickaël; Hirt, Heribert; Bergounioux, Catherine; Raynaud, Cécile; Benhamed, Moussa

    2015-01-01

    Chromatin architecture determines transcriptional accessibility to DNA and consequently gene expression levels in response to developmental and environmental stimuli. Recently, chromatin remodelers such as SWI/SNF complexes have been recognized as key regulators of chromatin architecture. To gain insight into the function of these complexes during root development, we have analyzed Arabidopsis knock-down lines for one sub-unit of SWI/SNF complexes: BAF60. Here, we show that BAF60 is a positive regulator of root development and cell cycle progression in the root meristem via its ability to down-regulate cytokinin production. By opposing both the deposition of active histone marks and the formation of a chromatin regulatory loop, BAF60 negatively regulates two crucial target genes for cytokinin biosynthesis (IPT3 and IPT7) and one cell cycle inhibitor (KRP7). Our results demonstrate that SWI/SNF complexes containing BAF60 are key factors governing the equilibrium between formation and dissociation of a chromatin loop controlling phytohormone production and cell cycle progression.

  14. Control of chromatin structure by long noncoding RNA

    PubMed Central

    Böhmdorfer, Gudrun; Wierzbicki, Andrzej T.

    2015-01-01

    Long noncoding RNA (lncRNA) is a pivotal factor regulating various aspects of genome activity. Genome regulation via DNA methylation and posttranslational histone modifications is a well-documented function of lncRNA in plants, fungi, and animals. Here, we summarize evidence showing that lncRNA also controls chromatin structure including nucleosome positioning and chromosome looping. We focus on data from plant experimental systems, discussed in the context of other eukaryotes. We explain the mechanisms of lncRNA-controlled chromatin remodeling and the implications of the functional interplay between noncoding transcription and several different chromatin remodelers. We propose that the unique properties of RNA make it suitable for controlling chromatin modifications and structure. PMID:26410408

  15. Chromatin mechanisms in the developmental control of imprinted gene expression.

    PubMed

    Sanli, Ildem; Feil, Robert

    2015-10-01

    Hundreds of protein-coding genes and regulatory non-coding RNAs (ncRNAs) are subject to genomic imprinting. The mono-allelic DNA methylation marks that control imprinted gene expression are somatically maintained throughout development, and this process is linked to specific chromatin features. Yet, at many imprinted genes, the mono-allelic expression is lineage or tissue-specific. Recent studies provide mechanistic insights into the developmentally-restricted action of the 'imprinting control regions' (ICRs). At several imprinted domains, the ICR expresses a long ncRNA that mediates chromatin repression in cis (and probably in trans as well). ICRs at other imprinted domains mediate higher-order chromatin structuration that enhances, or prevents, transcription of close-by genes. Here, we present how chromatin and ncRNAs contribute to developmental control of imprinted gene expression and discuss implications for disease. This article is part of a Directed Issue entitled: Epigenetics dynamics in development and disease.

  16. A remotely driven and controlled micro-gripper fabricated from light-induced deformation smart material

    NASA Astrophysics Data System (ADS)

    Huang, Chaolei; Lv, Jiu-an; Tian, Xiaojun; Wang, Yuechao; Liu, Jie; Yu, Yanlei

    2016-09-01

    Micro-gripper is an important tool to manipulate and assemble micro-scale objects. Generally, as micro-gripper is too small to be directly driven by general motors, it always needs special driving devices and suitable structure design. In this paper, two-finger micro-grippers are designed and fabricated, which utilize light-induced deformation smart material to make one of the two fingers. As the smart material is directly driven and controlled by remote lights instead of lines and motors, this light-driven mode simplifies the design of the two-finger micro-gripper and avoids special drivers and complex mechanical structure. In addition, a micro-manipulation experiment system is set up which is based on the light-driven micro-gripper. Experimental results show that this remotely light-driven micro-gripper has ability to manipulate and assemble micro-scale objects both in air and water. Furthermore, two micro-grippers can also work together for cooperation which can further enhance the assembly ability. On the other hand, this kind of remotely controllable micro-gripper that does not require on-board energy storage, can be used in mobile micro-robot as a manipulation hand.

  17. The Fun30 chromatin remodeler Fft3 controls nuclear organization and chromatin structure of insulators and subtelomeres in fission yeast.

    PubMed

    Steglich, Babett; Strålfors, Annelie; Khorosjutina, Olga; Persson, Jenna; Smialowska, Agata; Javerzat, Jean-Paul; Ekwall, Karl

    2015-03-01

    In eukaryotic cells, local chromatin structure and chromatin organization in the nucleus both influence transcriptional regulation. At the local level, the Fun30 chromatin remodeler Fft3 is essential for maintaining proper chromatin structure at centromeres and subtelomeres in fission yeast. Using genome-wide mapping and live cell imaging, we show that this role is linked to controlling nuclear organization of its targets. In fft3∆ cells, subtelomeres lose their association with the LEM domain protein Man1 at the nuclear periphery and move to the interior of the nucleus. Furthermore, genes in these domains are upregulated and active chromatin marks increase. Fft3 is also enriched at retrotransposon-derived long terminal repeat (LTR) elements and at tRNA genes. In cells lacking Fft3, these sites lose their peripheral positioning and show reduced nucleosome occupancy. We propose that Fft3 has a global role in mediating association between specific chromatin domains and the nuclear envelope.

  18. Control of trichome branching by Chromatin Assembly Factor-1

    PubMed Central

    Exner, Vivien; Gruissem, Wilhelm; Hennig, Lars

    2008-01-01

    Background Chromatin dynamics and stability are both required to control normal development of multicellular organisms. Chromatin assembly factor CAF-1 is a histone chaperone that facilitates chromatin formation and the maintenance of specific chromatin states. In plants and animals CAF-1 is essential for normal development, but it is poorly understood which developmental pathways require CAF-1 function. Results Mutations in all three CAF-1 subunits affect Arabidopsis trichome morphology and lack of CAF-1 function results in formation of trichomes with supernumerary branches. This phenotype can be partially alleviated by external sucrose. In contrast, other aspects of the CAF-1 mutant phenotype, such as defective meristem function and organ formation, are aggravated by external sucrose. Double mutant analyses revealed epistatic interactions between CAF-1 mutants and stichel, but non-epistatic interactions between CAF-1 mutants and glabra3 and kaktus. In addition, mutations in CAF-1 could partly suppress the strong overbranching and polyploidization phenotype of kaktus mutants. Conclusion CAF-1 is required for cell differentiation and regulates trichome development together with STICHEL in an endoreduplication-independent pathway. This function of CAF-1 can be partially substituted by application of exogenous sucrose. Finally, CAF-1 is also needed for the high degree of endoreduplication in kaktus mutants and thus for the realization of kaktus' extreme overbranching phenotype. PMID:18477400

  19. Optogenetic Control of Nuclear Protein Import in Living Cells Using Light-Inducible Nuclear Localization Signals (LINuS).

    PubMed

    Wehler, Pierre; Niopek, Dominik; Eils, Roland; Di Ventura, Barbara

    2016-01-01

    Many biological processes are regulated by the timely import of specific proteins into the nucleus. The ability to spatiotemporally control the nuclear import of proteins of interest therefore allows study of their role in a given biological process as well as controlling this process in space and time. The light-inducible nuclear localization signal (LINuS) was developed based on a natural plant photoreceptor that reversibly triggers the import of proteins of interest into the nucleus with blue light. Each LINuS is a small, genetically encoded domain that is fused to the protein of interest at the N or C terminus. These protocols describe how to carry out initial microscopy-based screening to assess which LINuS variant works best with a protein of interest. © 2016 by John Wiley & Sons, Inc. PMID:27258691

  20. A negative loop within the nuclear pore complex controls global chromatin organization

    PubMed Central

    Breuer, Manuel; Ohkura, Hiroyuki

    2015-01-01

    The nuclear pore complex (NPC) tethers chromatin to create an environment for gene regulation, but little is known about how this activity is regulated to avoid excessive tethering of the genome. Here we propose a negative regulatory loop within the NPC controlling the chromatin attachment state, in which Nup155 and Nup93 recruit Nup62 to suppress chromatin tethering by Nup155. Depletion of Nup62 severely disrupts chromatin distribution in the nuclei of female germlines and somatic cells, which can be reversed by codepleting Nup155. Thus, this universal regulatory system within the NPC is crucial to control large-scale chromatin organization in the nucleus. PMID:26341556

  1. Tuning the Binding Affinities and Reversion Kinetics of a Light Inducible Dimer Allows Control of Transmembrane Protein Localization.

    PubMed

    Zimmerman, Seth P; Hallett, Ryan A; Bourke, Ashley M; Bear, James E; Kennedy, Matthew J; Kuhlman, Brian

    2016-09-20

    Inducible dimers are powerful tools for controlling biological processes through colocalizing signaling molecules. To be effective, an inducible system should have a dissociation constant in the "off" state that is greater (i.e., weaker affinity) than the concentrations of the molecules that are being controlled, and in the "on" state a dissociation constant that is less (i.e., stronger affinity) than the relevant protein concentrations. Here, we reengineer the interaction between the light inducible dimer, iLID, and its binding partner SspB, to better control proteins present at high effective concentrations (5-100 μM). iLID contains a light-oxygen-voltage (LOV) domain that undergoes a conformational change upon activation with blue light and exposes a peptide motif, ssrA, that binds to SspB. The new variant of the dimer system contains a single SspB point mutation (A58V), and displays a 42-fold change in binding affinity when activated with blue light (from 3 ± 2 μM to 125 ± 40 μM) and allows for light-activated colocalization of transmembrane proteins in neurons, where a higher affinity switch (0.8-47 μM) was less effective because more colocalization was seen in the dark. Additionally, with a point mutation in the LOV domain (N414L), we lengthened the reversion half-life of iLID. This expanded suite of light induced dimers increases the variety of cellular pathways that can be targeted with light.

  2. Tuning the Binding Affinities and Reversion Kinetics of a Light Inducible Dimer Allows Control of Transmembrane Protein Localization.

    PubMed

    Zimmerman, Seth P; Hallett, Ryan A; Bourke, Ashley M; Bear, James E; Kennedy, Matthew J; Kuhlman, Brian

    2016-09-20

    Inducible dimers are powerful tools for controlling biological processes through colocalizing signaling molecules. To be effective, an inducible system should have a dissociation constant in the "off" state that is greater (i.e., weaker affinity) than the concentrations of the molecules that are being controlled, and in the "on" state a dissociation constant that is less (i.e., stronger affinity) than the relevant protein concentrations. Here, we reengineer the interaction between the light inducible dimer, iLID, and its binding partner SspB, to better control proteins present at high effective concentrations (5-100 μM). iLID contains a light-oxygen-voltage (LOV) domain that undergoes a conformational change upon activation with blue light and exposes a peptide motif, ssrA, that binds to SspB. The new variant of the dimer system contains a single SspB point mutation (A58V), and displays a 42-fold change in binding affinity when activated with blue light (from 3 ± 2 μM to 125 ± 40 μM) and allows for light-activated colocalization of transmembrane proteins in neurons, where a higher affinity switch (0.8-47 μM) was less effective because more colocalization was seen in the dark. Additionally, with a point mutation in the LOV domain (N414L), we lengthened the reversion half-life of iLID. This expanded suite of light induced dimers increases the variety of cellular pathways that can be targeted with light. PMID:27529180

  3. Engineering an improved light-induced dimer (iLID) for controlling the localization and activity of signaling proteins

    PubMed Central

    Guntas, Gurkan; Hallett, Ryan A.; Zimmerman, Seth P.; Williams, Tishan; Yumerefendi, Hayretin; Bear, James E.; Kuhlman, Brian

    2015-01-01

    The discovery of light-inducible protein–protein interactions has allowed for the spatial and temporal control of a variety of biological processes. To be effective, a photodimerizer should have several characteristics: it should show a large change in binding affinity upon light stimulation, it should not cross-react with other molecules in the cell, and it should be easily used in a variety of organisms to recruit proteins of interest to each other. To create a switch that meets these criteria we have embedded the bacterial SsrA peptide in the C-terminal helix of a naturally occurring photoswitch, the light-oxygen-voltage 2 (LOV2) domain from Avena sativa. In the dark the SsrA peptide is sterically blocked from binding its natural binding partner, SspB. When activated with blue light, the C-terminal helix of the LOV2 domain undocks from the protein, allowing the SsrA peptide to bind SspB. Without optimization, the switch exhibited a twofold change in binding affinity for SspB with light stimulation. Here, we describe the use of computational protein design, phage display, and high-throughput binding assays to create an improved light inducible dimer (iLID) that changes its affinity for SspB by over 50-fold with light stimulation. A crystal structure of iLID shows a critical interaction between the surface of the LOV2 domain and a phenylalanine engineered to more tightly pin the SsrA peptide against the LOV2 domain in the dark. We demonstrate the functional utility of the switch through light-mediated subcellular localization in mammalian cell culture and reversible control of small GTPase signaling. PMID:25535392

  4. Nonhistone Proteins Control Gene Expression in Reconstituted Chromatin

    PubMed Central

    Barrett, T.; Maryanka, D.; Hamlyn, P. H.; Gould, H. J.

    1974-01-01

    Chromatin was reconstituted from the purified DNA and histones of chicken erythrocytes and the nonhistone proteins of either chicken reticulocytes or chicken liver. Reconstituted chromatins, native chicken reticulocyte chromatin, and free DNA were transcribed with Escherichia coli RNA polymerase and the concentrations of globin-specific sequences in the RNA products were measured by hybridization with [3H]DNA complementary to chicken globin messenger RNA. Reticulocyte, but not liver, nonhistone proteins were shown to activate the globin genes in reconstituted erythrocyte chromatin. The transcripts of native and reconstituted chromatins were indistinguishable in respect of both the total yield of the RNA and the fractional yield of globin-specific sequences. Images PMID:4140516

  5. Coordinated Regulation of PPARγ Expression and Activity through Control of Chromatin Structure in Adipogenesis and Obesity

    PubMed Central

    Eeckhoute, Jérôme; Oger, Frédérik; Staels, Bart; Lefebvre, Philippe

    2012-01-01

    The nuclear receptor peroxisome proliferator-activated receptor gamma (PPARγ) is required for differentiation and function of mature adipocytes. Its expression is induced during adipogenesis where it plays a key role in establishing the transcriptome of terminally differentiated white fat cells. Here, we review findings indicating that PPARγ expression and activity are intricately regulated through control of chromatin structure. Hierarchical and combinatorial activation of transcription factors, noncoding RNAs, and chromatin remodelers allows for temporally controlled expression of PPARγ and its target genes through sequential chromatin remodelling. In obesity, these regulatory pathways may be altered and lead to modified PPARγ activity. PMID:22991504

  6. Controlled release of encapsulated bioactive volatiles by rupture of the capsule wall through the light-induced generation of a gas.

    PubMed

    Paret, Nicolas; Trachsel, Alain; Berthier, Damien L; Herrmann, Andreas

    2015-02-01

    The encapsulation of photolabile 2-oxoacetates in core-shell microcapsules allows the light-induced, controlled release of bioactive compounds. On irradiation with UVA light these compounds degrade to generate an overpressure of gas inside the capsules, which expands or breaks the capsule wall. Headspace measurements confirmed the light-induced formation of CO and CO2 and the successful release of the bioactive compound, while optical microscopy demonstrated the formation of gas bubbles, the cleavage of the capsule wall, and the leakage of the oil phase out of the capsule. The efficiency of the delivery system depends on the structure of the 2-oxoacetate, the quantity used with respect to the thickness of the capsule wall, and the intensity of the irradiating UVA light.

  7. Senataxin controls meiotic silencing through ATR activation and chromatin remodeling.

    PubMed

    Yeo, Abrey J; Becherel, Olivier J; Luff, John E; Graham, Mark E; Richard, Derek; Lavin, Martin F

    2015-01-01

    Senataxin, defective in ataxia oculomotor apraxia type 2, protects the genome by facilitating the resolution of RNA-DNA hybrids (R-loops) and other aspects of RNA processing. Disruption of this gene in mice causes failure of meiotic recombination and defective meiotic sex chromosome inactivation, leading to male infertility. Here we provide evidence that the disruption of Setx leads to reduced SUMOylation and disruption of protein localization across the XY body during meiosis. We demonstrate that senataxin and other DNA damage repair proteins, including ataxia telangiectasia and Rad3-related protein-interacting partner, are SUMOylated, and a marked downregulation of both ataxia telangiectasia and Rad3-related protein-interacting partner and TopBP1 leading to defective activation and signaling through ataxia telangiectasia and Rad3-related protein occurs in the absence of senataxin. Furthermore, chromodomain helicase DNA-binding protein 4, a component of the nucleosome remodeling and deacetylase chromatin remodeler that interacts with both ataxia telangiectasia and Rad3-related protein and senataxin was not recruited efficiently to the XY body, triggering altered histone acetylation and chromatin conformation in Setx (-/-) pachytene-staged spermatocytes. These results demonstrate that senataxin has a critical role in ataxia telangiectasia and Rad3-related protein- and chromodomain helicase DNA-binding protein 4-mediated transcriptional silencing and chromatin remodeling during meiosis providing greater insight into its critical role in gene regulation to protect against neurodegeneration. PMID:27462424

  8. Senataxin controls meiotic silencing through ATR activation and chromatin remodeling

    PubMed Central

    Yeo, Abrey J; Becherel, Olivier J; Luff, John E; Graham, Mark E; Richard, Derek; Lavin, Martin F

    2015-01-01

    Senataxin, defective in ataxia oculomotor apraxia type 2, protects the genome by facilitating the resolution of RNA–DNA hybrids (R-loops) and other aspects of RNA processing. Disruption of this gene in mice causes failure of meiotic recombination and defective meiotic sex chromosome inactivation, leading to male infertility. Here we provide evidence that the disruption of Setx leads to reduced SUMOylation and disruption of protein localization across the XY body during meiosis. We demonstrate that senataxin and other DNA damage repair proteins, including ataxia telangiectasia and Rad3-related protein-interacting partner, are SUMOylated, and a marked downregulation of both ataxia telangiectasia and Rad3-related protein-interacting partner and TopBP1 leading to defective activation and signaling through ataxia telangiectasia and Rad3-related protein occurs in the absence of senataxin. Furthermore, chromodomain helicase DNA-binding protein 4, a component of the nucleosome remodeling and deacetylase chromatin remodeler that interacts with both ataxia telangiectasia and Rad3-related protein and senataxin was not recruited efficiently to the XY body, triggering altered histone acetylation and chromatin conformation in Setx−/− pachytene-staged spermatocytes. These results demonstrate that senataxin has a critical role in ataxia telangiectasia and Rad3-related protein- and chromodomain helicase DNA-binding protein 4-mediated transcriptional silencing and chromatin remodeling during meiosis providing greater insight into its critical role in gene regulation to protect against neurodegeneration. PMID:27462424

  9. Chromatin Computation

    PubMed Central

    Bryant, Barbara

    2012-01-01

    In living cells, DNA is packaged along with protein and RNA into chromatin. Chemical modifications to nucleotides and histone proteins are added, removed and recognized by multi-functional molecular complexes. Here I define a new computational model, in which chromatin modifications are information units that can be written onto a one-dimensional string of nucleosomes, analogous to the symbols written onto cells of a Turing machine tape, and chromatin-modifying complexes are modeled as read-write rules that operate on a finite set of adjacent nucleosomes. I illustrate the use of this “chromatin computer” to solve an instance of the Hamiltonian path problem. I prove that chromatin computers are computationally universal – and therefore more powerful than the logic circuits often used to model transcription factor control of gene expression. Features of biological chromatin provide a rich instruction set for efficient computation of nontrivial algorithms in biological time scales. Modeling chromatin as a computer shifts how we think about chromatin function, suggests new approaches to medical intervention, and lays the groundwork for the engineering of a new class of biological computing machines. PMID:22567109

  10. Biotic Control of Surface pH and Evidence of Light-Induced H+ Pumping and Ca2+-H+ Exchange in a Tropical Crustose Coralline Alga

    PubMed Central

    Hofmann, Laurie C.; Koch, Marguerite; de Beer, Dirk

    2016-01-01

    Presently, an incomplete mechanistic understanding of tropical reef macroalgae photosynthesis and calcification restricts predictions of how these important autotrophs will respond to global change. Therefore, we investigated the mechanistic link between inorganic carbon uptake pathways, photosynthesis and calcification in a tropical crustose coralline alga (CCA) using microsensors. We measured pH, oxygen (O2), and calcium (Ca2+) dynamics and fluxes at the thallus surface under ambient (8.1) and low (7.8) seawater pH (pHSW) and across a range of irradiances. Acetazolamide (AZ) was used to inhibit extracellular carbonic anhydrase (CAext), which mediates hydrolysis of HCO3-, and 4,4′ diisothiocyanatostilbene-2,2′-disulphonate (DIDS) that blocks direct HCO3- uptake by anion exchange transport. Both inhibited photosynthesis, suggesting both diffusive uptake of CO2 via HCO3- hydrolysis to CO2 and direct HCO3- ion transport are important in this CCA. Surface pH was raised approximately 0.3 units at saturating irradiance, but less when CAext was inhibited. Surface pH was lower at pHSW 7.8 than pHSW 8.1 in the dark, but not in the light. The Ca2+ fluxes were large, complex and temporally variable, but revealed net Ca2+ uptake under all conditions. The temporal variability in Ca2+ dynamics was potentially related to localized dissolution during epithallial cell sloughing, a strategy of CCA to remove epiphytes. Simultaneous Ca2+ and pH dynamics suggest the presence of Ca2+/H+ exchange. Rapid light-induced H+ surface dynamics that continued after inhibition of photosynthesis revealed the presence of a light-mediated, but photosynthesis-independent, proton pump. Thus, the study indicates metabolic control of surface pH can occur in CCA through photosynthesis and light-inducible H+ pumps. Our results suggest that complex light-induced ion pumps play an important role in biological processes related to inorganic carbon uptake and calcification in CCA. PMID:27459463

  11. Biotic Control of Surface pH and Evidence of Light-Induced H+ Pumping and Ca2+-H+ Exchange in a Tropical Crustose Coralline Alga.

    PubMed

    Hofmann, Laurie C; Koch, Marguerite; de Beer, Dirk

    2016-01-01

    Presently, an incomplete mechanistic understanding of tropical reef macroalgae photosynthesis and calcification restricts predictions of how these important autotrophs will respond to global change. Therefore, we investigated the mechanistic link between inorganic carbon uptake pathways, photosynthesis and calcification in a tropical crustose coralline alga (CCA) using microsensors. We measured pH, oxygen (O2), and calcium (Ca2+) dynamics and fluxes at the thallus surface under ambient (8.1) and low (7.8) seawater pH (pHSW) and across a range of irradiances. Acetazolamide (AZ) was used to inhibit extracellular carbonic anhydrase (CAext), which mediates hydrolysis of HCO3-, and 4,4' diisothiocyanatostilbene-2,2'-disulphonate (DIDS) that blocks direct HCO3- uptake by anion exchange transport. Both inhibited photosynthesis, suggesting both diffusive uptake of CO2 via HCO3- hydrolysis to CO2 and direct HCO3- ion transport are important in this CCA. Surface pH was raised approximately 0.3 units at saturating irradiance, but less when CAext was inhibited. Surface pH was lower at pHSW 7.8 than pHSW 8.1 in the dark, but not in the light. The Ca2+ fluxes were large, complex and temporally variable, but revealed net Ca2+ uptake under all conditions. The temporal variability in Ca2+ dynamics was potentially related to localized dissolution during epithallial cell sloughing, a strategy of CCA to remove epiphytes. Simultaneous Ca2+ and pH dynamics suggest the presence of Ca2+/H+ exchange. Rapid light-induced H+ surface dynamics that continued after inhibition of photosynthesis revealed the presence of a light-mediated, but photosynthesis-independent, proton pump. Thus, the study indicates metabolic control of surface pH can occur in CCA through photosynthesis and light-inducible H+ pumps. Our results suggest that complex light-induced ion pumps play an important role in biological processes related to inorganic carbon uptake and calcification in CCA. PMID:27459463

  12. Light-induced click reactions.

    PubMed

    Tasdelen, Mehmet Atilla; Yagci, Yusuf

    2013-06-01

    Spatial and temporal control over chemical and biological processes, both in terms of "tuning" products and providing site-specific control, is one of the most exciting and rapidly developing areas of modern science. For synthetic chemists, the challenge is to discover and develop selective and efficient reactions capable of generating useful molecules in a variety of matrices. In recent studies, light has been recognized as a valuable method for determining where, when, and to what extent a process is started or stopped. Accordingly, this Minireview will present the fundamental aspects of light-induced click reactions, highlight the applications of these reactions to diverse fields of study, and discuss the potential for this methodology to be applied to the study of biomolecular systems.

  13. Dynamic cohesin-mediated chromatin architecture controls epithelial-mesenchymal plasticity in cancer.

    PubMed

    Yun, Jiyeon; Song, Sang-Hyun; Kim, Hwang-Phill; Han, Sae-Won; Yi, Eugene C; Kim, Tae-You

    2016-09-01

    Epithelial to mesenchymal transition (EMT) and mesenchymal to epithelial transition (MET) are important interconnected events in tumorigenesis controlled by complex genetic networks. However, the cues that activate EMT-initiating factors and the mechanisms that reversibly connect EMT/MET are not well understood. Here, we show that cohesin-mediated chromatin organization coordinates EMT/MET by regulating mesenchymal genes. We report that RAD21, a subunit of the cohesin complex, is expressed in epithelial breast cancer cells, whereas its expression is decreased in mesenchymal cancer. Depletion of RAD21 in epithelial cancer cells causes transcriptional activation of TGFB1 and ITGA5, inducing EMT. Reduced binding of RAD21 changes intrachromosomal chromatin interactions within the TGFB1 and ITGA5 loci, creating an active transcriptional environment. Similarly, stem cell-like cancer cells also show an open chromatin structure at both genes, which correlates with high expression levels and mesenchymal fate characteristics. Conversely, overexpression of RAD21 in mesenchymal cancer cells induces MET-specific expression patterns. These findings indicate that dynamic cohesin-mediated chromatin structures are responsible for the initiation and regulation of essential EMT-related cell fate changes in cancer. PMID:27466323

  14. Light-inducible genetic engineering and control of non-homologous end-joining in industrial eukaryotic microorganisms: LML 3.0 and OFN 1.0

    PubMed Central

    Zhang, Lei; Zhao, Xihua; Zhang, Guoxiu; Zhang, Jiajia; Wang, Xuedong; Zhang, Suping; Wang, Wei; Wei, Dongzhi

    2016-01-01

    Filamentous fungi play important roles in the production of plant cell-wall degrading enzymes. In recent years, homologous recombinant technologies have contributed significantly to improved enzymes production and system design of genetically manipulated strains. When introducing multiple gene deletions, we need a robust and convenient way to control selectable marker genes, especially when only a limited number of markers are available in filamentous fungi. Integration after transformation is predominantly nonhomologous in most fungi other than yeast. Fungal strains deficient in the non-homologous end-joining (NHEJ) pathway have limitations associated with gene function analyses despite they are excellent recipient strains for gene targets. We describe strategies and methods to address these challenges above and leverage the power of resilient NHEJ deficiency strains. We have established a foolproof light-inducible platform for one-step unmarked genetic modification in industrial eukaryotic microorganisms designated as ‘LML 3.0’, and an on-off control protocol of NHEJ pathway called ‘OFN 1.0’, using a synthetic light-switchable transactivation to control Cre recombinase-based excision and inversion. The methods provide a one-step strategy to sequentially modify genes without introducing selectable markers and NHEJ-deficiency. The strategies can be used to manipulate many biological processes in a wide range of eukaryotic cells. PMID:26857594

  15. NOTE: MRI observation of the light-induced release of a contrast agent from photo-controllable polymer micelles

    NASA Astrophysics Data System (ADS)

    Lepage, Martin; Jiang, Jinqiang; Babin, Jérôme; Qi, Bo; Tremblay, Luc; Zhao, Yue

    2007-05-01

    The encapsulation of molecules into nanocarriers is studied for its potential in delivering a high dose of anticancer drugs to a tumor, while minimizing side effects. Most systems either release their content in a non-specific manner or under specific environmental conditions such as temperature or pH. We have synthesized a novel class of photo-controllable polymer micelles that can stably encapsulate a hydrophilic compound and subsequently release it upon absorption of UV light. Here, we describe an in vitro magnetic resonance imaging assay that can evaluate the state of incorporation of a small Gd-based contrast agent. Our results indicate that the contrast agent alone can diffuse through a filter, but that the same agent incorporated into micelles cannot. After exposure to UV light, the micelles released the contrast agent, which could then diffuse through the filter.

  16. Single-Component TiO2 Tubular Microengines with Motion Controlled by Light-Induced Bubbles.

    PubMed

    Mou, Fangzhi; Li, Yan; Chen, Chuanrui; Li, Wei; Yin, Yixia; Ma, Huiru; Guan, Jianguo

    2015-06-01

    In this work, light-controlled bubble-propelled single-component metal oxide tubular microengines have for the first time been demonstrated. For such a simple single-component TiO2 tubular microengine in H2O2 aqueous solution under UV irradiation, when the inner diameter and length of the tube are regulated, the O2 molecules will nucleate and grow into bubbles preferentially on the inner concave surface rather than on the outer surface, resulting in a vital propulsion of the microengine. More importantly, the motion state and speed can be modulated reversibly, fast (the response time is less than 0.2 s) and wirelessly by adjusting UV irradiation. Consequently, the as-developed TiO2 tubular microengine promises potential challenged applications related to photocatalysis, such as "on-the-fly" photocatalytic degradation of organic pollutes and photocatalytic inactivation of bacteria due to the low cost, single component, and simple structure, as well as the facile fabrication in a large-scale.

  17. Photosynthetic control of the plasma membrane H+-ATPase in Vallisneria leaves. I. Regulation of activity during light-induced membrane hyperpolarization.

    PubMed

    Harada, Akiko; Okazaki, Yoshiji; Takagi, Shingo

    2002-04-01

    In mesophyll cells of the aquatic angiosperm Vallisneria gigantea Graebner, red, blue, or blue plus far-red light induced a typical membrane hyperpolarization, whereas far-red light alone had little effect. Both N,N'-dicyclohexylcarbodiimide, a potent inhibitor of H+-ATPase, and carbonylcyanide m-chlorophenylhydrazone, an uncoupler, produced a considerable membrane depolarization in the dark-adapted cells and a complete suppression of the light-induced hyperpolarization. Although 3-(3',4'-dichlorophenyl)-1,1-dimethylurea (DCMU), an inhibitor of photosynthetic electron transport, did not affect the membrane potential in darkness, it completely inhibited the light-induced membrane hyperpolarization. In vivo illumination of the leaves with red light caused a substantial decrease in the Km for ATP, not only of the vanadate-sensitive ATP-hydrolyzing activity in leaf homogenate, but also of the ATP-dependent H+-transporting activity in plasma membrane (PM) vesicles isolated from the leaves by aqueous polymer two-phase partitioning methods. The effects of red light were negated by the presence of DCMU during illumination. In vivo illumination with far-red light had no effect on the Km for ATP of H+-transporting activity. These results strongly suggest that an electrogenic component in the membrane potential of the mesophyll cell is generated by the PM H+-ATPase, and that photosynthesis-dependent modulation of the enzymatic activity of the PM H+-ATPase is involved in the light-induced membrane hyperpolarization. PMID:11941462

  18. miRNA-132 orchestrates chromatin remodeling and translational control of the circadian clock.

    PubMed

    Alvarez-Saavedra, Matías; Antoun, Ghadi; Yanagiya, Akiko; Oliva-Hernandez, Reynaldo; Cornejo-Palma, Daniel; Perez-Iratxeta, Carolina; Sonenberg, Nahum; Cheng, Hai-Ying M

    2011-02-15

    Mammalian circadian rhythms are synchronized to the external time by daily resetting of the suprachiasmatic nucleus (SCN) in response to light. As the master circadian pacemaker, the SCN coordinates the timing of diverse cellular oscillators in multiple tissues. Aberrant regulation of clock timing is linked to numerous human conditions, including cancer, cardiovascular disease, obesity, various neurological disorders and the hereditary disorder familial advanced sleep phase syndrome. Additionally, mechanisms that underlie clock resetting factor into the sleep and physiological disturbances experienced by night-shift workers and travelers with jet lag. The Ca(2+)/cAMP response element-binding protein-regulated microRNA, miR-132, is induced by light within the SCN and attenuates its capacity to reset, or entrain, the clock. However, the specific targets that are regulated by miR-132 and underlie its effects on clock entrainment remained elusive until now. Here, we show that genes involved in chromatin remodeling (Mecp2, Ep300, Jarid1a) and translational control (Btg2, Paip2a) are direct targets of miR-132 in the mouse SCN. Coordinated regulation of these targets underlies miR-132-dependent modulation of Period gene expression and clock entrainment: the mPer1 and mPer2 promoters are bound to and transcriptionally activated by MeCP2, whereas PAIP2A and BTG2 suppress the translation of the PERIOD proteins by enhancing mRNA decay. We propose that miR-132 is selectively enriched for chromatin- and translation-associated target genes and is an orchestrator of chromatin remodeling and protein translation within the SCN clock, thereby fine-tuning clock entrainment. These findings will further our understanding of mechanisms governing clock entrainment and its involvement in human diseases. PMID:21118894

  19. The Chromatin Remodeling Complex Chd4/NuRD Controls Striated Muscle Identity and Metabolic Homeostasis.

    PubMed

    Gómez-Del Arco, Pablo; Perdiguero, Eusebio; Yunes-Leites, Paula Sofia; Acín-Pérez, Rebeca; Zeini, Miriam; Garcia-Gomez, Antonio; Sreenivasan, Krishnamoorthy; Jiménez-Alcázar, Miguel; Segalés, Jessica; López-Maderuelo, Dolores; Ornés, Beatriz; Jiménez-Borreguero, Luis Jesús; D'Amato, Gaetano; Enshell-Seijffers, David; Morgan, Bruce; Georgopoulos, Katia; Islam, Abul B M M K; Braun, Thomas; de la Pompa, José Luis; Kim, Johnny; Enriquez, José A; Ballestar, Esteban; Muñoz-Cánoves, Pura; Redondo, Juan Miguel

    2016-05-10

    Heart muscle maintains blood circulation, while skeletal muscle powers skeletal movement. Despite having similar myofibrilar sarcomeric structures, these striated muscles differentially express specific sarcomere components to meet their distinct contractile requirements. The mechanism responsible is still unclear. We show here that preservation of the identity of the two striated muscle types depends on epigenetic repression of the alternate lineage gene program by the chromatin remodeling complex Chd4/NuRD. Loss of Chd4 in the heart triggers aberrant expression of the skeletal muscle program, causing severe cardiomyopathy and sudden death. Conversely, genetic depletion of Chd4 in skeletal muscle causes inappropriate expression of cardiac genes and myopathy. In both striated tissues, mitochondrial function was also dependent on the Chd4/NuRD complex. We conclude that an epigenetic mechanism controls cardiac and skeletal muscle structural and metabolic identities and that loss of this regulation leads to hybrid striated muscle tissues incompatible with life.

  20. Controllable fabrication of iron oxide/oxyhydroxide with diverse nanostructures and their excellent performance in visible light induced photocatalytic degradation of rhodamine B.

    PubMed

    Li, Hui; Wang, Taishan; Zhang, Yanjun; Jiang, Li; Shu, Chunying; Wang, Chunru

    2012-03-01

    Alpha-FeOOH and alpha-Fe2O3 with diverse morphologies (sea hedgehog-like, array-like, nanorod-like and nanoparticle-like) were synthesized through a simple and facile solvent-mediated method. The products with different morphologies can be prepared by adjusting the concentration of ferrous ions, reaction temperature and the pH value of the reaction solution in the rationally designed synthesis routes. All the products had a high BET surface area and exhibited an excellent catalytic ability in visible light induced degradation of rhodamine B.

  1. Gene activation and cell fate control in plants: a chromatin perspective.

    PubMed

    Engelhorn, Julia; Blanvillain, Robert; Carles, Cristel C

    2014-08-01

    In plants, environment-adaptable organogenesis extends throughout the lifespan, and iterative development requires repetitive rounds of activation and repression of several sets of genes. Eukaryotic genome compaction into chromatin forms a physical barrier for transcription; therefore, induction of gene expression requires alteration in chromatin structure. One of the present great challenges in molecular and developmental biology is to understand how chromatin is brought from a repressive to permissive state on specific loci and in a very specific cluster of cells, as well as how this state is further maintained and propagated through time and cell division in a cell lineage. In this review, we report recent discoveries implementing our knowledge on chromatin dynamics that modulate developmental gene expression. We also discuss how new data sets highlight plant specificities, likely reflecting requirement for a highly dynamic chromatin.

  2. Light-Inducible Gene Regulation with Engineered Zinc Finger Proteins

    PubMed Central

    Polstein, Lauren R.; Gersbach, Charles A.

    2014-01-01

    The coupling of light-inducible protein-protein interactions with gene regulation systems has enabled the control of gene expression with light. In particular, heterodimer protein pairs from plants can be used to engineer a gene regulation system in mammalian cells that is reversible, repeatable, tunable, controllable in a spatiotemporal manner, and targetable to any DNA sequence. This system, Light-Inducible Transcription using Engineered Zinc finger proteins (LITEZ), is based on the blue light-induced interaction of GIGANTEA and the LOV domain of FKF1 that drives the localization of a transcriptional activator to the DNA-binding site of a highly customizable engineered zinc finger protein. This chapter provides methods for modifying LITEZ to target new DNA sequences, engineering a programmable LED array to illuminate cell cultures, and using the modified LITEZ system to achieve spatiotemporal control of transgene expression in mammalian cells. PMID:24718797

  3. Xenopus Cdc45-dependent loading of DNA polymerase alpha onto chromatin under the control of S-phase Cdk.

    PubMed Central

    Mimura, S; Takisawa, H

    1998-01-01

    At the onset of S phase, chromosomal replication is initiated by the loading of DNA polymerase alpha onto replication origins. However, the molecular mechanisms for controlling the initiation are poorly understood. Using Xenopus egg extract, we report here the identification of a Xenopus homolog of Cdc45, a yeast protein essential for the initiation of replication, which is shown to be an essential molecule for the initiation of replication via the loading of DNA polymerase alpha onto chromatin. XCdc45, by physically interacting with the polymerase in the extract, became associated with chromatin only after nuclear formation. During S phase, XCdc45 co-localized with the polymerase in the nuclei, and the loading of the polymerase, which depended on endogenous XCdc45, was facilitated by exogenously added recombinant XCdc45. These findings, together with the apparent requirement of S-phase-cdk activity for the loading of XCdc45, suggest that XCdc45, under the control of S-phase cdk, plays a pivotal role in the loading of DNA polymerase alpha onto chromatin. PMID:9755170

  4. The nuclear oncogene SET controls DNA repair by KAP1 and HP1 retention to chromatin.

    PubMed

    Kalousi, Alkmini; Hoffbeck, Anne-Sophie; Selemenakis, Platonas N; Pinder, Jordan; Savage, Kienan I; Khanna, Kum Kum; Brino, Laurent; Dellaire, Graham; Gorgoulis, Vassilis G; Soutoglou, Evi

    2015-04-01

    Cells experience damage from exogenous and endogenous sources that endanger genome stability. Several cellular pathways have evolved to detect DNA damage and mediate its repair. Although many proteins have been implicated in these processes, only recent studies have revealed how they operate in the context of high-ordered chromatin structure. Here, we identify the nuclear oncogene SET (I2PP2A) as a modulator of DNA damage response (DDR) and repair in chromatin surrounding double-strand breaks (DSBs). We demonstrate that depletion of SET increases DDR and survival in the presence of radiomimetic drugs, while overexpression of SET impairs DDR and homologous recombination (HR)-mediated DNA repair. SET interacts with the Kruppel-associated box (KRAB)-associated co-repressor KAP1, and its overexpression results in the sustained retention of KAP1 and Heterochromatin protein 1 (HP1) on chromatin. Our results are consistent with a model in which SET-mediated chromatin compaction triggers an inhibition of DNA end resection and HR.

  5. A phospho-dependent mechanism involving NCoR and KMT2D controls a permissive chromatin state at Notch target genes

    PubMed Central

    Oswald, Franz; Rodriguez, Patrick; Giaimo, Benedetto Daniele; Antonello, Zeus A.; Mira, Laura; Mittler, Gerhard; Thiel, Verena N.; Collins, Kelly J.; Tabaja, Nassif; Cizelsky, Wiebke; Rothe, Melanie; Kühl, Susanne J.; Kühl, Michael; Ferrante, Francesca; Hein, Kerstin; Kovall, Rhett A.; Dominguez, Maria; Borggrefe, Tilman

    2016-01-01

    The transcriptional shift from repression to activation of target genes is crucial for the fidelity of Notch responses through incompletely understood mechanisms that likely involve chromatin-based control. To activate silenced genes, repressive chromatin marks are removed and active marks must be acquired. Histone H3 lysine-4 (H3K4) demethylases are key chromatin modifiers that establish the repressive chromatin state at Notch target genes. However, the counteracting histone methyltransferase required for the active chromatin state remained elusive. Here, we show that the RBP-J interacting factor SHARP is not only able to interact with the NCoR corepressor complex, but also with the H3K4 methyltransferase KMT2D coactivator complex. KMT2D and NCoR compete for the C-terminal SPOC-domain of SHARP. We reveal that the SPOC-domain exclusively binds to phosphorylated NCoR. The balance between NCoR and KMT2D binding is shifted upon mutating the phosphorylation sites of NCoR or upon inhibition of the NCoR kinase CK2β. Furthermore, we show that the homologs of SHARP and KMT2D in Drosophila also physically interact and control Notch-mediated functions in vivo. Together, our findings reveal how signaling can fine-tune a committed chromatin state by phosphorylation of a pivotal chromatin-modifier. PMID:26912830

  6. Dynamic long-range chromatin interactions control Myb proto-oncogene transcription during erythroid development

    PubMed Central

    Stadhouders, Ralph; Thongjuea, Supat; Andrieu-Soler, Charlotte; Palstra, Robert-Jan; Bryne, Jan Christian; van den Heuvel, Anita; Stevens, Mary; de Boer, Ernie; Kockx, Christel; van der Sloot, Antoine; van den Hout, Mirjam; van IJcken, Wilfred; Eick, Dirk; Lenhard, Boris; Grosveld, Frank; Soler, Eric

    2012-01-01

    The key haematopoietic regulator Myb is essential for coordinating proliferation and differentiation. ChIP-Sequencing and Chromosome Conformation Capture (3C)-Sequencing were used to characterize the structural and protein-binding dynamics of the Myb locus during erythroid differentiation. In proliferating cells expressing Myb, enhancers within the Myb-Hbs1l intergenic region were shown to form an active chromatin hub (ACH) containing the Myb promoter and first intron. This first intron was found to harbour the transition site from transcription initiation to elongation, which takes place around a conserved CTCF site. Upon erythroid differentiation, Myb expression is downregulated and the ACH destabilized. We propose a model for Myb activation by distal enhancers dynamically bound by KLF1 and the GATA1/TAL1/LDB1 complex, which primarily function as a transcription elongation element through chromatin looping. PMID:22157820

  7. Dynamic long-range chromatin interactions control Myb proto-oncogene transcription during erythroid development.

    PubMed

    Stadhouders, Ralph; Thongjuea, Supat; Andrieu-Soler, Charlotte; Palstra, Robert-Jan; Bryne, Jan Christian; van den Heuvel, Anita; Stevens, Mary; de Boer, Ernie; Kockx, Christel; van der Sloot, Antoine; van den Hout, Mirjam; van Ijcken, Wilfred; Eick, Dirk; Lenhard, Boris; Grosveld, Frank; Soler, Eric

    2012-02-15

    The key haematopoietic regulator Myb is essential for coordinating proliferation and differentiation. ChIP-Sequencing and Chromosome Conformation Capture (3C)-Sequencing were used to characterize the structural and protein-binding dynamics of the Myb locus during erythroid differentiation. In proliferating cells expressing Myb, enhancers within the Myb-Hbs1l intergenic region were shown to form an active chromatin hub (ACH) containing the Myb promoter and first intron. This first intron was found to harbour the transition site from transcription initiation to elongation, which takes place around a conserved CTCF site. Upon erythroid differentiation, Myb expression is downregulated and the ACH destabilized. We propose a model for Myb activation by distal enhancers dynamically bound by KLF1 and the GATA1/TAL1/LDB1 complex, which primarily function as a transcription elongation element through chromatin looping. PMID:22157820

  8. Replicating centromeric chromatin: Spatial and temporal control of CENP-A assembly

    SciTech Connect

    Nechemia-Arbely, Yael; Fachinetti, Daniele; Cleveland, Don W.

    2012-07-15

    The centromere is the fundamental unit for insuring chromosome inheritance. This complex region has a distinct type of chromatin in which histone H3 is replaced by a structurally different homologue identified in humans as CENP-A. In metazoans, specific DNA sequences are neither required nor sufficient for centromere identity. Rather, an epigenetic mark comprised of CENP-A containing chromatin is thought to be the major determinant of centromere identity. In this view, CENP-A deposition and chromatin assembly are fundamental processes for the maintenance of centromeric identity across mitotic and meiotic divisions. Several lines of evidence support CENP-A deposition in metazoans occurring at only one time in the cell cycle. Such cell cycle-dependent loading of CENP-A is found in divergent species from human to fission yeast, albeit with differences in the cell cycle point at which CENP-A is assembled. Cell cycle dependent CENP-A deposition requires multiple assembly factors for its deposition and maintenance. This review discusses the regulation of new CENP-A deposition and its relevance to centromere identity and inheritance.

  9. Autophagy in light-induced retinal damage.

    PubMed

    Chen, Yu; Perusek, Lindsay; Maeda, Akiko

    2016-03-01

    Vision is reliant upon converting photon signals to electrical information which is interpreted by the brain and therefore allowing us to receive information about our surroundings. However, when exposed to excessive light, photoreceptors and other types of cells in the retina can undergo light-induced cell death, termed light-induced retinal damage. In this review, we summarize our current knowledge regarding molecular events in the retina after excessive light exposure and mechanisms of light-induced retinal damage. We also introduce works which investigate potential roles of autophagy, an essential cellular mechanism required for maintaining homeostasis under stress conditions, in the illuminated retina and animal models of light-induced retinal damage.

  10. Distinct Roles of Chromatin Insulator Proteins in Control of the Drosophila Bithorax Complex.

    PubMed

    Savitsky, Mikhail; Kim, Maria; Kravchuk, Oksana; Schwartz, Yuri B

    2016-02-01

    Chromatin insulators are remarkable regulatory elements that can bring distant genomic sites together and block unscheduled enhancer-promoter communications. Insulators act via associated insulator proteins of two classes: sequence-specific DNA binding factors and "bridging" proteins. The latter are required to mediate interactions between distant insulator elements. Chromatin insulators are critical for correct expression of complex loci; however, their mode of action is poorly understood. Here, we use the Drosophila bithorax complex as a model to investigate the roles of the bridging proteins Cp190 and Mod(mdg4). The bithorax complex consists of three evolutionarily conserved homeotic genes Ubx, abd-A, and Abd-B, which specify anterior-posterior identity of the last thoracic and all abdominal segments of the fly. Looking at effects of CTCF, mod(mdg4), and Cp190 mutations on expression of the bithorax complex genes, we provide the first functional evidence that Mod(mdg4) acts in concert with the DNA binding insulator protein CTCF. We find that Mod(mdg4) and Cp190 are not redundant and may have distinct functional properties. We, for the first time, demonstrate that Cp190 is critical for correct regulation of the bithorax complex and show that Cp190 is required at an exceptionally strong Fub insulator to partition the bithorax complex into two topological domains.

  11. MiRNA-mediated regulation of the SWI/SNF chromatin remodeling complex controls pluripotency and endodermal differentiation in human ES cells

    PubMed Central

    Wade, Staton L.; Langer, Lee F.; Ward, James M.; Archer, Trevor K.

    2015-01-01

    MicroRNAs and chromatin remodeling complexes represent powerful epigenetic mechanisms that regulate the pluripotent state. miR-302 is a strong inducer of pluripotency, which is characterized by a distinct chromatin architecture. This suggests that miR-302 regulates global chromatin structure; however, a direct relationship between miR-302 and chromatin remodelers has not been established. Here, we provide data to show that miR-302 regulates Brg1 chromatin remodeling complex composition in human embryonic stem (hESs) cells through direct repression of the BAF53a and BAF170 subunits. With the subsequent overexpression of BAF170 in hESCs, we show that miR-302’s inhibition of BAF170 protein levels can affect the expression of genes involved in cell proliferation. Furthermore, miR-302-mediated repression of BAF170 regulates pluripotency by positively influencing mesendodermal differentiation. Overexpression of BAF170 in hESCs led to biased differentiation toward the ectoderm lineage during EB formation and severely hindered directed definitive endoderm differentiation. Taken together, these data uncover a direct regulatory relationship between miR-302 and the Brg1 chromatin remodeling complex that controls gene expression and cell fate decisions in hESCs and suggests that similar mechanisms are at play during early human development. PMID:26119756

  12. Focal Adhesion-Chromatin Linkage Controls Tumor Cell Resistance to Radio- and Chemotherapy

    PubMed Central

    Storch, Katja; Cordes, Nils

    2012-01-01

    Cancer resistance to therapy presents an ongoing and unsolved obstacle, which has clear impact on patient's survival. In order to address this problem, novel in vitro models have been established and are currently developed that enable data generation in a more physiological context. For example, extracellular-matrix- (ECM-) based scaffolds lead to the identification of integrins and integrin-associated signaling molecules as key promoters of cancer cell resistance to radio- and chemotherapy as well as modern molecular agents. In this paper, we discuss the dynamic nature of the interplay between ECM, integrins, cytoskeleton, nuclear matrix, and chromatin organization and how this affects the response of tumor cells to various kinds of cytotoxic anticancer agents. PMID:22778951

  13. Transcriptional Control by PARP-1: Chromatin Modulation, Enhancer-binding, Coregulation, and Insulation

    PubMed Central

    Kraus, W. Lee

    2008-01-01

    Summary The regulation of gene expression requires a wide array of protein factors that can modulate chromatin structure, act at enhancers, function as transcriptional coregulators, or regulate insulator function. Poly(ADP-ribose) polymerase-1 (PARP-1), an abundant and ubiquitous nuclear enzyme that catalyzes the NAD+-dependent addition of ADP-ribose polymers on a variety of nuclear proteins, has been implicated in all of these functions. Recent biochemical, genomic, proteomic, and cell-based studies have highlighted the role of PARP-1 in each of these processes and provided new insights about the molecular mechanisms governing PARP-1-dependent regulation of gene expression. In addition, these studies have demonstrated how PARP-1 functions as an integral part of cellular signaling pathways that culminate in gene regulatory outcomes. PMID:18450439

  14. Early programming of the oocyte epigenome temporally controls late prophase I transcription and chromatin remodelling

    PubMed Central

    Navarro-Costa, Paulo; McCarthy, Alicia; Prudêncio, Pedro; Greer, Christina; Guilgur, Leonardo G.; Becker, Jörg D.; Secombe, Julie; Rangan, Prashanth; Martinho, Rui G.

    2016-01-01

    Oocytes are arrested for long periods of time in the prophase of the first meiotic division (prophase I). As chromosome condensation poses significant constraints to gene expression, the mechanisms regulating transcriptional activity in the prophase I-arrested oocyte are still not entirely understood. We hypothesized that gene expression during the prophase I arrest is primarily epigenetically regulated. Here we comprehensively define the Drosophila female germ line epigenome throughout oogenesis and show that the oocyte has a unique, dynamic and remarkably diversified epigenome characterized by the presence of both euchromatic and heterochromatic marks. We observed that the perturbation of the oocyte's epigenome in early oogenesis, through depletion of the dKDM5 histone demethylase, results in the temporal deregulation of meiotic transcription and affects female fertility. Taken together, our results indicate that the early programming of the oocyte epigenome primes meiotic chromatin for subsequent functions in late prophase I. PMID:27507044

  15. Early programming of the oocyte epigenome temporally controls late prophase I transcription and chromatin remodelling.

    PubMed

    Navarro-Costa, Paulo; McCarthy, Alicia; Prudêncio, Pedro; Greer, Christina; Guilgur, Leonardo G; Becker, Jörg D; Secombe, Julie; Rangan, Prashanth; Martinho, Rui G

    2016-08-10

    Oocytes are arrested for long periods of time in the prophase of the first meiotic division (prophase I). As chromosome condensation poses significant constraints to gene expression, the mechanisms regulating transcriptional activity in the prophase I-arrested oocyte are still not entirely understood. We hypothesized that gene expression during the prophase I arrest is primarily epigenetically regulated. Here we comprehensively define the Drosophila female germ line epigenome throughout oogenesis and show that the oocyte has a unique, dynamic and remarkably diversified epigenome characterized by the presence of both euchromatic and heterochromatic marks. We observed that the perturbation of the oocyte's epigenome in early oogenesis, through depletion of the dKDM5 histone demethylase, results in the temporal deregulation of meiotic transcription and affects female fertility. Taken together, our results indicate that the early programming of the oocyte epigenome primes meiotic chromatin for subsequent functions in late prophase I.

  16. The SWI/SNF chromatin-remodeling complex modulates peripheral T cell activation and proliferation by controlling AP-1 expression.

    PubMed

    Jeong, Seung Min; Lee, Changjin; Lee, Sung Kyu; Kim, Jieun; Seong, Rho Hyun

    2010-01-22

    The SWI/SNF chromatin-remodeling complex has been implicated in the activation and proliferation of T cells. After T cell receptor signaling, the SWI/SNF complex rapidly associates with chromatin and controls gene expression in T cells. However, the process by which the SWI/SNF complex regulates peripheral T cell activation has not been elucidated. In this study, we show that the SWI/SNF complex regulates cytokine production and proliferation of T cells. During T cell activation, the SWI/SNF complex is recruited to the promoter of the transcription factor AP-1, and it increases the expression of AP-1. Increased expression of the SWI/SNF complex resulted in enhanced AP-1 activity, cytokine production, and proliferation of peripheral T cells, whereas knockdown of the SWI/SNF complex expression impaired the AP-1 expression and reduced the activation and proliferation of T cells. Moreover, mice that constitutively expressed the SWI/SNF complex in T cells were much more susceptible to experimentally induced autoimmune encephalomyelitis than the normal mice were. These results suggest that the SWI/SNF complex plays a critical role during T cell activation and subsequent immune responses.

  17. Controllable synthesis of 3D BiVO₄ superstructures with visible-light-induced photocatalytic oxidation of NO in the gas phase and mechanistic analysis.

    PubMed

    Ou, Man; Nie, Haoyu; Zhong, Qin; Zhang, Shule; Zhong, Lei

    2015-11-21

    A surfactant-free solvothermal method was developed for the controlled synthesis of diverse 3D ms-BiVO4 superstructures, including a flower, a double-layer half-open flower and a hollow tube with square cross-sections, via facilely adjusting the pH values with the aid of NH3·H2O. The effects of the morphologies of the prepared 3D ms-BiVO4 superstructure on the photocatalytic oxidation of NO were investigated, indicating that the enhanced photoactivity was not related to the surface area, but associated with the unique morphology, surface structure and good crystallinity. Moreover, the flower-like ms-BiVO4 photocatalyst with a more (040) reactive crystal plane exhibited higher photoactivity than those of other samples. The unique morphology helped with flushing the oxidation products accumulated on the surface of photocatalysts in the H2O2 system, and further improved the photoactivity. A trapping experiment was also conducted to examine the effects of the active species involved in the PCO of NO intuitively.

  18. Light-induced actuating nanotransducers.

    PubMed

    Ding, Tao; Valev, Ventsislav K; Salmon, Andrew R; Forman, Chris J; Smoukov, Stoyan K; Scherman, Oren A; Frenkel, Daan; Baumberg, Jeremy J

    2016-05-17

    Nanoactuators and nanomachines have long been sought after, but key bottlenecks remain. Forces at submicrometer scales are weak and slow, control is hard to achieve, and power cannot be reliably supplied. Despite the increasing complexity of nanodevices such as DNA origami and molecular machines, rapid mechanical operations are not yet possible. Here, we bind temperature-responsive polymers to charged Au nanoparticles, storing elastic energy that can be rapidly released under light control for repeatable isotropic nanoactuation. Optically heating above a critical temperature [Formula: see text] = 32 °C using plasmonic absorption of an incident laser causes the coatings to expel water and collapse within a microsecond to the nanoscale, millions of times faster than the base polymer. This triggers a controllable number of nanoparticles to tightly bind in clusters. Surprisingly, by cooling below [Formula: see text] their strong van der Waals attraction is overcome as the polymer expands, exerting nanoscale forces of several nN. This large force depends on van der Waals attractions between Au cores being very large in the collapsed polymer state, setting up a tightly compressed polymer spring which can be triggered into the inflated state. Our insights lead toward rational design of diverse colloidal nanomachines.

  19. Chromatin Immunoprecipitation.

    PubMed

    Wiehle, Laura; Breiling, Achim

    2016-01-01

    Chromatin immunoprecipitation (ChIP) is a valuable method to investigate protein-DNA interactions in vivo. Since its discovery it has been indispensable to identify binding sites and patterns of a variety of DNA-interacting proteins, such as transcription factors and regulators, modified histones, and epigenetic modifiers. The Polycomb repressors were the first proteins that have been mapped using this technique, which provided the mechanistic basis for the understanding of their biological function. Cross-linked (XChIP) or native (NChIP) chromatin from tissues or cultured cells is fragmented and the protein of interest is immunoprecipitated using a specific antibody. The co-precipitated DNA is then purified and subjected to analysis by region-specific PCR, DNA microarray (ChIP-on-chip), or next-generation sequencing (ChIP-seq). The assay can therefore produce information about the localization of the analyzed protein at specific candidate loci or throughout the entire genome. In this chapter, we provide a detailed protocol of the basic standard ChIP assay and some remarks about variations. PMID:27659971

  20. Light-induced olefin metathesis

    PubMed Central

    Vidavsky, Yuval

    2010-01-01

    Summary Light activation is a most desirable property for catalysis control. Among the many catalytic processes that may be activated by light, olefin metathesis stands out as both academically motivating and practically useful. Starting from early tungsten heterogeneous photoinitiated metathesis, up to modern ruthenium methods based on complex photoisomerisation or indirect photoactivation, this survey of the relevant literature summarises past and present developments in the use of light to expedite olefin ring-closing, ring-opening polymerisation and cross-metathesis reactions. PMID:21160912

  1. EKLF/KLF1, a Tissue-Restricted Integrator of Transcriptional Control, Chromatin Remodeling, and Lineage Determination

    PubMed Central

    Yien, Yvette Y.

    2013-01-01

    Erythroid Krüppel-like factor (EKLF or KLF1) is a transcriptional regulator that plays a critical role in lineage-restricted control of gene expression. KLF1 expression and activity are tightly controlled in a temporal and differentiation stage-specific manner. The mechanisms by which KLF1 is regulated encompass a range of biological processes, including control of KLF1 RNA transcription, protein stability, localization, and posttranslational modifications. Intact KLF1 regulation is essential to correctly regulate erythroid function by gene transcription and to maintain hematopoietic lineage homeostasis by ensuring a proper balance of erythroid/megakaryocytic differentiation. In turn, KLF1 regulates erythroid biology by a wide variety of mechanisms, including gene activation and repression by regulation of chromatin configuration, transcriptional initiation and elongation, and localization of gene loci to transcription factories in the nucleus. An extensive series of biochemical, molecular, and genetic analyses has uncovered some of the secrets of its success, and recent studies are highlighted here. These reveal a multilayered set of control mechanisms that enable efficient and specific integration of transcriptional and epigenetic controls and that pave the way for proper lineage commitment and differentiation. PMID:23090966

  2. The mobile nucleoporin Nup2p and chromatin-bound Prp20p function in endogenous NPC-mediated transcriptional control.

    PubMed

    Dilworth, David J; Tackett, Alan J; Rogers, Richard S; Yi, Eugene C; Christmas, Rowan H; Smith, Jennifer J; Siegel, Andrew F; Chait, Brian T; Wozniak, Richard W; Aitchison, John D

    2005-12-19

    Nuclear pore complexes (NPCs) govern macromolecular transport between the nucleus and cytoplasm and serve as key positional markers within the nucleus. Several protein components of yeast NPCs have been implicated in the epigenetic control of gene expression. Among these, Nup2p is unique as it transiently associates with NPCs and, when artificially tethered to DNA, can prevent the spread of transcriptional activation or repression between flanking genes, a function termed boundary activity. To understand this function of Nup2p, we investigated the interactions of Nup2p with other proteins and with DNA using immunopurifications coupled with mass spectrometry and microarray analyses. These data combined with functional assays of boundary activity and epigenetic variegation suggest that Nup2p and the Ran guanylyl-nucleotide exchange factor, Prp20p, interact at specific chromatin regions and enable the NPC to play an active role in chromatin organization by facilitating the transition of chromatin between activity states.

  3. Light-induced anodisation of silicon for solar cell passivation

    NASA Astrophysics Data System (ADS)

    Cui, J.; Wang, X.; Opila, R.; Lennon, A.

    2013-11-01

    This paper reports a new method for forming anodic oxides on silicon surfaces using the light-induced current of pn-junction solar cells to make p-type silicon surfaces anodic. The light-induced anodisation process enables anodic oxide layers as thick as 79 nm to be formed at room temperature in a faster, more uniform, and controllable manner compared to previously reported clip-based anodisation methods. Although the effective minority carrier lifetime decreased immediately after light-induced anodisation from initial values measured with an 17 nm thermally grown oxide on both wafer surfaces, the 1-sun implied open circuit voltage of wafers on which the thermally grown oxide on the p-type surface was replaced by an anodic oxide of the same thickness could be returned to its initial value of ˜635 mV (for 3-5 Ω-cm Cz silicon wafers) after a 400 °C anneal in oxygen and then forming gas. The passivation of the formed anodic oxide layers was stable for a period of 50 days providing the oxide was protected by a 75 nm thick silicon nitride capping layer.

  4. p63 and Brg1 control developmentally regulated higher-order chromatin remodelling at the epidermal differentiation complex locus in epidermal progenitor cells

    PubMed Central

    Mardaryev, Andrei N.; Gdula, Michal R.; Yarker, Joanne L.; Emelianov, Vladimir N.; Poterlowicz, Krzysztof; Sharov, Andrey A.; Sharova, Tatyana Y.; Scarpa, Julie A.; Chambon, Pierre; Botchkarev, Vladimir A.; Fessing, Michael Y.

    2014-01-01

    Chromatin structural states and their remodelling, including higher-order chromatin folding and three-dimensional (3D) genome organisation, play an important role in the control of gene expression. The role of 3D genome organisation in the control and execution of lineage-specific transcription programmes during the development and differentiation of multipotent stem cells into specialised cell types remains poorly understood. Here, we show that substantial remodelling of the higher-order chromatin structure of the epidermal differentiation complex (EDC), a keratinocyte lineage-specific gene locus on mouse chromosome 3, occurs during epidermal morphogenesis. During epidermal development, the locus relocates away from the nuclear periphery towards the nuclear interior into a compartment enriched in SC35-positive nuclear speckles. Relocation of the EDC locus occurs prior to the full activation of EDC genes involved in controlling terminal keratinocyte differentiation and is a lineage-specific, developmentally regulated event controlled by transcription factor p63, a master regulator of epidermal development. We also show that, in epidermal progenitor cells, p63 directly regulates the expression of the ATP-dependent chromatin remodeller Brg1, which binds to distinct domains within the EDC and is required for relocation of the EDC towards the nuclear interior. Furthermore, Brg1 also regulates gene expression within the EDC locus during epidermal morphogenesis. Thus, p63 and its direct target Brg1 play an essential role in remodelling the higher-order chromatin structure of the EDC and in the specific positioning of this locus within the landscape of the 3D nuclear space, as required for the efficient expression of EDC genes in epidermal progenitor cells during skin development. PMID:24346698

  5. Chromatin remodeling in plant development.

    PubMed

    Jarillo, José A; Piñeiro, Manuel; Cubas, Pilar; Martínez-Zapater, José M

    2009-01-01

    Plant development results from specific patterns of gene expression that are tightly regulated in a spatio-temporal manner. Chromatin remodeling plays a central role in establishing these expression patterns and maintaining epigenetic transcriptional states through successive rounds of mitosis that take place within a cell lineage. Plant epigenetic switches occur not only at the embryo stage, but also during postembryonic developmental transitions, suggesting that chromatin remodeling activities in plants can provide a higher degree of regulatory flexibility which probably underlies their developmental plasticity. Here, we highlight recent progress in the understanding of plant chromatin dynamic organization, facilitating the activation or repression of specific sets of genes involved in different developmental programs and integrating them with the response to environmental signals. Chromatin conformation controls gene expression both in actively dividing undifferentiated cells and in those already fate-determined. In this context, we first describe chromatin reorganization activities required to maintain meristem function stable through DNA replication and cell division. Organ initiation at the apex, with emphasis on reproductive development, is next discussed to uncover the chromatin events involved in the establishment and maintenance of expression patterns associated with differentiating cells; this is illustrated with the complex epigenetic regulation of the Arabidopsis floral repressor FLOWERING LOCUS C (FLC). Finally, we discuss the involvement of chromatin remodeling in plant responses to environmental cues and to different types of stress conditions.

  6. Chromatin remodelling and antisense-mediated up-regulation of the developmental switch gene eud-1 control predatory feeding plasticity

    PubMed Central

    Serobyan, Vahan; Xiao, Hua; Namdeo, Suryesh; Rödelsperger, Christian; Sieriebriennikov, Bogdan; Witte, Hanh; Röseler, Waltraud; Sommer, Ralf J.

    2016-01-01

    Phenotypic plasticity has been suggested to act through developmental switches, but little is known about associated molecular mechanisms. In the nematode Pristionchus pacificus, the sulfatase eud-1 was identified as part of a developmental switch controlling mouth-form plasticity governing a predatory versus bacteriovorous mouth-form decision. Here we show that mutations in the conserved histone-acetyltransferase Ppa-lsy-12 and the methyl-binding-protein Ppa-mbd-2 mimic the eud-1 phenotype, resulting in the absence of one mouth-form. Mutations in both genes cause histone modification defects and reduced eud-1 expression. Surprisingly, Ppa-lsy-12 mutants also result in the down-regulation of an antisense-eud-1 RNA. eud-1 and antisense-eud-1 are co-expressed and further experiments suggest that antisense-eud-1 acts through eud-1 itself. Indeed, overexpression of the antisense-eud-1 RNA increases the eud-1-sensitive mouth-form and extends eud-1 expression. In contrast, this effect is absent in eud-1 mutants indicating that antisense-eud-1 positively regulates eud-1. Thus, chromatin remodelling and antisense-mediated up-regulation of eud-1 control feeding plasticity in Pristionchus. PMID:27487725

  7. Metastable light induced defects in pentacene

    SciTech Connect

    Liguori, R.; Aprano, S.; Rubino, A.

    2014-02-21

    In this study we analyzed one of the environmental factors that could affect organic materials. Pentacene thin film samples were fabricated and the degradation of their electrical characteristics was measured when the devices were exposed to ultraviolet light irradiation. The results have been reported in terms of a trap density model, which provides a description of the dynamics of light induced electrically active defects in an organic semiconductor.

  8. Antisense RNA Controls LRP1 Sense Transcript Expression Through Interaction With a Chromatin-Associated Protein, HMGB2

    PubMed Central

    Yamanaka, Yasunari; Faghihi, Mohammad Ali; Magistri, Marco; Alvarez-Garcia, Oscar; Lotz, Martin; Wahlestedt, Claes

    2015-01-01

    SUMMARY Long non-coding RNAs (lncRNAs) including natural antisense transcripts (NATs) are expressed more extensively than previously anticipated, and have widespread roles in regulating gene expression. Nevertheless, the molecular mechanisms of action of the majority of NATs remain largely unknown. Here we identify a NAT of Low-density lipoprotein receptor-related protein 1 (Lrp1), referred to as Lrp1-AS, that negatively regulates Lrp1 expression. We show that Lrp1-AS directly binds to High mobility group box 2 (Hmgb2) and inhibits the activity of Hmgb2 to enhance Srebp1a-dependent transcription of Lrp1. Short oligonucleotides targeting Lrp1-AS inhibit the interaction of antisense transcript and Hmgb2 protein, and increase Lrp1 expression by enhancing Hmgb2 activity. qRT-PCR analysis of Alzheimer’s disease brain samples and aged-matched controls revealed upregulation of LRP1-AS and downregulation of LRP1. Our data suggest a new regulatory mechanism whereby a NAT interacts with a ubiquitous chromatin-associated protein to modulate its activity in a locus-specific fashion. PMID:25937287

  9. Isorefractive high internal phase emulsion organogels for light induced reactions.

    PubMed

    Zhang, Tao; Guo, Qipeng

    2016-03-25

    Isorefractive high internal phase emulsion (HIPE) organogels have been fabricated and investigated for light induced reactions. High transparency facilitates both the UV and visible light induced reactions within HIPE organogels. Transparent HIPE organogels are advantageous for light induced polymerizations, accelerating such polymerizations and enabling the preparation of large polyHIPE monoliths.

  10. Light-induced voltage alteration for integrated circuit analysis

    DOEpatents

    Cole, Jr., Edward I.; Soden, Jerry M.

    1995-01-01

    An apparatus and method are described for analyzing an integrated circuit (IC), The invention uses a focused light beam that is scanned over a surface of the IC to generate a light-induced voltage alteration (LIVA) signal for analysis of the IC, The LIVA signal may be used to generate an image of the IC showing the location of any defects in the IC; and it may be further used to image and control the logic states of the IC. The invention has uses for IC failure analysis, for the development of ICs, for production-line inspection of ICs, and for qualification of ICs.

  11. Light-induced voltage alteration for integrated circuit analysis

    DOEpatents

    Cole, E.I. Jr.; Soden, J.M.

    1995-07-04

    An apparatus and method are described for analyzing an integrated circuit (IC). The invention uses a focused light beam that is scanned over a surface of the IC to generate a light-induced voltage alteration (LIVA) signal for analysis of the IC. The LIVA signal may be used to generate an image of the IC showing the location of any defects in the IC; and it may be further used to image and control the logic states of the IC. The invention has uses for IC failure analysis, for the development of ICs, for production-line inspection of ICs, and for qualification of ICs. 18 figs.

  12. Light-induced scattering in photorefractive crystals

    NASA Astrophysics Data System (ADS)

    Rupp, R. A.; Drees, F. W.

    1986-04-01

    Light-induced scattering features in LiNbO3- and BaTiO3-crytals are compared with theories on holographic writing in photorefractive crystals. It is shown that they describe the experimental facts concerning the expected main scattering directions for a given incident polarization, the time development, the thickness and the wavelength dependence. Time records of the transmission offer a useful alternative for the determination of the photoconductivity. Furthermore, a new method for birefringence measurements is established. The high accuracy of this method is based on the automatic fulfillment of a phase matching condition by the anisotropically scattered radiation.

  13. Strain Differences in Light-Induced Retinopathy

    PubMed Central

    Polosa, Anna; Bessaklia, Hyba; Lachapelle, Pierre

    2016-01-01

    The purpose of this study was to better understand the role of ocular pigmentation and genetics in light-induced retinal damage. Adult pigmented [Long Evans (LE) and Brown Norway (BN)] and albino [Sprague Dawley (SD) and Lewis (LW)] rats were exposed to a bright cyclic light for 6 consecutive days and where compared with juvenile animals exposed to the same bright light environment from postnatal age 14 to 28. Flash ERGs and retinal histology were performed at predetermined days (D) post-light exposure. At D1, ERGs were similar in all adult groups with no recordable a-waves and residual b-waves. A transient recovery was noticed at D30 in the LW and LE only [b-wave: 18% and 25% of their original amplitude respectively]. Histology revealed that BN retina was the most damaged, while LE retina was best preserved. SD and LW rats were almost as damaged as BN rats. In contrast, the retina of juvenile BN was almost as resistant to the bright light exposure as that of juvenile LE rats. Our results strongly suggest that, although ocular pigmentation and genetic background are important factors in regulating the severity of light-induced retinal damage, the age of the animal at the onset of light exposure appears to be the most important determining factor. PMID:27355622

  14. A light-induced microwave oscillator

    NASA Technical Reports Server (NTRS)

    Yao, X. S.; Maleki, L.

    1995-01-01

    We describe a novel oscillator that converts continuous light energy into sta ble and spectrally pure microwave signals. This light-induced microwave oscillator (LIMO) consists of a pump laser and a feedback circuit, including an intensity modulator, an optical fiber delay line, a photodetector, an amplifier, and a filter. We develop a quasilinear theory and obtain expressions for the threshold condition, the amplitude, the frequency, the line width, and the spectral power density of the oscillation. We also present experimental data to compare with the theoretical results. Our findings indicate that the LIMO can generate ultrastable, spectrally pure microwave reference signals up to 75 GHz with a phase noise lower than -140 dBc/Hz at 10 kHz.

  15. Broadband Visible Light Induced NO Formation

    NASA Astrophysics Data System (ADS)

    Lubart, Rachel; Eichler, Maor; Friedmann, Harry; Savion, N.; Breitbart, Haim; Ankri, Rinat

    2009-06-01

    Nitric oxide formation is a potential mechanism for photobiomodulation because it is synthesized in cells by nitric oxide synthase (NOS), which contains both flavin and heme, and thus absorbs visible light. The purpose of this work was to study broadband visible light induced NO formation in various cells. Cardiac, endothelial, sperm cells and RAW 264.7 macrophages were illuminated with broadband visible light, 40-130 mW/cm2, 2.4-39 J/cm2, and nitric oxide production was quantified by using the Griess reagent. The results showed that visible light illumination increased NO concentration both in sperm and endothelial cells, but not in cardiac cells. Activation of RAW 264.7 macrophages was very small. It thus appears that NO is involved in photobiomodulation, though different light parameters and illumination protocols are needed to induce NO in various cells.

  16. Visible-Light-Induced Click Chemistry.

    PubMed

    Mueller, Jan O; Schmidt, Friedrich G; Blinco, James P; Barner-Kowollik, Christopher

    2015-08-24

    A rapid and catalyst-free cycloaddition system for visible-light-induced click chemistry is reported. A readily accessible photoreactive 2H-azirine moiety was designed to absorb light at wavelengths above 400 nm. Irradiation with low-energy light sources thus enables efficient small-molecule synthesis with a diverse range of multiple-bond-containing compounds. Moreover, in order to demonstrate the efficiency of the current approach, quantitative ligation of the photoactivatable chromophore with functional polymeric substrates was performed and full conversion with irradiation times of only 1 min at ambient conditions was achieved. The current report thus presents a highly efficient method for applications involving selective cycloaddition to electron-deficient multiple-bond-containing materials.

  17. Broadband Visible Light Induced NO Formation

    SciTech Connect

    Lubart, Rachel; Eichler, Maor; Friedmann, Harry; Ankri, Rinat; Savion, N.; Breitbart, Haim

    2009-06-19

    Nitric oxide formation is a potential mechanism for photobiomodulation because it is synthesized in cells by nitric oxide synthase (NOS), which contains both flavin and heme, and thus absorbs visible light. The purpose of this work was to study broadband visible light induced NO formation in various cells. Cardiac, endothelial, sperm cells and RAW 264.7 macrophages were illuminated with broadband visible light, 40-130 mW/cm2, 2.4-39 J/cm2, and nitric oxide production was quantified by using the Griess reagent. The results showed that visible light illumination increased NO concentration both in sperm and endothelial cells, but not in cardiac cells. Activation of RAW 264.7 macrophages was very small. It thus appears that NO is involved in photobiomodulation, though different light parameters and illumination protocols are needed to induce NO in various cells.

  18. Light-Induced Dielectrophoretic Manipulation of DNA

    PubMed Central

    Hoeb, Marco; Rädler, Joachim O.; Klein, Stefan; Stutzmann, Martin; Brandt, Martin S.

    2007-01-01

    Light-induced dielectrophoretic movement of polystyrene beads and λ-DNA is studied using thin films of amorphous hydrogenated silicon as local photoaddressable electrodes with a diameter of 4 μm. Positive (high-field seeking) dielectrophoretic movement is observed for both types of objects. The absence of strong negative (low-field seeking) dielectrophoresis of DNA at high frequencies is in agreement with the similarity of the dielectric constants of DNA and water, the real part of the dielectric function. The corresponding imaginary part of the dielectric function governed by the conductivity of DNA can be determined from a comparison of the frequency dependence of the dielectrophoretic drift velocity with the Clausius-Mossotti relation. PMID:17483160

  19. Green light induces shade avoidance symptoms.

    PubMed

    Zhang, Tingting; Maruhnich, Stefanie A; Folta, Kevin M

    2011-11-01

    Light quality and quantity affect plant adaptation to changing light conditions. Certain wavelengths in the visible and near-visible spectrum are known to have discrete effects on plant growth and development, and the effects of red, far-red, blue, and ultraviolet light have been well described. In this report, an effect of green light on Arabidopsis (Arabidopsis thaliana) rosette architecture is demonstrated using a narrow-bandwidth light-emitting diode-based lighting system. When green light was added to a background of constant red and blue light, plants exhibited elongation of petioles and upward leaf reorientation, symptoms consistent with those observed in a shaded light environment. The same green light-induced phenotypes were also observed in phytochrome (phy) and cryptochrome (cry) mutant backgrounds. To explore the molecular mechanism underlying the green light-induced response, the accumulation of shade-induced transcripts was measured in response to enriched green light environments. Transcripts that have been demonstrated to increase in abundance under far-red-induced shade avoidance conditions either decrease or exhibit no change when green light is added. However, normal far-red light-associated transcript accumulation patterns are observed in cryptochrome mutants grown with supplemental green light, indicating that the green-absorbing form of cryptochrome is the photoreceptor active in limiting the green light induction of shade-associated transcripts. These results indicate that shade symptoms can be induced by the addition of green light and that cryptochrome receptors and an unknown light sensor participate in acclimation to the enriched green environment.

  20. Light-induced chemical vapour deposition painting with titanium dioxide

    NASA Astrophysics Data System (ADS)

    Halary-Wagner, E.; Bret, T.; Hoffmann, P.

    2003-03-01

    Light-induced chemical vapour deposits of titanium dioxide are obtained from titanium tetra-isopropoxide (TTIP) in an oxygen and nitrogen atmosphere with a long pulse (250 ns) 308 nm XeCl excimer laser using a mask projection set-up. The demonstrated advantages of this technique are: (i) selective area deposition, (ii) precise control of the deposited thickness and (iii) low temperature deposition, enabling to use a wide range of substrates. A revolving mask system enables, in a single reactor load, to deposit shapes of controlled heights, which overlap to build up a complex pattern. Interferential multi-coloured deposits are achieved, and the process limitations (available colours and resolution) are discussed.

  1. Light-induced fluorescence for pulpal diagnosis

    NASA Astrophysics Data System (ADS)

    Ebihara, Arata; Liaw, Lih-Huei L.; Krasieva, Tatiana B.; Wilder-Smith, Petra B. B.

    2001-04-01

    A direct non-histological means of pulpal diagnosis remains elusive to clinical practice. Clinical vitality testing remains limited to electric, thermal criteria, or laser Doppler flowmetry. The goal of these investigations was to determine the feasibility of using light-induced fluorescence as a non-invasive modality for pulpal evaluation. Such a capability would, for example, permit expanded use of pulpotomy/pulpectomy techniques. Clinically healthy and diseased human extirpated pulpal tissues were used in this study. After excision, they were rapidly frozen and standard cryosections prepared. Measurement of tissue excitation/emission characteristics was performed using spectrographic analysis. A low-light level fluorescence microscopy system was then used to image autofluorescence localization and intensity at optimal excitation/detection parameters. Excitation/detection parameters used in this study included 405/605, 405/635, 405/670, 440/550, and 440/635. Autofluorescence intensities in healthy tissues were significantly stronger than those in diseased tissues at optimal parameters. It is postulated that autofluorescence characteristics are related to pathology- related structural changes in the pulp. This work provides the basis for further investigation into the relation between autofluorescence, histology and clinical symptoms.

  2. Light-induced atomic desorption: recent developments

    NASA Astrophysics Data System (ADS)

    Mariotti, E.; Atutov, S. N.; Biancalana, Valerio; Bocci, S.; Burchianti, A.; Marinelli, C.; Nasyrov, K. A.; Pieragnoli, B.; Moi, L.

    2001-04-01

    Light induced atomic desorption (LIAD) is an impressive manifestation of a new class of phenomena involving alkali atoms, dielectric films and light. LIAD consists of a huge emission of alkali atoms (experimentally proved for sodium, potassium, rubidium and cesium) from siloxane films when illuminated by laser or ordinary light. Most of the experiments have been performed in glass cells suitably coated by a thin film (of the order of 10 micrometer) either of poly - (dimethylsiloxane) (PDMS), a polymer, or of octamethylcyclotetrasiloxane (OCT), a crown molecule. LIAD is a combination of two processes: direct photo-desorption from the surface and diffusion within the siloxane layer. The photo-desorbed atoms are replaced by fresh atoms diffusing to the surface. Moreover, from the experimental data it comes out that the desorbing light increases atomic diffusion and hence the diffusion coefficient. To our knowledge this is the first time that such an effect is clearly observed, measured and discussed: LIAD represents a new class of photo-effects characterized by two simultaneous phenomena due to the light: surface desorption and fastened bulk diffusion.

  3. EDITORIAL Light-induced material organization Light-induced material organization

    NASA Astrophysics Data System (ADS)

    Vainos, Nikos; Rode, Andrei V.

    2010-12-01

    horizons to production processing (Koroleva et al). The use of femtosecond lasers enables polymerization for flexible production of micro-optics and integrated optics (Malinauskas et al). Laser beams of moderate intensity are used to create surface relief patterning in polymer and hybrid matter (Babeva et al) while the use of optimized acrylamide photopolymers results in submicron holographic structures (Trainer et al). In a different concept, the application of laser radiation forces in soft polymer matter offers intriguing, yet unexplored, means for the organization of dense structures and filaments in polymer solutes, pointing to nonlinear optical applications (Anyfantakis et al). Finally, high laser intensities are used for the processing of soft polymer and hybrid matter. In the two modes of operation available, laser-induced forward transfer of polymers is a promising alternative for the creation of controlled structures (Palla-Papavlu et al), while ablative structuring creates interfaces with enhanced properties by excimer laser irradiation at the deep ultraviolet 193 nm and 157 nm wavelengths (Athanasekos et al). Such methods provide flexible tools for the fabrication of optimized photonic sensor structures based on hybrid nanocomposites incorporating diffractive optic interfaces, a technology enabling the recent advent of remote point sensing of chemical and physical agents by light (Vasileiades et al). A substantial part of this work has been supported in the framework of COST MP0604 Action `Optical Micro-Manipulation by Nonlinear Nanophotonics' of the European Science Foundation. We are confident that this collection of papers on light-induced material organization will guide the reader in this emerging field, inspire the interested scientific community and stimulate further research and innovation in this exciting and growing field.

  4. Expanding the roles of chromatin insulators in nuclear architecture, chromatin organization and genome function.

    PubMed

    Schoborg, Todd; Labrador, Mariano

    2014-11-01

    Of the numerous classes of elements involved in modulating eukaryotic chromosome structure and function, chromatin insulators arguably remain the most poorly understood in their contribution to these processes in vivo. Indeed, our view of chromatin insulators has evolved dramatically since their chromatin boundary and enhancer blocking properties were elucidated roughly a quarter of a century ago as a result of recent genome-wide, high-throughput methods better suited to probing the role of these elements in their native genomic contexts. The overall theme that has emerged from these studies is that chromatin insulators function as general facilitators of higher-order chromatin loop structures that exert both physical and functional constraints on the genome. In this review, we summarize the result of recent work that supports this idea as well as a number of other studies linking these elements to a diverse array of nuclear processes, suggesting that chromatin insulators exert master control over genome organization and behavior.

  5. Direct interplay among histones, histone chaperones, and a chromatin boundary protein in the control of histone gene expression.

    PubMed

    Zunder, Rachel M; Rine, Jasper

    2012-11-01

    In Saccharomyces cerevisiae, the histone chaperone Rtt106 binds newly synthesized histone proteins and mediates their delivery into chromatin during transcription, replication, and silencing. Rtt106 is also recruited to histone gene regulatory regions by the HIR histone chaperone complex to ensure S-phase-specific expression. Here we showed that this Rtt106:HIR complex included Asf1 and histone proteins. Mutations in Rtt106 that reduced histone binding reduced Rtt106 enrichment at histone genes, leading to their increased transcription. Deletion of the chromatin boundary element Yta7 led to increased Rtt106:H3 binding, increased Rtt106 enrichment at histone gene regulatory regions, and decreased histone gene transcription at the HTA1-HTB1 locus. These results suggested a unique regulatory mechanism in which Rtt106 sensed the level of histone proteins to maintain the proper level of histone gene transcription. The role of these histone chaperones and Yta7 differed markedly among the histone gene loci, including the two H3-H4 histone gene pairs. Defects in silencing in rtt106 mutants could be partially accounted for by Rtt106-mediated changes in histone gene repression. These studies suggested that feedback mediated by histone chaperone complexes plays a pivotal role in regulating histone gene transcription.

  6. Parental Allele-Specific Chromatin Configuration in a Boundary–Imprinting-Control Element Upstream of the Mouse H19 Gene

    PubMed Central

    Khosla, Sanjeev; Aitchison, Alan; Gregory, Richard; Allen, Nicholas D.; Feil, Robert

    1999-01-01

    The mouse H19 gene is expressed from the maternal chromosome exclusively. A 2-kb region at 2 to 4 kb upstream of H19 is paternally methylated throughout development, and these sequences are necessary for the imprinted expression of both H19 and the 5′-neighboring Igf2 gene. In particular, on the maternal chromosome this element appears to insulate the Igf2 gene from enhancers located downstream of H19. We analyzed the chromatin organization of this element by assaying its sensitivity to nucleases in nuclei. Six DNase I hypersensitive sites (HS sites) were detected on the unmethylated maternal chromosome exclusively, the two most prominent of which mapped 2.25 and 2.75 kb 5′ to the H19 transcription initiation site. Five of the maternal HS sites were present in expressing and nonexpressing tissues and in embryonic stem (ES) cells. They seem, therefore, to reflect the maternal origin of the chromosome rather than the expression of H19. A sixth maternal HS site, at 3.45 kb upstream of H19, was detected in ES cells only. The nucleosomal organization of this element was analyzed in tissues and ES cells by micrococcal nuclease digestion. Specifically on the maternal chromosome, an unusual and strong banding pattern was obtained, suggestive of a nonnucleosomal organization. From our studies, it appears that the unusual chromatin organization with the presence of HS sites (maternal chromosome) and DNA methylation (paternal chromosome) in this element are mutually exclusive and reflect alternate epigenetic states. In addition, our data suggest that nonhistone proteins are associated with the maternal chromosome and that these might be involved in its boundary function. PMID:10082521

  7. Gearing up chromatin

    PubMed Central

    Mandemaker, Imke K; Vermeulen, Wim; Marteijn, Jurgen A

    2014-01-01

    During transcription, RNA polymerase may encounter DNA lesions, which causes stalling of transcription. To overcome the RNA polymerase blocking lesions, the transcribed strand is repaired by a dedicated repair mechanism, called transcription coupled nucleotide excision repair (TC-NER). After repair is completed, it is essential that transcription restarts. So far, the regulation and exact molecular mechanism of this transcriptional restart upon genotoxic damage has remained elusive. Recently, three different chromatin remodeling factors, HIRA, FACT, and Dot1L, were identified to stimulate transcription restart after DNA damage. These factors either incorporate new histones or establish specific chromatin marks that will gear up the chromatin to subsequently promote transcription recovery. This adds a new layer to the current model of chromatin remodeling necessary for repair and indicates that this specific form of transcription, i.e., the transcriptional restart upon DNA damage, needs specific chromatin remodeling events. PMID:24809693

  8. Arabidopsis BREVIPEDICELLUS interacts with the SWI2/SNF2 chromatin remodeling ATPase BRAHMA to regulate KNAT2 and KNAT6 expression in control of inflorescence architecture.

    PubMed

    Zhao, Minglei; Yang, Songguang; Chen, Chia-Yang; Li, Chenlong; Shan, Wei; Lu, Wangjin; Cui, Yuhai; Liu, Xuncheng; Wu, Keqiang

    2015-03-01

    BREVIPEDICELLUS (BP or KNAT1), a class-I KNOTTED1-like homeobox (KNOX) transcription factor in Arabidopsis thaliana, contributes to shaping the normal inflorescence architecture through negatively regulating other two class-I KNOX genes, KNAT2 and KNAT6. However, the molecular mechanism of BP-mediated transcription regulation remains unclear. In this study, we showed that BP directly interacts with the SWI2/SNF2 chromatin remodeling ATPase BRAHMA (BRM) both in vitro and in vivo. Loss-of-function BRM mutants displayed inflorescence architecture defects, with clustered inflorescences, horizontally orientated pedicels, and short pedicels and internodes, a phenotype similar to the bp mutants. Furthermore, the transcript levels of KNAT2 and KNAT6 were elevated in brm-3, bp-9 and brm-3 bp-9 double mutants. Increased histone H3 lysine 4 tri-methylation (H3K4me3) levels were detected in brm-3, bp-9 and brm-3 bp-9 double mutants. Moreover, BRM and BP co-target to KNAT2 and KNAT6 genes, and BP is required for the binding of BRM to KNAT2 and KNAT6. Taken together, our results indicate that BP interacts with the chromatin remodeling factor BRM to regulate the expression of KNAT2 and KNAT6 in control of inflorescence architecture.

  9. Chromatin and the genome integrity network

    PubMed Central

    Papamichos-Chronakis, Manolis; Peterson, Craig L.

    2013-01-01

    The maintenance of genome integrity is essential for organism survival and for the inheritance of traits to offspring. Genomic instability is caused by DNA damage, aberrant DNA replication or uncoordinated cell division, which can lead to chromosomal aberrations and gene mutations. Recently, chromatin regulators that shape the epigenetic landscape have emerged as potential gatekeepers and signalling coordinators for the maintenance of genome integrity. Here, we review chromatin functions during the two major pathways that control genome integrity: namely, repair of DNA damage and DNA replication. We also discuss recent evidence that suggests a novel role for chromatin-remodelling factors in chromosome segregation and in the prevention of aneuploidy. PMID:23247436

  10. Light-induced self-assembly of active rectification devices.

    PubMed

    Stenhammar, Joakim; Wittkowski, Raphael; Marenduzzo, Davide; Cates, Michael E

    2016-04-01

    Self-propelled colloidal objects, such as motile bacteria or synthetic microswimmers, have microscopically irreversible individual dynamics-a feature they share with all living systems. The incoherent behavior of individual swimmers can be harnessed (or "rectified") by microfluidic devices that create systematic motions that are impossible in equilibrium. We present a computational proof-of-concept study showing that such active rectification devices could be created directly from an unstructured "primordial soup" of light-controlled motile particles, solely by using spatially modulated illumination to control their local propulsion speed. Alongside both microscopic irreversibility and speed modulation, our mechanism requires spatial symmetry breaking, such as a chevron light pattern, and strong interactions between particles, such as volume exclusion, which cause a collisional slowdown at high density. Together, we show how these four factors create a novel, many-body rectification mechanism. Our work suggests that standard spatial light modulator technology might allow the programmable, light-induced self-assembly of active rectification devices from an unstructured particle bath.

  11. Light-induced self-assembly of active rectification devices

    PubMed Central

    Stenhammar, Joakim; Wittkowski, Raphael; Marenduzzo, Davide; Cates, Michael E.

    2016-01-01

    Self-propelled colloidal objects, such as motile bacteria or synthetic microswimmers, have microscopically irreversible individual dynamics—a feature they share with all living systems. The incoherent behavior of individual swimmers can be harnessed (or “rectified”) by microfluidic devices that create systematic motions that are impossible in equilibrium. We present a computational proof-of-concept study showing that such active rectification devices could be created directly from an unstructured “primordial soup” of light-controlled motile particles, solely by using spatially modulated illumination to control their local propulsion speed. Alongside both microscopic irreversibility and speed modulation, our mechanism requires spatial symmetry breaking, such as a chevron light pattern, and strong interactions between particles, such as volume exclusion, which cause a collisional slowdown at high density. Together, we show how these four factors create a novel, many-body rectification mechanism. Our work suggests that standard spatial light modulator technology might allow the programmable, light-induced self-assembly of active rectification devices from an unstructured particle bath. PMID:27051883

  12. Prenucleosomes and Active Chromatin

    PubMed Central

    Khuong, Mai T.; Fei, Jia; Ishii, Haruhiko; Kadonaga, James T.

    2016-01-01

    Chromatin consists of nucleosomes as well as nonnucleosomal histone-containing particles. Here we describe the prenucleosome, which is a stable conformational isomer of the nucleosome that associates with ~80 bp DNA. Prenucleosomes are formed rapidly upon the deposition of histones onto DNA and can be converted into canonical nucleosomes by an ATP-driven chromatin assembly factor such as ACF. Different lines of evidence reveal that there are prenucleosome-sized DNA-containing particles with histones in the upstream region of active promoters. Moreover, p300 acetylates histone H3K56 in prenucleosomes but not in nucleosomes, and H3K56 acetylation is found at active promoters and enhancers. These findings therefore suggest that there may be prenucleosomes or prenucleosome-like particles in the upstream region of active promoters. More generally, we postulate that prenucleosomes or prenucleosome-like particles are present at dynamic chromatin, whereas canonical nucleosomes are at static chromatin. PMID:26767995

  13. A green-light inducible lytic system for cyanobacterial cells

    PubMed Central

    2014-01-01

    Background Cyanobacteria are an attractive candidate for the production of biofuel because of their ability to capture carbon dioxide by photosynthesis and grow on non-arable land. However, because huge quantities of water are required for cultivation, strict water management is one of the greatest issues in algae- and cyanobacteria-based biofuel production. In this study, we aim to construct a lytic cyanobacterium that can be regulated by a physical signal (green-light illumination) for future use in the recovery of biofuel related compounds. Results We introduced T4 bacteriophage-derived lysis genes encoding holin and endolysin under the control of the green-light regulated cpcG2 promoter in Synechocystis sp. PCC 6803. When cells harboring the lysis genes were illuminated with both red and green light, we observed a considerable decrease in growth rate, a significant increase in cellular phycocyanin released in the medium, and a considerable fraction of dead cells. These effects were not observed when these cells were illuminated with only red light, or when cells not containing the lysis genes were grown under either red light or red and green light. These results indicate that our constructed green-light inducible lytic system was clearly induced by green-light illumination, resulting in lytic cells that released intracellular phycocyanin into the culture supernatant. This property suggests a future possibility to construct photosynthetic genetically modified organisms that are unable to survive under sunlight exposure. Expression of the self-lysis system with green-light illumination was also found to greatly increase the fragility of the cell membrane, as determined by subjecting the induced cells to detergent, osmotic-shock, and freeze-thaw treatments. Conclusions A green-light inducible lytic system was constructed in Synechocystis sp. PCC 6803. The engineered lytic cyanobacterial cells should be beneficial for the recovery of biofuels and related compounds

  14. Targeting Chromatin-Mediated Transcriptional Control of Gene Expression in Non-Small Cell Lung Cancer Therapy: Preclinical Rationale and Clinical Results.

    PubMed

    Pasini, Alice; Delmonte, Angelo; Tesei, Anna; Calistri, Daniele; Giordano, Emanuele

    2015-10-01

    Targeting chromatin-mediated transcriptional control of gene expression is nowadays considered a promising new strategy, transcending conventional anticancer therapy. As a result, molecules acting as DNA demethylating agents or histone deacetylase inhibitors (HDACi) have entered the clinical arena in the last decade. Given the evidence suggesting that epigenetic regulation is significantly involved in lung cancer development and progression, the potential of epigenetically active compounds to modulate gene expression and reprogram cancer cells to a less aggressive phenotype is, at present, a promising strategy. Accordingly, a large number of compounds that interact with the epigenetic machinery of gene expression regulation are now being developed and tested as potential antitumor agents, either alone or in combination with standard therapy. The preclinical rationale and clinical data concerning the pharmacological modulation of chromatin organization in non-small cell lung cancer (NSCLC) is described in this review. Although preclinical data suggest that a pharmacological treatment targeting the epigenetic machinery has relevant activity over the neoplastic phenotype of NSCLC cells, clinical results are disappointing, leading only to short periods of disease stabilization in NSCLC patients. This evidence calls for a significant rethinking of strategies for an effective epigenetic therapy of NSCLC. The synergistic effect of concurrent epigenetic therapies, use at low doses, the priming of current treatments with previous epigenetic drugs, and the selection of clinical trial populations based on epigenetic biomarkers/signatures appear to be the cornerstones of a mature therapeutic strategy aiming to establish new regimens for reprogramming malignant cells and improving the clinical history of affected patients. PMID:26347133

  15. The SWI/SNF chromatin remodeling complex exerts both negative and positive control over LET-23/EGFR-dependent vulval induction in Caenorhabditis elegans.

    PubMed

    Flibotte, Stephane; Kim, Bo Ram; Van de Laar, Emily; Brown, Louise; Moghal, Nadeem

    2016-07-01

    Signaling by the epidermal growth factor receptor (EGFR) generates diverse developmental patterns. This requires precise control over the location and intensity of signaling. Elucidation of these regulatory mechanisms is important for understanding development and disease pathogenesis. In Caenorhabditis elegans, LIN-3/EGF induces vulval formation in the mid-body, which requires LET-23/EGFR activation only in P6.p, the vulval progenitor nearest the LIN-3 source. To identify mechanisms regulating this signaling pattern, we screened for mutations that cooperate with a let-23 gain-of-function allele to cause ectopic vulval induction. Here, we describe a dominant gain-of-function mutation in swsn-4, a component of SWI/SNF chromatin remodeling complexes. Loss-of-function mutations in multiple SWI/SNF components reveal that weak reduction in SWI/SNF activity causes ectopic vulval induction, while stronger reduction prevents adoption of vulval fates, a phenomenon also observed with increasing loss of LET-23 activity. High levels of LET-23 expression in P6.p are thought to locally sequester LIN-3, thereby preventing ectopic vulval induction, with slight reductions in its expression interfering with LIN-3 sequestration, but not vulval fate signaling. We find that SWI/SNF positively regulates LET-23 expression in P6.p descendants, providing an explanation for the similarities between let-23 and SWI/SNF mutant phenotypes. However, SWI/SNF regulation of LET-23 expression is cell-specific, with SWI/SNF repressing its expression in the ALA neuron. The swsn-4 gain-of-function mutation affects the PTH domain, and provides the first evidence that its auto-inhibitory function in yeast Sth1p is conserved in metazoan chromatin remodelers. Finally, our work supports broad use of SWI/SNF in regulating EGFR signaling during development, and suggests that dominant SWI/SNF mutations in certain human congenital anomaly syndromes may be gain-of-functions. PMID:27207389

  16. The SWI/SNF chromatin remodeling complex exerts both negative and positive control over LET-23/EGFR-dependent vulval induction in Caenorhabditis elegans.

    PubMed

    Flibotte, Stephane; Kim, Bo Ram; Van de Laar, Emily; Brown, Louise; Moghal, Nadeem

    2016-07-01

    Signaling by the epidermal growth factor receptor (EGFR) generates diverse developmental patterns. This requires precise control over the location and intensity of signaling. Elucidation of these regulatory mechanisms is important for understanding development and disease pathogenesis. In Caenorhabditis elegans, LIN-3/EGF induces vulval formation in the mid-body, which requires LET-23/EGFR activation only in P6.p, the vulval progenitor nearest the LIN-3 source. To identify mechanisms regulating this signaling pattern, we screened for mutations that cooperate with a let-23 gain-of-function allele to cause ectopic vulval induction. Here, we describe a dominant gain-of-function mutation in swsn-4, a component of SWI/SNF chromatin remodeling complexes. Loss-of-function mutations in multiple SWI/SNF components reveal that weak reduction in SWI/SNF activity causes ectopic vulval induction, while stronger reduction prevents adoption of vulval fates, a phenomenon also observed with increasing loss of LET-23 activity. High levels of LET-23 expression in P6.p are thought to locally sequester LIN-3, thereby preventing ectopic vulval induction, with slight reductions in its expression interfering with LIN-3 sequestration, but not vulval fate signaling. We find that SWI/SNF positively regulates LET-23 expression in P6.p descendants, providing an explanation for the similarities between let-23 and SWI/SNF mutant phenotypes. However, SWI/SNF regulation of LET-23 expression is cell-specific, with SWI/SNF repressing its expression in the ALA neuron. The swsn-4 gain-of-function mutation affects the PTH domain, and provides the first evidence that its auto-inhibitory function in yeast Sth1p is conserved in metazoan chromatin remodelers. Finally, our work supports broad use of SWI/SNF in regulating EGFR signaling during development, and suggests that dominant SWI/SNF mutations in certain human congenital anomaly syndromes may be gain-of-functions.

  17. Light induced DEP for immobilizing and orienting Escherichia coli bacteria

    NASA Astrophysics Data System (ADS)

    Miccio, Lisa; Marchesano, Valentina; Mugnano, Martina; Grilli, Simonetta; Ferraro, Pietro

    2016-01-01

    Manipulating bacteria and understanding their behavior when interacting with different substrates are of fundamental importance for patterning, detection, and any other topics related to health-care, food-enterprise, etc. Here, we adopt an innovative dielectrophoretic (DEP) approach based on electrode-free DEP for investigating smart but simple strategies for immobilization and orientation of bacteria. Escherichia coli DH5-alpha strain has been selected as subject of the study. The light induced DEP is achieved through ferroelectric iron-doped lithium niobate crystals used as substrates. Due to the photorefractive (PR) property of such material, suitable light patterns allow writing spatial-charges-distribution inside its volume and the resultant electric fields are able to immobilize E. coli on the surface. The experiments showed that, after laser irradiation, about 80% of bacteria is blocked and oriented along a particular direction on the crystals within an area of few square centimeters. The investigation presented here could open the way for detection or patterning applications based on a new driving mechanism. Future perspectives also include the possibility to actively switch by light the DEP forces, through the writing/erasing characteristic of PR fields, to dynamically control biofilm spatial structure and arrangement.

  18. A light-induced shortcut in the planktonic microbial loop.

    PubMed

    Ptacnik, Robert; Gomes, Ana; Royer, Sarah-Jeanne; Berger, Stella A; Calbet, Albert; Nejstgaard, Jens C; Gasol, Josep M; Isari, Stamatina; Moorthi, Stefanie D; Ptacnikova, Radka; Striebel, Maren; Sazhin, Andrey F; Tsagaraki, Tatiana M; Zervoudaki, Soultana; Altoja, Kristi; Dimitriou, Panagiotis D; Laas, Peeter; Gazihan, Ayse; Martínez, Rodrigo A; Schabhüttl, Stefanie; Santi, Ioulia; Sousoni, Despoina; Pitta, Paraskevi

    2016-01-01

    Mixotrophs combine photosynthesis with phagotrophy to cover their demands in energy and essential nutrients. This gives them a competitive advantage under oligotropihc conditions, where nutrients and bacteria concentrations are low. As the advantage for the mixotroph depends on light, the competition between mixo- and heterotrophic bacterivores should be regulated by light. To test this hypothesis, we incubated natural plankton from the ultra-oligotrophic Eastern Mediterranean in a set of mesocosms maintained at 4 light levels spanning a 10-fold light gradient. Picoplankton (heterotrophic bacteria (HB), pico-sized cyanobacteria, and small-sized flagellates) showed the fastest and most marked response to light, with pronounced predator-prey cycles, in the high-light treatments. Albeit cell specific activity of heterotrophic bacteria was constant across the light gradient, bacterial abundances exhibited an inverse relationship with light. This pattern was explained by light-induced top-down control of HB by bacterivorous phototrophic eukaryotes (PE), which was evidenced by a significant inverse relationship between HB net growth rate and PE abundances. Our results show that light mediates the impact of mixotrophic bacterivores. As mixo- and heterotrophs differ in the way they remineralize nutrients, these results have far-reaching implications for how nutrient cycling is affected by light. PMID:27404551

  19. A light-induced shortcut in the planktonic microbial loop

    PubMed Central

    Ptacnik, Robert; Gomes, Ana; Royer, Sarah-Jeanne; Berger, Stella A.; Calbet, Albert; Nejstgaard, Jens C.; Gasol, Josep M.; Isari, Stamatina; Moorthi, Stefanie D.; Ptacnikova, Radka; Striebel, Maren; Sazhin, Andrey F.; Tsagaraki, Tatiana M.; Zervoudaki, Soultana; Altoja, Kristi; Dimitriou, Panagiotis D.; Laas, Peeter; Gazihan, Ayse; Martínez, Rodrigo A.; Schabhüttl, Stefanie; Santi, Ioulia; Sousoni, Despoina; Pitta, Paraskevi

    2016-01-01

    Mixotrophs combine photosynthesis with phagotrophy to cover their demands in energy and essential nutrients. This gives them a competitive advantage under oligotropihc conditions, where nutrients and bacteria concentrations are low. As the advantage for the mixotroph depends on light, the competition between mixo- and heterotrophic bacterivores should be regulated by light. To test this hypothesis, we incubated natural plankton from the ultra-oligotrophic Eastern Mediterranean in a set of mesocosms maintained at 4 light levels spanning a 10-fold light gradient. Picoplankton (heterotrophic bacteria (HB), pico-sized cyanobacteria, and small-sized flagellates) showed the fastest and most marked response to light, with pronounced predator-prey cycles, in the high-light treatments. Albeit cell specific activity of heterotrophic bacteria was constant across the light gradient, bacterial abundances exhibited an inverse relationship with light. This pattern was explained by light-induced top-down control of HB by bacterivorous phototrophic eukaryotes (PE), which was evidenced by a significant inverse relationship between HB net growth rate and PE abundances. Our results show that light mediates the impact of mixotrophic bacterivores. As mixo- and heterotrophs differ in the way they remineralize nutrients, these results have far-reaching implications for how nutrient cycling is affected by light. PMID:27404551

  20. Retino-hypothalamic regulation of light-induced murine sleep

    PubMed Central

    Muindi, Fanuel; Zeitzer, Jamie M.; Heller, Horace Craig

    2014-01-01

    The temporal organization of sleep is regulated by an interaction between the circadian clock and homeostatic processes. Light indirectly modulates sleep through its ability to phase shift and entrain the circadian clock. Light can also exert a direct, circadian-independent effect on sleep. For example, acute exposure to light promotes sleep in nocturnal animals and wake in diurnal animals. The mechanisms whereby light directly influences sleep and arousal are not well understood. In this review, we discuss the direct effect of light on sleep at the level of the retina and hypothalamus in rodents. We review murine data from recent publications showing the roles of rod-, cone- and melanopsin-based photoreception on the initiation and maintenance of light-induced sleep. We also present hypotheses about hypothalamic mechanisms that have been advanced to explain the acute control of sleep by light. Specifically, we review recent studies assessing the roles of the ventrolateral preoptic area (VLPO) and the suprachiasmatic nucleus (SCN). We also discuss how light might differentially promote sleep and arousal in nocturnal and diurnal animals respectively. Lastly, we suggest new avenues for research on this topic which is still in its early stages. PMID:25140132

  1. Chromatin organization as a possible factor in the control of susceptibility to radiation-induced AML in mice

    NASA Astrophysics Data System (ADS)

    Maranon, David G.

    C57BL/6). This tissue-dependency is consistent with the concept of tissue predisposition to certain kind of cancers, in which, for instance blood cells contain specific characteristics or nuclear organization not present in fibroblasts that could lead to AML. Using AML cells from actual radiation-induced tumors, the measurements done within the intact chromosome 2 from these AML samples showed a high proportion of cells with distances between the clusters markers that were similar to the distances seen for the small domain from normal BM cells. Therefore, from our data, deletion of chromosome 2 seemed to occur mainly in a non-random fashion because the PU.1 gene was deleted from the large domain in 8 out of 10 cases in an average proportion of ˜74% of the analyzed cells considering all AML cases. To explore and test the possible effect of the genomic imprinting on the structure and organization of the chromatin in both small and large domain from mouse chromosome 2, a different mouse model was used that allowed us to differentiate the parental origin of each chromosome 2 inherited after fertilization for the hybrid offspring (F1) obtained from crosses between a C3H/HeNCrl and Tirano/EiJ mouse strain. The latter has a Robertsonian translocation that involved chromosome 2 and 8, which allows tracking of a paternal or maternal copy of chromosome 2 in the F1 mice. Although such a CBA strain was not available, the C3H mouse strain is similarly sensitive to AML induction after radiation treatment, and chromosome 2 in this mouse model is hyper-radiosensitive as well. Then, if the small or closed and large or open configuration of the chromatin that was observed in the interphase is due to the genomic imprinting, we should be able to determine its parental origin. The experimental data did not show evidence of any influence in the chromosomal domain conformation in relation to the genomic imprinting occurring in mouse chromosome 2. No difference was seen for the maternal

  2. Chromatin organization as a possible factor in the control of susceptibility to radiation-induced AML in mice

    NASA Astrophysics Data System (ADS)

    Maranon, David G.

    C57BL/6). This tissue-dependency is consistent with the concept of tissue predisposition to certain kind of cancers, in which, for instance blood cells contain specific characteristics or nuclear organization not present in fibroblasts that could lead to AML. Using AML cells from actual radiation-induced tumors, the measurements done within the intact chromosome 2 from these AML samples showed a high proportion of cells with distances between the clusters markers that were similar to the distances seen for the small domain from normal BM cells. Therefore, from our data, deletion of chromosome 2 seemed to occur mainly in a non-random fashion because the PU.1 gene was deleted from the large domain in 8 out of 10 cases in an average proportion of ˜74% of the analyzed cells considering all AML cases. To explore and test the possible effect of the genomic imprinting on the structure and organization of the chromatin in both small and large domain from mouse chromosome 2, a different mouse model was used that allowed us to differentiate the parental origin of each chromosome 2 inherited after fertilization for the hybrid offspring (F1) obtained from crosses between a C3H/HeNCrl and Tirano/EiJ mouse strain. The latter has a Robertsonian translocation that involved chromosome 2 and 8, which allows tracking of a paternal or maternal copy of chromosome 2 in the F1 mice. Although such a CBA strain was not available, the C3H mouse strain is similarly sensitive to AML induction after radiation treatment, and chromosome 2 in this mouse model is hyper-radiosensitive as well. Then, if the small or closed and large or open configuration of the chromatin that was observed in the interphase is due to the genomic imprinting, we should be able to determine its parental origin. The experimental data did not show evidence of any influence in the chromosomal domain conformation in relation to the genomic imprinting occurring in mouse chromosome 2. No difference was seen for the maternal

  3. Atomic force microscope imaging of chromatin assembled in Xenopus laevis egg extract.

    PubMed

    Fu, Hongxia; Freedman, Benjamin S; Lim, Chwee Teck; Heald, Rebecca; Yan, Jie

    2011-06-01

    Gaps persist in our understanding of chromatin lower- and higher-order structures. Xenopus egg extracts provide a way to study essential chromatin components which are difficult to manipulate in living cells, but nanoscale imaging of chromatin assembled in extracts poses a challenge. We describe a method for preparing chromatin assembled in extracts for atomic force microscopy (AFM) utilizing restriction enzyme digestion followed by transferring to a mica surface. Using this method, we find that buffer dilution of the chromatin assembly extract or incubation of chromatin in solutions of low ionic strength results in loosely compacted chromatin fibers that are prone to unraveling into naked DNA. We also describe a method for direct AFM imaging of chromatin which does not utilize restriction enzymes and reveals higher-order fibers of varying widths. Due to the capability of controlling chromatin assembly conditions, we believe these methods have broad potential for studying physiologically relevant chromatin structures. PMID:21369955

  4. Epigenomic regulation of oncogenesis by chromatin remodeling.

    PubMed

    Kumar, R; Li, D-Q; Müller, S; Knapp, S

    2016-08-25

    Disruption of the intricate gene expression program represents one of major driving factors for the development, progression and maintenance of human cancer, and is often associated with acquired therapeutic resistance. At the molecular level, cancerous phenotypes are the outcome of cellular functions of critical genes, regulatory interactions of histones and chromatin remodeling complexes in response to dynamic and persistent upstream signals. A large body of genetic and biochemical evidence suggests that the chromatin remodelers integrate the extracellular and cytoplasmic signals to control gene activity. Consequently, widespread dysregulation of chromatin remodelers and the resulting inappropriate expression of regulatory genes, together, lead to oncogenesis. We summarize the recent developments and current state of the dysregulation of the chromatin remodeling components as the driving mechanism underlying the growth and progression of human tumors. Because chromatin remodelers, modifying enzymes and protein-protein interactions participate in interpreting the epigenetic code, selective chromatin remodelers and bromodomains have emerged as new frontiers for pharmacological intervention to develop future anti-cancer strategies to be used either as single-agent or in combination therapies with chemotherapeutics or radiotherapy. PMID:26804164

  5. Chromatin signatures of cancer

    PubMed Central

    Morgan, Marc A.; Shilatifard, Ali

    2015-01-01

    Changes in the pattern of gene expression play an important role in allowing cancer cells to acquire their hallmark characteristics, while genomic instability enables cells to acquire genetic alterations that promote oncogenesis. Chromatin plays central roles in both transcriptional regulation and the maintenance of genomic stability. Studies by cancer genome consortiums have identified frequent mutations in genes encoding chromatin regulatory factors and histone proteins in human cancer, implicating them as major mediators in the pathogenesis of both hematological malignancies and solid tumors. Here, we review recent advances in our understanding of the role of chromatin in cancer, focusing on transcriptional regulatory complexes, enhancer-associated factors, histone point mutations, and alterations in heterochromatin-interacting factors. PMID:25644600

  6. Nucleoporins and chromatin metabolism.

    PubMed

    Ptak, Christopher; Wozniak, Richard W

    2016-06-01

    Mounting evidence has implicated a group of proteins termed nucleoporins, or Nups, in various processes that regulate chromatin structure and function. Nups were first recognized as building blocks for nuclear pore complexes, but several members of this group of proteins also reside in the cytoplasm and within the nucleus. Moreover, many are dynamic and move between these various locations. Both at the nuclear envelope, as part of nuclear pore complexes, and within the nucleoplasm, Nups interact with protein complexes that function in gene transcription, chromatin remodeling, DNA repair, and DNA replication. Here, we review recent studies that provide further insight into the molecular details of these interactions and their role in regulating the activity of chromatin modifying factors. PMID:27085162

  7. Selective excitation of vibrational states by shaping of light-induced potentials

    PubMed

    Sola; Chang; Santamaria; Malinovsky; Krause

    2000-11-13

    In this Letter we describe a method for population transfer using intense, ultrafast laser pulses. The selectivity is accomplished by careful shaping of light-induced potentials (LIPs). Creation and control of the LIPs is accomplished by choosing pairs of pulses with proper frequency detunings and time delays. As an example, selective population transfer is demonstrated for a three-state model of the sodium dimer.

  8. Light induced cytosolic drug delivery from liposomes with gold nanoparticles.

    PubMed

    Lajunen, Tatu; Viitala, Lauri; Kontturi, Leena-Stiina; Laaksonen, Timo; Liang, Huamin; Vuorimaa-Laukkanen, Elina; Viitala, Tapani; Le Guével, Xavier; Yliperttula, Marjo; Murtomäki, Lasse; Urtti, Arto

    2015-04-10

    Externally triggered drug release at defined targets allows site- and time-controlled drug treatment regimens. We have developed liposomal drug carriers with encapsulated gold nanoparticles for triggered drug release. Light energy is converted to heat in the gold nanoparticles and released to the lipid bilayers. Localized temperature increase renders liposomal bilayers to be leaky and triggers drug release. The aim of this study was to develop a drug releasing system capable of releasing its cargo to cell cytosol upon triggering with visible and near infrared light signals. The liposomes were formulated using either heat-sensitive or heat- and pH-sensitive lipid compositions with star or rod shaped gold nanoparticles. Encapsulated fluorescent probe, calcein, was released from the liposomes after exposure to the light. In addition, the pH-sensitive formulations showed a faster drug release in acidic conditions than in neutral conditions. The liposomes were internalized into human retinal pigment epithelial cells (ARPE-19) and human umbilical vein endothelial cells (HUVECs) and did not show any cellular toxicity. The light induced cytosolic delivery of calcein from the gold nanoparticle containing liposomes was shown, whereas no cytosolic release was seen without light induction or without gold nanoparticles in the liposomes. The light activated liposome formulations showed a controlled content release to the cellular cytosol at a specific location and time. Triggering with visual and near infrared light allows good tissue penetration and safety, and the pH-sensitive liposomes may enable selective drug release in the intracellular acidic compartments (endosomes, lysosomes). Thus, light activated liposomes with gold nanoparticles are an attractive option for time- and site-specific drug delivery into the target cells.

  9. An Efficient Light-Inducible P53 Expression System for Inhibiting Proliferation of Bladder Cancer Cell

    PubMed Central

    Lin, Fan; Dong, Liang; Wang, Weiming; Liu, Yuchen; Huang, Weiren; Cai, Zhiming

    2016-01-01

    Optogenetic gene expression systems enable spatial-temporal modulation of gene transcription and cell behavior. Although applications in biomedicine are emerging, the utility of optogenetic gene switches remains elusive in cancer research due to the relative low gene activation efficiency. Here, we present an optimized CRISPR-Cas9-based light-inducible gene expression device that controls gene transcription in a dose-dependent manner. To prove the potential utility of this device, P53 was tested as a functional target in the bladder cancer cell models. It was illustrated that the light-induced P53 inhibited proliferation of 5637 and UMUC-3 cell effectively. The “light-on” gene expression system may demonstrate a novel therapeutic strategy for bladder cancer intervention. PMID:27766041

  10. Protective effect of taurine on the light-induced disruption of isolated frog rod outer segments

    SciTech Connect

    Pasantes-Morales, H.; Ademe, R.M.; Quesada, O.

    1981-01-01

    Isolated frog rod outer segments (ROS) incubated in a Krebs-bicarbonate medium, and illuminated for 2 h, show a profound alteration in their structure. This is characterized by distention of discs, vesiculation, and a marked swelling. The light-induced ROS disruption requires the presence of bicarbonate and sodium chloride. Replacement of bicarbonate by TRIS or HEPES protects ROS structure. Also, substitution of sodium chloride by sucrose or choline chloride maintains unaltered the ROS structure. Deletion of calcium, magnesium, or phosphate does not modify the effect produced by illumination. An increased accumulation of labeled bicarbonate and tritiated water is observed in illuminated ROS, as compared with controls in the dark. The presence of taurine, GABA, or glycine, at concentrations of 5-25 mM, effectively counteracts the light-induced ROS disruption. Taurine (25 mM) reduces labeled bicarbonate and tritiated water levels to those observed in the dark incubated ROS.

  11. Analysis of Chromatin Organisation

    ERIC Educational Resources Information Center

    Szeberenyi, Jozsef

    2011-01-01

    Terms to be familiar with before you start to solve the test: chromatin, nucleases, sucrose density gradient centrifugation, melting point, gel electrophoresis, ethidium bromide, autoradiography, Southern blotting, Northern blotting, Sanger sequencing, restriction endonucleases, exonucleases, linker DNA, chloroform extraction, nucleosomes,…

  12. An Overview of Chromatin-Regulating Proteins in Cells

    PubMed Central

    Zhang, Pingyu; Torres, Keila; Liu, Xiuping; Liu, Chang-gong; Pollock, Raphael E.

    2016-01-01

    In eukaryotic cells, gene expressions on chromosome DNA are orchestrated by a dynamic chromosome structure state that is largely controlled by chromatin-regulating proteins, which regulate chromatin structures, release DNA from the nucleosome, and activate or suppress gene expression by modifying nucleosome histones or mobilizing DNA-histone structure. The two classes of chromatin- regulating proteins are 1) enzymes that modify histones through methylation, acetylation, phosphorylation, adenosine diphosphate–ribosylation, glycosylation, sumoylation, or ubiquitylation and 2) enzymes that remodel DNA-histone structure with energy from ATP hydrolysis. Chromatin-regulating proteins, which modulate DNA-histone interaction, change chromatin conformation, and increase or decrease the binding of functional DNA-regulating protein complexes, have major functions in nuclear processes, including gene transcription and DNA replication, repair, and recombination. This review provides a general overview of chromatin-regulating proteins, including their classification, molecular functions, and interactions with the nucleosome in eukaryotic cells. PMID:26796306

  13. EP300 Protects from Light-Induced Retinopathy in Zebrafish

    PubMed Central

    Kawase, Reiko; Nishimura, Yuhei; Ashikawa, Yoshifumi; Sasagawa, Shota; Murakami, Soichiro; Yuge, Mizuki; Okabe, Shiko; Kawaguchi, Koki; Yamamoto, Hiroshi; Moriyuki, Kazumi; Yamane, Shinsaku; Tsuruma, Kazuhiro; Shimazawa, Masamitsu; Hara, Hideaki; Tanaka, Toshio

    2016-01-01

    Exposure of rhodopsin to bright white light can induce photoreceptor cell damage and degeneration. However, a comprehensive understanding of the mechanisms underlying light-induced retinopathy remains elusive. In this study, we performed comparative transcriptome analysis of three rodent models of light-induced retinopathy, and we identified 37 genes that are dysregulated in all three models. Gene ontology analysis revealed that this gene set is significantly associated with a cytokine signaling axis composed of signal transducer and activator of transcription 1 and 3 (STAT1/3), interleukin 6 signal transducer (IL6ST), and oncostatin M receptor (OSMR). Furthermore, the analysis suggested that the histone acetyltransferase EP300 may be a key upstream regulator of the STAT1/3–IL6ST/OSMR axis. To examine the role of EP300 directly, we developed a larval zebrafish model of light-induced retinopathy. Using this model, we demonstrated that pharmacological inhibition of EP300 significantly increased retinal cell apoptosis, decreased photoreceptor cell outer segments, and increased proliferation of putative Müller cells upon exposure to intense light. These results suggest that EP300 may protect photoreceptor cells from light-induced damage and that activation of EP300 may be a novel therapeutic approach for the treatment of retinal degenerative diseases. PMID:27242532

  14. Chromatin assembly using Drosophila systems.

    PubMed

    Fyodorov, Dmitry V; Levenstein, Mark E

    2002-05-01

    To successfully study chromatin structure and activity in vitro, it is essential to have a chromatin assembly system that will prepare extended nucleosome arrays with highly defined protein content that resemble bulk chromatin isolated from living cell nuclei in terms of periodicity and nucleosome positioning. The Drosophila ATP-dependent chromatin assembly system described in this unit meets these requirements. The end product of the reaction described here has highly periodic extended arrays with physiologic spacing and positioning of the nucleosomes.

  15. Activin/Nodal signaling and NANOG orchestrate human embryonic stem cell fate decisions by controlling the H3K4me3 chromatin mark

    PubMed Central

    Bertero, Alessandro; Madrigal, Pedro; Galli, Antonella; Hubner, Nina C.; Moreno, Inmaculada; Burks, Deborah; Brown, Stephanie; Pedersen, Roger A.; Gaffney, Daniel; Mendjan, Sasha; Pauklin, Siim

    2015-01-01

    Stem cells can self-renew and differentiate into multiple cell types. These characteristics are maintained by the combination of specific signaling pathways and transcription factors that cooperate to establish a unique epigenetic state. Despite the broad interest of these mechanisms, the precise molecular controls by which extracellular signals organize epigenetic marks to confer multipotency remain to be uncovered. Here, we use human embryonic stem cells (hESCs) to show that the Activin–SMAD2/3 signaling pathway cooperates with the core pluripotency factor NANOG to recruit the DPY30-COMPASS histone modifiers onto key developmental genes. Functional studies demonstrate the importance of these interactions for correct histone 3 Lys4 trimethylation and also self-renewal and differentiation. Finally, genetic studies in mice show that Dpy30 is also necessary to maintain pluripotency in the pregastrulation embryo, thereby confirming the existence of similar regulations in vivo during early embryonic development. Our results reveal the mechanisms by which extracellular factors coordinate chromatin status and cell fate decisions in hESCs. PMID:25805847

  16. The Breakdown of Stored Triacylglycerols Is Required during Light-Induced Stomatal Opening.

    PubMed

    McLachlan, Deirdre H; Lan, Jue; Geilfus, Christoph-Martin; Dodd, Antony N; Larson, Tony; Baker, Alison; Hõrak, Hanna; Kollist, Hannes; He, Zhesi; Graham, Ian; Mickelbart, Michael V; Hetherington, Alistair M

    2016-03-01

    Stomata regulate the uptake of CO2 and the loss of water vapor [1] and contribute to the control of water-use efficiency [2] in plants. Although the guard-cell-signaling pathway coupling blue light perception to ion channel activity is relatively well understood [3], we know less about the sources of ATP required to drive K(+) uptake [3-6]. Here, we show that triacylglycerols (TAGs), present in Arabidopsis guard cells as lipid droplets (LDs), are involved in light-induced stomatal opening. Illumination induces reductions in LD abundance, and this involves the PHOT1 and PHOT2 blue light receptors [3]. Light also induces decreases in specific TAG molecular species. We hypothesized that TAG-derived fatty acids are metabolized by peroxisomal β-oxidation to produce ATP required for stomatal opening. In silico analysis revealed that guard cells express all the genes required for β-oxidation, and we showed that light-induced stomatal opening is delayed in three TAG catabolism mutants (sdp1, pxa1, and cgi-58) and in stomata treated with a TAG breakdown inhibitor. We reasoned that, if ATP supply was delaying light-induced stomatal opening, then the activity of the plasma membrane H(+)-ATPase should be reduced at this time. Monitoring changes in apoplastic pH in the mutants showed that this was the case. Together, our results reveal a new role for TAGs in vegetative tissue and show that PHOT1 and PHOT2 are involved in reductions in LD abundance. Reductions in LD abundance in guard cells of the lycophyte Selaginella suggest that TAG breakdown may represent an evolutionarily conserved mechanism in light-induced stomatal opening. PMID:26898465

  17. Chromatin States Accurately Classify Cell Differentiation Stages

    PubMed Central

    Larson, Jessica L.; Yuan, Guo-Cheng

    2012-01-01

    Gene expression is controlled by the concerted interactions between transcription factors and chromatin regulators. While recent studies have identified global chromatin state changes across cell-types, it remains unclear to what extent these changes are co-regulated during cell-differentiation. Here we present a comprehensive computational analysis by assembling a large dataset containing genome-wide occupancy information of 5 histone modifications in 27 human cell lines (including 24 normal and 3 cancer cell lines) obtained from the public domain, followed by independent analysis at three different representations. We classified the differentiation stage of a cell-type based on its genome-wide pattern of chromatin states, and found that our method was able to identify normal cell lines with nearly 100% accuracy. We then applied our model to classify the cancer cell lines and found that each can be unequivocally classified as differentiated cells. The differences can be in part explained by the differential activities of three regulatory modules associated with embryonic stem cells. We also found that the “hotspot” genes, whose chromatin states change dynamically in accordance to the differentiation stage, are not randomly distributed across the genome but tend to be embedded in multi-gene chromatin domains, and that specialized gene clusters tend to be embedded in stably occupied domains. PMID:22363642

  18. The Chromatin Protein DUET/MMD1 Controls Expression of the Meiotic Gene TDM1 during Male Meiosis in Arabidopsis.

    PubMed

    Andreuzza, Sébastien; Nishal, Bindu; Singh, Aparna; Siddiqi, Imran

    2015-09-01

    Meiosis produces haploid cells essential for sexual reproduction. In yeast, entry into meiosis activates transcription factors which trigger a transcriptional cascade that results in sequential co-expression of early, middle and late meiotic genes. However, these factors are not conserved, and the factors and regulatory mechanisms that ensure proper meiotic gene expression in multicellular eukaryotes are poorly understood. Here, we report that DUET/MMD1, a PHD finger protein essential for Arabidopsis male meiosis, functions as a transcriptional regulator in plant meiosis. We find that DUET-PHD binds H3K4me2 in vitro, and show that this interaction is critical for function during meiosis. We also show that DUET is required for proper microtubule organization during meiosis II, independently of its function in meiosis I. Remarkably, DUET protein shows stage-specific expression, confined to diplotene. We identify two genes TDM1 and JAS with critical functions in cell cycle transitions and spindle organization in male meiosis, as DUET targets, with TDM1 being a direct target. Thus, DUET is required to regulate microtubule organization and cell cycle transitions during male meiosis, and functions as a direct transcription activator of the meiotic gene TDM1. Expression profiling showed reduced expression of a subset comprising about 12% of a known set of meiosis preferred genes in the duet mutant. Our results reveal the action of DUET as a transcriptional regulator during male meiosis in plants, and suggest that transcription of meiotic genes is under stagewise control in plants as in yeast.

  19. Functions of the Proteasome on Chromatin

    PubMed Central

    McCann, Tyler S.; Tansey, William P.

    2014-01-01

    The proteasome is a large self-compartmentalized protease complex that recognizes, unfolds, and destroys ubiquitylated substrates. Proteasome activities are required for a host of cellular functions, and it has become clear in recent years that one set of critical actions of the proteasome occur on chromatin. In this review, we discuss some of the ways in which proteasomes directly regulate the structure and function of chromatin and chromatin regulatory proteins, and how this influences gene transcription. We discuss lingering controversies in the field, the relative importance of proteolytic versus non-proteolytic proteasome activities in this process, and highlight areas that require further investigation. Our intention is to show that proteasomes are involved in major steps controlling the expression of the genetic information, that proteasomes use both proteolytic mechanisms and ATP-dependent protein remodeling to accomplish this task, and that much is yet to be learned about the full spectrum of ways that proteasomes influence the genome. PMID:25422899

  20. Chromatin and alternative splicing.

    PubMed

    Alló, M; Schor, I E; Muñoz, M J; de la Mata, M; Agirre, E; Valcárcel, J; Eyras, E; Kornblihtt, A R

    2010-01-01

    Alternative splicing affects more than 90% of human genes. Coupling between transcription and splicing has become crucial in the complex network underlying alternative splicing regulation. Because chromatin is the real template for nuclear transcription, changes in its structure, but also in the "reading" and "writing" of the histone code, could modulate splicing choices. Here, we discuss the evidence supporting these ideas, from the first proposal of chromatin affecting alternative splicing, performed 20 years ago, to the latest findings including genome-wide evidence that nucleosomes are preferentially positioned in exons. We focus on two recent reports from our laboratories that add new evidence to this field. The first report shows that a physiological stimulus such as neuron depolarization promotes intragenic histone acetylation (H3K9ac) and chromatin relaxation, causing the skipping of exon 18 of the neural cell adhesion molecule gene. In the second report, we show how specific histone modifications can be created at targeted gene regions as a way to affect alternative splicing: Using small interfering RNAs (siRNAs), we increased the levels of H3K9me2 and H3K27me3 in the proximity of alternative exon 33 of the human fibronectin gene, favoring its inclusion into mature messenger RNA (mRNA) through a mechanism that recalls RNA-mediated transcriptional gene silencing.

  1. The Chromatin Protein DUET/MMD1 Controls Expression of the Meiotic Gene TDM1 during Male Meiosis in Arabidopsis

    PubMed Central

    Andreuzza, Sébastien; Nishal, Bindu; Singh, Aparna; Siddiqi, Imran

    2015-01-01

    Meiosis produces haploid cells essential for sexual reproduction. In yeast, entry into meiosis activates transcription factors which trigger a transcriptional cascade that results in sequential co-expression of early, middle and late meiotic genes. However, these factors are not conserved, and the factors and regulatory mechanisms that ensure proper meiotic gene expression in multicellular eukaryotes are poorly understood. Here, we report that DUET/MMD1, a PHD finger protein essential for Arabidopsis male meiosis, functions as a transcriptional regulator in plant meiosis. We find that DUET-PHD binds H3K4me2 in vitro, and show that this interaction is critical for function during meiosis. We also show that DUET is required for proper microtubule organization during meiosis II, independently of its function in meiosis I. Remarkably, DUET protein shows stage-specific expression, confined to diplotene. We identify two genes TDM1 and JAS with critical functions in cell cycle transitions and spindle organization in male meiosis, as DUET targets, with TDM1 being a direct target. Thus, DUET is required to regulate microtubule organization and cell cycle transitions during male meiosis, and functions as a direct transcription activator of the meiotic gene TDM1. Expression profiling showed reduced expression of a subset comprising about 12% of a known set of meiosis preferred genes in the duet mutant. Our results reveal the action of DUET as a transcriptional regulator during male meiosis in plants, and suggest that transcription of meiotic genes is under stagewise control in plants as in yeast. PMID:26348709

  2. Chemical physics: Quantum control of light-induced reactions

    NASA Astrophysics Data System (ADS)

    Chandler, David W.

    2016-07-01

    An investigation of how ultracold molecules are broken apart by light reveals surprising, previously unobserved quantum effects. The work opens up avenues of research in quantum optics. See Letter p.122

  3. Electro-optic phase modulation in light induced self-written waveguides propagated in a 5CB doped photopolymer.

    PubMed

    Jemal, Abdelmonem; Ben Belgacem, Mohamed; Kamoun, Saber; Gargouri, Mohamed; Honorat Dorkenoo, Kokou D; Barsella, Alberto; Mager, Loïc

    2013-01-28

    We present the inscription of a Light Induced Self-Written (LISW) waveguide in a 4-cyano-4'-pentylbipheny (5CB) doped photopolymer. The dynamic reorientation of the 5CB molecules in the material under applied electric field leads to birefringence in LISW waveguide and thus allows the control of the phase of the guided mode. PMID:23389136

  4. Nanoparticle-Mediated, Light-Induced Phase Separations.

    PubMed

    Neumann, Oara; Neumann, Albert D; Silva, Edgar; Ayala-Orozco, Ciceron; Tian, Shu; Nordlander, Peter; Halas, Naomi J

    2015-12-01

    Nanoparticles that both absorb and scatter light, when dispersed in a liquid, absorb optical energy and heat a reduced fluid volume due to the combination of multiple scattering and optical absorption. This can induce a localized liquid-vapor phase change within the reduced volume without the requirement of heating the entire fluid. For binary liquid mixtures, this process results in vaporization of the more volatile component of the mixture. When subsequently condensed, these two steps of vaporization and condensation constitute a distillation process mediated by nanoparticles and driven by optical illumination. Because it does not require the heating of a large volume of fluid, this process requires substantially less energy than traditional distillation using thermal sources. We investigated nanoparticle-mediated, light-induced distillation of ethanol-H2O and 1-propanol-H2O mixtures, using Au-SiO2 nanoshells as the absorber-scatterer nanoparticle and nanoparticle-resonant laser irradiation to drive the process. For ethanol-H2O mixtures, the mole fraction of ethanol obtained in the light-induced process is substantially higher than that obtained by conventional thermal distillation, essentially removing the ethanol-H2O azeotrope that limits conventional distillation. In contrast, for 1-propanol-H2O mixtures the distillate properties resulting from light-induced distillation were very similar to those obtained by thermal distillation. In the 1-propanol-H2O system, a nanoparticle-mediated, light-induced liquid-liquid phase separation was also observed. PMID:26535465

  5. Optics of metal nanoparticle aggregates with light induced motion.

    PubMed

    Drachev, Vladimir P; Perminov, Sergey V; Rautian, Sergey G

    2007-07-01

    Light-induced forces between metal nanoparticles change the geometry of the aggregates and affect their optical properties. Light absorption, scattering and scattering of a probe beam are numerically studied with Newton's equations and the coupled dipole equations for penta-particle aggregates. The relative changes in optical responses are large compared with the linear, low-intensity limit and relatively fast with nanosecond characteristic times. Time and intensity dependencies are shown to be sensitive to the initial potential of the aggregation forces.

  6. Influenza Virus and Chromatin: Role of the CHD1 Chromatin Remodeler in the Virus Life Cycle

    PubMed Central

    Marcos-Villar, Laura; Pazo, Alejandra

    2016-01-01

    ABSTRACT Influenza A virus requires ongoing cellular transcription to carry out the cap-snatching process. Chromatin remodelers modify chromatin structure to produce an active or inactive conformation, which enables or prevents the recruitment of transcriptional complexes to specific genes; viral transcription thus depends on chromatin dynamics. Influenza virus polymerase associates with chromatin components of the infected cell, such as RNA polymerase II (RNAP II) or the CHD6 chromatin remodeler. Here we show that another CHD family member, CHD1 protein, also interacts with the influenza virus polymerase complex. CHD1 recognizes the H3K4me3 (histone 3 with a trimethyl group in lysine 4) histone modification, a hallmark of active chromatin. Downregulation of CHD1 causes a reduction in viral polymerase activity, viral RNA transcription, and the production of infectious particles. Despite the dependence of influenza virus on cellular transcription, RNAP II is degraded when viral transcription is complete, and recombinant viruses unable to degrade RNAP II show decreased pathogenicity in the murine model. We describe the CHD1–RNAP II association, as well as the parallel degradation of both proteins during infection with viruses showing full or reduced induction of degradation. The H3K4me3 histone mark also decreased during influenza virus infection, whereas a histone mark of inactive chromatin, H3K27me3, remained unchanged. Our results indicate that CHD1 is a positive regulator of influenza virus multiplication and suggest a role for chromatin remodeling in the control of the influenza virus life cycle. IMPORTANCE Although influenza virus is not integrated into the genome of the infected cell, it needs continuous cellular transcription to synthesize viral mRNA. This mechanism implies functional association with host genome expression and thus depends on chromatin dynamics. Influenza virus polymerase associates with transcription-related factors, such as RNA

  7. Chromatin modifications associated with diabetes.

    PubMed

    Keating, Samuel T; El-Osta, Assam

    2012-08-01

    Accelerated rates of vascular complications are associated with diabetes mellitus. Environmental factors including hyperglycaemia contribute to the progression of diabetic complications. Epidemiological and experimental animal studies identified poor glycaemic control as a major contributor to the development of complications. These studies suggest that early exposure to hyperglycaemia can instigate the development of complications that present later in the progression of the disease, despite improved glycaemic control. Recent experiments reveal a striking commonality associated with gene-activating hyperglycaemic events and chromatin modification. The best characterised to date are associated with the chemical changes of amino-terminal tails of histone H3. Enzymes that write specified histone tail modifications are not well understood in models of hyperglycaemia and metabolic memory as well as human diabetes. The best-characterised enzyme is the lysine specific Set7 methyltransferase. The contribution of Set7 to the aetiology of diabetic complications may extend to other transcriptional events through methylation of non-histone substrates. PMID:22639343

  8. Correlating in Vitro and in Vivo Activities of Light-Inducible Dimers: A Cellular Optogenetics Guide.

    PubMed

    Hallett, Ryan A; Zimmerman, Seth P; Yumerefendi, Hayretin; Bear, James E; Kuhlman, Brian

    2016-01-15

    Light-inducible dimers are powerful tools for cellular optogenetics, as they can be used to control the localization and activity of proteins with high spatial and temporal resolution. Despite the generality of the approach, application of light-inducible dimers is not always straightforward, as it is frequently necessary to test alternative dimer systems and fusion strategies before the desired biological activity is achieved. This process is further hindered by an incomplete understanding of the biophysical/biochemical mechanisms by which available dimers behave and how this correlates to in vivo function. To better inform the engineering process, we examined the biophysical and biochemical properties of three blue-light-inducible dimer variants (cryptochrome2 (CRY2)/CIB1, iLID/SspB, and LOVpep/ePDZb) and correlated these characteristics to in vivo colocalization and functional assays. We find that the switches vary dramatically in their dark and lit state binding affinities and that these affinities correlate with activity changes in a variety of in vivo assays, including transcription control, intracellular localization studies, and control of GTPase signaling. Additionally, for CRY2, we observe that light-induced changes in homo-oligomerization can have significant effects on activity that are sensitive to alternative fusion strategies. PMID:26474029

  9. Correlating in Vitro and in Vivo Activities of Light-Inducible Dimers: A Cellular Optogenetics Guide.

    PubMed

    Hallett, Ryan A; Zimmerman, Seth P; Yumerefendi, Hayretin; Bear, James E; Kuhlman, Brian

    2016-01-15

    Light-inducible dimers are powerful tools for cellular optogenetics, as they can be used to control the localization and activity of proteins with high spatial and temporal resolution. Despite the generality of the approach, application of light-inducible dimers is not always straightforward, as it is frequently necessary to test alternative dimer systems and fusion strategies before the desired biological activity is achieved. This process is further hindered by an incomplete understanding of the biophysical/biochemical mechanisms by which available dimers behave and how this correlates to in vivo function. To better inform the engineering process, we examined the biophysical and biochemical properties of three blue-light-inducible dimer variants (cryptochrome2 (CRY2)/CIB1, iLID/SspB, and LOVpep/ePDZb) and correlated these characteristics to in vivo colocalization and functional assays. We find that the switches vary dramatically in their dark and lit state binding affinities and that these affinities correlate with activity changes in a variety of in vivo assays, including transcription control, intracellular localization studies, and control of GTPase signaling. Additionally, for CRY2, we observe that light-induced changes in homo-oligomerization can have significant effects on activity that are sensitive to alternative fusion strategies.

  10. Cas9 Functionally Opens Chromatin.

    PubMed

    Barkal, Amira A; Srinivasan, Sharanya; Hashimoto, Tatsunori; Gifford, David K; Sherwood, Richard I

    2016-01-01

    Using a nuclease-dead Cas9 mutant, we show that Cas9 reproducibly induces chromatin accessibility at previously inaccessible genomic loci. Cas9 chromatin opening is sufficient to enable adjacent binding and transcriptional activation by the settler transcription factor retinoic acid receptor at previously unbound motifs. Thus, we demonstrate a new use for Cas9 in increasing surrounding chromatin accessibility to alter local transcription factor binding. PMID:27031353

  11. A synthetic erectile optogenetic stimulator enabling blue-light-inducible penile erection.

    PubMed

    Kim, Taeuk; Folcher, Marc; Doaud-El Baba, Marie; Fussenegger, Martin

    2015-05-11

    Precise spatiotemporal control of physiological processes by optogenetic devices inspired by synthetic biology may provide novel treatment opportunities for gene- and cell-based therapies. An erectile optogenetic stimulator (EROS), a synthetic designer guanylate cyclase producing a blue-light-inducible surge of the second messenger cyclic guanosine monophosphate (cGMP) in mammalian cells, enabled blue-light-dependent penile erection associated with occasional ejaculation after illumination of EROS-transfected corpus cavernosum in male rats. Photostimulated short-circuiting of complex psychological, neural, vascular, and endocrine factors to stimulate penile erection in the absence of sexual arousal may foster novel advances in the treatment of erectile dysfunction. PMID:25788334

  12. Heterogeneous nucleation and growth dynamics in the light-induced phase transition in vanadium dioxide

    DOE PAGESBeta

    Brady, Nathaniel F.; Appavoo, Kannatassen; Seo, Minah; Nag, Joyeeta; Prasankumar, Rohit P.; Haglund, Richard F.; Hilton, David J.

    2016-03-02

    Here we report on ultrafast optical investigations of the light-induced insulator-to-metal phase transition in vanadium dioxide with controlled disorder generated by substrate mismatch. These results reveal common dynamics of this optically-induced phase transition that are independent of this disorder. Lastly, above the fluence threshold for completing the transition to the rutile crystalline phase, we find a common time scale, independent of sample morphology, of 40.5 ± 2 ps that is consistent with nucleation and growth dynamics of the R phase from the parent M1 ground state.

  13. Heterogeneous nucleation and growth dynamics in the light-induced phase transition in vanadium dioxide

    NASA Astrophysics Data System (ADS)

    Brady, Nathaniel F.; Appavoo, Kannatassen; Seo, Minah; Nag, Joyeeta; Prasankumar, Rohit P.; Haglund, Richard F., Jr.; Hilton, David J.

    2016-03-01

    We report on ultrafast optical investigations of the light-induced insulator-to-metal phase transition in vanadium dioxide with controlled disorder generated by substrate mismatch. These results reveal common dynamics of this optically-induced phase transition that are independent of this disorder. Above the fluence threshold for completing the transition to the rutile crystalline phase, we find a common time scale, independent of sample morphology, of 40.5+/- 2 ps that is consistent with nucleation and growth dynamics of the R phase from the parent M1 ground state.

  14. A synthetic erectile optogenetic stimulator enabling blue-light-inducible penile erection.

    PubMed

    Kim, Taeuk; Folcher, Marc; Doaud-El Baba, Marie; Fussenegger, Martin

    2015-05-11

    Precise spatiotemporal control of physiological processes by optogenetic devices inspired by synthetic biology may provide novel treatment opportunities for gene- and cell-based therapies. An erectile optogenetic stimulator (EROS), a synthetic designer guanylate cyclase producing a blue-light-inducible surge of the second messenger cyclic guanosine monophosphate (cGMP) in mammalian cells, enabled blue-light-dependent penile erection associated with occasional ejaculation after illumination of EROS-transfected corpus cavernosum in male rats. Photostimulated short-circuiting of complex psychological, neural, vascular, and endocrine factors to stimulate penile erection in the absence of sexual arousal may foster novel advances in the treatment of erectile dysfunction.

  15. Light-induced metastable structural changes in hydrogenated amorphous silicon

    SciTech Connect

    Fritzsche, H.

    1996-09-01

    Light-induced defects (LID) in hydrogenated amorphous silicon (a-Si:H) and its alloys limit the ultimate efficiency of solar panels made with these materials. This paper reviews a variety of attempts to find the origin of and to eliminate the processes that give rise to LIDs. These attempts include novel deposition processes and the reduction of impurities. Material improvements achieved over the past decade are associated more with the material`s microstructure than with eliminating LIDs. We conclude that metastable LIDs are a natural by-product of structural changes which are generally associated with non-radiative electron-hole recombination in amorphous semiconductors.

  16. Preventing light-induced degradation in multicrystalline silicon

    SciTech Connect

    Lindroos, J. Boulfrad, Y.; Yli-Koski, M.; Savin, H.

    2014-04-21

    Multicrystalline silicon (mc-Si) is currently dominating the silicon solar cell market due to low ingot costs, but its efficiency is limited by transition metals, extended defects, and light-induced degradation (LID). LID is traditionally associated with a boron-oxygen complex, but the origin of the degradation in the top of the commercial mc-Si brick is revealed to be interstitial copper. We demonstrate that both a large negative corona charge and an aluminum oxide thin film with a built-in negative charge decrease the interstitial copper concentration in the bulk, preventing LID in mc-Si.

  17. FANCD2-controlled chromatin access of the Fanconi-associated nuclease FAN1 is crucial for the recovery of stalled replication forks.

    PubMed

    Chaudhury, Indrajit; Stroik, Daniel R; Sobeck, Alexandra

    2014-11-01

    Fanconi anemia (FA) is a cancer predisposition syndrome characterized by cellular hypersensitivity to DNA interstrand cross-links (ICLs). Within the FA pathway, an upstream core complex monoubiquitinates and recruits the FANCD2 protein to ICLs on chromatin. Ensuing DNA repair involves the Fanconi-associated nuclease 1 (FAN1), which interacts selectively with monoubiquitinated FANCD2 (FANCD2(Ub)) at ICLs. Importantly, FANCD2 has additional independent functions: it binds chromatin and coordinates the restart of aphidicolin (APH)-stalled replication forks in concert with the BLM helicase, while protecting forks from nucleolytic degradation by MRE11. We identified FAN1 as a new crucial replication fork recovery factor. FAN1 joins the BLM-FANCD2 complex following APH-mediated fork stalling in a manner dependent on MRE11 and FANCD2, followed by FAN1 nuclease-mediated fork restart. Surprisingly, APH-induced activation and chromatin recruitment of FAN1 occur independently of the FA core complex or the FAN1 UBZ domain, indicating that the FANCD2(Ub) isoform is dispensable for functional FANCD2-FAN1 cross talk during stalled fork recovery. In the absence of FANCD2, MRE11 exonuclease-promoted access of FAN1 to stalled forks results in severe FAN1-mediated nucleolytic degradation of nascent DNA strands. Thus, FAN1 nuclease activity at stalled replication forks requires tight regulation: too little inhibits fork restart, whereas too much causes fork degradation.

  18. FANCD2-Controlled Chromatin Access of the Fanconi-Associated Nuclease FAN1 Is Crucial for the Recovery of Stalled Replication Forks

    PubMed Central

    Chaudhury, Indrajit; Stroik, Daniel R.

    2014-01-01

    Fanconi anemia (FA) is a cancer predisposition syndrome characterized by cellular hypersensitivity to DNA interstrand cross-links (ICLs). Within the FA pathway, an upstream core complex monoubiquitinates and recruits the FANCD2 protein to ICLs on chromatin. Ensuing DNA repair involves the Fanconi-associated nuclease 1 (FAN1), which interacts selectively with monoubiquitinated FANCD2 (FANCD2Ub) at ICLs. Importantly, FANCD2 has additional independent functions: it binds chromatin and coordinates the restart of aphidicolin (APH)-stalled replication forks in concert with the BLM helicase, while protecting forks from nucleolytic degradation by MRE11. We identified FAN1 as a new crucial replication fork recovery factor. FAN1 joins the BLM-FANCD2 complex following APH-mediated fork stalling in a manner dependent on MRE11 and FANCD2, followed by FAN1 nuclease-mediated fork restart. Surprisingly, APH-induced activation and chromatin recruitment of FAN1 occur independently of the FA core complex or the FAN1 UBZ domain, indicating that the FANCD2Ub isoform is dispensable for functional FANCD2-FAN1 cross talk during stalled fork recovery. In the absence of FANCD2, MRE11 exonuclease-promoted access of FAN1 to stalled forks results in severe FAN1-mediated nucleolytic degradation of nascent DNA strands. Thus, FAN1 nuclease activity at stalled replication forks requires tight regulation: too little inhibits fork restart, whereas too much causes fork degradation. PMID:25135477

  19. Interplay between mismatch repair and chromatin assembly

    PubMed Central

    Schöpf, Barbara; Bregenhorn, Stephanie; Quivy, Jean-Pierre; Kadyrov, Farid A.; Almouzni, Genevieve; Jiricny, Josef

    2012-01-01

    Single strand nicks and gaps in DNA have been reported to increase the efficiency of nucleosome loading mediated by chromatin assembly factor 1 (CAF-1). However, on mismatch-containing substrates, these strand discontinuities are utilized by the mismatch repair (MMR) system as loading sites for exonuclease 1, at which degradation of the error-containing strand commences. Because packaging of DNA into chromatin might inhibit MMR, we were interested to learn whether chromatin assembly is differentially regulated on heteroduplex and homoduplex substrates. We now show that the presence of a mismatch in a nicked plasmid substrate delays nucleosome loading in human cell extracts. Our data also suggest that, once the mismatch is removed, repair of the single-stranded gap is accompanied by efficient nucleosome loading. We postulated that the balance between MMR and chromatin assembly might be governed by proliferating cell nuclear antigen (PCNA), the processivity factor of replicative DNA polymerases, which is loaded at DNA termini and which interacts with the MSH6 subunit of the mismatch recognition factor MutSα, as well as with CAF-1. We now show that this regulation might be more complex; MutSα and CAF-1 interact not only with PCNA, but also with each other. In vivo this interaction increases during S-phase and may be controlled by the phosphorylation status of the p150 subunit of CAF-1. PMID:22232658

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

    PubMed

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

    2016-06-01

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

  1. Transient light-induced intracellular oxidation revealed by redox biosensor

    SciTech Connect

    Kolossov, Vladimir L.; Beaudoin, Jessica N.; Hanafin, William P.; DiLiberto, Stephen J.; Kenis, Paul J.A.; Rex Gaskins, H.

    2013-10-04

    Highlights: •Time-resolved live cell imaging revealed light-induced oxidation. •Only the roGFP probe fused with glutaredoxin reveals photooxidation. •The transient oxidation is rapidly reduced by the cytosolic antioxidant system. •Intracellular photooxidation is media-dependent. •Oxidation is triggered exclusively by exposure to short wavelength excitation. -- Abstract: We have implemented a ratiometric, genetically encoded redox-sensitive green fluorescent protein fused to human glutaredoxin (Grx1-roGFP2) to monitor real time intracellular glutathione redox potentials of mammalian cells. This probe enabled detection of media-dependent oxidation of the cytosol triggered by short wavelength excitation. The transient nature of light-induced oxidation was revealed by time-lapse live cell imaging when time intervals of less than 30 s were implemented. In contrast, transient ROS generation was not observed with the parental roGFP2 probe without Grx1, which exhibits slower thiol-disulfide exchange. These data demonstrate that the enhanced sensitivity of the Grx1-roGFP2 fusion protein enables the detection of short-lived ROS in living cells. The superior sensitivity of Grx1-roGFP2, however, also enhances responsiveness to environmental cues introducing a greater likelihood of false positive results during image acquisition.

  2. Light-induced defects in hybrid lead halide perovskite

    NASA Astrophysics Data System (ADS)

    Sharia, Onise; Schneider, William

    One of the main challenges facing organohalide perovskites for solar application is stability. Solar cells must last decades to be economically viable alternatives to traditional energy sources. While some causes of instability can be avoided through engineering, light-induced defects can be fundamentally limiting factor for practical application of the material. Light creates large numbers of electron and hole pairs that can contribute to degradation processes. Using ab initio theoretical methods, we systematically explore first steps of light induced defect formation in methyl ammonium lead iodide, MAPbI3. In particular, we study charged and neutral Frenkel pair formation involving Pb and I atoms. We find that most of the defects, except negatively charged Pb Frenkel pairs, are reversible, and thus most do not lead to degradation. Negative Pb defects create a mid-gap state and localize the conduction band electron. A minimum energy path study shows that, once the first defect is created, Pb atoms migrate relatively fast. The defects have two detrimental effects on the material. First, they create charge traps below the conduction band. Second, they can lead to degradation of the material by forming Pb clusters.

  3. 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.

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

    PubMed

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

    2003-03-01

    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. CCSI: a database providing chromatin-chromatin spatial interaction information.

    PubMed

    Xie, Xiaowei; Ma, Wenbin; Songyang, Zhou; Luo, Zhenhua; Huang, Junfeng; Dai, Zhiming; Xiong, Yuanyan

    2016-01-01

    Distal regulatory elements have been shown to regulate gene transcription through spatial interactions, and single nucleotide polymorphisms (SNPs) are linked with distal gene expression by spatial proximity, which helps to explain the causal role of disease-associated SNPs in non-coding region. Therefore, studies on spatial interactions between chromatin have created a new avenue for elucidating the mechanism of transcriptional regulation in disease pathogenesis. Recently, a growing number of chromatin interactions have been revealed by means of 3C, 4C, 5C, ChIA-PET and Hi-C technologies. To interpret and utilize these interactions, we constructed chromatin-chromatin spatial interaction (CCSI) database by integrating and annotating 91 sets of chromatin interaction data derived from published literature, UCSC database and NCBI GEO database, resulting in a total of 3,017,962 pairwise interactions (false discovery rate < 0.05), covering human, mouse and yeast. A web interface has been designed to provide access to the chromatin interactions. The main features of CCSI are (i) showing chromatin interactions and corresponding genes, enhancers and SNPs within the regions in the search page; (ii) offering complete interaction datasets, enhancer and SNP information in the download page; and (iii) providing analysis pipeline for the annotation of interaction data. In conclusion, CCSI will facilitate exploring transcriptional regulatory mechanism in disease pathogenesis associated with spatial interactions among genes, regulatory regions and SNPs. Database URL: http://songyanglab.sysu.edu.cn/ccsi. PMID:26868054

  6. The Emerging Roles of ATP-Dependent Chromatin Remodeling Enzymes in Nucleotide Excision Repair

    PubMed Central

    Czaja, Wioletta; Mao, Peng; Smerdon, Michael J.

    2012-01-01

    DNA repair in eukaryotic cells takes place in the context of chromatin, where DNA, including damaged DNA, is tightly packed into nucleosomes and higher order chromatin structures. Chromatin intrinsically restricts accessibility of DNA repair proteins to the damaged DNA and impacts upon the overall rate of DNA repair. Chromatin is highly responsive to DNA damage and undergoes specific remodeling to facilitate DNA repair. How damaged DNA is accessed, repaired and restored to the original chromatin state, and how chromatin remodeling coordinates these processes in vivo, remains largely unknown. ATP-dependent chromatin remodelers (ACRs) are the master regulators of chromatin structure and dynamics. Conserved from yeast to humans, ACRs utilize the energy of ATP to reorganize packing of chromatin and control DNA accessibility by sliding, ejecting or restructuring nucleosomes. Several studies have demonstrated that ATP-dependent remodeling activity of ACRs plays important roles in coordination of spatio-temporal steps of different DNA repair pathways in chromatin. This review focuses on the role of ACRs in regulation of various aspects of nucleotide excision repair (NER) in the context of chromatin. We discuss current understanding of ATP-dependent chromatin remodeling by various subfamilies of remodelers and regulation of the NER pathway in vivo. PMID:23109894

  7. Ultrastructure of bovine sperm chromatin.

    PubMed

    Filho, Romualdo Morandi; Beletti, Marcelo Emilio; de Oliveira, Fabio

    2015-12-01

    Mammalian semen chromatin comprises DNA, protamine, and, at lower levels, other proteins. This constitution confers intense compaction to the chromatin, helping to protect the DNA and causing the head of the sperm to be very small, facilitating the safe transport of its genetic contents. It is known that changes in the sperm chromatin compaction lead to fertility problems in bulls, justifying studies of this structure. Although there are theoretical models of sperm chromatin because of its high compaction, there is no morphological evidence of such models. The aim of this study was to demonstrate the ultrastructure of bovine sperm chromatin in an attempt to corroborate the theoretical chromatin models existing today. The isolated bull sperm heads had their chromatin partially unpacked by chemical treatment using sodium dodecyl sulfate (SDS) and dithiothreitol (DTT) and were then embedded in Epon resin. Using an ultramicrotome, ultrathin sections were obtained, which were contrasted with uranyl acetate and lead citrate, and then viewed under transmission electron microscopy. The methodology used allowed the visualization of toroidal structures interconnected by a filamentous nuclear matrix, which is entirely consistent with the most current theoretical models. PMID:26515508

  8. Single Molecule Studies of Chromatin

    SciTech Connect

    Jeans, C; Colvin, M E; Thelen, M P; Noy, A

    2004-01-06

    The DNA in eukaryotic cells is tightly packaged as chromatin through interactions with histone proteins to form nucleosomes. These nucleosomes are themselves packed together through interactions with linker histone and non-histone proteins. In order for processes such as DNA replication, DNA repair, and transcription to occur, the chromatin fiber must be remodeled such that the necessary enzymes can access the DNA. The structure of the chromatin fiber beyond the level of the single nucleosome and the structural changes which accompany the remodeling process are poorly understood. We are studying the structures and forces behind the remodeling process through the use of atomic force microscopy (AFM). This allows both high-resolution imaging of the chromatin, and manipulation of individual fibers. Pulling a single chromatin fiber apart using the AFM tip yields information on the forces which hold the structure together. We have isolated chromatin fibers from chicken erythrocytes and Chinese hamster ovary cell lines. AFM images of these fibers will be presented, along with preliminary data from the manipulation of these fibers using the AFM tip. The implications of these data for the structure of chromatin undergoing the remodeling process are discussed.

  9. Chromatin Dynamics during Cellular Reprogramming

    PubMed Central

    Apostolou, Effie; Hochedlinger, Konrad

    2014-01-01

    Preface Induced pluripotency is a powerful tool to derive patient-specific stem cells. In addition, it provides a unique assay to study the interplay between transcription factors and chromatin structure. Here, we review the latest insights into chromatin dynamics inherent to induced pluripotency. Moreover, we compare and contrast these events with other physiological and pathological processes involving changes in chromatin and cell state, including germ cell maturation and tumorigenesis. We propose that an integrated view of these seemingly diverse processes could provide mechanistic insights into cell fate transitions in general and might lead to novel approaches in regenerative medicine and cancer treatment. PMID:24153299

  10. Chromatin organization: form to function.

    PubMed

    de Graaf, Carolyn A; van Steensel, Bas

    2013-04-01

    Recent developments in technology have made it possible to create high resolution genome-wide maps of histone marks, DNA binding proteins and physical interactions along genomic regions. Chromatin features are found together in different combinations, dividing the genome up into domains with distinct functional properties. Microscopy and chromatin conformation capture techniques have shown that the 3D structure of chromosomes is constrained by nuclear features and functional links between different parts of chromatin. These results provide insights about the 3D and domain organization of the genome and their connection to gene regulation and other nuclear functions. PMID:23274160

  11. Chromatin modifications and their function.

    PubMed

    Kouzarides, Tony

    2007-02-23

    The surface of nucleosomes is studded with a multiplicity of modifications. At least eight different classes have been characterized to date and many different sites have been identified for each class. Operationally, modifications function either by disrupting chromatin contacts or by affecting the recruitment of nonhistone proteins to chromatin. Their presence on histones can dictate the higher-order chromatin structure in which DNA is packaged and can orchestrate the ordered recruitment of enzyme complexes to manipulate DNA. In this way, histone modifications have the potential to influence many fundamental biological processes, some of which may be epigenetically inherited. PMID:17320507

  12. The Regulation of Chromatin by Dynamic SUMO Modifications.

    PubMed

    Wilson, Nicole R; Hochstrasser, Mark

    2016-01-01

    Protein modification by the small ubiquitin-related modifier (SUMO) protein regulates numerous cellular pathways and mounting evidence reveals a critical role for SUMO in modulating gene expression. Dynamic sumoylation of transcription factors, chromatin-modifying enzymes, histones, and other chromatin-associated factors significantly affects the transcriptional status of the eukaryotic genome. Recent studies have employed high-throughput ChIP-Seq analyses to gain clues regarding the role of the SUMO pathway in regulating chromatin-based transactions. Indeed, the global distribution of SUMO across chromatin reveals an important function for SUMO in controlling transcription, particularly of genes involved in protein synthesis. These newly appreciated patterns of genome-wide sumoylation will inform more directed studies aimed at analyzing how the dynamics of gene expression are controlled by posttranslational SUMO modification. PMID:27631795

  13. Light-induced structural changes in a monomeric bacteriophytochrome.

    PubMed

    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

    2016-09-01

    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

  14. Polymer-Fullerene Network Formation via Light-Induced Crosslinking.

    PubMed

    Sugawara, Yuuki; Hiltebrandt, Kai; Blasco, Eva; Barner-Kowollik, Christopher

    2016-09-01

    A facile and efficient methodology for the formation of polymer-fullerene networks via a light-induced reaction is reported. The photochemical crosslinking is based on a nitrile imine-mediated tetrazole-ene cycloaddition reaction, which proceeds catalyst-free under UV-light irradiation (λmax = 320 nm) at ambient temperature. A tetrazole-functionalized polymer (Mn = 6500 g mol(-1) , Ð = 1.3) and fullerene C60 are employed for the formation of the hybrid networks. The tetrazole-functionalized polymer as well as the fullerene-containing networks are carefully characterized by NMR spectrometry, size exclusion chromatography, infrared spectroscopy, and elemental analysis. Furthermore, thermal analysis of the fullerene networks and their precursors is carried out. The current contribution thus induces an efficient platform technology for fullerene-based network formation. PMID:27336692

  15. Light-induced suppression of endogenous circadian amplitude in humans

    NASA Technical Reports Server (NTRS)

    Jewett, Megan; Czeisler, Charles A.; Kronauer, Richard E.

    1991-01-01

    A recent demonstration that the phase of the human circadian pacemaker could be inverted using an unconventional three-cycle stimulus has led to an investigation of whether critically timed exposure to a more moderate stimulus could drive that oscillator toward its singularity, a phaseless position at which the amplitude of circadian oscillation is zero. It is reported here that exposure of humans to fewer cycles of bright light, centered around the time at which the human circadian pacemaker is most sensitive to light-induced phase shifts, can markedly attenuate endogenous cicadian amplitude. In some cases this results in an apparent loss of rhythmicity, as expected to occur in the region of singularity.

  16. 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.

  17. Light-Induced Metastability in Pure and Hydrogenated Amorphous Silicon

    SciTech Connect

    Queen, D. R.; Liu, X.; Karel, J.; Wang, Q.; Crandall, Richard S.; Metcalf, T. H.; Hellman, F.

    2015-10-01

    Light soaking is found to increase the specific heat C and internal friction Q-1 of pure (a-Si) and hydrogenated (a-Si:H) amorphous silicon. At the lowest temperatures, the increases in C and Q-1 are consistent with an increased density of two-level systems (TLS). The light-induced increase in C persists to room temperature. Neither the sound velocity nor shear modulus change with light soaking indicating that the Debye specific heat is unchanged which suggests that light soaking creates localized vibrational modes in addition to TLS. The increase can be reversibly added and removed by light soaking and annealing, respectively, suggesting that it is related to the Staebler-Wronski effect (SWE), even in a-Si without H, and involves a reversible nanoscale structural rearrangement that is facilitated by, but does not require, H to occur.

  18. Light-induced metastability in pure and hydrogenated amorphous silicon

    NASA Astrophysics Data System (ADS)

    Queen, D. R.; Liu, X.; Karel, J.; Wang, Q.; Crandall, R. S.; Metcalf, T. H.; Hellman, F.

    2015-10-01

    Light soaking is found to increase the specific heat C and internal friction Q-1 of pure (a-Si) and hydrogenated (a-Si:H) amorphous silicon. At the lowest temperatures, the increases in C and Q-1 are consistent with an increased density of two-level systems (TLS). The light-induced increase in C persists to room temperature. Neither the sound velocity nor shear modulus change with light soaking indicating that the Debye specific heat is unchanged which suggests that light soaking creates localized vibrational modes in addition to TLS. The increase can be reversibly added and removed by light soaking and annealing, respectively, suggesting that it is related to the Staebler-Wronski effect (SWE), even in a-Si without H, and involves a reversible nanoscale structural rearrangement that is facilitated by, but does not require, H to occur.

  19. Functional analysis of chloroplast early light inducible proteins (ELIPs)

    SciTech Connect

    Wetzel, Carolyn M

    2005-02-22

    The objectives of this project were to characterize gene expression patterns of early light inducible protein (ELIP) genes in Arabidopsis thaliana and in Lycopersicon esculentum, to identify knock mutants of the 2 ELIP genes in Arabidopsis, and to characterize the effects of the knockouts. Expression in Arabidopsis was studied in response to thylakoid electron transport chain (PETC) capacity, where it was found that there is a signal for expression associated with reduction of the PETC. Expression in response to salt was also studied, with different responses of the two gene copies. Knockout lines for ELIP1 and ELIP2 have been identified and are being characterized. In tomato, it was found that the single-copy ELIP gene is highly expressed in ripening fruit during the chloroplast-to-chromoplast transition. Studies of expression in tomato ripening mutants are ongoing.

  20. 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

  1. Light induced silver and copper plating on silver screen-printed contacts of silicon solar cells

    NASA Astrophysics Data System (ADS)

    Tutashkonko, S.; Kaminski-Cachopo, A.; Boulord, C.; Arès, R.; Aimez, V.; Lemiti, M.

    2011-09-01

    In this paper we present the results of solar cell's screen printed contacts thickening by light induced plating (LIP) of Cu and Ag. Light-induced and light-assisted plating techniques are compared. Plating bath current versus illumination intensity, the potentials of metallic anode, front and back surfaces of the solar cell were measured and analyzed for all possible plating modes. The current-voltage behaviour of cells under illumination in a plating bath for the cases of electrically insulated and non-insulated back-surface of a cell is analyzed and discussed. Finally, the exact values of current/voltage/illumination intensity for optimal depositions and a general recipe for their determination for different plating materials are given. The quality of deposited layers, state of contact-line and anti-reflective coating surface were controlled after plating by cross-section and planar-view SEM observations. The electrical properties of plated contacts and their effect on overall efficiency of solar cell were investigated by measuring contact-line resistance and dark- and light I-V solar cell measurements. The absence of short-circuits was verified by imaging with an infra-red camera.

  2. Chromatin fiber allostery and the epigenetic code

    NASA Astrophysics Data System (ADS)

    Lesne, Annick; Foray, Nicolas; Cathala, Guy; Forné, Thierry; Wong, Hua; Victor, Jean-Marc

    2015-02-01

    The notion of allostery introduced for proteins about fifty years ago has been extended since then to DNA allostery, where a locally triggered DNA structural transition remotely controls other DNA-binding events. We further extend this notion and propose that chromatin fiber allosteric transitions, induced by histone-tail covalent modifications, may play a key role in transcriptional regulation. We present an integrated scenario articulating allosteric mechanisms at different scales: allosteric transitions of the condensed chromatin fiber induced by histone-tail acetylation modify the mechanical constraints experienced by the embedded DNA, thus possibly controlling DNA-binding of allosteric transcription factors or further allosteric mechanisms at the linker DNA level. At a higher scale, different epigenetic constraints delineate different statistically dominant subsets of accessible chromatin fiber conformations, which each favors the assembly of dedicated regulatory complexes, as detailed on the emblematic example of the mouse Igf2-H19 gene locus and its parental imprinting. This physical view offers a mechanistic and spatially structured explanation of the observed correlation between transcriptional activity and histone modifications. The evolutionary origin of allosteric control supports to speak of an ‘epigenetic code’, by which events involved in transcriptional regulation are encoded in histone modifications in a context-dependent way.

  3. Vernalization-mediated chromatin changes.

    PubMed

    Zografos, Brett R; Sung, Sibum

    2012-07-01

    Proper flowering time is vital for reproductive fitness in flowering plants. In Arabidopsis, vernalization is mediated primarily through the repression of a MADS box transcription factor, FLOWERING LOCUS C (FLC). The induction of a plant homeodomain-containing protein, VERNALIZATION INSENSITIVE 3 (VIN3), by vernalizing cold is required for proper repression of FLC. One of a myriad of changes that occurs after VIN3 is induced is the establishment of FLC chromatin at a mitotically repressed state due to the enrichment of repressive histone modifications. VIN3 induction by cold is the earliest known event during the vernalization response and includes changes in histone modifications at its chromatin. Here, the current understanding of the vernalization-mediated chromatin changes in Arabidopsis is discussed, with a focus on the roles of shared chromatin-modifying machineries in regulating VIN3 and FLC gene family expression during the course of vernalization.

  4. Stress-induced chromatin changes in plants: of memories, metabolites and crop improvement.

    PubMed

    Vriet, Cécile; Hennig, Lars; Laloi, Christophe

    2015-04-01

    Exposure of plants to adverse environmental conditions leads to extensive transcriptional changes. Genome-wide approaches and gene function studies have revealed the importance of chromatin-level control in the regulation of stress-responsive gene expression. Advances in understanding chromatin modifications implicated in plant stress response and identifying proteins involved in chromatin-mediated transcriptional responses to stress are briefly presented in this review. We then highlight how chromatin-mediated gene expression changes can be coupled to the metabolic status of the cell, since many of the chromatin-modifying proteins involved in transcriptional regulation depend on cofactors and metabolites that are shared with enzymes in basic metabolism. Lastly, we discuss the stability and heritability of stress-induced chromatin changes and the potential of chromatin-based strategies for increasing stress tolerance of crops.

  5. Painting a Clearer Picture of Chromatin.

    PubMed

    Finn, Elizabeth H; Misteli, Tom; Shachar, Sigal

    2016-02-22

    Elucidating chromatin's 3D shape is critical to understanding its function, but the fine structure of chromatin domains remains poorly resolved. In a recent report in Nature, Boettiger et al. (2016) visualize chromatin in super-resolution, gaining unprecedented insight into chromatin architecture. PMID:26906730

  6. Light-induced scattering in laser radiation nonlinear optical limiting based on fullerene-containing media

    NASA Astrophysics Data System (ADS)

    Belousova, Inna M.; Grigor'ev, Vladimir A.; Danilov, Oleg B.; Kalintsev, Alexander G.; Kris'ko, A. V.; Mironova, N. G.; Yur'ev, Michail S.

    2001-03-01

    The contribution of light induced scattering to nonlinear optical limiting is theoretically and experimentally investigated. It is shown that light induced scattering is caused by fine-scale (1 divided by 10 micrometer) inhomogeneities formation, very low (comparable to spontaneous noise) laser beam inhomogeneities can evolve into light induced scattering. The numerical modeling of scattered radiation angular distribution and laser radiation attenuation in optical limiters was performed. The modeling results were compared with the experimental ones.

  7. The nucleotides responsible for the direct physical contact between the chromatin insulator protein CTCF and the H19 imprinting control region manifest parent of origin-specific long-distance insulation and methylation-free domains

    PubMed Central

    Pant, Vinod; Mariano, Piero; Kanduri, Chandrasekhar; Mattsson, Anita; Lobanenkov, Victor; Heuchel, Rainer; Ohlsson, Rolf

    2003-01-01

    The repression of the maternally inherited Igf2 allele has been proposed to depend on a methylation-sensitive chromatin insulator organized by the 11 zinc finger protein CTCF at the H19 imprinting control region (ICR). Here we document that point mutations of the nucleotides in physical contact with CTCF within the endogenous H19 ICR lead to loss of CTCF binding and Igf2 imprinting only when passaged through the female germline. This effect is accompanied by a significant loss of methylation protection of the maternally derived H19 ICR. Because CTCF interacts with other imprinting control regions, it emerges as a central factor responsible for interpreting and propagating gamete-derived epigenetic marks and for organizing epigenetically controlled expression domains. PMID:12629040

  8. The polymorphisms of the chromatin fiber

    NASA Astrophysics Data System (ADS)

    Boulé, Jean-Baptiste; Mozziconacci, Julien; Lavelle, Christophe

    2015-01-01

    In eukaryotes, the genome is packed into chromosomes, each consisting of large polymeric fibers made of DNA bound with proteins (mainly histones) and RNA molecules. The nature and precise 3D organization of this fiber has been a matter of intense speculations and debates. In the emerging picture, the local chromatin state plays a critical role in all fundamental DNA transactions, such as transcriptional control, DNA replication or repair. However, the molecular and structural mechanisms involved remain elusive. The purpose of this review is to give an overview of the tremendous efforts that have been made for almost 40 years to build physiologically relevant models of chromatin structure. The motivation behind building such models was to shift our representation and understanding of DNA transactions from a too simplistic ‘naked DNA’ view to a more realistic ‘coated DNA’ view, as a step towards a better framework in which to interpret mechanistically the control of genetic expression and other DNA metabolic processes. The field has evolved from a speculative point of view towards in vitro biochemistry and in silico modeling, but is still longing for experimental in vivo validations of the proposed structures or even proof of concept experiments demonstrating a clear role of a given structure in a metabolic transaction. The mere existence of a chromatin fiber as a relevant biological entity in vivo has been put into serious questioning. Current research is suggesting a possible reconciliation between theoretical studies and experiments, pointing towards a view where the polymorphic and dynamic nature of the chromatin fiber is essential to support its function in genome metabolism.

  9. Essential role of NF-E2 in remodeling of chromatin structure and transcriptional activation of the epsilon-globin gene in vivo by 5' hypersensitive site 2 of the beta-globin locus control region.

    PubMed Central

    Gong, Q H; McDowell, J C; Dean, A

    1996-01-01

    Much of our understanding of the process by which enhancers activate transcription has been gained from transient-transfection studies in which the DNA is not assembled with histones and other chromatin proteins as it is in the cell nucleus. To study the activation of a mammalian gene in a natural chromatin context in vivo, we constructed a minichromosome containing the human epsilon-globin gene and portions of the beta-globin locus control region (LCR). The minichromosomes replicate and are maintained at stable copy number in human erythroid cells. Expression of the minichromosomal epsilon-globin gene requires the presence of beta-globin LCR elements in cis, as is the case for the chromosomal gene. We determined the chromatin structure of the epsilon-globin gene in both the active and inactive states. The transcriptionally inactive locus is covered by an array of positioned nucleosomes extending over 1,400 bp. In minichromosomes with a (mu)LCR or DNase I-hypersensitive site 2 (HS2) which actively transcribe the epsilon-globin gene, the nucleosome at the promoter is altered or disrupted while positioning of nucleosomes in the rest of the locus is retained. All or virtually all minichromosomes are simultaneously hypersensitive to DNase I both at the promoter and at HS2. Transcriptional activation and promoter remodeling, as well as formation of the HS2 structure itself, depended on the presence of the NF-E2 binding motif in HS2. The nucleosome at the promoter which is altered upon activation is positioned over the transcriptional elements of the epsilon-globin gene, i.e., the TATA, CCAAT, and CACCC elements, and the GATA-1 site at -165. The simple availability of erythroid transcription factors that recognize these motifs is insufficient to allow expression. As in the chromosomal globin locus, regulation also occurs at the level of chromatin structure. These observations are consistent with the idea that one role of the beta-globin LCR is to maintain promoters free

  10. CHAPERONE-MEDIATED CHROMATIN ASSEMBLY AND TRANSCRIPTION REGULATION IN XENOPUS LAEVIS

    PubMed Central

    Onikubo, Takashi; Shechter, David

    2016-01-01

    Chromatin is the complex of DNA and histone proteins that is the physiological form of the eukaryotic genome. Chromatin is generally repressive for transcription, especially so during early metazoan development when maternal factors are explicitly in control of new zygotic gene expression. In the important model organism Xenopus laevis, maturing oocytes are transcriptionally active with reduced rates of chromatin assembly, while laid eggs and fertilized embryos have robust rates of chromatin assembly and are transcriptionally repressed. As the DNA-to-cytoplasmic ratio decreases approaching the mid-blastula transition (MBT) and the onset of zygotic transcription activation (ZGA), the chromatin assembly process changes with the concomitant reduction in maternal chromatin components. Chromatin assembly is mediated in part by histone chaperones that store maternal histones and release them into new zygotic chromatin. Here, we review literature on chromatin and transcription in frog embryos and cell-free extracts and highlight key insights demonstrating the roles of maternal and zygotic histone deposition and their relationship with transcriptional regulation. We explore the central historical and recent literature on the use of Xenopus embryos and the key contributions provided by experiments in cell-free oocyte and egg extracts for the interplay between histone chaperones, chromatin assembly, and transcriptional regulation. Ongoing and future studies in Xenopus cell free extracts will likely contribute essential new insights into the interplay between chromatin assembly and transcriptional regulation. PMID:27759155

  11. The chromatin landscape of Kaposi's sarcoma-associated herpesvirus.

    PubMed

    Toth, Zsolt; Brulois, Kevin; Jung, Jae U

    2013-05-01

    Kaposi's sarcoma-associated herpesvirus is an oncogenic γ-herpesvirus that causes latent infection in humans. In cells, the viral genome adopts a highly organized chromatin structure, which is controlled by a wide variety of cellular and viral chromatin regulatory factors. In the past few years, interrogation of the chromatinized KSHV genome by whole genome-analyzing tools revealed that the complex chromatin landscape spanning the viral genome in infected cells has important regulatory roles during the viral life cycle. This review summarizes the most recent findings regarding the role of histone modifications, histone modifying enzymes, DNA methylation, microRNAs, non-coding RNAs and the nuclear organization of the KSHV epigenome in the regulation of latent and lytic viral gene expression programs as well as their connection to KSHV-associated pathogenesis. PMID:23698402

  12. ISWI chromatin remodeling complexes in the DNA damage response

    PubMed Central

    Aydin, Özge Z; Vermeulen, Wim; Lans, Hannes

    2014-01-01

    Regulation of chromatin structure is an essential component of the DNA damage response (DDR), which effectively preserves the integrity of DNA by a network of multiple DNA repair and associated signaling pathways. Within the DDR, chromatin is modified and remodeled to facilitate efficient DNA access, to control the activity of repair proteins and to mediate signaling. The mammalian ISWI family has recently emerged as one of the major ATP-dependent chromatin remodeling complex families that function in the DDR, as it is implicated in at least 3 major DNA repair pathways: homologous recombination, non-homologous end-joining and nucleotide excision repair. In this review, we discuss the various manners through which different ISWI complexes regulate DNA repair and how they are targeted to chromatin containing damaged DNA. PMID:25486562

  13. ISWI chromatin remodeling complexes in the DNA damage response.

    PubMed

    Aydin, Özge Z; Vermeulen, Wim; Lans, Hannes

    2014-01-01

    Regulation of chromatin structure is an essential component of the DNA damage response (DDR), which effectively preserves the integrity of DNA by a network of multiple DNA repair and associated signaling pathways. Within the DDR, chromatin is modified and remodeled to facilitate efficient DNA access, to control the activity of repair proteins and to mediate signaling. The mammalian ISWI family has recently emerged as one of the major ATP-dependent chromatin remodeling complex families that function in the DDR, as it is implicated in at least 3 major DNA repair pathways: homologous recombination, non-homologous end-joining and nucleotide excision repair. In this review, we discuss the various manners through which different ISWI complexes regulate DNA repair and how they are targeted to chromatin containing damaged DNA.

  14. [Study of blue light induced DNA damage of retinal pigment epithelium(RPE) cells and the protection of vitamin C].

    PubMed

    Zhou, Jian Wei; Ren, Guo Liang; Zhang, Xiao Ming; Zhu, Xi; Lin, Hai Yan; Zhou, Ji Lin

    2003-10-01

    To evaluate protection of vitamin C on blue light-induced DNA damage of human retinal pigment epithelium (RPE) cells. The cultured RPE cells were divided into 3 groups: Control group (no blue light exposure), blue light exposure group (blue light exposure for 20 minutes) and blue light exposure + vitamin C group (blue light exposure + 100 mumol/L vitamin C). Travigen's comet assay kit and Euclid comet assay software were used to assay the DNA damage levels. The DNA percentage in the tail of electrophoretogram in the three groups were 18.44%, 54.42% and 32.43% respectively (p < 0.01). Tail moments were 8.2, 48.3, and 18.4 respectively (p < 0.01). Blue light could induce DNA damage to RPE cells but vitamin C could protect the RPE cells from the blue light-induced DNA damage.

  15. Environmental-stress-induced Chromatin Regulation and its Heritability

    PubMed Central

    Fang, Lei; Wuptra, Kenly; Chen, Danqi; Li, Hongjie; Huang, Shau-Ku; Jin, Chunyuan; Yokoyama, Kazunari K

    2014-01-01

    Chromatin is subject to proofreading and repair mechanisms during the process of DNA replication, as well as repair to maintain genetic and epigenetic information and genome stability. The dynamic structure of chromatin modulates various nuclear processes, including transcription and replication, by altering the accessibility of the DNA to regulatory factors. Structural changes in chromatin are affected by the chemical modification of histone proteins and DNA, remodeling of nucleosomes, incorporation of variant histones, noncoding RNAs, and nonhistone DNA-binding proteins. Phenotypic diversity and fidelity can be balanced by controlling stochastic switching of chromatin structure and dynamics in response to the environmental disruptors and endogenous stresses. The dynamic chromatin remodeling can, therefore, serve as a sensor, through which environmental and/or metabolic agents can alter gene expression, leading to global cellular changes involving multiple interactive networks. Furthermore its recent evidence also suggests that the epigenetic changes are heritable during the development. This review will discuss the environmental sensing system for chromatin regulation and genetic and epigenetic controls from developmental perspectives. PMID:25045581

  16. Environmental-stress-induced Chromatin Regulation and its Heritability.

    PubMed

    Fang, Lei; Wuptra, Kenly; Chen, Danqi; Li, Hongjie; Huang, Shau-Ku; Jin, Chunyuan; Yokoyama, Kazunari K

    2014-01-15

    Chromatin is subject to proofreading and repair mechanisms during the process of DNA replication, as well as repair to maintain genetic and epigenetic information and genome stability. The dynamic structure of chromatin modulates various nuclear processes, including transcription and replication, by altering the accessibility of the DNA to regulatory factors. Structural changes in chromatin are affected by the chemical modification of histone proteins and DNA, remodeling of nucleosomes, incorporation of variant histones, noncoding RNAs, and nonhistone DNA-binding proteins. Phenotypic diversity and fidelity can be balanced by controlling stochastic switching of chromatin structure and dynamics in response to the environmental disruptors and endogenous stresses. The dynamic chromatin remodeling can, therefore, serve as a sensor, through which environmental and/or metabolic agents can alter gene expression, leading to global cellular changes involving multiple interactive networks. Furthermore its recent evidence also suggests that the epigenetic changes are heritable during the development. This review will discuss the environmental sensing system for chromatin regulation and genetic and epigenetic controls from developmental perspectives.

  17. TOPOISOMERASE 6B is involved in chromatin remodelling associated with control of carbon partitioning into secondary metabolites and cell walls, and epidermal morphogenesis in Arabidopsis

    PubMed Central

    Mittal, Amandeep; Balasubramanian, Rajagopal; Cao, Jin; Singh, Prabhjeet; Subramanian, Senthil; Hicks, Glenn; Nothnagel, Eugene A.; Abidi, Noureddine; Janda, Jaroslav; Galbraith, David W.; Rock, Christopher D.

    2014-01-01

    Plant growth is continuous and modular, a combination that allows morphogenesis by cell division and elongation and serves to facilitate adaptation to changing environments. The pleiotropic phenotypes of the harlequin (hlq) mutant, isolated on the basis of ectopic expression of the abscisic acid (ABA)- and auxin-inducible proDc3:GUS reporter gene, were previously characterized. Mutants are skotomorphogenic, have deformed and collapsed epidermal cells which accumulate callose and starch, cell walls abundant in pectins and cell wall proteins, and abnormal and reduced root hairs and leaf trichomes. hlq and two additional alleles that vary in their phenotypic severity of starch accumulation in the light and dark have been isolated, and it is shown that they are alleles of bin3/hyp6/rhl3/Topoisomerase6B. Mutants and inhibitors affecting the cell wall phenocopy several of the traits displayed in hlq. A microarray analysis was performed, and coordinated expression of physically adjacent pairs/sets of genes was observed in hlq, suggesting a direct effect on chromatin. Histones, WRKY and IAA/AUX transcription factors, aquaporins, and components of ubiquitin-E3-ligase-mediated proteolysis, and ABA or biotic stress response markers as well as proteins involved in cellular processes affecting carbon partitioning into secondary metabolites were also identified. A comparative analysis was performed of the hlq transcriptome with other previously published TopoVI mutant transcriptomes, namely bin3, bin5, and caa39 mutants, and limited concordance between data sets was found, suggesting indirect or genotype-specific effects. The results shed light on the molecular mechanisms underlying the det/cop/fus-like pleiotropic phenotypes of hlq and support a broader role for TopoVI regulation of chromatin remodelling to mediate development in response to environmental and hormonal signals. PMID:24821950

  18. Chromatin beacons: global sampling of chromatin physical properties using chromatin charting lines.

    PubMed

    Amini, Aniça; Luo, Chongyuan; Lam, Eric

    2011-01-01

    The extent to which physical properties and intranuclear locations of chromatin can influence transcription output remains unclear and poorly quantified. Because the scale and resolution at which structural parameters can be queried are usually so different from the scale that transcription outputs are measured, the integration of these data is often indirect. To overcome this limitation in quantifying chromatin structural parameters at different locations in the genome, a Chromatin Charting collection with 277 transposon-tagged Arabidopsis lines has been established in order to discover correlations between gene expression and the physical properties of chromatin loci within the nuclei. In these lines, dispersed loci in the Arabidopsis genome are tagged with an identical transgene cassette containing a luciferase gene reporter, which permits the quantification of gene expressions in real time, and an ∼2 kb LacO repeat that acts as a "chromatin beacon" to facilitate the visual tracking of a tagged locus in living plants via the expression of LacI-GFP fusion proteins in trans. In this chapter, we describe the methods for visualizing and tracking these insertion loci in vivo and illustrate the potential of using this approach to correlate chromatin mobility with gene expression in living plants.

  19. Chromatin pattern by variogram analysis.

    PubMed

    Diaz, G; Zucca, A; Setzu, M D; Cappai, C

    1997-11-01

    Many cytological processes such as cell proliferation, differentiation, transformation, apoptosis, etc., are accompanied by specific chromatin changes, usually identified on the basis of the relative content of euchromatin and heterochromatin. In order to achieve a quantitative, non-subjective evaluation of the chromatin pattern, two different approaches may be undertaken, one consisting in the analysis of the several morphological features of chromatin grains (size, shape, density, arrangement, and distribution), and the second consisting in the analysis of the chromatin globally considered as a coherent texture. Although the second approach appears to be simpler and more suitable, methods of texture analysis--including those specifically designed for the analysis of the chromatin pattern--are rarely applied due mainly to the unsuitability of sampling procedures and the excessive crypticism of results. As an alternative to traditional texture analysis, we suggest a method supported by a sound mathematical theory and approximately 30 years of applications in the field of geostatistics. The method, called variogram, analyzes the intrinsic structure of data sampled at different distance intervals and directions, and outputs easily understandable results. Recently, variogram analysis has successfully been exported from geostatistics to other fields (for example, ecology and epidemiology) that make use of spatially referenced variables. Based on the fact that pixels represent a perfect array of data ordered at regular distance intervals and directions, the variogram can be adopted to explore nuclear images and recognize chromatin patterns. Variograms of different nuclei can be summarized by multivariate methods without the need of previous standardization of data. This allows comparison and discrimination of chromatin patterns from mixed cell populations. Preliminary data obtained from young neurons undergoing massive apoptosis reveal a self-consistent map of nuclear

  20. Chromatin modifications remodel cardiac gene expression.

    PubMed

    Mathiyalagan, Prabhu; Keating, Samuel T; Du, Xiao-Jun; El-Osta, Assam

    2014-07-01

    Signalling and transcriptional control involve precise programmes of gene activation and suppression necessary for cardiovascular physiology. Deep sequencing of DNA-bound transcription factors reveals a remarkable complexity of co-activators or co-repressors that serve to alter chromatin modification and regulate gene expression. The regulated complexes characterized by genome-wide mapping implicate the recruitment and exchange of proteins with specific enzymatic activities that include roles for histone acetylation and methylation in key developmental programmes of the heart. As for transcriptional changes in response to pathological stress, co-regulatory complexes are also differentially utilized to regulate genes in cardiac disease. Members of the histone deacetylase (HDAC) family catalyse the removal of acetyl groups from proteins whose pharmacological inhibition has profound effects preventing heart failure. HDACs interact with a complex co-regulatory network of transcription factors, chromatin-remodelling complexes, and specific histone modifiers to regulate gene expression in the heart. For example, the histone methyltransferase (HMT), enhancer of zeste homolog 2 (Ezh2), is regulated by HDAC inhibition and associated with pathological cardiac hypertrophy. The challenge now is to target the activity of enzymes involved in protein modification to prevent or reverse the expression of genes implicated with cardiac hypertrophy. In this review, we discuss the role of HDACs and HMTs with a focus on chromatin modification and gene function as well as the clinical treatment of heart failure. PMID:24812277

  1. A possible mechanism for visible-light-induced skin rejuvenation

    NASA Astrophysics Data System (ADS)

    Longo, Leonardo; Lubart, Rachel; Friedman, Harry; Lavie, R.

    2004-09-01

    In recent years there has been intensive research in the field of non-ablative skin rejuvenation. This comes as a response to the desire for a simple method of treating rhytids caused by aging, UV exposure and acne scars. In numerous studies intense visible light pulsed systems (20-30J/cm2) are used. The mechanism of action was supposed to be a selective heat induced denaturalization of dermal collagen that leads to subsequent reactive synthesis. In this study we suggest a different mechanism for photorejuvenation based on light induced Reactive Oxygen Species (ROS) formation. We irradiated collagen in-vitro with a broad band of visible light, 400-800 nm, 12-22J/cm2, and used the spin trapping coupled with electron paramagnetic resonance (EPR) spectroscopy to detect ROS. In vivo, we used dose 30 J in average (35 for acnis scars, 25 for wrinkles and redness). Irradiated collagen results in hydroxyl and methyl radicals formation. We propose, as a new concept, that visible light at the intensity used for skin rejuvenation, 20-30J/cm2, produces high amounts of ROS which destroy old collagen fibers encouraging the formation of new ones. On the other hand at inner depths of the skin, where the light intensity is much weaker, low amounts of ROS are formed which are well known to stimulate fibroblast proliferation.

  2. Diagnosis of dental caries using quantitative light-induced fluorescence

    NASA Astrophysics Data System (ADS)

    Amaechi, Bennett T.; Higham, Susan M.

    2001-10-01

    Current dental diagnostic methods can detect caries but cannot quantify the mineral status of the lesion. Quantitative Light-induced Fluorescence (QLF) measures the percentage fluorescence radiance change of demineralised enamel with respect to surround sound enamel, and related it directly to the amount of mineral lost during demineralisation. Demineralisation of teeth to produce caries-like lesions and the subsequent remineralisation of the lesions were monitored quantitatively and longitudinally with QLF. The influence of factors such as presence of plaque or saliva, lesion staining, lesion magnification, tooth thickness and developmental hypomineralisation, on the reproducibility of QLF imaging and analysis were investigated, Results showed that the integrated fluorescence change (hence the mineral loss) increased linearly with demineralisation time and decreased with increasing remineralisation time. Caries detection was limited by saliva or plaque, but enhanced by staining. QLF could not discriminate between developmental hypomineralisation and caries. Neither the variation in tooth thickness nor lesion magnification within the limit of a sharp image made a significant difference in QLF analysis. It was concluded that QLF could detect and quantitatively monitor the mineral changes in an incipient caries on a longitudinal basis, however detection may be limited by the presence of saliva or plaque or enhanced by staining.

  3. Ultraviolet light-induced inhibition of small nuclear RNA synthesis.

    PubMed

    Eliceiri, B P; Choudhury, K; Scott, Q O; Eliceiri, G L

    1989-03-01

    Two apparently distinct types of inhibition of the synthesis of U1, U2, U3, U4, and U5 small nuclear RNA, induced by ultraviolet (UV) radiation, have been described before: immediate and delayed. Our present observation can be summarized as follows: a) neither the immediate nor the delayed inhibition appear to be mediated by the formation of cyclobutane pyrimidine dimers, since they were not prevented by photoreactivating light, in ICR 2A frog cells; b) the inhibition of U1 RNA synthesis, monitored in HeLA cells within the first few minutes after irradiation, extrapolated to a substantial suppression at time zero of postirradiation cell incubation, providing further support for the proposal that the immediate inhibition is a reaction separate from the delayed UV light-induced inhibition of U1 RNA synthesis; c) the transition from the pattern of the immediate inhibition to that of the delayed inhibition (disappearance of the UV-resistant fraction of U1 RNA synthesis and increased rate of inhibition) occurred gradually, without an apparent threshold, within the first 2 hr of incubation after irradiation; and d) the incident UV dose that resulted in a 37% level of residual U1 RNA synthesis (D37) during the delayed inhibition was about 7 J/m2, with an apparent UV dose threshold, and was about 60 J/m2 for the immediate inhibition. PMID:2925798

  4. Early light-induced proteins protect Arabidopsis from photooxidative stress.

    PubMed

    Hutin, Claire; Nussaume, Laurent; Moise, Nicolae; Moya, Ismaël; Kloppstech, Klaus; Havaux, Michel

    2003-04-15

    The early light-induced proteins (ELIPs) belong to the multigenic family of light-harvesting complexes, which bind chlorophyll and absorb solar energy in green plants. ELIPs accumulate transiently in plants exposed to high light intensities. By using an Arabidopsis thaliana mutant (chaos) affected in the posttranslational targeting of light-harvesting complex-type proteins to the thylakoids, we succeeded in suppressing the rapid accumulation of ELIPs during high-light stress, resulting in leaf bleaching and extensive photooxidative damage. Constitutive expression of ELIP genes in chaos before light stress resulted in ELIP accumulation and restored the phototolerance of the plants to the wild-type level. Free chlorophyll, a generator of singlet oxygen in the light, was detected by chlorophyll fluorescence lifetime measurements in chaos leaves before the symptoms of oxidative stress appeared. Our findings indicate that ELIPs fulfill a photoprotective function that could involve either the binding of chlorophylls released during turnover of pigment-binding proteins or the stabilization of the proper assembly of those proteins during high-light stress. PMID:12676998

  5. Influence of Sugars on Blue Light-Induced Chloroplast Relocations

    PubMed Central

    Banaś, Agnieszka Katarzyna

    2007-01-01

    The aim of this study was to investigate the influence of sugars on blue light-induced chloroplast movements. Sucrose and glucose inhibited chloroplast responses in the detached leaves of Arabidopsis thaliana and in Lemna trisulca fronds in a concentration and time-dependent manner. The prolonged exposure necessary for inhibition indicates that sugars may act via altered gene expression. Overexpression of phototropin2, a photoreceptor responsible for the strong blue light response of chloroplasts, counteracted the sugar effect. This may suggest that sugars modify some component(s) of the phototropin2-mediated signal transduction pathway. The expression of PHOT2 was not suppressed by sugars in wild type plants, it was even upregulated by glucose. Impaired chloroplast movements were observed only in mature Arabidopsis plants. The mRNA of SAG12, a late senescence marker, was not detectable in the sugar-incubated leaves. The SAG13 mRNA level and its regulation by sugars were similar in wild type and PHOT2 overexpressor. Thus, the sugar insensitivity of 35S:PHOT2 chloroplast responses was not due to delayed senescence. The sugar-induced transduction pathway involved remains unclear. 3-O-methylglucose did not affect chloroplast movements suggesting the participation of a hexokinase-dependent pathway. Only the amplitude of avoidance response was reduced in gin2-1, a hexokinase1 null mutant. Probably other hexokinases, or glycolysis-associated signals play a role in the suppression of chloroplast responses. PMID:19516992

  6. Orthogonal light-induced self-assembly of nanoparticles using differently substituted azobenzenes.

    PubMed

    Manna, Debasish; Udayabhaskararao, Thumu; Zhao, Hui; Klajn, Rafal

    2015-10-12

    Precise control of the self-assembly of selected components within complex mixtures is a challenging goal whose realization is important for fabricating novel nanomaterials. Herein we show that by decorating the surfaces of metallic nanoparticles with differently substituted azobenzenes, it is possible to modulate the wavelength of light at which the self-assembly of these nanoparticles is induced. Exposing a mixture of two types of nanoparticles, each functionalized with a different azobenzene, to UV or blue light induces the selective self-assembly of only one type of nanoparticles. Irradiation with the other wavelength triggers the disassembly of the aggregates, and the simultaneous self-assembly of nanoparticles of the other type. By placing both types of azobenzenes on the same nanoparticles, we created unique materials ("frustrated" nanoparticles) whose self-assembly is induced irrespective of the wavelength of the incident light.

  7. Single Molecule Studies of Chromatin

    SciTech Connect

    Jeans, C; Thelen, M P; Noy, A

    2006-02-06

    In eukaryotic cells, DNA is packaged as chromatin, a highly ordered structure formed through the wrapping of the DNA around histone proteins, and further packed through interactions with a number of other proteins. In order for processes such as DNA replication, DNA repair, and transcription to occur, the structure of chromatin must be remodeled such that the necessary enzymes can access the DNA. A number of remodeling enzymes have been described, but our understanding of the remodeling process is hindered by a lack of knowledge of the fine structure of chromatin, and how this structure is modulated in the living cell. We have carried out single molecule experiments using atomic force microscopy (AFM) to study the packaging arrangements in chromatin from a variety of cell types. Comparison of the structures observed reveals differences which can be explained in terms of the cell type and its transcriptional activity. During the course of this project, sample preparation and AFM techniques were developed and optimized. Several opportunities for follow-up work are outlined which could provide further insight into the dynamic structural rearrangements of chromatin.

  8. Chromatin Preparation and Chromatin Immuno-precipitation from Drosophila Embryos.

    PubMed

    Löser, Eva; Latreille, Daniel; Iovino, Nicola

    2016-01-01

    This protocol provides specific details on how to perform Chromatin immunoprecipitation (ChIP) from Drosophila embryos. ChIP allows the matching of proteins or histone modifications to specific genomic regions. Formaldehyde-cross-linked chromatin is isolated and antibodies against the target of interest are used to determine whether the target is associated with a specific DNA sequence. This can be performed in spatial and temporal manner and it can provide information about the genome-wide localization of a given protein or histone modification if coupled with deep sequencing technology (ChIP-Seq). PMID:27659972

  9. Accelerated Chromatin Biochemistry Using DNA-Barcoded Nucleosome Libraries

    PubMed Central

    Nguyen, Uyen T. T.; Bittova, Lenka; Müller, Manuel M.; Fierz, Beat; David, Yael; Houck-Loomis, Brian; Feng, Vanessa; Dann, Geoffrey P.; Muir, Tom W.

    2014-01-01

    Elucidating the molecular details of how chromatin-associated factors deposit, remove and recognize histone posttranslational modification (‘PTM’) signatures remains a daunting task in the epigenetics field. Here, we introduce a versatile platform that greatly accelerates biochemical investigations into chromatin recognition and signaling. This technology is based on the streamlined semi-synthesis of DNA-barcoded nucleosome libraries with distinct combinations of PTMs. Chromatin immunoprecipitation of these libraries treated with purified chromatin effectors or the combined chromatin recognizing and modifying activities of the nuclear proteome is followed by multiplexed DNA-barcode sequencing. This ultrasensitive workflow allowed us to collect thousands of biochemical data points revealing the binding preferences of various nuclear factors for PTM patterns and how pre-existing PTMs, alone or synergistically, affect further PTM deposition via crosstalk mechanisms. We anticipate that the high-throughput and -sensitivity of the technology will help accelerate the decryption of the diverse molecular controls that operate at the level of chromatin. PMID:24997861

  10. Effect of captopril and melatonin on fibrotic rebuilding of the aorta in 24 hour light-induced hypertension.

    PubMed

    Repová-Bednárová, K; Aziriová, S; Hrenák, J; Krajčírovičová, K; Adamcová, M; Paulis, L; Simko, F

    2013-01-01

    Chronic continuous light exposure leads to melatonin deficiency along with complex neurohumoral activation resulting in hypertension development in rats. The aim of this study was to show, whether continuous light induces fibrotic rebuilding of the aorta and whether the treatment with melatonin or angiotensin converting enzyme inhibitor captopril can prevent these potential alterations. In a six-week experiment, 3-month-old Wistar rats were divided into 4 groups (ten per group): controls, rats exposed to continuous light, exposed to continuous light plus treated with captopril (100 mg/kg/24 h) and exposed to continuous light plus treated with melatonin (10 mg/kg/24 h). Systolic blood pressure (SBP) and collagen type I and III in the media of thoracic aorta were measured. Continuous light induced hypertension and fibrotic rebuilding of the aorta in terms of enhancement of collagen I and III concentration in the aortic media. Both captopril and melatonin prevented SBP rise and reduced collagen III concentration in the aorta. However, only melatonin reduced collagen I and the sum of collagen I and III in the aortic tissue. We conclude that in continuous light-induced hypertension, administration of melatonin, along with SBP reduction, decreases collagen I and III concentration in the aorta. It is suggested that antifibrotic effect of melatonin may reduce the stiffness of the aorta and small arteries and beneficially influence the nature of the pulse wave and peripheral vascular resistance.

  11. Light-Induced Changes of the Circadian Clock of Humans: Increasing Duration is More Effective than Increasing Light Intensity

    PubMed Central

    Dewan, Karuna; Benloucif, Susan; Reid, Kathryn; Wolfe, Lisa F.; Zee, Phyllis C.

    2011-01-01

    Study Objectives: To evaluate the effect of increasing the intensity and/or duration of exposure on light-induced changes in the timing of the circadian clock of humans. Design: Multifactorial randomized controlled trial, between and within subject design Setting: General Clinical Research Center (GCRC) of an academic medical center Participants: 56 healthy young subjects (20-40 years of age) Interventions: Research subjects were admitted for 2 independent stays of 4 nights/3 days for treatment with bright or dim-light (randomized order) at a time known to induce phase delays in circadian timing. The intensity and duration of the bright light were determined by random assignment to one of 9 treatment conditions (duration of 1, 2, or 3 hours at 2000, 4000, or 8000 lux). Measurements and Results: Treatment-induced changes in the dim light melatonin onset (DLMO) and dim light melatonin offset (DLMOff) were measured from blood samples collected every 20-30 min throughout baseline and post-treatment nights. Comparison by multi-factor analysis of variance (ANOVA) of light-induced changes in the time of the circadian melatonin rhythm for the 9 conditions revealed that changing the duration of the light exposure from 1 to 3 h increased the magnitude of light-induced delays. In contrast, increasing from moderate (2,000 lux) to high (8,000 lux) intensity light did not alter the magnitude of phase delays of the circadian melatonin rhythm. Conclusions: Results from the present study suggest that for phototherapy of circadian rhythm sleep disorders in humans, a longer period of moderate intensity light may be more effective than a shorter exposure period of high intensity light. Citation: Dewan K; Benloucif S; Reid K; Wolfe LF; Zee PC. Light-induced changes of the circadian clock of humans: increasing duration is more effective than increasing light intensity. SLEEP 2011;34(5):593-599. PMID:21532952

  12. Chromatin remodeling in nuclear cloning.

    PubMed

    Wade, Paul A; Kikyo, Nobuaki

    2002-05-01

    Nuclear cloning is a procedure to create new animals by injecting somatic nuclei into unfertilized oocytes. Recent successes in mammalian cloning with differentiated adult nuclei strongly indicate that oocyte cytoplasm contains unidentified remarkable reprogramming activities with the capacity to erase the previous memory of cell differentiation. At the heart of this nuclear reprogramming lies chromatin remodeling as chromatin structure and function define cell differentiation through regulation of the transcriptional activities of the cells. Studies involving the modification of chromatin elements such as selective uptake or release of binding proteins, covalent histone modifications including acetylation and methylation, and DNA methylation should provide significant insight into the molecular mechanisms of nuclear dedifferentiation and redifferentiation in oocyte cytoplasm.

  13. Light-Induced Alterations in Basil Ganglia Kynurenic Acid Levels

    NASA Technical Reports Server (NTRS)

    Sroufe, Angela E.; Whittaker, J. A.; Patrickson, J. W.; Orr, M. C.

    1997-01-01

    The metabolic synthesis, release and breakdown of several known CNS neurotransmitters have been shown to follow a circadian pattern entrained to the environmental light/dark cycle. The levels of excitatory amino acid (EAA) transmitters such as glutamate, have been shown to vary with environmental lighting conditions. Kynurenic Acid (KA), an endogenous tryptophan metabolite and glutamate receptor antagonist, has been reported to have neuroprotective effects against EAA-induced excitotoxic cell damage. Changes in KA's activity within the mammalian basal ganglia has been proposed as being contributory to neurotoxicity in Huntington's Disease. It is not known whether CNS KA levels follow a circadian pattern or exhibit light-induced fluctuations. However, because the symptoms of certain degenerative motor disorders seem to fluctuate with daily 24 hour rhythm, we initiated studies to determine if basal ganglia KA were influenced by the daily light/dark cycle and could influence motor function. Therefore in this study, HPLC-EC was utilized to determine if basal ganglia KA levels in tissue extracts from adult male Long-Evans rats (200-250g) entrained to 24 and 48 hours constant light and dark conditions, respectively. Samples were taken one hour before the onset of the subjective day and one hour prior to the onset of the subjective night in order to detect possible phase differences in KA levels and to allow for accumulation of factors expressed in association with the light or dark phase. Data analysis revealed that KA levels in the basal ganglia vary with environmental lighting conditions; being elevated generally during the dark. Circadian phase differences in KA levels were also evident during the subjective night and subjective day, respectively. Results from these studies are discussed with respect to potential cyclic changes in neuronal susceptibility to excitotoxic damage during the daily 24 hour cycle and its possible relevance to future therapeutic approaches in

  14. Light-induced changes of sensitivity in Limulus ventral photoreceptors

    PubMed Central

    1975-01-01

    The responses of Limulus ventral photoreceptors to brief test flashes and to longer adapting lights were measured under voltage clamp conditions. When the cell was dark adapted, there was a range of energy of the test flashes over which the peak amplitude of the responses (light-induced currents) was directly proportional to the flash energy. This was also true when test flashes were superposed on adapting stimuli but the proportionality constant (termed peak currently/photon) was reduced. The peak current/photon was attenuated more by brighter adapting stimuli than by less bright adapting stimuli. The peak current/photon is a measure of the sensitivity of the conductance- increase mechanism underlying the light response of the photo-receptor. The response elicited by an adapting stimulus had a large initial transient which declined to a smaller plateau. The peak current/photon decreased sharply during the declining phase of the transient and was relatively stable during the plateau. This indicates that the onset of light adaptation is delayed with respect to the onset of the response to the adapting stimulus. If the adaptational state just before the onset of each of a series of adapting stimuli was constant, the amplitude of the transient was a nearly linear function of intensity. When the total intensity was rapidly doubled (or halved) during a plateau response, the total current approximately doubled (or halved). We argue that the transition from transient to plateau, light-elicited changes of threshold, and the nonlinear function relating the plateau response to stimulus intensity all reflect changes of the responsiveness of the conductance-increase mechanism. PMID:1181378

  15. Light-induced metastable states in ferroelectric oxides

    NASA Astrophysics Data System (ADS)

    Liu, G. K.; Vikhnin, V. S.; Kapphan, S. E.

    2007-07-01

    New Raman scattering lines (at 463 cm-1 and at 156 cm-1) induced by strong enough optical pumping in nominally pure KTaO3 crystals are manifested. The model of such effect is proposed. This model is based on the light-induced formation of metastable polar clusters constructed from bi-polaronic excitons - Charge Transfer Vibronic Excitons (CTVEs) with their high degree alignment. The CTVEs are caused by photo-carriers with high local concentration which are trapped to local potential wells related with long-range defect fields. CTVE formation are realized in these potential wells due to significant easing of charge transfer fluctuations induced by photo-carrier screening effects. This model is effective also for explanation of giant dielectric constant inducing by strong illumination which was detected recently in KTaO3 and SrTiO3 by Japanese investigators [M. Takesada, T. Yagi, M. Itoh, S. Koshihara, J. Phys. Soc. Jpn. 72 (2003) 37; T. Hasegawa, S. Mouri, Y. Yamada, K. Tanaka, J. Phys. Soc. Jpn. 72 (2003) 41; I. Katayama, Y. Ichikawa, K. Tanaka, Phys. Rev. B 67 (2003) 100102(R)]. Another aspect of the present study was specific recombination luminescence of CTVEs which was investigated here with respect to the influence of additional IR pumping. The present investigation has led to experimental evidence of new, mainly non-linear CTVE with good defined metastable behavior. Such an essentially anharmonic CTVE with respect to charge transfer and lattice displacements was predicted recently in our work [V.S. Vikhnin, Solid State Commun. 127 (2003) 283]. Here, we present experimental evidence of the existence of a new type of exciton state.

  16. Paramecium tetraurelia chromatin assembly factor-1-like protein PtCAF-1 is involved in RNA-mediated control of DNA elimination.

    PubMed

    Ignarski, Michael; Singh, Aditi; Swart, Estienne C; Arambasic, Miroslav; Sandoval, Pamela Y; Nowacki, Mariusz

    2014-10-29

    Genome-wide DNA remodelling in the ciliate Paramecium is ensured by RNA-mediated trans-nuclear crosstalk between the germline and the somatic genomes during sexual development. The rearrangements include elimination of transposable elements, minisatellites and tens of thousands non-coding elements called internally eliminated sequences (IESs). The trans-nuclear genome comparison process employs a distinct class of germline small RNAs (scnRNAs) that are compared against the parental somatic genome to select the germline-specific subset of scnRNAs that subsequently target DNA elimination in the progeny genome. Only a handful of proteins involved in this process have been identified so far and the mechanism of DNA targeting is unknown. Here we describe chromatin assembly factor-1-like protein (PtCAF-1), which we show is required for the survival of sexual progeny and localizes first in the parental and later in the newly developing macronucleus. Gene silencing shows that PtCAF-1 is required for the elimination of transposable elements and a subset of IESs. PTCAF-1 depletion also impairs the selection of germline-specific scnRNAs during development. We identify specific histone modifications appearing during Paramecium development which are strongly reduced in PTCAF-1 depleted cells. Our results demonstrate the importance of PtCAF-1 for the epigenetic trans-nuclear cross-talk mechanism.

  17. Paramecium tetraurelia chromatin assembly factor-1-like protein PtCAF-1 is involved in RNA-mediated control of DNA elimination

    PubMed Central

    Ignarski, Michael; Singh, Aditi; Swart, Estienne C.; Arambasic, Miroslav; Sandoval, Pamela Y.; Nowacki, Mariusz

    2014-01-01

    Genome-wide DNA remodelling in the ciliate Paramecium is ensured by RNA-mediated trans-nuclear crosstalk between the germline and the somatic genomes during sexual development. The rearrangements include elimination of transposable elements, minisatellites and tens of thousands non-coding elements called internally eliminated sequences (IESs). The trans-nuclear genome comparison process employs a distinct class of germline small RNAs (scnRNAs) that are compared against the parental somatic genome to select the germline-specific subset of scnRNAs that subsequently target DNA elimination in the progeny genome. Only a handful of proteins involved in this process have been identified so far and the mechanism of DNA targeting is unknown. Here we describe chromatin assembly factor-1-like protein (PtCAF-1), which we show is required for the survival of sexual progeny and localizes first in the parental and later in the newly developing macronucleus. Gene silencing shows that PtCAF-1 is required for the elimination of transposable elements and a subset of IESs. PTCAF-1 depletion also impairs the selection of germline-specific scnRNAs during development. We identify specific histone modifications appearing during Paramecium development which are strongly reduced in PTCAF-1 depleted cells. Our results demonstrate the importance of PtCAF-1 for the epigenetic trans-nuclear cross-talk mechanism. PMID:25270876

  18. Paramecium tetraurelia chromatin assembly factor-1-like protein PtCAF-1 is involved in RNA-mediated control of DNA elimination.

    PubMed

    Ignarski, Michael; Singh, Aditi; Swart, Estienne C; Arambasic, Miroslav; Sandoval, Pamela Y; Nowacki, Mariusz

    2014-10-29

    Genome-wide DNA remodelling in the ciliate Paramecium is ensured by RNA-mediated trans-nuclear crosstalk between the germline and the somatic genomes during sexual development. The rearrangements include elimination of transposable elements, minisatellites and tens of thousands non-coding elements called internally eliminated sequences (IESs). The trans-nuclear genome comparison process employs a distinct class of germline small RNAs (scnRNAs) that are compared against the parental somatic genome to select the germline-specific subset of scnRNAs that subsequently target DNA elimination in the progeny genome. Only a handful of proteins involved in this process have been identified so far and the mechanism of DNA targeting is unknown. Here we describe chromatin assembly factor-1-like protein (PtCAF-1), which we show is required for the survival of sexual progeny and localizes first in the parental and later in the newly developing macronucleus. Gene silencing shows that PtCAF-1 is required for the elimination of transposable elements and a subset of IESs. PTCAF-1 depletion also impairs the selection of germline-specific scnRNAs during development. We identify specific histone modifications appearing during Paramecium development which are strongly reduced in PTCAF-1 depleted cells. Our results demonstrate the importance of PtCAF-1 for the epigenetic trans-nuclear cross-talk mechanism. PMID:25270876

  19. Plastid translation in organello and in vitro during light-induced development in Euglena.

    PubMed

    Miller, M E; Jurgenson, J E; Reardon, E M; Price, C A

    1983-12-10

    Plastids were isolated from dark-grown Euglena gracilis, from cells exposed to light for 3 h, and from normal, light-grown cells. Plastid protein synthesis was then measured either in organello, by incorporation of [35S]Met into isolated plastids, or in vitro, by programming wheat germ, reticulocyte, or Escherichia coli translation systems with RNA isolated from the plastids. Specific and total rates of protein synthesis in organello increased during light-induced development about 100-fold. In contrast, specific mRNA activity of plastid RNA increased no more than 3-fold, and the estimated total mRNA activity of plastids increased less than 10-fold. Protein synthesis in plastids appears therefore to be subject to strong regulation at a level other than that of transcription superimposed on weak transcriptional regulation. The synthesis of the large subunit of ribulose-bisphosphate carboxylase in particular appears to be under translational control. There is also qualitative evidence for regulation. Most plastid mRNAs, as indicated by translation in vitro, electrophoresis, and fluorography of their translation products, increase with light-induced development as a coordinate set. A second or proplastid set can be detected in RNAs from immature plastids, but not from mature chloroplasts. A few mRNAs appear only later in development, corresponding to a delayed set. Most translation products measured in organello also appear to belong to the coordinate set, a few to the proplastid and delayed sets, and a further few to a transient set, which appears only early in development.

  20. Stimulation of RNA polymerase I and II activities by 17 beta -estradiol receptor on chick liver chromatin.

    PubMed Central

    Dierks-Ventling, C; Bieri-Bonniot, F

    1977-01-01

    The endogenous transcriptional capacity (RNA polymerase I and II activity) of liver chromatin from chicks treated with 17 beta-estradiol for 24 h (E 24) was double that of the controls. E 24 chromatin contained estradiol receptor activity while control chromatin did not. Its presence suggested an implication in the enhanced activities of RNA polymerases of E 24 chromatin. When semi-purified estradiol receptor was added to control chromatin, the endogenous transcriptional capacity of this chromatin was greatly increased. Studies with alpha-amanitin showed that both RNA polymerase I and II were stimulated by the estradiol receptor. This stimulation was observed as long as homology of the system was maintained. Solubilized homologous RNA polymerases were stimulated much less by the hormone complex in the presence of heterologous DNA than with homologous chromatin. Prokaryotic RNA polymerase could not be stimulated by chick liver estradiol receptor in the presence of heterologous DNA. PMID:840645

  1. Using targeted chromatin regulators to engineer combinatorial and spatial transcriptional regulation.

    PubMed

    Keung, Albert J; Bashor, Caleb J; Kiriakov, Szilvia; Collins, James J; Khalil, Ahmad S

    2014-07-01

    The transcription of genomic information in eukaryotes is regulated in large part by chromatin. How a diverse array of chromatin regulator (CR) proteins with different functions and genomic localization patterns coordinates chromatin activity to control transcription remains unclear. Here, we take a synthetic biology approach to decipher the complexity of chromatin regulation by studying emergent transcriptional behaviors from engineered combinatorial, spatial, and temporal patterns of individual CRs. We fuse 223 yeast CRs to programmable zinc finger proteins. Site-specific and combinatorial recruitment of CRs to distinct intralocus locations reveals a range of transcriptional logic and behaviors, including synergistic activation, long-range and spatial regulation, and gene expression memory. Comparing these transcriptional behaviors with annotated CR complex and function terms provides design principles for the engineering of transcriptional regulation. This work presents a bottom-up approach to investigating chromatin-mediated transcriptional regulation and introduces chromatin-based components and systems for synthetic biology and cellular engineering.

  2. Chromatin states modify network motifs contributing to cell-specific functions

    PubMed Central

    Zhao, Hongying; Liu, Tingting; Liu, Ling; Zhang, Guanxiong; Pang, Lin; Yu, Fulong; Fan, Huihui; Ping, Yanyan; Wang, Li; Xu, Chaohan; Xiao, Yun; Li, Xia

    2015-01-01

    Epigenetic modification can affect many important biological processes, such as cell proliferation and apoptosis. It can alter chromatin conformation and contribute to gene regulation. To investigate how chromatin states associated with network motifs, we assembled chromatin state-modified regulatory networks by combining 269 ChIP-seq data and chromatin states in four cell types. We found that many chromatin states were significantly associated with network motifs, especially for feedforward loops (FFLs). These distinct chromatin state compositions contribute to different expression levels and translational control of targets in FFLs. Strikingly, the chromatin state-modified FFLs were highly cell-specific and, to a large extent, determined cell-selective functions, such as the embryonic stem cell-specific bivalent modification-related FFL with an important role in poising developmentally important genes for expression. Besides, comparisons of chromatin state-modified FFLs between cancerous/stem and primary cell lines revealed specific type of chromatin state alterations that may act together with motif structural changes cooperatively contribute to cell-to-cell functional differences. Combination of these alterations could be helpful in prioritizing candidate genes. Together, this work highlights that a dynamic epigenetic dimension can help network motifs to control cell-specific functions. PMID:26169043

  3. Broadly permissive intestinal chromatin underlies lateral inhibition and cell plasticity

    PubMed Central

    Kim, Tae-Hee; Li, Fugen; Ferreiro-Neira, Isabel; Ho, Li-Lun; Luyten, Annouck; Nalapareddy, Kodandaramireddy; Long, Henry; Verzi, Michael; Shivdasani, Ramesh A.

    2014-01-01

    Cells differentiate when transcription factors (TFs) bind accessible cis-regulatory elements to establish specific gene expression programs. In differentiating embryonic stem (ES) cells, chromatin at lineage-restricted genes becomes sequentially accessible1-4, probably by virtue of “pioneer” TF activity5, but tissues may utilize other strategies in vivo. Lateral inhibition is a pervasive process in which one cell forces a different identity on its neighbors6, and it is unclear how chromatin in equipotent progenitors undergoing lateral inhibition quickly enables distinct, transiently reversible cell fates. Here we report the chromatin and transcriptional underpinnings of differentiation in mouse small intestine crypts, where Notch signaling mediates lateral inhibition to assign progenitor cells into absorptive or secretory lineages7-9. Transcript profiles in isolated LGR5+ intestinal stem cells (ISC)10 and secretory and absorptive progenitors indicated that each cell population was distinct and the progenitors specified. Nevertheless, secretory and absorptive progenitors showed comparable levels of H3K4me2 and H3K27ac histone marks and DNaseI hypersensitivity - signifying accessible, permissive chromatin - at most of the same cis-elements. Enhancers acting uniquely in progenitors were well-demarcated in LGR5+ ISC, revealing early priming of chromatin for divergent transcriptional programs, and retained active marks well after lineages were specified. On this chromatin background, ATOH1, a secretory-specific TF, controls lateral inhibition through Delta-like Notch ligand genes and also drives numerous secretory lineage genes. Depletion of ATOH1 from specified secretory cells converted them into functional enterocytes, indicating prolonged responsiveness of marked enhancers to presence or absence of a key TF. Thus, lateral inhibition and intestinal crypt lineage plasticity involve interaction of a lineage-restricted TF with broadly permissive chromatin established

  4. Light-induced excess conductivity and the role of argon in the deposition of doping-modulated amorphous silicon superlattices

    SciTech Connect

    Su, F.; Levine, S.; Vanier, P.E.; Kampas, F.J.

    1985-09-15

    Amorphous silicon pnpn ... structures that exhibit the phenomenon of light-induced excess conductivity (LEC) have been deposited in a single-chamber glow discharge deposition system by simple control of gas flows. This phenomenon is negligible when the doped silane is undiluted but clearly evident when the silane is diluted in argon. Experiments were performed in which argon dilution was only used for specific regions of the structure. The LEC effect was found to occur if argon dilution was used during the deposition of any fraction of the superlattice layers. These experiments rule out mechanisms requiring phosphorus-boron defect complexes or interface states.

  5. Changes in chromatin structure associated with Alzheimer's disease.

    PubMed

    Lewis, P N; Lukiw, W J; De Boni, U; McLachlan, D R

    1981-11-01

    The enzyme micrococcal nuclease was used to examine the accessibility of chromatin extracted from brains of 13 patients with senile and presenile dementia of the Alzheimer type. Compared with chromatin extracted from brains of 8 patients without neurological signs or brain pathology and brains of 7 patients with nonAlzheimer dementia, Alzheimer chromatin was less accessible to this enzyme. Reduced accessibility was reflected by a reduced yield of mononucleosomes in comparison with dinucleosomes and larger oligomers. Both neuronal and glial chromatin were found to be similarly affected. The reduced yield of mononucleosomes from Alzheimer chromatin is not due to their increased breakdown, but is probably related to protein associated with the internucleosomal linker region that retards nuclease action. Dinucleosomes isolated from control and Alzheimer nuclease digests were examined for their protein complement. Three perchloric acid-soluble proteins situated in the histone H1 region of sodium dodecyl sulfate (SDS) gels were present in elevated levels in Alzheimer dinucleosomes. These results represent the first example of altered chromosomal proteins associated with a diseased state of the brain.

  6. Circadian rhythms and memory formation: regulation by chromatin remodeling.

    PubMed

    Sahar, Saurabh; Sassone-Corsi, Paolo

    2012-01-01

    Epigenetic changes, such as DNA methylation or histone modification, can remodel the chromatin and regulate gene expression. Remodeling of chromatin provides an efficient mechanism of transducing signals, such as light or nutrient availability, to regulate gene expression. CLOCK:BMAL1 mediated activation of clock-controlled genes (CCGs) is coupled to circadian changes in histone modification at their promoters. Several chromatin modifiers, such as the deacetylases SIRT1 and HDAC3 or methyltransferase MLL1, have been shown to be recruited to the promoters of the CCGs in a circadian manner. Interestingly, the central element of the core clock machinery, the transcription factor CLOCK, also possesses histone acetyltransferase activity. Rhythmic expression of the CCGs is abolished in the absence of these chromatin modifiers. Recent research has demonstrated that chromatin remodeling is at the cross-roads of circadian rhythms and regulation of metabolism and aging. It would be of interest to identify if similar pathways exist in the epigenetic regulation of memory formation. PMID:22470318

  7. CHROMATIN ASSEMBLY AND TRANSCRIPTIONAL CROSS-TALK IN XENOPUS LAEVIS OOCYTE AND EGG EXTRACTS

    PubMed Central

    Wang, Wei-Lin; Shechter, David

    2016-01-01

    Chromatin, primarily a complex of DNA and histone proteins, is the physiological form of the genome. Chromatin is generally repressive for transcription and other information transactions that occur on DNA. A wealth of post-translational modifications on canonical histones and histone variants encode regulatory information to recruit or repel effector proteins on chromatin, promoting and further repressing transcription and thereby form the basis of epigenetic information. During metazoan oogenesis, large quantities of histone proteins are synthesized and stored in preparation for the rapid early cell cycles of development and to elicit maternal control of chromatin assembly pathways. Oocyte and egg cell-free extracts of the frog Xenopus laevis are a compelling model system for the study of chromatin assembly and transcription precisely because they exist in an extreme state primed for rapid chromatin assembly or for transcriptional activity. We show that chromatin assembly rates are slower in X. laevis oocyte than in egg extracts, while conversely only oocyte extracts transcribe template plasmids. We demonstrate that rapid chromatin assembly in egg extracts represses RNA Polymerase II dependent transcription, while pre-binding of TATA-Binding Protein (TBP) to a template plasmid promotes transcription. Our experimental evidence presented here supports a model in which chromatin assembly and transcription are in competition and that the onset of zygotic genomic activation may be in part due to stable transcriptional complex assembly. PMID:27759158

  8. Rapid changes in protein phosphorylation associated with light-induced gravity perception in corn roots

    NASA Technical Reports Server (NTRS)

    McFadden, J. J.; Poovaiah, B. W.

    1988-01-01

    The effect of light and calcium depletion on in vivo protein phosphorylation was tested using dark-grown roots of Merit corn. Light caused rapid and specific promotion of phosphorylation of three polypeptides. Pretreatment of roots with ethylene glycol bis N,N,N',N' tetraacetic acid and A23187 prevented light-induced changes in protein phosphorylation. We postulate that these changes in protein phosphorylation are involved in the light-induced gravity response.

  9. Organisation of subunits in chromatin.

    PubMed

    Carpenter, B G; Baldwin, J P; Bradbury, E M; Ibel, K

    1976-07-01

    There is considerable current interest in the organisation of nucleosomes in chromatin. A strong X-ray and neutron semi-meridional diffraction peak at approximately 10 nm had previously been attributed to the interparticle specing of a linear array of nucleosomes. This diffraction peak could also result from a close packed helical array of nucleosomes. A direct test of these proposals is whether the 10 nm peak is truly meridional as would be expected for a linear array of nucleosomes or is slightly off the meridian as expected for a helical array. Neutron diffraction studies of H1-depleted chromatin support the latter alternative. The 10 nm peak has maxima which form a cross-pattern with semi-meridional angle of 8 to 9 degrees. This is consistent with a coil of nucleosomes of pitch 10 nm and outer diameter of approximately 30 nm. These dimensions correspond to about six nucleosomes per turn of the coli.

  10. Chromatin Structure in Telomere Dynamics

    PubMed Central

    Galati, Alessandra; Micheli, Emanuela; Cacchione, Stefano

    2013-01-01

    The establishment of a specific nucleoprotein structure, the telomere, is required to ensure the protection of chromosome ends from being recognized as DNA damage sites. Telomere shortening below a critical length triggers a DNA damage response that leads to replicative senescence. In normal human somatic cells, characterized by telomere shortening with each cell division, telomere uncapping is a regulated process associated with cell turnover. Nevertheless, telomere dysfunction has also been associated with genomic instability, cell transformation, and cancer. Despite the essential role telomeres play in chromosome protection and in tumorigenesis, our knowledge of the chromatin structure involved in telomere maintenance is still limited. Here we review the recent findings on chromatin modifications associated with the dynamic changes of telomeres from protected to deprotected state and their role in telomere functions. PMID:23471416

  11. Cohesin's role as an active chromatin domain anchorage revealed.

    PubMed

    Feig, Christine; Odom, Duncan T

    2013-12-11

    Cohesin is a conserved protein complex indispensible for proper cell division, because it secures sister-chromatid cohesion following DNA replication until segregation is required at the onset of anaphase. Recent studies have revealed functions beyond this, showing that cohesin binds to interphase chromatin regulating gene expression at select loci via long-range chromosomal interactions. In this issue of The EMBO Journal, Sofueva et al (2013) use a combination of chromatin conformation capture methods, classical FISH imaging, and loss-of-function studies to elegantly demonstrate how cohesin controls the 3D architectural organization of the genome.

  12. Reversible light induced conductance switching of asymmetric diarylethenes on gold: surface and electronic studies

    NASA Astrophysics Data System (ADS)

    Arramel, Affa; Pijper, Thomas C.; Kudernac, Tibor; Katsonis, Nathalie; van der Maas, Minko; Feringa, Ben L.; van Wees, Bart J.

    2013-09-01

    We report on the light-induced switching of conductance of a new generation of diarylethene switches embedded in an insulating matrix of dodecanethiol on Au(111), by using scanning tunneling microscopy (STM). The diarylethene switches we synthesize and study are modified diarylethenes where the thiophene unit at one side of the molecular backbone introduces an intrinsic asymmetry into the switch, which is expected to influence its photo-conductance properties. We show that reversible conversion between two distinguishable conductance states can be controlled via photoisomerisation of the switches by using alternative irradiation with UV (λ = 313 nm) or visible (λ > 420 nm) light. We addressed this phenomenon by using STM in ambient conditions, based on switching of the apparent height of the molecules which convert from 4-6 Å in their closed form to 0-1 Å in their open form. Furthermore, the levels of the frontier molecular orbital levels (HOMO and LUMO) were evaluated for these asymmetric switches by using Scanning Tunneling Spectroscopy at 77 K, which allowed us to determine a HOMO-LUMO energy gap of 2.24 eV.We report on the light-induced switching of conductance of a new generation of diarylethene switches embedded in an insulating matrix of dodecanethiol on Au(111), by using scanning tunneling microscopy (STM). The diarylethene switches we synthesize and study are modified diarylethenes where the thiophene unit at one side of the molecular backbone introduces an intrinsic asymmetry into the switch, which is expected to influence its photo-conductance properties. We show that reversible conversion between two distinguishable conductance states can be controlled via photoisomerisation of the switches by using alternative irradiation with UV (λ = 313 nm) or visible (λ > 420 nm) light. We addressed this phenomenon by using STM in ambient conditions, based on switching of the apparent height of the molecules which convert from 4-6 Å in their closed form to 0

  13. A positive but complex association between meiotic double-strand break hotspots and open chromatin in Saccharomyces cerevisiae

    PubMed Central

    Berchowitz, Luke E.; Hanlon, Sean E.; Lieb, Jason D.; Copenhaver, Gregory P.

    2009-01-01

    During meiosis, chromatin undergoes extensive changes to facilitate recombination, homolog pairing, and chromosome segregation. To investigate the relationship between chromatin organization and meiotic processes, we used formaldehyde-assisted isolation of regulatory elements (FAIRE) to map open chromatin during the transition from mitosis to meiosis in the budding yeast Saccharomyces cerevisiae. We found that meiosis-induced opening of chromatin is associated with meiotic DSB hotpots. The positive association between open chromatin and DSB hotspots is most prominent 3 h into meiosis, when the early meiotic genes DMC1 and HOP1 exhibit maximum transcription and the early recombination genes SPO11 and RAD51 are strongly up-regulated. While the degree of chromatin openness is positively associated with the occurrence of recombination hotspots, many hotspots occur outside of open chromatin. Of particular interest, many DSB hotspots that fell outside of meiotic open chromatin nonetheless occurred in chromatin that had recently been open during mitotic growth. Finally, we find evidence for meiosis-specific opening of chromatin at the regions adjacent to boundaries of subtelomeric sequences, which exhibit specific crossover control patterns hypothesized to be regulated by chromatin. PMID:19801530

  14. On the mechanochemical machinery underlying chromatin remodeling

    NASA Astrophysics Data System (ADS)

    Yusufaly, Tahir I.

    This dissertation discuss two recent efforts, via a unique combination of structural bioinformatics and density functional theory, to unravel some of the details concerning how molecular machinery within the eukaryotic cell nucleus controls chromatin architecture. The first, a study of the 5-methylation of cytosine in 5'-CG-3' : 5'-CG-3' base-pair steps, reveals that the methyl groups roughen the local elastic energy landscape of the DNA. This enhances the probability of the canonical B-DNA structure transitioning into the undertwisted A-like and overtwisted C-like forms seen in nucleosomes, or looped segments of DNA bound to histones. The second part focuses on the formation of salt bridges between arginine residues in histones and phosphate groups on the DNA backbone. The arginine residues are ob- served to apply a tunable mechanical load to the backbone, enabling precision-controlled activation of DNA deformations.

  15. Effect of saffron on rat sperm chromatin integrity

    PubMed Central

    Mardani, Mohammad; Vaez, Ahmad; Razavi, Shahnaz

    2014-01-01

    Background: Currently, relation between reactive oxygen species (ROS) ROS concentration and semen quality was indicated. Saffron has traditionally been not only considered as a food additive but also as a medicinal herb, which has a good antioxidant properties. Objective: The aim of this study was to evaluate the protection potency of saffron and vitamin E on sperm chromatin integrity. Materials and Methods: Thirty adult male Wistar rats divided equally into saffron (100 mg/kg), vitamin E (100 mg/kg) and control (0.5cc distilled water /day) groups. After 60 days, cauda epididymis dissected and sperm cells were used for analysis of sperm chromatin packaging by chromomycin A3 (CMA3) staining, and sperm chromatin susceptibility to acid denaturation by acridine orange (AO) staining. Results: The mean percentage of CMA3 positive sperm was significantly decreased in saffron and vitamin E groups relative to control group (p<0.001). Moreover, the AO staining results showed that the mean percentage of sperm with DNA damage was significantly decreased in saffron and vitamin E groups as compared with control group (p<0.001). Conclusion: Our results purposed that saffron can protect sperm against DNA damage and chromatin anomalies. PMID:25031579

  16. Rapid at-line pharmaceutical cleaning verification using a novel light induced fluorescence (LIF) sensor.

    PubMed

    Peles, Dana N; Ely, Kevin J; Crowder, Timothy M; Ponstingl, Mike

    2013-01-01

    A novel light emitting diode (LED) array-based light induced fluorescence (LIF) sensor is presented as an analytical methodology for at-line cleaning verification within the pharmaceutical industry. This sensor differs from conventional LIF sensors through the ability to dynamically control both the LED excitation array and detection parameters, enabling the exploitation of the optical power and detection sensitivity to rapidly detect trace concentrations of residual drug. This feature makes this sensor an ideal alternative to conventional cleaning verification analytical methodologies. In this study, the LIF sensor was validated as an analytical technique through the analysis of specificity, precision, linearity, limit of quantitation, and accuracy, with respect to solutions and swab extracts of a single pharmaceutical compound (Compound A). The validated system was then utilized for cleaning process optimization and subsequent routine cleaning process verification following three manufacturing campaigns. The LIF sensor enabled a significant improvement in the analysis time for quantitative detection of Compound A; individual swab and rinsate extracts were analyzed in less than 1 min. The results presented herein effectively demonstrate the ability of the novel LIF sensor to efficiently function as a valid at-line analytical methodology for cleaning verification.

  17. Mesophyll-localized phytochromes gate stress- and light-inducible anthocyanin accumulation in Arabidopsis thaliana

    PubMed Central

    Oh, Sookyung; Warnasooriya, Sankalpi N; Montgomery, Beronda L

    2014-01-01

    Abiotic stress and light induce anthocyanin accumulation in Arabidopsis. Here, we demonstrate that mesophyll-localized phytochromes regulate nitrogen-, phosphate- and cold-induced anthocyanin accumulation in shoots of Arabidopsis. Whereas ecotype-dependent differences result in distinct total levels of anthocyanin accumulation in response to light, cold, or nutrient-deficient treatments, phytochromes generally gate light- and/or stress-induced anthocyanin accumulation in shoots, as plants depleted of mesophyll-localized phytochromes lack or have highly attenuated induction of anthocyanins. Observed interactions between light and stress were found to be wavelength dependent, with red and far-red light stimulating higher total levels of anthocyanin accumulation under cold temperatures, especially in response to nitrogen limitation, whereas blue light did not. The roots of plants depleted of mesophyll-localized phytochromes still respond to nutrient deficiency as determined by elongation of primary roots and root hair elongation when plants are grown under nitrogen- or phosphate-limited conditions. Plants which are constitutively deficient in photoreceptors in both shoots and roots, i.e., phy or cry mutants, exhibit defects in light- and stress-induced anthocyanin accumulation and defects in root development. Taken together, these results suggest that the response to nutrient limitation in roots and shoots is under distinct control by spatial-specific pools of phytochromes in Arabidopsis. PMID:24535251

  18. Diet-mediated alteration of chromatin structure.

    PubMed

    Castro, C E; Armstrong-Major, J; Ramirez, M E

    1986-08-01

    Higher-order chromatin structure and the process of transcription are related. The significance of a nutritional state's altering chromatin structure lies in the potential role of that nutritional state in the regulation of gene expression. In rats short-term feeding of semisynthetic diets varying in the proportion of carbohydrate, protein, or fat alters the configuration of liver chromatin as measured by sensitivity to micrococcal nuclease (EC 3.1.31.1). A carbohydrate-rich, fat-free diet increases the sensitivity of rat liver chromatin to micrococcal nuclease and decreases the nucleosome repeat length. In contrast, a protein-free diet or a diet deficient in magnesium or zinc decreases the sensitivity of liver nuclear chromatin to micrococcal nuclease. Diet-mediated mechanisms that alter chromatin structure are now unknown, but the continued study of nutritional interaction with the genome should identify the responsible features as well as their significance to gene function.

  19. Proteomics of a fuzzy organelle: interphase chromatin

    PubMed Central

    Kustatscher, Georg; Hégarat, Nadia; Wills, Karen L H; Furlan, Cristina; Bukowski-Wills, Jimi-Carlo; Hochegger, Helfrid; Rappsilber, Juri

    2014-01-01

    Chromatin proteins mediate replication, regulate expression, and ensure integrity of the genome. So far, a comprehensive inventory of interphase chromatin has not been determined. This is largely due to its heterogeneous and dynamic composition, which makes conclusive biochemical purification difficult, if not impossible. As a fuzzy organelle, it defies classical organellar proteomics and cannot be described by a single and ultimate list of protein components. Instead, we propose a new approach that provides a quantitative assessment of a protein's probability to function in chromatin. We integrate chromatin composition over a range of different biochemical and biological conditions. This resulted in interphase chromatin probabilities for 7635 human proteins, including 1840 previously uncharacterized proteins. We demonstrate the power of our large-scale data-driven annotation during the analysis of cyclin-dependent kinase (CDK) regulation in chromatin. Quantitative protein ontologies may provide a general alternative to list-based investigations of organelles and complement Gene Ontology. PMID:24534090

  20. Nanoscale histone localization in live cells reveals reduced chromatin mobility in response to DNA damage

    PubMed Central

    Liu, Jing; Vidi, Pierre-Alexandre; Lelièvre, Sophie A.; Irudayaraj, Joseph M. K.

    2015-01-01

    ABSTRACT Nuclear functions including gene expression, DNA replication and genome maintenance intimately rely on dynamic changes in chromatin organization. The movements of chromatin fibers might play important roles in the regulation of these fundamental processes, yet the mechanisms controlling chromatin mobility are poorly understood owing to methodological limitations for the assessment of chromatin movements. Here, we present a facile and quantitative technique that relies on photoactivation of GFP-tagged histones and paired-particle tracking to measure chromatin mobility in live cells. We validate the method by comparing live cells to ATP-depleted cells and show that chromatin movements in mammalian cells are predominantly energy dependent. We also find that chromatin diffusion decreases in response to DNA breaks induced by a genotoxic drug or by the ISceI meganuclease. Timecourse analysis after cell exposure to ionizing radiation indicates that the decrease in chromatin mobility is transient and precedes subsequent increased mobility. Future applications of the method in the DNA repair field and beyond are discussed. PMID:25501817

  1. The condensed chromatin fiber: an allosteric chemo-mechanical machine for signal transduction and genome processing

    NASA Astrophysics Data System (ADS)

    Lesne, Annick; Bécavin, Christophe; Victor, Jean–Marc

    2012-02-01

    Allostery is a key concept of molecular biology which refers to the control of an enzyme activity by an effector molecule binding the enzyme at another site rather than the active site (allos = other in Greek). We revisit here allostery in the context of chromatin and argue that allosteric principles underlie and explain the functional architecture required for spacetime coordination of gene expression at all scales from DNA to the whole chromosome. We further suggest that this functional architecture is provided by the chromatin fiber itself. The structural, mechanical and topological features of the chromatin fiber endow chromosomes with a tunable signal transduction from specific (or nonspecific) effectors to specific (or nonspecific) active sites. Mechanical constraints can travel along the fiber all the better since the fiber is more compact and regular, which speaks in favor of the actual existence of the (so-called 30 nm) chromatin fiber. Chromatin fiber allostery reconciles both the physical and biochemical approaches of chromatin. We illustrate this view with two supporting specific examples. Moreover, from a methodological point of view, we suggest that the notion of chromatin fiber allostery is particularly relevant for systemic approaches. Finally we discuss the evolutionary power of allostery in the context of chromatin and its relation to modularity.

  2. Chromatin insulators: lessons from the fly.

    PubMed

    Gurudatta, B V; Corces, Victor G

    2009-07-01

    Chromatin insulators are DNA-protein complexes with broad functions in nuclear biology. Drosophila has at least five different types of insulators; recent results suggest that these different insulators share some components that may allow them to function through common mechanisms. Data from genome-wide localization studies of insulator proteins indicate a possible functional specialization, with different insulators playing distinct roles in nuclear biology. Cells have developed mechanisms to control insulator activity by recruiting specialized proteins or by covalent modification of core components. Current results suggest that insulators set up cell-specific blueprints of nuclear organization that may contribute to the establishment of different patterns of gene expression during cell differentiation and development.

  3. A model for chromatin structure.

    PubMed Central

    Li, H J

    1975-01-01

    A model for chromatin structure is presented. (a) Each of four histone species, H2A (IIbl or f2a2), H2B (IIb2 or f2b), H3 (III or f3) and H4 (IV or f2al) can form a parallel dimer. (b) These dimers can form two tetramers, (H2A)2(H2b)2 and (H3)2(H4)2. (C) These two tetramers bind a segment of DNA and condense it into a "C" segments. (d) The adjacent segments, termed extended or "E" segments, are bound by histone H1 (I or fl) for the major fraction of chromatin; the other "E" regions can be either bound by non-histone proteins or free of protein binding. (e) The binding of histones causes a structural distortion of the DNA which, depending upon the external conditions, may generate the formation of either an open structure with a heterogeneous and non-uniform supercoil or a compact structure with a string of beads. The model is supported by experimental data on histone-histone interaction, histone-DNA interaction and histone subunit-DNA interaction. PMID:1101222

  4. Light-induced crawling of crystals on a glass surface

    PubMed Central

    Uchida, Emi; Azumi, Reiko; Norikane, Yasuo

    2015-01-01

    Motion is an essential process for many living organisms and for artificial robots and machines. To date, creating self-propelled motion in nano-to-macroscopic-sized objects has been a challenging issue for scientists. Herein, we report the directional and continuous motion of crystals on a glass surface when irradiated simultaneously with two different wavelengths, using simple azobenzenes as a photoresponsive organic compound. The direction of the motion can be controlled by the position of the light sources, and the crystals can even climb vertical surfaces. The motion is driven by crystallization and melting at the front and rear edges of the crystal, respectively, via photochemical conversion between the crystal and liquid phases induced by the trans–cis isomerization of azobenzenes. This finding could lead to remote-controlled micrometre-sized vehicles and valves on solid substrates. PMID:26084483

  5. Light-induced crawling of crystals on a glass surface.

    PubMed

    Uchida, Emi; Azumi, Reiko; Norikane, Yasuo

    2015-01-01

    Motion is an essential process for many living organisms and for artificial robots and machines. To date, creating self-propelled motion in nano-to-macroscopic-sized objects has been a challenging issue for scientists. Herein, we report the directional and continuous motion of crystals on a glass surface when irradiated simultaneously with two different wavelengths, using simple azobenzenes as a photoresponsive organic compound. The direction of the motion can be controlled by the position of the light sources, and the crystals can even climb vertical surfaces. The motion is driven by crystallization and melting at the front and rear edges of the crystal, respectively, via photochemical conversion between the crystal and liquid phases induced by the trans-cis isomerization of azobenzenes. This finding could lead to remote-controlled micrometre-sized vehicles and valves on solid substrates.

  6. Light-induced crawling of crystals on a glass surface.

    PubMed

    Uchida, Emi; Azumi, Reiko; Norikane, Yasuo

    2015-01-01

    Motion is an essential process for many living organisms and for artificial robots and machines. To date, creating self-propelled motion in nano-to-macroscopic-sized objects has been a challenging issue for scientists. Herein, we report the directional and continuous motion of crystals on a glass surface when irradiated simultaneously with two different wavelengths, using simple azobenzenes as a photoresponsive organic compound. The direction of the motion can be controlled by the position of the light sources, and the crystals can even climb vertical surfaces. The motion is driven by crystallization and melting at the front and rear edges of the crystal, respectively, via photochemical conversion between the crystal and liquid phases induced by the trans-cis isomerization of azobenzenes. This finding could lead to remote-controlled micrometre-sized vehicles and valves on solid substrates. PMID:26084483

  7. Light-induced crawling of crystals on a glass surface

    NASA Astrophysics Data System (ADS)

    Uchida, Emi; Azumi, Reiko; Norikane, Yasuo

    2015-06-01

    Motion is an essential process for many living organisms and for artificial robots and machines. To date, creating self-propelled motion in nano-to-macroscopic-sized objects has been a challenging issue for scientists. Herein, we report the directional and continuous motion of crystals on a glass surface when irradiated simultaneously with two different wavelengths, using simple azobenzenes as a photoresponsive organic compound. The direction of the motion can be controlled by the position of the light sources, and the crystals can even climb vertical surfaces. The motion is driven by crystallization and melting at the front and rear edges of the crystal, respectively, via photochemical conversion between the crystal and liquid phases induced by the trans-cis isomerization of azobenzenes. This finding could lead to remote-controlled micrometre-sized vehicles and valves on solid substrates.

  8. Optogenetic control of nuclear protein export

    PubMed Central

    Niopek, Dominik; Wehler, Pierre; Roensch, Julia; Eils, Roland; Di Ventura, Barbara

    2016-01-01

    Active nucleocytoplasmic transport is a key mechanism underlying protein regulation in eukaryotes. While nuclear protein import can be controlled in space and time with a portfolio of optogenetic tools, protein export has not been tackled so far. Here we present a light-inducible nuclear export system (LEXY) based on a single, genetically encoded tag, which enables precise spatiotemporal control over the export of tagged proteins. A constitutively nuclear, chromatin-anchored LEXY variant expands the method towards light inhibition of endogenous protein export by sequestering cellular CRM1 receptors. We showcase the utility of LEXY for cell biology applications by regulating a synthetic repressor as well as human p53 transcriptional activity with light. LEXY is a powerful addition to the optogenetic toolbox, allowing various novel applications in synthetic and cell biology. PMID:26853913

  9. [On the nature of the light-induced component of dark respiration of plants].

    PubMed

    Ivlev, A A; Dubinskiĭ, Iu A

    2011-01-01

    The data on the isotope composition of carbon of CO2 of the light-induced dark respiration component have been analyzed using the oscillation model of photosynthesis. It was concluded that this component originates during the transformation of sucrose accumulated by the plant in the oxygenase phase of photosynthetic oscillations in the light period into organic acids. The transformation occurs in the dark period. It this process, C-3 and C-4 atoms, which determine the "heavy" isotope composition of carbon of CO2 of the light-induced dark respiration component are split off from the hexose link of sucrose. PMID:21950073

  10. CHD5 is required for spermiogenesis and chromatin condensation.

    PubMed

    Zhuang, Tiangang; Hess, Rex A; Kolla, Venkatadri; Higashi, Mayumi; Raabe, Tobias D; Brodeur, Garrett M

    2014-02-01

    Haploid spermatids undergo extensive cellular, molecular and morphological changes to form spermatozoa during spermiogenesis. Abnormalities in these steps can lead to serious male fertility problems, from oligospermia to complete azoospermia. CHD5 is a chromatin-remodeling nuclear protein expressed almost exclusively in the brain and testis. Male Chd5 knockout (KO) mice have deregulated spermatogenesis, characterized by immature sloughing of spermatids, spermiation failure, disorganization of the spermatogenic cycle and abnormal head morphology in elongating spermatids. This results in the inappropriate placement and juxtaposition of germ cell types within the epithelium. Sperm that did enter the epididymis displayed irregular shaped sperm heads, and retained cytoplasmic components. These sperm also stained positively for acidic aniline, indicating improper removal of histones and lack of proper chromatin condensation. Electron microscopy showed that spermatids in the seminiferous tubules of Chd5 KO mice have extensive nuclear deformation, with irregular shaped heads of elongated spermatids, and lack the progression of chromatin condensation in an anterior-to-posterior direction. However, the mRNA expression levels of other important genes controlling spermatogenesis were not affected. Chd5 KO mice also showed decreased H4 hyperacetylation beginning at stage IX, step 9, which is vital for the histone-transition protein replacement in spermiogenesis. Our data indicate that CHD5 is required for normal spermiogenesis, especially for spermatid chromatin condensation.

  11. Chromatin Remodelers: From Function to Dysfunction.

    PubMed

    Längst, Gernot; Manelyte, Laura

    2015-01-01

    Chromatin remodelers are key players in the regulation of chromatin accessibility and nucleosome positioning on the eukaryotic DNA, thereby essential for all DNA dependent biological processes. Thus, it is not surprising that upon of deregulation of those molecular machines healthy cells can turn into cancerous cells. Even though the remodeling enzymes are very abundant and a multitude of different enzymes and chromatin remodeling complexes exist in the cell, the particular remodeling complex with its specific nucleosome positioning features must be at the right place at the right time in order to ensure the proper regulation of the DNA dependent processes. To achieve this, chromatin remodeling complexes harbor protein domains that specifically read chromatin targeting signals, such as histone modifications, DNA sequence/structure, non-coding RNAs, histone variants or DNA bound interacting proteins. Recent studies reveal the interaction between non-coding RNAs and chromatin remodeling complexes showing importance of RNA in remodeling enzyme targeting, scaffolding and regulation. In this review, we summarize current understanding of chromatin remodeling enzyme targeting to chromatin and their role in cancer development. PMID:26075616

  12. Open chromatin reveals the functional maize genome

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Every cellular process mediated through nuclear DNA must contend with chromatin. As results from ENCODE show, open chromatin assays can efficiently integrate across diverse regulatory elements, revealing functional non-coding genome. In this study, we use a MNase hypersensitivity assay to discover o...

  13. Expression-Dependent Folding of Interphase Chromatin

    PubMed Central

    Jerabek, Hansjoerg; Heermann, Dieter W.

    2012-01-01

    Multiple studies suggest that chromatin looping might play a crucial role in organizing eukaryotic genomes. To investigate the interplay between the conformation of interphase chromatin and its transcriptional activity, we include information from gene expression profiles into a polymer model for chromatin that incorporates genomic loops. By relating loop formation to transcriptional activity, we are able to generate chromosome conformations whose structural and topological properties are consistent with experimental data. The model particularly allows to reproduce the conformational variations that are known to occur between highly and lowly expressed chromatin regions. As previously observed in experiments, lowly expressed regions of the simulated polymers are much more compact. Due to the changes in loop formation, the distributions of chromatin loops are also expression-dependent and exhibit a steeper decay in highly active regions. As a results of entropic interaction between differently looped parts of the chromosome, we observe topological alterations leading to a preferential positioning of highly transcribed loci closer to the surface of the chromosome territory. Considering the diffusional behavior of the chromatin fibre, the simulations furthermore show that the higher the expression level of specific parts of the chromatin fibre is, the more dynamic they are. The results exhibit that variations of loop formation along the chromatin fibre, and the entropic changes that come along with it, do not only influence the structural parameters on the local scale, but also effect the global chromosome conformation and topology. PMID:22649534

  14. Molecular-scale dynamics of light-induced spin cross-over in a two-dimensional layer.

    PubMed

    Bairagi, Kaushik; Iasco, Olga; Bellec, Amandine; Kartsev, Alexey; Li, Dongzhe; Lagoute, Jérôme; Chacon, Cyril; Girard, Yann; Rousset, Sylvie; Miserque, Frédéric; Dappe, Yannick J; Smogunov, Alexander; Barreteau, Cyrille; Boillot, Marie-Laure; Mallah, Talal; Repain, Vincent

    2016-01-01

    Spin cross-over molecules show the unique ability to switch between two spin states when submitted to external stimuli such as temperature, light or voltage. If controlled at the molecular scale, such switches would be of great interest for the development of genuine molecular devices in spintronics, sensing and for nanomechanics. Unfortunately, up to now, little is known on the behaviour of spin cross-over molecules organized in two dimensions and their ability to show cooperative transformation. Here we demonstrate that a combination of scanning tunnelling microscopy measurements and ab initio calculations allows discriminating unambiguously between both states by local vibrational spectroscopy. We also show that a single layer of spin cross-over molecules in contact with a metallic surface displays light-induced collective processes between two ordered mixed spin-state phases with two distinct timescale dynamics. These results open a way to molecular scale control of two-dimensional spin cross-over layers. PMID:27425776

  15. Molecular-scale dynamics of light-induced spin cross-over in a two-dimensional layer

    NASA Astrophysics Data System (ADS)

    Bairagi, Kaushik; Iasco, Olga; Bellec, Amandine; Kartsev, Alexey; Li, Dongzhe; Lagoute, Jérôme; Chacon, Cyril; Girard, Yann; Rousset, Sylvie; Miserque, Frédéric; Dappe, Yannick J.; Smogunov, Alexander; Barreteau, Cyrille; Boillot, Marie-Laure; Mallah, Talal; Repain, Vincent

    2016-07-01

    Spin cross-over molecules show the unique ability to switch between two spin states when submitted to external stimuli such as temperature, light or voltage. If controlled at the molecular scale, such switches would be of great interest for the development of genuine molecular devices in spintronics, sensing and for nanomechanics. Unfortunately, up to now, little is known on the behaviour of spin cross-over molecules organized in two dimensions and their ability to show cooperative transformation. Here we demonstrate that a combination of scanning tunnelling microscopy measurements and ab initio calculations allows discriminating unambiguously between both states by local vibrational spectroscopy. We also show that a single layer of spin cross-over molecules in contact with a metallic surface displays light-induced collective processes between two ordered mixed spin-state phases with two distinct timescale dynamics. These results open a way to molecular scale control of two-dimensional spin cross-over layers.

  16. Molecular-scale dynamics of light-induced spin cross-over in a two-dimensional layer

    PubMed Central

    Bairagi, Kaushik; Iasco, Olga; Bellec, Amandine; Kartsev, Alexey; Li, Dongzhe; Lagoute, Jérôme; Chacon, Cyril; Girard, Yann; Rousset, Sylvie; Miserque, Frédéric; Dappe, Yannick J; Smogunov, Alexander; Barreteau, Cyrille; Boillot, Marie-Laure; Mallah, Talal; Repain, Vincent

    2016-01-01

    Spin cross-over molecules show the unique ability to switch between two spin states when submitted to external stimuli such as temperature, light or voltage. If controlled at the molecular scale, such switches would be of great interest for the development of genuine molecular devices in spintronics, sensing and for nanomechanics. Unfortunately, up to now, little is known on the behaviour of spin cross-over molecules organized in two dimensions and their ability to show cooperative transformation. Here we demonstrate that a combination of scanning tunnelling microscopy measurements and ab initio calculations allows discriminating unambiguously between both states by local vibrational spectroscopy. We also show that a single layer of spin cross-over molecules in contact with a metallic surface displays light-induced collective processes between two ordered mixed spin-state phases with two distinct timescale dynamics. These results open a way to molecular scale control of two-dimensional spin cross-over layers. PMID:27425776

  17. Light-Induced Alterations in Striatal Neurochemical Profiles

    NASA Technical Reports Server (NTRS)

    Sroufe, Angela E.; Whittaker, J. A.; Patrickson, J. W.

    1997-01-01

    Much of our present knowledge regarding circadian rhythms and biological activity during space flight has been derived from those missions orbiting the Earth. During space missions, astronauts can become exposed to bright/dark cycles that vary considerably from those that entrain the mammalian biological timing system to the 24-hour cycle found on Earth. As a spacecraft orbits the Earth, the duration of the light/dark period experienced becomes a function of the time it takes to circumnavigate the planet which in turn depends upon the altitude of the craft. Orbiting the Earth at an altitude of 200-800 km provides a light/dark cycle lasting between 80 and 140 minutes, whereas a voyage to the moon or even another planet would provide a light condition of constant light. Currently, little is known regarding the effects of altered light/dark cycles on neurochemical levels within the central nervous system (CNS). Many biochemical, physiological and behavioral phenomena are under circadian control, governed primarily by the hypothalamic suprachiasmatic nucleus. As such, these phenomena are subject to influence by the environmental light/dark cycle. Circadian variations in locomotor and behavioral activities have been correlated to both the environmental light/dark cycle and to dopamine (DA) levels within the CNS. It has been postulated by Martin-Iverson et al. that DA's role in the control of motor activity is subject to modulation by circadian rhythms (CR), environmental lighting and excitatory amino acids (EAAs). In addition, DA and EAA receptor regulated pathways are involved in both the photic entrainment of CR and the control of motor activity. The cellular mechanisms by which DA and EAA-receptor ligands execute these functions, is still unclear. In order to help elucidate these mechanisms, we set out to determine the effects of altered environmental light/dark cycles on CNS neurotransmitter levels. In this study, we focused on the striatum, a region of the brain

  18. Light-induced Adhesion of Spirogyra Cells to Glass.

    PubMed

    Nagata, Y

    1977-04-01

    Adhesion of Spirogyra (tentatively, Spirogyra fluviatilis) cells to glass is described. The cells of an algal filament can adhere to a substrate only when they are located at the end of the filament. Rapid adhesion is induced by blue-violet light (blue adhesion) as well as by temperature shift (about 6 C --> about 22 C) or shaking (dark adhesion). Adherent cells detach in 1 hour in the absence of one of these stimuli. Slow adhesion is induced by red light (red adhesion) 1 hour after irradiation, and may be controlled by phytochrome. A cell once caused to adhere by red light does not release from the glass.Adhesion seems to be maintained by a cementing substance, probably qa mucoprotein. A transparent material which appears around the tip of the cell may be the cementing substance.

  19. Inheritance of epigenetic chromatin silencing

    PubMed Central

    David-Rus, Diana; Mukhopadhyay, Swagatam; Lebowitz, Joel L.; Sengupta, Anirvan M.

    2010-01-01

    Maintenance of alternative chromatin states through cell divisions pose some fundamental constraints on the dynamics of histone modifications. In this paper, we study the systems biology of epigenetic inheritance by defining and analyzing general classes of mathematical models. We discuss how the number of modification states involved plays an essential role in the stability of epigenetic states. In addition, DNA duplication and the consequent dilution of marked histones act as a large perturbation for a stable state of histone modifications. The requirement that this large perturbation falls into the basin of attraction of the original state sometimes leads to additional constraints on effective models. Two such models, inspired by two different biological systems, are compared in their fulfilling the requirements of multistability and of recovery after DNA duplication. We conclude that in the presence of multiple histone modifications that characterize alternative epigenetic stable states, these requirements are more easily fulfilled. PMID:19174167

  20. Computational strategies to address chromatin structure problems

    NASA Astrophysics Data System (ADS)

    Perišić, Ognjen; Schlick, Tamar

    2016-06-01

    While the genetic information is contained in double helical DNA, gene expression is a complex multilevel process that involves various functional units, from nucleosomes to fully formed chromatin fibers accompanied by a host of various chromatin binding enzymes. The chromatin fiber is a polymer composed of histone protein complexes upon which DNA wraps, like yarn upon many spools. The nature of chromatin structure has been an open question since the beginning of modern molecular biology. Many experiments have shown that the chromatin fiber is a highly dynamic entity with pronounced structural diversity that includes properties of idealized zig-zag and solenoid models, as well as other motifs. This diversity can produce a high packing ratio and thus inhibit access to a majority of the wound DNA. Despite much research, chromatin’s dynamic structure has not yet been fully described. Long stretches of chromatin fibers exhibit puzzling dynamic behavior that requires interpretation in the light of gene expression patterns in various tissue and organisms. The properties of chromatin fiber can be investigated with experimental techniques, like in vitro biochemistry, in vivo imagining, and high-throughput chromosome capture technology. Those techniques provide useful insights into the fiber’s structure and dynamics, but they are limited in resolution and scope, especially regarding compact fibers and chromosomes in the cellular milieu. Complementary but specialized modeling techniques are needed to handle large floppy polymers such as the chromatin fiber. In this review, we discuss current approaches in the chromatin structure field with an emphasis on modeling, such as molecular dynamics and coarse-grained computational approaches. Combinations of these computational techniques complement experiments and address many relevant biological problems, as we will illustrate with special focus on epigenetic modulation of chromatin structure.

  1. How the cell cycle impacts chromatin architecture and influences cell fate

    PubMed Central

    Ma, Yiqin; Kanakousaki, Kiriaki; Buttitta, Laura

    2015-01-01

    Since the earliest observations of cells undergoing mitosis, it has been clear that there is an intimate relationship between the cell cycle and nuclear chromatin architecture. The nuclear envelope and chromatin undergo robust assembly and disassembly during the cell cycle, and transcriptional and post-transcriptional regulation of histone biogenesis and chromatin modification is controlled in a cell cycle-dependent manner. Chromatin binding proteins and chromatin modifications in turn influence the expression of critical cell cycle regulators, the accessibility of origins for DNA replication, DNA repair, and cell fate. In this review we aim to provide an integrated discussion of how the cell cycle machinery impacts nuclear architecture and vice-versa. We highlight recent advances in understanding cell cycle-dependent histone biogenesis and histone modification deposition, how cell cycle regulators control histone modifier activities, the contribution of chromatin modifications to origin firing for DNA replication, and newly identified roles for nucleoporins in regulating cell cycle gene expression, gene expression memory and differentiation. We close with a discussion of how cell cycle status may impact chromatin to influence cell fate decisions, under normal contexts of differentiation as well as in instances of cell fate reprogramming. PMID:25691891

  2. Local light-induced magnetization using nanodots and chiral molecules.

    PubMed

    Dor, Oren Ben; Morali, Noam; Yochelis, Shira; Baczewski, Lech Tomasz; Paltiel, Yossi

    2014-11-12

    With the increasing demand for miniaturization, nanostructures are likely to become the primary components of future integrated circuits. Different approaches are being pursued toward achieving efficient electronics, among which are spin electronics devices (spintronics). In principle, the application of spintronics should result in reducing the power consumption of electronic devices. Recently a new, promising, effective approach for spintronics has emerged, using spin selectivity in electron transport through chiral molecules. In this work, using chiral molecules and nanocrystals, we achieve local spin-based magnetization generated optically at ambient temperatures. Through the chiral layer, a spin torque can be transferred without permanent charge transfer from the nanocrystals to a thin ferromagnetic layer, creating local perpendicular magnetization. We used Hall sensor configuration and atomic force microscopy (AFM) to measure the induced local magnetization. At low temperatures, anomalous spin Hall effects were measured using a thin Ni layer. The results may lead to optically controlled spintronics logic devices that will enable low power consumption, high density, and cheap fabrication.

  3. Light-induced color changes of microgel-based etalons.

    PubMed

    Gao, Yongfeng; Serpe, Michael J

    2014-06-11

    Poly(N-isopropylacrylamide) (pNIPAm) microgel-based etalons were used to fabricate systems that change visual color in response to light exposure. These systems were fabricated by adding pH responsive microgel-based etalons to a solution composed of the photoacid o-nitrobenzaldehyde (o-NBA). Upon exposure of this system to ultraviolet (UV) irradiation, the photoacid released a proton, lowering the pH of the solution. Since the pNIPAm microgel-based etalon was responsive to pH, the etalon changed its optical properties and, hence, visual color. We went on to show that patterned etalons could be fabricated, which only contained pH-responsive microgels in specific regions. These etalons only changed color in the pH-responsive regions, to yield patterns that change color upon UV light exposure. Finally, the color of the etalon was shown to be fully reversible and could be switched multiple times. These unique systems could potentially be used for display technologies, and as a controlled/triggered drug delivery system. PMID:24916052

  4. 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

  5. Increased Sensitivity to Light-Induced Melatonin Suppression in Premenstrual Dysphoric Disorder

    PubMed Central

    Parry, Barbara L.; Meliska, Charles J.; Sorenson, Diane L.; Lopez, Ana; Martínez, Luis Fernando; Hauger, Richard L.; Elliott, Jeffrey A.

    2010-01-01

    Increased sensitivity to light-induced melatonin suppression characterizes some, but not all, patients with bipolar illness or seasonal affective disorder. The aim of this study was to test the hypothesis that patients with premenstrual dysphoric disorder (PMDD), categorized as a depressive disorder in DSM-IV, have altered sensitivity to 200 lux light during mid-follicular (MF) and late-luteal (LL) menstrual cycle phases compared with normal control (NC) women. As an extension of a pilot study in which we administered 500 lux to 8 PMDD and 5 NC subjects, in the present study we administered 200 lux to 10 PMDD and 13 NC subjects during MF and LL menstrual cycle phases. We admitted subjects to the General Clinical Research Center (GCRC) in dim light (< 50 lux) to dark (during sleep) conditions at 16:00 h where nurses inserted an intravenous catheter at 17:00 h and collected plasma samples for melatonin at 30-min intervals from 18:00 to 10:00 h, including between 00:00 and 01:00 h for baseline values, between 01:30 and 03:00 h during the 200 lux light exposure administered from 01:00-03:00 h, and at 03:30 and 04:00 h after the light exposure. Median % melatonin suppression was significantly greater in PMDD (30.8%) vs. NC (−0.2%) women (p = 0.040), and was significantly greater in PMDD in the MF (30.8%) than in the LL (−0.15%) phase (p = 0.047). Additionally, in the LL (but not the MF) phase, % suppression after 200 lux light was significantly positively correlated with serum estradiol level (p = 0.007) in PMDD patients, but not in NC subjects (p > .05). PMID:20795885

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

    PubMed

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

    2015-09-01

    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 phyB(Lys996Arg)-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.

  7. Human Genome Replication Proceeds through Four Chromatin States

    PubMed Central

    Julienne, Hanna; Zoufir, Azedine; Audit, Benjamin; Arneodo, Alain

    2013-01-01

    Advances in genomic studies have led to significant progress in understanding the epigenetically controlled interplay between chromatin structure and nuclear functions. Epigenetic modifications were shown to play a key role in transcription regulation and genome activity during development and differentiation or in response to the environment. Paradoxically, the molecular mechanisms that regulate the initiation and the maintenance of the spatio-temporal replication program in higher eukaryotes, and in particular their links to epigenetic modifications, still remain elusive. By integrative analysis of the genome-wide distributions of thirteen epigenetic marks in the human cell line K562, at the 100 kb resolution of corresponding mean replication timing (MRT) data, we identify four major groups of chromatin marks with shared features. These states have different MRT, namely from early to late replicating, replication proceeds though a transcriptionally active euchromatin state (C1), a repressive type of chromatin (C2) associated with polycomb complexes, a silent state (C3) not enriched in any available marks, and a gene poor HP1-associated heterochromatin state (C4). When mapping these chromatin states inside the megabase-sized U-domains (U-shaped MRT profile) covering about 50% of the human genome, we reveal that the associated replication fork polarity gradient corresponds to a directional path across the four chromatin states, from C1 at U-domains borders followed by C2, C3 and C4 at centers. Analysis of the other genome half is consistent with early and late replication loci occurring in separate compartments, the former correspond to gene-rich, high-GC domains of intermingled chromatin states C1 and C2, whereas the latter correspond to gene-poor, low-GC domains of alternating chromatin states C3 and C4 or long C4 domains. This new segmentation sheds a new light on the epigenetic regulation of the spatio-temporal replication program in human and provides a

  8. Dynamic chromatin: the regulatory domain organization of eukaryotic gene loci.

    PubMed

    Bonifer, C; Hecht, A; Saueressig, H; Winter, D M; Sippel, A E

    1991-10-01

    It is hypothesized that nuclear DNA is organized in topologically constrained loop domains defining basic units of higher order chromatin structure. Our studies are performed in order to investigate the functional relevance of this structural subdivision of eukaryotic chromatin for the control of gene expression. We used the chicken lysozyme gene locus as a model to examine the relation between chromatin structure and gene function. Several structural features of the lysozyme locus are known: the extension of the region of general DNAasel sensitivity of the active gene, the location of DNA-sequences with high affinity for the nuclear matrix in vitro, and the position of DNAasel hypersensitive chromatin sites (DHSs). The pattern of DHSs changes depending on the transcriptional status of the gene. Functional studies demonstrated that DHSs mark the position of cis-acting regulatory elements. Additionally, we discovered a novel cis-activity of the border regions of the DNAasel sensitive domain (A-elements). By eliminating the position effect on gene expression usually observed when genes are randomly integrated into the genome after transfection, A-elements possibly serve as punctuation marks for a regulatory chromatin domain. Experiments using transgenic mice confirmed that the complete structurally defined lysozyme gene domain behaves as an independent regulatory unit, expressing the gene in a tissue specific and position independent manner. These expression features were lost in transgenic mice carrying a construct, in which the A-elements as well as an upstream enhancer region were deleted, indicating the lack of a locus activation function on this construct. Experiments are designed in order to uncover possible hierarchical relationships between the different cis-acting regulatory elements for stepwise gene activation during cell differentiation. We are aiming at the definition of the basic structural and functional requirements for position independent and high

  9. Dynamic chromatin: the regulatory domain organization of eukaryotic gene loci.

    PubMed

    Bonifer, C; Hecht, A; Saueressig, H; Winter, D M; Sippel, A E

    1991-10-01

    It is hypothesized that nuclear DNA is organized in topologically constrained loop domains defining basic units of higher order chromatin structure. Our studies are performed in order to investigate the functional relevance of this structural subdivision of eukaryotic chromatin for the control of gene expression. We used the chicken lysozyme gene locus as a model to examine the relation between chromatin structure and gene function. Several structural features of the lysozyme locus are known: the extension of the region of general DNAasel sensitivity of the active gene, the location of DNA-sequences with high affinity for the nuclear matrix in vitro, and the position of DNAasel hypersensitive chromatin sites (DHSs). The pattern of DHSs changes depending on the transcriptional status of the gene. Functional studies demonstrated that DHSs mark the position of cis-acting regulatory elements. Additionally, we discovered a novel cis-activity of the border regions of the DNAasel sensitive domain (A-elements). By eliminating the position effect on gene expression usually observed when genes are randomly integrated into the genome after transfection, A-elements possibly serve as punctuation marks for a regulatory chromatin domain. Experiments using transgenic mice confirmed that the complete structurally defined lysozyme gene domain behaves as an independent regulatory unit, expressing the gene in a tissue specific and position independent manner. These expression features were lost in transgenic mice carrying a construct, in which the A-elements as well as an upstream enhancer region were deleted, indicating the lack of a locus activation function on this construct. Experiments are designed in order to uncover possible hierarchical relationships between the different cis-acting regulatory elements for stepwise gene activation during cell differentiation. We are aiming at the definition of the basic structural and functional requirements for position independent and high

  10. Reply to Comment on Light-induced atomic desorption and diffusion of Rb from porous alumina

    SciTech Connect

    Villalba, S.; Failache, H.; Lezama, A.

    2010-11-15

    We argue that the model used in our paper [Phys. Rev. A 81, 032901 (2010)] for the analysis of the experimental study of light-induced atomic desorption in porous alumina is the simplest consistent approach to a previously unexplored physical system.

  11. Light induced electrical and macroscopic changes in hydrogenated polymorphous silicon solar cells

    NASA Astrophysics Data System (ADS)

    Kim, K. H.; Johnson, E. V.; Abramov, A.; Cabarrocas, P. Roca i.

    2012-07-01

    We report on light-induced electrical and macroscopic changes in hydrogenated polymorphous silicon (pm-Si:H) PIN solar cells. To explain the particular light-soaking behavior of such cells - namely an increase of the open circuit voltage (Voc) and a rapid drop of the short circuit current density (Jsc) - we correlate these effects to changes in hydrogen incorporation and structural properties in the layers of the cells. Numerous techniques such as current-voltage characteristics, infrared spectroscopy, hydrogen exodiffusion, Raman spectroscopy, atomic force microscopy, scanning electron microscopy and spectroscopic ellipsometry are used to study the light-induced changes from microscopic to macroscopic scales (up to tens of microns). Such comprehensive use of complementary techniques lead us to suggest that light-soaking produces the diffusion of molecular hydrogen, hydrogen accumulation at p-layer/substrate interface and localized delamination of the interface. Based on these results we propose that light-induced degradation of PIN solar cells has to be addressed from not only as a material issue, but also a device point of view. In particular we bring experimental evidence that localized delamination at the interface between the p-layer and SnO2 substrate by light-induced hydrogen motion causes the rapid drop of Jsc.

  12. Electronic and structural response of materials to fast intense laser pulses, including light-induced superconductivity

    NASA Astrophysics Data System (ADS)

    Allen, Roland E.

    2016-06-01

    This is a very brief discussion of some experimental and theoretical studies of materials responding to fast intense laser pulses, with emphasis on those cases where the electronic response and structural response are both potentially important (and ordinarily coupled). Examples are nonthermal insulator-to-metal transitions and light-induced superconductivity in cuprates, fullerenes, and an organic Mott insulator.

  13. Structural specifics of light-induced metastable states in copper(II)-nitroxide molecular magnets.

    PubMed

    Barskaya, I Yu; Veber, S L; Fokin, S V; Tretyakov, E V; Bagryanskaya, E G; Ovcharenko, V I; Fedin, M V

    2015-12-28

    Although light-induced magnetostructural switching in copper(II)-nitroxide molecular magnets Cu(hfac)2L(R) has been known for several years, structural characterization of metastable photoinduced states has not yet been accomplished due to significant technical demands. In this work we apply, for the first time, variable-temperature FTIR spectroscopy with photoexcitation to investigate the structural specifics of light-induced states in the Cu(hfac)2L(R) family represented by (i) Cu(hfac)2L(Me) comprising two-spin copper(II)-nitroxide clusters, and (ii) Cu(hfac)2L(Pr) comprising three-spin nitroxide-copper(II)-nitroxide clusters. The light-induced state of Cu(hfac)2L(Me) manifests the same set of vibrational bands as the corresponding thermally-induced state, implying their similar structures. For the second compound Cu(hfac)2L(Pr), the coordination environment of copper(II) is similar in light- and thermally-induced states, but distinct differences are found for packing of the peripheral n-propyl substituent of nitroxide. Thus, generally the structures of the corresponding thermally- and light-induced states in molecular magnets Cu(hfac)2L(R) might differ, and FTIR spectroscopy provides a useful approach for revealing and elucidating such differences.

  14. Light Induced C-C Coupling of 2-Chlorobenzazoles with Carbamates, Alcohols, and Ethers.

    PubMed

    Lipp, Alexander; Lahm, Günther; Opatz, Till

    2016-06-01

    A light induced, transition-metal-free C-C coupling reaction of 2-chlorobenzazoles with aliphatic carbamates, alcohols, and ethers is presented. Inexpensive reagents, namely sodium acetate, benzophenone, water, and acetonitrile, are employed in a simple reaction protocol using a cheap and widely available 25 W energy saving UV-A lamp at ambient temperature. PMID:27128627

  15. The formation of light-induced gratings in the rigid eosine K solution in gelatin

    NASA Astrophysics Data System (ADS)

    Vorob'ev, A. A.; Kolchanova, S. A.; Sizykh, A. G.; Sul'Kis, I. G.

    1992-03-01

    The mechanism of the formation of light-induced amplitude gratings in the rigid eosine K solution in gelatin is investigated. It is shown that spatial modulation of the absorptance of the recording medium is caused by the transformation of the dye into a colorless form in the process of photosensitized proton transfer from gelatin to the eosine.

  16. Polyamines may regulate S-phase progression but not the dynamic changes of chromatin during the cell cycle.

    PubMed

    Laitinen, J; Stenius, K; Eloranta, T O; Hölttä, E

    1998-02-01

    Several studies suggest that polyamines may stabilize chromatin and play a role in its structural alterations. In line with this idea, we found here by chromatin precipitation and micrococcal nuclease (MNase) digestion analyses, that spermidine and spermine stabilize or condense the nucleosomal organization of chromatin in vitro. We then investigated the possible physiological role of polyamines in the nucleosomal organization of chromatin during the cell cycle in Chinese hamster ovary (CHO) cells deficient in ornithine decarboxylase (ODC) activity. An extended polyamine deprivation (for 4 days) was found to arrest 70% of the odc- cells in S phase. MNase digestion analyses revealed that these cells have a highly loosened and destabilized nucleosomal organization. However, no marked difference in the chromatin structure was detected between the control and polyamine-depleted cells following the synchronization of the cells at the S-phase. We also show in synchronized cells that polyamine deprivation retards the traverse of the cells through the S phase already in the first cell cycle. Depletion of polyamines had no significant effect on the nucleosomal organization of chromatin in G1-early S. The polyamine-deprived cells were also capable of condensing the nucleosomal organization of chromatin in the S/G2 phase of the cell cycle. These data indicate that polyamines do not regulate the chromatin condensation state during the cell cycle, although they might have some stabilizing effect on the chromatin structure. Polyamines may, however, play an important role in the control of S-phase progression. PMID:9443076

  17. Surviving an identity crisis: a revised view of chromatin insulators in the genomics era.

    PubMed

    Matzat, Leah H; Lei, Elissa P

    2014-03-01

    The control of complex, developmentally regulated loci and partitioning of the genome into active and silent domains is in part accomplished through the activity of DNA-protein complexes termed chromatin insulators. Together, the multiple, well-studied classes of insulators in Drosophila melanogaster appear to be generally functionally conserved. In this review, we discuss recent genomic-scale experiments and attempt to reconcile these newer findings in the context of previously defined insulator characteristics based on classical genetic analyses and transgenic approaches. Finally, we discuss the emerging understanding of mechanisms of chromatin insulator regulation. This article is part of a Special Issue entitled: Chromatin and epigenetic regulation of animal development.

  18. CYCLIN H;1 Regulates Drought Stress Responses and Blue Light-Induced Stomatal Opening by Inhibiting Reactive Oxygen Species Accumulation in Arabidopsis1[C][W][OA

    PubMed Central

    Zhou, Xiao Feng; Jin, Yin Hua; Yoo, Chan Yul; Lin, Xiao-Li; Kim, Woe-Yeon; Yun, Dae-Jin; Bressan, Ray A.; Hasegawa, Paul M.; Jin, Jing Bo

    2013-01-01

    Arabidopsis (Arabidopsis thaliana) CYCLIN-DEPENDENT KINASE Ds (CDKDs) phosphorylate the C-terminal domain of the largest subunit of RNA polymerase II. Arabidopsis CYCLIN H;1 (CYCH;1) interacts with and activates CDKDs; however, the physiological function of CYCH;1 has not been determined. Here, we report that CYCH;1, which is localized to the nucleus, positively regulates blue light-induced stomatal opening. Reduced-function cych;1 RNA interference (cych;1 RNAi) plants exhibited a drought tolerance phenotype. CYCH;1 is predominantly expressed in guard cells, and its expression was substantially down-regulated by dehydration. Transpiration of intact leaves was reduced in cych;1 RNAi plants compared with the wild-type control in light but not in darkness. CYCH;1 down-regulation impaired blue light-induced stomatal opening but did not affect guard cell development or abscisic acid-mediated stomatal closure. Microarray and real-time polymerase chain reaction analyses indicated that CYCH;1 did not regulate the expression of abscisic acid-responsive genes or light-induced stomatal opening signaling determinants, such as MYB60, MYB61, Hypersensitive to red and blue1, and Protein phosphatase7. CYCH;1 down-regulation induced the expression of redox homeostasis genes, such as LIPOXYGENASE3 (LOX3), LOX4, ARABIDOPSIS GLUTATHIONE PEROXIDASE 7 (ATGPX7), EARLY LIGHT-INDUCIBLE PROTEIN1 (ELIP1), and ELIP2, and increased hydrogen peroxide production in guard cells. Furthermore, loss-of-function mutations in CDKD;2 or CDKD;3 did not affect responsiveness to drought stress, suggesting that CYCH;1 regulates the drought stress response in a CDKD-independent manner. We propose that CYCH;1 regulates blue light-mediated stomatal opening by controlling reactive oxygen species homeostasis. PMID:23656895

  19. Chromatin maintenance by a molecular motor protein

    PubMed Central

    Sung, Myong-Hee; Misteli, Tom

    2011-01-01

    The kinesin motor protein KIF4 performs essential functions in mitosis. Like other mitotic kinesins, loss of KIF4 causes spindle defects, aneuploidy, genomic instability and ultimately tumor formation. However, KIF4 is unique among molecular motors in that it resides in the cell nucleus throughout interphase, suggesting a non-mitotic function as well. Here we identify a novel cellular function for a molecular motor protein by demonstrating that KIF4 acts as a modulator of large-scale chromatin architecture during interphase. KIF4 binds globally to chromatin and its absence leads to chromatin decondensation and loss of heterochromatin domains. KIF4-dependent chromatin decondensation has functional consequences by causing replication defects and global mis-regulation of gene expression programs. KIF4 exerts its function in chromatin architecture via regulation of ADP-ribosylation of core and linker histones and by physical interaction and recruitment of chromatin assembly proteins during S-phase. These observations document a novel function for a molecular motor protein in establishment and maintenance of higher order chromatin structure. PMID:22130187

  20. Targeting of cohesin by transcriptionally silent chromatin.

    PubMed

    Chang, Chuang-Rung; Wu, Ching-Shyi; Hom, Yolanda; Gartenberg, Marc R

    2005-12-15

    Eukaryotic DNA replication produces sister chromatids that are linked together until anaphase by cohesin, a ring-shaped protein complex that is thought to act by embracing both chromatids. Cohesin is enriched at centromeres, as well as discrete sites along chromosome arms where transcription positions the complex between convergent gene pairs. A relationship between cohesin and Sir-mediated transcriptional silencing has also begun to emerge. Here we used fluorescence microscopy and site-specific recombination to characterize interactions between newly replicated copies of the silent HMR mating-type locus. HMR was tagged with lac-GFP and flanked by binding sites for an inducible site-specific recombinase. Excision of the locus in cells with sister chromatids produced two chromatin circles that remained associated with one another. Pairing of the circles required silent chromatin, cohesin, and the RSC chromatin-remodeling complex. Chromatin immunoprecipitation showed that targeting of cohesin to the locus is Sir-dependent, and functional tests showed that silent chromatin acts in a continuous fashion to maintain cohesion. Remarkably, loss of silencing led to loss of cohesin from linear chromosomal templates but not from excised chromatin circles. The results are consistent with a model in which cohesin binds silent chromatin via topological linkage to individual chromatids. PMID:16319193

  1. Chromatin remodelling initiation during human spermiogenesis

    PubMed Central

    De Vries, Marieke; Ramos, Liliana; Housein, Zjwan; De Boer, Peter

    2012-01-01

    Summary During the last phase of spermatogenesis, spermiogenesis, haploid round spermatids metamorphose towards spermatozoa. Extensive cytoplasmic reduction and chromatin remodelling together allow a dramatic decrease of cellular, notably nuclear volume. DNA packing by a nucleosome based chromatin structure is largely replaced by a protamine based one. At the cytoplasmic level among others the acrosome and perinuclear theca (PNT) are formed. In this study we describe the onset of chromatin remodelling to occur concomitantly with acrosome and PNT development. In spread human round spermatid nuclei, we show development of a DAPI-intense doughnut-like structure co-localizing with the acrosomal sac and sub acrosomal PNT. At this structure we observe the first gradual decrease of nucleosomes and several histones. Histone post-translational modifications linked to chromatin remodelling such as H4K8ac and H4K16ac also delineate the doughnut, that is furthermore marked by H3K9me2. During the capping phase of acrosome development, the size of the doughnut-like chromatin domain increases, and this area often is marked by uniform nucleosome loss and the first appearance of transition protein 2 and protamine 1. In the acrosome phase at nuclear elongation, chromatin remodelling follows the downward movement of the marginal ring of the acrosome. Our results indicate that acrosome development and chromatin remodelling are interacting processes. In the discussion we relate chromatin remodelling to the available data on the nuclear envelope and the linker of nucleoskeleton and cytoskeleton (LINC) complex of spermatids, suggesting a signalling route for triggering chromatin remodelling. PMID:23213436

  2. The light induced changes in a-Si:H materials and solar cells -- Where we are now

    SciTech Connect

    Wronski, C.R.

    1997-07-01

    The quest for understanding and especially controlling the reversible light induced changes in a-Si:H based materials has been ongoing for the last twenty years. This has been accompanied by a corresponding large effort in minimizing their effects on more efficient a-Si:H based solar cells. Despite the complexities in both the phenomena as well as the solar cells, progress has been made in both the scientific and technological arenas. This paper briefly reviews primarily studies on the characterization and reduction of the metastable changes in materials and the correlation of these changes with those in efficient solar cells. It will discuss the impact of studies on materials as well as the continuous advances made with engineering of solar cell structures on their improved stabilized performance.

  3. Characterization of chick liver chromatin and analysis of its in vitro transcription products

    PubMed Central

    Dierks-Ventling, Christa; Stalder, Jürg; Gautschi, Johannes

    1978-01-01

    Carefully controlled preparation of chromatin from purified chick liver nuclei yielded over 50% native chromatin as shown by the analysis of the nucleosome pattern after micrococcal nuclease digestion. The size of DNA in this chromatin as analyzed on alkaline sucrose gradients varied from 10S to 19S, the majority being 14S. All endogenous RNA polymerases were represented in the chromatin preparation although to different extents: RNA polymerase I was the most and RNA polymerase II the least abundant. Initiation studies showed that endogenous RNA polymerase II was capable of initiating RNA chains during 5 min. Saturation of chromatin with purified homologous RNA polymerase II increased initiation to 10 min. The addition of heparin caused the RNA transcribed to be larger in size and of increased yield. Chromatin transcription with added purified RNA polymerase II in the presence of heparin produced RNA as large as 32S. A chromatin preparation of this kind would therefore be suitable to transcribe any eukaryotic gene invitro provided additional homologous RNA polymerase II is used. Images PMID:566911

  4. Chromatin Fiber Dynamics under Tension and Torsion

    PubMed Central

    Lavelle, Christophe; Victor, Jean-Marc; Zlatanova, Jordanka

    2010-01-01

    Genetic and epigenetic information in eukaryotic cells is carried on chromosomes, basically consisting of large compact supercoiled chromatin fibers. Micromanipulations have recently led to great advances in the knowledge of the complex mechanisms underlying the regulation of DNA transaction events by nucleosome and chromatin structural changes. Indeed, magnetic and optical tweezers have allowed opportunities to handle single nucleosomal particles or nucleosomal arrays and measure their response to forces and torques, mimicking the molecular constraints imposed in vivo by various molecular motors acting on the DNA. These challenging technical approaches provide us with deeper understanding of the way chromatin dynamically packages our genome and participates in the regulation of cellular metabolism. PMID:20480035

  5. Unraveling chromatin structure using magnetic tweezers

    NASA Astrophysics Data System (ADS)

    van Noort, John

    2010-03-01

    The compact, yet dynamic organization of chromatin plays an essential role in regulating gene expression. Although the static structure of chromatin fibers has been studied extensively, the controversy about the higher order folding remains. The compaction of eukaryotic DNA into chromatin has been implicated in the regulation of all DNA processes. To understand the relation between gene regulation and chromatin structure it is essential to uncover the mechanisms by which chromatin fibers fold and unfold. We used magnetic tweezers to probe the mechanical properties of individual nucleosomes and chromatin fibers consisting of a single, well-defined array of 25 nucleosomes. From these studies five major features appeared upon forced extension of chromatin fibers: the elastic stretching of chromatin's higher order structure, the breaking of internucleosomal contacts, unwrapping of the first turn of DNA, unwrapping of the second turn of DNA, and the dissociation of histone octamers. These events occur sequentially at the increasing force. Neighboring nucleosomes stabilize DNA folding into a nucleosome relative to isolated nucleosomes. When an array of nucleosomes is folded into a 30 nm fiber, representing the first level of chromatin condensation, the fiber stretched like a Hookian spring at forces up to 4 pN. Together with a nucleosome-nucleosome stacking energy of 14 kT this points to a solenoid as the underlying topology of the 30 nm fiber. Surprisingly, linker histones do not affect the length or stiffness of the fibers, but stabilize fiber folding up to forces of 7 pN. The stiffness of the folded chromatin fiber points at histone tails that mediate nucleosome stacking. Fibers with a nucleosome repeat length of 167 bp instead of 197 bp are significantly stiffer, consistent with a two-start helical arrangement. The extensive thermal breathing of the chromatin fiber that is a consequence of the observed high compliance provides a structural basis for understanding the

  6. Regulation of oncogene-induced cell cycle exit and senescence by chromatin modifiers

    PubMed Central

    David, Gregory

    2012-01-01

    Oncogene activation leads to dramatic changes in numerous biological pathways controlling cellular division, and results in the initiation of a transcriptional program that promotes transformation. Conversely, it also triggers an irreversible cell cycle exit called cellular senescence, which allows the organism to counteract the potentially detrimental uncontrolled proliferation of damaged cells. Therefore, a tight transcriptional control is required at the onset of oncogenic signal, coordinating both positive and negative regulation of gene expression. Not surprisingly, numerous chromatin modifiers contribute to the cellular response to oncogenic stress. While these chromatin modifiers were initially thought of as mere mediators of the cellular response to oncogenic stress, recent studies have uncovered a direct and specific regulation of chromatin modifiers by oncogenic signals. We review here the diverse functions of chromatin modifiers in the cellular response to oncogenic stress, and discuss the implications of these findings on the regulation of cell cycle progression and proliferation by activated oncogenes. PMID:22825329

  7. Diabetic retinopathy alters light-induced clock gene expression and dopamine levels in the mouse retina

    PubMed Central

    Lahouaoui, Hasna; Coutanson, Christine; Cooper, Howard M.; Bennis, Mohamed

    2016-01-01

    Purpose Diabetic retinopathy is one of the most common consequences of diabetes that affects millions of working-age adults worldwide and leads to progressive degeneration of the retina, visual loss, and blindness. Diabetes is associated with circadian disruption of the central and peripheral circadian clocks, but the mechanisms responsible for such alterations are unknown. Using a streptozotocin (STZ)-induced model of diabetes, we investigated whether diabetes alters 1) the circadian regulation of clock genes in the retina and in the central clocks, 2) the light response of clock genes in the retina, and/or 3) light-driven retinal dopamine (DA), a major output marker of the retinal clock. Methods To quantify circadian expression of clock and clock-controlled genes, retinas and suprachiasmatic nucleus (SCN) from the same animals were collected every 4 h in circadian conditions, 12 weeks post-diabetes. Induction of Per1, Per2, and c-fos mRNAs was quantified in the retina after the administration of a pulse of monochromatic light (480 nm, 1.17×1014 photons/cm2/s, 15 min) at circadian time 16. Gene expression was assessed with real-time reverse transcription PCR (RT–PCR). Pooled retinas from the control and STZ-diabetic mice were collected 2 h after light ON and light OFF (Zeitgeber time (ZT)2 and ZT14), and DA and its metabolite were analyzed with high-performance liquid chromatography (HPLC). Results We found variable effects of diabetes on the expression of clock genes in the retina and only slight differences in phase and/or amplitude in the SCN. c-fos and Per1 induction by a 480 nm light pulse was abolished in diabetic animals at 12 weeks post-induction of diabetes in comparison with the control mice, suggesting a deficit in light-induced neuronal activation of the retinal clock. Finally, we quantified a 56% reduction in the total number of tyrosine hydroxylase (TH) immunopositive cells, associated with a decrease in DA levels during the subjective day (ZT2

  8. Chromatin Domains: The Unit of Chromosome Organization.

    PubMed

    Dixon, Jesse R; Gorkin, David U; Ren, Bing

    2016-06-01

    How eukaryotic chromosomes fold inside the nucleus is an age-old question that remains unanswered today. Early biochemical and microscopic studies revealed the existence of chromatin domains and loops as a pervasive feature of interphase chromosomes, but the biological implications of such organizational features were obscure. Genome-wide analysis of pair-wise chromatin interactions using chromatin conformation capture (3C)-based techniques has shed new light on the organization of chromosomes in interphase nuclei. Particularly, the finding of cell-type invariant, evolutionarily conserved topologically associating domains (TADs) in a broad spectrum of cell types has provided a new molecular framework for the study of animal development and human diseases. Here, we review recent progress in characterization of such chromatin domains and delineation of mechanisms of their formation in animal cells. PMID:27259200

  9. Predictive Computational Modeling of Chromatin Folding

    NASA Astrophysics Data System (ADS)

    di Pierro, Miichele; Zhang, Bin; Wolynes, Peter J.; Onuchic, Jose N.

    In vivo, the human genome folds into well-determined and conserved three-dimensional structures. The mechanism driving the folding process remains unknown. We report a theoretical model (MiChroM) for chromatin derived by using the maximum entropy principle. The proposed model allows Molecular Dynamics simulations of the genome using as input the classification of loci into chromatin types and the presence of binding sites of loop forming protein CTCF. The model was trained to reproduce the Hi-C map of chromosome 10 of human lymphoblastoid cells. With no additional tuning the model was able to predict accurately the Hi-C maps of chromosomes 1-22 for the same cell line. Simulations show unknotted chromosomes, phase separation of chromatin types and a preference of chromatin of type A to sit at the periphery of the chromosomes.

  10. HIRA orchestrates a dynamic chromatin landscape in senescence and is required for suppression of neoplasia

    PubMed Central

    Cole, John J.; Nelson, David M.; Dikovskaya, Dina; Faller, William J.; Vizioli, Maria Grazia; Hewitt, Rachael N.; Anannya, Orchi; McBryan, Tony; Manoharan, Indrani; van Tuyn, John; Morrice, Nicholas; Pchelintsev, Nikolay A.; Ivanov, Andre; Brock, Claire; Drotar, Mark E.; Nixon, Colin; Clark, William; Sansom, Owen J.; Anderson, Kurt I.; King, Ayala; Blyth, Karen

    2014-01-01

    Cellular senescence is a stable proliferation arrest that suppresses tumorigenesis. Cellular senescence and associated tumor suppression depend on control of chromatin. Histone chaperone HIRA deposits variant histone H3.3 and histone H4 into chromatin in a DNA replication-independent manner. Appropriately for a DNA replication-independent chaperone, HIRA is involved in control of chromatin in nonproliferating senescent cells, although its role is poorly defined. Here, we show that nonproliferating senescent cells express and incorporate histone H3.3 and other canonical core histones into a dynamic chromatin landscape. Expression of canonical histones is linked to alternative mRNA splicing to eliminate signals that confer mRNA instability in nonproliferating cells. Deposition of newly synthesized histones H3.3 and H4 into chromatin of senescent cells depends on HIRA. HIRA and newly deposited H3.3 colocalize at promoters of expressed genes, partially redistributing between proliferating and senescent cells to parallel changes in expression. In senescent cells, but not proliferating cells, promoters of active genes are exceptionally enriched in H4K16ac, and HIRA is required for retention of H4K16ac. HIRA is also required for retention of H4K16ac in vivo and suppression of oncogene-induced neoplasia. These results show that HIRA controls a specialized, dynamic H4K16ac-decorated chromatin landscape in senescent cells and enforces tumor suppression. PMID:25512559

  11. Probabilistic modelling of chromatin code landscape reveals functional diversity of enhancer-like chromatin states

    PubMed Central

    Zhou, Jian; Troyanskaya, Olga G.

    2016-01-01

    Interpreting the functional state of chromatin from the combinatorial binding patterns of chromatin factors, that is, the chromatin codes, is crucial for decoding the epigenetic state of the cell. Here we present a systematic map of Drosophila chromatin states derived from data-driven probabilistic modelling of dependencies between chromatin factors. Our model not only recapitulates enhancer-like chromatin states as indicated by widely used enhancer marks but also divides these states into three functionally distinct groups, of which only one specific group possesses active enhancer activity. Moreover, we discover a strong association between one specific enhancer state and RNA Polymerase II pausing, linking transcription regulatory potential and chromatin organization. We also observe that with the exception of long-intron genes, chromatin state transition positions in transcriptionally active genes align with an absolute distance to their corresponding transcription start site, regardless of gene length. Using our method, we provide a resource that helps elucidate the functional and spatial organization of the chromatin code landscape. PMID:26841971

  12. Chromatin Dynamics During DNA Replication and Uncharacterized Replication Factors determined by Nascent Chromatin Capture (NCC) Proteomics

    PubMed Central

    Alabert, Constance; Bukowski-Wills, Jimi-Carlo; Lee, Sung-Bau; Kustatscher, Georg; Nakamura, Kyosuke; de Lima Alves, Flavia; Menard, Patrice; Mejlvang, Jakob; Rappsilber, Juri; Groth, Anja

    2014-01-01

    SUMMARY To maintain genome function and stability, DNA sequence and its organization into chromatin must be duplicated during cell division. Understanding how entire chromosomes are copied remains a major challenge. Here, we use Nascent Chromatin Capture (NCC) to profile chromatin proteome dynamics during replication in human cells. NCC relies on biotin-dUTP labelling of replicating DNA, affinity-purification and quantitative proteomics. Comparing nascent chromatin with mature post-replicative chromatin, we provide association dynamics for 3995 proteins. The replication machinery and 485 chromatin factors like CAF-1, DNMT1, SUV39h1 are enriched in nascent chromatin, whereas 170 factors including histone H1, DNMT3, MBD1-3 and PRC1 show delayed association. This correlates with H4K5K12diAc removal and H3K9me1 accumulation, while H3K27me3 and H3K9me3 remain unchanged. Finally, we combine NCC enrichment with experimentally derived chromatin probabilities to predict a function in nascent chromatin for 93 uncharacterized proteins and identify FAM111A as a replication factor required for PCNA loading. Together, this provides an extensive resource to understand genome and epigenome maintenance. PMID:24561620

  13. Light induced dielectric constant of Alumina doped lead silicate glass based on silica sands

    NASA Astrophysics Data System (ADS)

    Diantoro, Markus; Natalia, Desi Ayu; Mufti, Nandang; Hidayat, Arif

    2016-04-01

    Numerous studies on glass ceramic compounds have been conducted intensively. Two major problems to be solved are to simplify the fabrication process by reducing melting temperature as well as improving various properties for various fields of technological application. To control the dielectric constant, the researchers generally use a specific dopant. So far there is no comprehensive study to control the dielectric constant driven by both of dopant and light intensity. In this study it is used Al2O3 dopant to increase the light induced dielectric constant of the glass. The source of silica was taken from local silica sands of Bancar Tuban. The sands were firstly leached using hydrochloric acid to improve the purity of silica which was investigated by means of XRF. Fabricating the glass samples were performed by using melting-glass method. Silica powder was mixed with various ratio of SiO2:Na2CO3:PbO:Al2O3. Subsequently, a mixture of various Al2O3 doped lead silicate glasses were melted at 970°C and directy continued by annealed at 300°C. The samples were investigated by XRD, FTIR, SEM-EDX and measuring dielectric constant was done using dc-capacitance meter with various light intensities. The investigation result of XRD patterns showed that the crystal structures of the samples are amorphous state. The introduction of Al2O3 does not alter the crystal structure, but significantly change the structure of the functional glass bonding PbO-SiO2 which was shown by the FTIR spectra. It was noted that some new peak peaks were exist in the doped samples. Measuring result of dielectricity shows that the dielectric constant of glass increases with the addition of Al2O3. Increasing the light intensity gives rise to increase their dielectric constant in general. A detail observation of the dielectric seen that there are discontinuous step-like of dielectric. Most likely a specific quantization mechanism occurs when glass exposed under light.

  14. A chromatin insulator determines the nuclear localization of DNA.

    PubMed

    Gerasimova, T I; Byrd, K; Corces, V G

    2000-11-01

    Chromatin insulators might regulate gene expression by controlling the subnuclear organization of DNA. We found that a DNA sequence normally located inside of the nucleus moved to the periphery when the gypsy insulator was placed within the sequence. The presence of the gypsy insulator also caused two sequences, normally found in different regions of the nucleus, to come together at a single location. Alterations in this subnuclear organization imposed by the gypsy insulator correlated with changes in gene expression that took place during the heat-shock response. These global changes in transcription were accompanied by dramatic alterations in the distribution of insulator proteins and DNA. The results suggest that the nuclear organization imposed by the gypsy insulator on the chromatin fiber is important for gene expression. PMID:11106742

  15. JOINING THE DOTS: FROM CHROMATIN REMODELING TO NEURONAL PLASTICITY

    PubMed Central

    Zocchi, Loredana; Sassone-Corsi, Paolo

    2010-01-01

    SUMMARY In recent years spectacular advances in the field of epigenetics have taken place. Multiple lines of evidence that connect epigenetic regulation to brain functions have been accumulating. Neurons daily convert a variety of external stimuli into rapid or long-lasting changes in gene expression. Control is achieved through several post-translational modifications that occur both on DNA and chromatin. Specific modifications mediate many developmental processes and adult brain functions, such as synaptic plasticity and memory. In this review, we focus on critical chromatin remodeling events that mediate long-lasting neuronal responses. The challenging goal is to reach sufficient understanding of these epigenetic pathways in the brain so that they may be useful for future development of specific pharmacological strategies. PMID:20471240

  16. Synaptic, transcriptional, and chromatin genes disrupted in autism

    PubMed Central

    De Rubeis, Silvia; He, Xin; Goldberg, Arthur P.; Poultney, Christopher S.; Samocha, Kaitlin; Cicek, A Ercument; Kou, Yan; Liu, Li; Fromer, Menachem; Walker, Susan; Singh, Tarjinder; Klei, Lambertus; Kosmicki, Jack; Fu, Shih-Chen; Aleksic, Branko; Biscaldi, Monica; Bolton, Patrick F.; Brownfeld, Jessica M.; Cai, Jinlu; Campbell, Nicholas J.; Carracedo, Angel; Chahrour, Maria H.; Chiocchetti, Andreas G.; Coon, Hilary; Crawford, Emily L.; Crooks, Lucy; Curran, Sarah R.; Dawson, Geraldine; Duketis, Eftichia; Fernandez, Bridget A.; Gallagher, Louise; Geller, Evan; Guter, Stephen J.; Hill, R. Sean; Ionita-Laza, Iuliana; Gonzalez, Patricia Jimenez; Kilpinen, Helena; Klauck, Sabine M.; Kolevzon, Alexander; Lee, Irene; Lei, Jing; Lehtimäki, Terho; Lin, Chiao-Feng; Ma'ayan, Avi; Marshall, Christian R.; McInnes, Alison L.; Neale, Benjamin; Owen, Michael J.; Ozaki, Norio; Parellada, Mara; Parr, Jeremy R.; Purcell, Shaun; Puura, Kaija; Rajagopalan, Deepthi; Rehnström, Karola; Reichenberg, Abraham; Sabo, Aniko; Sachse, Michael; Sanders, Stephan J.; Schafer, Chad; Schulte-Rüther, Martin; Skuse, David; Stevens, Christine; Szatmari, Peter; Tammimies, Kristiina; Valladares, Otto; Voran, Annette; Wang, Li-San; Weiss, Lauren A.; Willsey, A. Jeremy; Yu, Timothy W.; Yuen, Ryan K.C.; Cook, Edwin H.; Freitag, Christine M.; Gill, Michael; Hultman, Christina M.; Lehner, Thomas; Palotie, Aarno; Schellenberg, Gerard D.; Sklar, Pamela; State, Matthew W.; Sutcliffe, James S.; Walsh, Christopher A.; Scherer, Stephen W.; Zwick, Michael E.; Barrett, Jeffrey C.; Cutler, David J.; Roeder, Kathryn; Devlin, Bernie; Daly, Mark J.; Buxbaum, Joseph D.

    2014-01-01

    Summary The genetic architecture of autism spectrum disorder involves the interplay of common and rare variation and their impact on hundreds of genes. Using exome sequencing, analysis of rare coding variation in 3,871 autism cases and 9,937 ancestry-matched or parental controls implicates 22 autosomal genes at a false discovery rate (FDR) < 0.05, and a set of 107 autosomal genes strongly enriched for those likely to affect risk (FDR < 0.30). These 107 genes, which show unusual evolutionary constraint against mutations, incur de novo loss-of-function mutations in over 5% of autistic subjects. Many of the genes implicated encode proteins for synaptic, transcriptional, and chromatin remodeling pathways. These include voltage-gated ion channels regulating propagation of action potentials, pacemaking, and excitability-transcription coupling, as well as histone-modifying enzymes and chromatin remodelers, prominently histone post-translational modifications involving lysine methylation/demethylation. PMID:25363760

  17. Chromatin remodelers: We are the drivers!!

    PubMed

    Tyagi, Monica; Imam, Nasir; Verma, Kirtika; Patel, Ashok K

    2016-07-01

    Chromatin is a highly dynamic structure that imparts structural organization to the genome and regulates the gene expression underneath. The decade long research in deciphering the significance of epigenetics in maintaining cellular integrity has embarked the focus on chromatin remodeling enzymes. These drivers have been categorized as readers, writers and erasers with each having significance of their own. Largely, on the basis of structure, ATP dependent chromatin remodelers have been grouped into 4 families; SWI/SNF, ISWI, IN080 and CHD. It is still unclear to what degree these enzymes are swayed by local DNA sequences when shifting a nucleosome to different positions. The ability of regulating active and repressive transcriptional state via open and close chromatin architecture has been well studied however, the significance of chromatin remodelers in regulating transcription at each step i.e. initiation, elongation and termination require further attention. The authors have highlighted the significance and role of different chromatin remodelers in transcription, DNA repair and histone variant deposition. PMID:27429206

  18. Links between genome replication and chromatin landscapes.

    PubMed

    Sequeira-Mendes, Joana; Gutierrez, Crisanto

    2015-07-01

    Post-embryonic organogenesis in plants requires the continuous production of cells in the organ primordia, their expansion and a coordinated exit to differentiation. Genome replication is one of the most important processes that occur during the cell cycle, as the maintenance of genomic integrity is of primary relevance for development. As it is chromatin that must be duplicated, a strict coordination occurs between DNA replication, the deposition of new histones, and the introduction of histone modifications and variants. In turn, the chromatin landscape affects several stages during genome replication. Thus, chromatin accessibility is crucial for the initial stages and to specify the location of DNA replication origins with different chromatin signatures. The chromatin landscape also determines the timing of activation during the S phase. Genome replication must occur fully, but only once during each cell cycle. The re-replication avoidance mechanisms rely primarily on restricting the availability of certain replication factors; however, the presence of specific histone modifications are also revealed as contributing to the mechanisms that avoid re-replication, in particular for heterochromatin replication. We provide here an update of genome replication mostly focused on data from Arabidopsis, and the advances that genomic approaches are likely to provide in the coming years. The data available, both in plants and animals, point to the relevance of the chromatin landscape in genome replication, and require a critical evaluation of the existing views about the nature of replication origins, the mechanisms of origin specification and the relevance of epigenetic modifications for genome replication.

  19. Chromatin structure in scrapie and Alzheimer's disease.

    PubMed

    McLachlan, D R; Lukiw, W J; Cho, H J; Carp, R I; Wisniewski, H

    1986-11-01

    Scrapie affected brains exhibit a number of pathological features in common with the human neurodegenerative condition, Alzheimer's disease. The present report describes studies on chromatin structure seen in these two disease processes. Chromatin associated proteins influence transcriptional activity of DNA through an effect upon chromatin structure. We examined chromatin structure by: measuring the capacity of the enzyme micrococcal nuclease to release mono- and dinucleosomes from isolated nuclei and measuring DNA-histone interactions by examining the effect of ambient tonicity upon the release of chromatin proteins. In two strains of mice infected with two strains of scrapie agent there was reduced accessibility to micrococcal nuclease and an increased content on dinucleosomes of the histone H1 and H1(0) types. These changes precede clinical signs of scrapie and resemble those found in the human conditions of Alzheimer's and Pick's disease. Scrapie mouse brain differs from Alzheimer brain in that scrapie does not alter histone-DNA interactions as monitored by ionically induced histone release from chromatin. Despite similarities, the scrapie agent appears to operate upon different molecular mechanisms than those found in Alzheimer's disease.

  20. Chromatin insulation by a transcriptional activator

    PubMed Central

    Sutter, Nathan B.; Scalzo, David; Fiering, Steven; Groudine, Mark; Martin, David I. K.

    2003-01-01

    In eukaryotic genomes, transcriptionally active regions are interspersed with silent chromatin that may repress genes in its vicinity. Chromatin insulators are elements that can shield a locus from repressive effects of flanking chromatin. Few such elements have been characterized in higher eukaryotes, but transcriptional activating elements are an invariant feature of active loci and have been shown to suppress transgene silencing. Hence, we have assessed the ability of a transcriptional activator to cause chromatin insulation, i.e., to relieve position effects at transgene integration sites in cultured cells. The transgene contained a series of binding sites for the metal-inducible transcriptional activator MTF, linked to a GFP reporter. Clones carrying single integrated transgenes were derived without selection for expression, and in most clones the transgene was silent. Induction of MTF resulted in transition of the transgene from the silent to the active state, prolongation of the active state, and a marked narrowing of the range of expression levels at different genomic sites. At one genomic site, prolonged induction of MTF resulted in suppression of transgene silencing that persisted after withdrawal of the induction stimulus. These results are consistent with MTF acting as a chromatin insulator and imply that transcriptional activating elements can insulate active loci against chromatin repression. PMID:12547916

  1. Overexpression of plasma membrane H+-ATPase in guard cells promotes light-induced stomatal opening and enhances plant growth.

    PubMed

    Wang, Yin; Noguchi, Ko; Ono, Natsuko; Inoue, Shin-ichiro; Terashima, Ichiro; Kinoshita, Toshinori

    2014-01-01

    Stomatal pores surrounded by a pair of guard cells in the plant epidermis control gas exchange between plants and the atmosphere in response to light, CO2, and the plant hormone abscisic acid. Light-induced stomatal opening is mediated by at least three key components: the blue light receptor phototropin (phot1 and phot2), plasma membrane H(+)-ATPase, and plasma membrane inward-rectifying K(+) channels. Very few attempts have been made to enhance stomatal opening with the goal of increasing photosynthesis and plant growth, even though stomatal resistance is thought to be the major limiting factor for CO2 uptake by plants. Here, we show that transgenic Arabidopsis plants overexpressing H(+)-ATPase using the strong guard cell promoter GC1 showed enhanced light-induced stomatal opening, photosynthesis, and plant growth. The transgenic plants produced larger and increased numbers of rosette leaves, with ∼42-63% greater fresh and dry weights than the wild type in the first 25 d of growth. The dry weights of total flowering stems of 45-d-old transgenic plants, including seeds, siliques, and flowers, were ∼36-41% greater than those of the wild type. In addition, stomata in the transgenic plants closed normally in response to darkness and abscisic acid. In contrast, the overexpression of phototropin or inward-rectifying K(+) channels in guard cells had no effect on these phenotypes. These results demonstrate that stomatal aperture is a limiting factor in photosynthesis and plant growth, and that manipulation of stomatal opening by overexpressing H(+)-ATPase in guard cells is useful for the promotion of plant growth.

  2. Light-induced oxidation in semihard cheeses. Evaluation of methods used to determine levels of oxidation.

    PubMed

    Mortensen, Grith; Sørensen, John; Stapelfeldt, Henrik

    2002-07-17

    Light-induced oxidation in Havarti cheese (38% fat) stored in the dark and exposed to fluorescent light was evaluated by an array of chemical, physical, and spectroscopic methods. Light-induced changes were noticeable already after short exposure times (<12 h). A clear differentiation between samples stored in the dark and samples exposed to 1000 lx fluorescent light was obtained by means of the following methods: color measurements (a values), peroxide value determinations, and evaluations of volatile oxidation products by solid-phase microextraction gas chromatography (SPME-GC). The expected changes in peroxide values in relation to storage time were not evident. Measuring free radicals by electron spin resonance spectrometry could not be done to distinguish between samples, possibly due to the conversion of radicals during sample preparation. However, significant light-exposure effects on secondary oxidation products, detected by SPME-GC, were noted for 1-pentanol, 1-hexanol, nonanal, and benzaldehyde. PMID:12105971

  3. Absolute Configuration from Different Multifragmentation Pathways in Light-Induced Coulomb Explosion Imaging.

    PubMed

    Pitzer, Martin; Kastirke, Gregor; Kunitski, Maksim; Jahnke, Till; Bauer, Tobias; Goihl, Christoph; Trinter, Florian; Schober, Carl; Henrichs, Kevin; Becht, Jasper; Zeller, Stefan; Gassert, Helena; Waitz, Markus; Kuhlins, Andreas; Sann, Hendrik; Sturm, Felix; Wiegandt, Florian; Wallauer, Robert; Schmidt, Lothar Ph H; Johnson, Allan S; Mazenauer, Manuel; Spenger, Benjamin; Marquardt, Sabrina; Marquardt, Sebastian; Schmidt-Böcking, Horst; Stohner, Jürgen; Dörner, Reinhard; Schöffler, Markus; Berger, Robert

    2016-08-18

    The absolute configuration of individual small molecules in the gas phase can be determined directly by light-induced Coulomb explosion imaging (CEI). Herein, this approach is demonstrated for ionization with a single X-ray photon from a synchrotron light source, leading to enhanced efficiency and faster fragmentation as compared to previous experiments with a femtosecond laser. In addition, it is shown that even incomplete fragmentation pathways of individual molecules from a racemic CHBrClF sample can give access to the absolute configuration in CEI. This leads to a significant increase of the applicability of the method as compared to the previously reported complete break-up into atomic ions and can pave the way for routine stereochemical analysis of larger chiral molecules by light-induced CEI. PMID:27298209

  4. Modification of enzymatic activity following laser irradiation through the light-induced electric field

    NASA Astrophysics Data System (ADS)

    Amat, Albert; Waynant, Ronald W.

    2006-02-01

    When cells are irradiated with visible and near-infrared wavelengths a variety of stimulatory effects are observed in their metabolism. To explain the observed light effects, researchers try to identify the chromophores that are involved in the processes. However, the mechanism of light absorption by a chromophore does not explain many of the experimental observations and therefore the primary mechanism for cellular light responses remains unproven. In addition to the ability of photons to produce electronic excitation in chromophores, light induces an alternating electric field in a medium that is able to interact with polar structures and produce dipole transitions. The effect of the light induced electric field in enzymatic molecules is analyzed in the present article, and it will be described how enzymatic activity is enhanced by this mechanism.

  5. Experimental evidence on removing copper and light-induced degradation from silicon by negative charge

    SciTech Connect

    Boulfrad, Yacine Lindroos, Jeanette; Yli-Koski, Marko; Savin, Hele; Wagner, Matthias; Wolny, Franziska

    2014-11-03

    In addition to boron and oxygen, copper is also known to cause light-induced degradation (LID) in silicon. We have demonstrated previously that LID can be prevented by depositing negative corona charge onto the wafer surfaces. Positively charged interstitial copper ions are proposed to diffuse to the negatively charged surface and consequently empty the bulk of copper. In this study, copper out-diffusion was confirmed by chemical analysis of the near surface region of negatively/positively charged silicon wafer. Furthermore, LID was permanently removed by etching the copper-rich surface layer after negative charge deposition. These results demonstrate that (i) copper can be effectively removed from the bulk by negative charge, (ii) under illumination copper forms a recombination active defect in the bulk of the wafer causing severe light induced degradation.

  6. Experimental study on light induced influence model to mice using support vector machine

    NASA Astrophysics Data System (ADS)

    Ji, Lei; Zhao, Zhimin; Yu, Yinshan; Zhu, Xingyue

    2014-08-01

    Previous researchers have made studies on different influences created by light irradiation to animals, including retinal damage, changes of inner index and so on. However, the model of light induced damage to animals using physiological indicators as features in machine learning method is never founded. This study was designed to evaluate the changes in micro vascular diameter, the serum absorption spectrum and the blood flow influenced by light irradiation of different wavelengths, powers and exposure time with support vector machine (SVM). The micro images of the mice auricle were recorded and the vessel diameters were calculated by computer program. The serum absorption spectrums were analyzed. The result shows that training sample rate 20% and 50% have almost the same correct recognition rate. Better performance and accuracy was achieved by third-order polynomial kernel SVM quadratic optimization method and it worked suitably for predicting the light induced damage to organisms.

  7. Till disassembly do us part: a happy marriage of nuclear envelope and chromatin.

    PubMed

    Tsuchiya, Yuichi

    2008-02-01

    A characteristic feature of eukaryotic cells is the presence of nuclear envelope (NE) which separates genomic DNA from cytoplasm. NE is composed of inner nuclear membrane (INM), which interacts with chromatin, and outer nuclear membrane, which is connected to endoplasmic reticulum. Nuclear pore complexes are inserted into NE to form transport channels between nucleus and cytoplasm. In metazoan cells, an intermediate filament-based meshwork called as nuclear lamina exists between INM and chromatin. Sophisticated collaboration of these molecular machineries is necessary for the structure and functions of NE. Recent research advances have revealed that NE dynamically communicates with chromatin and cytoskeleton to control multiple nuclear functions. In this mini review, I briefly summarize the basic concepts and current topics of functional relationships between NE and chromatin.

  8. Non-coding RNAs: novel players in chromatin-regulation during viral latency.

    PubMed

    Eilebrecht, Sebastian; Schwartz, Christian; Rohr, Olivier

    2013-08-01

    Chromatin structure plays an essential role during gene expression regulation not only in the case of the host cellular genome, but also during the viral life cycle. Epigenetic chromatin marks thereby define, whether a gene promoter is accessible for the transcription machinery or whether a repressive heterochromatin state is established. The heterochromatin-mediated repression of lytic viral genes results in viral latency, enabling the virus to persist dormant without being recognized by the host immune system, but keeping the potential for reactivation. Arising new systems biology approaches are starting to uncover an unexpected multiplicity and variety of non-coding (nc)RNAs playing important roles during chromatin structure control, likely constituting a novel layer in epigenetic regulation. In this review we give an overview of chromatin-regulatory viral and host cellular ncRNAs and their links to viral latency. PMID:23660570

  9. Application of the Protein Semisynthesis Strategy to the Generation of Modified Chromatin

    PubMed Central

    Holt, Matthew; Muir, Tom

    2016-01-01

    Histone proteins are subject to a host of posttranslational modifications (PTMs) that modulate chromatin structure and function. Such control is achieved by the direct alteration of the intrinsic physical properties of the chromatin fiber or by regulating the recruitment and activity of a host of trans-acting nuclear factors. The sheer number of histone PTMs presents a formidable barrier to understanding the molecular mechanisms at the heart of epigenetic regulation of eukaryotic genomes. One aspect of this multifarious problem, namely how to access homogeneously modified chromatin for biochemical studies, is well suited to the sensibilities of the organic chemist. Indeed, recent years have witnessed a critical role for synthetic protein chemistry methods in generating the raw materials needed for studying how histone PTMs regulate chromatin biochemistry. This review focuses on what is arguably the most powerful, and widely employed, of these chemical strategies, namely histone semisynthesis via the chemical ligation of peptide fragments. PMID:25784050

  10. Genetic dissection of light-induced Ca2+ influx into Drosophila photoreceptors

    PubMed Central

    1994-01-01

    Invertebrate photoreceptors use the inositol-lipid signaling cascade for phototransduction. A useful approach to dissect this pathway and its regulation has been provided by the isolation of Drosophila visual mutants. We measured extracellular changes of Ca2+ [delta Ca2+]o in Drosophila retina using Ca(2+)-selective microelectrodes in both the transient receptor potential (trp) mutant, in which the calcium permeability of the light-sensitive channels is greatly diminished and in the inactivation-but-no-afterpotential C (inaC) mutant which lacks photoreceptor-specific protein kinase C (PKC). Illumination induced a decrease in extracellular [Ca2+] with kinetics and magnitude that changed with light intensity. Compared to wild-type, the light-induced decrease in [Ca2+]o (the Ca2+ signal) was diminished in trp but significantly enhanced in inaC. The enhanced Ca2+ signal was diminished in the double mutant inaC;trp indicating that the effect of the trp mutation overrides the enhancement observed in the absence of eye-PKC. We suggest that the decrease in [Ca2+]o reflects light-induced Ca2+ influx into the photoreceptors and that the trp mutation blocks a large fraction of this Ca2+ influx, while the absence of eye specific PKC leads to enhancement of light-induced Ca2+ influx. This suggestion was supported by Ca2+ measurements in isolated ommatidia loaded with the fluorescent Ca2+ indicator, Ca Green-5N, which indicated an approximately threefold larger light-induced increase in cellular Ca2+ in inaC relative to WT. Our observations are consistent with the hypothesis that TRP is a light activated Ca2+ channel and that the increased Ca2+ influx observed in the absence of PKC is mediated mainly via the TRP channel. PMID:7699363

  11. Light-induced noncentrosymmetry in acceptor-donor-substituted azobenzene solutions

    NASA Astrophysics Data System (ADS)

    Zhao, Jiang; Si, Jinhai; Wang, Yougui; Ye, Peixian; Fu, Xingfa; Qiu, Ling; Shen, Yuquan

    1995-10-01

    Light-induced noncentrosymmetry was achieved experimentally in acceptor-donor-substituted azobenzene solutions and observed by phase-matched nondegenerate six-wave mixing. The microscopic origin of the induced noncentrosymmetry was found to be orientational hole burning, which was distinguished directly with net orientation of molecules by experimental observations. The decay time of the induced noncentrosymmetry depended on the rotational orientation time of the sample's molecule, which varied linearly with the viscosity of the solvent.

  12. Identification of novel light-induced genes in the suprachiasmatic nucleus

    PubMed Central

    Porterfield, Veronica M; Piontkivska, Helen; Mintz, Eric M

    2007-01-01

    Background The transmission of information about the photic environment to the circadian clock involves a complex array of neurotransmitters, receptors, and second messenger systems. Exposure of an animal to light during the subjective night initiates rapid transcription of a number of immediate-early genes in the suprachiasmatic nucleus of the hypothalamus. Some of these genes have known roles in entraining the circadian clock, while others have unknown functions. Using laser capture microscopy, microarray analysis, and quantitative real-time PCR, we performed a comprehensive screen for changes in gene expression immediately following a 30 minute light pulse in suprachiasmatic nucleus of mice. Results The results of the microarray screen successfully identified previously known light-induced genes as well as several novel genes that may be important in the circadian clock. Newly identified light-induced genes include early growth response 2, proviral integration site 3, growth-arrest and DNA-damage-inducible 45 beta, and TCDD-inducible poly(ADP-ribose) polymerase. Comparative analysis of promoter sequences revealed the presence of evolutionarily conserved CRE and associated TATA box elements in most of the light-induced genes, while other core clock genes generally lack this combination of promoter elements. Conclusion The photic signalling cascade in the suprachiasmatic nucleus activates an array of immediate-early genes, most of which have unknown functions in the circadian clock. Detected evolutionary conservation of CRE and TATA box elements in promoters of light-induced genes suggest that the functional role of these elements has likely remained the same over evolutionary time across mammalian orders. PMID:18021443

  13. Factors affecting light-induced excess conductivity in doping-modulated amorphous silicon superlattices

    SciTech Connect

    Su, F.; Levine, S.; Vanier, P.E.; Kampas, F.J.

    1986-03-15

    Doping-modulated amorphous silicon semiconducting films which exhibit the phenomenon of light-induced excess conductivity (LEC) have been made by silane glow discharge in a single-chamber system. This phenomenon shows a strong dependence on substrate temperature and process gas composition. The LEC effect decreases for very small and very large layer thickness. There also seems to be an optimum defect density for producing large effects.

  14. Spin Hall effects for cold atoms in a light induced gauge potential

    SciTech Connect

    Zhu, Shi-Liang; Fu, Hao; Wu, C.-J.; Zhang, S.-C.; Duan, L.-M. /Michigan U., MCTP

    2010-03-16

    We propose an experimental scheme to observe spin Hall effects with cold atoms in a light induced gauge potential. Under an appropriate configuration, the cold atoms moving in a spatially varying laser field experience an effective spin-dependent gauge potential. Through numerical simulation, we demonstrate that such a gauge field leads to observable spin Hall currents under realistic conditions. We also discuss the quantum spin Hall state in an optical lattice.

  15. Rise kinetics of light-induced modulation of absorption for a CdS crystal

    NASA Technical Reports Server (NTRS)

    Long, E. R., Jr.; Conway, E. J.

    1976-01-01

    An experimental study has been made of the rise kinetics for changes in optical absorption in a single crystal of CdS which was bulk excited by pulsed laser light. The experimental data were compared to calculations from a simple model involving a bimolecular process. Experimental and calculated values agreed to within the experimental error and confirmed that light-induced modulation of absorption is a bimolecular process.

  16. Mechanism of UV light-induced photorelaxation in isolated rat aorta.

    PubMed

    Kim, J H; Hong, Y; Shim, C S

    2000-12-01

    Isolated rat thoracic aorta which is pharmacologically precontracted by phenylephrine induces photorelaxation when exposed to long wave length UV-light. The aim of the present study was to characterize the mechanism of UV-light induced by photorelaxation in the rat aorta. 1. UV light relaxed both endothelium-intact and -denuded rat aortic rings contracted by phenylephrine. The magnitude of relaxation on UV light was dependent on the exposure time and slightly greatly in endothelium-denuded rings than in endothelium-intact preparations. 2. L-NAME (10 nM-100 uM) but not D-NAME completely inhibited the photorelaxation in a concentration dependent manner. 3. The UV-induced relaxation was inhibited by methylene blue (1 -100 uM), and verapamil (100 nM), and removal of extracellular Ca2+. In contrast, UV-light induced photorelaxation was potentiated by N(w)-nitro-Larginine (L-NOARG) treatment. 4. In immunocytochemical analysis of UV-light induced iNOS and eNOS expression in rat aortas, at which expression levels were increased in a time-dependent manner on UV-irradiation in aortic endothelium and smooth muscle, respectively. These results suggest that UV light-induced photorelaxation may be due to nitric oxide from exogenously administered L-arginine as well as endogenous nitric oxide donors such as amino acid and arginine derivatives. Additional suggestion is that UV light stimulates the expression of nitric oxide synthases, and its activity for nitric oxide generation is dependent on cytosolic Ca2+ originated from extracellular space.

  17. Comment on ''Light-induced atomic desorption and diffusion of Rb from porous alumina''

    SciTech Connect

    RePbilas, Krzysztof

    2010-11-15

    In a recent article [Phys. Rev. A 81, 037801 (2010)] a theory of light-induced atomic desorption for Rb in porous alumina is proposed. We point out that both the main assumption of this theory (the diffusion inside the pores treated as a random walk with the adsorption to the inner surface of the pores at any step) and several further hypotheses supporting the theoretical model require a revision.

  18. Blue-light-induced rapid chloroplast de-anchoring in Vallisneria epidermal cells.

    PubMed

    Sakai, Yuuki; Inoue, Shin-ichiro; Harada, Akiko; Shimazaki, Ken-Ichiro; Takagi, Shingo

    2015-01-01

    In the outer periclinal cytoplasm of leaf epidermal cells of an aquatic angiosperm Vallisneria, blue light induces "chloroplast de-anchoring", a rapid decline in the resistance of chloroplasts against centrifugal force. Chloroplast de-anchoring is known induced within 1 min of irradiation with high-fluence-rate blue light specifically, preceding the commencement of chloroplasts migration toward the anticlinal cytoplasm. However, its regulatory mechanism has remained elusive, although pharmacological analysis suggested that a calcium release from intracellular calcium stores is necessary for the response. In search of the responsible photoreceptors, immunoblotting analysis using antibodies against phototropins demonstrated that cross-reactive polypeptides of 120-kDa exist in the plasma-membrane fraction prepared from the leaves. In vitro phosphorylation analysis revealed that 120-kDa polypeptides were phosphorylated by exposure to blue light in a fluence-dependent manner. The blue-light-induced phosphorylation activity was sensitive to a Ser/Thr kinase inhibitor, staurosporine, and unusually was retained at a high level for a long time in darkness. Furthermore, phototropin gene homologs (Vallisneria PHOTOTROPIN1 and PHOTOTROPIN2) expressed in leaves were isolated. We propose that calcium-regulated chloroplast de-anchoring, possibly mediated by phototropins, is an initial process of the blue-light-induced avoidance response of chloroplasts in Vallisneria.

  19. Blue-light-induced rapid chloroplast de-anchoring in Vallisneria epidermal cells.

    PubMed

    Sakai, Yuuki; Inoue, Shin-ichiro; Harada, Akiko; Shimazaki, Ken-Ichiro; Takagi, Shingo

    2015-01-01

    In the outer periclinal cytoplasm of leaf epidermal cells of an aquatic angiosperm Vallisneria, blue light induces "chloroplast de-anchoring", a rapid decline in the resistance of chloroplasts against centrifugal force. Chloroplast de-anchoring is known induced within 1 min of irradiation with high-fluence-rate blue light specifically, preceding the commencement of chloroplasts migration toward the anticlinal cytoplasm. However, its regulatory mechanism has remained elusive, although pharmacological analysis suggested that a calcium release from intracellular calcium stores is necessary for the response. In search of the responsible photoreceptors, immunoblotting analysis using antibodies against phototropins demonstrated that cross-reactive polypeptides of 120-kDa exist in the plasma-membrane fraction prepared from the leaves. In vitro phosphorylation analysis revealed that 120-kDa polypeptides were phosphorylated by exposure to blue light in a fluence-dependent manner. The blue-light-induced phosphorylation activity was sensitive to a Ser/Thr kinase inhibitor, staurosporine, and unusually was retained at a high level for a long time in darkness. Furthermore, phototropin gene homologs (Vallisneria PHOTOTROPIN1 and PHOTOTROPIN2) expressed in leaves were isolated. We propose that calcium-regulated chloroplast de-anchoring, possibly mediated by phototropins, is an initial process of the blue-light-induced avoidance response of chloroplasts in Vallisneria. PMID:25231366

  20. Light-induced melatonin suppression at night after exposure to different wavelength composition of morning light.

    PubMed

    Kozaki, Tomoaki; Kubokawa, Ayaka; Taketomi, Ryunosuke; Hatae, Keisuke

    2016-03-11

    Bright nocturnal light has been shown to suppress melatonin secretion. However, bright light exposure during the day might reduce light-induced melatonin suppression at night. The human circadian system is sensitive to short wavelength light. This study evaluated the preventive effect of different wavelengths of daytime light on light-induced melatonin suppression at night. Twelve male subjects were exposed to various light conditions (dim, white, and bluish white light) between the hours of 09:00 and 10:30 (daytime light conditions). They were then exposed to light (300lx) again between 01:00 and 02:30 (night-time light exposure). Subjects provided saliva samples before (00:55) and after night-time light exposure (02:30). A two-tailed paired t-test yielded significant decrements in melatonin concentrations after night-time light exposure under daytime dim and white light conditions. No significant differences were found in melatonin concentrations between pre- and post-night-time light exposure with bluish-white light. Present findings suggest that daytime blue light exposure has an acute preventive impact on light-induced melatonin suppression in individuals with a general life rhythm (sleep/wake schedule). These findings may be useful for implementing artificial light environments for humans in, for example, hospitals and underground shopping malls to reduce health risks.

  1. Light-induced melatonin suppression at night after exposure to different wavelength composition of morning light.

    PubMed

    Kozaki, Tomoaki; Kubokawa, Ayaka; Taketomi, Ryunosuke; Hatae, Keisuke

    2016-03-11

    Bright nocturnal light has been shown to suppress melatonin secretion. However, bright light exposure during the day might reduce light-induced melatonin suppression at night. The human circadian system is sensitive to short wavelength light. This study evaluated the preventive effect of different wavelengths of daytime light on light-induced melatonin suppression at night. Twelve male subjects were exposed to various light conditions (dim, white, and bluish white light) between the hours of 09:00 and 10:30 (daytime light conditions). They were then exposed to light (300lx) again between 01:00 and 02:30 (night-time light exposure). Subjects provided saliva samples before (00:55) and after night-time light exposure (02:30). A two-tailed paired t-test yielded significant decrements in melatonin concentrations after night-time light exposure under daytime dim and white light conditions. No significant differences were found in melatonin concentrations between pre- and post-night-time light exposure with bluish-white light. Present findings suggest that daytime blue light exposure has an acute preventive impact on light-induced melatonin suppression in individuals with a general life rhythm (sleep/wake schedule). These findings may be useful for implementing artificial light environments for humans in, for example, hospitals and underground shopping malls to reduce health risks. PMID:26777427

  2. Light-induced biocidal action of conjugated polyelectrolytes supported on colloids.

    PubMed

    Chemburu, Sireesha; Corbitt, Thomas S; Ista, Linnea K; Ji, Eunkyung; Fulghum, Julia; Lopez, Gabriel P; Ogawa, Katsu; Schanze, Kirk S; Whitten, David G

    2008-10-01

    A series of water soluble, cationic conjugated polyelectrolytes (CPEs) with backbones based on a poly(phenylene ethynylene) repeat unit structure and tetraakylammonium side groups exhibit a profound light-induced biocidal effect. The present study examines the biocidal activity of the CPEs, correlating this activity with the photophysical properties of the polymers. The photophysical properties of the CPEs are studied in solution, and the results demonstrate that direct excitation produces a triplet excited-state in moderate yield, and the triplet is shown to be effective at sensitizing the production of singlet oxygen. Using the polymers in a format where they are physisorbed or covalently grafted to the surface of colloidal silica particles (5 and 30 microm diameter), we demonstrate that they exhibit light-activated biocidal activity, effectively killing Cobetia marina and Pseudomonas aeruginosa. The light-induced biocidal activity is also correlated with a requirement for oxygen suggesting that interfacial generation of singlet oxygen is the crucial step in the light-induced biocidal activity.

  3. Stress-Induced Chromatin Changes: A Critical View on Their Heritability

    PubMed Central

    Pecinka, Ales; Mittelsten Scheid, Ortrun

    2012-01-01

    The investigation of stress responses has been a focus of plant research, breeding and biotechnology for a long time. Insight into stress perception, signaling and genetic determinants of resistance has recently been complemented by growing evidence for substantial stress-induced changes at the chromatin level. These affect specific sequences or occur genome-wide and are often correlated with transcriptional regulation. The majority of these changes only occur during stress exposure, and both expression and chromatin states typically revert to the pre-stress state shortly thereafter. Other changes result in the maintenance of new chromatin states and modified gene expression for a longer time after stress exposure, preparing an individual for developmental decisions or more effective defence. Beyond this, there are claims for stress-induced heritable chromatin modifications that are transmitted to progeny, thereby improving their characteristics. These effects resemble the concept of Lamarckian inheritance of acquired characters and represent a challenge to the uniqueness of DNA sequence-based inheritance. However, with the growing insight into epigenetic regulation and transmission of chromatin states, it is worth investigating these phenomena carefully. While genetic changes (mainly transposon mobility) in response to stress-induced interference with chromatin are well documented and heritable, in our view there is no unambiguous evidence for transmission of exclusively chromatin-controlled stress effects to progeny. We propose a set of criteria that should be applied to substantiate the data for stress-induced, chromatin-encoded new traits. Well-controlled stress treatments, thorough phenotyping and application of refined genome-wide epigenetic analysis tools should be helpful in moving from interesting observations towards robust evidence. PMID:22457398

  4. Photocarrier Radiometry Investigation of Light-Induced Degradation of Boron-Doped Czochralski-Grown Silicon Without Surface Passivation

    NASA Astrophysics Data System (ADS)

    Wang, Qian; Li, Bincheng

    2016-04-01

    Light-induced degradation (LID) effects of boron-doped Cz silicon wafers without surface passivation are investigated in details by photocarrier radiometry (PCR). The resistivity of all samples is in the range of 0.006 Ω {\\cdot } {cm} to 38 Ω {\\cdot } {cm}. It is found that light-induced changes in surface state occupation have a great effect on LID under illumination. With the increasing contribution of light-induced changes in surface state occupation, the generation rate of the defect decreases. The light-induced changes in surface state occupation and light-induced degradation dominate the temporal behaviors of the excess carrier density of high- and low-resistivity Si wafers, respectively. Moreover, the temporal behaviors of PCR signals of these samples under laser illumination with different powers, energy of photons, and multiple illuminations were also analyzed to understand the light-induced change of material properties. Based on the nonlinear dependence of PCR signal on the excitation power, a theoretical model taking into account both light-induced changes in surface state occupation and LID processes was proposed to explain those temporal behaviors.

  5. A Computer Lab Exploring Evolutionary Aspects of Chromatin Structure and Dynamics for an Undergraduate Chromatin Course

    ERIC Educational Resources Information Center

    Eirin-Lopez, Jose M.

    2013-01-01

    The study of chromatin constitutes one of the most active research fields in life sciences, being subject to constant revisions that continuously redefine the state of the art in its knowledge. As every other rapidly changing field, chromatin biology requires clear and straightforward educational strategies able to efficiently translate such a…

  6. The accessible chromatin landscape of the human genome

    PubMed Central

    Thurman, Robert E.; Rynes, Eric; Humbert, Richard; Vierstra, Jeff; Maurano, Matthew T.; Haugen, Eric; Sheffield, Nathan C.; Stergachis, Andrew B.; Wang, Hao; Vernot, Benjamin; Garg, Kavita; Sandstrom, Richard; Bates, Daniel; Canfield, Theresa K.; Diegel, Morgan; Dunn, Douglas; Ebersol, Abigail K.; Frum, Tristan; Giste, Erika; Harding, Lisa; Johnson, Audra K.; Johnson, Ericka M.; Kutyavin, Tanya; Lajoie, Bryan; Lee, Bum-Kyu; Lee, Kristen; London, Darin; Lotakis, Dimitra; Neph, Shane; Neri, Fidencio; Nguyen, Eric D.; Reynolds, Alex P.; Roach, Vaughn; Safi, Alexias; Sanchez, Minerva E.; Sanyal, Amartya; Shafer, Anthony; Simon, Jeremy M.; Song, Lingyun; Vong, Shinny; Weaver, Molly; Zhang, Zhancheng; Zhang, Zhuzhu; Lenhard, Boris; Tewari, Muneesh; Dorschner, Michael O.; Hansen, R. Scott; Navas, Patrick A.; Stamatoyannopoulos, George; Iyer, Vishwanath R.; Lieb, Jason D.; Sunyaev, Shamil R.; Akey, Joshua M.; Sabo, Peter J.; Kaul, Rajinder; Furey, Terrence S.; Dekker, Job; Crawford, Gregory E.; Stamatoyannopoulos, John A.

    2013-01-01

    DNaseI hypersensitive sites (DHSs) are markers of regulatory DNA and have underpinned the discovery of all classes of cis-regulatory elements including enhancers, promoters, insulators, silencers, and locus control regions. Here we present the first extensive map of human DHSs identified through genome-wide profiling in 125 diverse cell and tissue types. We identify ~2.9 million DHSs that encompass virtually all known experimentally-validated cis-regulatory sequences and expose a vast trove of novel elements, most with highly cell-selective regulation. Annotating these elements using ENCODE data reveals novel relationships between chromatin accessibility, transcription, DNA methylation, and regulatory factor occupancy patterns. We connect ~580,000 distal DHSs with their target promoters, revealing systematic pairing of different classes of distal DHSs and specific promoter types. Patterning of chromatin accessibility at many regulatory regions is choreographed with dozens to hundreds of co-activated elements, and the trans-cellular DNaseI sensitivity pattern at a given region can predict cell type-specific functional behaviors. The DHS landscape shows signatures of recent functional evolutionary constraint. However, the DHS compartment in pluripotent and immortalized cells exhibits higher mutation rates than that in highly differentiated cells, exposing an unexpected link between chromatin accessibility, proliferative potential and patterns of human variation. PMID:22955617

  7. The insulation of genes from external enhancers and silencing chromatin

    PubMed Central

    Burgess-Beusse, Bonnie; Farrell, Catherine; Gaszner, Miklos; Litt, Michael; Mutskov, Vesco; Recillas-Targa, Felix; Simpson, Melanie; West, Adam; Felsenfeld, Gary

    2002-01-01

    Insulators are DNA sequence elements that can serve in some cases as barriers to protect a gene against the encroachment of adjacent inactive condensed chromatin. Some insulators also can act as blocking elements to protect against the activating influence of distal enhancers associated with other genes. Although most of the insulators identified so far derive from Drosophila, they also are found in vertebrates. An insulator at the 5′ end of the chicken β-globin locus marks a boundary between an open chromatin domain and a region of constitutively condensed chromatin. Detailed analysis of this element shows that it possesses both enhancer blocking activity and the ability to screen reporter genes against position effects. Enhancer blocking is associated with binding of the protein CTCF; sites that bind CTCF are found at other critical points in the genome. Protection against position effects involves other properties that appear to be associated with control of histone acetylation and methylation. Insulators thus are complex elements that can help to preserve the independent function of genes embedded in a genome in which they are surrounded by regulatory signals they must ignore. PMID:12154228

  8. The nss mutation or lanthanum inhibits light-induced Ca2+ influx into fly photoreceptors.

    PubMed

    Rom-Glas, A; Sandler, C; Kirschfeld, K; Minke, B

    1992-11-01

    Ion-selective calcium microelectrodes were inserted into the compound eyes of the wild-type sheep blowfly Lucilia or into the retina of the no steady state (nss) mutant of Lucilia. These electrodes monitored light-induced changes in the extracellular concentration of calcium (delta[Ca2+]o) together with the extracellularly recorded receptor potential. Prolonged dim lights induced a steady reduction in [Ca2+]o during light in the retina of normal Lucilia, while relatively little change in [Ca2+]o was observed in the retina of the nss mutant. Prolonged intense light induced a multiphasic change in [Ca2+]o: the [Ca2+]o signal became transient, reaching a minimum within 6 s after light onset, and then rose to a nearly steady-state phase below the dark concentration. When lights were turned off, a rapid increase in [Ca2+]o was observed, reaching a peak above the dark level and then declining again to the dark level within 1 min. In analogy to similar studies conduced in the honeybee drone, we suggest that the reduction in [Ca2+]o reflects light-induced Ca2+ influx into the photoreceptors, while the subsequent increase in [Ca2+]o reflects the activation of the Na-Ca exchange which extrudes Ca2+ from the cells. In the nss mutant in response to intense prolonged light, the receptor potential declines to baseline during light while the Ca2+ signal is almost abolished, revealing only a short transient reduction in [Ca2+]o. Application of lanthanum (La3+), but not nickel (Ni2+), into the retinal extracellular space of normal Lucilia mimicked the effect of the nss mutation on the receptor potential, while complete elimination of the Ca2+ signal in a reversible manner was observed. The results suggest that La3+ and the nss mutation inhibit light-induced Ca2+ influex into the photoreceptor in a manner similar to the action of the trp mutation in Drosophila, which has been shown to block specifically a light-activated Ca2+ channel necessary to maintain light excitation.

  9. Inhibition by acrolein of light-induced stomatal opening through inhibition of inward-rectifying potassium channels in Arabidopsis thaliana.

    PubMed

    Islam, Md Moshiul; Ye, Wenxiu; Matsushima, Daiki; Khokon, Md Atiqur Rahman; Munemasa, Shintaro; Nakamura, Yoshimasa; Murata, Yoshiyuki

    2015-01-01

    Acrolein is a reactive α,β-unsaturated aldehyde derived from lipid peroxides, which are produced in plants under a variety of stress. We investigated effects of acrolein on light-induced stomatal opening using Arabidopsis thaliana. Acrolein inhibited light-induced stomatal opening in a dose-dependent manner. Acrolein at 100 μM inhibited plasma membrane inward-rectifying potassium (Kin) channels in guard cells. Acrolein at 100 μM inhibited Kin channel KAT1 expressed in a heterologous system using Xenopus leaves oocytes. These results suggest that acrolein inhibits light-induced stomatal opening through inhibition of Kin channels in guard cells.

  10. POD Nanoparticles Expressing GDNF Provide Structural and Functional Rescue of Light-induced Retinal Degeneration in an Adult Mouse

    PubMed Central

    Read, Sarah P; Cashman, Siobhan M; Kumar-Singh, Rajendra

    2010-01-01

    Peptide for ocular delivery (POD) is a novel cationic cell-penetrating peptide (CPP) which, when conjugated with polyethylene glycol (PEG-POD), can deliver plasmid DNA to the retinal pigment epithelium (RPE) of adult murine retina. PEG-POD nanoparticles containing an expression cassette for glial cell line–derived neurotrophic factor (PEG–POD~GDNF) were investigated for their ability to inhibit light-induced photoreceptor apoptosis. PEG-POD~GDNF, control nanoparticles, or buffer were injected into the subretinal space of adult murine retina and retinal degeneration induced by blue light. Animals injected with PEG-POD~GDNF showed a significant reduction (3.9–7.7 fold) in apoptosis relative to control-injected animals. The thickness of the outer nuclear layer (ONL) of the superior retina of PEG-POD~GDNF-injected eyes was significantly greater (23.6–39.3%) than control-injected retina 14 days post-light treatment. PEG-POD~GDNF-injected eyes showed a 27–39% greater functional response relative to controls, as measured by electroretinogram (ERG) 7 days post-light treatment. This is one of only two studies demonstrating histological and functional rescue of a mouse model of retinal degeneration following nonviral administration of a transgene into adult retina. Although rescue is short lived for clinical application, this study represents an important step in the development of nonviral gene therapy for retinal diseases. PMID:20700110

  11. Chromatin Ring Formation at Plant Centromeres.

    PubMed

    Schubert, Veit; Ruban, Alevtina; Houben, Andreas

    2016-01-01

    We observed the formation of chromatin ring structures at centromeres of somatic rye and Arabidopsis chromosomes. To test whether this behavior is present also in other plant species and tissues we analyzed Arabidopsis, rye, wheat, Aegilops and barley centromeres during cell divisions and in interphase nuclei by immunostaining and FISH. Furthermore, structured illumination microscopy (super-resolution) was applied to investigate the ultrastructure of centromere chromatin beyond the classical refraction limit of light. It became obvious, that a ring formation at centromeres may appear during mitosis, meiosis and in interphase nuclei in all species analyzed. However, varying centromere structures, as ring formations or globular organized chromatin fibers, were identified in different tissues of one and the same species. In addition, we found that a chromatin ring formation may also be caused by subtelomeric repeats in barley. Thus, we conclude that the formation of chromatin rings may appear in different plant species and tissues, but that it is not specific for centromere function. Based on our findings we established a model describing the ultrastructure of plant centromeres and discuss it in comparison to previous models proposed for animals and plants. PMID:26913037

  12. Chromatin associations in Arabidopsis interphase nuclei

    PubMed Central

    Schubert, Veit; Rudnik, Radoslaw; Schubert, Ingo

    2014-01-01

    The arrangement of chromatin within interphase nuclei seems to be caused by topological constraints and related to gene expression depending on tissue and developmental stage. In yeast and animals it was found that homologous and heterologous chromatin association are required to realize faithful expression and DNA repair. To test whether such associations are present in plants we analyzed Arabidopsis thaliana interphase nuclei by FISH using probes from different chromosomes. We found that chromatin fiber movement and variable associations, although in general relatively seldom, may occur between euchromatin segments along chromosomes, sometimes even over large distances. The combination of euchromatin segments bearing high or low co-expressing genes did not reveal different association frequencies probably due to adjacent genes of deviating expression patterns. Based on previous data and on FISH analyses presented here, we conclude that the global interphase chromatin organization in A. thaliana is relatively stable, due to the location of its 10 centromeres at the nuclear periphery and of the telomeres mainly at the centrally localized nucleolus. Nevertheless, chromatin movement enables a flexible spatial genome arrangement in plant nuclei. PMID:25431580

  13. Chromatin Ring Formation at Plant Centromeres

    PubMed Central

    Schubert, Veit; Ruban, Alevtina; Houben, Andreas

    2016-01-01

    We observed the formation of chromatin ring structures at centromeres of somatic rye and Arabidopsis chromosomes. To test whether this behavior is present also in other plant species and tissues we analyzed Arabidopsis, rye, wheat, Aegilops and barley centromeres during cell divisions and in interphase nuclei by immunostaining and FISH. Furthermore, structured illumination microscopy (super-resolution) was applied to investigate the ultrastructure of centromere chromatin beyond the classical refraction limit of light. It became obvious, that a ring formation at centromeres may appear during mitosis, meiosis and in interphase nuclei in all species analyzed. However, varying centromere structures, as ring formations or globular organized chromatin fibers, were identified in different tissues of one and the same species. In addition, we found that a chromatin ring formation may also be caused by subtelomeric repeats in barley. Thus, we conclude that the formation of chromatin rings may appear in different plant species and tissues, but that it is not specific for centromere function. Based on our findings we established a model describing the ultrastructure of plant centromeres and discuss it in comparison to previous models proposed for animals and plants. PMID:26913037

  14. Two-step Crosslinking for Analysis of Protein-Chromatin Interactions

    PubMed Central

    Tian, Bing; Yang, Jun; Brasier, Allan R.

    2013-01-01

    Eukaryotic gene regulation is controlled, in part, by inducible transcription factors binding regulatory sequences in a tissue-specific and hormone-responsive manner. The development of methods for analysis of transcription factor interaction within native chromatin has been a significant advance for the systematic analyses of the timing of gene regulation and studies on the effects of chromatin modifying enzymes on promoter accessibility. Cross-linking-ChIP (XChIP) is a specific method involving formaldehyde mediated protein-chromatin fixation to preserve the interaction for subsequent target identification. However, the conventional single-step cross-linking technique does not preserve all protein-DNA interactions, especially for transcription factors in hyper-dynamic equilibrium with chromatin or for coactivator interactions. Here we describe a versatile, efficient “two-step” XChIP method that involves sequential protein-protein fixation followed by protein-DNA fixation. This method has been used successfully for analysis of chromatin binding for transcription factors (NF-κB, STAT3), polymerases (RNA Pol II), coactivators (CBP/p300, CDK9) and chromatin structural proteins (modified histones). Modifications of DNA extraction and sonication suitable for downstream target identification by quantitative genomic PCR and next generation sequencing are described. PMID:22113271

  15. Multivalency governs HP1α association dynamics with the silent chromatin state

    PubMed Central

    Kilic, Sinan; Bachmann, Andreas L.; Bryan, Louise C.; Fierz, Beat

    2015-01-01

    Multivalent interactions between effector proteins and histone post-translational modifications are an elementary mechanism of dynamic chromatin signalling. Here we elucidate the mechanism how heterochromatin protein 1α (HP1α), a multivalent effector, is efficiently recruited to the silent chromatin state (marked by trimethylated H3 at Lys9, H3K9me3) while remaining highly dynamic. Employing chemically defined nucleosome arrays together with single-molecule total internal reflection fluorescence microscopy (smTIRFM), we demonstrate that the HP1α residence time on chromatin depends on the density of H3K9me3, as dissociated factors can rapidly rebind at neighbouring sites. Moreover, by chemically controlling HP1α dimerization we find that effector multivalency prolongs chromatin retention and, importantly, accelerates the association rate. This effect results from increased avidity together with strengthened nonspecific chromatin interactions of dimeric HP1α. We propose that accelerated chromatin binding is a key feature of effector multivalency, allowing for fast and efficient competition for binding sites in the crowded nuclear compartment. PMID:26084584

  16. Chk1 protects against chromatin bridges by constitutively phosphorylating BLM serine 502 to inhibit BLM degradation.

    PubMed

    Petsalaki, Eleni; Dandoulaki, Maria; Morrice, Nick; Zachos, George

    2014-09-15

    Chromatin bridges represent incompletely segregated chromosomal DNA connecting the anaphase poles and can result in chromosome breakage. The Bloom's syndrome protein helicase (BLM, also known as BLMH) suppresses formation of chromatin bridges. Here, we show that cells deficient in checkpoint kinase 1 (Chk1, also known as CHEK1) exhibit higher frequency of chromatin bridges and reduced BLM protein levels compared to controls. Chk1 inhibition leads to BLM ubiquitylation and proteasomal degradation during interphase. Furthermore, Chk1 constitutively phosphorylates human BLM at serine 502 (S502) and phosphorylated BLM localises to chromatin bridges. Mutation of S502 to a non-phosphorylatable alanine residue (BLM-S502A) reduces the stability of BLM, whereas expression of a phospho-mimicking BLM-S502D, in which S502 is mutated to aspartic acid, stabilises BLM and prevents chromatin bridges in Chk1-deficient cells. In addition, wild-type but not BLM-S502D associates with cullin 3, and cullin 3 depletion rescues BLM accumulation and localisation to chromatin bridges after Chk1 inhibition. We propose that Chk1 phosphorylates BLM-S502 to inhibit cullin-3-mediated BLM degradation during interphase. These results suggest that Chk1 prevents deleterious anaphase bridges by stabilising BLM.

  17. Mechanical model of the nucleosome and chromatin.

    PubMed

    Bishop, Thomas C; Zhmudsky, Oleksandr O

    2002-04-01

    A theoretical framework for evaluating the approximate energy and dynamic properties associated with the folding of DNA into nucleosomes and chromatin is presented. Experimentally determined elastic constants of linear DNA and a simple fold geometry are assumed in order to derive elastic constants for extended and condensed chromatin. The model predicts the Young s modulus of extended and condensed chromatin to within an order of magnitude of experimentally determined values. Thus we demonstrate that the elastic properties of DNA are a primary determinant of the elastic properties of the higher order folded states. The derived elastic constants are used to predict the speed of propagation of small amplitude waves that excite an extension(sound), twist, bend or shear motion in each folded state. Taken together the results demonstrate that folding creates a hierarchy of time, length and energy scales.

  18. [Comparative characteristics of chromatin endonuclease fragments].

    PubMed

    Miul'berg, A A; Tishchenko, L I; Domkina, L K

    1977-05-01

    Soluble fragments of chromatin obtained by Ca, Mg-dependent endonuclease digest of rat liver nuclei, have been separated by gel chromatography on Sepharose 4B into three zones, containing oligomers, tetramers--dimers and monomers, respectively. The content of nonhistone proteins and particularly lysine-rich histones is decreased with a transition from theoligomers to monomers. The average protein/DNA ratio of the monomers is equal to 1.36 and that of histone/DNA ratio--to 0.82. The dependence of the degree of chromatin digest by endonuclease on its protein content and conditions of isolation and incubation of nuclei is discussed. The chromatin monomer formed appears to be made up of a nucleosome and short portions of spacer DNA bound to some part of histone HI and nonhistone proteins. PMID:889964

  19. Chromatin Remodeling, DNA Damage Repair and Aging

    PubMed Central

    Liu, Baohua; Yip, Raymond KH; Zhou, Zhongjun

    2012-01-01

    Cells are constantly exposed to a variety of environmental and endogenous conditions causing DNA damage, which is detected and repaired by conserved DNA repair pathways to maintain genomic integrity. Chromatin remodeling is critical in this process, as the organization of eukaryotic DNA into compact chromatin presents a natural barrier to all DNA-related events. Studies on human premature aging syndromes together with normal aging have suggested that accumulated damages might lead to exhaustion of resources that are required for physiological functions and thus accelerate aging. In this manuscript, combining the present understandings and latest findings, we focus mainly on discussing the role of chromatin remodeling in the repair of DNA double-strand breaks (DSBs) and regulation of aging. PMID:23633913

  20. The Chromatin Fiber: Multiscale Problems and Approaches

    PubMed Central

    Ozer, Gungor; Luque, Antoni; Schlick, Tamar

    2015-01-01

    The structure of chromatin, affected by many factors from DNA linker lengths to posttranslational modifications, is crucial to the regulation of eukaryotic cells. Combined experimental and computational methods have led to new insights into its structural and dynamical features, from interactions due to the flexible core histone tails of the nucleosomes to the physical mechanism driving the formation of chromosomal domains. Here we present a perspective of recent advances in chromatin modeling techniques at the atomic, mesoscopic, and chromosomal scales with a view toward developing multiscale computational strategies to integrate such findings. Innovative modeling methods that connect molecular to chromosomal scales are crucial for interpreting experiments and eventually deciphering the complex dynamic organization and function of chromatin in the cell. PMID:26057099

  1. Nucleosome dynamics during chromatin remodeling in vivo

    PubMed Central

    Ramachandran, Srinivas; Henikoff, Steven

    2016-01-01

    ABSTRACT Precise positioning of nucleosomes around regulatory sites is achieved by the action of chromatin remodelers, which use the energy of ATP to slide, evict or change the composition of nucleosomes. Chromatin remodelers act to bind nucleosomes, disrupt histone-DNA interactions and translocate the DNA around the histone core to reposition nucleosomes. Hence, remodeling is expected to involve nucleosomal intermediates with a structural organization that is distinct from intact nucleosomes. We describe the identification of a partially unwrapped nucleosome structure using methods that map histone-DNA contacts genome-wide. This alternative nucleosome structure is likely formed as an intermediate or by-product during nucleosome remodeling by the RSC complex. Identification of the loss of histone-DNA contacts during chromatin remodeling by RSC in vivo has implications for the regulation of transcriptional initiation. PMID:26933790

  2. Chromatin Higher-order Structure and Dynamics

    PubMed Central

    Woodcock, Christopher L.; Ghosh, Rajarshi P.

    2010-01-01

    The primary role of the nucleus as an information storage, retrieval, and replication site requires the physical organization and compaction of meters of DNA. Although it has been clear for many years that nucleosomes constitute the first level of chromatin compaction, this contributes a relatively small fraction of the condensation needed to fit the typical genome into an interphase nucleus or set of metaphase chromosomes, indicating that there are additional “higher order” levels of chromatin condensation. Identifying these levels, their interrelationships, and the principles that govern their occurrence has been a challenging and much discussed problem. In this article, we focus on recent experimental advances and the emerging evidence indicating that structural plasticity and chromatin dynamics play dominant roles in genome organization. We also discuss novel approaches likely to yield important insights in the near future, and suggest research areas that merit further study. PMID:20452954

  3. Nuclease digestion studies of chromatin structure

    SciTech Connect

    Deutsch, S.M.

    1987-01-01

    Micrococcal nuclease, which preferentially cleaves linker DNA in chromatin, was immobilized by covalent attachment to CNBr-activated agarose beads and used to study the accessibility of linker DNA in chromatin fibers prepared from chicken erythrocyte nuclei. This immobilized nuclease was able to cleave chromatin fibers into the typical pattern of fragments corresponding to multiples of mononucleosomes. Cleavage from only the ends of the fibers was ruled out by examining the products of cleavage of fibers end-labelled with /sup 35/P. Comparison of the rate of digestion by immobilized and soluble micrococcal nuclease indicated that the fiber structure does not significantly affect access to linker DNA. The absence of an effect of reducing temperatures on the rate of digestion of fibers, as compared to short oligonucleosomes, indicated that breathing motions to allow access to the fiber interior were not required for cleavage of linker DNA.

  4. Open chromatin reveals the functional maize genome

    PubMed Central

    Rodgers-Melnick, Eli; Vera, Daniel L.; Bass, Hank W.

    2016-01-01

    Cellular processes mediated through nuclear DNA must contend with chromatin. Chromatin structural assays can efficiently integrate information across diverse regulatory elements, revealing the functional noncoding genome. In this study, we use a differential nuclease sensitivity assay based on micrococcal nuclease (MNase) digestion to discover open chromatin regions in the maize genome. We find that maize MNase-hypersensitive (MNase HS) regions localize around active genes and within recombination hotspots, focusing biased gene conversion at their flanks. Although MNase HS regions map to less than 1% of the genome, they consistently explain a remarkably large amount (∼40%) of heritable phenotypic variance in diverse complex traits. MNase HS regions are therefore on par with coding sequences as annotations that demarcate the functional parts of the maize genome. These results imply that less than 3% of the maize genome (coding and MNase HS regions) may give rise to the overwhelming majority of phenotypic variation, greatly narrowing the scope of the functional genome. PMID:27185945

  5. CHD chromatin remodelers and the transcription cycle.

    PubMed

    Murawska, Magdalena; Brehm, Alexander

    2011-01-01

    It is well established that ATP-dependent chromatin remodelers modulate DNA access of transcription factors and RNA polymerases by "opening" or "closing" chromatin structure. However, this view is far too simplistic. Recent findings have demonstrated that these enzymes not only set the stage for the transcription machinery to act but are actively involved at every step of the transcription process. As a consequence, they affect initiation, elongation, termination and RNA processing. In this review we will use the CHD family as a paradigm to illustrate the progress that has been made in revealing these new concepts.

  6. Rapid and unbiased extraction of chromatin associated RNAs from purified native chromatin.

    PubMed

    Zhou, Zhongwu; Yang, Yi; Konieczny, Stephen F; Irudayaraj, Joseph M K

    2015-12-24

    An ultra fast and unbiased method that uses salicylic acid coated magnetic nanoparticles (SAMNPs) and magnetophoretic chromatography is developed to extract chromatin associated RNAs (CARs). The SAMNPs were first used for enriching cells from the cell culture media and further used for capturing chromatin after cells were lysed. The formed SAMNPs-chromatin complexes were transferred to a viscous polyethylene glycol (PEG) solution stored in a 200-μl pipette tip. Due to the difference in viscosities, a bi-layer liquid was formed inside the pipette tip. The SAMNPs-chromatin complexes were separated from the free SAMNPs and free RNA-SAMNPs complexes by applying an external magnetic field. The CARs were further extracted from the SAMNP-chromatin complexes directly. The extracted CARs were reverse transcribed as cDNA and further characterized by real-time qPCR. The total assay time taken for cell separation, chromatin purification and chromatin associated RNAs extraction can be accomplished in less than 2h. PMID:26643718

  7. Light-induced gradual activation of photosystem II in dark-grown Norway spruce seedlings.

    PubMed

    Pavlovič, Andrej; Stolárik, Tibor; Nosek, Lukáš; Kouřil, Roman; Ilík, Petr

    2016-06-01

    Gymnosperms, unlike angiosperms, are able to synthesize chlorophyll and form photosystems in complete darkness. Photosystem I (PSI) formed under such conditions is fully active, but photosystem II (PSII) is present in its latent form with inactive oxygen evolving complex (OEC). In this work we have studied light-induced gradual changes in PSII function in dark-grown cotyledons of Norway spruce (Picea abies) via the measurement of chlorophyll a fluorescence rise, absorption changes at 830 nm, thermoluminescence glow curves (TL) and protein analysis. The results indicate that in dark-grown cotyledons, alternative reductants were able to act as electron donors to PSII with inactive OEC. Illumination of cotyledons for 5 min led to partial activation of PSII, which was accompanied by detectable oxygen evolution, but still a substantial number of PSII centers remained in the so called PSII-Q(B)-non-reducing form. Interestingly, even 24 h long illumination was not sufficient for the full activation of PSII centers. This was evidenced by a weak attachment of PsbP protein and the absence of PsbQ protein in PSII particles, the absence of PSII supercomplexes, the suboptimal maximum yield of PSII photochemistry, the presence of C band in TL curve and also the presence of up-shifted Q band in TL in DCMU-treated cotyledons. This slow light-induced activation of PSII in dark-grown cotyledons could contribute to the prevention of PSII overexcitation before the light-induced increase in PSI/PSII ratio allows effective operation of linear electron flow. PMID:26901522

  8. Light-induced gradual activation of photosystem II in dark-grown Norway spruce seedlings.

    PubMed

    Pavlovič, Andrej; Stolárik, Tibor; Nosek, Lukáš; Kouřil, Roman; Ilík, Petr

    2016-06-01

    Gymnosperms, unlike angiosperms, are able to synthesize chlorophyll and form photosystems in complete darkness. Photosystem I (PSI) formed under such conditions is fully active, but photosystem II (PSII) is present in its latent form with inactive oxygen evolving complex (OEC). In this work we have studied light-induced gradual changes in PSII function in dark-grown cotyledons of Norway spruce (Picea abies) via the measurement of chlorophyll a fluorescence rise, absorption changes at 830 nm, thermoluminescence glow curves (TL) and protein analysis. The results indicate that in dark-grown cotyledons, alternative reductants were able to act as electron donors to PSII with inactive OEC. Illumination of cotyledons for 5 min led to partial activation of PSII, which was accompanied by detectable oxygen evolution, but still a substantial number of PSII centers remained in the so called PSII-Q(B)-non-reducing form. Interestingly, even 24 h long illumination was not sufficient for the full activation of PSII centers. This was evidenced by a weak attachment of PsbP protein and the absence of PsbQ protein in PSII particles, the absence of PSII supercomplexes, the suboptimal maximum yield of PSII photochemistry, the presence of C band in TL curve and also the presence of up-shifted Q band in TL in DCMU-treated cotyledons. This slow light-induced activation of PSII in dark-grown cotyledons could contribute to the prevention of PSII overexcitation before the light-induced increase in PSI/PSII ratio allows effective operation of linear electron flow.

  9. Beneficial protective effect of pramipexole on light-induced retinal damage in mice.

    PubMed

    Shibagaki, Keiichi; Okamoto, Kazuyoshi; Katsuta, Osamu; Nakamura, Masatsugu

    2015-10-01

    We investigated the effects of pramipexole, a potent dopamine receptor D2/D3 agonist, on light-induced retinal damage in mice, H2O2-induced retinal pigment epithelium ARPE-19 cell injury in humans, and hydroxyl radical scavenging activity in a cell-free system. Pramipexole (0.1 and 1 mg/kg body weight) was orally administered to mice 1 h before light exposure (5000 lux, 2 h). Electrophysiological and morphologic studies were performed to evaluate the effects of the pramipexole on light-induced retinal damage in mice. Pramipexole significantly prevented the reduction of the a- and b-wave electroretinogram (ERG) amplitudes caused by light exposure in a dose-dependent manner. In parallel, damage to the inner and outer segments (IS/OS) of the photoreceptors, loss of photoreceptor nuclei, and the number of Tdt-mediated dUTP nick-end labeling (TUNEL)-positive cells in the outer nuclear layer (ONL) caused by light exposure were notably ameliorated by pramipexole. Additionally, pramipexole suppressed H2O2-induced ARPE-19 cell death in vitro in a concentration-dependent manner. The effect of pramipexole was significant at concentrations of 10(-6) M or higher. Pramipexole also significantly prevented H2O2-induced activation of caspases-3/7 and the intracellular accumulation of reactive oxygen species (ROS) in a concentration-dependent manner ranging from 10(-5) to 10(-3) M. Furthermore, pramipexole increased the scavenging activity toward a hydroxyl radical generated from H2O2 in a Fenton reaction. Our results suggest that pramipexole protects against light-induced retinal damage as an antioxidant and that it may be a novel and effective therapy for retinal degenerative disorders, such as dry age-related macular degeneration.

  10. Simulation of light-induced degradation of μc-Si in a-Si/μc-Si tandem solar cells by the diode equivalent circuit

    NASA Astrophysics Data System (ADS)

    Weicht, J. A.; Hamelmann, F. U.; Behrens, G.

    2016-02-01

    Silicon-based thin film tandem solar cells consist of one amorphous (a-Si) and one microcrystalline (μc-Si) silicon solar cell. The Staebler - Wronski effect describes the light- induced degradation and temperature-dependent healing of defects of silicon-based solar thin film cells. The solar cell degradation depends strongly on operation temperature. Until now, only the light-induced degradation (LID) of the amorphous layer was examined in a-Si/μc-Si solar cells. The LID is also observed in pc-Si single function solar cells. In our work we show the influence of the light-induced degradation of the μc-Si layer on the diode equivalent circuit. The current-voltage-curves (I-V-curves) for the initial state of a-Si/pc-Si modules are measured. Afterwards the cells are degraded under controlled conditions at constant temperature and constant irradiation. At fixed times the modules are measured at standard test conditions (STC) (AM1.5, 25°C cell temperature, 1000 W/m2) for controlling the status of LID. After the degradation the modules are annealed at dark conditions for several hours at 120°C. After the annealing the dangling bonds in the amorphous layer are healed, while the degradation of the pc-Si is still present, because the healing of defects in pc-Si solar cells needs longer time or higher temperatures. The solar cells are measured again at STC. With this laboratory measured I-V-curves we are able to separate the values of the diode model: series Rs and parallel resistance Rp, saturation current Is and diode factor n.

  11. Cold-Atom Physics Using Ultrathin Optical Fibers: Light-Induced Dipole Forces and Surface Interactions

    SciTech Connect

    Sague, G.; Vetsch, E.; Alt, W.; Meschede, D.; Rauschenbeutel, A.

    2007-10-19

    The strong evanescent field around ultrathin unclad optical fibers bears a high potential for detecting, trapping, and manipulating cold atoms. Introducing such a fiber into a cold-atom cloud, we investigate the interaction of a small number of cold cesium atoms with the guided fiber mode and with the fiber surface. Using high resolution spectroscopy, we observe and analyze light-induced dipole forces, van der Waals interaction, and a significant enhancement of the spontaneous emission rate of the atoms. The latter can be assigned to the modification of the vacuum modes by the fiber.

  12. Robust Measurement of Thin-Film Photovoltaic Modules Exhibiting Light-Induced Transients: Preprint

    SciTech Connect

    Deceglie, Michael, G.; Silverman, Timothy J.; Marion, Bill; Kurtz, Sarah R.

    2015-09-09

    Light-induced changes to the current-voltage characteristic of thin-film photovoltaic modules (i.e. light-soaking effects) frustrate the repeatable measurement of their operating power. We describe best practices for mitigating, or stabilizing, light-soaking effects for both CdTe and CIGS modules to enable robust, repeatable, and relevant power measurements. We motivate the practices by detailing how modules react to changes in different stabilization methods. We also describe and demonstrate a method for validating alternative stabilization procedures, such as those relying on forward bias in the dark. Reliable measurements of module power are critical for qualification testing, reliability testing, and power rating.

  13. Light-induced phenomena in one-component gas: The transport phenomena

    NASA Astrophysics Data System (ADS)

    Chermyaninov, I. V.; Chernyak, V. G.

    2016-09-01

    The article presents the theory of transport processes in a one-component gas located in the capillary under the action of resonant laser radiation and the temperature and pressure gradients. The expressions for the kinetic coefficients determining heat and mass transport in the gas are obtained on the basis of the modified Boltzmann equations for the excited and unexcited particles. The Onsager reciprocal relations for cross kinetic coefficients are proven for all Knudsen numbers and for any law interaction of gas particles with each other and boundary surface. Light-induced phenomena associated with the possible non-equilibrium stationary states of system are analyzed.

  14. Light-Induced Resistance Effect Observed in Nano Au Films Covered Two-Dimensional Colloidal Crystals.

    PubMed

    Liu, Shuai; Huang, Meizhen; Yao, Yanjie; Wang, Hui; Jin, Kui-juan; Zhan, Peng; Wang, Zhenlin

    2015-09-01

    Tailoring resistance response using periodic nanostructures is one of the key issues in the current research. Two-dimensional colloidal crystals (CCs) structure is one of popular periodic nanospheres' structures and most of reports are focused on anomalous transmission of light or biomedical applications. In this work, a light-induced resistance effect is observed on silicon-based Au films covered CCs, featuring a remarkable resistance change as much as 56% and resistance switching characteristic. The diffusion and recombination of photocarriers is the crucial factor for this effect. This finding will expand photoelectricity functionality and be useful for future development of CC-based photoelectric devices.

  15. Light-induced absorption instability in weakly reduced congruent Er:LiNbO3 crystal

    NASA Astrophysics Data System (ADS)

    Zhang, D.-L.; Zhang, J.; Wang, Y.-F.; Zhu, D.-S.; Wu, Z.-K.; Pun, E. Y. B.

    2005-05-01

    Light-induced absorption (LIA) characteristics in weakly reduced (or strongly annealed) congruent and/or vapor transport equilibration (VTE)-treated Er-doped LiNbO3 crystals have been investigated in comparison with their corresponding as-grown ones and undoped crystals by using a polarized 632.8-nm beam as probe light and another polarized 632.8- or 488-nm beam as pump light. Under He-Ne pump, the LIA was observed only in strongly reduced pure VTE LiNbO3 crystal. Under 488-nm pump, LIA is still not observed in the doped or undoped as-grown crystals. The weakly reduced VTE-treated Er(0.2 mol %):LiNbO3 crystal displays weak and stable LIA. On the other hand, the corresponding weakly reduced congruent crystal displays a rather unpredictable light-induced absorption instability phenomenon. The instability was shown by the random competition of the LIA and light-induced transparency (LIT). When both crystals were further reduced, the VTE sample still shows stable LIA but with increased LIA, while the LIA in the congruent sample also becomes stable enough. The instability was experimentally proved to be associated with the presence of the Er3+ ion that performs the role of an extrinsic defect instead of photoluminescence. A three-level model is suggested that consists of a deep level (the bipolaron) and two shallow levels: the small polaron level and the level with respect to the Er3+ ion. The model has been employed to qualitatively explain the LIA characteristics of the weakly reduced congruent Er:LiNbO3 crystal, including the the instability, the effect of the state of reduction, the pump intensity and the pump-probe polarization dependences. The inhomogeneity of the defects caused by the weak reduction and the simultaneous participation of the two shallow levels in the light-induced electron-transport process result in the random competition between LIA and LIT, and consequently result in the LIA instability.

  16. Three components in the light-induced current of the Limulus ventral photoreceptor.

    PubMed Central

    Deckert, A; Nagy, K; Helrich, C S; Stieve, H

    1992-01-01

    1. Light-induced currents were measured in Limulus ventral nerve photoreceptors using a two-electrode voltage clamp. Three kinetically distinct components in the light-induced current could be distinguished by varying the light adaptation state of the photoreceptor and the intensity of the stimulus light. 2. The components could be partly separated by choosing appropriate stimulus intensities and dark adaptation time. Thus the properties of the components could be separately studied. The first component is the first to recover after a light adaptation, appears temporally first in the light-induced response, has the lowest activation threshold and is the smallest. The second component needs a longer time to recover after an adapting illumination and its kinetics differ from that of the other components. Applying a bright stimulus to a dark-adapted cell a third component can be observed late in the response. 3. The time to peak of the first and the third components depended on the stimulus intensity, but not on the dark adaptation time. The time to peak of the second component became shorter the longer the dark adaptation time. For a constant adaptation state the time to the maximum of component 2 was independent, but those of components 1 and 3 were dependent on the membrane voltage. 4. To exclude the possibility of the contribution of voltage-gated currents, light-activated currents were measured at clamp potentials more negative than -50 mV after adding 4-aminopyridine into the bath solution or injecting tetraethyl-ammonium chloride into the cell. The properties of the three components remained unchanged under these conditions. 5. The I-V curve of the first component was flat at negative membrane potentials and had a strong outward rectification at positive membrane potentials. The I-V curve of component 3 showed a negative resistance at potentials more negative than about -30 mV. In contrast, the I-V curve for the second component was always nearly linear. 6. No

  17. Light-Induced Resistance Effect Observed in Nano Au Films Covered Two-Dimensional Colloidal Crystals.

    PubMed

    Liu, Shuai; Huang, Meizhen; Yao, Yanjie; Wang, Hui; Jin, Kui-juan; Zhan, Peng; Wang, Zhenlin

    2015-09-01

    Tailoring resistance response using periodic nanostructures is one of the key issues in the current research. Two-dimensional colloidal crystals (CCs) structure is one of popular periodic nanospheres' structures and most of reports are focused on anomalous transmission of light or biomedical applications. In this work, a light-induced resistance effect is observed on silicon-based Au films covered CCs, featuring a remarkable resistance change as much as 56% and resistance switching characteristic. The diffusion and recombination of photocarriers is the crucial factor for this effect. This finding will expand photoelectricity functionality and be useful for future development of CC-based photoelectric devices. PMID:26314930

  18. Formation kinetics of copper-related light-induced degradation in crystalline silicon

    SciTech Connect

    Lindroos, J. Savin, H.

    2014-12-21

    Light-induced degradation (LID) is a deleterious effect in crystalline silicon, which is considered to originate from recombination-active boron-oxygen complexes and/or copper-related defects. Although LID in both cases appears as a fast initial decay followed by a second slower degradation, we show that the time constant of copper-related degradation increases with increasing boron concentration in contrast to boron-oxygen LID. Temperature-dependent analysis reveals that the defect formation is limited by copper diffusion. Finally, interface defect density measurements confirm that copper-related LID is dominated by recombination in the wafer bulk.

  19. Blue and green light-induced phototropism in Arabidopsis thaliana and Lactuca sativa L. seedlings

    SciTech Connect

    Steinitz, B.; Ren, Z.; Poff, K.L.

    1985-01-01

    Exposure time-response curves for blue and green light-induced phototropic bending in hypocotyls of Arabidopsis thaliana (L.) Heynh. and Lactuca sativa L. seedlings are presented. These seedlings show significant phototropic sensitivity up to 540 to 550 nanometers. Since wavelengths longer than 560 nanometers do not induce phototropic bending, it is suggested that the response to 510 to 550 nanometers light is mediated by the specific blue light photoreceptor of phototropism. The authors advise care in the use of green safelights for studies of phototropism.

  20. UV light induced photodegradation of organic dye by ZnO nanocatalysts

    SciTech Connect

    Sumesh, C. K.; Patel, Bhavin; Parekh, Kinnari

    2013-06-03

    Ultraviolet light induced photocatalytic activity of ZnO nanocatalyst prepared using a wet chemical precipitation route and mineralization of the methyl orange (MO) dye has been carried out in a photocatalytic reactor. The degradation of the MO was monitored spectrophotometrically and showed a decolorization efficiency of 92% after nine hours of irradiation in the MO-ZnO/UV light system. The blue shifting of maximum peak position of the MO and the formation of extra peak at 247 nm during irradiation time advances revealed that MO degrades in the form of intermediates during the photocatalytic process.

  1. Multiple phytochromes are involved in red-light-induced enhancement of first-positive phototropism in Arabidopsis thaliana.

    PubMed Central

    Janoudi, A K; Gordon, W R; Wagner, D; Quail, P; Poff, K L

    1997-01-01

    The amplitude of phototropic curvature to blue light is enhanced by a prior exposure of seedlings to red light. This enhancement is mediated by phytochrome. Fluence-response relationships have been constructed for red-light-induced enhancement in the phytochrome A (phyA) null mutant, the phytochrome B- (phyB) deficient mutant, and in two transgenic lines of Rabidopsis thaliana that overexpress either phyA or phyB. These fluence-response relationships demonstrate the existence of two response in enhancement, a response in the very-low-to-low-fluence range, and a response in the high-fluence range. Only the response in the high-fluence range is present in the phyA null mutant. In contrast, the phyB-deficient mutant is indistinguishable from the wild-type parent in red-light responsiveness. These data indiacate that phyA is necessary for the very-low-to-low but not the high-influence response, and that phyB is not necessary for either response range. Based on these results, the high-fluence response, if controlled by a single phytochrome, must be controlled by aphytochorme other than phyA of phyB. Overexpression of phyA has a negative effect and overexpression of phyB has an enhancing effect in the high-fluence range. These results suggest that overexpression of either phytochrome perturbs the function of the endogenous photoreceptor system in an unpredictable fashion. PMID:9085579

  2. The HT1 protein kinase is essential for red light-induced stomatal opening and genetically interacts with OST1 in red light and CO2 -induced stomatal movement responses.

    PubMed

    Matrosova, Anastasia; Bogireddi, Hanumakumar; Mateo-Peñas, Alfonso; Hashimoto-Sugimoto, Mimi; Iba, Koh; Schroeder, Julian I; Israelsson-Nordström, Maria

    2015-12-01

    The question of whether red light-induced stomatal opening is mediated by a photosynthesis-derived reduction in intercellular [CO2 ] (Ci ) remains controversial and genetic analyses are needed. The Arabidopsis thaliana protein kinase HIGH TEMPERATURE 1 (HT1) is a negative regulator of [CO2 ]-induced stomatal closing and ht1-2 mutant plants do not show stomatal opening to low [CO2 ]. The protein kinase mutant ost1-3 exhibits slowed stomatal responses to CO2 . The functions of HT1 and OPEN STOMATA 1 (OST1) to changes in red, blue light or [CO2 ] were analyzed. For comparison we assayed recessive ca1ca4 carbonic anhydrase double mutant plants, based on their slowed stomatal response to CO2 . Here, we report a strong impairment in ht1 in red light-induced stomatal opening whereas blue light was able to induce stomatal opening. The effects on photosynthetic performance in ht1 were restored when stomatal limitation of CO2 uptake, by control of [Ci ], was eliminated. HT1 was found to interact genetically with OST1 both during red light- and low [CO2 ]-induced stomatal opening. Analyses of ca1ca4 plants suggest that more than a low [Ci ]-dependent pathway may function in red light-induced stomatal opening. These results demonstrate that HT1 is essential for red light-induced stomatal opening and interacts genetically with OST1 during stomatal responses to red light and altered [CO2 ]. PMID:26192339

  3. The HT1 protein kinase is essential for red light-induced stomatal opening and genetically interacts with OST1 in red light and CO2 -induced stomatal movement responses.

    PubMed

    Matrosova, Anastasia; Bogireddi, Hanumakumar; Mateo-Peñas, Alfonso; Hashimoto-Sugimoto, Mimi; Iba, Koh; Schroeder, Julian I; Israelsson-Nordström, Maria

    2015-12-01

    The question of whether red light-induced stomatal opening is mediated by a photosynthesis-derived reduction in intercellular [CO2 ] (Ci ) remains controversial and genetic analyses are needed. The Arabidopsis thaliana protein kinase HIGH TEMPERATURE 1 (HT1) is a negative regulator of [CO2 ]-induced stomatal closing and ht1-2 mutant plants do not show stomatal opening to low [CO2 ]. The protein kinase mutant ost1-3 exhibits slowed stomatal responses to CO2 . The functions of HT1 and OPEN STOMATA 1 (OST1) to changes in red, blue light or [CO2 ] were analyzed. For comparison we assayed recessive ca1ca4 carbonic anhydrase double mutant plants, based on their slowed stomatal response to CO2 . Here, we report a strong impairment in ht1 in red light-induced stomatal opening whereas blue light was able to induce stomatal opening. The effects on photosynthetic performance in ht1 were restored when stomatal limitation of CO2 uptake, by control of [Ci ], was eliminated. HT1 was found to interact genetically with OST1 both during red light- and low [CO2 ]-induced stomatal opening. Analyses of ca1ca4 plants suggest that more than a low [Ci ]-dependent pathway may function in red light-induced stomatal opening. These results demonstrate that HT1 is essential for red light-induced stomatal opening and interacts genetically with OST1 during stomatal responses to red light and altered [CO2 ].

  4. Profiling of the Chromatin-associated Proteome Identifies HP1BP3 as a Novel Regulator of Cell Cycle Progression *

    PubMed Central

    Dutta, Bamaprasad; Ren, Yan; Hao, Piliang; Sim, Kae Hwan; Cheow, Esther; Adav, Sunil; Tam, James P.; Sze, Siu Kwan

    2014-01-01

    The chromatin-associated proteome (chromatome) regulates cellular gene expression by restricting access of transcriptional machinery to template DNA, and dynamic re-modeling of chromatin structure is required to regulate critical cell functions including growth and replication, DNA repair and recombination, and oncogenic transformation in progression to cancer. Central to the control of these processes is efficient regulation of the host cell cycle, which is maintained by rapid changes in chromatin conformation during normal cycle progression. A global overview of chromatin protein organization is therefore essential to fully understand cell cycle regulation, but the influence of the chromatome and chromatin binding topology on host cell cycle progression remains poorly defined. Here we used partial MNase digestion together with iTRAQ-based high-throughput quantitative proteomics to quantify chromatin-associated proteins during interphase progression. We identified a total of 481 proteins with high confidence that were involved in chromatin-dependent events including transcriptional regulation, chromatin re-organization, and DNA replication and repair, whereas the quantitative data revealed the temporal interactions of these proteins with chromatin during interphase progression. When combined with biochemical and functional assays, these data revealed a strikingly dynamic association of protein HP1BP3 with the chromatin complex during different stages of interphase, and uncovered a novel regulatory role for this molecule in transcriptional regulation. We report that HP1BP3 protein maintains heterochromatin integrity during G1–S progression and regulates the duration of G1 phase to critically influence cell proliferative capacity. PMID:24830416

  5. Synergistic effect of IFN-γ gene on LIGHT-induced apoptosis in HepG2 cells via down regulation of Bcl-2.

    PubMed

    Han, Bing; Wu, Li-Qun; Ma, Xiang; Wang, Zheng-Hua; Li, Jin-Peng; Bi, Chong-Yao; Yong, Sun

    2011-08-01

    To detect the expression of anti-apoptotic factor Bcl-2 and Survivin in transferred HepG2 cells and evaluate the synergistic effect of IFN-γ gene on LIGHT-induced apoptosis signal transduction pathways, the full-length ORF of LIGHT and IFN-γ gene were cloned into pcDNA4 and verified by DNA sequencing. After being optimized by EGFP, recombinant LIGHT and IFN-γ were transferred into the HepG2 cells mediated by a cationic liposome in vitro. The expression of LIGHT and IFN-γ was identified in the supernatants by ELISA. The HepG2 cells were divided into three groups: the control, LIGHT gene transfection alone, and simultaneous transfection of LIGHT and IFN-γ genes. The cell apoptosis and expression of Bcl-2 and Survivin in cell lysate were detected through FCM. After transfection, the apoptosis rate of HepG2 cells was increased with the prolonged time, and the apoptosis rate of LIGHT group was higher than the control group, while the LIGHT/IFN-γ group was higher than the LIGHT group P < 0.01). The expression of Bcl-2 and Survivin in LIGHT group and LIGHT/IFN-γ group decreased dramatically compared with the control group. LIGHT gene alone can result in significant inhibition of HepG2 cells proliferation. INF-γ can synergistically precede LIGHT-induced apoptotic processes through down-regulation of Bcl-2 expression, but not survivin expression.

  6. Light induced heterogeneous ozone processing on the pesticides adsorbed on silica particles

    NASA Astrophysics Data System (ADS)

    Socorro, J.; Désert, M.; Quivet, E.; Gligorovski, S.; Wortham, H.

    2013-12-01

    In France, in 2010, the sales of pesticides reached 1.8 billion euros for 61 900 tons of active ingredients, positioning France as a first European consumer of pesticides, as reported by the European Crop Protection Association. About 19 million hectares of crops are sprayed annually with pesticides, i.e., 35% of the total surface area of France. This corresponds to an average pesticide dose of 3.2 kg ha-1. The consumption of herbicide and fungicide is favoured in comparison to the use of insecticides in France and the other European countries, as well. The partitioning of pesticides between the gas and particulate phases influences the atmospheric fate of these compounds such as their photo-chemical degradation. There is much uncertainty concerning the behavior of the pesticides in the atmosphere. Especially, there is a gap of knowledge concerning the degradation of the pesticides induced by heterogeneous reactions in absence and especially in presence of solar light. Considering that most of the pesticides currently used are semi-volatile, it is of crucial importance to investigate the heterogeneous reactivity of particulate pesticides with light and with atmospheric oxidants such as ozone and OH radical. The aim of the present work is to evaluate the light induced heterogeneous ozonation of suspended pesticide particles. 8 pesticides (cyprodinil, deltamethrin, difenoconazole, fipronil, oxadiazon, pendimethalin, permethrin and tetraconazole) were chosen for their physico-chemical properties and their concentration levels in the PACA (Région Provence-Alpes-Côte d'Azur) region, France. Silica particles with well-known properties were chosen as model particles of atmospheric relevance. Kinetic rate constants were determined to allow estimate the atmospheric lifetimes relating to ozone. The rate constants were determined as follows: k = (6.6 × 0.2) 10-19, (7.2 × 0.3) 10-19, (5.1 × 0.5) 10-19, (3.9 × 0.3) 10-19 [cm3 molecules-1 s-1] for Cyprodinil

  7. Chromatin regulation: how complex does it get?

    PubMed

    Meier, Karin; Brehm, Alexander

    2014-11-01

    Gene transcription is tightly regulated at different levels to ensure that the transcriptome of the cell is appropriate for developmental stage and cell type. The chromatin state in which a gene is embedded determines its expression level to a large extent. Activation or repression of transcription is typically accomplished by the recruitment of chromatin-associated multisubunit protein complexes that combine several molecular tools, such as histone-binding and chromatin-modifying activities. Recent biochemical purifications of such complexes have revealed a substantial diversity. On the one hand, complexes that were thought to be unique have been revealed to be part of large complex families. On the other hand, protein subunits that were thought to only exist in separate complexes have been shown to coexist in novel assemblies. In this review we discuss our current knowledge of repressor complexes that contain MBT domain proteins and/or the CoREST co-repressor and use them as a paradigm to illustrate the unexpected heterogeneity and tool sharing of chromatin regulating protein complexes. These recent insights also challenge the ways we define and think about protein complexes in general. PMID:25482055

  8. The great repression: chromatin and cryptic transcription.

    PubMed

    Hennig, Bianca P; Fischer, Tamás

    2013-01-01

    The eukaryotic chromatin structure is essential in correctly defining transcription units. Impairing this structure can activate cryptic promoters, and lead to the accumulation of aberrant RNA transcripts. Here we discuss critical pathways that are responsible for the repression of cryptic transcription and the maintenance of genome integrity.

  9. Trivalent chromatin marks the way in.

    PubMed

    Hysolli, Eriona; Park, In-Hyun

    2013-11-01

    Recently in Cell, Wapinski et al. (2013) investigated the epigenetic mechanisms underlying the direct conversion of fibroblasts to induced neurons (iNs). They found that Ascl1 acts as a pioneer factor at neurogenic loci marked by a closed "trivalent" chromatin state in cells permissive to direct conversion, but not in restrictive cell types. PMID:24209756

  10. Histone variants: key players of chromatin.

    PubMed

    Biterge, Burcu; Schneider, Robert

    2014-06-01

    Histones are fundamental structural components of chromatin. Eukaryotic DNA is wound around an octamer of the core histones H2A, H2B, H3, and H4. Binding of linker histone H1 promotes higher order chromatin organization. In addition to their structural role, histones impact chromatin function and dynamics by, e.g., post-translational histone modifications or the presence of specific histone variants. Histone variants exhibit differential expression timings (DNA replication-independent) and mRNA characteristics compared to canonical histones. Replacement of canonical histones with histone variants can affect nucleosome stability and help to create functionally distinct chromatin domains. In line with this, several histone variants have been implicated in the regulation of cellular processes such as DNA repair and transcriptional activity. In this review, we focus on recent progress in the study of core histone variants H2A.X, H2A.Z, macroH2A, H3.3, and CENP-A, as well as linker histone H1 variants, their functions and their links to development and disease.

  11. Chemical biology: Chromatin chemistry goes cellular

    NASA Astrophysics Data System (ADS)

    Fischle, Wolfgang; Schwarzer, Dirk; Mootz, Henning D.

    2015-05-01

    Analysing post-translational modifications of histone proteins as they occur within chromatin is challenging due to their large number and chemical diversity. A major step forward has now been achieved by using split intein chemistry to engineer functionalized histones within cells.

  12. Chromatin regulation: How complex does it get?

    PubMed Central

    Meier, Karin; Brehm, Alexander

    2014-01-01

    Gene transcription is tightly regulated at different levels to ensure that the transcriptome of the cell is appropriate for developmental stage and cell type. The chromatin state in which a gene is embedded determines its expression level to a large extent. Activation or repression of transcription is typically accomplished by the recruitment of chromatin-associated multisubunit protein complexes that combine several molecular tools, such as histone-binding and chromatin-modifying activities. Recent biochemical purifications of such complexes have revealed a substantial diversity. On the one hand, complexes that were thought to be unique have been revealed to be part of large complex families. On the other hand, protein subunits that were thought to only exist in separate complexes have been shown to coexist in novel assemblies. In this review we discuss our current knowledge of repressor complexes that contain MBT domain proteins and/or the CoREST co-repressor and use them as a paradigm to illustrate the unexpected heterogeneity and tool sharing of chromatin regulating protein complexes. These recent insights also challenge the ways we define and think about protein complexes in general. PMID:25482055

  13. Unraveling the mechanisms of chromatin fibril packaging.

    PubMed

    Gavrilov, Alexey A; Shevelyov, Yuri Y; Ulianov, Sergey V; Khrameeva, Ekaterina E; Kos, Pavel; Chertovich, Alexander; Razin, Sergey V

    2016-05-01

    Recent data indicate that eukaryotic chromosomes are organized into Topologically Associating Domains (TADs); however, the mechanisms underlying TAD formation remain obscure. Based on the results of Hi-C analysis performed on 4 Drosophila melanogaster cell lines, we have proposed that specific properties of nucleosomes in active and repressed chromatin play a key role in the formation of TADs. Our computer simulations showed that the ability of "inactive" nucleosomes to stick to each other and the lack of such ability in "active" nucleosomes is sufficient for spatial segregation of these types of chromatin, which is revealed in the Hi-C analysis as TAD/inter-TAD partitioning. However, some Drosophila and mammalian TADs contain both active and inactive chromatin, a fact that does not fit this model. Herein, we present additional arguments for the model by postulating that transcriptionally active chromatin is extruded on the surface of a TAD, and discuss the possible impact of this organization on the enhancer-promoter communication and on the segregation of TADs. PMID:27249516

  14. Epigenetic chromatin silencing: bistability and front propagation

    NASA Astrophysics Data System (ADS)

    Sedighi, Mohammad; Sengupta, Anirvan M.

    2007-12-01

    The role of post-translational modification of histones in eukaryotic gene regulation is well recognized. Epigenetic silencing of genes via heritable chromatin modifications plays a major role in cell fate specification in higher organisms. We formulate a coarse-grained model of chromatin silencing in yeast and study the conditions under which the system becomes bistable, allowing for different epigenetic states. We also study the dynamics of the boundary between the two locally stable states of chromatin: silenced and unsilenced. The model could be of use in guiding the discussion on chromatin silencing in general. In the context of silencing in budding yeast, it helps us understand the phenotype of various mutants, some of which may be non-trivial to see without the help of a mathematical model. One such example is a mutation that reduces the rate of background acetylation of particular histone side chains that competes with the deacetylation by Sir2p. The resulting negative feedback due to a Sir protein depletion effect gives rise to interesting counter-intuitive consequences. Our mathematical analysis brings forth the different dynamical behaviors possible within the same molecular model and guides the formulation of more refined hypotheses that could be addressed experimentally.

  15. Epigenetic chromatin silencing: bistability and front propagation

    PubMed Central

    Sedighi, Mohammad; Sengupta, Anirvan M

    2008-01-01

    The role of post-translational modification of histones in eukaryotic gene regulation is well recognized. Epigenetic silencing of genes via heritable chromatin modifications plays a major role in cell fate specification in higher organisms. We formulate a coarse-grained model of chromatin silencing in yeast and study the conditions under which the system becomes bistable, allowing for different epigenetic states. We also study the dynamics of the boundary between the two locally stable states of chromatin: silenced and unsilenced. The model could be of use in guiding the discussion on chromatin silencing in general. In the context of silencing in budding yeast, it helps us understand the phenotype of various mutants, some of which may be non-trivial to see without the help of a mathematical model. One such example is a mutation that reduces the rate of background acetylation of particular histone side chains that competes with the deacetylation by Sir2p. The resulting negative feedback due to a Sir protein depletion effect gives rise to interesting counter-intuitive consequences. Our mathematical analysis brings forth the different dynamical behaviors possible within the same molecular model and guides the formulation of more refined hypotheses that could be addressed experimentally. PMID:17991991

  16. Impaired Mitochondrial Energy Production Causes Light-Induced Photoreceptor Degeneration Independent of Oxidative Stress.

    PubMed

    Jaiswal, Manish; Haelterman, Nele A; Sandoval, Hector; Xiong, Bo; Donti, Taraka; Kalsotra, Auinash; Yamamoto, Shinya; Cooper, Thomas A; Graham, Brett H; Bellen, Hugo J

    2015-07-01

    Two insults often underlie a variety of eye diseases including glaucoma, optic atrophy, and retinal degeneration--defects in mitochondrial function and aberrant Rhodopsin trafficking. Although mitochondrial defects are often associated with oxidative stress, they have not been linked to Rhodopsin trafficking. In an unbiased forward genetic screen designed to isolate mutations that cause photoreceptor degeneration, we identified mutations in a nuclear-encoded mitochondrial gene, ppr, a homolog of human LRPPRC. We found that ppr is required for protection against light-induced degeneration. Its function is essential to maintain membrane depolarization of the photoreceptors upon repetitive light exposure, and an impaired phototransduction cascade in ppr mutants results in excessive Rhodopsin1 endocytosis. Moreover, loss of ppr results in a reduction in mitochondrial RNAs, reduced electron transport chain activity, and reduced ATP levels. Oxidative stress, however, is not induced. We propose that the reduced ATP level in ppr mutants underlies the phototransduction defect, leading to increased Rhodopsin1 endocytosis during light exposure, causing photoreceptor degeneration independent of oxidative stress. This hypothesis is bolstered by characterization of two other genes isolated in the screen, pyruvate dehydrogenase and citrate synthase. Their loss also causes a light-induced degeneration, excessive Rhodopsin1 endocytosis and reduced ATP without concurrent oxidative stress, unlike many other mutations in mitochondrial genes that are associated with elevated oxidative stress and light-independent photoreceptor demise. PMID:26176594

  17. Light induced fluorescence evaluation: A novel concept for caries diagnosis and excavation.

    PubMed

    Gugnani, Neeraj; Pandit, Ik; Srivastava, Nikhil; Gupta, Monika; Gugnani, Shalini

    2011-10-01

    In the era of minimal invasive dentistry, every effort should be directed to preserve the maximum tooth structure during cavity preparation. However, while making cavities, clinicians usually get indecisive at what point caries excavation should be stopped, so as to involve only the infected dentin. Apparent lack of valid clinical markers, difficulties with the use of caries detector dyes and chemo mechanical caries removal systems carve out a need for an improved system, which would be helpful to differentiate between the healthy and infected dentin during caries excavation. Light induced fluorescence evaluation is a novel concept implicated for caries detection and for making decisions while cavity preparation. This paper describes a few cases that explain the clinical applicability of this concept, using the SoproLife camera that works on this principle. Autofluorescence masking effect was found to be helpful for caries detection and the red fluorescence in the treatment mode was found helpful in deciding 'when to stop the excavation process.' Light induced fluorescence evaluation - Diagnosis - Treatment concept concept can be used as a guide for caries detection and excavation. It also facilitates decision making for stopping the caries excavation so as to involve infected dentin only.

  18. Light induced fluorescence evaluation: A novel concept for caries diagnosis and excavation

    PubMed Central

    Gugnani, Neeraj; Pandit, IK; Srivastava, Nikhil; Gupta, Monika; Gugnani, Shalini

    2011-01-01

    In the era of minimal invasive dentistry, every effort should be directed to preserve the maximum tooth structure during cavity preparation. However, while making cavities, clinicians usually get indecisive at what point caries excavation should be stopped, so as to involve only the infected dentin. Apparent lack of valid clinical markers, difficulties with the use of caries detector dyes and chemo mechanical caries removal systems carve out a need for an improved system, which would be helpful to differentiate between the healthy and infected dentin during caries excavation. Light induced fluorescence evaluation is a novel concept implicated for caries detection and for making decisions while cavity preparation. This paper describes a few cases that explain the clinical applicability of this concept, using the SoproLife camera that works on this principle. Autofluorescence masking effect was found to be helpful for caries detection and the red fluorescence in the treatment mode was found helpful in deciding ‘when to stop the excavation process.’ Light induced fluorescence evaluation – Diagnosis - Treatment concept concept can be used as a guide for caries detection and excavation. It also facilitates decision making for stopping the caries excavation so as to involve infected dentin only. PMID:22144816

  19. Two Light-Induced Processes in the Photoreceptor Cells of Limulus Ventral Eye

    PubMed Central

    Lisman, J. E.; Brown, J. E.

    1971-01-01

    The dark-adapted current-voltage (I-V) curve of a ventral photoreceptor cell of Limulus, measured by a voltage-clamp technique, has a high slope-resistance region more negative than resting voltage, a lower slope-resistance region between resting voltage and zero, and a negative slope-resistance region more positive than 0 v. With illumination, we find no unique voltage at which there is no light-induced current. At the termination of illumination, the I-V curve changes quickly, then recovers very slowly to a dark-adapted configuration. The voltage-clamp currents during and after illumination can be interpreted to arise from two separate processes. One process (fast) changes quickly with change in illumination, has a reversal potential at +20 mv, and has an I-V curve with positive slope resistance at all voltages. These properties are consistent with a light-induced change in membrane conductance to sodium ions. The other process (slow) changes slowly with changes in illumination, generates light-activated current at +20 mv, and has an I-V curve with a large region of negative slope resistance. The mechanism of this process cannot as yet be identified. PMID:5122373

  20. Microscopic theory of light-induced deformation in amorphous side-chain azobenzene polymers.

    PubMed

    Toshchevikov, V; Saphiannikova, M; Heinrich, G

    2009-04-16

    We propose a microscopic theory of light-induced deformation of side-chain azobenzene polymers taking into account the internal structure of polymer chains. Our theory is based on the fact that interaction of chromophores with the polarized light leads to the orientation anisotropy of azobenzene macromolecules which is accompanied by the appearance of mechanical stress. It is the first microscopic theory which provides the value of the light-induced stress larger than the yield stress. This result explains a possibility for the inscription of surface relief gratings in glassy side-chain azobenzene polymers. For some chemical architectures, elongation of a sample demonstrates a nonmonotonic behavior with the light intensity and can change its sign (a stretched sample starts to be uniaxially compressed), in agreement with experiments. Using a viscoplastic approach, we show that the irreversible strain of a sample, which remains after the light is switched off, decreases with increasing temperature and can disappear at certain temperature below the glass transition temperature. This theoretical prediction is also confirmed by recent experiments.

  1. Impaired Mitochondrial Energy Production Causes Light-Induced Photoreceptor Degeneration Independent of Oxidative Stress

    PubMed Central

    Jaiswal, Manish; Haelterman, Nele A.; Sandoval, Hector; Xiong, Bo; Donti, Taraka; Kalsotra, Auinash; Yamamoto, Shinya; Cooper, Thomas A.; Graham, Brett H.; Bellen, Hugo J.

    2015-01-01

    Two insults often underlie a variety of eye diseases including glaucoma, optic atrophy, and retinal degeneration—defects in mitochondrial function and aberrant Rhodopsin trafficking. Although mitochondrial defects are often associated with oxidative stress, they have not been linked to Rhodopsin trafficking. In an unbiased forward genetic screen designed to isolate mutations that cause photoreceptor degeneration, we identified mutations in a nuclear-encoded mitochondrial gene, ppr, a homolog of human LRPPRC. We found that ppr is required for protection against light-induced degeneration. Its function is essential to maintain membrane depolarization of the photoreceptors upon repetitive light exposure, and an impaired phototransduction cascade in ppr mutants results in excessive Rhodopsin1 endocytosis. Moreover, loss of ppr results in a reduction in mitochondrial RNAs, reduced electron transport chain activity, and reduced ATP levels. Oxidative stress, however, is not induced. We propose that the reduced ATP level in ppr mutants underlies the phototransduction defect, leading to increased Rhodopsin1 endocytosis during light exposure, causing photoreceptor degeneration independent of oxidative stress. This hypothesis is bolstered by characterization of two other genes isolated in the screen, pyruvate dehydrogenase and citrate synthase. Their loss also causes a light-induced degeneration, excessive Rhodopsin1 endocytosis and reduced ATP without concurrent oxidative stress, unlike many other mutations in mitochondrial genes that are associated with elevated oxidative stress and light-independent photoreceptor demise. PMID:26176594

  2. Fatty Acid Transport Protein 4 (FATP4) Prevents Light-Induced Degeneration of Cone and Rod Photoreceptors by Inhibiting RPE65 Isomerase

    PubMed Central

    Li, Songhua; Lee, Jungsoo; Zhou, Yongdong; Gordon, William C.; Hill, James M.; Bazan, Nicolas G.; Miner, Jeffrey H.; Jin, Minghao

    2013-01-01

    While Rhodopsin is essential for sensing light for vision, it also mediates light-induced apoptosis of photoreceptors in mouse. RPE65, which catalyzes isomerization of all-trans retinyl fatty acid esters to 11-cis retinol (11cROL) in the visual cycle, controls the rhodopsin regeneration rate and photoreceptor susceptibility to light-induced degeneration. Mutations in RPE65 have been linked to blindness in affected children. Despite such importance, the mechanism that regulates RPE65 function remains unclear. Through unbiased expression screening of a bovine retinal pigment epithelium (RPE) cDNA library, we have identified elongation of very long-chain fatty acids-like 1 (ELOVL1) and fatty acid transport protein 4 (FATP4), which each have very long-chain fatty acid acyl-CoA synthetase (VLCFA-ACS) activity, as negative regulators of RPE65. We found that the VLCFA derivative lignoceroyl (C24:0)-CoA inhibited synthesis of 11cROL, whereas palmitoyl (C16:0)-CoA promoted synthesis of 11cROL. We further found that competition of FATP4 with RPE65 for the substrate of RPE65 was also involved in the mechanisms by which FATP4 inhibits synthesis of 11cROL. FATP4 was predominantly expressed in RPE, and the FATP4-deficient RPE showed significantly higher isomerase activity. Consistent with these results, the regeneration rate of 11-cis retinaldehyde and the recovery rate for rod light sensitivity were faster in FATP4-deficient mice than wild-type mice. Moreover, FATP4-deficient mice displayed increased accumulation of the cytotoxic all-trans retinaldehyde and hyper susceptibility to light-induced photoreceptor degeneration. Our findings demonstrate that ELOVL1, FATP4, and their products comprise the regulatory elements of RPE65 and play important roles in protecting photoreceptors from degeneration induced by light damage. PMID:23407971

  3. [Studies on the light-induced reversible xanthophyll-conversions in Chlorella and spinach leaves].

    PubMed

    Hager, A

    1967-06-01

    1. Using new methods in thin-layer chromatography, experiments were carried out to prove the light-induced changes in the quantity of various xanthophylls in Chlorella and spinach leaves. The probable connection of these interconversions to electron transport in photosynthesis was demonstrated. 2. The kinetics of these xanthophyll conversions were investigated during strong illumination and in the succeeding dark period (Chlorella). Already after illumination of 1 min one can detect a decrease of the di-epoxide xanthophyll violaxanthin and a corresponding increase of the epoxide-free zeaxanthin. The intermediate of this interconversion is the mono-epoxide antheraxanthin. Neoxanthin exhibits no change in concentration under the given light intensity and an illumination time of 60 min and more; the same result can be observed with the other carotenoids (α-carotene, β-carotene, lutein, lutein-5,6-epoxyd) and the chlorophylls a and b. 3. The light-induced formation of zeaxanthin is not correlated with those pigment interconversions which are photooxidative in their nature and which may be detected only after long illuminations. However, by using damaged, e.g., briefly heated Chlorella cells, a photooxidative-induced decrease of carotenes and chlorophyll a and a smaller decrease of xanthophylls and chlorophyll b could already be demonstrated after illumination of 15 min. In this case the ratio xanthophylls/ carotenes increases. 4. The transformation violaxanthin → antheraxanthin → zeaxanthin ("forward-reaction") is induced not only by an illumination with white light (point 2) but also with red light (>600 nm); that means the reaction proceeds at a wavelength which cannot be absorbed by the xanthophylls themselves. Chlorophyll acts as light-acceptor. 5. The "forward-reaction" does not proceed after the cells have been heated for a short time. The presence of inhibitors of light-reaction II in photosynthesis such as o-phenanthroline, hydroxylamine and DCMU entirely

  4. Understanding RNA-Chromatin Interactions Using Chromatin Isolation by RNA Purification (ChIRP).

    PubMed

    Chu, Ci; Chang, Howard Y

    2016-01-01

    ChIRP is a novel and easy-to-use technique for studying long noncoding RNA (lncRNA)-chromatin interactions. RNA and chromatin are cross-linked in vivo using formaldehyde or glutaraldehyde, and purified using biotinylated antisense oligonucleotides that hybridize to the target RNA. Co-precipitated DNA is then purified and analyzed by quantitative PCR (qPCR) or high-throughput sequencing. PMID:27659979

  5. Direct chromatin PCR (DC-PCR): hypotonic conditions allow differentiation of chromatin states during thermal cycling.

    PubMed

    Vatolin, Sergei; Khan, Shahper N; Reu, Frederic J

    2012-01-01

    Current methods to study chromatin configuration are not well suited for high throughput drug screening since they require large cell numbers and multiple experimental steps that include centrifugation for isolation of nuclei or DNA. Here we show that site specific chromatin analysis can be achieved in one step by simply performing direct chromatin PCR (DC-PCR) on cells. The basic underlying observation was that standard hypotonic PCR buffers prevent global cellular chromatin solubilization during thermal cycling while more loosely organized chromatin can be amplified. Despite repeated heating to >90 °C, 41 of 61 tested 5' sequences of silenced genes (CDKN2A, PU.1, IRF4, FOSB, CD34) were not amplifiable while 47 could be amplified from expressing cells. Two gene regions (IRF4, FOSB) even required pre-heating of cells in isotonic media to allow this differentiation; otherwise none of 19 assayed sequences yielded PCR products. Cells with baseline expression or epigenetic reactivation gave similar DC-PCR results. Silencing during differentiation of CD34 positive cord blood cells closed respective chromatin while treatment of myeloma cells with an IRF4 transcriptional inhibitor opened a site to DC-PCR that was occupied by RNA polymerase II and NFκB as determined by ChIP. Translation into real-time PCR can not be achieved with commercial real-time PCR buffers which potently open chromatin, but even with simple ethidium bromide addition to standard PCR mastermix we were able to identify hits in small molecules screens that suppressed IRF4 expression or reactivated CDKN2A in myeloma cells using densitometry or visual inspection of PCR plates under UV light. While need in drug development inspired this work, application to genome-wide analysis appears feasible using phi29 for selective amplification of open cellular chromatin followed by library construction from supernatants since such supernatants yielded similar results as gene specific DC-PCR.

  6. Dynamic reprogramming of chromatin: paradigmatic palimpsests and HES factors

    PubMed Central

    Kok, Kurtulus; Arnosti, David N.

    2015-01-01

    Temporal and spatial control of transcription in development is dictated to a great extent by transcriptional repressors. Some repressor complexes, such as Polycomp-group proteins, induce relatively long-term non-permissive states, whereas others such as hairy/enhancer of split (HES) family repressors are linked to dynamically modulated chromatin states associated with cycling expression of target genes. The mode of action and specificity of repressors involved in mediating this latter form of epigenetic control are unknown. Oscillating expression of HES repressors controlled by signaling pathways such as Notch suggests that the entire ensemble of HES–associated co-repressors and histone modifying complexes readily cycle on and off genes. Dynamic interactions between these factors and chromatin seem to be crucial in maintaining multipotency of progenitor cells, but the significance of such interactions in more differentiated cells is less well understood. We discuss here how genome-wide analyses and real-time gene expression measurements of HES regulated genes can help decipher the detailed mechanisms and biological importance of highly dynamic transcriptional switching mediated by epigenetic changes. PMID:25713582

  7. Critical electrolyte concentration of silk gland chromatin of the sugarcane borer Diatraea saccharalis, induced using agrochemicals.

    PubMed

    Santos, S A; Fermino, F; Moreira, B M T; Araujo, K F; Falco, J R P; Ruvolo-Takasusuki, M C C

    2014-01-01

    The sugarcane borer Diatraea saccharalis is widely known as the main pest of sugarcane crop, causing increased damage to the entire fields. Measures to control this pest involve the use of chemicals and biological control with Cotesia flavipes wasps. In this study, we evaluated the insecticides fipronil (Frontline; 0.0025%), malathion (Malatol Bio Carb; 0.4%), cipermetrina (Galgotrin; 10%), and neem oil (Natuneem; 100%) and the herbicide nicosulfuron (Sanson 40 SC; 100%) in the posterior region silk glands of 3rd- and 5th-instar D. saccharalis by studying the variation in the critical electrolyte concentration (CEC). Observations of 3rd-instar larvae indicated that malathion, cipermetrina, and neem oil induced increased chromatin condensation that may consequently disable genes. Tests with fipronil showed no alteration in chromatin condensation. With the use of nicosulfuron, there was chromatin and probable gene decompaction. In the 5th-instar larvae, the larval CEC values indicated that malathion and neem oil induced increased chromatin condensation. The CEC values for 5th-instar larvae using cipermetrina, fipronil, and nicosulfuron indicated chromatin unpacking. These observations led us to conclude that the quantity of the pesticide does not affect the mortality of these pests, can change the conformation of complexes of DNA, RNA, and protein from the posterior region of silk gland cells of D. saccharalis, activating or repressing the expression of genes related to the defense mechanism of the insect and contributing to the selection and survival of resistant individuals. PMID:25299111

  8. The many faces of plant chromatin: Meeting summary of the 4th European workshop on plant chromatin 2015, Uppsala, Sweden.

    PubMed

    Mozgová, Iva; Köhler, Claudia; Gaudin, Valérie; Hennig, Lars

    2015-01-01

    In June 2015, the fourth European Workshop on Plant Chromatin took place in Uppsala, Sweden, bringing together 80 researchers studying various aspects of plant chromatin and epigenetics. The intricate relationships between plant chromatin dynamics and gene expression change, chromatin organization within the plant cell nucleus, and the impact of chromatin structure on plant development were discussed. Among the main highlights of the meeting were an ever-growing list of newly identified players in chromatin structure establishment and the development of novel tools and approaches to foster our understanding of chromatin-mediated gene regulation, taking into account the context of the plant cell nucleus and its architecture. In this report, we summarize some of the main advances and prospects of plant chromatin research presented at this meeting. PMID:26646904

  9. Chromatin remodelling complex RSC promotes base excision repair in chromatin of Saccharomyces cerevisiae.

    PubMed

    Czaja, Wioletta; Mao, Peng; Smerdon, Michael J

    2014-04-01

    The base excision repair (BER) pathway is a conserved DNA repair system required to maintain genomic integrity and prevent mutagenesis in all eukaryotic cells. Nevertheless, how BER operates in vivo (i.e. in the context of chromatin) is poorly understood. We have investigated the role of an essential ATP-dependent chromatin remodelling (ACR) complex RSC (Remodels the Structure of Chromatin) in BER of intact yeast cells. We show that depletion of STH1, the ATPase subunit of RSC, causes enhanced sensitivity to the DNA alkylating agent methyl methanesulfonate (MMS) and results in a substantial inhibition of BER, at the GAL1 locus and in the genome overall. Consistent with this observation, the DNA in chromatin is less accessible to micrococcal nuclease digestion in the absence of RSC. Quantitative PCR results indicate that repair deficiency in STH1 depleted cells is not due to changes in the expression of BER genes. Collectively, our data indicates the RSC complex promotes efficient BER in chromatin. These results provide, for the first time, a link between ATP-dependent chromatin remodelling and BER in living cells.

  10. DNA repair choice defines a common pathway for recruitment of chromatin regulators

    PubMed Central

    Bennett, Gwendolyn; Papamichos-Chronakis, Manolis; Peterson, Craig L.

    2013-01-01

    DNA double-strand break (DSB) repair is essential for maintenance of genome stability. Recent work has implicated a host of chromatin regulators in the DNA damage response, and although several functional roles have been defined, the mechanisms that control their recruitment to DNA lesions remain unclear. Here, we find that efficient DSB recruitment of the INO80, SWR-C, NuA4, SWI/SNF, and RSC enzymes is inhibited by the non-homologous end joining machinery, and that their recruitment is controlled by early steps of homologous recombination. Strikingly, we find no significant role for H2A.X phosphorylation (γH2AX) in the recruitment of chromatin regulators, but rather their recruitment coincides with reduced levels of γH2AX. Our work indicates that cell cycle position plays a key role in DNA repair pathway choice and that recruitment of chromatin regulators is tightly coupled to homologous recombination. PMID:23811932

  11. Photolabile acetals as profragrances: the effect of structural modifications on the light-induced release of volatile aldehydes on cotton.

    PubMed

    Trachsel, Alain; Buchs, Barbara; Herrmann, Andreas

    Because volatile compounds evaporate from surfaces that are usually exposed to daylight, photoresponsive delivery systems are particularly suitable to control their release. In the present study, we investigated 4,4-diphenyl-4H-benzo[d][1,3]dioxins as profragrances for the light-induced delivery of aldehydes in functional perfumery. The efficiency of fragrance release was investigated on cotton after direct and indirect surface deposition from a fabric softening formulation as a function of the substitution pattern of the profragrance structure. Dynamic headspace analysis above the cotton surface demonstrated that the structure of the profragrance had a much larger effect on the fragrance release than did the amount of deposition on the target surface. Although some trends observed for the photolysis in solution also applied to the reaction on cotton, it is not generally possible to predict the photochemical behaviour of structurally different precursors on surfaces from their solution properties. The fact that the present system performed on a dry surface makes it an interesting light-triggered delivery vehicle for other classes of bioactive volatile compounds, such as pheromones or agrochemicals. PMID:27509886

  12. Plastid movement impaired 2, a new gene involved in normal blue-light-induced chloroplast movements in Arabidopsis.

    PubMed

    Luesse, Darron R; DeBlasio, Stacy L; Hangarter, Roger P

    2006-08-01

    Chloroplasts move in a light-dependent manner that can modulate the photosynthetic potential of plant cells. Identification of genes required for light-induced chloroplast movement is beginning to define the molecular machinery that controls these movements. In this work, we describe plastid movement impaired 2 (pmi2), a mutant in Arabidopsis (Arabidopsis thaliana) that displays attenuated chloroplast movements under intermediate and high light intensities while maintaining a normal movement response under low light intensities. In wild-type plants, fluence rates below 20 micromol m(-2) s(-1) of blue light lead to chloroplast accumulation on the periclinal cell walls, whereas light intensities over 20 micromol m(-2) s(-1) caused chloroplasts to move toward the anticlinal cell walls (avoidance response). However, at light intensities below 75 micromol m(-2) s(-1), chloroplasts in pmi2 leaves move to the periclinal walls; 100 micromol m(-2) s(-1) of blue light is required for chloroplasts in pmi2 to move to the anticlinal cell walls, indicating a shift in the light threshold for the avoidance response in the mutant. The pmi2 mutation has been mapped to a gene that encodes a protein of unknown function with a large coiled-coil domain in the N terminus and a putative P loop. PMI2 shares sequence and structural similarity with PMI15, another unknown protein in Arabidopsis that, when mutated, causes a defect in chloroplast avoidance under high-light intensities.

  13. Mechanisms of ATP-Dependent Chromatin Remodeling Motors.

    PubMed

    Zhou, Coral Y; Johnson, Stephanie L; Gamarra, Nathan I; Narlikar, Geeta J

    2016-07-01

    Chromatin remodeling motors play essential roles in all DNA-based processes. These motors catalyze diverse outcomes ranging from sliding the smallest units of chromatin, known as nucleosomes, to completely disassembling chromatin. The broad range of actions carried out by these motors on the complex template presented by chromatin raises many stimulating mechanistic questions. Other well-studied nucleic acid motors provide examples of the depth of mechanistic understanding that is achievable from detailed biophysical studies. We use these studies as a guiding framework to discuss the current state of knowledge of chromatin remodeling mechanisms and highlight exciting open questions that would continue to benefit from biophysical analyses. PMID:27391925

  14. A unique chromatin signature uncovers early developmental enhancers in humans.

    PubMed

    Rada-Iglesias, Alvaro; Bajpai, Ruchi; Swigut, Tomek; Brugmann, Samantha A; Flynn, Ryan A; Wysocka, Joanna

    2011-02-10

    Cell-fate transitions involve the integration of genomic information encoded by regulatory elements, such as enhancers, with the cellular environment. However, identification of genomic sequences that control human embryonic development represents a formidable challenge. Here we show that in human embryonic stem cells (hESCs), unique chromatin signatures identify two distinct classes of genomic elements, both of which are marked by the presence of chromatin regulators p300 and BRG1, monomethylation of histone H3 at lysine 4 (H3K4me1), and low nucleosomal density. In addition, elements of the first class are distinguished by the acetylation of histone H3 at lysine 27 (H3K27ac), overlap with previously characterized hESC enhancers, and are located proximally to genes expressed in hESCs and the epiblast. In contrast, elements of the second class, which we term 'poised enhancers', are distinguished by the absence of H3K27ac, enrichment of histone H3 lysine 27 trimethylation (H3K27me3), and are linked to genes inactive in hESCs and instead are involved in orchestrating early steps in embryogenesis, such as gastrulation, mesoderm formation and neurulation. Consistent with the poised identity, during differentiation of hESCs to neuroepithelium, a neuroectoderm-specific subset of poised enhancers acquires a chromatin signature associated with active enhancers. When assayed in zebrafish embryos, poised enhancers are able to direct cell-type and stage-specific expression characteristic of their proximal developmental gene, even in the absence of sequence conservation in the fish genome. Our data demonstrate that early developmental enhancers are epigenetically pre-marked in hESCs and indicate an unappreciated role of H3K27me3 at distal regulatory elements. Moreover, the wealth of new regulatory sequences identified here provides an invaluable resource for studies and isolation of transient, rare cell populations representing early stages of human embryogenesis.

  15. Chromatin structure and gene expression in Alzheimer's disease.

    PubMed

    Lukiw, W J; Crapper McLachlan, D R

    1990-04-01

    Light micrococcal nuclease digestion was used to examine DNA associated with nucleosome populations isolated from Alzheimer's disease (AD) affected superior temporal lobe neocortical nuclei. 46.1% of the immediate 5' upstream DNA sequence of the single copy neurofilament light chain (NF-L) gene was found to be associated with a mononucleosome fraction in control neocortices. This fraction was reduced to 7.4% in age-matched AD-affected neocortex. No differences in accessibility to the nuclease probe was found between AD-affected and control temporal grey matter nuclei for the human prion HuPrP gene or for the NF-L gene in nuclei isolated from the primary visual cortex or the cerebellum. An AvaI restriction endonuclease site, located 124 base pairs upstream from the TATAA box in the NF-L leader sequence, was also found to be occluded in AD-affected nuclei. From this and previous data we conclude that within the AD-affected nucleus, focused changes in neuronal chromatin conformation occur. Increases in the packing density of chromatin may reduce transcription and alter the ability of neurons to generate sufficient levels of gene products to maintain normal neocortical function.

  16. The landscape of accessible chromatin in mammalian preimplantation embryos.

    PubMed

    Wu, Jingyi; Huang, Bo; Chen, He; Yin, Qiangzong; Liu, Yang; Xiang, Yunlong; Zhang, Bingjie; Liu, Bofeng; Wang, Qiujun; Xia, Weikun; Li, Wenzhi; Li, Yuanyuan; Ma, Jing; Peng, Xu; Zheng, Hui; Ming, Jia; Zhang, Wenhao; Zhang, Jing; Tian, Geng; Xu, Feng; Chang, Zai; Na, Jie; Yang, Xuerui; Xie, Wei

    2016-06-30

    In mammals, extensive chromatin reorganization is essential for reprogramming terminally committed gametes to a totipotent state during preimplantation development. However, the global chromatin landscape and its dynamics in this period remain unexplored. Here we report a genome-wide map of accessible chromatin in mouse preimplantation embryos using an improved assay for transposase-accessible chromatin with high throughput sequencing (ATAC-seq) approach with CRISPR/Cas9-assisted mitochondrial DNA depletion. We show that despite extensive parental asymmetry in DNA methylomes, the chromatin accessibility between the parental genomes is globally comparable after major zygotic genome activation (ZGA). Accessible chromatin in early embryos is widely shaped by transposable elements and overlaps extensively with putative cis-regulatory sequences. Unexpectedly, accessible chromatin is also found near the transcription end sites of active genes. By integrating the maps of cis-regulatory elements and single-cell transcriptomes, we construct the regulatory network of early development, which helps to identify the key modulators for lineage specification. Finally, we find that the activities of cis-regulatory elements and their associated open chromatin diminished before major ZGA. Surprisingly, we observed many loci showing non-canonical, large open chromatin domains over the entire transcribed units in minor ZGA, supporting the presence of an unusually permissive chromatin state. Together, these data reveal a unique spatiotemporal chromatin configuration that accompanies early mammalian development. PMID:27309802

  17. Global genome nucleotide excision repair is organized into domains that promote efficient DNA repair in chromatin

    PubMed Central

    Yu, Shirong; Evans, Katie; Bennett, Mark; Webster, Richard M.; Leadbitter, Matthew; Teng, Yumin; Waters, Raymond

    2016-01-01

    The rates at which lesions are removed by DNA repair can vary widely throughout the genome, with important implications for genomic stability. To study this, we measured the distribution of nucleotide excision repair (NER) rates for UV-induced lesions throughout the budding yeast genome. By plotting these repair rates in relation to genes and their associated flanking sequences, we reveal that, in normal cells, genomic repair rates display a distinctive pattern, suggesting that DNA repair is highly organized within the genome. Furthermore, by comparing genome-wide DNA repair rates in wild-type cells and cells defective in the global genome–NER (GG-NER) subpathway, we establish how this alters the distribution of NER rates throughout the genome. We also examined the genomic locations of GG-NER factor binding to chromatin before and after UV irradiation, revealing that GG-NER is organized and initiated from specific genomic locations. At these sites, chromatin occupancy of the histone acetyl-transferase Gcn5 is controlled by the GG-NER complex, which regulates histone H3 acetylation and chromatin structure, thereby promoting efficient DNA repair of UV-induced lesions. Chromatin remodeling during the GG-NER process is therefore organized into these genomic domains. Importantly, loss of Gcn5 significantly alters the genomic distribution of NER rates; this has implications for the effects of chromatin modifiers on the distribution of mutations that arise throughout the genome. PMID:27470111

  18. The ChroP Approach Combines ChIP and Mass Spectrometry to Dissect Locus-specific Proteomic Landscapes of Chromatin

    PubMed Central

    Soldi, Monica; Bonaldi, Tiziana

    2014-01-01

    Chromatin is a highly dynamic nucleoprotein complex made of DNA and proteins that controls various DNA-dependent processes. Chromatin structure and function at specific regions is regulated by the local enrichment of histone post-translational modifications (hPTMs) and variants, chromatin-binding proteins, including transcription factors, and DNA methylation. The proteomic characterization of chromatin composition at distinct functional regions has been so far hampered by the lack of efficient protocols to enrich such domains at the appropriate purity and amount for the subsequent in-depth analysis by Mass Spectrometry (MS). We describe here a newly designed chromatin proteomics strategy, named ChroP (Chromatin Proteomics), whereby a preparative chromatin immunoprecipitation is used to isolate distinct chromatin regions whose features, in terms of hPTMs, variants and co-associated non-histonic proteins, are analyzed by MS. We illustrate here the setting up of ChroP for the enrichment and analysis of transcriptionally silent heterochromatic regions, marked by the presence of tri-methylation of lysine 9 on histone H3. The results achieved demonstrate the potential of ChroP in thoroughly characterizing the heterochromatin proteome and prove it as a powerful analytical strategy for understanding how the distinct protein determinants of chromatin interact and synergize to establish locus-specific structural and functional configurations. PMID:24747196

  19. Minireview: Conversing With Chromatin: The Language of Nuclear Receptors

    PubMed Central

    2014-01-01

    Nuclear receptors are transcription factors that are activated by physiological stimuli to bind DNA in the context of chromatin and regulate complex biological pathways. Major advances in nuclear receptor biology have been aided by genome scale examinations of receptor interactions with chromatin. In this review, we summarize the roles of the chromatin landscape in regulating nuclear receptor function. Chromatin acts as a central integrator in the nuclear receptor-signaling axis, operating in distinct temporal modalities. Chromatin effects nuclear receptor action by specifying its genomic localization and interactions with regulatory elements. On receptor binding, changes in chromatin operate as an effector of receptor signaling to modulate transcriptional events. Chromatin is therefore an integral component of the pathways that guide nuclear receptor action in cell-type-specific and cell state-dependent manners. PMID:24196351

  20. Quantification of chromatin condensation level by image processing.

    PubMed

    Irianto, Jerome; Lee, David A; Knight, Martin M

    2014-03-01

    The level of chromatin condensation is related to the silencing/activation of chromosomal territories and therefore impacts on gene expression. Chromatin condensation changes during cell cycle, progression and differentiation, and is influenced by various physicochemical and epigenetic factors. This study describes a validated experimental technique to quantify chromatin condensation. A novel image processing procedure is developed using Sobel edge detection to quantify the level of chromatin condensation from nuclei images taken by confocal microscopy. The algorithm was developed in MATLAB and used to quantify different levels of chromatin condensation in chondrocyte nuclei achieved through alteration in osmotic pressure. The resulting chromatin condensation parameter (CCP) is in good agreement with independent multi-observer qualitative visual assessment. This image processing technique thereby provides a validated unbiased parameter for rapid and highly reproducible quantification of the level of chromatin condensation.

  1. Minireview: Conversing with chromatin: the language of nuclear receptors.

    PubMed

    Biddie, Simon C; John, Sam

    2014-01-01

    Nuclear receptors are transcription factors that are activated by physiological stimuli to bind DNA in the context of chromatin and regulate complex biological pathways. Major advances in nuclear receptor biology have been aided by genome scale examinations of receptor interactions with chromatin. In this review, we summarize the roles of the chromatin landscape in regulating nuclear receptor function. Chromatin acts as a central integrator in the nuclear receptor-signaling axis, operating in distinct temporal modalities. Chromatin effects nuclear receptor action by specifying its genomic localization and interactions with regulatory elements. On receptor binding, changes in chromatin operate as an effector of receptor signaling to modulate transcriptional events. Chromatin is therefore an integral component of the pathways that guide nuclear receptor action in cell-type-specific and cell state-dependent manners. PMID:24196351

  2. Effect of rabbit age on sperm chromatin structure.

    PubMed

    Gogol, P; Bochenek, M; Smorag, Z

    2002-04-01

    The aim of this study was to determine the relationship between the age of male rabbits and the sperm chromatin structure. The studies involved the semen of New Zealand White rabbits between 5 and 28 months of age. A flow cytometry and sperm chromatin structure assay (SCSA) method was used to determine chromatin structure. The results of cytometric chromatin structure assay suggested a relatively high stability of sperm chromatin in the rabbit. Between 6 and 16 months of age, the mean percentage of sperm with damaged chromatin was the lowest and ranged from 1.7 to 2.4%. Decreased sperm chromatin stability was found in ejaculates taken from male rabbits less than 5 months and more than 20 months of age. PMID:11975746

  3. Evaluation of dental enamel caries assessment using Quantitative Light Induced Fluorescence and Optical Coherence Tomography.

    PubMed

    Maia, Ana Marly Araújo; de Freitas, Anderson Zanardi; de L Campello, Sergio; Gomes, Anderson Stevens Leônidas; Karlsson, Lena

    2016-06-01

    An in vitro study of morphological alterations between sound dental structure and artificially induced white spot lesions in human teeth, was performed through the loss of fluorescence by Quantitative Light-Induced Fluorescence (QLF) and the alterations of the light attenuation coefficient by Optical Coherence Tomography (OCT). To analyze the OCT images using a commercially available system, a special algorithm was applied, whereas the QLF images were analyzed using the software available in the commercial system employed. When analyzing the sound region against white spot lesions region by QLF, a reduction in the fluorescence intensity was observed, whilst an increase of light attenuation by the OCT system occurred. Comparison of the percentage of alteration between optical properties of sound and artificial enamel caries regions showed that OCT processed images through the attenuation of light enhanced the tooth optical alterations more than fluorescence detected by QLF System. QLF versus OCT imaging of enamel caries: a photonics assessment.

  4. DNA Photonics — Probing Light-Induced Dynamics in DNA on the Femtosecond Timescale

    NASA Astrophysics Data System (ADS)

    Wang, Qiang; Fiebig, Torsten

    In Chap. 10, Wang and Fiebig discuss about a new field, DNA photonics that is important to understand the role of DNA as a functional building block in molecular nanoscale devices, and is also expected to shed light on the complex interactions between structural and electronic properties of DNA. The latter is important for biomedical applications such as DNA-targeted drug design. In this chapter, the authors present experimental data from several different classes of functionalized DNA systems and illustrate the relationship between the structural dynamics and charge injection/migration using state-of-the art femtosecond broadband spectroscopy. They also highlight the importance of the initial electronic excitation for modelling electron transfer rates and point out that ultrafast electronic energy migration, dissipation, and (de)localization must be included into the theoretical description of light-induced dynamics in DNA.

  5. Flicker-light induced visual phenomena: frequency dependence and specificity of whole percepts and percept features.

    PubMed

    Allefeld, Carsten; Pütz, Peter; Kastner, Kristina; Wackermann, Jiří

    2011-12-01

    Flickering light induces visual hallucinations in human observers. Despite a long history of the phenomenon, little is known about the dependence of flicker-induced subjective impressions on the flicker frequency. We investigate this question using Ganzfeld stimulation and an experimental paradigm combining a continuous frequency scan (1-50 Hz) with a focus on re-occurring, whole percepts. On the single-subject level, we find a high degree of frequency stability of percepts. To generalize across subjects, we apply two rating systems, (1) a set of complex percept classes derived from subjects' reports and (2) an enumeration of elementary percept features, and determine distributions of occurrences over flicker frequency. We observe a stronger frequency specificity for complex percept classes than elementary percept features. Comparing the similarity relations among percept categories to those among frequency profiles, we observe that though percepts are preferentially induced by particular frequencies, the frequency does not unambiguously determine the experienced percept. PMID:21123084

  6. Light-induced reorientation and birefringence in polymeric dispersions of nano-sized crystals.

    PubMed

    Termine, Roberto; Aiello, Iolinda; Godbert, Nicolas; Ghedini, Mauro; Golemme, A

    2008-05-12

    Nanocrystals (50-250 nm) of a Palladium complex within a polyisobutylmethacrylate matrix were prepared by a phase separation method. In these dispersions, a light-induced birefringence with Deltan approximately 10(-3) was induced, without the application of an electric field. This effect was related to the photoconducting properties of the dispersion. Evidence for charge photogeneration without any applied field was obtained. The photorefractive behaviour of the material confirmed that the nanocrystals reorientation is a consequence of photoconducting properties. A light-generated electric field approximaely E 3 V/microm was estimated. These results illustrate the potential of materials with a nano-crystalline dispersion morphology as light-responsive media.

  7. Light-induced atomic desorption in a compact system for ultracold atoms

    PubMed Central

    Torralbo-Campo, Lara; Bruce, Graham D.; Smirne, Giuseppe; Cassettari, Donatella

    2015-01-01

    In recent years, light-induced atomic desorption (LIAD) of alkali atoms from the inner surface of a vacuum chamber has been employed in cold atom experiments for the purpose of modulating the alkali background vapour. This is beneficial because larger trapped atom samples can be loaded from vapour at higher pressure, after which the pressure is reduced to increase the lifetime of the sample. We present an analysis, based on the case of rubidium atoms adsorbed on pyrex, of various aspects of LIAD that are useful for this application. Firstly, we study the intensity dependence of LIAD by fitting the experimental data with a rate-equation model, from which we extract a correct prediction for the increase in trapped atom number. Following this, we quantify a figure of merit for the utility of LIAD in cold atom experiments and we show how it can be optimised for realistic experimental parameters. PMID:26458325

  8. In situ transmission electron microscopy of light-induced photocatalytic reactions.

    PubMed

    Cavalca, F; Laursen, A B; Kardynal, B E; Dunin-Borkowski, R E; Dahl, S; Wagner, J B; Hansen, T W

    2012-02-24

    Transmission electron microscopy (TEM) makes it possible to obtain insight into the structure, composition and reactivity of photocatalysts, which are of fundamental interest for sustainable energy research. Such insight can be used for further material optimization. Here, we combine conventional TEM analysis of photocatalysts with environmental TEM (ETEM) and photoactivation using light. Two novel types of TEM specimen holder that enable in situ illumination are developed to study light-induced phenomena in photoactive materials, systems and photocatalysts at the nanoscale under working conditions. The technological development of the holders is described and two representative photo-induced phenomena are studied: the photodegradation of Cu₂O and the photodeposition of Pt onto a GaN:ZnO photocatalyst.

  9. Experimental studies of collective excitations of a BEC in light-induced gauge fields

    NASA Astrophysics Data System (ADS)

    Li, Chuan-Hsun; Niffenegger, Robert; Blasing, David; Olson, Abraham; Chen, Yong P.

    2015-05-01

    We present our experimental studies of collective modes including spin dipole mode and scissors mode of a 87Rb Bose-Einstein condensate (BEC) in the presence of Raman light-induced gauge fields and synthetic spin-orbit coupling (SOC). By Raman dressing the mf spin states within the F =1 manifold, we engineer atoms' energy-momentum dispersion to create synthetic SOC, and spin dependent synthetic electric and magnetic fields. We have used spin dependent synthetic electric fields to make two BECs with different spins oscillate and collide in the optical trap. We have studied the effects of SOC on both the momentum damping and thermalization behaviors of the BECs when undergoing such spin dipole oscillations. We have also used spatially dependent synthetic electric fields to excite the scissors mode, which has been used as a probe for superfluidity. We have investigated the effects of the synthetic gauge fields and SOC on the measured scissors mode.

  10. Modeling of coherent ultrafast magneto-optical experiments: Light-induced molecular mean-field model

    SciTech Connect

    Hinschberger, Y.; Hervieux, P.-A.

    2015-12-28

    We present calculations which aim to describe coherent ultrafast magneto-optical effects observed in time-resolved pump-probe experiments. Our approach is based on a nonlinear semi-classical Drude-Voigt model and is used to interpret experiments performed on nickel ferromagnetic thin film. Within this framework, a phenomenological light-induced coherent molecular mean-field depending on the polarizations of the pump and probe pulses is proposed whose microscopic origin is related to a spin-orbit coupling involving the electron spins of the material sample and the electric field of the laser pulses. Theoretical predictions are compared to available experimental data. The model successfully reproduces the observed experimental trends and gives meaningful insight into the understanding of magneto-optical rotation behavior in the ultrafast regime. Theoretical predictions for further experimental studies are also proposed.

  11. Theory of light-induced drift of electrons in coupled quantum wells

    NASA Astrophysics Data System (ADS)

    Stockman, Mark I.; Muratov, Leonid S.; George, Thomas F.

    1992-10-01

    A theory of the new effect of light-induced drift (LID) in coupled potential wells is developed on the basis of the density-matrix method. The effect appears when light excites intersubband electronic transitions. LID manifests itself as the photocurrent of the two-dimensional electron gas in the well plane, which depends on coherent electron tunneling between the coupled wells. The theory shows the effect to possess distinctive features such as a characteristic antisymmetric spectral contour consisting of four alternating positive and negative peaks and the change of sign of the LID current with the sign change of the bias normal to the quantum-well plane. The quantitative estimates for GaAs wells show the LID current to be readily detectable.

  12. Light-induced depigmentation in planarians models the pathophysiology of acute porphyrias.

    PubMed

    Stubenhaus, Bradford M; Dustin, John P; Neverett, Emily R; Beaudry, Megan S; Nadeau, Leanna E; Burk-McCoy, Ethan; He, Xinwen; Pearson, Bret J; Pellettieri, Jason

    2016-05-31

    Porphyrias are disorders of heme metabolism frequently characterized by extreme photosensitivity. This symptom results from accumulation of porphyrins, tetrapyrrole intermediates in heme biosynthesis that generate reactive oxygen species when exposed to light, in the skin of affected individuals. Here we report that in addition to producing an ommochrome body pigment, the planarian flatworm Schmidtea mediterranea generates porphyrins in its subepithelial pigment cells under physiological conditions, and that this leads to pigment cell loss when animals are exposed to intense visible light. Remarkably, porphyrin biosynthesis and light-induced depigmentation are enhanced by starvation, recapitulating a common feature of some porphyrias - decreased nutrient intake precipitates an acute manifestation of the disease. Our results establish planarians as an experimentally tractable animal model for research into the pathophysiology of acute porphyrias, and potentially for the identification of novel pharmacological interventions capable of alleviating porphyrin-mediated photosensitivity or decoupling dieting and fasting from disease pathogenesis.

  13. Light-induced avian glaucoma as an animal model for human primary glaucoma.

    PubMed

    Lauber, J K

    1987-01-01

    Glaucoma can be induced in domestic chicks at the will of the investigator, by the simple device of rearing the chicks under continuous light. This light-induced avian glaucoma (LIAG) is presented as an animal model system for human open-angle glaucoma. A number of morphological and physiological findings in LIAG are reviewed, and the LIAG system is compared with several other glaucoma model systems, in dogs, rabbits and monkeys. Intraocular pressure in LIAG has been demonstrated to be responsive to several anti-glaucoma drugs, and the system could be used for further drug testing. Thus it is suggested that LIAG may be especially useful in studies seeking to understand human glaucoma, and how to forestall it, or treat it. As well, a prolonged "pre-glaucoma" period is available to the investigator working with LIAG, during which a pathological course is already underway in the eye, but intraocular pressure has not yet gone up. PMID:3332676

  14. Light-induced atomic desorption and diffusion of Rb from porous alumina

    SciTech Connect

    Villalba, S.; Failache, H.; Lezama, A.

    2010-03-15

    We present a study of light-induced atom desorption (LIAD) of an alkali-metal atom (Rb) in porous alumina. We observe the variation due to LIAD of the rubidium density in a vapor cell as a function of illumination time, intensity, and wavelength. The simple and regular structure of the alumina pores allows a description of the atomic diffusion in the porous medium in which the diffusion constant only depends on the known pore geometry and the atomic sticking time to the pore wall. A simple one-dimensional theoretical model is presented which reproduces the essential features of the observed signals. Fitting of the model to the experimental data gives access to the diffusion constant and consequently the atom-wall sticking time and its dependence on light intensity and wavelength. The nonmonotonic dependence of the LIAD yield on the illumination light frequency is indicative of the existence of Rb clusters in the porous medium.

  15. In search of the pathways for light-induced pacemaker resetting in the suprachiasmatic nucleus.

    PubMed

    Meijer, Johanna H; Schwartz, William J

    2003-06-01

    Within the suprachiasmatic nucleus (SCN) of the mammalian hypothalamus is a circadian pacemaker that functions as a clock. Its endogenous period is adjusted to the external 24-h light-dark cycle, primarily by light-induced phase shifts that reset the pacemaker's oscillation. Evidence using a wide variety of neurobiological and molecular genetic tools has elucidated key elements that comprise the visual input pathway for SCN photoentrainment in rodents. Important questions remain regarding the intracellular signals that reset the autoregulatory molecular loop within photoresponsive cells in the SCN's retino-recipient subdivision, as well as the intercellular coupling mechanisms that enable SCN tissue to generate phase shifts of overt behavioral and physiological circadian rhythms such as locomotion and SCN neuronal firing rate. Multiple neurotransmitters, protein kinases, and photoinducible genes add to system complexity, and we still do not fully understand how dawn and dusk light pulses ultimately produce bidirectional, advancing and delaying phase shifts for pacemaker entrainment. PMID:12828281

  16. Light-Induced Reversible Self-Assembly of Gold Nanoparticles Surface-Immobilized with Coumarin Ligands.

    PubMed

    He, Huibin; Feng, Miao; Chen, Qidi; Zhang, Xinqi; Zhan, Hongbing

    2016-01-18

    A novel light-induced reversible self-assembly (LIRSA) system is based on the reversible photodimerization and photocleavage of coumarin groups on the surface of gold nanoparticles (AuNPs) in THF solution. Facilitated by coumarin groups, light irradiation at 365 nm triggers the stable assembly of monodisperse AuNPs; the resulting self-assembly system can be disassembled back to the disassembled state by a relatively short exposure to benign UV light. The reversible self-assembly cycle can be repeated 4 times. A specific concentration range of coumarin ligand and the THF solvent were identified to be the two predominant factors that contribute to the LIRSA of AuNPs. This is the first successful application of reversible photodimerization based on a coumarin derivative in the field of AuNP LIRSA. This LIRSA system may provide unique opportunities for the photoregulated synthesis of many adjustable nanostructures and devices.

  17. Dynamics of light-induced FeB pair dissociation in crystalline silicon

    SciTech Connect

    Geerligs, L.J.; Macdonald, Daniel

    2004-11-29

    The dynamics of light-induced dissociation of iron-boron (FeB) pairs in p-type crystalline silicon is investigated. The dissociation is observed to be a single-exponential process which is balanced with thermal repairing. The dissociation rate is proportional to the square of the carrier generation rate and the inverse square of the FeB concentration. This suggests that the dissociation process involves two recombination or electron capture events. A proportionality constant of 5x10{sup -15} s describes the dissociation rate well in the absence of other significant recombination channels. The dissociation rate decreases in the presence of other recombination channels. These results can be used for reliable detection of iron in silicon devices and materials, and for further elucidation of the electronically driven FeB dissociation reaction.

  18. Combination of light-induced effect and gate bias stress in organic phototransistors

    NASA Astrophysics Data System (ADS)

    Liguori, R.; Sheets, W. C.; Bezzeccheri, E.; Facchetti, A.; Rubino, A.

    2016-05-01

    In this work, the photoresponse of pentacene-based thin film transistors fabricated with a photocurable polymer insulator was investigated under visible and ultraviolet illumination. A simple model was developed to distinguish a photoconductive and a photovoltaic effect, that is, a direct photocurrent and a current enhancement caused by a threshold voltage shift. The direction of the light-induced threshold translation is affected by measurement conditions (e.g. integration time and voltage range) and is related to the nature of the trap states, specifically those located in the pentacene film near the interface with the polymer. In particular, it was shown that, thanks to this phenomenon, the photosensitivity of the fabricated phototransistors could be modulated by the gate bias applied during illumination.

  19. Light-Induced Temperature Transitions in Biodegradable Polymer and Nanorod Composites**

    PubMed Central

    Hribar, Kolin C.; Metter, Robert B.; Ifkovits, Jamie L.; Troxler, Thomas

    2010-01-01

    Shape-memory materials (including polymers, metals, and ceramics) are those that are processed into a temporary shape and respond to some external stimuli (e.g., temperature) to undergo a transition back to a permanent shape.[1, 2] Shape memory polymers are finding use in a range of applications from aerospace to fabrics, to biomedical devices and microsystem components.[3–5] For many applications, it would be beneficial to initiate heating with an external trigger (e.g., transdermal light exposure). In this work, we formulated composites of gold nanorods (<1% by volume) and biodegradable networks, where exposure to infrared light induced heating and consequently, shape transitions. The heating is repeatable and tunable based on nanorod concentration and light intensity and the nanorods did not alter the cytotoxicity or in vivo tissue response to the networks. PMID:19408258

  20. Light induced chemical vapour deposition of titanium oxide thin films at room temperature

    NASA Astrophysics Data System (ADS)

    Halary, E.; Benvenuti, G.; Wagner, F.; Hoffmann, P.

    2000-02-01

    High resolution patterned deposition of titania is achieved by light induced chemical vapour deposition (LICVD), by imaging a mask onto a glass substrate. A long pulse XeCl Excimer laser (308 nm) provides, by perpendicular irradiation, the energy to convert titanium tetraisopropoxide (TTIP) vapour into titanium dioxide films, in an oxygen atmosphere, on unheated glass substrates. The amorphous titania deposits contain about 6% carbon contamination according to X-ray photoelectron spectroscopy (XPS) measurements. The deposition rate increases with increasing laser fluence until a maximum value is reached, then remains constant over a wide range, and finally decreases with further fluence increase due to titania ablation or thermal effects. The film thickness increases linearly with the number of pulses after a nucleation period. The strong influence of the laser pulse repetition rate on the growth rate and the thickness profile are reported.

  1. Visible Light-Induced Photoredox Construction of Trifluoromethylated Quaternary Carbon Centers from Trifluoromethylated Tertiary Bromides.

    PubMed

    Huan, Feng; Chen, Qing-Yun; Guo, Yong

    2016-08-19

    A mild, operationally simple, visible light-induced photoredox method for constructing novel trifluoromethylated quaternary carbon centers from trifluoromethylated tertiary bromides has been developed. Using this method, a wide range of alkenes were successfully bifunctionalized to γ-butyrolactams. As for electron-rich alkenes, reactions catalyzed by Ir(dF(CF3)ppy)2(dtbbpy)(PF6) were kinetic processes with high yields and short times. For styrenes, reactions catalyzed by Ir(ppy)2(dtbbpy)(PF6) were thermodynamic processes with moderate yields and prolonged reaction times. For aliphatic alkenes, the reactions were neither thermodynamic nor kinetic and fac-Ir(ppy)3 was used as catalyst. Thus, reactions were not as efficient as electron-rich alkenes. The atom-transfer radical addition reactions of trifluoromethylated tertiary bromides with alkynes were also achieved. The configuration of products we separated was E type only. Some of the products exhibited bactericidal activity.

  2. Visible Light-Induced Photoredox Construction of Trifluoromethylated Quaternary Carbon Centers from Trifluoromethylated Tertiary Bromides.

    PubMed

    Huan, Feng; Chen, Qing-Yun; Guo, Yong

    2016-08-19

    A mild, operationally simple, visible light-induced photoredox method for constructing novel trifluoromethylated quaternary carbon centers from trifluoromethylated tertiary bromides has been developed. Using this method, a wide range of alkenes were successfully bifunctionalized to γ-butyrolactams. As for electron-rich alkenes, reactions catalyzed by Ir(dF(CF3)ppy)2(dtbbpy)(PF6) were kinetic processes with high yields and short times. For styrenes, reactions catalyzed by Ir(ppy)2(dtbbpy)(PF6) were thermodynamic processes with moderate yields and prolonged reaction times. For aliphatic alkenes, the reactions were neither thermodynamic nor kinetic and fac-Ir(ppy)3 was used as catalyst. Thus, reactions were not as efficient as electron-rich alkenes. The atom-transfer radical addition reactions of trifluoromethylated tertiary bromides with alkynes were also achieved. The configuration of products we separated was E type only. Some of the products exhibited bactericidal activity. PMID:27438228

  3. Light-induced atomic desorption in a compact system for ultracold atoms.

    PubMed

    Torralbo-Campo, Lara; Bruce, Graham D; Smirne, Giuseppe; Cassettari, Donatella

    2015-01-01

    In recent years, light-induced atomic desorption (LIAD) of alkali atoms from the inner surface of a vacuum chamber has been employed in cold atom experiments for the purpose of modulating the alkali background vapour. This is beneficial because larger trapped atom samples can be loaded from vapour at higher pressure, after which the pressure is reduced to increase the lifetime of the sample. We present an analysis, based on the case of rubidium atoms adsorbed on pyrex, of various aspects of LIAD that are useful for this application. Firstly, we study the intensity dependence of LIAD by fitting the experimental data with a rate-equation model, from which we extract a correct prediction for the increase in trapped atom number. Following this, we quantify a figure of merit for the utility of LIAD in cold atom experiments and we show how it can be optimised for realistic experimental parameters. PMID:26458325

  4. Batch and Flow Synthesis of Disulfides by Visible-Light-Induced TiO2 Photocatalysis.

    PubMed

    Bottecchia, Cecilia; Erdmann, Nico; Tijssen, Patricia M A; Milroy, Lech-Gustav; Brunsveld, Luc; Hessel, Volker; Noël, Timothy

    2016-07-21

    A mild and practical method for the preparation of disulfides through visible-light-induced photocatalytic aerobic oxidation of thiols has been developed. The method involves the use of TiO2 as a heterogeneous photocatalyst. The catalyst's high stability and recyclability makes this method highly practical. The reaction can be substantially accelerated in a continuous-flow packed-bed reactor, which enables a safe and reliable scale-up of the reaction conditions. The batch and flow protocol described herein can be applied to a diverse set of thiol substrates for the preparation of homo- and hetero-dimerized disulfides. Furthermore, biocompatible reaction conditions (i.e., room temperature, visible light, neutral buffer solution, and no additional base) have been developed, which permits the rapid and chemoselective modification of densely functionalized peptide substrates without recourse to complex purification steps.

  5. A tunable azine covalent organic framework platform for visible light-induced hydrogen generation

    PubMed Central

    Vyas, Vijay S.; Haase, Frederik; Stegbauer, Linus; Savasci, Gökcen; Podjaski, Filip; Ochsenfeld, Christian; Lotsch, Bettina V.

    2015-01-01

    Hydrogen evolution from photocatalytic reduction of water holds promise as a sustainable source of carbon-free energy. Covalent organic frameworks (COFs) present an interesting new class of photoactive materials, which combine three key features relevant to the photocatalytic process, namely crystallinity, porosity and tunability. Here we synthesize a series of water- and photostable 2D azine-linked COFs from hydrazine and triphenylarene aldehydes with varying number of nitrogen atoms. The electronic and steric variations in the precursors are transferred to the resulting frameworks, thus leading to a progressively enhanced light-induced hydrogen evolution with increasing nitrogen content in the frameworks. Our results demonstrate that by the rational design of COFs on a molecular level, it is possible to precisely adjust their structural and optoelectronic properties, thus resulting in enhanced photocatalytic activities. This is expected to spur further interest in these photofunctional frameworks where rational supramolecular engineering may lead to new material applications. PMID:26419805

  6. Theory of light-induced effective magnetic field in Rashba ferromagnets

    NASA Astrophysics Data System (ADS)

    Qaiumzadeh, Alireza; Titov, Mikhail

    2016-07-01

    Motivated by recent experiments on all-optical magnetization reversal in conductive ferromagnetic thin films we use nonequilibrium formalism to calculate the effective magnetic field induced in a Rashba ferromagnet by a short laser pulse. The main contribution to the effect originates in the direct optical transitions between spin-split subbands. The resulting effective magnetic field is inversely proportional to the impurity scattering rate and can reach the amplitude of a few Tesla in the systems like Co/Pt bilayers. We show that the total light-induced effective magnetic field in ferromagnetic systems is the sum of two contributions: a helicity dependent term, which is an even function of magnetization, and a helicity independent term, which is an odd function of magnetization. The primary role of the spin-orbit interaction is to widen the frequency range for direct optical transitions.

  7. Batch and Flow Synthesis of Disulfides by Visible-Light-Induced TiO2 Photocatalysis.

    PubMed

    Bottecchia, Cecilia; Erdmann, Nico; Tijssen, Patricia M A; Milroy, Lech-Gustav; Brunsveld, Luc; Hessel, Volker; Noël, Timothy

    2016-07-21

    A mild and practical method for the preparation of disulfides through visible-light-induced photocatalytic aerobic oxidation of thiols has been developed. The method involves the use of TiO2 as a heterogeneous photocatalyst. The catalyst's high stability and recyclability makes this method highly practical. The reaction can be substantially accelerated in a continuous-flow packed-bed reactor, which enables a safe and reliable scale-up of the reaction conditions. The batch and flow protocol described herein can be applied to a diverse set of thiol substrates for the preparation of homo- and hetero-dimerized disulfides. Furthermore, biocompatible reaction conditions (i.e., room temperature, visible light, neutral buffer solution, and no additional base) have been developed, which permits the rapid and chemoselective modification of densely functionalized peptide substrates without recourse to complex purification steps. PMID:27329945

  8. Light-induced effects-impacts to module performance measurements and reliability testing: An overview

    NASA Astrophysics Data System (ADS)

    Wronski, C. R.

    1985-10-01

    The stability of solar cells is a key factor in determining the reliability of photovoltaic modules and is of great interest in the case of solar cells having a new technology which has not yet been fully developed. In particular this question arises with hydrogenated amorphous silicon (a-Si) solar cells because a-Si exhibits reversible light induced changes in its electronic properties, commonly referred to as the Staebler-Wronski effect (SWE). Continuous progress is being made in the peak conversion efficiencies of a-Si solar cells and efficiencies in excess of 11% have been achieved. However, stability is still a problem. ARCO Solar reports results on solar cells which, after over a year's exposure to sunlight, under open circuit conditions, still have about 7% conversion efficiency. Other results show a region of fast degradation for about a month, after which the degradation diminishes rapidly.

  9. Mapping Recombination Initiation Sites Using Chromatin Immunoprecipitation.

    PubMed

    He, Yan; Wang, Minghui; Sun, Qi; Pawlowski, Wojciech P

    2016-01-01

    Genome-wide maps of recombination sites provide valuable information not only on the recombination pathway itself but also facilitate the understanding of genome dynamics and evolution. Here, we describe a chromatin immunoprecipitation (ChIP) protocol to map the sites of recombination initiation in plants with maize used as an example. ChIP is a method that allows identification of chromosomal sites occupied by specific proteins. Our protocol utilizes RAD51, a protein involved in repair of double-strand breaks (DSBs) that initiate meiotic recombination, to identify DSB formation hotspots. Chromatin is extracted from meiotic flowers, sheared and enriched in fragments bound to RAD51. Genomic location of the protein is then identified by next-generation sequencing. This protocol can also be used in other species of plants, animals, and fungi. PMID:27511175

  10. Calorie restriction and the exercise of chromatin

    PubMed Central

    Vaquero, Alejandro; Reinberg, Danny

    2009-01-01

    Since the earliest stages of evolution, organisms have faced the challenge of sensing and adapting to environmental changes for their survival under compromising conditions such as food depletion or stress. Implicit in these responses are mechanisms developed during evolution that include the targeting of chromatin to allow or prevent expression of fundamental genes and to protect genome integrity. Among the different approaches to study these mechanisms, the analysis of the response to a moderate reduction of energy intake, also known as calorie restriction (CR), has become one of the best sources of information regarding the factors and pathways involved in metabolic adaptation from lower to higher eukaryotes. Furthermore, responses to CR are involved in life span regulation—conserved from yeast to mammals—and therefore have garnered major research interest. Herein we review current knowledge of responses to CR at the molecular level and their functional link to chromatin. PMID:19608767

  11. Regulation of chromatin by histone modifications

    PubMed Central

    Bannister, Andrew J; Kouzarides, Tony

    2011-01-01

    Chromatin is not an inert structure, but rather an instructive DNA scaffold that can respond to external cues to regulate the many uses of DNA. A principle component of chromatin that plays a key role in this regulation is the modification of histones. There is an ever-growing list of these modifications and the complexity of their action is only just beginning to be understood. However, it is clear that histone modifications play fundamental roles in most biological processes that are involved in the manipulation and expression of DNA. Here, we describe the known histone modifications, define where they are found genomically and discuss some of their functional consequences, concentrating mostly on transcription where the majority of characterisation has taken place. PMID:21321607

  12. Heat- and light-induced detachment of the light harvesting complex from isolated photosystem I supercomplexes.

    PubMed

    Nellaepalli, Sreedhar; Zsiros, Ottó; Tóth, Tünde; Yadavalli, Venkateswarlu; Garab, Győző; Subramanyam, Rajagopal; Kovács, László

    2014-08-01

    In a previous study, using photosystem I enriched stroma thylakoid membrane vesicles, we have shown that the light harvesting complexes of this photosystem are prone to heat- and light-induced, thermo-optically driven detachment from the supercomplex [43]. We have also shown that the splitting of the supercomplex occurs in a gradual and specific manner, selectively affecting the different constituents of the antenna complexes. Here we further analyse these heat- and light-induced processes in isolated Photosystem I supercomplex using circular dichroism and 77K fluorescence emission spectroscopy and immuno blotting, and obtain further details on the sequence of events of the dissociation process as well as on the thermal stability of the different components. Our absorption and circular dichroism spectroscopy and immuno blotting data show that the dissociation of LHCI from PSI-LHCI supercomplex starts above 50°C. Also, the low temperature fluorescence emission spectra depicts decrease of maximum fluorescence emission at 730nm and an increase of the intensity at 685nm, and about 10nm blue-shifts, from 730 to 720nm and from 685 to 676nm, respectively, indicating the heat (50°C) induced detachment of LHCI from PSI core complexes. The reaction centre proteins are highly stable even at high temperatures. Lhca2 is more heat stable than the other light harvesting protein complexes of PSI, whereas Lhca4 and Lhca3 are rather labile. Combined heat and light treatments significantly enhances the disorganization of PSI-LHCI supercomplexes, indicating a thermo-optic mechanism, which might have significant role under combined heat and light stress conditions.

  13. Light-induced activation of class II cyclobutane pyrimidine dimer photolyases.

    PubMed

    Okafuji, Asako; Biskup, Till; Hitomi, Kenichi; Getzoff, Elizabeth D; Kaiser, Gebhard; Batschauer, Alfred; Bacher, Adelbert; Hidema, Jun; Teranishi, Mika; Yamamoto, Kazuo; Schleicher, Erik; Weber, Stefan

    2010-05-01

    Light-induced activation of class II cyclobutane pyrimidine dimer (CPD) photolyases of Arabidopsis thaliana and Oryza sativa has been examined by UV/Vis and pulsed Davies-type electron-nuclear double resonance (ENDOR) spectroscopy, and the results compared with structure-known class I enzymes, CPD photolyase and (6-4) photolyase. By ENDOR spectroscopy, the local environment of the flavin adenine dinucleotide (FAD) cofactor is probed by virtue of proton hyperfine couplings that report on the electron-spin density at the positions of magnetic nuclei. Despite the amino-acid sequence dissimilarity as compared to class I enzymes, the results indicate similar binding motifs for FAD in the class II photolyases. Furthermore, the photoreduction kinetics starting from the FAD cofactor in the fully oxidized redox state, FAD(ox), have been probed by UV/Vis spectroscopy. In Escherichia coli (class I) CPD photolyase, light-induced generation of FADH from FAD(ox), and subsequently FADH(-) from FADH, proceeds in a step-wise fashion via a chain of tryptophan residues. These tryptophans are well conserved among the sequences and within all known structures of class I photolyases, but completely lacking from the equivalent positions of class II photolyase sequences. Nevertheless, class II photolyases show photoreduction kinetics similar to those of the class I enzymes. We propose that a different, but also effective, electron-transfer cascade is conserved among the class II photolyases. The existence of such electron transfer pathways is supported by the observation that the catalytically active fully reduced flavin state obtained by photoreduction is maintained even under oxidative conditions in all three classes of enzymes studied in this contribution. PMID:20227927

  14. Origin of Light-Induced Spin-Correlated Radical Pairs in Cryptochrome

    PubMed Central

    Weber, Stefan; Biskup, Till; Okafuji, Asako; Marino, Anthony R.; Berthold, Thomas; Link, Gerhard; Hitomi, Kenichi; Getzoff, Elizabeth D.; Schleicher, Erik; Norris, James R.

    2012-01-01

    Blue-light excitation of cryptochromes and homologs uniformly triggers electron transfer (ET) from the protein surface to the flavin-adenine dinucleotide (FAD) cofactor. A cascade of three conserved tryptophan residues has been considered to be critically involved in this photoreaction. If the FAD is initially in its fully oxidized (diamagnetic) redox state, light-induced ET via the tryptophan triad generates a series of short-lived spin-correlated radical pairs comprising an FAD radical and a tryptophan radical. Coupled doublet-pair species of this type have been proposed as the basis, e.g., of a biological magnetic compass in migratory birds, and were found critical for some cryptochrome functions in vivo. In this contribution, a cryptochrome-like protein (CRYD) derived from Xenopus laevis has been examined as a representative system. The terminal radical-pair state FAD•⋯W324• of X. laevis CRYD has been characterized in detail by time-resolved electron-paramagnetic resonance (TREPR) at X-band microwave frequency (9.68 GHz) and magnetic fields around 345 mT, and at Q-band (34.08 GHz) at around 1215 mT. Different precursor states – singlet versus triplet – of radical-pair formation have been considered in spectral simulations of the experimental electron-spin polarized TREPR signals. Conclusively, we present evidence for a singlet-state precursor of FAD•⋯W324• radical-pair generation because at both magnetic fields, where radical pairs were studied by TREPR, net-zero electron-spin polarization has been detected. Neither a spin-polarized triplet precursor nor a triplet at thermal equilibrium can explain such an electron-spin polarization. It turns out that a two-microwave-frequency TREPR approach is essential to draw conclusions on the nature of the precursor electronic states in light-induced spin-correlated radical pair formations. PMID:20684534

  15. [PHF10 isoforms are phosphorylated in the PBAF mammalian chromatin remodeling complex].

    PubMed

    Brechalov, A V; Valieva, M E; Georgieva, S G; Soshnikova, N V

    2016-01-01

    Chromatin remodeling complex PBAF(SWI/SNF) alters the structure of chromatin and controls gene expression. PHF10 is a specific subunit of PBAF complex and is expressed as four isoforms in mammalian cells. We demonstrated that all isoforms are expressed in various human cell types of different histological origins. All four isoforms are extensively phosphorylated and their phosphorylation level is depended on the cell type. Phosphorylation of PHF10 isoforms occurs while they are incorporated as a subunit of the PBAF complex, and therefore phosphorylation of PHF10 isoforms may play an essential role in regulation of PBAF complex's function and mechanism of action. PMID:27239853

  16. Gatekeepers of Chromatin: Small Metabolites Elicit Big Changes in Gene Expression

    PubMed Central

    Kaochar, Salma; Tu, Benjamin P.

    2012-01-01

    Eukaryotes are constantly fine-tuning their gene expression programs in response to the demands of the environment and the availability of nutrients. Such dynamic regulation of the genome necessitates versatile chromatin architecture. Rapid changes in transcript levels are brought about via a wide range of posttranslational modifications of the histone proteins that control chromatin structure. Many enzymes responsible for these modifications have been identified and they require various metabolic cofactors or substrates for their activity. Herein, we highlight recent developments that have begun to reveal particular cellular metabolites that might in fact be underappreciated regulators of gene expression through their ability to modulate particular histone modifications. PMID:22944281

  17. Chromatin immunoprecipitation and deep sequencing in Xenopus tropicalis and Xenopus laevis

    PubMed Central

    Wills, Andrea E.; Gupta, Rakhi; Chuong, Edward; Baker, Julie C.

    2014-01-01

    Chromatin immunoprecipitation and deep sequencing (ChIP-SEQ) represents a powerful tool for identifying the genomic targets of transcription factors, chromatin remodeling factors, and histone modifications. The frogs Xenopus laevis and Xenopus tropicalis have historically been outstanding model systems for embryology and cell biology, with emerging utility as highly accessible embryos for genome-wide studies. Here we focus on the particular strengths and limitations of Xenopus cell biology and genomics as they apply to ChIP-SEQ, and outline a methodology for ChIP-SEQ in both species, providing detailed strategies for sample preparation, antibody selection, quality control, sequencing library preparation, and basic analysis. PMID:24064036

  18. Premature chromatin condensation upon accumulation of NIMA.

    PubMed Central

    O'Connell, M J; Norbury, C; Nurse, P

    1994-01-01

    The NIMA protein kinase of Aspergillus nidulans is required for the G2/M transition of the cell cycle. Mutants lacking NIMA arrest without morphological characteristics of mitosis, but they do contain an activated p37nimX kinase (the Aspergillus homologue of p34cdc2). To gain a better understanding of NIMA function we have investigated the effects of expressing various NIMA constructs in Aspergillus, fission yeast and human cells. Our experiments have shown that the instability of the NIMA protein requires sequences in the non-catalytic C-terminus of the protein. Removal of this domain results in a stable protein that, once accumulated, promotes a lethal premature condensation of chromatin without any other aspects of mitosis. Similar effects were also observed in fission yeast and human cells accumulating Aspergillus NIMA. This phenotype is independent of cell cycle progression and does not require p34cdc2 kinase activity. As gain of NIMA function by accumulation results in premature chromatin condensation, and loss of NIMA function results in an inability to enter mitosis, we propose that NIMA functions in G2 to promote the condensation of chromatin normally associated with entry into mitosis. Images PMID:7957060

  19. The role of chromatin conformations in diffusional transport of chromatin-binding proteins: Cartesian lattice simulations

    NASA Astrophysics Data System (ADS)

    Wedemeier, Annika; Zhang, Ting; Merlitz, Holger; Wu, Chen-Xu; Langowski, Jörg

    2008-04-01

    In this paper, a lattice model for the diffusional transport of chromatin-binding particles in the interphase cell nucleus is proposed. Sliding effects are studied in dense networks of chromatin fibers created by three different methods: Randomly distributed, noninterconnected obstacles, a random walk chain model with an attractive step potential, and a self-avoiding random walk chain model with a hard repulsive core and attractive surroundings. By comparing a discrete and continuous version of the random walk chain model, we demonstrate that lattice discretization does not alter the diffusion of chromatin-binding particles. The influence of conformational properties of the fiber network on the particle sliding is investigated in detail while varying occupation volume, sliding probability, chain length, and persistence length. It is observed that adjacency of the monomers, the excluded volume effect incorporated in the self-avoiding random walk model, and the persistence length affect the chromatin-binding particle diffusion. It is demonstrated that sliding particles sense local chain structures. When plotting the diffusion coefficient as a function of the accessible volume for diffusing particles, the data fall onto master curves depending on the persistence length. However, once intersegment transfer is involved, chromatin-binding proteins no longer perceive local chain structures.

  20. Coupled effects of director orientations and boundary conditions on light induced bending of monodomain nematic liquid crystalline polymer plates

    NASA Astrophysics Data System (ADS)

    You, Yue; Xu, Changwei; Ding, Shurong; Huo, Yongzhong

    2012-12-01

    A photo-chromic liquid crystal polymers (LCPs) is a smart material for large light-activated variation or bending to transfer luminous energy into mechanical energy. We study the light induced behavior by modeling planar and homeotropic nematic network polymer plates. We effectively illustrate some reported experimental outcomes and theoretically predict some possible bending patterns. This paper constructs an understanding between the bending behaviors and interactions among the alignments, aspect ratios and boundary conditions, etc. Our work provides information on optimizing light induced bending in the process of micro-opto-mechanical system (MOMS) design.

  1. Effects of hydroxyl radical scavengers KCN and CO on ultraviolet light-induced activation of crude soluble guanylate cyclase

    SciTech Connect

    Karlsson, J.O.; Axelsson, K.L.; Andersson, R.G.

    1985-01-01

    The crude soluble guanylate cyclase (GC) from bovine mesenteric artery was stimulated by ultraviolet (UV) light (366 nm). Addition of free radical scavengers, dimethylsulfoxide or superoxide dismutase and/or catalase to the GC assay did not abolish the stimulatory effect of UV light. On the contrary, the UV light-induced activation was enhanced in the presence of these scavengers. KCN (1 mM) did not affect the UV light-induced activation, while 0.1 mM of CO potentiated the activation. These results may indicate that UV light is operating through a direct interaction with the ferrous form of the GC-heme.

  2. SATB1 Packages Densely Looped, Transcriptionally Active Chromatin for Coordinated Expression of Cytokine Genes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    SATB1 (special AT-rich sequence binding protein 1) organizes cell type–specific nuclear architecture by anchoring specialized DNA sequences and recruiting chromatin remodeling factors to control gene transcription. We studied the role of SATB1 in regulating the coordinated expression of Il5, Il4 and...

  3. Sperm chromatin dispersion by formaldehyde in Wistar rats.

    PubMed

    Betancourt-Martínez, N D; Jiménez-Villarreal, J; Carranza-Rosales, P; Guzmán-Delgado, N E; Leyva Orasma, C; Viveros Valdez, E; Morán-Martínez, J

    2015-01-01

    Formaldehyde (FA) is an environmental xenobiotic, which is genotoxic and carcinogenic to humans and animals; it induces DNA damage, mutations, and clastogenicity during critical cytogenetic events. FA-mediated oxidative stress is an important mechanism that has been associated with the induction of cytotoxic and genotoxic damage. Therefore, the objective of this study was to evaluate the dispersion of sperm chromatin and reproductive parameters induced by exposure to different concentrations of FA in Wistar rats. Compared to the percentage of sperm with fragmented DNA in the control group (18.10 ± 8.62%), the percentage of sperm with fragmented DNA increased following exposure to 5, 10, and 30 mg FA/kg body weight (29.60 ± 8.44, 85.20 ± 20.94 and 96.0 ± 7.87, respectively; P = 0.0001). Histopathological alterations were evident, especially in the seminiferous tubules. In conclusion, this study provides experimental evidence concerning the genotoxicity of FA, with particular reference to the decreased sperm concentration and motility and increased dispersion of DNA chromatin in rats.

  4. Molecular basis for chromatin binding and regulation of MLL5.

    PubMed

    Ali, Muzaffar; Rincón-Arano, Héctor; Zhao, Wei; Rothbart, Scott B; Tong, Qiong; Parkhurst, Susan M; Strahl, Brian D; Deng, Lih-Wen; Groudine, Mark; Kutateladze, Tatiana G

    2013-07-01

    The human mixed-lineage leukemia 5 (MLL5) protein mediates hematopoietic cell homeostasis, cell cycle, and survival; however, the molecular basis underlying MLL5 activities remains unknown. Here, we show that MLL5 is recruited to gene-rich euchromatic regions via the interaction of its plant homeodomain finger with the histone mark H3K4me3. The 1.48-Å resolution crystal structure of MLL5 plant homeodomain in complex with the H3K4me3 peptide reveals a noncanonical binding mechanism, whereby K4me3 is recognized through a single aromatic residue and an aspartate. The binding induces a unique His-Asp swapping rearrangement mediated by a C-terminal α-helix. Phosphorylation of H3T3 and H3T6 abrogates the association with H3K4me3 in vitro and in vivo, releasing MLL5 from chromatin in mitosis. This regulatory switch is conserved in the Drosophila ortholog of MLL5, UpSET, and suggests the developmental control for targeting of H3K4me3. Together, our findings provide first insights into the molecular basis for the recruitment, exclusion, and regulation of MLL5 at chromatin. PMID:23798402

  5. Molecular basis for chromatin binding and regulation of MLL5

    PubMed Central

    Ali, Muzaffar; Rincón-Arano, Héctor; Zhao, Wei; Rothbart, Scott B.; Tong, Qiong; Parkhurst, Susan M.; Strahl, Brian D.; Deng, Lih-Wen; Groudine, Mark; Kutateladze, Tatiana G.

    2013-01-01

    The human mixed-lineage leukemia 5 (MLL5) protein mediates hematopoietic cell homeostasis, cell cycle, and survival; however, the molecular basis underlying MLL5 activities remains unknown. Here, we show that MLL5 is recruited to gene-rich euchromatic regions via the interaction of its plant homeodomain finger with the histone mark H3K4me3. The 1.48-Å resolution crystal structure of MLL5 plant homeodomain in complex with the H3K4me3 peptide reveals a noncanonical binding mechanism, whereby K4me3 is recognized through a single aromatic residue and an aspartate. The binding induces a unique His–Asp swapping rearrangement mediated by a C-terminal α-helix. Phosphorylation of H3T3 and H3T6 abrogates the association with H3K4me3 in vitro and in vivo, releasing MLL5 from chromatin in mitosis. This regulatory switch is conserved in the Drosophila ortholog of MLL5, UpSET, and suggests the developmental control for targeting of H3K4me3. Together, our findings provide first insights into the molecular basis for the recruitment, exclusion, and regulation of MLL5 at chromatin. PMID:23798402

  6. Synaptic, transcriptional and chromatin genes disrupted in autism.

    PubMed

    De Rubeis, Silvia; He, Xin; Goldberg, Arthur P; Poultney, Christopher S; Samocha, Kaitlin; Cicek, A Erucment; Kou, Yan; Liu, Li; Fromer, Menachem; Walker, Susan; Singh, Tarinder; Klei, Lambertus; Kosmicki, Jack; Shih-Chen, Fu; Aleksic, Branko; Biscaldi, Monica; Bolton, Patrick F; Brownfeld, Jessica M; Cai, Jinlu; Campbell, Nicholas G; Carracedo, Angel; Chahrour, Maria H; Chiocchetti, Andreas G; Coon, Hilary; Crawford, Emily L; Curran, Sarah R; Dawson, Geraldine; Duketis, Eftichia; Fernandez, Bridget A; Gallagher, Louise; Geller, Evan; Guter, Stephen J; Hill, R Sean; Ionita-Laza, Juliana; Jimenz Gonzalez, Patricia; Kilpinen, Helena; Klauck, Sabine M; Kolevzon, Alexander; Lee, Irene; Lei, Irene; Lei, Jing; Lehtimäki, Terho; Lin, Chiao-Feng; Ma'ayan, Avi; Marshall, Christian R; McInnes, Alison L; Neale, Benjamin; Owen, Michael J; Ozaki, Noriio; Parellada, Mara; Parr, Jeremy R; Purcell, Shaun; Puura, Kaija; Rajagopalan, Deepthi; Rehnström, Karola; Reichenberg, Abraham; Sabo, Aniko; Sachse, Michael; Sanders, Stephan J; Schafer, Chad; Schulte-Rüther, Martin; Skuse, David; Stevens, Christine; Szatmari, Peter; Tammimies, Kristiina; Valladares, Otto; Voran, Annette; Li-San, Wang; Weiss, Lauren A; Willsey, A Jeremy; Yu, Timothy W; Yuen, Ryan K C; Cook, Edwin H; Freitag, Christine M; Gill, Michael; Hultman, Christina M; Lehner, Thomas; Palotie, Aaarno; Schellenberg, Gerard D; Sklar, Pamela; State, Matthew W; Sutcliffe, James S; Walsh, Christiopher A; Scherer, Stephen W; Zwick, Michael E; Barett, Jeffrey C; Cutler, David J; Roeder, Kathryn; Devlin, Bernie; Daly, Mark J; Buxbaum, Joseph D

    2014-11-13

    The genetic architecture of autism spectrum disorder involves the interplay of common and rare variants and their impact on hundreds of genes. Using exome sequencing, here we show that analysis of rare coding variation in 3,871 autism cases and 9,937 ancestry-matched or parental controls implicates 22 autosomal genes at a false discovery rate (FDR) < 0.05, plus a set of 107 autosomal genes strongly enriched for those likely to affect risk (FDR < 0.30). These 107 genes, which show unusual evolutionary constraint against mutations, incur de novo loss-of-function mutations in over 5% of autistic subjects. Many of the genes implicated encode proteins for synaptic formation, transcriptional regulation and chromatin-remodelling pathways. These include voltage-gated ion channels regulating the propagation of action potentials, pacemaking and excitability-transcription coupling, as well as histone-modifying enzymes and chromatin remodellers-most prominently those that mediate post-translational lysine methylation/demethylation modifications of histones.

  7. Capture of associated targets on chromatin links long-distance chromatin looping to transcriptional coordination.

    PubMed

    Bourgo, Ryan J; Singhal, Hari; Greene, Geoffrey L

    2016-01-01

    Here we describe a sensitive and novel method of identifying endogenous DNA-DNA interactions. Capture of Associated Targets on CHromatin (CATCH) uses efficient capture and enrichment of specific genomic loci of interest through hybridization and subsequent purification via complementary biotinylated oligonucleotide. The CATCH assay requires no enzymatic digestion or ligation, requires little starting material, provides high-quality data, has excellent reproducibility and is completed in less than 24 h. Efficacy is demonstrated through capture of three disparate loci, which demonstrate unique subsets of long-distance chromatin interactions enriched for both enhancer marks and oestrogen receptor-binding sites. In each experiment, CATCH-seq peaks representing long-distance chromatin interactions were centred near the TSS of genes, and, critically, the genes identified as physically interacting are shown to be transcriptionally coexpressed. These interactions could potentially create transcriptional hubs for the regulation of gene expression programmes. PMID:27634217

  8. Capture of associated targets on chromatin links long-distance chromatin looping to transcriptional coordination

    PubMed Central

    Bourgo, Ryan J.; Singhal, Hari; Greene, Geoffrey L.

    2016-01-01

    Here we describe a sensitive and novel method of identifying endogenous DNA–DNA interactions. Capture of Associated Targets on CHromatin (CATCH) uses efficient capture and enrichment of specific genomic loci of interest through hybridization and subsequent purification via complementary biotinylated oligonucleotide. The CATCH assay requires no enzymatic digestion or ligation, requires little starting material, provides high-quality data, has excellent reproducibility and is completed in less than 24 h. Efficacy is demonstrated through capture of three disparate loci, which demonstrate unique subsets of long-distance chromatin interactions enriched for both enhancer marks and oestrogen receptor-binding sites. In each experiment, CATCH-seq peaks representing long-distance chromatin interactions were centred near the TSS of genes, and, critically, the genes identified as physically interacting are shown to be transcriptionally coexpressed. These interactions could potentially create transcriptional hubs for the regulation of gene expression programmes. PMID:27634217

  9. Chromatin remodelers Isw1 and Chd1 maintain chromatin structure during transcription by preventing histone exchange

    PubMed Central

    Smolle, Michaela; Venkatesh, Swaminathan; Gogol, Madelaine M.; Li, Hua; Zhang, Ying; Florens, Laurence; Washburn, Michael P.; Workman, Jerry L.

    2012-01-01

    Set2-mediated methylation of histone H3 Lys36 (H3K36) is a mark associated with the coding sequences of actively transcribed genes, yet plays a negative role during transcription elongation. It prevents trans-histone exchange over coding regions and signals for histone deacetylation in the wake of RNA polymerase II (RNAPII) passage. We have found that in Saccharomyces cerevisiae the Isw1b chromatin-remodeling complex is specifically recruited to open reading frames (ORFs) by H3K36 methylation through the PWWP domain of its Ioc4 subunit in vivo and in vitro. Isw1b acts in conjunction with Chd1 to regulate chromatin structure by preventing trans-histone exchange from taking place over coding regions and thus maintains chromatin integrity during transcription elongation by RNA polymerase II. PMID:22922743

  10. Development of a multivariate light-induced fluorescence (LIF) PAT tool for in-line quantitative analysis of pharmaceutical granules in a V-blender.

    PubMed

    Guay, Jean-Maxime; Lapointe-Garant, Pierre-Philippe; Gosselin, Ryan; Simard, Jean-Sébastien; Abatzoglou, Nicolas

    2014-04-01

    Process analytical technologies (PAT) enable process insight, process control and real-time testing. Light-induced fluorescence (LIF) spectroscopy is especially well suited for low-concentration ingredients as, in many cases, it is the most sensitive probe of the in-line PAT toolbox. This study is aimed at verifying the applicability of a multivariate LIF analyzer to monitor granulated powder blends in industrial settings. Its targets are to: (1) evaluate the critical parameters of powders to obtain robust, precise and accurate concentration predictions and (2) assess technology performance for in-line monitoring of blending operations. Varying dye properties, moisture levels and particle sizes have been shown to have the most significant impact on fluorescence emission. Reliable quantitative models can be obtained by controlling and/or mitigating these factors. PMID:24373731

  11. Global Chromatin Domain Organization of the Drosophila Genome

    PubMed Central

    de Wit, Elzo; Braunschweig, Ulrich; Greil, Frauke; Bussemaker, Harmen J.; van Steensel, Bas

    2008-01-01

    In eukaryotes, neighboring genes can be packaged together in specific chromatin structures that ensure their coordinated expression. Examples of such multi-gene chromatin domains are well-documented, but a global view of the chromatin organization of eukaryotic genomes is lacking. To systematically identify multi-gene chromatin domains, we constructed a compendium of genome-scale binding maps for a broad panel of chromatin-associated proteins in Drosophila melanogaster. Next, we computationally analyzed this compendium for evidence of multi-gene chromatin domains using a novel statistical segmentation algorithm. We find that at least 50% of all fly genes are organized into chromatin domains, which often consist of dozens of genes. The domains are characterized by various known and novel combinations of chromatin proteins. The genes in many of the domains are coregulated during development and tend to have similar biological functions. Furthermore, during evolution fewer chromosomal rearrangements occur inside chromatin domains than outside domains. Our results indicate that a substantial portion of the Drosophila genome is packaged into functionally coherent, multi-gene chromatin domains. This has broad mechanistic implications for gene regulation and genome evolution. PMID:18369463

  12. Sodium butyrate induced structural changes in HeLa cell chromatin

    SciTech Connect

    Reczek, P.R.; Weissman, D.; Huvos, P.E.; Fasman, G.D.

    1982-01-01

    Postsynthetic modifications of core histones by treatment of HeLa S3 cells with 5 mM sodium butyrate lead to alterations in the structure of high molecular weight chromatin. Whole chromatin from butyrate-treated cells, which results in highly acetylated core histones, has an ellipticity (theta)/sub 282.5/ of 3700 deg cm/sup 2/ dmol/sup -1/ (0.2 mM EDTA, pH 7.4) that is 1200 deg cm/sup 2/ dmol/sup -1/ less than chromatin from untreated HeLa cells, suggesting a more condensed structure. No difference in the circular dichroism spectra was observed in Hl-stripped, high molecular weight chromatin obtained from control and butyrate-treated cells at low (0.2 mM EDTA, pH 7.4) ionic strength.Thermal denaturation profiles of high molecular weight chromatin were resolved into three transitions and exhibited a shifting of hyperchromicity from transition I to transition III, at a higher T/sub m/, with butyrate treatment of HeLa cells, further indicating a more compact structure. Thermal denaturation profiles of Hl-stripped chromatin were not affected by butyrate treatment. Ionic strength studies in the range of 0-5 mM NaH/sub 2/PO/sub 4/, 0.2 mM EDTA, pH 7.4, of high molecular weight chromatin exhibited a decrease in (theta)/sub 282.5/ and a shifting of hyperchromicity from transition I to transition III with increasing ionic strength. Control high molecular weight chromatin was more sensitive to changes in ionic strength than its highly acetylated counterpart. These results suggest that acetylation of histones alone does not result in a change in histone-DNA interaction but other changes associated with butyrate treatment most probably cause a more condensed structure, of the fraction studied herein, which is mediated by Hl or other materials removed during stripping in 0.35 M NaCl.

  13. Sodium butyrate induced structural changes in HeLa cell chromatin

    SciTech Connect

    Reczek, P.R.; Weissman, D.; Huvos, P.E.; Fasman, G.D.

    1982-03-02

    Postsynthetic modifications of core histones by treatment of HeLa S3 cells with 5 mM sodium butyrate lead to alterations in the structure of high molecular weight chromatin. Whole chromatin from butyrate-treated cells, which results in highly acetylated core histones, has an ellipticity (THETA)/sub 282.5/ of 3700 deg cm/sup 2/ dmol/sup -1/ (0.2 mM EDTA, pH 7.4) that is 1200 deg cm/sup 2/ dmol/sup -1/ less than chromatin from untreated HeLa cells, suggesting a more condensed structure. No difference in the circular dichroism spectra was observed in Hl-stripped, high molecular weight chromatin obtained from control and butyrate-treated cells at low (0.2 mM EDTA, pH 7.4) ionic strength. Thermal denaturation profiles of high molecular weight chromatin were resolved into three transitions and exhibited a shifting of hyperchromicity from transition I to transition III, at a higher T/sub m/, with butyrate treatment of HeLa cells, further indicating a more compact structure. Thermal denaturation profiles of Hl-stripped chromatin were not affected by butyrate treatment. Ionic strength studies in the range of 0-5 mM NaH/sub 2/PO/sub 4/, 0.2 mM EDTA, pH 7.4, of high molecular weight chromatin exhibited a decrease in (THETA)/sub 282.5/ and shifting of hyperchromicity from transition I to transition III with increasing ionic strength. Control high molecular weight chromatin was more sensitive to changes in ionic strength than its highly acetylated counterpart. These results suggest that acetylation of histones alone does not result in a change in histone-DNA interaction but other changes associated with butyrate treatment most probably cause a more condensed structure, of the fraction studied herein, which is mediated by Hl or other materials removed during stripping in 0.35 M NaCl.

  14. H3K4 monomethylation dictates nucleosome dynamics and chromatin remodeling at stress-responsive genes.

    PubMed

    Nadal-Ribelles, Mariona; Mas, Glòria; Millán-Zambrano, Gonzalo; Solé, Carme; Ammerer, Gustav; Chávez, Sebastián; Posas, Francesc; de Nadal, Eulàlia

    2015-05-26

    Chromatin remodeling is essential for proper adaptation to extracellular stimuli. The p38-related Hog1 SAPK is an important regulator of transcription that mediates chromatin remodeling upon stress. Hog1 targets the RSC chromatin remodeling complex to stress-responsive genes and rsc deficient cells display reduced induction of gene expression. Here we show that the absence of H3K4 methylation, either achieved by deletion of the SET1 methyltransferase or by amino acid substitution of H3K4, bypasses the requirement of RSC for stress-responsive gene expression. Monomethylation of H3K4 is specifically inhibiting RSC-independent chromatin remodeling and thus, it prevents osmostress-induced gene expression. The absence of H3K4 monomethylation permits that the association of alternative remodelers with stress-responsive genes and the Swr1 complex (SWR-C) is instrumental in the induction of gene expression upon stress. Accordingly, the absence of SWR-C or histone H2A.Z results in compromised chromatin remodeling and impaired gene expression in the absence of RSC and H3K4 methylation. These results indicate that expression of stress-responsive genes is controlled by two remodeling mechanisms: RSC in the presence of monomethylated H3K4, and SWR-C in the absence of H3K4 monomethylation. Our findings point to a novel role for H3K4 monomethylation in dictating the specificity of chromatin remodeling, adding an extra layer of regulation to the transcriptional stress response.

  15. Effect of imaging geometry on evaluating natural white-spot lesions using quantitative light-induced fluorescence.

    PubMed

    Ando, Masatoshi; Eckert, George J; Stookey, George K; Zero, Domenick T

    2004-01-01

    The objective of this study was to determine the effect of imaging geometry on evaluating natural white-spot lesions with quantitative light-induced fluorescence (QLF). A total of 34 specimens were prepared from extracted human premolars and permanent molars with white spots on the interproximal surface. The specimens were each adjusted to a final thickness of 3.0 mm. Images were acquired with the QLF system perpendicular to the white spots and at 5 degrees intervals up to 30 degrees above and below the perpendicular. The specimens were rotated around the buccolingual axis of the tooth (pitch angle) and around the long axis of the tooth (roll angle). The averages of fluorescence loss (DeltaF, %) and lesion size (mm2) were determined with QLF. Another variable, DeltaQ, which was defined as the fluorescence loss integrated over the lesion size (% x mm2), was also calculated. DeltaF was smaller when lesions were viewed from the cervical direction (angles less than 90 degrees ), and became bigger when viewed from the coronal direction. Roll angle did not significantly affect DeltaF. Apparent lesion size diminished with deviations from 90 degrees in both directions for pitch and roll angles. DeltaQ was affected by pitch and roll angles with the largest value at 90 degrees and values decreasing in both directions from 90 degrees. In general, there were significant differences for angles larger than 20 degrees from the perpendicular for all three QLF variables. This study suggests that angle is an important factor to control when performing QLF studies; however, small changes (deviations within 20 degrees ) have a minimal effect on QLF variables. PMID:14684976

  16. TD-DFT study of the light-induced spin crossover of Fe(III) complexes.

    PubMed

    Saureu, Sergi; de Graaf, Coen

    2016-01-14

    Two light-induced spin-crossover Fe(III) compounds have been studied with time-dependent density functional theory (TD-DFT) to investigate the deactivation mechanism and the role of the ligand-field states as intermediates in this process. The B3LYP* functional has previously shown its ability to accurately describe (light-induced) spin-crossover in Fe(II) complexes. Here, we establish its performance for Fe(III) systems using [Fe(qsal)2](+) (Hqsal = 2-[(8-quinolinylimino)methyl]phenol) and [Fe(pap)2](+) (Hpap = 2-(2-pyridylmethyleneamino)phenol) as test cases comparing the B3LYP* results to experimental information and to multiconfigurational wave function results. In addition to rather accurate high spin (HS) and low spin (LS) state geometries, B3LYP* also predicts ligand-to-metal charge transfer (LMCT) states with large oscillator strength in the energy range where the UV-VIS spectrum shows an intense absorption band, whereas optically allowed π-π* excitations on the ligands were calculated at higher energy. Subsequently, we have generated a two-dimensional potential energy surface of the HS and LS states varying the Fe-N and Fe-O distances. LMCT and metal centered (MC) excited states were followed along the approximate minimal energy path that connects the minima of the HS and LS on this surface. The (2)LMCT state has a minimum in the same region as the initial LS state, where we also observe a crossing with the intermediate spin (IS) state. Upon the expansion of the coordination sphere of the Fe(III) ion, the IS state crosses with the HS state and further expansion of the coordination sphere leads to the excited spin state trapping as observed in experiment. The calculation of the intersystem crossing rates reveals that the deactivation from (2)LMCT → IS → HS competes with the (2)LMCT → IS → LS pathway, in line with the low efficiency encountered in experiments. PMID:26660866

  17. A role for chromatin topology in imprinted domain regulation.

    PubMed

    MacDonald, William A; Sachani, Saqib S; White, Carlee R; Mann, Mellissa R W

    2016-02-01

    Recently, many advancements in genome-wide chromatin topology and nuclear architecture have unveiled the complex and hidden world of the nucleus, where chromatin is organized into discrete neighbourhoods with coordinated gene expression. This includes the active and inactive X chromosomes. Using X chromosome inactivation as a working model, we utilized publicly available datasets together with a literature review to gain insight into topologically associated domains, lamin-associated domains, nucleolar-associating domains, scaffold/matrix attachment regions, and nucleoporin-associated chromatin and their role in regulating monoallelic expression. Furthermore, we comprehensively review for the first time the role of chromatin topology and nuclear architecture in the regulation of genomic imprinting. We propose that chromatin topology and nuclear architecture are important regulatory mechanisms for directing gene expression within imprinted domains. Furthermore, we predict that dynamic changes in chromatin topology and nuclear architecture play roles in tissue-specific imprint domain regulation during early development and differentiation.

  18. Difunctionalization of Alkenes via the Visible-Light-Induced Trifluoromethylarylation/1,4-Aryl Shift/Desulfonylation Cascade Reactions.

    PubMed

    Zheng, Lewei; Yang, Chao; Xu, ZhaoZhong; Gao, Fei; Xia, Wujiong

    2015-06-01

    A novel visible-light-induced trifluoromethylarylation/1,4-aryl shift/desulfonylation cascade reaction using CF3SO2Cl as CF3 source was described. The protocol provides an efficient approach for the synthesis of α-aryl-β-trifluoromethyl amides and/or CF3-containing oxindoles as well as the isoquinolinediones under benign conditions.

  19. Additive effect of mPer1 and mPer2 antisense oligonucleotides on light-induced phase shift.

    PubMed

    Wakamatsu, H; Takahashi, S; Moriya, T; Inouye, S T; Okamura, H; Akiyama, M; Shibata, S

    2001-01-22

    It is well known that light induces both mPer1 and mPer2 mRNA in the suprachiasmatic nucleus. We have reported that mPer1 antisense oligonucleotides (ODNs) inhibited the light-induced phase delays of mouse locomotor rhythm. In this study, we asked whether both or either mPer1 or mPer2 expression is necessary to induce the phase shift. We examined the effects of inhibition of mRNA expression on light-induced phase delays of mouse circadian behavior rhythm. Light-induced phase delays were moderately attenuated by microinjection of mPer1 or mPer2 antisense ODN, but not by mPer3 antisense or mPer1, mPer2 scrambled ODNs, whereas following simultaneous injection of both mPer1 and mPer2 antisense ODNs they disappeared. The present results suggest that acute induction of mPer1 and mPer2 gene play an additive effect on photic entrainment. PMID:11201072

  20. The Effects of TiO2 Nanodot Films with RGD Immobilization on Light-Induced Cell Sheet Technology

    PubMed Central

    Yu, Meng-Liu; Yu, Meng-Fei; Zhu, Li-Qin; Wang, Tian-Tian; Zhou, Yi; Wang, Hui-Ming

    2015-01-01

    Cell sheet technology is a new strategy in tissue engineering which could be possible to implant into the body without a scaffold. In order to get an integrated cell sheet, a light-induced method via UV365 is used for cell sheet detachment from culture dishes. In this study, we investigated the possibility of cell detachment and growth efficiency on TiO2 nanodot films with RGD immobilization on light-induced cell sheet technology. Mouse calvaria-derived, preosteoblastic (MC3T3-E1) cells were cultured on TiO2 nanodot films with (TR) or without (TN) RGD immobilization. After cells were cultured with or without 5.5 mW/cm2 UV365 illumination, cell morphology, cell viability, osteogenesis related RNA and protein expression, and cell detachment ability were compared, respectively. Light-induced cell detachment was possible when cells were cultured on TR samples. Also, cells cultured on TR samples showed better cell viability, alongside higher protein and RNA expression than on TN samples. This study provides a new biomaterial for light-induced cell/cell sheet harvesting. PMID:26417596

  1. Ubiquitin-specific Protease 7 Regulates Nucleotide Excision Repair through Deubiquitinating XPC Protein and Preventing XPC Protein from Undergoing Ultraviolet Light-induced and VCP/p97 Protein-regulated Proteolysis*

    PubMed Central

    He, Jinshan; Zhu, Qianzheng; Wani, Gulzar; Sharma, Nidhi; Han, Chunhua; Qian, Jiang; Pentz, Kyle; Wang, Qi-en; Wani, Altaf A.

    2014-01-01

    Ubiquitin specific protease 7 (USP7) is a known deubiquitinating enzyme for tumor suppressor p53 and its downstream regulator, E3 ubiquitin ligase Mdm2. Here we report that USP7 regulates nucleotide excision repair (NER) via deubiquitinating xeroderma pigmentosum complementation group C (XPC) protein, a critical damage recognition factor that binds to helix-distorting DNA lesions and initiates NER. XPC is ubiquitinated during the early stage of NER of UV light-induced DNA lesions. We demonstrate that transiently compromising cellular USP7 by siRNA and chemical inhibition leads to accumulation of ubiquitinated forms of XPC, whereas complete USP7 deficiency leads to rapid ubiquitin-mediated XPC degradation upon UV irradiation. We show that USP7 physically interacts with XPC in vitro and in vivo. Overexpression of wild-type USP7, but not its catalytically inactive or interaction-defective mutants, reduces the ubiquitinated forms of XPC. Importantly, USP7 efficiently deubiquitinates XPC-ubiquitin conjugates in deubiquitination assays in vitro. We further show that valosin-containing protein (VCP)/p97 is involved in UV light-induced XPC degradation in USP7-deficient cells. VCP/p97 is readily recruited to DNA damage sites and colocalizes with XPC. Chemical inhibition of the activity of VCP/p97 ATPase causes an increase in ubiquitinated XPC on DNA-damaged chromatin. Moreover, USP7 deficiency severely impairs the repair of cyclobutane pyrimidine dimers and, to a lesser extent, affects the repair of 6-4 photoproducts. Taken together, our findings uncovered an important role of USP7 in regulating NER via deubiquitinating XPC and by preventing its VCP/p97-regulated proteolysis. PMID:25118285

  2. NET23/STING Promotes Chromatin Compaction from the Nuclear Envelope

    PubMed Central

    de las Heras, Jose I.; Saiz-Ros, Natalia; Makarov, Alexandr A.; Lazou, Vassiliki; Meinke, Peter; Waterfall, Martin; Kelly, David A.; Schirmer, Eric C.

    2014-01-01

    Changes in the peripheral distribution and amount of condensed chromatin are observed in a number of diseases linked to mutations in the lamin A protein of the nuclear envelope. We postulated that lamin A interactions with nuclear envelope transmembrane proteins (NETs) that affect chromatin structure might be altered in these diseases and so screened thirty-one NETs for those that promote chromatin compaction as determined by an increase in the number of chromatin clusters of high pixel intensity. One of these, NET23 (also called STING, MITA, MPYS, ERIS, Tmem173), strongly promoted chromatin compaction. A correlation between chromatin compaction and endogenous levels of NET23/STING was observed for a number of human cell lines, suggesting that NET23/STING may contribute generally to chromatin condensation. NET23/STING has separately been found to be involved in innate immune response signaling. Upon infection cells make a choice to either apoptose or to alter chromatin architecture to support focused expression of interferon genes and other response factors. We postulate that the chromatin compaction induced by NET23/STING may contribute to this choice because the cells expressing NET23/STING eventually apoptose, but the chromatin compaction effect is separate from this as the condensation was still observed when cells were treated with Z-VAD to block apoptosis. NET23/STING-induced compacted chromatin revealed changes in epigenetic marks including changes in histone methylation and acetylation. This indicates a previously uncharacterized nuclear role for NET23/STING potentially in both innate immune signaling and general chromatin architecture. PMID:25386906

  3. Aging by epigenetics-A consequence of chromatin damage?

    SciTech Connect

    Sedivy, John M. Banumathy, Gowrishankar; Adams, Peter D.

    2008-06-10

    Chromatin structure is not fixed. Instead, chromatin is dynamic and is subject to extensive developmental and age-associated remodeling. In some cases, this remodeling appears to counter the aging and age-associated diseases, such as cancer, and extend organismal lifespan. However, stochastic non-deterministic changes in chromatin structure might, over time, also contribute to the break down of nuclear, cell and tissue function, and consequently aging and age-associated diseases.

  4. NET23/STING promotes chromatin compaction from the nuclear envelope.

    PubMed

    Malik, Poonam; Zuleger, Nikolaj; de las Heras, Jose I; Saiz-Ros, Natalia; Makarov, Alexandr A; Lazou, Vassiliki; Meinke, Peter; Waterfall, Martin; Kelly, David A; Schirmer, Eric C

    2014-01-01

    Changes in the peripheral distribution and amount of condensed chromatin are observed in a number of diseases linked to mutations in the lamin A protein of the nuclear envelope. We postulated that lamin A interactions with nuclear envelope transmembrane proteins (NETs) that affect chromatin structure might be altered in these diseases and so screened thirty-one NETs for those that promote chromatin compaction as determined by an increase in the number of chromatin clusters of high pixel intensity. One of these, NET23 (also called STING, MITA, MPYS, ERIS, Tmem173), strongly promoted chromatin compaction. A correlation between chromatin compaction and endogenous levels of NET23/STING was observed for a number of human cell lines, suggesting that NET23/STING may contribute generally to chromatin condensation. NET23/STING has separately been found to be involved in innate immune response signaling. Upon infection cells make a choice to either apoptose or to alter chromatin architecture to support focused expression of interferon genes and other response factors. We postulate that the chromatin compaction induced by NET23/STING may contribute to this choice because the cells expressing NET23/STING eventually apoptose, but the chromatin compaction effect is separate from this as the condensation was still observed when cells were treated with Z-VAD to block apoptosis. NET23/STING-induced compacted chromatin revealed changes in epigenetic marks including changes in histone methylation and acetylation. This indicates a previously uncharacterized nuclear role for NET23/STING potentially in both innate immune signaling and general chromatin architecture. PMID:25386906

  5. NET23/STING promotes chromatin compaction from the nuclear envelope.

    PubMed

    Malik, Poonam; Zuleger, Nikolaj; de las Heras, Jose I; Saiz-Ros, Natalia; Makarov, Alexandr A; Lazou, Vassiliki; Meinke, Peter; Waterfall, Martin; Kelly, David A; Schirmer, Eric C

    2014-01-01

    Changes in the peripheral distribution and amount of condensed chromatin are observed in a number of diseases linked to mutations in the lamin A protein of the nuclear envelope. We postulated that lamin A interactions with nuclear envelope transmembrane proteins (NETs) that affect chromatin structure might be altered in these diseases and so screened thirty-one NETs for those that promote chromatin compaction as determined by an increase in the number of chromatin clusters of high pixel intensity. One of these, NET23 (also called STING, MITA, MPYS, ERIS, Tmem173), strongly promoted chromatin compaction. A correlation between chromatin compaction and endogenous levels of NET23/STING was observed for a number of human cell lines, suggesting that NET23/STING may contribute generally to chromatin condensation. NET23/STING has separately been found to be involved in innate immune response signaling. Upon infection cells make a choice to either apoptose or to alter chromatin architecture to support focused expression of interferon genes and other response factors. We postulate that the chromatin compaction induced by NET23/STING may contribute to this choice because the cells expressing NET23/STING eventually apoptose, but the chromatin compaction effect is separate from this as the condensation was still observed when cells were treated with Z-VAD to block apoptosis. NET23/STING-induced compacted chromatin revealed changes in epigenetic marks including changes in histone methylation and acetylation. This indicates a previously uncharacterized nuclear role for NET23/STING potentially in both innate immune signaling and general chromatin architecture.

  6. The light-induced transcriptome of the zebrafish pineal gland reveals complex regulation of the circadian clockwork by light.

    PubMed

    Ben-Moshe, Zohar; Alon, Shahar; Mracek, Philipp; Faigenbloom, Lior; Tovin, Adi; Vatine, Gad D; Eisenberg, Eli; Foulkes, Nicholas S; Gothilf, Yoav

    2014-04-01

    Light constitutes a primary signal whereby endogenous circadian clocks are synchronized ('entrained') with the day/night cycle. The molecular mechanisms underlying this vital process are known to require gene activation, yet are incompletely understood. Here, the light-induced transcriptome in the zebrafish central clock organ, the pineal gland, was characterized by messenger RNA (mRNA) sequencing (mRNA-seq) and microarray analyses, resulting in the identification of multiple light-induced mRNAs. Interestingly, a considerable portion of the molecular clock (14 genes) is light-induced in the pineal gland. Four of these genes, encoding the transcription factors dec1, reverbb1, e4bp4-5 and e4bp4-6, differentially affected clock- and light-regulated promoter activation, suggesting that light-input is conveyed to the core clock machinery via diverse mechanisms. Moreover, we show that dec1, as well as the core clock gene per2, is essential for light-entrainment of rhythmic locomotor activity in zebrafish larvae. Additionally, we used microRNA (miRNA) sequencing (miR-seq) and identified pineal-enhanced and light-induced miRNAs. One such miRNA, miR-183, is shown to downregulate e4bp4-6 mRNA through a 3'UTR target site, and importantly, to regulate the rhythmic mRNA levels of aanat2, the key enzyme in melatonin synthesis. Together, this genome-wide approach and functional characterization of light-induced factors indicate a multi-level regulation of the circadian clockwork by light. PMID:24423866

  7. Formaldehyde crosslinking: a tool for the study of chromatin complexes.

    PubMed

    Hoffman, Elizabeth A; Frey, Brian L; Smith, Lloyd M; Auble, David T

    2015-10-30

    Formaldehyde has been used for decades to probe macromolecular structure and function and to trap complexes, cells, and tissues for further analysis. Formaldehyde crosslinking is routinely employed for detection and quantification of protein-DNA interactions, interactions between chromatin proteins, and interactions between distal segments of the chromatin fiber. Despite widespread use and a rich biochemical literature, important aspects of formaldehyde behavior in cells have not been well described. Here, we highlight features of formaldehyde chemistry relevant to its use in analyses of chromatin complexes, focusing on how its properties may influence studies of chromatin structure and function.

  8. Interaction of sulfur mustard with rat liver salt fractionated chromatin.

    PubMed

    Jafari, Mahvash; Nateghi, M; Rabbani, A

    2010-01-01

    In this study, the interaction of an alkylating agent, sulfur mustard (SM) with rat liver active (S1 and S2) and inactive (P2) chromatin was investigated employing UV/vis spectroscopy and gel electrophoreses. The results show that SM affects the chromatin structure in a dose-dependent manner. The binding of SM to fractions is different. At lower concentrations (<500 microM), SM seems to unfold the structure and at higher concentrations, it induces aggregation and condensation of chromatin possibly via forming cross-links between the chromatin components. The extent of condensation in S2 is higher when compared to the P2 fraction.

  9. The centromere: chromatin foundation for the kinetochore machinery.

    PubMed

    Fukagawa, Tatsuo; Earnshaw, William C

    2014-09-01

    Since discovery of the centromere-specific histone H3 variant CENP-A, centromeres have come to be defined as chromatin structures that establish the assembly site for the complex kinetochore machinery. In most organisms, centromere activity is defined epigenetically, rather than by specific DNA sequences. In this review, we describe selected classic work and recent progress in studies of centromeric chromatin with a focus on vertebrates. We consider possible roles for repetitive DNA sequences found at most centromeres, chromatin factors and modifications that assemble and activate CENP-A chromatin for kinetochore assembly, plus the use of artificial chromosomes and kinetochores to study centromere function. PMID:25203206

  10. Formaldehyde crosslinking: a tool for the study of chromatin complexes.

    PubMed

    Hoffman, Elizabeth A; Frey, Brian L; Smith, Lloyd M; Auble, David T

    2015-10-30

    Formaldehyde has been used for decades to probe macromolecular structure and function and to trap complexes, cells, and tissues for further analysis. Formaldehyde crosslinking is routinely employed for detection and quantification of protein-DNA interactions, interactions between chromatin proteins, and interactions between distal segments of the chromatin fiber. Despite widespread use and a rich biochemical literature, important aspects of formaldehyde behavior in cells have not been well described. Here, we highlight features of formaldehyde chemistry relevant to its use in analyses of chromatin complexes, focusing on how its properties may influence studies of chromatin structure and function. PMID:26354429

  11. Isolation of In Vivo SUMOylated Chromatin-Bound Proteins.

    PubMed

    Bawa-Khalfe, Tasneem

    2016-01-01

    SUMO posttranslational modification directs gene transcription and epigenetic programming to support normal cell function. The dynamic nature of SUMO-modification makes it difficult to identify endogenous protein substrates. Isolation of chromatin-bound SUMO targets is exceptionally challenging, as conventional immunoprecipitation assays are inefficient at concentrating this protein population. This chapter describes a protocol that effectively precipitates chromatin-associated fractions of SUMOylated heterochromatin protein 1α in cultured cells. Techniques to enrich endogenous SUMO substrates at the chromatin are also demonstrated and discussed. This approach could be adapted to evaluate chromatin-bound SUMO targets in additional in vivo systems. PMID:27631808

  12. Epigenetics: Beyond Chromatin Modifications and Complex Genetic Regulation1

    PubMed Central

    Eichten, Steven R.; Schmitz, Robert J.; Springer, Nathan M.

    2014-01-01

    Chromatin modifications and epigenetics may play important roles in many plant processes, including developmental regulation, responses to environmental stimuli, and local adaptation. Chromatin modifications describe biochemical changes to chromatin state, such as alterations in the specific type or placement of histones, modifications of DNA or histones, or changes in the specific proteins or RNAs that associate with a genomic region. The term epigenetic is often used to describe a variety of unexpected patterns of gene regulation or inheritance. Here, we specifically define epigenetics to include the key aspects of heritability (stable transmission of gene expression states through mitotic or meiotic cell divisions) and independence from DNA sequence changes. We argue against generically equating chromatin and epigenetics; although many examples of epigenetics involve chromatin changes, those chromatin changes are not always heritable or may be influenced by genetic changes. Careful use of the terms chromatin modifications and epigenetics can help separate the biochemical mechanisms of regulation from the inheritance patterns of altered chromatin states. Here, we also highlight examples in which chromatin modifications and epigenetics affect important plant processes. PMID:24872382

  13. Increased chromatin fragmentation and reduced acrosome integrity in spermatozoa of red deer from lead polluted sites.

    PubMed

    Castellanos, Pilar; del Olmo, Enrique; Fernández-Santos, M Rocío; Rodríguez-Estival, Jaime; Garde, J Julián; Mateo, Rafael

    2015-02-01

    Vertebrates are constantly exposed to a diffuse pollution of heavy metals existing in the environment, but in some cases, the proximity to emission sources like mining activity increases the risk of developing adverse effects of these pollutants. Here we have studied lead (Pb) levels in spermatozoa and testis, and chromatin damage and levels of endogenous antioxidant activity in spermatozoa of red deer (Cervus elaphus) from a Pb mining area (n=37) and a control area (n=26). Deer from the Pb-polluted area showed higher Pb levels in testis parenchyma, epididymal cauda and spermatozoa, lower values of acrosome integrity, higher activity of glutathione peroxidase (GPx) and higher values of DNA fragmentation (X-DFI) and stainability (HDS) in sperm than in the control area. These results indicate that mining pollution can produce damage on chromatin and membrane spermatozoa in wildlife. The study of chromatin fragmentation has not been studied before in spermatozoa of wildlife species, and the sperm chromatin structure assay (SCSA) has been revealed as a successful tool for this purpose in species in which the amount of sperm that can be collected is very limited.

  14. Chromatin Immunoprecipitation Assay for the Identification of Arabidopsis Protein-DNA Interactions In Vivo.

    PubMed

    Komar, Dorota N; Mouriz, Alfonso; Jarillo, José A; Piñeiro, Manuel

    2016-01-14

    Intricate gene regulatory networks orchestrate biological processes and developmental transitions in plants. Selective transcriptional activation and silencing of genes mediate the response of plants to environmental signals and developmental cues. Therefore, insights into the mechanisms that control plant gene expression are essential to gain a deep understanding of how biological processes are regulated in plants. The chromatin immunoprecipitation (ChIP) technique described here is a procedure to identify the DNA-binding sites of proteins in genes or genomic regions of the model species Arabidopsis thaliana. The interactions with DNA of proteins of interest such as transcription factors, chromatin proteins or posttranslationally modified versions of histones can be efficiently analyzed with the ChIP protocol. This method is based on the fixation of protein-DNA interactions in vivo, random fragmentation of chromatin, immunoprecipitation of protein-DNA complexes with specific antibodies, and quantification of the DNA associated with the protein of interest by PCR techniques. The use of this methodology in Arabidopsis has contributed significantly to unveil transcriptional regulatory mechanisms that control a variety of plant biological processes. This approach allowed the identification of the binding sites of the Arabidopsis chromatin protein EBS to regulatory regions of the master gene of flowering FT. The impact of this protein in the accumulation of particular histone marks in the genomic region of FT was also revealed through ChIP analysis.

  15. Crystal structure of the nucleosome containing ultraviolet light-induced cyclobutane pyrimidine dimer.

    PubMed

    Horikoshi, Naoki; Tachiwana, Hiroaki; Kagawa, Wataru; Osakabe, Akihisa; Matsumoto, Syota; Iwai, Shigenori; Sugasawa, Kaoru; Kurumizaka, Hitoshi

    2016-02-26

    The cyclobutane pyrimidine dimer (CPD) is induced in genomic DNA by ultraviolet (UV) light. In mammals, this photolesion is primarily induced within nucleosomal DNA, and repaired exclusively by the nucleotide excision repair (NER) pathway. However, the mechanism by which the CPD is accommodated within the nucleosome has remained unknown. We now report the crystal structure of a nucleosome containing CPDs. In the nucleosome, the CPD induces only limited local backbone distortion, and the affected bases are accommodated within the duplex. Interestingly, one of the affected thymine bases is located within 3.0 Å from the undamaged complementary adenine base, suggesting the formation of complementary hydrogen bonds in the nucleosome. We also found that UV-DDB, which binds the CPD at the initial stage of the NER pathway, also efficiently binds to the nucleosomal CPD. These results provide important structural and biochemical information for understanding how the CPD is accommodated and recognized in chromatin.

  16. Nucleophile sensitivity of Drosophila TRPA1 underlies light-induced feeding deterrence

    PubMed Central

    Du, Eun Jo; Ahn, Tae Jung; Wen, Xianlan; Seo, Dae-Won; Na, Duk L; Kwon, Jae Young; Choi, Myunghwan; Kim, Hyung-Wook; Cho, Hana; Kang, KyeongJin

    2016-01-01

    Solar irradiation including ultraviolet (UV) light causes tissue damage by generating reactive free radicals that can be electrophilic or nucleophilic due to unpaired electrons. Little is known about how free radicals induced by natural sunlight are rapidly detected and avoided by animals. We discover that Drosophila Transient Receptor Potential Ankyrin 1 (TRPA1), previously known only as an electrophile receptor, sensitively detects photochemically active sunlight through nucleophile sensitivity. Rapid light-dependent feeding deterrence in Drosophila was mediated only by the TRPA1(A) isoform, despite the TRPA1(A) and TRPA1(B) isoforms having similar electrophile sensitivities. Such isoform dependence re-emerges in the detection of structurally varied nucleophilic compounds and nucleophilicity-accompanying hydrogen peroxide (H2O2). Furthermore, these isoform-dependent mechanisms require a common set of TRPA1(A)-specific residues dispensable for electrophile detection. Collectively, TRPA1(A) rapidly responds to natural sunlight intensities through its nucleophile sensitivity as a receptor of photochemically generated radicals, leading to an acute light-induced behavioral shift in Drosophila. DOI: http://dx.doi.org/10.7554/eLife.18425.001 PMID:27656903

  17. Comparison of amorphous silicon absorber materials: Light-induced degradation and solar cell efficiency

    NASA Astrophysics Data System (ADS)

    Stuckelberger, M.; Despeisse, M.; Bugnon, G.; Schüttauf, J.-W.; Haug, F.-J.; Ballif, C.

    2013-10-01

    Several amorphous silicon (a-Si:H) deposition conditions have been reported to produce films that degrade least under light soaking when incorporated into a-Si:H solar cells. However, a systematic comparison of these a-Si:H materials has never been presented. In the present study, different plasma-enhanced chemical vapor deposition conditions, yielding standard low-pressure VHF a-Si:H, protocrystalline, polymorphous, and high-pressure RF a-Si:H materials, are compared with respect to their optical properties and their behavior when incorporated into single-junction solar cells. A wide deposition parameter space has been explored in the same deposition system varying hydrogen dilution, deposition pressure, temperature, frequency, and power. From the physics of layer growth, to layer properties, to solar cell performance and light-induced degradation, a consistent picture of a-Si:H materials that are currently used for a-Si:H solar cells emerges. The applications of these materials in single-junction, tandem, and triple-junction solar cells are discussed, as well as their deposition compatibility with rough substrates, taking into account aspects of voltage, current, and charge collection. In sum, this contributes to answering the question, "Which material is best for which type of solar cell?"

  18. A new photoacoustic method based on the modulation of the light induced absorption coefficient

    NASA Astrophysics Data System (ADS)

    Engel, S.; Wenisch, C.; Müller, F. A.; Gräf, S.

    2016-04-01

    The present study reports on a new photoacoustic (PA) measurement method that is suitable for the investigation of light induced absorption effects including e.g. excited state absorption. Contrary to the modulation of the radiation intensity used in conventional PA-methods, the key principle of this novel setup is based on the modulation of the induced absorption coefficient by light. For this purpose, a pump-probe setup with a pulsed pump laser beam and a continuous probe laser beam is utilized. In this regime, the potential influence of heat on the PA-signal is much smaller when compared to arrangements with pulsed probe beam and continuous pump beam. Beyond that, the negative effect of thermal lenses can be neglected. Thus, the measurement technique is well-suited for materials exhibiting a strong absorption at the pump wavelength. The quantitative analysis of the induced absorption coefficient was achieved by the calibration of the additional PA-signal caused by the continuous probe laser to the PA-signal resulting from the pulsed pump laser using thallium bromoiodide (KRS-5) as sample material.

  19. Light-induced EPR study of charge transfer in poly(3-hexylthiophene)/fullerene bulk heterojunction

    SciTech Connect

    Krinichnyi, V. I.; Yudanova, E. I.; Denisov, N. N.

    2009-07-28

    The first results of the light-induced EPR study of magnetic, relaxation, and dynamic parameters of charge carriers background photoinduced by optical photons (1.7-3.4 eV) in poly(3-hexylthiophene)/fullerene bulk heterojunctions are described. All magnetic resonance parameters for positively charged polaron and negatively charged fullerene ion-radical in radical pairs photoinduced in the composite were determined separately by the steady-state microwave saturation method. Paramagnetic susceptibility of charge carriers reflects their activation dynamics and exchange interaction. A decay of long-living radical pairs depends on the spatial distance between photoinduced charge carriers. The one-dimensional polaron diffusion along the polymer chain and fullerene rotation near the main molecular axis was shown to follow activation Elliot hopping model and to be governed by photon energy. The difference in activation energies of the charge carriers' dynamics and in their dependence on the exciting photon energy proves their noninteracting character in the polymer/fullerene composite. Main magnetic, relaxation and dynamics parameters of charge carriers are governed by the photon energy band due to inhomogeneity of distribution of polymer and fullerene domains in the composite.

  20. Light-induced cooling of active medium of CW TEA CO2 laser

    NASA Astrophysics Data System (ADS)

    Azharonok, Viktor V.; Filatova, Irina I.; Shimanovich, Vladimir D.

    2003-10-01

    In the present paper a gas kinetic temperature change of active medium of high-power TEA CO2 laser that is conditioned by a self-influence of laser radiation on plasma parameters, is investigated. The active medium was pumped by a self-sustained transverse glow discharge. The gas kinetic temperature Tg of plasma has been deduced from the half-width of rotationally unresolved spectral bands of the (2+)N2. It is shown that the laser radiation propagation through the inverse medium causes a cooling of the active medium. The degree of the gas mixture cooling δTg~5K at W~2.2 W/2.2 W/cm3 and δTg~60 K at W~4.4 W/cm3. We suppose that the effect of the active medium cooling is connected with the change of a kinetic of V-T relaxation in asymmetrical mode of the active medium cooling is connected with the change of a kinetic of V-T relaxation in asymmetrical mode of the active medium cooling is connected with with the change of a kinetic of V-T relaxation in asymmetrical mode of vibrationally-excited CO2 molecule when the lasing takes place in the laser resonator. Analytical estimation of light-induced temperature change δT*g of fast-flow TEA CO2-laser active medium are compared with the experimental ones.

  1. Light-induced negative differential resistance in graphene/Si-quantum-dot tunneling diodes.

    PubMed

    Lee, Kyeong Won; Jang, Chan Wook; Shin, Dong Hee; Kim, Jong Min; Kang, Soo Seok; Lee, Dae Hun; Kim, Sung; Choi, Suk-Ho; Hwang, Euyheon

    2016-01-01

    One of the interesing tunneling phenomena is negative differential resistance (NDR), the basic principle of resonant-tunneling diodes. NDR has been utilized in various semiconductor devices such as frequency multipliers, oscillators, relfection amplifiers, logic switches, and memories. The NDR in graphene has been also reported theoretically as well as experimentally, but should be further studied to fully understand its mechanism, useful for practical device applications. Especially, there has been no observation about light-induced NDR (LNDR) in graphene-related structures despite very few reports on the LNDR in GaAs-based heterostructures. Here, we report first observation of LNDR in graphene/Si quantum dots-embedded SiO2 (SQDs:SiO2) multilayers (MLs) tunneling diodes. The LNDR strongly depends on temperature (T) as well as on SQD size, and the T dependence is consistent with photocurrent (PC)-decay behaviors. With increasing light power, the PC-voltage curves are more structured with peak-to-valley ratios over 2 at room temperature. The physical mechanism of the LNDR, governed by resonant tunneling of charge carriers through the minibands formed across the graphene/SQDs:SiO2 MLs and by their nonresonant phonon-assisted tunneling, is discussed based on theoretical considerations.

  2. Visible Light Induces Melanogenesis in Human Skin through a Photoadaptive Response.

    PubMed

    Randhawa, Manpreet; Seo, InSeok; Liebel, Frank; Southall, Michael D; Kollias, Nikiforos; Ruvolo, Eduardo

    2015-01-01

    Visible light (400-700 nm) lies outside of the spectral range of what photobiologists define as deleterious radiation and as a result few studies have studied the effects of visible light range of wavelengths on skin. This oversight is important considering that during outdoors activities skin is exposed to the full solar spectrum, including visible light, and to multiple exposures at different times and doses. Although the contribution of the UV component of sunlight to skin damage has been established, few studies have examined the effects of non-UV solar radiation on skin physiology in terms of inflammation, and limited information is available regarding the role of visible light on pigmentation. The purpose of this study was to determine the effect of visible light on the pro-pigmentation pathways and melanin formation in skin. Exposure to visible light in ex-vivo and clinical studies demonstrated an induction of pigmentation in skin by visible light. Results showed that a single exposure to visible light induced very little pigmentation whereas multiple exposures with visible light resulted in darker and sustained pigmentation. These findings have potential implications on the management of photo-aggravated pigmentary disorders, the proper use of sunscreens, and the treatment of depigmented lesions.

  3. Effect of a Complex Lutein Formula in an Animal Model for Light-Induced Retinal Degeneration.

    PubMed

    Cheng, Yin-Pin; Ke, Chia-Ying; Kuo, Chih-Chieh; Lee, Yih-Jing

    2016-08-31

    Several retinal degenerative diseases cause vision loss and retinal cell death. Currently, people face prolonged exposure to digital screens, rendering vision protection from light exposure a critical topic. In this study, we designed a complex lutein formula (CLF) by combining several natural compounds: Calendula officinalis, Lycium barbarum, Vaccinium myrtillus, Cassia obtusifolia, and Rhodiola rosea. In addition, we evaluated the protective effects of the formula on retinal functions in an animal model for light-induced retinal degeneration. We employed electroretinography to analyse retinal function, and conducted a histological examination of the morphological changes in the retina treated under various conditions. We revealed that the retinal function in animals exposed to light for 7 days decreased significantly; however, the retinal function of animals that had received the CLF exhibited superior performance, despite light exposure. In addition, a greater portion of the outer nuclear layer (ONL) (i.e. the nuclei of photoreceptors) in these animals was preserved compared with the animals that had not received the formula after 7 days of light exposure. These results revealed that our dietary CLF supplement attenuated retinal function loss resulting from long-term light exposure. PMID:27426260

  4. Iterative experiment design guides the characterization of a light-inducible gene expression circuit

    PubMed Central

    Ruess, Jakob; Parise, Francesca; Milias-Argeitis, Andreas; Khammash, Mustafa; Lygeros, John

    2015-01-01

    Systems biology rests on the idea that biological complexity can be better unraveled through the interplay of modeling and experimentation. However, the success of this approach depends critically on the informativeness of the chosen experiments, which is usually unknown a priori. Here, we propose a systematic scheme based on iterations of optimal experiment design, flow cytometry experiments, and Bayesian parameter inference to guide the discovery process in the case of stochastic biochemical reaction networks. To illustrate the benefit of our methodology, we apply it to the characterization of an engineered light-inducible gene expression circuit in yeast and compare the performance of the resulting model with models identified from nonoptimal experiments. In particular, we compare the parameter posterior distributions and the precision to which the outcome of future experiments can be predicted. Moreover, we illustrate how the identified stochastic model can be used to determine light induction patterns that make either the average amount of protein or the variability in a population of cells follow a desired profile. Our results show that optimal experiment design allows one to derive models that are accurate enough to precisely predict and regulate the protein expression in heterogeneous cell populations over extended periods of time. PMID:26085136

  5. Kinetic and thermodynamic analysis of the light-induced processes in plant and cyanobacterial phytochromes.

    PubMed

    Chizhov, Igor; Zorn, Björn; Manstein, Dietmar J; Gärtner, Wolfgang

    2013-11-01

    The light-induced processes of the biological photoreceptor phytochrome (recombinant phyA of oat and recombinant CphA from the cyanobacterium Tolypothrix PCC7601) have been investigated in a time-resolved manner in the temperature range from 0 to 30°C. Both proteins were heterologously expressed and assembled in vitro with phycocyanobilin. The Pr state of plant phytochrome phyA is converted to the Pfr state after formation of four intermediates with an overall quantum yield of ~18%. The reversal reaction (Pfr-to-Pr) shows several intermediates, all of which, even the first detectable one, exhibit already all spectral features of the Pr state. The canonical phytochrome CphA from Tolypothrix showed a similar intermediate sequence as its plant ortholog. Whereas the kinetics for the forward reaction (Pr-to-Pfr) was nearly identical for both proteins, the reverse process (Pr formation) in the cyanobacterial phytochrome was slower by a factor of three. As found for the Pfr-to-Pr intermediates in the plant protein, also in CphA all detectable intermediates showed the spectral features of the Pr form. For both phytochromes, activation parameters for both the forward and the backward reaction pathways were determined. PMID:24209867

  6. Analysis of Light-Induced Transmembrane Ion Gradients and Membrane Potential in Photosystem I Proteoliposomes

    SciTech Connect

    Pennisi, Cristian P.; Greenbaum, Elias; Yoshida, Ken

    2010-01-01

    Photosystem I (PSI) complexes can support a light-driven electrochemical gradient for protons, which is the driving force for energy-conserving reactions across biological membranes. In this work, a computational model that enables a quantitative description of the light-induced proton gradients across the membrane of PSI proteoliposomes is presented. Using a set of electrodiffusion equations, a compartmental model of a vesicle suspended in aqueous medium was studied. The light-mediated proton movement was modeled as a single proton pumping step with backpressure of the electric potential. The model fits determinations of pH obtained from PSI proteoliposomes illuminated in the presence of mediators of cyclic electron transport. The model also allows analysis of the proton gradients in relation to the transmembrane ion fluxes and electric potential. Sensitivity analysis enabled a determination of the parameters that have greater influence on steady-state levels and onset/decay rates of transmembrane pH and electric potential. This model could be used as a tool for optimizing PSI proteoliposomes for photo-electrochemical applications.

  7. Quantified light-induced fluorescence, review of a diagnostic tool in prevention of oral disease

    NASA Astrophysics Data System (ADS)

    de Josselin de Jong, Elbert; Higham, Susan M.; Smith, Philip W.; van Daelen, Catherina J.; van der Veen, Monique H.

    2009-05-01

    Diagnostic methods for the use in preventive dentistry are being developed continuously. Few of these find their way into general practice. Although the general trend in medicine is to focus on disease prevention and early diagnostics, in dentistry this is still not the case. Nevertheless, in dental research some of these methods seem to be promising for near future use by the general dental professional. In this paper an overview is given of a method called quantitative light-induced fluorescence or (QLF) in which visible and harmless light excites the teeth in the patient's mouth to produce fluorescent images, which can be stored on disk and computer analyzed. White spots (early dental caries) are detected and quantified as well as bacterial metabolites on and in the teeth. An overview of research to validate the technique and modeling to further the understanding of the technique by Monte Carlo simulation is given and it is shown that the fluorescence phenomena can be described by the simulation model in a qualitative way. A model describing the visibility of red fluorescence from within the dental tissue is added, as this was still lacking in current literature. An overview is given of the clinical images made with the system and of the extensive research which has been done. The QLF™ technology has been shown to be of importance when used in clinical trials with respect to the testing of toothpastes and preventive treatments. It is expected that the QLF™ technology will soon find its way into the general dental practice.

  8. Light-induced negative differential resistance in graphene/Si-quantum-dot tunneling diodes.

    PubMed

    Lee, Kyeong Won; Jang, Chan Wook; Shin, Dong Hee; Kim, Jong Min; Kang, Soo Seok; Lee, Dae Hun; Kim, Sung; Choi, Suk-Ho; Hwang, Euyheon

    2016-01-01

    One of the interesing tunneling phenomena is negative differential resistance (NDR), the basic principle of resonant-tunneling diodes. NDR has been utilized in various semiconductor devices such as frequency multipliers, oscillators, relfection amplifiers, logic switches, and memories. The NDR in graphene has been also reported theoretically as well as experimentally, but should be further studied to fully understand its mechanism, useful for practical device applications. Especially, there has been no observation about light-induced NDR (LNDR) in graphene-related structures despite very few reports on the LNDR in GaAs-based heterostructures. Here, we report first observation of LNDR in graphene/Si quantum dots-embedded SiO2 (SQDs:SiO2) multilayers (MLs) tunneling diodes. The LNDR strongly depends on temperature (T) as well as on SQD size, and the T dependence is consistent with photocurrent (PC)-decay behaviors. With increasing light power, the PC-voltage curves are more structured with peak-to-valley ratios over 2 at room temperature. The physical mechanism of the LNDR, governed by resonant tunneling of charge carriers through the minibands formed across the graphene/SQDs:SiO2 MLs and by their nonresonant phonon-assisted tunneling, is discussed based on theoretical considerations. PMID:27465107

  9. Cyanobacterial high-light-inducible proteins--Protectors of chlorophyll-protein synthesis and assembly.

    PubMed

    Komenda, Josef; Sobotka, Roman

    2016-03-01

    Cyanobacteria contain a family of genes encoding one-helix high-light-inducible proteins (Hlips) that are homologous to light harvesting chlorophyll a/b-binding proteins of plants and algae. Based on various experimental approaches used for their study, a spectrum of functions that includes regulation of chlorophyll biosynthesis, transient chlorophyll binding, quenching of singlet oxygen and non-photochemical quenching of absorbed energy is ascribed to Hlips. However, these functions had not been supported by conclusive experimental evidence until recently when it became clear that Hlips are able to quench absorbed light energy and assist during terminal step(s) of the chlorophyll biosynthesis and early stages of Photosystem II assembly. In this review we summarize and discuss the present knowledge about Hlips and provide a model of how individual members of the Hlip family operate during the biogenesis of chlorophyll-proteins, namely Photosystem II. This article is part of a Special Issue entitled Organization and dynamics of bioenergetic systems in bacteria, edited by Conrad Mullineaux.

  10. Microstructuring of Si(100) by light induced dry etching in the VUV

    NASA Astrophysics Data System (ADS)

    Streller, U.; Krabbe, A.; Raaf, H.; Schwentner, N.

    1998-02-01

    Light-induced dry etching of Si(100) in the VUV range using synchrotron radiation (SR) and a halogen-containing gas (XeF2) has been investigated with respect to selectivity, anisotropy, quantum efficiency, optimal wavelength, spatial resolution and quality of the photochemical etching processes. Microstructuring of Si with XeF2can be optimized to achieve etched structures in the sub-micrometre range by increasing the contrast in choosing a wavelength with minimal unselective etching. The strength of unselective etching is strongly wavelength dependent and follows the XeF2gas phase absorption coefficient. Fragments from dissociation of the XeF2reach the Si surface and thus cause unselective etching. Optimal dry etching occurs for wavelengths around 120 nm because the selectivity is high due to an excitation of a surface layer and also the quantum efficiency is very large. An efficiency of 10 removed Si atoms per incoming photon, which exceeds that in the visible spectral range by more than four orders of magnitude, combined with the higher spatial resolution at 120 nm compared to the conventional excimer laser and I-line wavelengths and the availability of optical materials for imaging present a perspective for generating line densities in the Gbit range.

  11. LSD1 and HY5 antagonistically regulate red light induced-programmed cell death in Arabidopsis.

    PubMed

    Chai, Tingting; Zhou, Jun; Liu, Jian; Xing, Da

    2015-01-01

    Programmed cell death (PCD) in plant is triggered by abiotic and biotic stress. Light-dependent PCD is unique to plants. Light-induced PCD also requires reactive oxygen species (ROS) and salicylic acid (SA). In this study, lesion simulating disease1 (LSD1) and elongated hypocotyl 5 (HY5) perform opposite roles to regulate excess red light (RL)-triggered PCD associated with ROS and SA production. Under RL, the lsd1 mutant released more ROS and SA and displayed a stronger cell death rate than the hy5 mutant. It was shown that active LSD1 converted into inactive form by changing the redox status of the plastoquinone pool, and HY5 interacted with phytochrome B (phyB) to promote PCD in response to RL. LSD1 inhibited the enhanced disease susceptibility 1 (EDS1) expression by upregulating SR1, whereas HY5 enhanced the enhanced EDS1 expression by binding to the G-box of the EDS1 promoter. This study suggested that LSD1 and HY5 antagonistically modulated EDS1-dependent ROS and SA signaling; thus, PCD was mediated in response to RL.

  12. Iterative experiment design guides the characterization of a light-inducible gene expression circuit.

    PubMed

    Ruess, Jakob; Parise, Francesca; Milias-Argeitis, Andreas; Khammash, Mustafa; Lygeros, John

    2015-06-30

    Systems biology rests on the idea that biological complexity can be better unraveled through the interplay of modeling and experimentation. However, the success of this approach depends critically on the informativeness of the chosen experiments, which is usually unknown a priori. Here, we propose a systematic scheme based on iterations of optimal experiment design, flow cytometry experiments, and Bayesian parameter inference to guide the discovery process in the case of stochastic biochemical reaction networks. To illustrate the benefit of our methodology, we apply it to the characterization of an engineered light-inducible gene expression circuit in yeast and compare the performance of the resulting model with models identified from nonoptimal experiments. In particular, we compare the parameter posterior distributions and the precision to which the outcome of future experiments can be predicted. Moreover, we illustrate how the identified stochastic model can be used to determine light induction patterns that make either the average amount of protein or the variability in a population of cells follow a desired profile. Our results show that optimal experiment design allows one to derive models that are accurate enough to precisely predict and regulate the protein expression in heterogeneous cell populations over extended periods of time.

  13. Light-Induced Polar pH Changes in Leaves of Elodea canadensis1

    PubMed Central

    Elzenga, J. Theo M.; Prins, Hidde B. A.

    1989-01-01

    Leaves of the submerged aquatic Elodea canadensis Michx. exhibit a light induced polar pH reaction. In this study, the effects of light intensity and dissolved inorganic carbon concentration on this polar reaction were examined. At a light intensity of 100 watts per square meter the leaf showed a polar pH response when the dissolved inorganic carbon concentration was less than about 1 millimolar. The polar reaction was suppressed at a higher dissolved inorganic carbon concentration. This suppression was not due to the buffering capacity of bicarbonate. Because another weak acid, acetate, did not inhibit the polarity, but even had a small stimulatory effect, the effect of bicarbonate is also not due to acidification of the cytoplasm. The suppression of the polar reaction by CO2/HCO3− was relieved when the light intensity was increased. Apparently there is competition for product(s) of the photosynthetic light reactions between processes generating the polar reaction and the carbon fixation reactions. The possibility that the redox state of the cell regulates the generation of the polar reaction is discussed. PMID:16667044

  14. Quantification of Canine Dental Plaque Using Quantitative Light-Induced Fluorescence.

    PubMed

    Wallis, Corrin; Gill, Yadvinder; Colyer, Alison; Davis, Ian; Allsopp, Judi; Komarov, Gleb; Higham, Susan; Harris, Stephen

    2016-03-01

    The aim of this work was to evaluate Quantitative Light-induced Fluorescence (QLF) as an alternative to the established Logan and Boyce method for determining plaque coverage of dogs' teeth. In a series of studies in conscious and anesthetized dogs, QLF showed good intra-photographer repeatability (coefficient of variation [CV] of 7.5% for undisclosed teeth) and inter-photographer reproducibility (CV of 3.2% for undisclosed teeth and 8.5% for disclosed teeth). The QLF software accurately identifies areas of plaque as demonstrated by comparison to the variability of 5 human scorers, manually marking plaque on QLF-acquired images (P = 0.1). There was good agreement with the modified Logan and Boyce method in the percentage reduction in plaque accumulation measured when dogs were fed an oral care chew versus no chew. To see a 15% difference in plaque accumulation, which is considered sufficient by the Veterinary Oral Health Council to differentiate between 2 treatments, a retrospective power analysis (90%) of the data established that only 7 dogs would be required, compared to 19 dogs for the modified Logan and Boyce method. QLF is a reliable method for measuring dental plaque in dogs with the added advantage that it is not subjective and requires fewer animals. PMID:27487653

  15. Analysis of light-induced transmembrane ion gradients and membrane potential in Photosystem I proteoliposomes.

    PubMed

    Pennisi, Cristian Pablo; Greenbaum, Elias; Yoshida, Ken

    2010-01-01

    Photosystem I (PSI) complexes can support a light-driven electrochemical gradient for protons, which is the driving force for energy-conserving reactions across biological membranes. In this work, a computational model that enables a quantitative description of the light-induced proton gradients across the membrane of PSI proteoliposomes is presented. Using a set of electrodiffusion equations, a compartmental model of a vesicle suspended in aqueous medium was studied. The light-mediated proton movement was modeled as a single proton pumping step with backpressure of the electric potential. The model fits determinations of pH obtained from PSI proteoliposomes illuminated in the presence of mediators of cyclic electron transport. The model also allows analysis of the proton gradients in relation to the transmembrane ion fluxes and electric potential. Sensitivity analysis enabled a determination of the parameters that have greater influence on steady-state levels and onset/decay rates of transmembrane pH and electric potential. This model could be used as a tool for optimizing PSI proteoliposomes for photo-electrochemical applications.

  16. Enhancement of light-induced degradation under reverse bias in hydrogenated nanocrystalline silicon solar cells

    NASA Astrophysics Data System (ADS)

    Yue, Guozhen; Yan, Baojie; Yang, Jeffrey; Guha, Subhendu

    2005-10-01

    The nature of light- and current-induced metastabilities under electrical bias in hydrogenated nanocrystalline silicon (nc-Si:H) solar cells has been found to be different from those in hydrogenated amorphous silicon (a-Si:H)-based solar cells. First, a forward-bias current injection in the dark does not cause any degradation in nc-Si:H cell performance. The phenomenon is explained by the percolation transport through crystalline paths, where the excess carrier recombination does not cause degradation. Second, a reverse bias does not reduce, but enhances the light-induced degradation in the nc-Si:H cell performance. The enhancement increases with the magnitude of the applied reverse bias. By measuring the quantum efficiency losses and color (blue, wavelength=390 nm and red, wavelength=670 nm) fill factors, we suggest that the reverse-bias-enhanced defect generation mostly takes place in the grain-boundary regions. Light-soaking experiments using light with different spectra show that a reverse bias under white light causes more enhancement in the degradation than under blue light (wavelength shorter than 650 nm). No degradation occurs under red light (wavelength longer than 665 nm) in either open-circuit or reverse-bias condition. A ``back-to-back'' diode model is proposed to explain these phenomena in terms of the heterogeneity of the material structure.

  17. Light-induced depigmentation in planarians models the pathophysiology of acute porphyrias

    PubMed Central

    Stubenhaus, Bradford M; Dustin, John P; Neverett, Emily R; Beaudry, Megan S; Nadeau, Leanna E; Burk-McCoy, Ethan; He, Xinwen; Pearson, Bret J; Pellettieri, Jason

    2016-01-01

    Porphyrias are disorders of heme metabolism frequently characterized by extreme photosensitivity. This symptom results from accumulation of porphyrins, tetrapyrrole intermediates in heme biosynthesis that generate reactive oxygen species when exposed to light, in the skin of affected individuals. Here we report that in addition to producing an ommochrome body pigment, the planarian flatworm Schmidtea mediterranea generates porphyrins in its subepithelial pigment cells under physiological conditions, and that this leads to pigment cell loss when animals are exposed to intense visible light. Remarkably, porphyrin biosynthesis and light-induced depigmentation are enhanced by starvation, recapitulating a common feature of some porphyrias – decreased nutrient intake precipitates an acute manifestation of the disease. Our results establish planarians as an experimentally tractable animal model for research into the pathophysiology of acute porphyrias, and potentially for the identification of novel pharmacological interventions capable of alleviating porphyrin-mediated photosensitivity or decoupling dieting and fasting from disease pathogenesis. DOI: http://dx.doi.org/10.7554/eLife.14175.001 PMID:27240733

  18. Visible-light-induced instability in amorphous metal-oxide based TFTs for transparent electronics

    SciTech Connect

    Ha, Tae-Jun

    2014-10-15

    We investigate the origin of visible-light-induced instability in amorphous metal-oxide based thin film transistors (oxide-TFTs) for transparent electronics by exploring the shift in threshold voltage (V{sub th}). A large hysteresis window in amorphous indium-gallium-zinc-oxide (a-IGZO) TFTs possessing large optical band-gap (≈3 eV) was observed in a visible-light illuminated condition whereas no hysteresis window was shown in a dark measuring condition. We also report the instability caused by photo irradiation and prolonged gate bias stress in oxide-TFTs. Larger V{sub th} shift was observed after photo-induced stress combined with a negative gate bias than the sum of that after only illumination stress and only negative gate bias stress. Such results can be explained by trapped charges at the interface of semiconductor/dielectric and/or in the gate dielectric which play a role in a screen effect on the electric field applied by gate voltage, for which we propose that the localized-states-assisted transitions by visible-light absorption can be responsible.

  19. Light-induced negative differential resistance in graphene/Si-quantum-dot tunneling diodes

    PubMed Central

    Lee, Kyeong Won; Jang, Chan Wook; Shin, Dong Hee; Kim, Jong Min; Kang, Soo Seok; Lee, Dae Hun; Kim, Sung; Choi, Suk-Ho; Hwang, Euyheon

    2016-01-01

    One of the interesing tunneling phenomena is negative differential resistance (NDR), the basic principle of resonant-tunneling diodes. NDR has been utilized in various semiconductor devices such as frequency multipliers, oscillators, relfection amplifiers, logic switches, and memories. The NDR in graphene has been also reported theoretically as well as experimentally, but should be further studied to fully understand its mechanism, useful for practical device applications. Especially, there has been no observation about light-induced NDR (LNDR) in graphene-related structures despite very few reports on the LNDR in GaAs-based heterostructures. Here, we report first observation of LNDR in graphene/Si quantum dots-embedded SiO2 (SQDs:SiO2) multilayers (MLs) tunneling diodes. The LNDR strongly depends on temperature (T) as well as on SQD size, and the T dependence is consistent with photocurrent (PC)-decay behaviors. With increasing light power, the PC-voltage curves are more structured with peak-to-valley ratios over 2 at room temperature. The physical mechanism of the LNDR, governed by resonant tunneling of charge carriers through the minibands formed across the graphene/SQDs:SiO2 MLs and by their nonresonant phonon-assisted tunneling, is discussed based on theoretical considerations. PMID:27465107

  20. Parameters affecting light-induced excess conductivity in amorphous silicon doping-modulated multilayers

    SciTech Connect

    Su, F.C.; Levine, S.; Vanier, P.E.

    1986-01-01

    The phenomenon of light-induced excess conductivity (LEC) which occurs in a-Si:H npnp doping-modulated multilayers is found experimentally to be dependent on several different factors. The concentrations of the dopants in n-type and p-type layers affect the Fermi level position, the height of the barriers, and also the density of defects. These parameters are altered by different choices of inert gas diluent (Ar or He) and substrate temperature T/sub s/. For a given set of deposition conditions, the LEC effect can be maximized by varying the layer thickness. With undiluted silane at T/sub s/ = 250/sup 0/C, the effect was relatively small, reaching a maximum in relatively thick layers (540 A). The largest effects were obtained for films deposited from silane diluted in helium, using thinner (330 A) layers. However, for films deposited from silane diluted in argon, the magnitude of the effect and optimum layer thickness was intermediate (440 A). When T/sub s/ was varied, a minimum in LEC was found near 200 to 250/sup 0/C. The influence of internal field was examined by using nini, pipi and npnp multilayers. The internal field is a necessary factor to observe a large LEC effect. A compensated film shows a small LEC effect.

  1. Visible-light-induced degradation of rhodamine B by nanosized Bi2WO6.

    PubMed

    Fu, Hongbo; Pan, Chengshi; Yao, Wenqing; Zhu, Yongfa

    2005-12-01

    Visible-light-induced photodegradation of rhodamine B over nanosized Bi2WO6 has been observed. Bi2WO6 exhibited a high photoactivity to photodegrade rhodamine B in the central pH solution under visible irradiation (lambda > 420 nm). After five recycles for the photodegradation of rhodamine B, the catalyst did not exhibit any significant loss of activity, confirming the photocatalyst is essentially stable. The total organic carbon measurement displayed that a high degree of mineralization was achieved in the present photochemical system. The results of density functional theory calculation illuminated that the visible-light absorption band in the Bi2WO6 catalyst is attributed to the band transition from the hybrid orbitals of Bi6s and O2p to the W5d orbitals. The Bi2WO6-assisted photocatalytic degradation of rhodamine occurs via two competitive processes: a photocatalytic process and a photosensitized process. The transformation of rhodamine is mainly via the photocatalytic process. Kinetic studies by using electron spin resonance and the radical scavenger technologies suggest that *OH is not the dominant photooxidant. Direct hole transfers and O2*- could take part in Bi2WO6 photocatalysis. This study provided a possible treatment approach for organic pollutants by using visible light in aqueous ecosystems.

  2. Light-induced degradation in compensated p- and n-type Czochralski silicon wafers

    NASA Astrophysics Data System (ADS)

    Geilker, Juliane; Kwapil, Wolfram; Rein, Stefan

    2011-03-01

    Light-induced degradation (LID) due to boron-oxygen complex formation seriously diminishes the minority carrier lifetime of p-type Czochralski-grown (Cz) wafers. Depending linearly on the boron concentration NA in uncompensated silicon, the boron-oxygen defect density was suggested to depend on the net doping concentration p0 = NA - ND in compensated p-type samples, containing similar amounts of boron and phosphorus [D. Macdonald, F. Rougieux, A. Cuevas, et al., Journal of Applied Physics 105, 093704 (2009)]. However, this dependency contradicts observations of LID in compensated n-type silicon wafers [T. Schutz-Kuchly, J. Veirman, S. Dubois, et al., Applied Physics Letters 96, 1 (2010)], which are confirmed in this study by investigating the boron-oxygen complex formation on a large variety of compensated p- and n-type samples. In spite of their high boron content, compensated n-type samples may show a less pronounced LID than p-type samples containing less boron. Our experiments indicate that in compensated silicon, the defect concentration is only a function of the compensation ratio RC = (NA + ND)/(NA - ND).

  3. Understanding Light-Induced Degradation of c-Si Solar Cells: Preprint

    SciTech Connect

    Sopori, B.; Basnyat, P.; Devayajanam, S.; Shet, S.; Mehta, V.; Binns, J.; Appel, J.

    2012-06-01

    We discuss results of our investigations toward understanding bulk and surface components of light-induced degradation (LID) in low-Fe c-Si solar cells. The bulk effects, arising from boron-oxygen defects, are determined by comparing degradation of cell parameters and their thermal recovery, with that of the minority-carrier lifetime (964;) in sister wafers. We found that the recovery of 964; in wafers takes a much longer annealing time compared to that of the cell. We also show that cells having SiN:H coating experience a surface degradation (ascribed to surface recombination). The surface LID is seen as an increase in the q/2kT component of the dark saturation current (J02). The surface LID does not recover fully upon annealing and is attributed to degradation of the SiN:H-Si interface. This behavior is also exhibited by mc-Si cells that have very low oxygen content and do not show any bulk degradation.

  4. Evolution of light-induced vapor generation at a liquid-immersed metallic nanoparticle.

    PubMed

    Fang, Zheyu; Zhen, Yu-Rong; Neumann, Oara; Polman, Albert; García de Abajo, F Javier; Nordlander, Peter; Halas, Naomi J

    2013-04-10

    When an Au nanoparticle in a liquid medium is illuminated with resonant light of sufficient intensity, a nanometer scale envelope of vapor-a "nanobubble"-surrounding the particle, is formed. This is the nanoscale onset of the well-known process of liquid boiling, occurring at a single nanoparticle nucleation site, resulting from the photothermal response of the nanoparticle. Here we examine bubble formation at an individual metallic nanoparticle in detail. Incipient nanobubble formation is observed by monitoring the plasmon resonance shift of an individual, illuminated Au nanoparticle, when its local environment changes from liquid to vapor. The temperature on the nanoparticle surface is monitored during this process, where a dramatic temperature jump is observed as the nanoscale vapor layer thermally decouples the nanoparticle from the surrounding liquid. By increasing the intensity of the incident light or decreasing the interparticle separation, we observe the formation of micrometer-sized bubbles resulting from the coalescence of nanoparticle-"bound" vapor envelopes. These studies provide the first direct and quantitative analysis of the evolution of light-induced steam generation by nanoparticles from the nanoscale to the macroscale, a process that is of fundamental interest for a growing number of applications.

  5. Ultraviolet light-induced atom desorption for large rubidium and potassium magneto-optical traps

    SciTech Connect

    Klempt, C.; Zoest, T. van; Henninger, T.; Topic, O.; Rasel, E.; Ertmer, W.; Arlt, J.

    2006-01-15

    We show that light-induced atom desorption (LIAD) can be used as a flexible atomic source for large {sup 87}Rb and {sup 40}K magneto-optical traps. The use of LIAD at short wavelengths allows for fast switching of the desired vapor pressure and permits experiments with long trapping and coherence times. The wavelength dependence of the LIAD effect for both species was explored in a range from 630 to 253 nm in an uncoated quartz cell and a stainless steel chamber. Only a few mW/cm{sup 2} of near-UV light produce partial pressures that are high enough to saturate a magneto-optical trap at 3.5x10{sup 9} {sup 87}Rb atoms or 7x10{sup 7} {sup 40}K atoms. Loading rates as high as 1.2x10{sup 9} {sup 87}Rb atoms/s and 8x10{sup 7} {sup 40}K atoms/s were achieved without the use of a secondary atom source. After the desorption light is turned off, the pressure quickly decays back to equilibrium with a time constant as short as 200 {mu}s, allowing for long trapping lifetimes after the MOT loading phase.

  6. Light-induced morphological plasticity in the scleractinian coral Goniastrea pectinata and its functional significance

    NASA Astrophysics Data System (ADS)

    Ow, Y. X.; Todd, P. A.

    2010-09-01

    Environment-induced i.e., phenotypically plastic, changes in morphology, are potentially an important life-history component of sessile corals. Previous reciprocal transplant experiments have demonstrated depth-related responses in various coral species, but the potential adaptive significance is rarely investigated. To test for small-scale morphological plasticity in the massive coral Goniastrea pectinata Ehrenberg 1834, fragments from five colonies were reciprocally transplanted between two depths at Raffles Lighthouse (Pulau Satumu), Singapore. After 163 days, all fragments were collected, cleared of tissue, and examined. Reaction norms and multivariate analysis of variance describe light-induced changes in corallite architecture and genotype × environment interactions. In fragments transplanted to the shallow station, calices were deeper, and septa were shorter than in fragments transplanted to the deep station. To explore the functional significance of this plasticity, a two-dimensional model of corallite shape was constructed. The induced calice morphology of the shallow-water transplants was efficient at shading, possibly to protect tissue from excess radiation, whereas the calice morphology found in the deep-water transplants was more efficient at capturing light when irradiance was low.

  7. Thermodynamic theory of light-induced material transport in amorphous azobenzene polymer films.

    PubMed

    Saphiannikova, Marina; Neher, Dieter

    2005-10-20

    It was discovered 10 years ago that the exposure of an initially flat layer of an azobenzene-containing polymer to an inhomogeneous light pattern leads to the formation of surface relief structures, accompanied by a mass transport over several micrometers. However, the driving force of this process is still unclear. We propose a new thermodynamic approach that explains a number of experimental findings including the light-induced deformation of free-standing films and the formation of surface relief gratings for main inscription geometries. Our basic assumption is that under homogeneous illumination, an initially isotropic sample should stretch itself along the polarization direction to compensate the entropy decrease produced by the photoinduced reorientation of azobenzene chromophores. The magnitude of the elastic stress, estimated by taking the derivative of the free energy over the sample deformation, is shown to be sufficient to induce plastic deformation of the polymer film. Orientational distributions of chromophores predicted by our model are compared with those deduced from Raman intensity measurements.

  8. A Robust Metal-Organic Framework for Dynamic Light-Induced Swing Adsorption of Carbon Dioxide.

    PubMed

    Li, Haiqing; Martinez, Marta Rubio; Perry, Zachary; Zhou, Hong-Cai; Falcaro, Paolo; Doblin, Christian; Lim, Seng; Hill, Anita J; Halstead, Barry; Hill, Matthew R

    2016-08-01

    Adsorbents for CO2 capture need to demonstrate efficient release. Light-induced swing adsorption (LISA) is an attractive new method to release captured CO2 that utilizes solar energy rather than electricity. MOFs, which can be tailored for use in LISA owing to their chemical functionality, are often unstable in moist atmospheres, precluding their use. A MOF is used that can release large quantities of CO2 via LISA and is resistant to moisture across a large pH range. PCN-250 undergoes LISA, with UV flux regulating the CO2 desorption capacity. Furthermore, under UV light, the azo residues within PCN-250 have constrained, local, structural flexibility. This is dynamic, rapidly switching back to the native state. Reusability tests demonstrate a 7.3 % and 4.9 % loss in both adsorption and LISA capacity after exposure to water for five cycles. These minimal changes confirm the structural robustness of PCN-250 and its great potential for triggered release applications. PMID:27273621

  9. Laser Light Induced Photosensitization Of Lymphomas Cells And Normal Bone Marrow Cells

    NASA Astrophysics Data System (ADS)

    Gulliya, Kirpal S.; Pervaiz, Shazib; Nealon, Don G.; VanderMeulen, David L.

    1988-06-01

    Dye mediated, laser light induced photosensitization was tested in an in vitro model for its efficacy in eliminating the contaminating tumor cells for ex vivo autologous bone marrow purging. Daudi and U-937 cells (3 x 106/ml) in RPMI-1640 supplemented with 0.25% human albumin were mixed with 20 µg/ml and 25 µg/ml of MC-540, respectively. These cell-dye mixtures were then exposed to 514 nm argon laser light. Identical treatment was given to the normal bone marrow cells. Viability was determined by the trypan blue exclusion method. Results show that at 31.2 J/cm2 irradiation, 99.9999% Daudi cells were killed while 87% of the normal bone marrow cells survived. No regrowth of Daudi cells was observed for 30 days in culture. However, a light dose of 93.6 J/cm2 was required to obtain 99.999% U-937 cell kill with 80% normal bone marrow cell survival. Mixing of irradiated bone marrow cells with an equal number of lymphoma cells did not interfere with the photodynamic killing of lymphoma cells. Exposure of cells to low doses of recombinant interferon-alpha prior to photodynamic therapy increased the viability of lymphoma cells.

  10. Light-induced negative differential resistance in graphene/Si-quantum-dot tunneling diodes

    NASA Astrophysics Data System (ADS)

    Lee, Kyeong Won; Jang, Chan Wook; Shin, Dong Hee; Kim, Jong Min; Kang, Soo Seok; Lee, Dae Hun; Kim, Sung; Choi, Suk-Ho; Hwang, Euyheon

    2016-07-01

    One of the interesing tunneling phenomena is negative differential resistance (NDR), the basic principle of resonant-tunneling diodes. NDR has been utilized in various semiconductor devices such as frequency multipliers, oscillators, relfection amplifiers, logic switches, and memories. The NDR in graphene has been also reported theoretically as well as experimentally, but should be further studied to fully understand its mechanism, useful for practical device applications. Especially, there has been no observation about light-induced NDR (LNDR) in graphene-related structures despite very few reports on the LNDR in GaAs-based heterostructures. Here, we report first observation of LNDR in graphene/Si quantum dots-embedded SiO2 (SQDs:SiO2) multilayers (MLs) tunneling diodes. The LNDR strongly depends on temperature (T) as well as on SQD size, and the T dependence is consistent with photocurrent (PC)-decay behaviors. With increasing light power, the PC-voltage curves are more structured with peak-to-valley ratios over 2 at room temperature. The physical mechanism of the LNDR, governed by resonant tunneling of charge carriers through the minibands formed across the graphene/SQDs:SiO2 MLs and by their nonresonant phonon-assisted tunneling, is discussed based on theoretical considerations.

  11. Light-hormone interaction in the red-light-induced suppression of photomorphogenesis in rice seedlings.

    PubMed

    Roy, Ansuman; Sahoo, Dinabandhu; Tripathy, Baishnab C

    2016-03-01

    Red light perceived by the shoot bottom suppresses photomorphogenesis in rice seedlings mediated by phytochrome A. Shoots of these seedlings grown in red light having their shoot bottom exposed were deficient in chlorophyll and accumulated high concentration of trans-zeatin riboside. However, reduced presence of isopentynyl adenosine, dihydrozeatin riboside was observed in shoots of red-light-grown non-green seedlings in comparison to green seedling. The message abundance of cytokinin receptor (OsHK5), transporters (OsENT1, OsENT2), and response regulators (OsRR4, OsRR10) was downregulated in these red-light-grown non-green seedlings. Attenuation of greening process was reversed by application of exogenous cytokinin analogue, benzyladenine, or supplementing red light with blue light. In the same vein, the suppression of gene expression of cytokinin receptor, transporters, and type-A response regulators was reversed in red-light-grown seedlings treated with benzyladenine suggesting that the disarrayed cytokinin (CK) signaling cascade is responsible for non-greening of seedlings grown in red light. The reversal of red-light-induced suppression of photomorphogenesis by blue light and benzyladenine demonstrates the interaction of light and cytokinin signaling cascades in the regulation of photomorphogenesis. Partial reversal of greening process by exogenous application of benzyladenine suggests, apart from CKs perception, transportation and responsiveness, other factors are also involved in modulation of suppression of photomorphogenesis by red light.

  12. 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

  13. Light-induced potentials ignite dissociation of N{sub 2}{sup 2+}

    SciTech Connect

    Coffee, Ryan N.; Fang Li; Gibson, George N.

    2006-04-15

    Direct ionization to dissociative potential curves is the dominant explanation for intense-field dissociative ionization of N{sub 2}. In this article we contradict this notion by showing that the dissociation of N{sub 2}{sup 2+} adiabatically follows the avoided crossing formed by the vertical bar X {sup 3}{pi}{sub u},n> and vertical bar D {sup 3}{pi}{sub g},n-1> dressed curves. Dissociation along this light-induced molecular potential implies that one photon is absorbed and adds to the kinetic release of the fragments. We compare the fragmentation energies for three different laser wavelengths and find that nitrogen shows photon absorption whereas iodine does not. From this we conclude that one must account for the absorbed photon when interpreting the time-of-flight spectra for molecules with appreciable nuclear motion during the laser pulse. In nitrogen, doing so allows us to identify enhanced ionization of the dication at 2.2 A independent of laser wavelength.

  14. Light-induced fading of the PSL signal from irradiated herbs and spices

    NASA Astrophysics Data System (ADS)

    Alberti, A.; Corda, U.; Fuochi, P.; Bortolin, E.; Calicchia, A.; Onori, S.

    2007-08-01

    Reliability of the photo-stimulated luminescence (PSL) technique, as screening method for irradiated food identification, has been tested with three kinds of herbs and spices (oregano, red pepper and fennel), prepared in two different ways (granular: i.e. seeds and flakes, or powdered), over a long period of storage with different light exposures. The irradiated samples kept in the dark gave always a positive response (the sample is correctly classified as "irradiated") for the overall examination period. The samples kept under ambient light conditions, in typical commercial glass containers, exhibited a reduction of the PSL signal, more or less pronounced depending on the type of food and packaging. The different PSL response of the irradiated samples is to be related to the quantity and quality of the mineral debris present in the individual food. It was also found that, for the same type of food, the light-induced fading was much stronger for the flaked and seed samples than for the corresponding powder samples, the penetrating capability of light being much more inhibited in powdered than in whole seeds or flaked form samples. The observed light bleaching of the PSL signal in irradiated herbs and spices is of practical relevance since it may lead to false negative classifications.

  15. Light-induced atom desorption from glass surfaces characterized by X-ray photoelectron spectroscopy

    NASA Astrophysics Data System (ADS)

    Kumagai, Ryo; Hatakeyama, Atsushi

    2016-07-01

    We analyzed the surfaces of vitreous silica (quartz) and borosilicate glass (Pyrex) substrates exposed to rubidium (Rb) vapor by X-ray photoelectron spectroscopy (XPS) to understand the surface conditions of alkali metal vapor cells. XPS spectra indicated that Rb atoms adopted different bonding states in quartz and Pyrex. Furthermore, Rb atoms in quartz remained in the near-surface region, while they diffused into the bulk in Pyrex. For these characterized surfaces, we measured light-induced atom desorption (LIAD) of Rb atoms. Clear differences in time evolution, photon energy dependence, and substrate temperature dependence were found; the decay of LIAD by continuous ultraviolet irradiation for quartz was faster than that for Pyrex, a monotonic increase in LIAD with increasing photon energy from 1.8 to 4.3 eV was more prominent for quartz, and LIAD from quartz was more efficient at higher temperatures in the range from 300 to 580 K, while that from Pyrex was almost independent of temperature.

  16. Light-Induced SO2 Photochemistry at the Mineral Dust Surface

    NASA Astrophysics Data System (ADS)

    Styler, S. A.; Doussin, J.; Formenti, P.; Donaldson, D.

    2013-12-01

    The uptake of SO2 by mineral dust is believed to proceed first by formation of surface-bound sulfite, which can subsequently be oxidized to sulfate not only by co-sorbed O3 and NO2 but also by photooxidants such as Fe and Ti present within the dust itself. In the first phase of this study, we investigated the effect of light upon SO2 uptake by Fe2O3, TiO2, illite, feldspar, and mineral dust samples obtained from Niger, Tunisia, and China. We determined the initial uptake coefficient of SO2 at the surface of dust samples under both light and dark conditions using a photochemical Knudsen cell, and then measured the relative quantities of sulfite and sulfate formed at the surface of these films using ion chromatography. In the second phase of this study, which was performed in the CESAM atmospheric chamber, we explored the possibility that light-induced production of surface-sorbed sulfate might result in enhanced dust hygroscopicity by measuring changes in dust particle size distribution as a function of exposure to SO2 and light under a range of relative humidity conditions.

  17. Interphase Chromosome Conformation and Chromatin-chromatin Interactions in Human Epithelial Cells Cultured Under Different Gravity Conditions

    NASA Technical Reports Server (NTRS)

    Zhang, Ye; Hada, Megumi; Wu, Honglu

    2014-01-01

    On a multi-mega base pair scale of the DNA, the arrangement of chromatin is non-random. In M10 epithelial cells, both telomere regions tend to be located towards the exterior of the chromosome domain, whereas the rest p-arm of the chromatin region towards the interior. In contrast, most of the q-arm of the chromatin is found in the peripheral of the domain. In lymphocytes, the p-arm chromatin regions towards the interior in close proximity with each other, whereas two q-arm regions are nearness in space. It indicates that G0 lymphocytes may lack secondary 3D chromatin folding. There chromatin folding patterns are consistent with our previous finding of non-random distribution of intra-chromosomal exchanges. In simulated microgravity conditions, the chromosome conformation may be altered and new regions in close proximity, especially to region 2 are suggested.

  18. Mi2β Shows Chromatin Enzyme Specificity by Erasing a DNase I-hypersensitive Site Established by ACF*S⃞

    PubMed Central

    Ishii, Haruhiko; Du, Hansen; Zhang, Zhaoqing; Henderson, Angus; Sen, Ranjan; Pazin, Michael J.

    2009-01-01

    ATP-dependent chromatin-remodeling enzymes are linked to changes in gene expression; however, it is not clear how the multiple remodeling enzymes found in eukaryotes differ in function and work together. In this report, we demonstrate that the ATP-dependent remodeling enzymes ACF and Mi2β can direct consecutive, opposing chromatin-remodeling events, when recruited to chromatin by different transcription factors. In a cell-free system based on the immunoglobulin heavy chain gene enhancer, we show that TFE3 induces a DNase I-hypersensitive site in an ATP-dependent reaction that requires ACF following transcription factor binding to chromatin. In a second step, PU.1 directs Mi2β to erase an established DNase I-hypersensitive site, in an ATP-dependent reaction subsequent to PU.1 binding to chromatin, whereas ACF will not support erasure. Erasure occurred without displacing the transcription factor that initiated the site. Other tested enzymes were unable to erase the DNase I-hypersensitive site. Establishing and erasing the DNase I-hypersensitive site required transcriptional activation domains from TFE3 and PU.1, respectively. Together, these results provide important new mechanistic insight into the combinatorial control of chromatin structure. PMID:19158090

  19. From the chromatin interaction network to the organization of the human genome into replication N/U-domains

    NASA Astrophysics Data System (ADS)

    Boulos, Rasha E.; Julienne, Hanna; Baker, Antoine; Chen, Chun-Long; Petryk, Nataliya; Kahli, Malik; dʼAubenton-Carafa, Yves; Goldar, Arach; Jensen, Pablo; Hyrien, Olivier; Thermes, Claude; Arneodo, Alain; Audit, Benjamin

    2014-11-01

    The three-dimensional (3D) architecture of the mammalian nucleus is now being unraveled thanks to the recent development of chromatin conformation capture (3C) technologies. Here we report the results of a combined multiscale analysis of genome-wide mean replication timing and chromatin conformation data that reveal some intimate relationships between chromatin folding and human DNA replication. We previously described megabase replication N/U-domains as mammalian multiorigin replication units, and showed that their borders are ‘master’ replication initiation zones that likely initiate cascades of origin firing responsible for the stereotypic replication of these domains. Here, we demonstrate that replication N/U-domains correspond to the structural domains of self-interacting chromatin, and that their borders act as insulating regions both in high-throughput 3C (Hi-C) data and high-resolution 3C (4C) experiments. Further analyses of Hi-C data using a graph-theoretical approach reveal that N/U-domain borders are long-distance, interconnected hubs of the chromatin interaction network. Overall, these results and the observation that a well-defined ordering of chromatin states exists from N/U-domain borders to centers suggest that ‘master’ replication initiation zones are at the heart of a high-order, epigenetically controlled 3D organization of the human genome.

  20. Histone target selection within chromatin: an exemplary case of teamwork

    PubMed Central

    Lalonde, Marie-Eve; Cheng, Xue; Côté, Jacques

    2014-01-01

    Histone modifiers like acetyltransferases, methyltransferases, and demethylases are critical regulators of most DNA-based nuclear processes, de facto controlling cell cycle progression and cell fate. These enzymes perform very precise post-translational modifications on specific histone residues, which in turn are recognized by different effector modules/proteins. We now have a better understanding of how these enzymes exhibit such specificity. As they often reside in multisubunit complexes, they use associated factors to target their substrates within chromatin structure and select specific histone mark-bearing nucleosomes. In this review, we cover the current understanding of how histone modifiers select their histone targets. We also explain how different experimental approaches can lead to conflicting results about the histone specificity and function of these enzymes. PMID:24831698