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Sample records for control light-induced chromatin

  1. Organization of higher-level chromatin structures (chromomere, chromonema and chromatin block) examined using visible light-induced chromatin photo-stabilization.

    PubMed

    Sheval, E V; Prusov, A N; Kireev, I I; Fais, D; Polyakov, V Yu

    2002-01-01

    The method of chromatin photo-stabilization by the action of visible light in the presence of ethidium bromide was used for investigation of higher-level chromatin structures in isolated nuclei. As a model we used rat hepatocyte nuclei isolated in buffers which stabilized or destabilized nuclear matrix. Several higher-level chromatin structures were visualized: 100nm globules-chromomeres, chains of chromomeres-chromonemata, aggregates of chromomeres-blocks of condensed chromatin. All these structures were completely destroyed by 2M NaCl extraction independent of the matrix state, and DNA was extruded from the residual nuclei (nuclear matrices) into a halo. These results show that nuclear matrix proteins do not play the main role in the maintenance of higher-level chromatin structures. Preliminary irradiation led to the reduction of the halo width in the dose-dependent manner. In regions of condensed chromatin of irradiated nucleoids there were discrete complexes consisting of DNA fibers radiating from an electron-dense core and resembling the decondensed chromomeres or the rosette-like structures. As shown by the analysis of proteins bound to irradiated nuclei upon high-salt extraction, irradiation presumably stabilized the non-histone proteins. These results suggest that in interphase nuclei loop domains are folded into discrete higher-level chromatin complexes (chromomeres). These complexes are possibly maintained by putative non-histone proteins, which are extracted with high-salt buffers from non-irradiated nuclei. PMID:12127937

  2. Snapshots: Chromatin Control of Viral Infection

    PubMed Central

    Knipe, David M.; Lieberman, Paul M.; Jung, Jae U.; McBride, Alison A.; Morris, Kevin V.; Ott, Melanie; Margolis, David; Nieto, Amelia; Nevels, Michael; Parks, Robin J.; Kristie, Thomas M.

    2012-01-01

    Like their cellular host counterparts, many invading viral pathogens must contend with, modulate, and utilize the host cell’s chromatin machinery to promote efficient lytic infection or control persistent-latent states. While not intended to be comprehensive, this review represents a compilation of conceptual snapshots of the dynamic interplay of viruses with the chromatin environment. Contributions focus on chromatin dynamics during infection, viral circumvention of cellular chromatin repression, chromatin organization of large DNA viruses, tethering and persistence, viral interactions with cellular chromatin modulation machinery, and control of viral latency-reactivation cycles. PMID:23217624

  3. 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

  4. 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

  5. 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

  6. Pioneer transcription factors, chromatin dynamics, and cell fate control.

    PubMed

    Zaret, Kenneth S; Mango, Susan E

    2016-04-01

    Among the diverse transcription factors that are necessary to elicit changes in cell fate, both in embryonic development and in cellular reprogramming, a subset of factors are capable of binding to their target sequences on nucleosomal DNA and initiating regulatory events in silent chromatin. Such 'pioneer transcription factors' initiate cooperative interactions with other regulatory proteins to elicit changes in local chromatin structure. As a consequence of pioneer factor binding, the local chromatin can either become open and competent for activation, closed and repressed, or transcriptionally active. Understanding how pioneer factors initiate chromatin dynamics and how such can be blocked at heterochromatic sites provides insights into controlling cell fate transitions at will. PMID:26826681

  7. 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

  8. 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

  9. Controllable 3D alginate hydrogel patterning via visible-light induced electrodeposition.

    PubMed

    Dai, Gaole; Wan, Wenfeng; Zhao, Yuliang; Wang, Zixun; Li, Wenjun; Shi, Peng; Shen, Yajing

    2016-01-01

    The fabrication of alginate hydrogel in 3D has recently received increasing attention owing to its distinct efficacy as biocompatible scaffold for 3D cell culture, biomedical and tissue engineering. We report a controllable 3D alginate hydrogel patterning method by developing a visible-light induced electrodeposition chip. The chip mainly consists of a photoconductive titanyl phthalocyanine (TiOPc) anode plate, an indium tin oxide (ITO) cathode plate and the mixed solution (1% sodium alginate and 0.25% CaCO3 nano particles) between them. After a designed visible-light pattern is projected onto the TiOPc plate, the produced H(+) by electrolysis will trigger Ca(2+) near the anode (illuminated area), and then the gelation of calcium alginate patterns, as desired, happens controllably. In addition, we further establish an exponential model to elucidate the gel growth v.s. time and current density. The results indicate that the proposed method is able to fabricate various 3D alginate hydrogel patterns in a well controllable manner, and maintain the laden cells at high survival rate (>98% right after gel formation). This research paves an alternative way for 3D alginate hydrogel patterning with high controllability and productivity, which would benefit the research in biomedical and tissue engineering. PMID:27108617

  10. Light induced controlled release of fragrances by Norrish type II photofragmentation of alkyl phenyl ketones.

    PubMed

    Levrand, Barbara; Herrmann, Andreas

    2002-11-01

    The use of alkyl phenyl ketones as delivery systems for the controlled release of fragrances was investigated by photoirradiation of undegassed solutions with a xenon lamp as well as natural sunlight. A large variety of precursor compounds was prepared efficiently in a few reaction steps from commercially available starting materials. The Norrish type II photofragmentation was found to be the predominant reaction pathway to yield the desired perfumery alkenes and acetophenones in polar and apolar solution. Systematic GC-MS analysis of the irradiated solutions allowed identification of a series of side products that are due to the presence of oxygen. A detailed analysis of the product distribution after irradiation was carried out for a series of 4-alkoxy-1-phenylbutanone derivatives. Besides the expected acetophenones, vinyl ethers and phenylcyclobutanols, the formation of alkyl formates, alcohols and 4-oxo-4-phenylbutanoates was observed. The product distribution as influenced by solvent polarity, precursor concentration and substituent effects was investigated. The utility of alkyl phenyl ketones as precursors for the light induced controlled release of fragrances under natural daylight conditions was also demonstrated. PMID:12659532

  11. 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.

  12. Droplet Trajectory Control Using Light-Induced Thermocapillary Effects in a Microchannel

    NASA Astrophysics Data System (ADS)

    Won, June; Kang, Seungmin; Song, Simon

    2015-11-01

    Controlling droplets is one of the important functions on a microfluidic chip. Marangoni effects induced by interfacial tension gradient has been paid attention due to its strong driving force on a droplet by means of droplet control. Solutalcapillary effects occurs when the interfacial tension gradient is induced due to the transport of surfactant molecules. We aim to investigate light-induced solutalcapillary effects on a droplet trajectory. Unlike few previous studies, we illuminate a continuous phase with a laser beam, in order to minimize possible damage or property change to target molecules contained in droplets. A mixture solution of black metallic ink and oleic acid is used for the continuous phase fluid. DI-water is the disperse phase. As a result, we found that the trajectory shifting increases with increasing the laser power and the droplet diameter and decreasing the droplet velocity. The magnitude of Marangoni force was estimated to be about 100 nN by assuming quasi-equilibrium between drag force and Marangoni force. As an application of this technique, we successfully routed droplets toward one of three outlets at higher than 95% success rate on demand.

  13. Optical Control of Protein–Protein Interactions via Blue Light-Induced Domain Swapping

    PubMed Central

    2015-01-01

    The design of new optogenetic tools for controlling protein function would be facilitated by the development of protein scaffolds that undergo large, well-defined structural changes upon exposure to light. Domain swapping, a process in which a structural element of a monomeric protein is replaced by the same element of another copy of the same protein, leads to a well-defined change in protein structure. We observe domain swapping in a variant of the blue light photoreceptor photoactive yellow protein in which a surface loop is replaced by a well-characterized protein–protein interaction motif, the E-helix. In the domain-swapped dimer, the E-helix sequence specifically binds a partner K-helix sequence, whereas in the monomeric form of the protein, the E-helix sequence is unable to fold into a binding-competent conformation and no interaction with the K-helix is seen. Blue light irradiation decreases the extent of domain swapping (from Kd = 10 μM to Kd = 300 μM) and dramatically enhances the rate, from weeks to <1 min. Blue light-induced domain swapping thus provides a novel mechanism for controlling of protein–protein interactions in which light alters both the stability and the kinetic accessibility of binding-competent states. PMID:25003701

  14. Controllable light-induced conic structures in silicon nanowire arrays by metal-assisted chemical etching

    NASA Astrophysics Data System (ADS)

    Zhang, Shenli; Wang, Xinwei; Liu, Hong; Shen, Wenzhong

    2014-01-01

    Silicon nanowires (SiNWs) have long been considered a promising material due to their extraordinary electrical and optical properties. As a simple, highly efficient fabrication method for SiNWs, metal-assisted chemical etching (MACE) has been intensively studied over recent years. However, effective control by modulation of simple parameters is still a challenging topic and some key questions still remain in the mechanistic processes. In this work, a novel method to manipulate SiNWs with a light-modulated MACE process has been systematically investigated. Conic structures consisting of inclined and clustered SiNWs can be generated and effectively modified by the incident light while new patterns such as ‘bamboo shoot’ arrays can also be formed under certain conditions. More importantly, detailed study has revealed a new top-down ‘diverting etching’ model of the conic structures in this process, different from the previously proposed ‘bending’ model. As a consequence of this mechanism, preferential lateral mass transport of silver particles occurs. Evidence suggests a relationship of this phenomenon to the inhomogeneous distribution of the light-induced electron-hole pairs beneath the etching front. Study on the morphological change and related mechanism will hopefully open new routes to understand and modulate the formation of SiNWs and other nanostructures.

  15. The Fun30 Chromatin Remodeler Fft3 Controls Nuclear Organization and Chromatin Structure of Insulators and Subtelomeres in Fission Yeast

    PubMed Central

    Khorosjutina, Olga; Persson, Jenna; Smialowska, Agata; Javerzat, Jean-Paul; Ekwall, Karl

    2015-01-01

    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. PMID:25798942

  16. Keeping it quiet: chromatin control of gammaherpesvirus latency

    PubMed Central

    Lieberman, Paul M.

    2015-01-01

    Summary The human gammaherpesviruses Epstein-Barr virus (EBV) and Kaposi’s sarcoma-associated herpesvirus (KSHV) establish long-term latent infections associated with diverse human cancers. Viral oncogenesis depends on the ability of the latent viral genome to persist in host nuclei as episomes that express a restricted, yet dynamic pattern of viral genes. Multiple epigenetic events control viral episome generation and maintenance. This Review highlights some of the recent findings on the role of chromatin assembly, histone and DNA modifications, and higher-order chromosome structures that enable gammaherpesvirus to establish stable latent infections that mediate viral pathogenesis. PMID:24192651

  17. 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

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed

    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

  20. 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

  1. Linker histone variants control chromatin dynamics during early embryogenesis

    PubMed Central

    Saeki, Hideaki; Ohsumi, Keita; Aihara, Hitoshi; Ito, Takashi; Hirose, Susumu; Ura, Kiyoe; Kaneda, Yasufumi

    2005-01-01

    Complex transitions in chromatin structure produce changes in genome function during development in metazoa. Linker histones, the last component of nucleosomes to be assembled into chromatin, comprise considerably divergent subtypes as compared with core histones. In all metazoa studied, their composition changes dramatically during early embryogenesis concomitant with zygotic gene activation, leading to distinct functional changes that are still poorly understood. Here, we show that early embryonic linker histone B4, which is maternally expressed, is functionally different from somatic histone H1 in influencing chromatin structure and dynamics. We developed a chromatin assembly system with nucleosome assembly protein-1 as a linker histone chaperone. This assay system revealed that maternal histone B4 allows chromatin to be remodeled by ATP-dependent chromatin remodeling factor, whereas somatic histone H1 prevents this remodeling. Structural analysis shows that histone B4 does not significantly restrict the accessibility of linker DNA. These findings define the functional significance of developmental changes in linker histone variants. We propose a model that holds that maternally expressed linker histones are key molecules specifying nuclear dynamics with respect to embryonic totipotency. PMID:15821029

  2. Embryonic transcription is controlled by maternally defined chromatin state

    PubMed Central

    Hontelez, Saartje; van Kruijsbergen, Ila; Georgiou, Georgios; van Heeringen, Simon J.; Bogdanovic, Ozren; Lister, Ryan; Veenstra, Gert Jan C.

    2015-01-01

    Histone-modifying enzymes are required for cell identity and lineage commitment, however little is known about the regulatory origins of the epigenome during embryonic development. Here we generate a comprehensive set of epigenome reference maps, which we use to determine the extent to which maternal factors shape chromatin state in Xenopus embryos. Using α-amanitin to inhibit zygotic transcription, we find that the majority of H3K4me3- and H3K27me3-enriched regions form a maternally defined epigenetic regulatory space with an underlying logic of hypomethylated islands. This maternal regulatory space extends to a substantial proportion of neurula stage-activated promoters. In contrast, p300 recruitment to distal regulatory regions requires embryonic transcription at most loci. The results show that H3K4me3 and H3K27me3 are part of a regulatory space that exerts an extended maternal control well into post-gastrulation development, and highlight the combinatorial action of maternal and zygotic factors through proximal and distal regulatory sequences. PMID:26679111

  3. 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

  4. 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. PMID:25589352

  5. Chromatin Remodeling and Transcriptional Control in Innate Immunity: Emergence of Akirin2 as a Novel Player.

    PubMed

    Tartey, Sarang; Takeuchi, Osamu

    2015-01-01

    Transcriptional regulation of inflammatory gene expression has been at the forefront of studies of innate immunity and is coordinately regulated by transcription factors, including NF-κB, and chromatin modifiers. The growing evidence for involvement of chromatin in the regulation of gene expression in innate immune cells, has uncovered an evolutionarily conserved role of microbial sensing and chromatin remodeling. Toll-like receptors and RIG-I-like receptors trigger these signaling pathways leading to transcriptional expression of a set of genes involved in inflammation. Tightly regulated control of this gene expression is a paramount, and often foremost, goal of most biological endeavors. In this review, we will discuss the recent progress about the molecular mechanisms governing control of pro-inflammatory gene expression by an evolutionarily conserved novel nuclear protein Akirin2 in macrophages and its emergence as an essential link between NF-κB and chromatin remodelers for transcriptional regulation. PMID:26287257

  6. Chromatin Remodeling and Transcriptional Control in Innate Immunity: Emergence of Akirin2 as a Novel Player

    PubMed Central

    Tartey, Sarang; Takeuchi, Osamu

    2015-01-01

    Transcriptional regulation of inflammatory gene expression has been at the forefront of studies of innate immunity and is coordinately regulated by transcription factors, including NF-κB, and chromatin modifiers. The growing evidence for involvement of chromatin in the regulation of gene expression in innate immune cells, has uncovered an evolutionarily conserved role of microbial sensing and chromatin remodeling. Toll-like receptors and RIG-I-like receptors trigger these signaling pathways leading to transcriptional expression of a set of genes involved in inflammation. Tightly regulated control of this gene expression is a paramount, and often foremost, goal of most biological endeavors. In this review, we will discuss the recent progress about the molecular mechanisms governing control of pro-inflammatory gene expression by an evolutionarily conserved novel nuclear protein Akirin2 in macrophages and its emergence as an essential link between NF-κB and chromatin remodelers for transcriptional regulation. PMID:26287257

  7. 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

  8. 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

  9. Role of Ge:As ratio in controlling the light-induced response of a-Ge(x)As(35-x)Se65 thin films.

    PubMed

    Khan, Pritam; Jain, H; Adarsh, K V

    2014-01-01

    In this paper, we present interesting results on the quantification of photodarkening (PD), photobleaching (PB) and transient PD (TPD) in a-Ge(x)As(35-x)Se65 thin films as a function of network rigidity. Composition dependent light-induced responses of these samples indicate that there exist two parallel competing mechanisms of instantaneous PD arising from the As part of the network, and PB arising from the Ge part of the network. Raman spectra of the as-prepared and illuminated samples provide first direct evidence of the light-induced structural changes: an increase in AsSe3/2 pyramidal and GeSe4/2 corner-sharing tetrahedra units together with new Ge-O bond formation and decrease in energetically unstable edge sharing GeSe4/2 tetrahedra. Importantly, for a fixed Se concentration, Ge:As ratio plays the critical role in controlling the net light-induced response rather than the much believed rigidity of the glassy network. PMID:24504158

  10. Role of Ge:As ratio in controlling the light-induced response of a-GexAs35-xSe65 thin films

    NASA Astrophysics Data System (ADS)

    Khan, Pritam; Jain, H.; Adarsh, K. V.

    2014-02-01

    In this paper, we present interesting results on the quantification of photodarkening (PD), photobleaching (PB) and transient PD (TPD) in a-GexAs35-xSe65 thin films as a function of network rigidity. Composition dependent light-induced responses of these samples indicate that there exist two parallel competing mechanisms of instantaneous PD arising from the As part of the network, and PB arising from the Ge part of the network. Raman spectra of the as-prepared and illuminated samples provide first direct evidence of the light-induced structural changes: an increase in AsSe3/2 pyramidal and GeSe4/2 corner-sharing tetrahedra units together with new Ge-O bond formation and decrease in energetically unstable edge sharing GeSe4/2 tetrahedra. Importantly, for a fixed Se concentration, Ge:As ratio plays the critical role in controlling the net light-induced response rather than the much believed rigidity of the glassy network.

  11. Electrically-driven light-induced control of liquid crystal in a cell with fullerene-containing layer

    NASA Astrophysics Data System (ADS)

    Boychuk, V.; Ouskova, E.; Reznikov, Yurii

    2003-12-01

    We report on the first observation of surface-mediated reorientation effect in LC with fullerene-containing aligning polymer. We found a strong light-induced change of the Friedericksz transition voltage in a dc-field. The Friedericksz transition was measured in a LC cell containing reference and command surfaces. The reference surface, covered with the photoaligning material fluoro-polyvinyl-cinnamate (PVCN-F), was irradiated with polarized UV-light providing strong unidirectional planar alignment. The command surface was covered with a mixture of PVCN-F and fullerene in a 2:1 ratio. This layer was also irradiated with UV-light to obtain unidirectional planar alignment. The 90°-twist cell (thickness ~ 30 μm) was filled with LC 5CB in the nematic phase. We found a strong increase of the Friedericksz transition voltage as the intensity of the incident beam from He-Ne laser was increased. The effect was reversible and depended on the sign of electric field applied to the cell. We suggest that the increase of Friedericksz transition voltage arises from charge injection into the LC bulk from the fullerene-containing alignment layer. An enrichment of the ion concentration near the surface causes a redistribution of the electric field in the cell, localizing it more strongly near the surface, and, thus, leading to an increase of the voltage necessary to reorient the director.

  12. First photoswitchable neurotransmitter transporter inhibitor: light-induced control of γ-aminobutyric acid transporter 1 (GAT1) activity in mouse brain.

    PubMed

    Quandt, Gabriele; Höfner, Georg; Pabel, Jörg; Dine, Julien; Eder, Matthias; Wanner, Klaus T

    2014-08-14

    Inhibition of mGAT1, the most abundant GABA transporter in the brain, enhances GABA signaling and alleviates symptoms of CNS disorders such as epilepsy assumed to be associated with low GABA levels. We have now developed a potent and subtype selective photoswitchable inhibitor of this transporter, which for the first time extends the photoswitch concept for the light-induced control of ligand affinity to active membrane transporters. The new inhibitor exhibited reduced activity upon irradiation with light, as demonstrated in GABA uptake assays and electrophysiological experiments with brain slices, and might be used as a tool compound for deepening the understanding of mGAT1 function in brain. PMID:25025595

  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. 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

  15. 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

  16. 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

  17. Imprinting control regions (ICRs) are marked by mono-allelic bivalent chromatin when transcriptionally inactive

    PubMed Central

    Maupetit-Méhouas, Stéphanie; Montibus, Bertille; Nury, David; Tayama, Chiharu; Wassef, Michel; Kota, Satya K.; Fogli, Anne; Cerqueira Campos, Fabiana; Hata, Kenichiro; Feil, Robert; Margueron, Raphael; Nakabayashi, Kazuhiko; Court, Franck; Arnaud, Philippe

    2016-01-01

    Parental allele-specific expression of imprinted genes is mediated by imprinting control regions (ICRs) that are constitutively marked by DNA methylation imprints on the maternal or paternal allele. Mono-allelic DNA methylation is strictly required for the process of imprinting and has to be faithfully maintained during the entire life-span. While the regulation of DNA methylation itself is well understood, the mechanisms whereby the opposite allele remains unmethylated are unclear. Here, we show that in the mouse, at maternally methylated ICRs, the paternal allele, which is constitutively associated with H3K4me2/3, is marked by default by H3K27me3 when these ICRs are transcriptionally inactive, leading to the formation of a bivalent chromatin signature. Our data suggest that at ICRs, chromatin bivalency has a protective role by ensuring that DNA on the paternal allele remains unmethylated and protected against spurious and unscheduled gene expression. Moreover, they provide the proof of concept that, beside pluripotent cells, chromatin bivalency is the default state of transcriptionally inactive CpG island promoters, regardless of the developmental stage, thereby contributing to protect cell identity. PMID:26400168

  18. Visible-light-induced synthesis of pH-responsive composite hydrogels for controlled delivery of the anticonvulsant drug pregabalin.

    PubMed

    Cevik, Ozlem; Gidon, Dogan; Kizilel, Seda

    2015-01-01

    We report here a novel method for the synthesis of a pH-responsive composite using visible light. Formation of the pH-responsive layer is based on poly(methacrylic acid-g-ethylene glycol) as the macromer, eosin Y as the photoinitiator and triethanolamine as the co-initiator. The hydrogel was functionalized with hydrophobic domains through incorporation of crosslinked styrene-butadiene-styrene (SBS) copolymer into the pH-responsive prepolymer. Swelling ratios were decreased with the addition of SBS, and resulted in high hydrogel crosslink density. The composite allowed for controlled release of an anticonvulsant model drug, pregabalin, under neutral pH condition and the release was analyzed to describe the mode of transport through the network. In vitro human fibroblast survival assay and in vivo rabbit implantation experiments demonstrated that this hybrid network is not toxic and has desirable biocompatibility properties. This is the first report about the synthesis of a pH-responsive network incorporating crosslinked SBS synthesized under visible light. The approach for multifunctional membranes could allow the incorporation of molecules with specific functionalities so that sequential molecule delivery in response to specific stimuli could be achieved. PMID:25242648

  19. Control of alternative end joining by the chromatin remodeler p400 ATPase

    PubMed Central

    Taty-Taty, Gemael-Cedrick; Chailleux, Catherine; Quaranta, Muriel; So, Ayeong; Guirouilh-Barbat, Josée; Lopez, Bernard S.; Bertrand, Pascale; Trouche, Didier; Canitrot, Yvan

    2016-01-01

    Repair of DNA double-strand breaks occurs in a chromatin context that needs to be modified and remodeled to allow suitable access to the different DNA repair machineries. Of particular importance for the maintenance of genetic stability is the tight control of error-prone pathways, such as the alternative End Joining pathway. Here, we show that the chromatin remodeler p400 ATPase is a brake to the use of alternative End Joining. Using specific intracellular reporter susbstrates we observed that p400 depletion increases the frequency of alternative End Joining events, and generates large deletions following repair of double-strand breaks. This increase of alternative End Joining events is largely dependent on CtIP-mediated resection, indicating that it is probably related to the role of p400 in late steps of homologous recombination. Moreover, p400 depletion leads to the recruitment of poly(ADP) ribose polymerase (PARP) and DNA ligase 3 at DNA double-strand breaks, driving to selective killing by PARP inhibitors. All together these results show that p400 acts as a brake to prevent alternative End Joining-dependent genetic instability and underline its potential value as a clinical marker. PMID:26578561

  20. 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. PMID:27166947

  1. The Forkhead Transcription Factor FOXM1 Controls Cell Cycle-Dependent Gene Expression through an Atypical Chromatin Binding Mechanism

    PubMed Central

    Chen, Xi; Müller, Gerd A.; Quaas, Marianne; Fischer, Martin; Han, Namshik; Stutchbury, Benjamin; Engeland, Kurt

    2013-01-01

    There are nearly 50 forkhead (FOX) transcription factors encoded in the human genome and, due to sharing a common DNA binding domain, they are all thought to bind to similar DNA sequences. It is therefore unclear how these transcription factors are targeted to specific chromatin regions to elicit specific biological effects. Here, we used chromatin immunoprecipitation followed by sequencing (ChIP-seq) to investigate the genome-wide chromatin binding mechanisms used by the forkhead transcription factor FOXM1. In keeping with its previous association with cell cycle control, we demonstrate that FOXM1 binds and regulates a group of genes which are mainly involved in controlling late cell cycle events in the G2 and M phases. However, rather than being recruited through canonical RYAAAYA forkhead binding motifs, FOXM1 binding is directed via CHR (cell cycle genes homology region) elements. FOXM1 binds these elements through protein-protein interactions with the MMB transcriptional activator complex. Thus, we have uncovered a novel and unexpected mode of chromatin binding of a FOX transcription factor that allows it to specifically control cell cycle-dependent gene expression. PMID:23109430

  2. Long-range looping of a locus control region drives tissue-specific chromatin packing within a multigene cluster.

    PubMed

    Tsai, Yu-Cheng; Cooke, Nancy E; Liebhaber, Stephen A

    2016-06-01

    The relationships of higher order chromatin organization to mammalian gene expression remain incompletely defined. The human Growth Hormone (hGH) multigene cluster contains five gene paralogs. These genes are selectively activated in either the pituitary or the placenta by distinct components of a remote locus control region (LCR). Prior studies have revealed that appropriate activation of the placental genes is dependent not only on the actions of the LCR, but also on the multigene composition of the cluster itself. Here, we demonstrate that the hGH LCR 'loops' over a distance of 28 kb in primary placental nuclei to make specific contacts with the promoters of the two GH genes in the cluster. This long-range interaction sequesters the GH genes from the three hCS genes which co-assemble into a tightly packed 'hCS chromatin hub'. Elimination of the long-range looping, via specific deletion of the placental LCR components, triggers a dramatic disruption of the hCS chromatin hub. These data reveal a higher-order structural pathway by which long-range looping from an LCR impacts on local chromatin architecture that is linked to tissue-specific gene regulation within a multigene cluster. PMID:26893355

  3. Long-range looping of a locus control region drives tissue-specific chromatin packing within a multigene cluster

    PubMed Central

    Tsai, Yu-Cheng; Cooke, Nancy E.; Liebhaber, Stephen A.

    2016-01-01

    The relationships of higher order chromatin organization to mammalian gene expression remain incompletely defined. The human Growth Hormone (hGH) multigene cluster contains five gene paralogs. These genes are selectively activated in either the pituitary or the placenta by distinct components of a remote locus control region (LCR). Prior studies have revealed that appropriate activation of the placental genes is dependent not only on the actions of the LCR, but also on the multigene composition of the cluster itself. Here, we demonstrate that the hGH LCR ‘loops’ over a distance of 28 kb in primary placental nuclei to make specific contacts with the promoters of the two GH genes in the cluster. This long-range interaction sequesters the GH genes from the three hCS genes which co-assemble into a tightly packed ‘hCS chromatin hub’. Elimination of the long-range looping, via specific deletion of the placental LCR components, triggers a dramatic disruption of the hCS chromatin hub. These data reveal a higher-order structural pathway by which long-range looping from an LCR impacts on local chromatin architecture that is linked to tissue-specific gene regulation within a multigene cluster. PMID:26893355

  4. Chromatin remodeling — a novel strategy to control excessive alcohol drinking

    PubMed Central

    Warnault, V; Darcq, E; Levine, A; Barak, S; Ron, D

    2013-01-01

    Harmful excessive use of alcohol has a severe impact on society and it remains one of the major causes of morbidity and mortality in the population. However, mechanisms that underlie excessive alcohol consumption are still poorly understood, and thus available medications for alcohol use disorders are limited. Here, we report that changing the level of chromatin condensation by affecting DNA methylation or histone acetylation limits excessive alcohol drinking and seeking behaviors in rodents. Specifically, we show that decreasing DNA methylation by inhibiting the activity of DNA methyltransferase (DNMT) with systemic administration of the FDA-approved drug, 5-azacitidine (5-AzaC) prevents excessive alcohol use in mice. Similarly, we find that increasing histone acetylation via systemic treatment with several histone deacetylase (HDAC) inhibitors reduces mice binge-like alcohol drinking. We further report that systemic administration of the FDA-approved HDAC inhibitor, SAHA, inhibits the motivation of rats to seek alcohol. Importantly, the actions of both DNMT and HDAC inhibitors are specific for alcohol, as no changes in saccharin or sucrose intake were observed. In line with these behavioral findings, we demonstrate that excessive alcohol drinking increases DNMT1 levels and reduces histone H4 acetylation in the nucleus accumbens (NAc) of rodents. Together, our findings illustrate that DNA methylation and histone acetylation control the level of excessive alcohol drinking and seeking behaviors in preclinical rodent models. Our study therefore highlights the possibility that DNMT and HDAC inhibitors can be used to treat harmful alcohol abuse. PMID:23423140

  5. Photoreceptor IRBP prevents light induced injury.

    PubMed

    Sun, Zhongcui; Zhang, Meng; Liu, Wei; Tian, Jie; Xu, Gezhi

    2016-01-01

    Interphotoreceptor retinoid-binding protein (IRBP) is a classic inducer of experimental autoimmune uveoretinitis (EAU). Although IRBP causes neuronal loss in susceptible animals, resistant animals such as Sprague-Dawley (SPD) rats can benefit from the evoked protective autoimmune responses. The aim of the present study was to analyze the neuroprotective effects of IRBP against light-induced photoreceptor degeneration. We immunized 75 male SPD rats with IRBP and the rats were then exposed to blue light for 24 hours (IRBP group). Seventy five rats were included in the control group. We found that the number of apoptotic cells in the outer nuclear layer (ONL) peaked on 1 day after light exposure, and the ONL thickness decreased significantly on day 3. OX42-positive cells appeared in the ONL immediately after light exposure, and their number peaked on day 3, and changed from resting ramified cells to activated amoeboid cells. Compared with the control group (n=75), the IRBP group showed less apoptotic cells, a thicker ONL, and reduced expression of tumor necrosis factor-alpha. These outcomes indicate the IRPB might protect retinal photoreceptors against light-induced injury. PMID:27100484

  6. Population Variation and Genetic Control of Modular Chromatin Architecture in Humans.

    PubMed

    Waszak, Sebastian M; Delaneau, Olivier; Gschwind, Andreas R; Kilpinen, Helena; Raghav, Sunil K; Witwicki, Robert M; Orioli, Andrea; Wiederkehr, Michael; Panousis, Nikolaos I; Yurovsky, Alisa; Romano-Palumbo, Luciana; Planchon, Alexandra; Bielser, Deborah; Padioleau, Ismael; Udin, Gilles; Thurnheer, Sarah; Hacker, David; Hernandez, Nouria; Reymond, Alexandre; Deplancke, Bart; Dermitzakis, Emmanouil T

    2015-08-27

    Chromatin state variation at gene regulatory elements is abundant across individuals, yet we understand little about the genetic basis of this variability. Here, we profiled several histone modifications, the transcription factor (TF) PU.1, RNA polymerase II, and gene expression in lymphoblastoid cell lines from 47 whole-genome sequenced individuals. We observed that distinct cis-regulatory elements exhibit coordinated chromatin variation across individuals in the form of variable chromatin modules (VCMs) at sub-Mb scale. VCMs were associated with thousands of genes and preferentially cluster within chromosomal contact domains. We mapped strong proximal and weak, yet more ubiquitous, distal-acting chromatin quantitative trait loci (cQTL) that frequently explain this variation. cQTLs were associated with molecular activity at clusters of cis-regulatory elements and mapped preferentially within TF-bound regions. We propose that local, sequence-independent chromatin variation emerges as a result of genetic perturbations in cooperative interactions between cis-regulatory elements that are located within the same genomic domain. PMID:26300124

  7. Organization of the GAL1-GAL10 intergenic control region chromatin.

    PubMed Central

    Lohr, D

    1984-01-01

    A defined, "far upstream" promoter element, the Upstream Activator Sequence (UAS), which mediates the galactose dependent induction of expression of the GAL10 gene in yeast, is the locus of an anomalous, mainly expression independent chromatin structure. The UAS chromatin shows three symmetrical DNase I hypersensitive sites in brief digests, a loss of the 10 bp DNase I ladder pattern in more extensive digests and an enhanced staphylococcal nuclease sensitivity. This anomalous structure is confined to a small region of the UAS. The surrounding chromatin, including the TATA box regions shows a more typical, but expression dependent nucleoprotein, probably nucleosomal, organization. Such an arrangement may be a common feature of eukaryotic genes. Images PMID:6095201

  8. 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

  9. 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

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

    PubMed

    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

    2016-06-01

    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

  11. The BAF60 subunit of the SWI/SNF chromatin-remodeling complex directly controls the formation of a gene loop at FLOWERING LOCUS C in Arabidopsis.

    PubMed

    Jégu, Teddy; Latrasse, David; Delarue, Marianne; Hirt, Heribert; Domenichini, Séverine; Ariel, Federico; Crespi, Martin; Bergounioux, Catherine; Raynaud, Cécile; Benhamed, Moussa

    2014-02-01

    SWI/SNF complexes mediate ATP-dependent chromatin remodeling to regulate gene expression. Many components of these complexes are evolutionarily conserved, and several subunits of Arabidopsis thaliana SWI/SNF complexes are involved in the control of flowering, a process that depends on the floral repressor FLOWERING LOCUS C (FLC). BAF60 is a SWI/SNF subunit, and in this work, we show that BAF60, via a direct targeting of the floral repressor FLC, induces a change at the high-order chromatin level and represses the photoperiod flowering pathway in Arabidopsis. BAF60 accumulates in the nucleus and controls the formation of the FLC gene loop by modulation of histone density, composition, and posttranslational modification. Physiological analysis of BAF60 RNA interference mutant lines allowed us to propose that this chromatin-remodeling protein creates a repressive chromatin configuration at the FLC locus. PMID:24510722

  12. Replicating centromeric chromatin: spatial and temporal control of CENP-A assembly

    PubMed Central

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

    2013-01-01

    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. PMID:22561213

  13. 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.

  14. Light induced self-written waveguides interactions in photopolymer media.

    PubMed

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

    2015-08-10

    We present experimental and theoretical study of the interaction of Light Induced Self-Written (LISW) waveguides in photopolymers. We show that the diffusion of the monomer controls the refractive index distribution. Consequently it influences the interaction between the LISW channels allowing the observation of anti-crossing behavior or the propagation of an array of non interacting LISW waveguides. PMID:26367937

  15. Coordinated control of dCTCF and gypsy chromatin insulators in Drosophila

    PubMed Central

    Gerasimova, Tatiana I.; Lei, Elissa P.; Bushey, Ashley M.; Corces, Victor G.

    2008-01-01

    SUMMARY CTCF plays a central role in vertebrate insulators and forms part of the Fab-8 insulator in Drosophila. dCTCF is present at hundreds of sites in the Drosophila genome, where it is located at the boundaries between bands and interbands in polytene chromosomes. dCTCF co-localizes with CP190, which is required for proper binding of dCTCF to chromatin, but not with the other gypsy insulator proteins Su(Hw) or Mod(mdg4)2.2. Mutations in the CP190 gene affect Fab-8 insulator activity, suggesting that CP190 is an essential component of both gypsy and dCTCF insulators. dCTCF is present at specific nuclear locations forming large insulator bodies that overlap with those formed by Su(Hw), Mod(mdg4)2.2 and CP190. The results suggest that Su(Hw) and dCTCF may be the DNA-binding components of two different subsets of insulators that share CP190 and cooperate in the formation of insulator bodies to regulate the organization of the chromatin fiber in the nucleus. PMID:18082602

  16. Control of α-herpesvirus IE gene expression by HCF-1 coupled chromatin modification activities

    PubMed Central

    Kristie, Thomas M.; Liang, Yu; Vogel, Jodi L.

    2009-01-01

    Summary The immediate early genes of the α-herpesviruses HSV and VZV are transcriptionally regulated by viral and cellular factors in a complex combinatorial manner. Despite this complexity and the apparent redundancy of activators, the expression of the viral IE genes is critically dependent upon the cellular transcriptional coactivator HCF-1. Although the role of HCF-1 had remained elusive, recent studies have demonstrated that the protein is a component of multiple chromatin modification complexes including the Set1/MLL1 histone H3K4 methyltransferases. Studies using model viral promoter-reporter systems as well as analyses of components recruited to the viral genome during the initiation of infection have elucidated the significance of HCF-1 chromatin modification complexes in contributing to the final state of modified histones assembled on the viral IE promoters. Strikingly, the absence of HCF-1 results in the accumulation of nucleosomes bearing repressive marks on the viral IE promoters and silencing of viral gene expression. PMID:19682612

  17. MiRNA-Mediated Regulation of the SWI/SNF Chromatin Remodeling Complex Controls Pluripotency and Endodermal Differentiation in Human ESCs.

    PubMed

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

    2015-10-01

    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 cells (hESCs) 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

  18. 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. PMID:26325327

  19. A platform for controlled dual-drug delivery to the retina: protective effects against light-induced retinal damage in rats.

    PubMed

    Nagai, Nobuhiro; Kaji, Hirokazu; Onami, Hideyuki; Katsukura, Yuki; Ishikawa, Yumi; Nezhad, Zhaleh Kashkouli; Sampei, Kaori; Iwata, Satoru; Ito, Shuntaro; Nishizawa, Matsuhiko; Nakazawa, Toru; Osumi, Noriko; Mashima, Yukihiko; Abe, Toshiaki

    2014-10-01

    Controlled transscleral co-delivery of two drugs, edaravone (EDV) and unoprostone (UNO), using a platform that comprises a microfabricated reservoir, controlled-release cover, and drug formulations, which are made of photopolymerized poly(ethyleneglycol) dimethacrylates, shows synergistic retinal neuroprotection against light injury in rats when compared with single-drug-loaded devices. The device would offer a safer therapeutic method than intravitreal injections for retinal disease treatments. PMID:24753450

  20. 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

  1. 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

  2. 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

    2016-01-01

    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

  3. 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

  4. SIRT1-dependent regulation of chromatin and transcription: linking NAD(+) metabolism and signaling to the control of cellular functions.

    PubMed

    Zhang, Tong; Kraus, W Lee

    2010-08-01

    Sirtuins comprise a family of NAD(+)-dependent protein deacetylases and ADP-ribosyltransferases. Mammalian SIRT1 - a homolog of yeast Sir2, the prototypical member of the sirtuin family - is an important regulator of metabolism, cell differentiation and senescence, stress response, and cancer. As an NAD(+)-dependent enzyme, SIRT1 regulates gene expression programs in response to cellular metabolic status, thereby coordinating metabolic adaptation of the whole organism. Several important mechanisms have emerged for SIRT1-dependent regulation of transcription. First, SIRT1 can modulate chromatin function through direct deacetylation of histones as well as by promoting alterations in the methylation of histones and DNA, leading to the repression of transcription. The latter is accomplished through the recruitment of other nuclear enzymes to chromatin for histone methylation and DNA CpG methylation, suggesting a broader role of SIRT1 in epigenetic regulation. Second, SIRT1 can interact and deacetylate a broad range of transcription factors and coregulators, thereby regulating target gene expression both positively and negatively. Cellular energy state, specifically NAD(+) metabolism, plays a major role in the regulation of SIRT1 activity. Recent studies on the NAD(+) biosynthetic enzymes in the salvage pathway, nicotinamide phosphoribosyltransferase (NAMPT) and nicotinamide mononucleotide adenylyltransferase 1 (NMNAT-1), have revealed important functions for these enzymes in SIRT1-dependent transcription regulation. The collective molecular actions of SIRT1 control specific patterns of gene expression that modulate a wide variety of physiological outcomes. PMID:19879981

  5. 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. PMID:26451402

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

    PubMed Central

    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.

    2005-01-01

    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. PMID:16365162

  7. 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. PMID:27140648

  8. 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

  9. 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

  10. Chromatin, epigenetics and stem cells.

    PubMed

    Roloff, Tim C; Nuber, Ulrike A

    2005-03-01

    Epigenetics is a term that has changed its meaning with the increasing biological knowledge on developmental processes. However, its current application to stem cell biology is often imprecise and is conceptually problematic. This article addresses two different subjects, the definition of epigenetics and chromatin states of stem and differentiated cells. We describe mechanisms that regulate chromatin changes and provide an overview of chromatin states of stem and differentiated cells. Moreover, a modification of the current epigenetics definition is proposed that is not restricted by the heritability of gene expression throughout cell divisions and excludes translational gene expression control. PMID:15819395

  11. 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.

  12. 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

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

    PubMed

    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

  14. Regulation of cellular chromatin state

    PubMed Central

    Mishra, Rakesh K; Dhawan, Jyotsna

    2010-01-01

    The identity and functionality of eukaryotic cells is defined not just by their genomic sequence which remains constant between cell types, but by their gene expression profiles governed by epigenetic mechanisms. Epigenetic controls maintain and change the chromatin state throughout development, as exemplified by the setting up of cellular memory for the regulation and maintenance of homeotic genes in proliferating progenitors during embryonic development. Higher order chromatin structure in reversibly arrested adult stem cells also involves epigenetic regulation and in this review we highlight common trends governing chromatin states, focusing on quiescence and differentiation during myogenesis. Together, these diverse developmental modules reveal the dynamic nature of chromatin regulation providing fresh insights into the role of epigenetic mechanisms in potentiating development and differentiation. PMID:20592864

  15. 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

  16. 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.

  17. Histone H2A.Z controls a critical chromatin remodeling step required for DNA double-strand break repair

    PubMed Central

    Xu, Ye; Ayrapetov, Marina K.; Xu, Chang; Gursoy-Yuzugullu, Ozge; Hu, Yiduo; Price, Brendan D.

    2012-01-01

    Chromatin remodeling during DNA double-strand break (DSB) repair is required to facilitate access to and repair of DSBs. This remodeling requires increased acetylation of histones and a shift in nucleosome organization to create open, relaxed chromatin domains. However, the underlying mechanism driving changes in nucleosome structure at DSBs is poorly defined. Here, we demonstrate that histone H2A.Z is exchanged onto nucleosomes at DSBs by the p400 remodeling ATPase. H2A.Z exchange at DSBs shifts the chromatin to an open conformation, and is required for acetylation and ubiquitination of histones and for loading of the brca1 complex. H2A.Z exchange also restricts single-stranded DNA production by nucleases and is required for loading of the Ku70/80 DSB repair protein. H2A.Z exchange therefore promotes specific patterns of histone modification and reorganization of the chromatin architecture, leading to the assembly of a chromatin template which is an efficient substrate for the DSB repair machinery. PMID:23122415

  18. Light-induced optomechanical forces in graphene waveguides

    NASA Astrophysics Data System (ADS)

    Guizal, Brahim; Antezza, Mauro

    2016-03-01

    We show that the electromagnetic forces generated by the excitations of a mode in graphene-based optomechanical systems are highly tunable by varying the graphene chemical potential, and orders of magnitude stronger than usual non-graphene-based devices, in both attractive and repulsive regimes. We analyze coupled waveguides made of two parallel graphene sheets, either suspended or supported by dielectric slabs, and study the interplay between the light-induced force and the Casimir-Lifshitz interaction. These findings pave the way to advanced possibilities of control and fast modulation for optomechanical devices and sensors at the nano- and microscales.

  19. 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.

  20. 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.

  1. Molecular basis for the redox control of nuclear transport of the structural chromatin protein Hmgb1

    SciTech Connect

    Hoppe, George . E-mail: hoppeg@ccf.org; Talcott, Katherine E.; Bhattacharya, Sanjoy K.; Crabb, John W.; Sears, Jonathan E.

    2006-11-01

    Oxidative stress can induce a covalent disulfide bond between protein and peptide thiols that is reversible through enzymatic catalysis. This process provides a post-translational mechanism for control of protein function and may also protect thiol groups from irreversible oxidation. High mobility group protein B1 (Hmgb1), a DNA-binding structural chromosomal protein and transcriptional co-activator was identified as a substrate of glutaredoxin. Hmgb1 contains 3 cysteines, Cys23, 45, and 106. In mild oxidative conditions, Cys23 and Cys45 readily form an intramolecular disulfide bridge, whereas Cys106 remains in the reduced form. The disulfide bond between Cys23 and Cys45 is a target of glutathione-dependent reduction by glutaredoxin. Endogenous Hmgb1 as well as GFP-tagged wild-type Hmgb1 co-localize in the nucleus of CHO cells. While replacement of Hmgb1 Cys23 and/or 45 with serines did not affect the nuclear distribution of the mutant proteins, Cys106-to-Ser and triple cysteine mutations impaired nuclear localization of Hmgb1. Our cysteine targeted mutational analysis suggests that Cys23 and 45 induce conformational changes in response to oxidative stress, whereas Cys106 appears to be critical for the nucleocytoplasmic shuttling of Hmgb1.

  2. 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

  3. Differential Control of Xanthophylls and Light-Induced Stress Proteins, as Opposed to Light-Harvesting Chlorophyll a/b Proteins, during Photosynthetic Acclimation of Barley Leaves to Light Irradiance

    PubMed Central

    Montané, Marie-Hélène; Tardy, Florence; Kloppstech, Klaus; Havaux, Michel

    1998-01-01

    Barley (Hordeum vulgare L.) plants were grown at different photon flux densities ranging from 100 to 1800 μmol m−2 s−1 in air and/or in atmospheres with reduced levels of O2 and CO2. Low O2 and CO2 partial pressures allowed plants to grow under high photosystem II (PSII) excitation pressure, estimated in vivo by chlorophyll fluorescence measurements, at moderate photon flux densities. The xanthophyll-cycle pigments, the early light-inducible proteins, and their mRNA accumulated with increasing PSII excitation pressure irrespective of the way high excitation pressure was obtained (high-light irradiance or decreased CO2 and O2 availability). These findings indicate that the reduction state of electron transport chain components could be involved in light sensing for the regulation of nuclear-encoded chloroplast gene expression. In contrast, no correlation was found between the reduction state of PSII and various indicators of the PSII light-harvesting system, such as the chlorophyll a-to-b ratio, the abundance of the major pigment-protein complex of PSII (LHCII), the mRNA level of LHCII, the light-saturation curve of O2 evolution, and the induced chlorophyll-fluorescence rise. We conclude that the chlorophyll antenna size of PSII is not governed by the redox state of PSII in higher plants and, consequently, regulation of early light-inducible protein synthesis is different from that of LHCII. PMID:9733542

  4. The BAF60 Subunit of the SWI/SNF Chromatin-Remodeling Complex Directly Controls the Formation of a Gene Loop at FLOWERING LOCUS C in Arabidopsis[W

    PubMed Central

    Jégu, Teddy; Latrasse, David; Delarue, Marianne; Hirt, Heribert; Domenichini, Séverine; Ariel, Federico; Crespi, Martin; Bergounioux, Catherine; Raynaud, Cécile; Benhamed, Moussa

    2014-01-01

    SWI/SNF complexes mediate ATP-dependent chromatin remodeling to regulate gene expression. Many components of these complexes are evolutionarily conserved, and several subunits of Arabidopsis thaliana SWI/SNF complexes are involved in the control of flowering, a process that depends on the floral repressor FLOWERING LOCUS C (FLC). BAF60 is a SWI/SNF subunit, and in this work, we show that BAF60, via a direct targeting of the floral repressor FLC, induces a change at the high-order chromatin level and represses the photoperiod flowering pathway in Arabidopsis. BAF60 accumulates in the nucleus and controls the formation of the FLC gene loop by modulation of histone density, composition, and posttranslational modification. Physiological analysis of BAF60 RNA interference mutant lines allowed us to propose that this chromatin-remodeling protein creates a repressive chromatin configuration at the FLC locus. PMID:24510722

  5. 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

  6. 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.

  7. 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.

  8. 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.

  9. Localized light-induced protein dimerization in living cells using a photocaged dimerizer

    PubMed Central

    Ballister, Edward R.; Aonbangkhen, Chanat; Mayo, Alyssa M.; Lampson, Michael A.; Chenoweth, David M.

    2015-01-01

    Regulated protein localization is critical for many cellular processes. Several techniques have been developed for experimental control over protein localization, including chemically induced and light-induced dimerization, which both provide temporal control. Light-induced dimerization offers the distinct advantage of spatial precision within subcellular length scales. A number of elegant systems have been reported that utilize natural light-sensitive proteins to induce dimerization via direct protein–protein binding interactions, but the application of these systems at cellular locations beyond the plasma membrane has been limited. Here we present a new technique to rapidly and reversibly control protein localization in living cells with subcellular spatial resolution using a cell-permeable, photoactivatable chemical inducer of dimerization. We demonstrate light-induced recruitment of a cytosolic protein to individual centromeres, kinetochores, mitochondria and centrosomes in human cells, indicating that our system is widely applicable to many cellular locations. PMID:25400104

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. Chromatin-to-nucleoprotamine transition is controlled by the histone H2B variant TH2B

    PubMed Central

    Montellier, Emilie; Boussouar, Fayçal; Rousseaux, Sophie; Zhang, Kai; Buchou, Thierry; Fenaille, François; Shiota, Hitoshi; Debernardi, Alexandra; Héry, Patrick; Curtet, Sandrine; Jamshidikia, Mahya; Barral, Sophie; Holota, Hélène; Bergon, Aurélie; Lopez, Fabrice; Guardiola, Philippe; Pernet, Karin; Imbert, Jean; Petosa, Carlo; Tan, Minjia; Zhao, Yingming; Gérard, Matthieu; Khochbin, Saadi

    2013-01-01

    The conversion of male germ cell chromatin to a nucleoprotamine structure is fundamental to the life cycle, yet the underlying molecular details remain obscure. Here we show that an essential step is the genome-wide incorporation of TH2B, a histone H2B variant of hitherto unknown function. Using mouse models in which TH2B is depleted or C-terminally modified, we show that TH2B directs the final transformation of dissociating nucleosomes into protamine-packed structures. Depletion of TH2B induces compensatory mechanisms that permit histone removal by up-regulating H2B and programming nucleosome instability through targeted histone modifications, including lysine crotonylation and arginine methylation. Furthermore, after fertilization, TH2B reassembles onto the male genome during protamine-to-histone exchange. Thus, TH2B is a unique histone variant that plays a key role in the histone-to-protamine packing of the male genome and guides genome-wide chromatin transitions that both precede and follow transmission of the male genome to the egg. PMID:23884607

  15. 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

  16. Use of chromatin remodeling ATPases as RNAi targets for parental control of western corn rootworm (Diabrotica virgifera virgifera) and Neotropical brown stink bug (Euschistus heros).

    PubMed

    Fishilevich, Elane; Vélez, Ana M; Khajuria, Chitvan; Frey, Meghan L F; Hamm, Ronda L; Wang, Haichuan; Schulenberg, Greg A; Bowling, Andrew J; Pence, Heather E; Gandra, Premchand; Arora, Kanika; Storer, Nicholas P; Narva, Kenneth E; Siegfried, Blair D

    2016-04-01

    RNA interference (RNAi) is a gene silencing mechanism that is present in animals and plants and is triggered by double stranded RNA (dsRNA) or small interfering RNA (siRNA), depending on the organism. In the western corn rootworm (WCR), Diabrotica virgifera virgifera LeConte (Coleoptera: Chrysomelidae), RNAi can be achieved by feeding rootworms dsRNA added to artificial diet or plant tissues transformed to express dsRNA. The effect of RNAi depends on the targeted gene function and can range from an absence of phenotypic response to readily apparent responses, including lethality. Furthermore, RNAi can directly affect individuals that consume dsRNA or the effect may be transferred to the next generation. Our previous work described the potential use of genes involved in embryonic development as a parental RNAi technology for the control of WCR. In this study, we describe the use of chromatin-remodeling ATPases as target genes to achieve parental gene silencing in two insect pests, a coleopteran, WCR, and a hemipteran, the Neotropical brown stink bug, Euschistus heros Fabricius (Hemiptera: Pentatomidae). Our results show that dsRNA targeting chromatin-remodeling ATPase transcripts, brahma, mi-2, and iswi strongly reduced the fecundity of the exposed females in both insect species. Additionally, knockdown of chd1 reduced the fecundity of E. heros. PMID:26873291

  17. 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

  18. A chromatin perspective of adipogenesis

    PubMed Central

    Musri, Melina M; Gomis, Ramon

    2010-01-01

    The transcriptional cascade governing adipogenesis has been thoroughly examined throughout the years. Transcription factors PPARγ and C/EBPα are universally recognized as the master regulators of adipocyte differentiation and together they direct the establishment of the gene expression pattern of mature adipose cells. However, this familiar landscape has been considerably broadened in recent years by the identification of novel factors that participate in the regulation of adipogenesis, either favoring or inhibiting it, through their effects on chromatin. Epigenetic signals and chromatin-modifying proteins contribute to adipogenesis and, through regulation of the phenotypic maintenance of the mature adipocytes, to the control of metabolism. In this review we intend to summarize the recently described epigenetic events that participate in adipogenesis and their connections with the main factors that constitute the classical transcriptional cascade. PMID:20592861

  19. Chromatin deregulation in disease.

    PubMed

    Mirabella, Anne C; Foster, Benjamin M; Bartke, Till

    2016-03-01

    The regulation of chromatin by epigenetic mechanisms plays a central role in gene expression and is essential for development and maintenance of cell identity and function. Aberrant chromatin regulation is observed in many diseases where it leads to defects in epigenetic gene regulation resulting in pathological gene expression programmes. These defects are caused by inherited or acquired mutations in genes encoding enzymes that deposit or remove DNA and histone modifications and that shape chromatin architecture. Chromatin deregulation often results in neurodevelopmental disorders and intellectual disabilities, frequently linked to physical and developmental abnormalities, but can also cause neurodegenerative diseases, immunodeficiency, or muscle wasting syndromes. Epigenetic diseases can either be of monogenic origin or manifest themselves as complex multifactorial diseases such as in congenital heart disease, autism spectrum disorders, or cancer in which mutations in chromatin regulators are contributing factors. The environment directly influences the epigenome and can induce changes that cause or predispose to diseases through risk factors such as stress, malnutrition or exposure to harmful chemicals. The plasticity of chromatin regulation makes targeting the enzymatic machinery an attractive strategy for therapeutic intervention and an increasing number of small molecule inhibitors against a variety of epigenetic regulators are in clinical use or under development. In this review, we will give an overview of the molecular lesions that underlie epigenetic diseases, and we will discuss the impact of the environment and prospects for epigenetic therapies. PMID:26188466

  20. 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

  1. 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. PMID:27051883

  2. 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

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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

  8. 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.

  9. 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

  10. 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

  11. 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

  12. 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

  13. 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

  14. Studies on chromatin. II. Isolation and characterization of chromatin subunits.

    PubMed Central

    Bakayev, V V; Melnickov, A A; Osicka, V D; Varshausky, A J

    1975-01-01

    Earlier findings /1-10/ bearing on a subunit organization of chromatin were confirmed and in some points detailed. Besides this, a large-scale isolation of chromatin subunits; their protein composition, electron microscopic appearance and CsCl banding pattern are described. Although the purified chromatin subunit contains all five histones, the relative content of histone H1 i in it is two times lower than that in the original chromatin. tit is shown that a mild digestion of chromatin with staphylococcal nuclease produced not only separate chromatin subunits and their "oligomers' but also deoxyribonucleoprotein particles which sediment more slowly than subunits. It appears that these particles and subunits are produced from different initial structures in the chromatin. Finally, a crystallization of the purified chromatin subunit as a cetyltrimethyl ammonium salt is described. Images PMID:1178523

  15. Chromatin remodeling in cardiovascular development and physiology

    PubMed Central

    Han, Pei; Hang, Calvin T.; Yang, Jin; Chang, Ching-Pin

    2010-01-01

    Chromatin regulation provides an important means of controlling cardiac gene expression under different physiological and pathological conditions. Processes that direct the development of normal embryonic hearts and pathology of stressed adult hearts may share general mechanisms that govern cardiac gene expression by chromatin-regulating factors. These common mechanisms may provide a framework for us to investigate the interactions among diverse chromatin remodelers/modifiers and various transcription factors in the fine regulation of gene expression, essential for all aspects of cardiovascular biology. Aberrant cardiac gene expression, triggered by a variety of pathological insults, can cause heart diseases in both animals and humans. The severity of cardiomyopathy and heart failure correlates strongly with abnormal cardiac gene expression. Therefore, controlling cardiac gene expression presents a promising approach to the treatment of human cardiomyopathy. This review focuses on the roles of ATP-dependent chromatin-remodeling factors and chromatin-modifying enzymes in the control of gene expression during cardiovascular development and disease. PMID:21293009

  16. 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

  17. Chromatin dynamics associated with HIV-1 Tat activated transcription

    PubMed Central

    Easley, Rebecca; Van Duyne, Rachel; Coley, Will; Guendel, Irene; Dadgar, Sherry; Kehn-Hall, Kylene; Kashanchi, Fatah

    2009-01-01

    Summary Chromatin remodeling is an essential event for HIV-1 transcription. Over the last two decades this field of research has come to the forefront, as silencing of the HIV-1 provirus through chromatin modifications has been linked to latency. Here, we focus on chromatin remodeling, especially in relation to the transactivator Tat, and review the most important and newly emerging studies that investigate remodeling mechanisms. We begin by discussing covalent modifications that can alter chromatin structure including acetylation, deacetylation, and methylation, as well as topics addressing the interplay between chromatin remodeling and splicing. Next, we focus on complexes that use the energy of ATP to remove or secure nucleosomes and can additionally act to control HIV-1 transcription. Finally, we cover recent literature on viral microRNAs which have been shown to alter chromatin structure by inducing methylation or even by remodeling nucleosomes. PMID:19716452

  18. 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,…

  19. Chromatin and DNA replication.

    PubMed

    MacAlpine, David M; Almouzni, Geneviève

    2013-08-01

    The size of a eukaryotic genome presents a unique challenge to the cell: package and organize the DNA to fit within the confines of the nucleus while at the same time ensuring sufficient dynamics to allow access to specific sequences and features such as genes and regulatory elements. This is achieved via the dynamic nucleoprotein organization of eukaryotic DNA into chromatin. The basic unit of chromatin, the nucleosome, comprises a core particle with 147 bp of DNA wrapped 1.7 times around an octamer of histones. The nucleosome is a highly versatile and modular structure, both in its composition, with the existence of various histone variants, and through the addition of a series of posttranslational modifications on the histones. This versatility allows for both short-term regulatory responses to external signaling, as well as the long-term and multigenerational definition of large functional chromosomal domains within the nucleus, such as the centromere. Chromatin organization and its dynamics participate in essentially all DNA-templated processes, including transcription, replication, recombination, and repair. Here we will focus mainly on nucleosomal organization and describe the pathways and mechanisms that contribute to assembly of this organization and the role of chromatin in regulating the DNA replication program. PMID:23751185

  20. 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

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

    PubMed

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

    2015-04-01

    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

  2. Light-Induced Surface Patterning of Silica.

    PubMed

    Kang, Hong Suk; Lee, Seungwoo; Choi, Jaeho; Lee, Hongkyung; Park, Jung-Ki; Kim, Hee-Tak

    2015-10-27

    Manipulating the size and shape of silica precursor patterns using simple far-field light irradiation and transforming such reconfigured structures into inorganic silica patterns by pyrolytic conversion are demonstrated. The key concept of our work is the use of an azobenzene incorporated silica precursor (herein, we refer to this material as azo-silane composite) as ink in a micromolding process. The moving direction of azo-silane composite is parallel to light polarization direction; in addition, the amount of azo-silane composite movement can be precisely determined by controlling light irradiation time. By exploiting this peculiar phenomenon, azo-silane composite patterns produced using the micromolding technique are arbitrarily manipulated to obtain various structural features including high-resolution size or sophisticated shape. The photoreconfigured patterns formed with azo-silane composites are then converted into pure silica patterns through pyrolytic conversion. The pyrolytic converted silica patterns are uniformly formed over a large area, ensuring crack-free formation and providing high structural fidelity. Therefore, this optical manipulation technique, in conjunction with the pyrolytic conversion process, opens a promising route to the design of silica patterns with finely tuned structural features in terms of size and shape. This platform for designing silica structures has significant value in various nanotechnology fields including micro/nanofluidic channel for lab-on-a-chip devices, transparent superhydrophobic surfaces, and optoelectronic devices. PMID:26389813

  3. 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

  4. Amelioration of light-induced retinal degeneration by a calcium overload blocker. Flunarizine.

    PubMed

    Edward, D P; Lam, T T; Shahinfar, S; Li, J; Tso, M O

    1991-04-01

    Although free radical formation and lipid peroxidation have been implicated in photoreceptor degeneration following continuous light exposure, recent evidence led us to hypothesize that excessive stimulation of the photoreceptor cells in prolonged light exposure may cause intracellular calcium overload and consequent photoreceptor cell injury. To test this hypothesis, we studied the effects of flunarizine hydrochloride, a calcium overload blocker that inhibits the inositol 1,4,5-triphosphate-induced release of intracellular stores of calcium, in an established rat model of light-induced retinal degeneration. Light and electron microscopic examination of the flunarizine-treated retinas revealed remarkable preservation of the retinal pigment epithelium, rod inner and outer segments, nuclei, and synapses of the photoreceptor cells at all phases of the recovery period. This observation was further supported by morphometric evaluation of the outer nuclear layer thickness, which revealed a greater preservation of the photoreceptor nuclei in the drug-treated animals at 6 and 14 days after exposure. In addition, the rhodopsin levels in the flunarizine-treated retinas were also significantly higher than in the controls in all phases of recovery. The ability of flunarizine to ameliorate light-induced retinal degeneration in the rat supports our hypothesis that elevated intracellular calcium may indeed play a role in light-induced photoreceptor degeneration. PMID:2012559

  5. 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

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

    PubMed Central

    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.

    2016-01-01

    Summary 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, 4, 5, 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

  7. Chromatin retention of DNA damage sensors DDB2 and XPC through loss of p97 segregase causes genotoxicity

    PubMed Central

    Puumalainen, Marjo-Riitta; Lessel, Davor; Rüthemann, Peter; Kaczmarek, Nina; Bachmann, Karin; Ramadan, Kristijan; Naegeli, Hanspeter

    2014-01-01

    DNA damage recognition subunits like DDB2 and XPC protect the human skin from ultraviolet (UV) light-induced genome instability and cancer, as demonstrated by the devastating inherited syndrome xeroderma pigmentosum. Here, we show that the beneficial DNA repair response triggered by these two genome caretakers critically depends on a dynamic spatiotemporal regulation of their homeostasis. The prolonged retention of DDB2 and XPC in chromatin, due to a failure to readily remove both recognition subunits by the ubiquitin-dependent p97/VCP/Cdc48 segregase complex, leads to impaired DNA excision repair of UV lesions. Surprisingly, the ensuing chromosomal aberrations in p97-deficient cells are alleviated by a concomitant down regulation of DDB2 or XPC. Also, genome instability resulting from an excess of DDB2 persisting in UV-irradiated cells is prevented by concurrent p97 over-expression. Our findings demonstrate that DNA damage sensors and repair initiators acquire unexpected genotoxic properties if not controlled by timely extraction from chromatin. PMID:24770583

  8. Id2 leaves the chromatin of the E2F4–p130-controlled c-myc promoter during hepatocyte priming for liver regeneration

    PubMed Central

    Rodríguez, José L.; Sandoval, Juan; Serviddio, Gaetano; Sastre, Juan; Morante, María; Perrelli, Maria-Giulia; Martínez-Chantar, María L.; Viña, José; Viña, Juan R.; Mato, José M.; Ávila, Matías A.; Franco, Luis; López-Rodas, Gerardo; Torres, Luis

    2006-01-01

    The Id (inhibitor of DNA binding or inhibitor of differentiation) helix–loop–helix proteins are involved in the regulation of cell growth, differentiation and cancer. The fact that the molecular mechanisms of liver regeneration are not completely understood prompted us to study the fate of Id2 in proliferating liver. Id2 increases in liver regeneration after partial hepatectomy, following the early induction of its gene. Co-immunoprecipitation shows that Id2 forms a complex with E2F4, p130 and mSin3A in quiescent liver and all these components are present at the c-myc promoter as shown using ChIP (chromatin immunoprecipitation). Activation of c-myc during hepatocyte priming (G0–G1 transition) correlates with the dissociation of Id2 and HDAC (histone deacetylase), albeit p130 remains bound at least until 6 h. Moreover, as the G0–G1 transition progresses, Id2 and HDAC again bind the c-myc promoter concomitantly with the repression of this gene. The time course of c-myc binding to the Id2 promoter, as determined by ChIP assays is compatible with a role of the oncoprotein as a transcriptional inducer of Id2 in liver regeneration. Immunohistochemical analysis shows that Id2 also increases in proliferating hepatocytes after bile duct ligation. In this case, the pattern of Id2 presence in the c-myc promoter parallels that found in regenerating liver. Our results may suggest a control role for Id2 in hepatocyte priming, through a p130 dissociation-independent regulation of c-myc. PMID:16776654

  9. 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

  10. 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

  11. 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

  12. 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

  13. 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

  14. Cas9 Functionally Opens Chromatin

    PubMed Central

    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

  15. Mechanism of chromatin remodeling.

    PubMed

    Lorch, Yahli; Maier-Davis, Barbara; Kornberg, Roger D

    2010-02-23

    Results from biochemical and structural studies of the RSC chromatin-remodeling complex prompt a proposal for the remodeling mechanism: RSC binding to the nucleosome releases the DNA from the histone surface and initiates DNA translocation (through one or a small number of DNA base pairs); ATP binding completes translocation, and ATP hydrolysis resets the system. Binding energy thus plays a central role in the remodeling process. RSC may disrupt histone-DNA contacts by affecting histone octamer conformation and through extensive interaction with the DNA. Bulging of the DNA from the octamer surface is possible, and twisting is unavoidable, but neither is the basis of remodeling. PMID:20142505

  16. Chromatin and epigenetic features of long-range gene regulation

    PubMed Central

    Harmston, Nathan; Lenhard, Boris

    2013-01-01

    The precise regulation of gene transcription during metazoan development is controlled by a complex system of interactions between transcription factors, histone modifications and modifying enzymes and chromatin conformation. Developments in chromosome conformation capture technologies have revealed that interactions between regions of chromatin are pervasive and highly cell-type specific. The movement of enhancers and promoters in and out of higher-order chromatin structures within the nucleus are associated with changes in expression and histone modifications. However, the factors responsible for mediating these changes and determining enhancer:promoter specificity are still not completely known. In this review, we summarize what is known about the patterns of epigenetic and chromatin features characteristic of elements involved in long-range interactions. In addition, we review the insights into both local and global patterns of chromatin interactions that have been revealed by the latest experimental and computational methods. PMID:23766291

  17. Mapping chromatin modifications in nanochannels

    NASA Astrophysics Data System (ADS)

    Lim, Shuang Fang; Karpusenko, Alena; Riehn, Robert

    2013-03-01

    DNA and chromatin are elongated to a fixed fraction of their contour length when introduced into quasi-1d nanochannels. Because single molecules are analyzed, their hold great potential for the analysis for the genetic analysis of material from single cells. In this study, we have reconstituted chromatin with histones from a variety of sources, and mapped the modification profile of the chromatin. We monitored methylation and acetylation patterns of the histone tail protein residues using fluorescently labelled antibodies. Using those, we distinguished chromatin reconstituted from chicken erythrocytes, calf thymus, and HeLa cells. We discuss prospects for profiling histone modifications for whole chromosomes from single cells.

  18. Chromatin dynamics: Interplay between remodeling enzymes and histone modifications

    PubMed Central

    Swygert, Sarah G.; Peterson, Craig L.

    2014-01-01

    Chromatin dynamics play an essential role in regulating the accessibility of genomic DNA for a variety of nuclear processes, including gene transcription and DNA repair. The posttranslational modification of the core histones and the action of ATP-dependent chromatin remodeling enzymes represent two primary mechanisms by which chromatin dynamics are controlled and linked to nuclear events. Although there are examples in which a histone modification or a remodeling enzyme may be sufficient to drive a chromatin transition, these mechanisms typically work in concert to integrate regulatory inputs, leading to a coordinated alteration in chromatin structure and function. Indeed, site-specific histone modifications can facilitate the recruitment of chromatin remodeling enzymes to particular genomic regions, or they can regulate the efficiency or the outcome of a chromatin remodeling reaction. Conversely, chromatin remodeling enzymes can also influence, and sometimes directly modulate, the modification state of histones. These functional interactions are generally complex, frequently transient, and often require the association of myriad additional factors. PMID:24583555

  19. 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

  20. 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.

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

    PubMed

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

    2016-03-31

    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 [Formula: see text] ps that is consistent with nucleation and growth dynamics of the R phase from the parent M1 ground state. PMID:26932975

  2. 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.

  3. MicroRNA-7 Compromises p53 Protein-dependent Apoptosis by Controlling the Expression of the Chromatin Remodeling Factor SMARCD1.

    PubMed

    Hong, Chun-Fu; Lin, Shu-Yu; Chou, Yu-Ting; Wu, Cheng-Wen

    2016-01-22

    We previously demonstrated that the epidermal growth factor receptor (EGFR) up-regulated miR-7 to promote tumor growth during lung cancer oncogenesis. Several lines of evidence have suggested that alterations in chromatin remodeling components contribute to cancer initiation and progression. In this study, we identified SMARCD1 (SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin, subfamily d, member 1) as a novel target gene of miR-7. miR-7 expression reduced SMARCD1 protein expression in lung cancer cell lines. We used luciferase reporters carrying wild type or mutated 3'UTR of SMARCD1 and found that miR-7 blocked SMARCD1 expression by binding to two seed regions in the 3'UTR of SMARCD1 and down-regulated SMARCD1 mRNA expression. Additionally, upon chemotherapy drug treatment, miR-7 down-regulated p53-dependent apoptosis-related gene BAX (BCL2-associated X protein) and p21 expression by interfering with the interaction between SMARCD1 and p53, thereby reducing caspase3 cleavage and the downstream apoptosis cascades. We found that although SMARCD1 sensitized lung cancer cells to chemotherapy drug-induced apoptosis, miR-7 enhanced the drug resistance potential of lung cancer cells against chemotherapy drugs. SMARCD1 was down-regulated in patients with non-small cell lung cancer and lung adenocarcinoma cell lines, and SMARCD1 and miR-7 expression levels were negatively correlated in clinical samples. Our investigation into the involvement of the EGFR-regulated microRNA pathway in the SWI/SNF chromatin remodeling complex suggests that EGFR-mediated miR-7 suppresses the coupling of the chromatin remodeling factor SMARCD1 with p53, resulting in increased chemo-resistance of lung cancer cells. PMID:26542803

  4. 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.

  5. 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.

  6. Chromatin decondensed by acetylation shows an elevated radiation response

    SciTech Connect

    Nackerdien, Z.; Michie, J.; Boehm, L.

    1989-02-01

    V-79 Chinese hamster lung fibroblasts exposed to 5 mM n-sodium butyrate were irradiated with 60Co gamma rays and cell survival was determined by the cell colony assay. In a separate set of experiments the acetylated chromatin obtained from these cells was irradiated and the change of molecular weight of the DNA was evaluated by alkaline sucrose density centrifugation. At a survival level of 10(-2) to 10(-4) cells exposed to butyrate were found to be 1.3-1.4 times more radiosensitive than control cells. Exposure of isolated chromatin to 100 Gy of 60Co gamma irradiation generated 0.9 +/- 0.03 single-strand breaks (ssb) per 10 Gy per 10(8) Da and 2.0 +/- 0.3 ssb/10 Gy/10(8) Da for control and acetylated chromatin, respectively. The elevated radiation sensitivity of chromatin relaxed by acetylation is in good agreement with previous results on chromatin expanded by histone H1 depletion. Packing and accessibility of DNA in chromatin appear to be major factors which influence the radiation sensitivity. The intrinsic radiation sensitivity of chromatin in various packing states is discussed in light of the variation of radiation sensitivity of whole cells in the cell cycle which incorporates repair.

  7. 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

  8. 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

  9. 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

  10. 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.

  11. 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.

  12. 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.

  13. Preimplantation Mouse Embryo Selection Guided by Light-Induced Dielectrophoresis

    PubMed Central

    Valley, Justin K.; Swinton, Paul; Boscardin, W. John; Lue, Tom F.; Rinaudo, Paolo F.; Wu, Ming C.; Garcia, Maurice M.

    2010-01-01

    Selection of optimal quality embryos for in vitro fertilization (IVF) transfer is critical to successful live birth outcomes. Currently, embryos are chosen based on subjective assessment of morphologic developmental maturity. A non-invasive means to quantitatively measure an embryo's developmental maturity would reduce the variability introduced by the current standard. We present a method that exploits the scaling electrical properties of pre-transfer embryos to quantitatively discern embryo developmental maturity using light-induced dielectrophoresis (DEP). We show that an embryo's DEP response is highly correlated with its developmental stage. Uniquely, this technique allows one to select, in sequence and under blinded conditions, the most developmentally mature embryos among a mixed cohort of morphologically indistinguishable embryos cultured in optimized and sub-optimal culture media. Following assay, embryos continue to develop normally in vitro. Light-induced dielectrophoresis provides a non-invasive, quantitative, and reproducible means to select embryos for applications including IVF transfer and embryonic stem cell harvest. PMID:20405021

  14. Light-induced vegetative anthocyanin pigmentation in Petunia

    PubMed Central

    Albert, Nick W.; Lewis, David H.; Zhang, Huaibi; Irving, Louis J.; Jameson, Paula E.; Davies, Kevin M.

    2009-01-01

    The Lc petunia system, which displays enhanced, light-induced vegetative pigmentation, was used to investigate how high light affects anthocyanin biosynthesis, and to assess the effects of anthocyanin pigmentation upon photosynthesis. Lc petunia plants displayed intense purple anthocyanin pigmentation throughout the leaves and stems when grown under high-light conditions, yet remain acyanic when grown under shade conditions. The coloured phenotypes matched with an accumulation of anthocyanins and flavonols, as well as the activation of the early and late flavonoid biosynthetic genes required for flavonol and anthocyanin production. Pigmentation in Lc petunia only occurred under conditions which normally induce a modest amount of anthocyanin to accumulate in wild-type Mitchell petunia [Petunia axillaris×(Petunia axillaris×Petunia hybrida cv. ‘Rose of Heaven’)]. Anthocyanin pigmentation in Lc petunia leaves appears to screen underlying photosynthetic tissues, increasing light saturation and light compensation points, without reducing the maximal photosynthetic assimilation rate (Amax). In the Lc petunia system, where the bHLH factor Leaf colour is constitutively expressed, expression of the bHLH (Lc) and WD40 (An11) components of the anthocyanin regulatory system were not limited, suggesting that the high-light-induced anthocyanin pigmentation is regulated by endogenous MYB transcription factors. PMID:19380423

  15. 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.

  16. 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

  17. Persistent Chromatin Modifications Induced by High Fat Diet.

    PubMed

    Leung, Amy; Trac, Candi; Du, Juan; Natarajan, Rama; Schones, Dustin E

    2016-05-13

    Obesity is a highly heritable complex disease that results from the interaction of multiple genetic and environmental factors. Formerly obese individuals are susceptible to metabolic disorders later in life, even after lifestyle changes are made to mitigate the obese state. This is reminiscent of the metabolic memory phenomenon originally observed for persistent complications in diabetic patients, despite subsequent glycemic control. Epigenetic modifications represent a potential mediator of this observed memory. We previously demonstrated that a high fat diet leads to changes in chromatin accessibility in the mouse liver. The regions of greatest chromatin changes in accessibility are largely strain-dependent, indicating a genetic component in diet-induced chromatin alterations. We have now examined the persistence of diet-induced chromatin accessibility changes upon diet reversal in two strains of mice. We find that a substantial fraction of loci that undergo chromatin accessibility changes with a high fat diet remains in the remodeled state after diet reversal in C57BL/6J mice. In contrast, the vast majority of diet-induced chromatin accessibility changes in A/J mice are transient. Our data also indicate that the persistent chromatin accessibility changes observed in C57BL/6J mice are associated with specific transcription factors and histone post-translational modifications. The persistent loci identified here are likely to be contributing to the overall phenotype and are attractive targets for therapeutic intervention. PMID:27006400

  18. CTCF-Mediated Functional Chromatin Interactome in Pluripotent Cells

    PubMed Central

    Handoko, Lusy; Xu, Han; Li, Guoliang; Ngan, Chew Yee; Chew, Elaine; Schnapp, Marie; Lee, Charlie Wah Heng; Ye, Chaopeng; Ping, Joanne Lim Hui; Mulawadi, Fabianus; Wong, Eleanor; Sheng, Jianpeng; Zhang, Yubo; Poh, Thompson; Chan, Chee Seng; Kunarso, Galih; Shahab, Atif; Bourque, Guillaume; Cacheux-Rataboul, Valere; Sung, Wing-Kin; Ruan, Yijun; Wei, Chia-Lin

    2011-01-01

    Mammalian genomes are viewed as functional organizations that orchestrate spatial and temporal gene regulation. CTCF, the most characterized insulator-binding protein, has been implicated as a key genome organizer. Yet, little is known about CTCF-associated higher order chromatin structures at a global scale. Here, we applied Chromatin Interaction Analysis by Paired-End-Tag sequencing to elucidate the CTCF-chromatin interactome in pluripotent cells. From this analysis, 1,480 cis and 336 trans interacting loci were identified with high reproducibility and precision. Associating these chromatin interaction loci with their underlying epigenetic states, promoter activities, enhancer binding and nuclear lamina occupancy, we uncovered five distinct chromatin domains that suggest potential new models of CTCF function in chromatin organization and transcriptional control. Specifically, CTCF interactions demarcate chromatin-nuclear membrane attachments and influence proper gene expression through extensive crosstalk between promoters and regulatory elements. This highly complex nuclear organization offers insights towards the unifying principles governing genome plasticity and function. PMID:21685913

  19. 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

  20. Effects of Combined Ketamine/Xylazine Anesthesia on Light Induced Retinal Degeneration in Rats

    PubMed Central

    Bolz, Sylvia; Eslava-Schmalbach, Javier; Willmann, Gabriel; Zhour, Ahmad; Zrenner, Eberhart; Fischer, M. Dominik; Gekeler, Florian

    2012-01-01

    Objectives To explore the effect of ketamine-xylazine anesthesia on light-induced retinal degeneration in rats. Methods Rats were anesthetized with ketamine and xylazine (100 and 5 mg, respectively) for 1 h, followed by a recovery phase of 2 h before exposure to 16,000 lux of environmental illumination for 2 h. Functional assessment by electroretinography (ERG) and morphological assessment by in vivo imaging (optical coherence tomography), histology (hematoxylin/eosin staining, TUNEL assay) and immunohistochemistry (GFAP and rhodopsin staining) were performed at baseline (ERG), 36 h, 7 d and 14 d post-treatment. Non-anesthetized animals treated with light damage served as controls. Results Ketamine-xylazine pre-treatment preserved retinal function and protected against light-induced retinal degeneration. In vivo retinal imaging demonstrated a significant increase of outer nuclear layer (ONL) thickness in the non-anesthetized group at 36 h (p<0.01) and significant reduction one week (p<0.01) after light damage. In contrast, ketamine-xylazine pre-treated animals showed no significant alteration of total retinal or ONL thickness at either time point (p>0.05), indicating a stabilizing and/or protective effect with regard to phototoxicity. Histology confirmed light-induced photoreceptor cell death and Müller cells gliosis in non-anesthetized rats, especially in the superior hemiretina, while ketamine-xylazine treated rats showed reduced photoreceptor cell death (TUNEL staining: p<0.001 after 7 d), thicker ONL and longer IS/OS. Fourteen days after light damage, a reduction of standard flash induced a-wave amplitudes and a-wave slopes (p = 0.01) and significant alterations in parameters of the scotopic sensitivity function (e.g. Vmax of the Naka Rushton fit p = 0.03) were observed in non-treated vs. ketamine-xylazine treated animals. Conclusions Our results suggest that pre-treatment with ketamine-xylazine anesthesia protects retinas against light damage

  1. 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.

  2. Neutrophil extracellular traps: Is immunity the second function of chromatin?

    PubMed Central

    2012-01-01

    Neutrophil extracellular traps (NETs) are made of processed chromatin bound to granular and selected cytoplasmic proteins. NETs are released by white blood cells called neutrophils, maybe as a last resort, to control microbial infections. This release of chromatin is the result of a unique form of cell death, dubbed “NETosis.” Here we review our understanding of how NETs are made, their function in infections and as danger signals, and their emerging importance in autoimmunity and coagulation. PMID:22945932

  3. Light-induced metastable defects or light-induced metastable H atoms in a-Si:H films?

    SciTech Connect

    Godet, C.

    1997-07-01

    In hydrogenated amorphous silicon (a-Si:H) films, the increase of the metastable defect density under high-intensity illumination is usually described by an empirical two-parameter stretched-exponential time dependence (characteristic time {tau}{sub SE} and dispersion parameter {beta}). In this study, a clearly different (one-parameter) analytic function is obtained from a microscopic model based on the formation of metastable H (MSH) atoms in a-Si:H films. Assuming that MSH atoms are the only mobile species, only three chemical reactions are significant: MSH are produced from doubly hydrogenated (SiH HSi) configurations and trapped either at broken bonds or Si-H bonds, corresponding respectively to light-induced annealing (LIA) and light-induced creation (LIC) of defects. Competition between trapping sites results in a saturation of N(t) at a steady-state value N{sub ss}. A one-parameter fit of this analytical function to experimental data is generally good, indicating that the use of a statistical distribution of trap energies is not necessary.

  4. 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

  5. Light-induced long-range hydrogen motion in a-Si:H at room temperature

    NASA Astrophysics Data System (ADS)

    Cheong, Hyeonsik M.; Lee, S.-H.; Nelson, B. P.; Mascarenhas, A.; Deb, S. K.

    2001-03-01

    We demonstrate that one can detect minuscule amounts of hydrogen diffusion out of a-Si:H under illumination at room temperature, by monitoring the changes in the Raman spectrum of a-WO3 as a function of illumination. The Staebler-Wronski effect, the light-induce creation of metastable defects in hydrogenated amorphous silicon (a-Si:H), has been one of the major problems that has limited the performance of solar cells based on this material. The recently suggested ¡®hydrogen collision model¡¯ can explain many aspects of the Staebler-Wronski effect, but assumes that the photogenerated mobile hydrogen atoms can move a long distance at room temperature. However, light-induced hydrogen motion in a-Si:H has not been experimentally observed at room temperature. We utilized the high sensitivity of the Raman spectrum of electrochromic a-WO3 to hydrogen insertion to probe the long-range motion of hydrogen at room temperature. We deposited a thin (200 nm) layer of a-WO3 on top of a-Si:H, and under illumination, a change in the Raman spectrum was detected. By comparing the Raman signal changes with those for control experiments where hydrogen is electrochemically inserted into a-WO_3, we can estimate semiquantitatively the amount of hydrogen that diffuses out of the a-Si:H layer.

  6. Light-induced degradation of storage starch in turions of Spirodela polyrhiza depends on nitrate.

    PubMed

    Appenroth, Klaus-J; Ziegler, Paul

    2008-10-01

    Light induces both the germination of turions of the duckweed Spirodela polyrhiza and the degradation of the reserve starch stored in the turions. The germination photoresponse requires nitrate, and we show here that nitrate is also needed for the light-induced degradation of the turion starch. Ammonium cannot substitute for nitrate in this regard, and nitrate thus acts specifically as signal to promote starch degradation in the turions. Irradiation with continuous red light leads to starch degradation via auto-phosphorylation of starch-associated glucan, water dikinase (GWD), phosphorylation of the turion starch and enhanced binding of alpha-amylase to starch granules. The present study shows that all of these processes require the presence of nitrate, and that nitrate exerts its effect on starch degradation at a point between the absorption of light by phytochrome and the auto-phosphorylation of the GWD. Nitrate acts to coordinate carbon and nitrogen metabolism in germinating turions: starch will only be broken down when sufficient nitrogen is present to ensure appropriate utilization of the released carbohydrate. These data constitute the first report of control over the initiation of reserve starch degradation by nitrate. PMID:18643949

  7. 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.

  8. Light-Induced Degradation of Thin Film Silicon Solar Cells

    NASA Astrophysics Data System (ADS)

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

    2016-02-01

    Silicon-wafer based solar cells are still domination the market for photovoltaic energy conversion. However, most of the silicon is used only for mechanical stability, while only a small percentage of the material is needed for the light absorption. Thin film silicon technology reduces the material demand to just some hundred nanometer thickness. But even in a tandem stack (amorphous and microcrystalline silicon) the efficiencies are lower, and light-induced degradation is an important issue. The established standard tests for characterisation are not precise enough to predict the performance of thin film silicon solar cells under real conditions, since many factors do have an influence on the degradation. We will show some results of laboratory and outdoor measurements that we are going to use as a base for advanced modelling and simulation methods.

  9. 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.

  10. 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.

  11. 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

  12. 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.

  13. 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

  14. 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

  15. Effect of irradiation and endogenous nucleases on rat liver chromatin

    SciTech Connect

    Gelderblom, D.; Smit, B.J.; Boehm, L.

    1984-08-01

    The assessment of the consequences of irradiation on chromatin is complicated by endogenous nucleases. Isolation and prolonged storage of rat liver nuclei in buffers containing divalent metal ions activates these enzymes and promotes the degradation of chromatin. Irradiation of rat liver nuclei to dose levels of 20,000 rad under conditions in which endogenous nucleases are inhibited and analysis of the irradiated chromatin by sucrose density gradient centrifugation gave no evidence for monosomes or oligosomes. When chromatin from irradiated nuclei was digested with micrococcal nuclease, the levels of monosomes and oligosomes were identical to those of micrococcal nuclease digests of unirradiated control nuclei. These results suggest that irradiation results in neither a direct fragmentation of linkers nor the sensitization of linkers for subsequent cleavage by micrococcal nuclease.

  16. 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

  17. 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

  18. 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

    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

    2014-08-01

    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

  19. 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

  20. Stem cell factors in plants: chromatin connections.

    PubMed

    Kornet, N; Scheres, B

    2008-01-01

    The progression of pluripotent stem cells to differentiated cell lineages requires major shifts in cell differentiation programs. In both mammals and higher plants, this process appears to be controlled by a dedicated set of transcription factors, many of which are kingdom specific. These divergent transcription factors appear to operate, however, together with a shared suite of factors that affect the chromatin state. It is of major importance to investigate whether such shared global control mechanisms indicate a common mechanistic basis for preservation of the stem cell state, initiation of differentiation programs, and coordination of cell state transitions. PMID:19150963

  1. 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.

  2. Can chromatin conformation technologies bring light into human molecular pathology?

    PubMed

    Kubiak, Marta; Lewandowska, Marzena Anna

    2015-01-01

    Regulation of gene expression in eukaryotes involves many complex processes, in which chromatin structure plays an important role. In addition to the epigenetic effects, such as DNA methylation and phosphorylation or histone modifications, gene expression is also controlled by the spatial organization of chromatin. For example, distant regulatory elements (enhancers, insulators) may come into direct physical interaction with target genes or other regulatory elements located in genomic regions of up to several hundred kilobases in size. Such long-range interactions result in the formation of chromatin loops. In the last several years, there has been a rapid increase in our knowledge of the spatial organization of chromatin in the nucleus through the chromosome conformation capture (3C) technology. Here we review and compare the original 3C and 3C-based methods including chromosome conformation capture-on-chip (4C), chromosome conformation capture carbon copy (5C), hi-resolution chromosome confomation capture (HiC). In this article, we discuss different aspects of how the nuclear organization of chromatin is associated with gene expression regulation and how this knowledge is useful in translational medicine and clinical applications. We demonstrate that the knowledge of the chromatin 3D organization may help understand the mechanisms of gene expression regulation of genes involved in the development of human diseases, such as CFTR (responsible for cystic fibrosis) or IGFBP3 (associated with breast cancer pathogenesis). Additionally, 3C-derivative methods have been also useful in the diagnosis of some leukemia subtypes. PMID:26328275

  3. Mammalian sperm chromatin as a model for chromatin function in DNA degradation and DNA replication.

    PubMed

    Ortega, Michael A; Sil, Payel; Ward, W Steven

    2011-02-01

    Reproductive biology is considered a specialty field, however, an argument can be made that it is instead generally applicable to many fields of biology. The one-cell embryo is presented here as a model system for the study of eukaryotic DNA replication, apoptotic DNA degradation, and signaling mechanisms between the cytoplasm and nucleus. Two unique aspects of this system combine to make it particularly useful for the study of chromatin function. First, the evolutionary pressure that lead to the extreme condensation of mammalian sperm DNA resulted in a cell with virtually inert chromatin, no DNA replication or transcription ongoing in the sperm cell, and all of the cells in a G(0) state. This chromatin is suddenly transformed into actively transcribing and replicating DNA upon fertilization. Therefore, the sperm chromatin is poised to become active but does not yet possess sufficient components present in somatic chromatin structure for all these processes. The second unique aspect of this system is that the one cell embryo houses two distinct nuclei, termed pronuclei, through the first round of DNA synthesis. This means the sperm cell can be experimentally manipulated to test the affects of the various treatments on the biological functions of interest. Experimental manipulations of the system have already revealed a certain level of plasticity in the coordination of both the timing of DNA synthesis in the two pronuclei and in the response to cellular signals by each pronucleus involved with the progression through the G1/S checkpoint, including the degradation of DNA in the paternal pronucleus. The fact that two nuclei in the same cytoplasm can undergo different responses infers a level of autonomy in the nuclear control of the cell cycle. Thus, the features of mammalian fertilization can provide unique insights for the normal biology of the cell cycle in somatic cells. PMID:21204750

  4. Light-induced hopping conductivity in a transparent oxide

    NASA Astrophysics Data System (ADS)

    Medvedeva, J. E.; Freeman, A. J.; Bertoni, M. I.; Mason, T. O.

    2004-03-01

    Recently, Hayashi et al (K. Hayashi et al), Nature 419, 462 (2002) found a way to convert a transparent oxide into a persistent conductor using UV light. The simplicity of the insulator-conductor conversion (hydrogen annealing followed by UV irradiation) and the resulting drastic change in conductivity (by 10 orders of magnitude) makes this material an extremely attractive starting point for optoelectronic applications. Despite careful experimental studies, no definitive understanding has been reached on the underlying mechanism responsible for this new dramatic effect. Here we demonstrate that ab-initio calculations provide a detailed explanation of the experimental findings and reveal the origin of the light-induced conductivity. We (i) show that the charge transport, associated with photo-excitation of an electron from hydrogen, occurs by electron hopping, (ii) determine the exact paths for the carrier migration and (iii) derive the temperature behavior of the hopping conductivity. We predict the strong dependence of the transport on the particular hopping centers and their spatial arrangement which is confirmed by our measurements, and investigate the possibility of varying the conductivity by proper doping.

  5. Light-induced currents in Xenopus oocytes expressing bovine rhodopsin.

    PubMed Central

    Knox, B E; Khorana, H G; Nasi, E

    1993-01-01

    1. We have investigated the functioning of bovine rod opsin, which is efficiently synthesized from RNA made by in vitro transcription, following injection into Xenopus oocytes. We found that oocytes expressing the gene for opsin exhibit light-dependent ionic currents only after pigment generation by incubation with 11-cis-retinal. These currents are similar to the endogenous muscarinic acetylcholine (ACh) response of oocytes, but their amplitude is substantially smaller. 2. In order to optimize the conditions for obtaining light-induced currents in RNA-injected oocytes, the native ACh response was examined under several conditions. It was found that elevated external calcium markedly enhances the muscarinic response and that these currents have a non-linear dependence on membrane voltage, increasing substantially with depolarization. 3. Using the optimal conditions for evoking the largest ACh responses, (28 mM [Ca2+]o, 0 mV, omission of serum and Hepes from the media), the light-evoked currents obtained in RNA-injected oocytes were remarkably enhanced, and responses to multiple light stimuli could be obtained. 4. The light response appeared to desensitize, even after long periods of recovery and pigment regeneration. By contrast, the ACh responses continued to appear normal. These results suggest that desensitization of photoresponses expressed in Xenopus oocytes involve changes at early stages of the pathway, resulting in a reduced ability of rhodopsin to couple to the endogenous signalling system. Images Fig. 3 PMID:7692039

  6. 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.

  7. 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.

  8. 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

  9. Highly efficient visible light-induced O₂ generation by self-assembled nanohybrids of inorganic nanosheets and polyoxometalate nanoclusters.

    PubMed

    Gunjakar, Jayavant L; Kim, Tae Woo; Kim, In Young; Lee, Jang Mee; Hwang, Seong-Ju

    2013-01-01

    Unusually high photocatalytic activity of visible light-induced O₂ generation can be achieved by electrostatically-derived self-assembly between exfoliated Zn-Cr-LDH 2D nanosheets and POM 0D nanoclusters (W₇O₂₄⁶⁻ and V₁₀O₂₈⁶⁻) acting as an electron acceptor. This self-assembly can provide a high flexibility in the control of the chemical composition and pore structure of the resulting LDH-based nanohybrids. The hybridization with POM nanoclusters remarkably enhances the photocatalytic activity of the pristine Zn-Cr-LDH, which is attributable to the formation of porous structure and depression of charge recombination. Of prime interest is that the excellent photocatalytic activity of the as-prepared Zn-Cr-LDH-POM nanohybrid for visible light-induced O₂ generation can be further enhanced by calcination at 200 °C, leading to the very high apparent quantum yield of ∼75.2% at 420 nm. The present findings clearly demonstrate that the self-assembly of LDH-POM is fairly powerful in synthesizing novel LDH-based porous nanohybrid photocatalyst for visible light-induced O₂ generation. PMID:23801108

  10. Highly Efficient Visible Light-Induced O2 Generation by Self-Assembled Nanohybrids of Inorganic Nanosheets and Polyoxometalate Nanoclusters

    PubMed Central

    Gunjakar, Jayavant L.; Kim, Tae Woo; Kim, In Young; Lee, Jang Mee; Hwang, Seong-Ju

    2013-01-01

    Unusually high photocatalytic activity of visible light-induced O2 generation can be achieved by electrostatically-derived self-assembly between exfoliated Zn-Cr-LDH 2D nanosheets and POM 0D nanoclusters (W7O246− and V10O286−) acting as an electron acceptor. This self-assembly can provide a high flexibility in the control of the chemical composition and pore structure of the resulting LDH-based nanohybrids. The hybridization with POM nanoclusters remarkably enhances the photocatalytic activity of the pristine Zn-Cr-LDH, which is attributable to the formation of porous structure and depression of charge recombination. Of prime interest is that the excellent photocatalytic activity of the as-prepared Zn-Cr-LDH-POM nanohybrid for visible light-induced O2 generation can be further enhanced by calcination at 200 °C, leading to the very high apparent quantum yield of ∼75.2% at 420 nm. The present findings clearly demonstrate that the self-assembly of LDH–POM is fairly powerful in synthesizing novel LDH-based porous nanohybrid photocatalyst for visible light-induced O2 generation. PMID:23801108

  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. Global quantitative modeling of chromatin factor interactions.

    PubMed

    Zhou, Jian; Troyanskaya, Olga G

    2014-03-01

    Chromatin is the driver of gene regulation, yet understanding the molecular interactions underlying chromatin factor combinatorial patterns (or the "chromatin codes") remains a fundamental challenge in chromatin biology. Here we developed a global modeling framework that leverages chromatin profiling data to produce a systems-level view of the macromolecular complex of chromatin. Our model ultilizes maximum entropy modeling with regularization-based structure learning to statistically dissect dependencies between chromatin factors and produce an accurate probability distribution of chromatin code. Our unsupervised quantitative model, trained on genome-wide chromatin profiles of 73 histone marks and chromatin proteins from modENCODE, enabled making various data-driven inferences about chromatin profiles and interactions. We provided a highly accurate predictor of chromatin factor pairwise interactions validated by known experimental evidence, and for the first time enabled higher-order interaction prediction. Our predictions can thus help guide future experimental studies. The model can also serve as an inference engine for predicting unknown chromatin profiles--we demonstrated that with this approach we can leverage data from well-characterized cell types to help understand less-studied cell type or conditions. PMID:24675896

  13. 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

  14. 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

  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. Chromatin Structure Regulates Gene Conversion

    PubMed Central

    Cummings, W. Jason; Yabuki, Munehisa; Ordinario, Ellen C; Bednarski, David W; Quay, Simon; Maizels, Nancy

    2007-01-01

    Homology-directed repair is a powerful mechanism for maintaining and altering genomic structure. We asked how chromatin structure contributes to the use of homologous sequences as donors for repair using the chicken B cell line DT40 as a model. In DT40, immunoglobulin genes undergo regulated sequence diversification by gene conversion templated by pseudogene donors. We found that the immunoglobulin Vλ pseudogene array is characterized by histone modifications associated with active chromatin. We directly demonstrated the importance of chromatin structure for gene conversion, using a regulatable experimental system in which the heterochromatin protein HP1 (Drosophila melanogaster Su[var]205), expressed as a fusion to Escherichia coli lactose repressor, is tethered to polymerized lactose operators integrated within the pseudo-Vλ donor array. Tethered HP1 diminished histone acetylation within the pseudo-Vλ array, and altered the outcome of Vλ diversification, so that nontemplated mutations rather than templated mutations predominated. Thus, chromatin structure regulates homology-directed repair. These results suggest that histone modifications may contribute to maintaining genomic stability by preventing recombination between repetitive sequences. PMID:17880262

  17. Immobilization of the nematode Caenorhabditis elegans with addressable light-induced heat knockdown (ALINK).

    PubMed

    Chuang, Han-Sheng; Chen, Hsiang-Yu; Chen, Chang-Shi; Chiu, Wen-Tai

    2013-08-01

    Caenorhabditis (C.) elegans is a model animal used in genetics, neuroscience, and developmental biology. Researchers often immobilize squirming worms to obtain high-quality images for analysis. However, current methods usually require physical contact or anesthetics. This can cause injuries to worm bodies or neuron disturbances. This study presents an alternative technique, called addressable light-induced heat knockdown (ALINK), to effectively immobilize worms by using light-induced sublethal heat. A microchip composed of an indium-tin-oxide (ITO) glass plate and an ITO glass plate coated with a photoconductive layer (a-Si:H) was produced. Worms to be immobilized were immersed in a liquid medium and sandwiched between the two plates. When the worms were irradiated with a focused laser beam in the presence of electric fields (referred to as an optoelectric treatment), the optoelectric effect heated the liquid medium. The neural functions of the worms shut down temporarily when a critical temperature (>31 °C) was reached. Their neural functions resumed after the heat source was removed. A temperature above 37 °C killed all worms. Using short-wavelength light reduced the worms' recovery time. An equivalent circuit was modeled to predict the operating modes, and an optoelectric treatment with a high-concentration medium enhanced rapid heating. A safe operating range (20 Vpp (peak-to-peak voltage), 100 kHz to 10 MHz, 31 to 37 °C) to induce heat knockdown (KD) was also investigated. The results show that the heat KD was well controlled, autonomous, and reversible. This technique can be used for worm immobilization. PMID:23719845

  18. Light-Induced Reversible Change of Roughness and Thickness of Photosensitive Polymer Brushes.

    PubMed

    Kopyshev, Alexey; Galvin, Casey J; Patil, Rohan R; Genzer, Jan; Lomadze, Nino; Feldmann, David; Zakrevski, Juri; Santer, Svetlana

    2016-07-27

    We investigate light-induced changes in thickness and roughness of photosensitive polymer brushes containing azobenzene cationic surfactants by atomic force microscopy (AFM) in real time during light irradiation. Because the cis-state of azobenzene unit requires more free volume than its trans counterpart, the UV light-induced expansion of polymer thin films associated with the trans-to-cis isomerism of azobenzene groups is expected to occur. This phenomenon is well documented in physisorbed polymer films containing azobenzene groups. In contrast, photosensitive polymer brushes show a decrease in thickness under UV irradiation. We have found that the azobenzene surfactants in their trans-state form aggregates within the brush. Under irradiation, the surfactants undergo photoisomerization to the cis-state, which is more hydrophilic. As a consequence, the aggregates within the brush are disrupted, and the polymer brush contracts. When subsequently irradiated with blue light the polymer brush thickness returns back to its initial value. This behavior is related to isomerization of the surfactant to the more hydrophobic trans-state and subsequent formation of surfactant aggregates within the polymer brush. The photomechanical function of the dry polymer brush, i.e., contraction and expansion, was found to be reversible with repeated irradiation cycles and requires only a few seconds for switching. In addition to the thickness change, the roughness of the brush also changes reversibly between a few Angstroms (blue light) and several nanometers (UV light). Photosensitive polymer brushes represent smart films with light responsive thickness and roughness that could be used for generating dynamic fluctuating surfaces, the function of which can be turned on and off in a controllable manner on a nanometer length scale. PMID:27351592

  19. 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

  20. Chromatin immunoprecipitation and an open chromatin assay in zebrafish erythrocytes.

    PubMed

    Yang, S; Ott, C J; Rossmann, M P; Superdock, M; Zon, L I; Zhou, Y

    2016-01-01

    Zebrafish is an excellent genetic and developmental model for the study of vertebrate development and disease. Its ability to produce an abundance of transparent, externally developed embryos has facilitated large-scale genetic and chemical screens for the identification of critical genes and chemical factors that modulate developmental pathways. These studies can have profound implications for the diagnosis and treatment of a variety of human diseases. Recent advancements in molecular and genomic studies have provided valuable tools and resources for comprehensive and high-resolution analysis of epigenomes during cell specification and lineage differentiation throughout development. In this chapter, we describe two simple methods to evaluate protein-DNA interaction and chromatin architecture in erythrocytes from adult zebrafish. These are chromatin immunoprecipitation coupled with next-generation sequencing (ChIP-seq) and an assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq). These techniques, together with gene expression profiling, are useful for analyzing epigenomic regulation of cell specification, differentiation, and function during zebrafish development in both normal and disease models. PMID:27443937

  1. Looking at plant cell cycle from the chromatin window

    PubMed Central

    Desvoyes, Bénédicte; Fernández-Marcos, María; Sequeira-Mendes, Joana; Otero, Sofía; Vergara, Zaida; Gutierrez, Crisanto

    2014-01-01

    The cell cycle is defined by a series of complex events, finely coordinated through hormonal, developmental and environmental signals, which occur in a unidirectional manner and end up in producing two daughter cells. Accumulating evidence reveals that chromatin is not a static entity throughout the cell cycle. In fact, there are many changes that include nucleosome remodeling, histone modifications, deposition and exchange, among others. Interestingly, it is possible to correlate the occurrence of several of these chromatin-related events with specific processes necessary for cell cycle progression, e.g., licensing of DNA replication origins, the E2F-dependent transcriptional wave in G1, the activation of replication origins in S-phase, the G2-specific transcription of genes required for mitosis or the chromatin packaging occurring in mitosis. Therefore, an emerging view is that chromatin dynamics must be considered as an intrinsic part of cell cycle regulation. In this article, we review the main features of several key chromatin events that occur at defined times throughout the cell cycle and discuss whether they are actually controlling the transit through specific cell cycle stages. PMID:25120553

  2. Micron-scale coherence in interphase chromatin dynamics

    PubMed Central

    Zidovska, Alexandra; Weitz, David A.; Mitchison, Timothy J.

    2013-01-01

    Chromatin structure and dynamics control all aspects of DNA biology yet are poorly understood, especially at large length scales. We developed an approach, displacement correlation spectroscopy based on time-resolved image correlation analysis, to map chromatin dynamics simultaneously across the whole nucleus in cultured human cells. This method revealed that chromatin movement was coherent across large regions (4–5 µm) for several seconds. Regions of coherent motion extended beyond the boundaries of single-chromosome territories, suggesting elastic coupling of motion over length scales much larger than those of genes. These large-scale, coupled motions were ATP dependent and unidirectional for several seconds, perhaps accounting for ATP-dependent directed movement of single genes. Perturbation of major nuclear ATPases such as DNA polymerase, RNA polymerase II, and topoisomerase II eliminated micron-scale coherence, while causing rapid, local movement to increase; i.e., local motions accelerated but became uncoupled from their neighbors. We observe similar trends in chromatin dynamics upon inducing a direct DNA damage; thus we hypothesize that this may be due to DNA damage responses that physically relax chromatin and block long-distance communication of forces. PMID:24019504

  3. Arabidopsis FHY3 and FAR1 Regulate Light-Induced myo-Inositol Biosynthesis and Oxidative Stress Responses by Transcriptional Activation of MIPS1.

    PubMed

    Ma, Lin; Tian, Tian; Lin, Rongcheng; Deng, Xing-Wang; Wang, Haiyang; Li, Gang

    2016-04-01

    myo-Inositol-1-phosphate synthase (MIPS) catalyzes the limiting step of inositol biosynthesis and has crucial roles in plant growth and development. In response to stress, the transcription of MIPS1 is induced and the biosynthesis of inositol or inositol derivatives is promoted by unknown mechanisms. Here, we found that the light signaling protein FAR-RED ELONGATED HYPOCOTYL3 (FHY3) and its homolog FAR-RED IMPAIRED RESPONSE1 (FAR1) regulate light-induced inositol biosynthesis and oxidative stress responses by activating the transcription of MIPS1. Disruption of FHY3 and FAR1 caused light-induced cell death after dark-light transition, precocious leaf senescence, and increased sensitivity to oxidative stress. Reduction of salicylic acid (SA) accumulation by overexpression of SALICYLIC ACID 3-HYDROXYLASE largely suppressed the cell death phenotype of fhy3 far1 mutant plants, suggesting that FHY3- and FAR1-mediated cell death is dependent on SA. Furthermore, comparative analysis of chromatin immunoprecipitation sequencing and microarray results revealed that FHY3 and FAR1 directly target both MIPS1 and MIPS2. The fhy3 far1 mutant plants showed severely decreased MIPS1/2 transcript levels and reduced inositol levels. Conversely, constitutive expression of MIPS1 partially rescued the inositol contents, caused reduced transcript levels of SA-biosynthesis genes, and prevented oxidative stress in fhy3 far1. Taken together, our results indicate that the light signaling proteins FHY3 and FAR1 directly bind the promoter of MIPS1 to activate its expression and thereby promote inositol biosynthesis to prevent light-induced oxidative stress and SA-dependent cell death. PMID:26714049

  4. Glycolytic metabolism influences global chromatin structure

    PubMed Central

    Liu, Xue-Song; Little, John B.; Yuan, Zhi-Min

    2015-01-01

    Metabolic rewiring, specifically elevated glycolytic metabolism is a hallmark of cancer. Global chromatin structure regulates gene expression, DNA repair, and also affects cancer progression. But the interrelationship between tumor metabolism and chromatin architecture remain unclear. Here we show that increased glycolysis in cancer cells promotes an open chromatin configuration. Using complementary methods including Micrococcal nuclease (MNase) digestion assay, electron microscope and immunofluorescence staining, we demonstrate that glycolysis inhibition by pharmacological and genetic approaches was associated with induction of compacted chromatin structure. This condensed chromatin status appeared to result chiefly from histone hypoacetylation as restoration of histone acetylation with an HDAC inhibitor reversed the compacted chromatin state. Interestingly, glycolysis inhibition-induced chromatin condensation impeded DNA repair efficiency leading to increased sensitivity of cancer cells to DNA damage drugs, which may represent a novel molecular mechanism that can be exploited for cancer therapy. PMID:25784656

  5. 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

  6. Dynamic chromatin organization: Role in development and disease.

    PubMed

    Kuznetsova, Tatyana; Stunnenberg, Hendrik G

    2016-07-01

    The spatial organization of chromatin in the nucleus is important for proper regulation of gene expression. The cell-type specific transcription program is mainly controlled by distal regulatory elements, which can dynamically engage in long-range interactions with their target genes. These long-range interactions mostly occur within insulated genomic domains and are constrained by global organization of the chromatin, providing an extra layer of regulation. Genetic alterations can lead to disruption of spatial organization and consequently aberrant gene expression. In this review we will discuss the multiple layers of chromatin organization, how this organization changes during development and how its disruption can lead do aberrant gene expression and disease. PMID:27179794

  7. Light Induced Processes for the Synthesis of Polymers With Complex Structures

    NASA Astrophysics Data System (ADS)

    Durmaz, Yasemin Y.; Tasdelen, M. Atilla; Aydogan, Binnur; Kahveci, Muhammet U.; Yagci, Yusuf

    Light induced reactions are based on the absorption of light that excites the electrons of a molecule and can, under favorable circumstances, lead to dissociation, isomerization, abstraction, electron or energy transfer, and bond formation. These reactions have been the subject of many studies in various fields including organic chemistry, molecular biology, electronics etc. Light induced reactions can advantageously be utilized in the field of polymer chemistry. Among them, light induced polymerization is of enormous commercial importance. Techniques such as curing of coatings on wood, metal and paper, adhesives, printing inks and photoresists are based on photopolymerization. There are some other interesting applications, including production of laser video discs and curing of acrylate dental fillings. In this chapter, general methods for the light induced polymerization processes involving radical and ionic reactions are described. Special emphasize is devoted to their application to more complex macromolecular structures such as block, graft and star copolymers, and polymer nanocomposites based on clay and metal.

  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. 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.

  10. Identification of lamin B-regulated chromatin regions based on chromatin landscapes.

    PubMed

    Zheng, Xiaobin; Kim, Youngjo; Zheng, Yixian

    2015-07-15

    Lamins, the major structural components of the nuclear lamina (NL) found beneath the nuclear envelope, are known to interact with most of the nuclear peripheral chromatin in metazoan cells. Although NL-chromatin associations correlate with a repressive chromatin state, the role of lamins in tethering chromatin to NL and how such tether influences gene expression have remained challenging to decipher. Studies suggest that NL proteins regulate chromatin in a context-dependent manner. Therefore understanding the context of chromatin states based on genomic features, including chromatin-NL interactions, is important to the study of lamins and other NL proteins. By modeling genome organization based on combinatorial patterns of chromatin association with lamin B1, core histone modification, and core and linker histone occupancy, we report six distinct large chromatin landscapes, referred to as histone lamin landscapes (HiLands)-red (R), -orange (O), -yellow (Y), -green (G), -blue (B), and -purple (P), in mouse embryonic stem cells (mESCs). This HiLands model demarcates the previously mapped lamin-associated chromatin domains (LADs) into two HiLands, HiLands-B and HiLands-P, which are similar to facultative and constitutive heterochromatins, respectively. Deletion of B-type lamins in mESCs caused a reduced interaction between regions of HiLands-B and NL as measured by emerin-chromatin interaction. Our findings reveal the importance of analyzing specific chromatin types when studying the function of NL proteins in chromatin tether and regulation. PMID:25995381

  11. Efficient cell migration requires global chromatin condensation

    PubMed Central

    Gerlitz, Gabi; Bustin, Michael

    2010-01-01

    Cell migration is a fundamental process that is necessary for the development and survival of multicellular organisms. Here, we show that cell migration is contingent on global condensation of the chromatin fiber. Induction of directed cell migration by the scratch-wound assay leads to decreased DNaseI sensitivity, alterations in the chromatin binding of architectural proteins and elevated levels of H4K20me1, H3K27me3 and methylated DNA. All these global changes are indicative of increased chromatin condensation in response to induction of directed cell migration. Conversely, chromatin decondensation inhibited the rate of cell migration, in a transcription-independent manner. We suggest that global chromatin condensation facilitates nuclear movement and reshaping, which are important for cell migration. Our results support a role for the chromatin fiber that is distinct from its known functions in genetic processes. PMID:20530575

  12. Regulation of chromatin structure by poly(ADP-ribosyl)ation

    PubMed Central

    Beneke, Sascha

    2012-01-01

    The interaction of DNA with proteins in the context of chromatin has to be tightly regulated to achieve so different tasks as packaging, transcription, replication and repair. The very rapid and transient post-translational modification of proteins by poly(ADP-ribose) has been shown to take part in all four. Originally identified as immediate cellular answer to a variety of genotoxic stresses, already early data indicated the ability of this highly charged nucleic acid-like polymer to modulate nucleosome structure, the basic unit of chromatin. At the same time the enzyme responsible for synthesizing poly(ADP-ribose), the zinc-finger protein poly(ADP-ribose) polymerase-1 (PARP1), was shown to control transcription initiation as basic factor TFIIC within the RNA-polymerase II machinery. Later research focused more on PARP-mediated regulation of DNA repair and cell death, but in the last few years, transcription as well as chromatin modulation has re-appeared on the scene. This review will discuss the impact of PARP1 on transcription and transcription factors, its implication in chromatin remodeling for DNA repair and probably also replication, and its role in controlling epigenetic events such as DNA methylation and the functionality of the insulator protein CCCTC-binding factor. PMID:22969794

  13. Open chromatin in pluripotency and reprogramming

    PubMed Central

    Meshorer, Eran; Ramalho-Santos, Miguel

    2013-01-01

    Pluripotent stem cells can be derived from embryos or induced from adult cells by reprogramming. They are unique from any other stem cell in that they can give rise to all cell types of the body. Recent findings indicate that a particularly open chromatin state contributes to maintenance of pluripotency. Two emerging principles are that: specific factors maintain a globally open chromatin state that is accessible for transcriptional activation; and other chromatin regulators contribute locally to the silencing of lineage-specific genes until differentiation is triggered. These same principles may apply during reacquisition of an open chromatin state upon reprogramming to pluripotency, and during de-differentiation in cancer. PMID:21179060

  14. Single cell correlation fractal dimension of chromatin

    PubMed Central

    Récamier, Vincent; Izeddin, Ignacio; Bosanac, Lana; Dahan, Maxime; Proux, Florence; Darzacq, Xavier

    2014-01-01

    Chromatin is a major nuclear component, and it is an active matter of debate to understand its different levels of spatial organization, as well as its implication in gene regulation. Measurements of nuclear chromatin compaction were recently used to understand how DNA is folded inside the nucleus and to detect cellular dysfunctions such as cancer. Super-resolution imaging opens new possibilities to measure chromatin organization in situ. Here, we performed a direct measure of chromatin compaction at the single cell level. We used histone H2B, one of the 4 core histone proteins forming the nucleosome, as a chromatin density marker. Using photoactivation localization microscopy (PALM) and adaptive optics, we measured the three-dimensional distribution of H2B with nanometric resolution. We computed the distribution of distances between every two points of the chromatin structure, namely the Ripley K(r) distribution. We found that the K(r) distribution of H2B followed a power law, leading to a precise measurement of the correlation fractal dimension of chromatin of 2.7. Moreover, using photoactivable GFP fused to H2B, we observed dynamic evolution of chromatin sub-regions compaction. As a result, the correlation fractal dimension of chromatin reported here can be interpreted as a dynamically maintained non-equilibrium state. PMID:24637833

  15. 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.

  16. 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

  17. Light-induced gene transfer from packaged DNA enveloped in a dendrimeric photosensitizer

    NASA Astrophysics Data System (ADS)

    Nishiyama, Nobuhiro; Iriyama, Aya; Jang, Woo-Dong; Miyata, Kanjiro; Itaka, Keiji; Inoue, Yuji; Takahashi, Hidenori; Yanagi, Yasuo; Tamaki, Yasuhiro; Koyama, Hiroyuki; Kataoka, Kazunori

    2005-12-01

    The control of gene transfection in the body is a core issue in gene therapy. Photochemical internalization is a technology that allows light-induced delivery of DNA, drugs or other biological factors directly inside cells. Usually it requires that a photosensitizer be added to the drug-delivery system to photochemically destabilize the endosomal membrane. Here we present a system for in vivo DNA delivery in which these two components are assembled into one structure. This is a ternary complex composed of a core containing DNA packaged with cationic peptides and enveloped in the anionic dendrimer phthalocyanine, which provides the photosensitizing action. The ternary complex showed more than 100-fold photochemical enhancement of transgene expression in vitro with reduced photocytotoxicity. In an animal experiment, subconjuctival injection of the ternary complex followed by laser irradiation resulted in transgene expression only in the laser-irradiated site. This work demonstrates a new biomedical application for dendrimers, and the first success in the photochemical-internalization-mediated gene delivery in vivo.

  18. Dim-Red-Light-Induced Increase in Polar Auxin Transport in Cucumber Seedlings1

    PubMed Central

    Shinkle, James R.; Kadakia, Rajan; Jones, Alan M.

    1998-01-01

    We have developed and characterized a system to analyze light effects on auxin transport independent of photosynthetic effects. Polar transport of [3H]indole-3-acetic acid through hypocotyl segments from etiolated cucumber (Cucumis sativus L.) seedlings was increased in seedlings grown in dim-red light (DRL) (0.5 μmol m−2 s−1) relative to seedlings grown in darkness. Both transport velocity and transport intensity (export rate) were increased by at least a factor of 2. Tissue formed in DRL completely acquired the higher transport capacity within 50 h, but tissue already differentiated in darkness acquired only a partial increase in transport capacity within 50 h of DRL, indicating a developmental window for light induction of commitment to changes in auxin transport. This light-induced change probably manifests itself by alteration of function of the auxin efflux carrier, as revealed using specific transport inhibitors. Relative to dark controls, DRL-grown seedlings were differentially less sensitive to two inhibitors of polar auxin transport, N-(naphth-1-yl) phthalamic acid and 2,3,5-triiodobenzoic acid. On the basis of these data, we propose that the auxin efflux carrier is a key target of light regulation during photomorphogenesis. PMID:9536069

  19. Identification of lamin B–regulated chromatin regions based on chromatin landscapes

    PubMed Central

    Zheng, Xiaobin; Kim, Youngjo; Zheng, Yixian

    2015-01-01

    Lamins, the major structural components of the nuclear lamina (NL) found beneath the nuclear envelope, are known to interact with most of the nuclear peripheral chromatin in metazoan cells. Although NL–chromatin associations correlate with a repressive chromatin state, the role of lamins in tethering chromatin to NL and how such tether influences gene expression have remained challenging to decipher. Studies suggest that NL proteins regulate chromatin in a context-dependent manner. Therefore understanding the context of chromatin states based on genomic features, including chromatin–NL interactions, is important to the study of lamins and other NL proteins. By modeling genome organization based on combinatorial patterns of chromatin association with lamin B1, core histone modification, and core and linker histone occupancy, we report six distinct large chromatin landscapes, referred to as histone lamin landscapes (HiLands)-red (R), -orange (O), -yellow (Y), -green (G), -blue (B), and -purple (P), in mouse embryonic stem cells (mESCs). This HiLands model demarcates the previously mapped lamin-associated chromatin domains (LADs) into two HiLands, HiLands-B and HiLands-P, which are similar to facultative and constitutive heterochromatins, respectively. Deletion of B-type lamins in mESCs caused a reduced interaction between regions of HiLands-B and NL as measured by emerin–chromatin interaction. Our findings reveal the importance of analyzing specific chromatin types when studying the function of NL proteins in chromatin tether and regulation. PMID:25995381

  20. Regeneration of chromatin-bound and membrane lipids from liver and thymus of V-irradiated rats

    SciTech Connect

    Kaznacheev, Yu.S.; Kolomiitseva, I.K.; Kulagina, T.P.; Markevich, L.N.

    1985-06-20

    This paper compares the regeneration of nuclear and chromatin lipids from the liver and thymus of control and irradiated rats according to the criterion of the incorporation of (/sup 14/C) acetate. The chromatin-bound lipids were found to have high metabolic activity, which was sharply pronounced in thymus cells. The corresponding lipids of intact nuclei suggests that the chromatin lipids are structurally separate from the rest of the nuclear lipids.

  1. Computational strategies to address chromatin structure problems.

    PubMed

    Perišić, Ognjen; Schlick, Tamar

    2016-01-01

    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. PMID:27345617

  2. 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

  3. Structure, Assembly and Reading of Centromeric Chromatin

    PubMed Central

    Maddox, Paul S; Corbett, Kevin D; Desai, Arshad

    2011-01-01

    Centromeres are epigenetically defined chromatin domains marked by the presence of the histone H3 variant CENP-A. Here we review recent structural and biochemical work on CENP-A, and advances in understanding the mechanisms that propagate and read centromeric chromatin domains. PMID:22178421

  4. Chromatin Remodelers: From Function to Dysfunction

    PubMed Central

    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

  5. Organization of spacer DNA in chromatin.

    PubMed Central

    Lohr, D; Van Holde, K E

    1979-01-01

    Detailed analysis of the DNA fragment patterns produced by DNase I digestion of yeast, HeLa, and chicken erythrocyte nuclei reveals surprising features of nucleosome phasing. First, the spacer regions in phased yeast chromatin must be of lengths (10m + 5) base pairs, where m = 0, 1, 2,....This feature is not seen in parallel studies of chicken erythrocyte chromatin. The 5-base pair increment in the yeast spacer imposes interesting restraints on the higher order structure of yeast chromatin. Second, we have been able to simulate the DNase I cutting patterns and get good agreement with the observed yeast patterns. Third, three different chromatins show a long range periodicity in the DNase I digest pattern, with a period half that of the staphylococcal nuclease repeat. These results suggest that the amount of chromatin observed in discrete extended-ladder bands is a minimum estimate of phasing and in fact phasing may be a more general feature. Images PMID:392519

  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. 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

  9. 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

  10. 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.

  11. Light-induced effects in dye-doped liquid crystals: role of space charges

    NASA Astrophysics Data System (ADS)

    Simoni, F.; Lucchetti, L.

    2014-10-01

    We report the experimental demonstration that both the extra-ordinarily large nonlinear response and the light-induced permanent reorientation in liquid crystals doped by the azo-dye Methyl-Red originates from the modification of the charge density on the irradiated surface. By recording the sample response by applying dc or ac voltage, it is shown that in the latter case no permanent anchoring is possible. It is also demonstrated the limited role of photo-isomerization that gives a contribution to the nonlinear reorientation process only in the high dose regime. The effects on light-induced tuning of the Freedericksz transition are also reported.

  12. Hantzsch Ester as a Photosensitizer for the Visible-Light-Induced Debromination of Vicinal Dibromo Compounds.

    PubMed

    Chen, Wenxin; Tao, Huachen; Huang, Wenhao; Wang, Guoqiang; Li, Shuhua; Cheng, Xu; Li, Guigen

    2016-07-01

    The debromination of vicinal dibromo compounds to generate alkenes usually requires harsh reaction conditions and the addition of catalysts. Just recently the visible-light-induced debromination of vicinal dibromo compounds emerged as a possible alternative to commonly used methods, but the substrate scope of this reaction is limited and a photocatalyst is necessary for the successful conversion of the starting compounds. A catalyst-free visible-light-induced debromination of vicinal dibromo compounds with a base-activated Hantzsch ester as photosensitizer is reported. The method has a wide substrate scope and a broad functional-group compatibility. PMID:27128783

  13. 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

  14. 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.

  15. 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

  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. Chromatin fiber polymorphism triggered by variations of DNA linker lengths

    PubMed Central

    Collepardo-Guevara, Rosana; Schlick, Tamar

    2014-01-01

    Deciphering the factors that control chromatin fiber structure is key to understanding fundamental chromosomal processes. Although details remain unknown, it is becoming clear that chromatin is polymorphic depending on internal and external factors. In particular, different lengths of the linker DNAs joining successive nucleosomes (measured in nucleosome-repeat lengths or NRLs) that characterize different cell types and cell cycle stages produce different structures. NRL is also nonuniform within single fibers, but how this diversity affects chromatin fiber structure is not clear. Here we perform Monte Carlo simulations of a coarse-grained oligonucleosome model to help interpret fiber structure subject to intrafiber NRL variations, as relevant to proliferating cells of interphase chromatin, fibers subject to remodeling factors, and regulatory DNA sequences. We find that intrafiber NRL variations have a profound impact on chromatin structure, with a wide range of different architectures emerging (highly bent narrow forms, canonical and irregular zigzag fibers, and polymorphic conformations), depending on the NRLs mixed. This stabilization of a wide range of fiber forms might allow NRL variations to regulate both fiber compaction and selective DNA exposure. The polymorphic forms spanning canonical to sharply bent structures, like hairpins and loops, arise from large NRL variations and are surprisingly more compact than uniform NRL structures. They are distinguished by tail-mediated far-nucleosome interactions, in addition to the near-nucleosome interactions of canonical 30-nm fibers. Polymorphism is consistent with chromatin’s diverse biological functions and heterogeneous constituents. Intrafiber NRL variations, in particular, may contribute to fiber bending and looping and thus to distant communication in associated regulatory processes. PMID:24847063

  18. 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

  19. Purification of RNA Polymerase I-Associated Chromatin from Yeast Cells.

    PubMed

    Bruckmann, Astrid; Linnemann, Jan; Perez-Fernandez, Jorge

    2016-01-01

    The native template of all eukaryotic nuclear RNA polymerases is chromatin. To understand how transcription occurs in vivo, it is important to define the chromatin environment of transcribing RNA Pols. Here, we describe a method used to characterize the distribution and the protein environment of RNA Pol I on ribosomal DNA during transcription in the yeast S. cerevisiae. The method is based on conventional chromatin immunoprecipitation and we propose quality control analyses at different steps of the procedure. Finally, the obtained samples are a useful source for downstream analyses by semiquantitative mass spectrometry or quantitative PCR. PMID:27576721

  20. 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

  1. 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. PMID:25313442

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

    PubMed Central

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

    2015-01-01

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

  3. 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

  4. Ordered Arrays of Native Chromatin Molecules for High-Resolution Imaging and Analysis

    PubMed Central

    Cerf, Aline; Tian, Harvey C.; Craighead, Harold G.

    2012-01-01

    Individual chromatin molecules contain valuable genetic and epigenetic information. To date, there have not been reliable techniques available for the controlled stretching and manipulation of individual chromatin fragments for high-resolution imaging and analysis of these molecules. We report the controlled stretching of single chromatin fragments extracted from two different cancerous cell types (M091 and HeLa) characterized through fluorescence microscopy and atomic force microscopy (AFM). Our method combines soft-lithography with molecular stretching to form ordered arrays of more than 250,000 individual chromatin fragments immobilized into a beads-on-a-string structure on a solid transparent support. Using fluorescence microscopy and AFM, we verified the presence of histone proteins after the stretching and transfer process. PMID:22816516

  5. Light-induced inhibition of laccase in Pycnoporus sanguineus.

    PubMed

    Hernández, Christian A; Perroni, Yareni; Pérez, José Antonio García; Rivera, Beatriz Gutiérrez; Alarcón, Enrique

    2016-03-01

    The aim was to determine which specific regions of the visible light spectrum were responsible for the induction or inhibition of laccase in Pycnoporus sanguineus. Cultures were exposed to various bandwidth lights: blue (460 nm), green (525 nm), white (a combination of 460 and 560 nm), red (660 nm), and darkness. The results indicate that short wavelengths strongly inhibit the production of laccase: green (3.76 ± 1.12 U/L), blue (1.94 ± 0.36 U/L), and white (1.05 ± 0.21 U/L) in proportions of 85.8, 92.6, and 96.0%, respectively; whereas long wavelengths inhibit laccase production only partially i.e., red light (14.05 ± 4.79 U/L) in a proportion of 46.8%. Maximum activity was induced in absence of visible light (30 °C, darkness), i.e., 30.76 ± 4.0 U/L. It is concluded that the production of laccase in P. sanguineus responds to light stimuli [measured as wavelengths and lx] and that it does so inversely. This can be explained as an ecological mechanism of environmental recognition, given that P. sanguineus develops inside lignocellulose structures in conditions of darkness. The presence of short wavelength light (460-510 nm) would indicate that the organism finds itself in an external environment, unprovided of lignin, and that it is therefore unnecessary to secrete laccase. This possible new regulation in the laccase production in P. sanguineus has important biotechnological implications, for it would be possible to control the production of laccase using light stimuli. PMID:26233233

  6. An Analysis of Light-Induced Retroactive Inhibition in Pigeon Short-Term Memory

    ERIC Educational Resources Information Center

    Roberts, William A.; Grant, Douglas S.

    1978-01-01

    Grant and Roberts found that houselight presented throughout the delay period on a delayed matching-to-sample task caused pigeons to demonstrate a much lower level of accuracy than was found when the delay was spent in darkness. A series of experiments was carried out to examine possible mechanisms responsible for this light-induced retroactive…

  7. The regulatory mechanism underlying light-inducible production of carotenoids in nonphototrophic bacteria.

    PubMed

    Takano, Hideaki

    2016-07-01

    Light is a ubiquitous environmental factor serving as an energy source and external stimulus. Here, I review the conserved molecular mechanism of light-inducible production of carotenoids in three nonphototrophic bacteria: Streptomyces coelicolor A3(2), Thermus thermophilus HB27, and Bacillus megaterium QM B1551. A MerR family transcriptional regulator, LitR, commonly plays a central role in their light-inducible carotenoid production. Genetic and biochemical studies on LitR proteins revealed a conserved function: LitR in complex with adenosyl B12 (AdoB12) has a light-sensitive DNA-binding activity and thus suppresses the expression of the Crt biosynthesis gene cluster. The in vitro DNA-binding and transcription assays showed that the LitR-AdoB12 complex serves as a repressor allowing transcription initiation by RNA polymerase in response to illumination. The existence of novel light-inducible genes and the unique role of the megaplasmid were revealed by the transcriptomic analysis of T. thermophilus. The findings suggest that LitR is a general regulator responsible for the light-inducible carotenoid production in the phylogenetically divergent nonphototrophic bacteria, and that LitR performs diverse physiological functions in bacteria. PMID:26967471

  8. 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

  9. Light-induced resistive switching in silicon-based metal-insulator-semiconductor structures

    NASA Astrophysics Data System (ADS)

    Tikhov, S. V.; Gorshkov, O. N.; Koryazhkina, M. N.; Antonov, I. N.; Kasatkin, A. P.

    2016-05-01

    We have studied light-induced resistive switching in metal-insulator-semiconductor structures based on silicon covered with a tunneling-thin SiO2 layer and nanometer-thick layer of antimony. The role of an insulator was played by yttria-stabilized zirconia.

  10. 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. PMID:26571045

  11. CYCLIN H;1 regulates drought stress responses and blue light-induced stomatal opening by inhibiting reactive oxygen species accumulation in Arabidopsis.

    PubMed

    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

    2013-06-01

    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

  12. Nucleosome structure in chromatin from heated cells

    SciTech Connect

    Warters, R.L.; Roti Roti, J.L.; Winward, R.T.

    1980-12-01

    The effect of hyperthermia (40 to 80/sup 0/C) on the nucleosome structure of mammalian chromatin was determined using the enzyme micrococcal nuclease. At equivalent fractional DNA digestion it was found that neither the size of DNA nor the total fraction of cellular DNA associated with nucleosome structure is altered by heat exposure up to 48/sup 0/C for 30 min. It is proposed that this heat-induced reduction in the accessibility to nuclease attack of DNA in chromatin from heated cells is due to the increased protein mass associated with chromatin.

  13. Highly condensed chromatins are formed adjacent to subtelomeric and decondensed silent chromatin in fission yeast

    PubMed Central

    Matsuda, Atsushi; Chikashige, Yuji; Ding, Da-Qiao; Ohtsuki, Chizuru; Mori, Chie; Asakawa, Haruhiko; Kimura, Hiroshi; Haraguchi, Tokuko; Hiraoka, Yasushi

    2015-01-01

    It is generally believed that silent chromatin is condensed and transcriptionally active chromatin is decondensed. However, little is known about the relationship between the condensation levels and gene expression. Here we report the condensation levels of interphase chromatin in the fission yeast Schizosaccharomyces pombe examined by super-resolution fluorescence microscopy. Unexpectedly, silent chromatin is less condensed than the euchromatin. Furthermore, the telomeric silent regions are flanked by highly condensed chromatin bodies, or ‘knobs'. Knob regions span ∼50 kb of sequence devoid of methylated histones. Knob condensation is independent of HP1 homologue Swi6 and other gene silencing factors. Disruption of methylation at lysine 36 of histone H3 (H3K36) eliminates knob formation and gene repression at the subtelomeric and adjacent knob regions. Thus, epigenetic marks at H3K36 play crucial roles in the formation of a unique chromatin structure and in gene regulation at those regions in S. pombe. PMID:26205977

  14. 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.

  15. Photocatalytic Reactive Oxygen Species Formation by Semiconductor-Metal Hybrid Nanoparticles. Toward Light-Induced Modulation of Biological Processes.

    PubMed

    Waiskopf, Nir; Ben-Shahar, Yuval; Galchenko, Michael; Carmel, Inbal; Moshitzky, Gilli; Soreq, Hermona; Banin, Uri

    2016-07-13

    Semiconductor-metal hybrid nanoparticles manifest efficient light-induced spatial charge separation at the semiconductor-metal interface, as demonstrated by their use for hydrogen generation via water splitting. Here, we pioneer a study of their functionality as efficient photocatalysts for the formation of reactive oxygen species. We observed enhanced photocatalytic activity forming hydrogen peroxide, superoxide, and hydroxyl radicals upon light excitation, which was significantly larger than that of the semiconductor nanocrystals, attributed to the charge separation and the catalytic function of the metal tip. We used this photocatalytic functionality for modulating the enzymatic activity of horseradish peroxidase as a model system, demonstrating the potential use of hybrid nanoparticles as active agents for controlling biological processes through illumination. The capability to produce reactive oxygen species by illumination on-demand enhances the available peroxidase-based tools for research and opens the path for studying biological processes at high spatiotemporal resolution, laying the foundation for developing novel therapeutic approaches. PMID:27224678

  16. Engineered apoptotic nucleases for chromatin research.

    PubMed

    Xiao, Fei; Widlak, Piotr; Garrard, William T

    2007-01-01

    We have created new genomics tools for chromatin research by genetically engineering the human and mouse major apoptotic nucleases that are responsible for internucleosomal DNA cleavage, DNA fragmentation factor (DFF). Normally, in its inactive form, DFF is a heterodimer composed of a 45-kDa chaperone inhibitor subunit (DFF45 or ICAD), and a 40-kDa latent endonuclease subunit (DFF40 or CAD). Upon caspase-3 cleavage of DFF45, DFF40 forms active endonuclease homo-oligomers. Although Saccharomyces cerevisiae lacks DFF, expression of caspase-3 is lethal in this organism, but expression of the highly sequence-specific tobacco etch virus protease (TEVP) is harmless. Therefore, we inserted TEVP cleavage sites immediately downstream of the two caspase-3 cleavage sites within DFF45, generating a novel form of DFF (DFF-T) whose nuclease activity proved to be exclusively under the control of TEVP. We demonstrate that co-expression of TEVP and DFF-T under galactose control results in nucleosomal DNA laddering and cell death in S. cerevisiae. We also created synthetic DFF genes with optimized codons for high-level expression in Eschericia coli or S. cerevisiae. We further demonstrate the excellence of the synthetic gene products for in vitro mapping of the nucleosome positions and hypersensitive sites in specific genes such as the yeast PHO5. PMID:17626049

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

    PubMed

    Rai, Taranjit Singh; 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; Adams, Peter D

    2014-12-15

    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

  18. 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

  19. 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.

  20. Pulling chromatin apart: Unstacking or Unwrapping?

    PubMed Central

    2012-01-01

    Background Understanding the mechanical properties of chromatin is an essential step towards deciphering the physical rules of gene regulation. In the past ten years, many single molecule experiments have been carried out, and high resolution measurements of the chromatin fiber stiffness are now available. Simulations have been used in order to link those measurements with structural cues, but so far no clear agreement among different groups has been reached. Results We revisit here some of the most precise experimental results obtained with carefully reconstituted fibers. Conclusions We show that the mechanical properties of the chromatin fiber can be quantitatively accounted for by the stiffness of the DNA molecule and the 3D structure of the chromatin fiber. PMID:23186373

  1. 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

  2. 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

  3. 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

  4. Recruitment of Phosphorylated Chromatin Assembly Factor 1 to Chromatin after UV Irradiation of Human Cells

    PubMed Central

    Martini, Emmanuelle; Roche, Danièle M.J.; Marheineke, Kathrin; Verreault, Alain; Almouzni, Geneviève

    1998-01-01

    The subcellular distribution and posttranslational modification of human chromatin assembly factor 1 (CAF-1) have been investigated after UV irradiation of HeLa cells. In an asynchronous cell population only a subfraction of the two large CAF-1 subunits, p150 and p60, were found to exist in a chromatin-associated fraction. This fraction is most abundant during S phase in nonirradiated cells and is much reduced in G2 cells. After UV irradiation, the chromatin-associated form of CAF-1 dramatically increased in all cells irrespective of their position in the cell cycle. Such chromatin recruitment resembles that seen for PCNA, a DNA replication and repair factor. The chromatin-associated fraction of p60 was predominantly hypophosphorylated in nonirradiated G2 cells. UV irradiation resulted in the rapid recruitment to chromatin of phosphorylated forms of the p60 subunit. Furthermore, the amount of the p60 and p150 subunits of CAF-1 associated with chromatin was a function of the dose of UV irradiation. Consistent with these in vivo observations, we found that the amount of CAF-1 required to stimulate nucleosome assembly during the repair of UV photoproducts in vitro depended upon both the number of lesions and the phosphorylation state of CAF-1. The recruitment of CAF-1 to chromatin in response to UV irradiation of human cells described here supports a physiological role for CAF-1 in linking chromatin assembly to DNA repair. PMID:9813080

  5. Chromatin remodeling by nucleosome disassembly in vitro.

    PubMed

    Lorch, Yahli; Maier-Davis, Barbara; Kornberg, Roger D

    2006-02-28

    The RSC chromatin-remodeling complex completely disassembles a nucleosome in the presence of the histone chaperone Nap1 and ATP. Disassembly occurs in a stepwise manner, with the removal of H2A/H2B dimers, followed by the rest of the histones and the release of naked DNA. RSC and related chromatin-remodeling complexes may be responsible for the removal of promoter nucleosomes during transcriptional activation in vivo. PMID:16492771

  6. Nucleosome repeat lengths and columnar chromatin structure.

    PubMed

    Trifonov, Edward N

    2016-06-01

    Thorough quantitative study of nucleosome repeat length (NRL) distributions, conducted in 1992 by J. Widom, resulted in a striking observation that the linker lengths between the nucleosomes are quantized. Comparison of the NRL average values with the MNase cut distances predicted from the hypothetical columnar structure of chromatin (this work) shows a close correspondence between the two. This strongly suggests that the NRL distribution, actually, reflects the dominant role of columnar chromatin structure common for all eukaryotes. PMID:26208520

  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. TWIN SISTER OF FT, GIGANTEA, and CONSTANS have a positive but indirect effect on blue light-induced stomatal opening in Arabidopsis.

    PubMed

    Ando, Eigo; Ohnishi, Masato; Wang, Yin; Matsushita, Tomonao; Watanabe, Aiko; Hayashi, Yuki; Fujii, Miho; Ma, Jian Feng; Inoue, Shin-ichiro; Kinoshita, Toshinori

    2013-07-01

    FLOWERING LOCUS T (FT) is the major regulatory component controlling photoperiodic floral transition. It is expressed in guard cells and affects blue light-induced stomatal opening induced by the blue-light receptor phototropins phot1 and phot2. Roles for other flowering regulators in stomatal opening have yet to be determined. We show in Arabidopsis (Arabidopsis thaliana) that TWIN SISTER OF FT (TSF), CONSTANS (CO), and GIGANTEA (GI) provide a positive effect on stomatal opening. TSF, which is the closest homolog of FT, was transcribed in guard cells, and light-induced stomatal opening was repressed in tsf-1, a T-DNA insertion mutant of TSF. Overexpression of TSF in a phot1 phot2 mutant background gave a constitutive open-stomata phenotype. Then, we examined whether CO and GI, which are upstream regulators of FT and TSF in photoperiodic flowering, are involved in stomatal opening. Similar to TSF, light-induced stomatal opening was suppressed in the GI and CO mutants gi-1 and co-1. A constitutive open-stomata phenotype was observed in GI and CO overexpressors with accompanying changes in the transcription of both FT and TSF. In photoperiodic flowering, photoperiod is sensed by photoreceptors such as the cryptochromes cry1 and cry2. We examined stomatal phenotypes in a cry1 cry2 mutant and in CRY2 overexpressors. Light-induced stomatal opening was suppressed in cry1 cry2, and the transcription of FT and TSF was down-regulated. In contrast, the stomata in CRY2 overexpressors opened even in the dark, and FT and TSF transcription was up-regulated. We conclude that the photoperiodic flowering components TSF, GI, and CO positively affect stomatal opening. PMID:23669744

  9. 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

  10. 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

  11. 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. PMID:17999983

  12. 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

  13. Chromatin assembly during S phase: contributions from histone deposition, DNA replication and the cell division cycle.

    PubMed

    Krude, T; Keller, C

    2001-05-01

    During S phase of the eukaryotic cell division cycle, newly replicated DNA is rapidly assembled into chromatin. Newly synthesised histones form complexes with chromatin assembly factors, mediating their deposition onto nascent DNA and their assembly into nucleosomes. Chromatin assembly factor 1, CAF-1, is a specialised assembly factor that targets these histones to replicating DNA by association with the replication fork associated protein, proliferating cell nuclear antigen, PCNA. Nucleosomes are further organised into ordered arrays along the DNA by the activity of ATP-dependent chromatin assembly and spacing factors such as ATP-utilising chromatin assembly and remodelling factor ACE An additional level of controlling chromatin assembly pathways has become apparent by the observation of functional requirements for cyclin-dependent protein kinases, casein kinase II and protein phosphatases. In this review, we will discuss replication-associated histone deposition and nucleosome assembly pathways, and we will focus in particular on how nucleosome assembly is linked to DNA replication and how it may be regulated by the cell cycle control machinery. PMID:11437228

  14. 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.

  15. Human transcriptional interactome of chromatin contribute to gene co-expression

    PubMed Central

    2010-01-01

    Background Transcriptional interactome of chromatin is one of the important mechanisms in gene transcription regulation. By chromatin conformation capture and 3D FISH experiments, several chromatin interactions cases among sequence-distant genes or even inter-chromatin genes were reported. However, on genomics level, there is still little evidence to support these mechanisms. Recently based on Hi-C experiment, a genome-wide picture of chromatin interactions in human cells was presented. It provides a useful material for analysing whether the mechanism of transcriptional interactome is common. Results The main work here is to demonstrate whether the effects of transcriptional interactome on gene co-expression exist on genomic level. While controlling the effects of transcription factors control similarities (TCS), we tested the correlation between Hi-C interaction and the mutual ranks of gene co-expression rates (provided by COXPRESdb) of intra-chromatin gene pairs. We used 6,084 genes with both TF annotation and co-expression information, and matched them into 273,458 pairs with similar Hi-C interaction ranks in different cell types. The results illustrate that co-expression is strongly associated with chromatin interaction. Further analysis using GO annotation reveals potential correlation between gene function similarity, Hi-C interaction and their co-expression. Conclusions According to the results in this research, the intra-chromatin interactome may have relation to gene function and associate with co-expression. This study provides evidence for illustrating the effect of transcriptional interactome on transcription regulation. PMID:21156067

  16. 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

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

    PubMed Central

    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. PMID:24367097

  18. Chimeras of Channelrhodopsin-1 and -2 from Chlamydomonas reinhardtii Exhibit Distinctive Light-induced Structural Changes from Channelrhodopsin-2*

    PubMed Central

    Inaguma, Asumi; Tsukamoto, Hisao; Kato, Hideaki E.; Kimura, Tetsunari; Ishizuka, Toru; Oishi, Satomi; Yawo, Hiromu; Nureki, Osamu; Furutani, Yuji

    2015-01-01

    Channelrhodopsin-2 (ChR2) from the green alga Chlamydomonas reinhardtii functions as a light-gated cation channel that has been developed as an optogenetic tool to stimulate specific nerve cells in animals and control their behavior by illumination. The molecular mechanism of ChR2 has been extensively studied by a variety of spectroscopic methods, including light-induced difference Fourier transform infrared (FTIR) spectroscopy, which is sensitive to structural changes in the protein upon light activation. An atomic structure of channelrhodopsin was recently determined by x-ray crystallography using a chimera of channelrhodopsin-1 (ChR1) and ChR2. Electrophysiological studies have shown that ChR1/ChR2 chimeras are less desensitized upon continuous illumination than native ChR2, implying that there are some structural differences between ChR2 and chimeras. In this study, we applied light-induced difference FTIR spectroscopy to ChR2 and ChR1/ChR2 chimeras to determine the molecular basis underlying these functional differences. Upon continuous illumination, ChR1/ChR2 chimeras exhibited structural changes distinct from those in ChR2. In particular, the protonation state of a glutamate residue, Glu-129 (Glu-90 in ChR2 numbering), in the ChR chimeras is not changed as dramatically as in ChR2. Moreover, using mutants stabilizing particular photointermediates as well as time-resolved measurements, we identified some differences between the major photointermediates of ChR2 and ChR1/ChR2 chimeras. Taken together, our data indicate that the gating and desensitizing processes in ChR1/ChR2 chimeras are different from those in ChR2 and that these differences should be considered in the rational design of new optogenetic tools based on channelrhodopsins. PMID:25796616

  19. 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. PMID:24367097

  20. 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.

  1. 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

  2. [Light-induced production and consumption of oxygen by chloroplasts: activation and inhibition].

    PubMed

    Chan Van, N i; Nikandrov, V V; Brin, G P; Krasnovskii, A A

    1977-07-01

    Light-induced production and consumption of oxygen by pea chloroplasts are activated at certain concentrations of the solvents (diethyl ester, methyl alcohol, dimethylsulfoxide) and detergent Triton X-100. At higher concentrations of the compounds studied both reactions are inhibited. The uncouplers (methylamine and carbonyl cyanide-3-chlorophenylhydrazone) activate these processes. The agents studied have a similar effect on the processes of light-induced production and consumption of oxygen, which are limited by a common link bound to the phosphorylation site in photosystem I. The effects observed suggest that the inhibition may be due to inhibition of photosystem II, whereas the activation may be largely due to an action on photosystem I. PMID:907797

  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. 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.

  5. Ab initio investigation of light-induced relativistic spin-flip effects in magneto-optics

    NASA Astrophysics Data System (ADS)

    Mondal, Ritwik; Berritta, Marco; Carva, Karel; Oppeneer, Peter M.

    2015-05-01

    Excitation of a metallic ferromagnet such as Ni with an intensive femtosecond laser pulse causes an ultrafast demagnetization within approximately 300 fs. It was proposed that the ultrafast demagnetization measured in femtosecond magneto-optical experiments could be due to relativistic light-induced processes. We perform an ab initio investigation of the influence of relativistic effects on the magneto-optical response of Ni. To this end, first, we develop a response theory formulation of the additional appearing ultrarelativistic terms in the Foldy-Wouthuysen transformed Dirac Hamiltonian due to the electromagnetic field, and second, we compute the influence of relativistic light-induced spin-flip transitions on the magneto-optics. Our ab initio calculations of relativistic spin-flip optical excitations predict that these can give only a very small contribution (≤0.1 %) to the laser-induced magnetization change in Ni.

  6. Light-induced cross transport phenomena in a single-component gas

    SciTech Connect

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

    2013-07-15

    The cross transport processes that occur in a single-component gas in a capillary and are caused by resonance laser radiation and pressure and temperature gradients are studied. An expression for entropy production is derived using a system of kinetic Boltzmann equations in a linear approximation. The kinetic coefficients that determine the transport processes are shown to satisfy the Onsager reciprocal relations at any Knudsen numbers and any character of the elastic interaction of gas particles with the capillary surface. The light-induced baro- and thermoeffects that take place in a closed heat-insulated system in the field of resonance laser radiation are considered. Analytical expressions are obtained for the Onsager coefficients in an almost free-molecular regime. The light-induced pressure and temperature gradients that appear in a closed heat-insulated capillary under typical experimental conditions are numerically estimated.

  7. Light-induced Changes of the Carotenoid Levels in Chloroplast Envelopes 1

    PubMed Central

    Siefermann-Harms, Dorothea; Joyard, Jacques; Douce, Roland

    1978-01-01

    The carotenoid content of thylakoids and envelopes isolated from dark-or light-treated spinach (Spinacia oleracea L.) chloroplasts was compared. In thylakoids, light induced a decrease of violaxanthin parallel with a stoichiometric increase of zeaxanthin due to violaxanthin deepoxidation. In envelopes, violaxanthin was also decreased and the relative decrease was similar to thylakoids, but zeaxanthin increase was small resulting in an over-all decrease of the amount of envelope carotenoids. When violaxanthin deepoxidation in thylakoids was partly inhibited by 10 nm nigericin, violaxanthin decrease in the envelope was inhibited to a similar degree. These observations together with the absence of deepoxidase activity in isolated envelopes plus added stroma proteins suggest that light-induced violaxanthin decrease in the envelope is not caused by an envelope or stroma deepoxidase but results from violaxanthin exchange between envelope and thylakoids. PMID:16660330

  8. 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

  9. Nucleolin: dual roles in rDNA chromatin transcription.

    PubMed

    Durut, Nathalie; Sáez-Vásquez, Julio

    2015-02-01

    Nucleolin is a major nucleolar protein conserved in all eukaryotic organisms. It is a multifunctional protein involved in different cellular aspects like chromatin organization and stability, DNA and RNA metabolism, assembly of ribonucleoprotein complexes, cytokinesis, cell proliferation and stress response. The multifunctionality of nucleolin is linked to its tripartite structure, post-translational modifications and its ability of shuttling from and to the nucleolus/nucleoplasm and cytoplasm. Nucleolin has been now studied for many years and its activities and properties have been described in a number of excellent reviews. Here, we overview the role of nucleolin in RNA polymerase I (RNAPI) transcription and describe recent results concerning its functional interaction with rDNA chromatin organization. For a long time, nucleolin has been associated with rRNA gene expression and pre-rRNA processing. However, the functional connection between nucleolin and active versus inactive rRNA genes is still not fully understood. Novel evidence indicates that the nucleolin protein might be required for controlling the transcriptional ON/OFF states of rDNA chromatin in both mammals and plants. PMID:25225127

  10. Changing Chromatin Fiber Conformation by Nucleosome Repositioning

    PubMed Central

    Müller, Oliver; Kepper, Nick; Schöpflin, Robert; Ettig, Ramona; Rippe, Karsten; Wedemann, Gero

    2014-01-01

    Chromatin conformation is dynamic and heterogeneous with respect to nucleosome positions, which can be changed by chromatin remodeling complexes in the cell. These molecular machines hydrolyze ATP to translocate or evict nucleosomes, and establish loci with regularly and more irregularly spaced nucleosomes as well as nucleosome-depleted regions. The impact of nucleosome repositioning on the three-dimensional chromatin structure is only poorly understood. Here, we address this issue by using a coarse-grained computer model of arrays of 101 nucleosomes considering several chromatin fiber models with and without linker histones, respectively. We investigated the folding of the chain in dependence of the position of the central nucleosome by changing the length of the adjacent linker DNA in basepair steps. We found in our simulations that these translocations had a strong effect on the shape and properties of chromatin fibers: i), Fiber curvature and flexibility at the center were largely increased and long-range contacts between distant nucleosomes on the chain were promoted. ii), The highest destabilization of the fiber conformation occurred for a nucleosome shifted by two basepairs from regular spacing, whereas effects of linker DNA changes of ∼10 bp in phase with the helical twist of DNA were minimal. iii), A fiber conformation can stabilize a regular spacing of nucleosomes inasmuch as favorable stacking interactions between nucleosomes are facilitated. This can oppose nucleosome translocations and increase the energetic costs for chromatin remodeling. Our computational modeling framework makes it possible to describe the conformational heterogeneity of chromatin in terms of nucleosome positions, and thus advances theoretical models toward a better understanding of how genome compaction and access are regulated within the cell. PMID:25418099

  11. 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…

  12. Involvement of All-trans-retinal in Acute Light-induced Retinopathy of Mice*S⃞

    PubMed Central

    Maeda, Akiko; Maeda, Tadao; Golczak, Marcin; Chou, Steven; Desai, Amar; Hoppel, Charles L.; Matsuyama, Shigemi; Palczewski, Krzysztof

    2009-01-01

    Exposure to bright light can cause visual dysfunction and retinal photoreceptor damage in humans and experimental animals, but the mechanism(s) remain unclear. We investigated whether the retinoid cycle (i.e. the series of biochemical reactions required for vision through continuous generation of 11-cis-retinal and clearance of all-trans-retinal, respectively) might be involved. Previously, we reported that mice lacking two enzymes responsible for clearing all-trans-retinal, namely photoreceptor-specific ABCA4 (ATP-binding cassette transporter 4) and RDH8 (retinol dehydrogenase 8), manifested retinal abnormalities exacerbated by light and associated with accumulation of diretinoid-pyridinium-ethanolamine (A2E), a condensation product of all-trans-retinal and a surrogate marker for toxic retinoids. Now we show that these mice develop an acute, light-induced retinopathy. However, cross-breeding these animals with lecithin:retinol acyltransferase knock-out mice lacking retinoids within the eye produced progeny that did not exhibit such light-induced retinopathy until gavaged with the artificial chromophore, 9-cis-retinal. No significant ocular accumulation of A2E occurred under these conditions. These results indicate that this acute light-induced retinopathy requires the presence of free all-trans-retinal and not, as generally believed, A2E or other retinoid condensation products. Evidence is presented that the mechanism of toxicity may include plasma membrane permeability and mitochondrial poisoning that lead to caspase activation and mitochondria-associated cell death. These findings further understanding of the mechanisms involved in light-induced retinal degeneration. PMID:19304658

  13. Catalyst free visible light induced cycloaddition as an avenue for polymer ligation.

    PubMed

    Lederhose, Paul; Wüst, Kilian N R; Barner-Kowollik, Christopher; Blinco, James P

    2016-05-21

    The current study introduces a tetrazole species able to perform a rapid, visible light induced nitrile imine-mediated tetrazole-ene cycloaddition (NITEC). Full conversion of the tetrazole species under mild, catalyst free conditions is reported. Importantly, the visible light ligation technology is applied as a method for the modification and ligation of polymers featuring the rapid, clean and exclusive formation of the desired cycloadduct. PMID:27004740

  14. Light-induced changes in the absorption spectrum of bacteriorhodopsin under two-wavelength excitation

    NASA Astrophysics Data System (ADS)

    Koklyushkin, A. V.; Korolev, A. E.

    2004-09-01

    The results of spectrophotometric measurements of nonlinear light-induced changes in the absorption spectrum of bacteriorhodopsin D96N occurring upon simultaneous excitation at the wavelengths 633 and 441 nm in the excitation intensity range typical for recording of dynamic holograms are presented. The quantitative conditions under which the action of the radiation at one wavelength reduces the change in the optical density caused by the radiation at the other wavelength are determined.

  15. 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.

  16. 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

  17. 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.

  18. Visible-Light-Induced Specific Desulfurization of Cysteinyl Peptide and Glycopeptide in Aqueous Solution.

    PubMed

    Gao, Xiao-Fei; Du, Jing-Jing; Liu, Zheng; Guo, Jun

    2016-03-01

    Visible-light-induced specific desulfurization of cysteinyl peptides has been explored. The photocatalytic desulfurization catalyzed by Ru(bpy)3(2+) can proceed efficiently at room temperature in aqueous solution or in binary mixtures of aqueous/organic solvent and be compatible with the presence of residues of amino acids, carbohydrates, and various sulfur-containing functional groups. This approach was successfully applied to synthesize linear and cyclic peptides through the ligation-desulfurization protocol. PMID:26892036

  19. Hysteresis upon light-induced hydrodynamic reorientation of the director of a nematic liquid crystal

    SciTech Connect

    Akopyan, R S; Alaverdyan, R B; Vardanyan, A S; Chilingaryan, Yu S

    2000-08-31

    Oscillations and hysteresis in the behaviour of the director of a nematic liquid crystal were observed upon its light-induced hydrodynamic reorientation caused by direct volume expansion. The light propagated through the liquid crystal placed between crossed polarisers provides the feedback. This light falls back on the liquid crystal and is absorbed by producing the volume expansion. A theory is suggested that describes the observed behaviour of the director of the nematic liquid crystal. (laser applications and other topics in quantum electronics)

  20. Spatial Symmetry Breaking in the Belousov-Zhabotinsky Reaction with Light-Induced Remote Communication

    SciTech Connect

    Hildebrand, M.; Skodt, H.; Showalter, K.

    2001-08-20

    Domains containing spiral waves form on a stationary background in a photosensitive Belousov-Zhabotinsky reaction with light-induced alternating nonlocal feedback. Complex behavior of colliding and splitting wave fragments is found with feedback radii comparable to the spiral wavelength. A linear stability analysis of the uniform stationary states in an Oregonator model reveals a spatial symmetry breaking instability. Numerical simulations show behavior in agreement with that found experimentally and also predict a variety of other new patterns.

  1. Ambient temperature catalyst-free light-induced preparation of macrocyclic aliphatic polyesters.

    PubMed

    Josse, Thomas; Altintas, Ozcan; Oehlenschlaeger, Kim K; Dubois, Philippe; Gerbaux, Pascal; Coulembier, Olivier; Barner-Kowollik, Christopher

    2014-02-25

    The light induced, catalyst-free ambient temperature preparation of macrocyclic aliphatic polyesters is pioneered. Based on the photo-induced Diels-Alder reaction of orthoquinodimethane and acrylate moieties, cyclic polyesters of high purity are readily synthesized. Considering the high tolerance to functional groups and the orthogonality of the ligation, the reported protocol can be easily transferred to a large range of polymers, complex topologies (tadpole, sun-shaped, jellyfish, etc.) and applications. PMID:24413149

  2. The chromatin scaffold protein SAFB1 renders chromatin permissive for DNA damage signaling.

    PubMed

    Altmeyer, Matthias; Toledo, Luis; Gudjonsson, Thorkell; Grøfte, Merete; Rask, Maj-Britt; Lukas, Claudia; Akimov, Vyacheslav; Blagoev, Blagoy; Bartek, Jiri; Lukas, Jiri

    2013-10-24

    Although the general relevance of chromatin modifications for genotoxic stress signaling, cell-cycle checkpoint activation, and DNA repair is well established, how these modifications reach initial thresholds in order to trigger robust responses remains largely unexplored. Here, we identify the chromatin-associated scaffold attachment factor SAFB1 as a component of the DNA damage response and show that SAFB1 cooperates with histone acetylation to allow for efficient γH2AX spreading and genotoxic stress signaling. SAFB1 undergoes a highly dynamic exchange at damaged chromatin in a poly(ADP-ribose)-polymerase 1- and poly(ADP-ribose)-dependent manner and is required for unperturbed cell-cycle checkpoint activation and guarding cells against replicative stress. Altogether, our data reveal that transient recruitment of an architectural chromatin component is required in order to overcome physiological barriers by making chromatin permissive for DNA damage signaling, whereas the ensuing exclusion of SAFB1 may help prevent excessive signaling. PMID:24055346

  3. Light-induced processes on atoms and clusters confined in nanoporous silica and organic films

    NASA Astrophysics Data System (ADS)

    Moi, L.; Burchianti, A.; Bogi, A.; Marinelli, C.; Maibohm, C.; Mariotti, E.

    2007-03-01

    The study of light induced processes on atoms and nanoparticles confined in organic films or in dielectric structures is motivated both by fundamental interest and applications in optics and photonics. Depending on the light intensity and frequency and the kind of confinement, different processes can be activated. Among them photodesorption processes have a key role. Non thermal light induced atomic desorption has been observed from siloxane and paraffin films previously exposed to alkali vapors. This effect has been extensively investigated and used both to develop photo-atom sources and to load magneto-optical traps. Recently we observed huge photodesorption of alkali atoms embedded in nanoporous silica. In this case the atomic photodesorption causes, by properly tuning the light frequency, either formation or evaporation of clusters inside the silica matrix. Green-blue light desorbs isolated adatoms from the glass surface eventually producing clusters, whereas red-near infrared (NIR) light causes cluster evaporation due to direct excitation of surface plasmon oscillations. Green-blue light induces cluster formation taking advantage of the dense atomic vapor, which diffuses through the glass nano-cavities. Both processes are reversible and even visible to the naked eye. By alternatively illuminating the porous glass sample with blue-green and red-NIR light we demonstrate that the glass remembers the illumination sequences behaving as an effective rereadable and rewritable optical medium.

  4. Light-induced Voc increase and decrease in high-efficiency amorphous silicon solar cells

    NASA Astrophysics Data System (ADS)

    Stuckelberger, M.; Riesen, Y.; Despeisse, M.; Schüttauf, J.-W.; Haug, F.-J.; Ballif, C.

    2014-09-01

    High-efficiency amorphous silicon (a-Si:H) solar cells were deposited with different thicknesses of the p-type amorphous silicon carbide layer on substrates of varying roughness. We observed a light-induced open-circuit voltage (Voc) increase upon light soaking for thin p-layers, but a decrease for thick p-layers. Further, the Voc increase is enhanced with increasing substrate roughness. After correction of the p-layer thickness for the increased surface area of rough substrates, we can exclude varying the effective p-layer thickness as the cause of the substrate roughness dependence. Instead, we explain the observations by an increase of the dangling-bond density in both the p-layer—causing a Voc increase—and in the intrinsic absorber layer, causing a Voc decrease. We present a mechanism for the light-induced increase and decrease, justified by the investigation of light-induced changes of the p-layer and supported by Advanced Semiconductor Analysis simulation. We conclude that a shift of the electron quasi-Fermi level towards the conduction band is the reason for the observed Voc enhancements, and poor amorphous silicon quality on rough substrates enhances this effect.

  5. 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.

  6. Targeting chromatin to improve radiation response

    PubMed Central

    Olcina, M M; O'Dell, S

    2015-01-01

    Chromatin, the structure formed by the wrapping of approximately 146 base pairs of DNA around an octamer of histones, has a profound impact on numerous DNA-based processes. Chromatin modifications and chromatin remodellers have recently been implicated in important aspects of the DNA damage response including facilitating the initial sensing of the damage as well as subsequent recruitment of repair factors. Radiation is an effective cancer therapy for a large number of tumours, and there is considerable interest in finding approaches that might further increase the efficacy of radiotherapy. The use of radiation leads to the generation of DNA damage and, therefore, agents that can affect the sensing and repair of DNA damage may have an impact on overall radiation efficacy. The chromatin modifications as well as chromatin modifiers that have been associated with the DNA damage response will be summarized in this review. An emphasis will be placed on those processes that can be pharmacologically manipulated with currently available inhibitors. The rationale for the use of these inhibitors in combination with radiation will also be described. PMID:25513745

  7. PROTOCOLS: Chromatin Immunoprecipitation from Arabidopsis Tissues

    PubMed Central

    Yamaguchi, Nobutoshi; Winter, Cara M.; Wu, Miin-Feng; Kwon, Chang Seob; William, Dilusha A.; Wagner, Doris

    2014-01-01

    The ability of proteins to associate with genomic DNA in the context of chromatin is critical for many nuclear processes including transcription, replication, recombination, and DNA repair. Chromatin immunoprecipication (ChIP) is a practical and useful technique for characterizing protein / DNA association in vivo. The procedure generally includes six steps: (1) crosslinking the protein to the DNA; (2) isolating the chromatin; (3) chromatin fragmentation; (4) imunoprecipitation with antibodies against the protein of interest; (5) DNA recovery; and (6) PCR identification of factor associated DNA sequences. In this protocol, we describe guidelines, experimental setup, and conditions for ChIP in intact Arabidopsis tissues. This protocol has been used to study association of histone modifications, of chromatin remodeling ATPases, as well as of sequence-specific transcription factors with the genomic DNA in various Arabidopsis thaliana tissues. The protocol described focuses on ChIP-qPCR, but can readily be adapted for use in ChIP-chip or ChIP-seq experiments. The entire procedure can be completed within 3 days. PMID:24653666

  8. 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

  9. 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

  10. NuMA Influences Higher Order Chromatin Organization in Human Mammary Epithelium

    PubMed Central

    Abad, Patricia C.; Lewis, Jason; Mian, I. Saira; Knowles, David W.; Sturgis, Jennifer; Badve, Sunil; Xie, Jun

    2007-01-01

    The coiled-coil protein NuMA is an important contributor to mitotic spindle formation and stabilization. A potential role for NuMA in nuclear organization or gene regulation is suggested by the observations that its pattern of nuclear distribution depends upon cell phenotype and that it interacts and/or colocalizes with transcription factors. To date, the precise contribution of NuMA to nuclear function remains unclear. Previously, we observed that antibody-induced alteration of NuMA distribution in growth-arrested and differentiated mammary epithelial structures (acini) in three-dimensional culture triggers the loss of acinar differentiation. Here, we show that in mammary epithelial cells, NuMA is present in both the nuclear matrix and chromatin compartments. Expression of a portion of the C terminus of NuMA that shares sequence similarity with the chromatin regulator HPC2 is sufficient to inhibit acinar differentiation and results in the redistribution of NuMA, chromatin markers acetyl-H4 and H4K20m, and regions of deoxyribonuclease I-sensitive chromatin compared with control cells. Short-term alteration of NuMA distribution with anti-NuMA C-terminus antibodies in live acinar cells indicates that changes in NuMA and chromatin organization precede loss of acinar differentiation. These findings suggest that NuMA has a role in mammary epithelial differentiation by influencing the organization of chromatin. PMID:17108325

  11. Light-induced pH changes in the intact retinae of normal and early diabetic rats.

    PubMed

    Dmitriev, Andrey V; Henderson, Desmond; Linsenmeier, Robert A

    2016-04-01

    Double-barreled H(+)-selective microelectrodes were used to measure local extracellular concentration of H(+) ([H(+)]o) in the retina of dark-adapted anesthetized Long-Evans rats. The microelectrode advanced in steps of 30 μm throughout the retina from the vitreal surface to retinal pigment epithelium and then to the choroid, recording changes in [H(+)]o evoked by light stimulation. Recordings were performed in diabetic rats 1-3 months after intraperitoneal injection of streptozotocin and the results were compared with data obtained in age-matched control animals. Brief light stimulation (2.5 s) evoked changes of [H(+)]o with amplitudes of a few nM. Throughout the retina, there was a transient initial acidification for ∼200 ms followed by steady alkalinization, although amplitudes and kinetics of these components were slightly variable in different retinal layers. No significant difference was found when the light-induced [H(+)]o changes recorded in various retinal layers of early diabetic rats were compared with the [H(+)]o changes from corresponding layers of control animals. Also, when H(+)-selective microelectrodes were located in the retinal pigment epithelium (RPE) layer, an increase in H(+) was recorded, whose time course and amplitude were similar in control and diabetic rats. However, a striking difference between light-induced [H(+)]o changes in controls and diabetics was observed in the choriocapillaris, in the thin layer (10-20 μm) distal to the basal membrane of the RPE. In control rats, choroidal [H(+)]o decreased in a few cases, but much more often practically did not change. In contrast, diabetic rats demonstrated either an increase (in half of the cases) or no change in choroidal [H(+)]o. The data suggest that the active participation of the choroidal blood supply in stabilization of [H(+)]o could be partially compromised already at early stages of diabetes in rats. Interestingly, it appeared that the acid removal by the choroidal

  12. 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. PMID:25144495

  13. 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

  14. Bacterial chromatin: converging views at different scales.

    PubMed

    Dame, Remus T; Tark-Dame, Mariliis

    2016-06-01

    Bacterial genomes are functionally organized and compactly folded into a structure referred to as bacterial chromatin or the nucleoid. An important role in genome folding is attributed to Nucleoid-Associated Proteins, also referred to as bacterial chromatin proteins. Although a lot of molecular insight in the mechanisms of operation of these proteins has been generated in the test tube, knowledge on genome organization in the cellular context is still lagging behind severely. Here, we discuss important advances in the understanding of three-dimensional genome organization due to the application of Chromosome Conformation Capture and super-resolution microscopy techniques. We focus on bacterial chromatin proteins whose proposed role in genome organization is supported by these approaches. Moreover, we discuss recent insights into the interrelationship between genome organization and genome activity/stability in bacteria. PMID:26942688

  15. 4D chromatin dynamics in cycling cells

    PubMed Central

    Strickfaden, Hilmar; Zunhammer, Andreas; van Koningsbruggen, Silvana; Köhler, Daniela

    2010-01-01

    This live cell study of chromatin dynamics in four dimensions (space and time) in cycling human cells provides direct evidence for three hypotheses first proposed by Theodor Boveri in seminal studies of fixed blastomeres from Parascaris equorum embryos: (I) Chromosome territory (CT) arrangements are stably maintained during interphase. (II) Chromosome proximity patterns change profoundly during prometaphase. (III) Similar CT proximity patterns in pairs of daughter nuclei reflect symmetrical chromosomal movements during anaphase and telophase, but differ substantially from the arrangement in mother cell nucleus. Hypothesis I could be confirmed for the majority of interphase cells. A minority, however, showed complex, rotational movements of CT assemblies with large-scale changes of CT proximity patterns, while radial nuclear arrangements were maintained. A new model of chromatin dynamics is proposed. It suggests that long-range DNA-DNA interactions in cell nuclei may depend on a combination of rotational CT movements and locally constrained chromatin movements. PMID:21327076

  16. 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

  17. 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

  18. Open chromatin reveals the functional maize genome.

    PubMed

    Rodgers-Melnick, Eli; Vera, Daniel L; Bass, Hank W; Buckler, Edward S

    2016-05-31

    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

  19. 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

  20. 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.

  1. [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

  2. 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

  3. Linker Histones Incorporation Maintains Chromatin Fiber Plasticity

    PubMed Central

    Recouvreux, Pierre; Lavelle, Christophe; Barbi, Maria; Conde e Silva, Natalia; Le Cam, Eric; Victor, Jean-Marc; Viovy, Jean-Louis

    2011-01-01

    Genomic DNA in eukaryotic cells is organized in supercoiled chromatin fibers, which undergo dynamic changes during such DNA metabolic processes as transcription or replication. Indeed, DNA-translocating enzymes like polymerases produce physical constraints in vivo. We used single-molecule micromanipulation by magnetic tweezers to study the response of chromatin to mechanical constraints in the same range as those encountered in vivo. We had previously shown that under positive torsional constraints, nucleosomes can undergo a reversible chiral transition toward a state of positive topology. We demonstrate here that chromatin fibers comprising linker histones present a torsional plasticity similar to that of naked nucleosome arrays. Chromatosomes can undergo a reversible chiral transition toward a state of positive torsion (reverse chromatosome) without loss of linker histones. PMID:21641318

  4. Nucleosome dynamics during chromatin remodeling in vivo.

    PubMed

    Ramachandran, Srinivas; Henikoff, Steven

    2016-01-01

    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

  5. 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

  6. 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

  7. 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.

  8. Chromatin Compaction Protects Genomic DNA from Radiation Damage

    PubMed Central

    Takata, Hideaki; Hanafusa, Tomo; Mori, Toshiaki; Shimura, Mari; Iida, Yutaka; Ishikawa, Kenichi; Yoshikawa, Kenichi; Yoshikawa, Yuko; Maeshima, Kazuhiro

    2013-01-01

    Genomic DNA is organized three-dimensionally in the nucleus, and is thought to form compact chromatin domains. Although chromatin compaction is known to be essential for mitosis, whether it confers other advantages, particularly in interphase cells, remains unknown. Here, we report that chromatin compaction protects genomic DNA from radiation damage. Using a newly developed solid-phase system, we found that the frequency of double-strand breaks (DSBs) in compact chromatin after ionizing irradiation was 5–50-fold lower than in decondensed chromatin. Since radical scavengers inhibited DSB induction in decondensed chromatin, condensed chromatin had a lower level of reactive radical generation after ionizing irradiation. We also found that chromatin compaction protects DNA from attack by chemical agents. Our findings suggest that genomic DNA compaction plays an important role in maintaining genomic integrity. PMID:24130727

  9. Chromatin higher-order structures and gene regulation

    PubMed Central

    Li, Guohong

    2011-01-01

    Genomic DNA in the eukaryotic nucleus is hierarchically packaged by histones into chromatin to fit inside the nucleus. The dynamics of higher-order chromatin compaction play a critical role in transcription and other biological processes inherent to DNA. Many factors, including histone variants, histone modifications, DNA methylation and the binding of non-histone architectural proteins regulate the structure of chromatin. Although the structure of nucleosomes, the fundamental repeating unit of chromatin, is clear, there is still much discussion on the higher-order levels of chromatin structure. In this review, we focus on the recent progress in elucidating the structure of the 30-nm chromatin fiber. We also discuss the structural plasticity/dynamics and epigenetic inheritance of higher-order chromatin and the roles of chromatin higher-order organization in eukaryotic gene regulation. PMID:21342762

  10. Light induced anisotropy and gyrotropy in the media on the basis of azo indicators

    NASA Astrophysics Data System (ADS)

    Shaverdova, Valentina; Petrova, Svetlana; Purtseladze, Anna; Tarasashvili, Lado; Obolashvili, Nino

    2011-02-01

    Azo indicators are well known in which when changing acidity they changes their properties. It was natural to expect also their appreciable changes of their polarization properties. The results of the carried out experimental research in recording media on the basis of azo indicators- homolog of the Methyl orange introduced into the polymeric matrix are presented in this work. According to the technology developed by us, the samples for the reception of which solvents with various degree of acidity, within values pH 1.68-12.45 have been created. Samples were irradiated by the light of argon laser (488 nm) actinic for them. Measurement of light induced anisotropy was carried out on a registering recorder and can be described by means of one parameter- the effective anisotropy. As standards the samples of dyes for the reception of which neutral solvent was used have been considered. In a number of dyes the values of effective anisotropy in alkaline and acid media exceed its values concerning corresponding standards. The higher homolog -Heptyl orange and Benzyl orange which are weak or insoluble in water, become water-soluble when using solvents both with acid and alkaline reaction. The interval of appearance of light induced anisotropy has been expanded. We have used the method of the zero-ellipsometry for the research arising in the same samples light induced gyrotropy. Values of circular dichroism and circular birefringence in investigated layers in neutral media have been calculated also at various values pH. In the work the received results are discussed and analyzed.

  11. 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

  12. Light-induced membrane potential and pH gradient in Halobacterium halobium envelope vesicles.

    PubMed

    Renthal, R; Lanyi, J K

    1976-05-18

    Illumination of envelope vesicles prepared from Halobacterium halobium cells causes translocation of protons from inside to outside, due to the light-induced cycling of bacteriorhodopsin. This process results in a pH gradient across the membranes, an electrical potential, and the movements of K+ and Na+. The electrical potential was estimated by following the fluorescence of a cyanine dye, 3,3'-dipentyloxadicarbocyanine. Illumination of H. halobium vesicles resulted in a rapid, reversible decrease of the dye fluorescence, by as much as 35%. This effect was not seen in nonvesicular patches of purple membrane. Observation of maximal fluorescence decreases upon ilumination of vesicles required an optimal dye/membrane protein ratio. The pH optimum for the lightinduced fluorescence decrease was 6.0. The decrease was linear with actinic light intensity up to about 4 X 10(5) ergs cn-2 s-1. Valinomycin, gramicidin, and triphenylmethylphosphonium ion all abolished the fluorescence changes. However, the light-induced pH change was enhanced by these agents. Conversely, buffered vesicles showed no pH change but gave the same or larger fluorescence changes. Thus, we have identified the fluorescence decrease with a light-induced membrane potential, inside negative. By using valinomycin-K+-induced membrane potentials, we calibrated the fluorescence decrease with calculated Nernst diffusion potentials. We found a linear dependence between potential and fluorescence decrease of 3 mV/%, up to 90 mV. When the envelope vesicles were illuminated, the total proton-motive force generated was dependent on the presence of Na+ and K+ and their concentration gradients across the membrane. In general, K+ appeared to be more permeable than Na+ and, thus, permitted development of greater pH gradients and lower electrical potentials. By calculating the total proton-motive force from the sum of the pH and potential terms, we found that the vesicles can produce proton-motive forces near--200 m

  13. 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. PMID:26213307

  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. Chromosomes without a 30-nm chromatin fiber

    PubMed Central

    Joti, Yasumasa; Hikima, Takaaki; Nishino, Yoshinori; Kamada, Fukumi; Hihara, Saera; Takata, Hideaki; Ishikawa, Tetsuya; Maeshima, Kazuhiro

    2012-01-01

    How is a long strand of genomic DNA packaged into a mitotic chromosome or nucleus? The nucleosome fiber (beads-on-a-string), in which DNA is wrapped around core histones, has long been assumed to be folded into a 30-nm chromatin fiber, and a further helically folded larger fiber. However, when frozen hydrated human mitotic cells were observed using cryoelectron microscopy, no higher-order structures that included 30-nm chromatin fibers were found. To investigate the bulk structure of mitotic chromosomes further, we performed small-angle X-ray scattering (SAXS), which can detect periodic structures in noncrystalline materials in solution. The results were striking: no structural feature larger than 11 nm was detected, even at a chromosome-diameter scale (~1 μm). We also found a similar scattering pattern in interphase nuclei of HeLa cells in the range up to ~275 nm. Our findings suggest a common structural feature in interphase and mitotic chromatins: compact and irregular folding of nucleosome fibers occurs without a 30-nm chromatin structure. PMID:22825571

  16. Chromatin-modifying and -remodeling complexes.

    PubMed

    Kornberg, R D; Lorch, Y

    1999-04-01

    Nucleosomes have long been known to inhibit DNA transactions on chromosomes and a remarkable abundance of multiprotein complexes that either enhance or relieve this inhibition have been described. Most is known about chromatin-remodeling complexes that perturb nucleosome structure. PMID:10322131

  17. Monte Carlo simulation of chromatin stretching.

    PubMed

    Aumann, Frank; Lankas, Filip; Caudron, Maïwen; Langowski, Jörg

    2006-04-01

    We present Monte Carlo (MC) simulations of the stretching of a single chromatin fiber. The model approximates the DNA by a flexible polymer chain with Debye-Hückel electrostatics and uses a two-angle zigzag model for the geometry of the linker DNA connecting the nucleosomes. The latter are represented by flat disks interacting via an attractive Gay-Berne potential. Our results show that the stiffness of the chromatin fiber strongly depends on the linker DNA length. Furthermore, changing the twisting angle between nucleosomes from 90 degrees to 130 degrees increases the stiffness significantly. An increase in the opening angle from 22 degrees to 34 degrees leads to softer fibers for small linker lengths. We observe that fibers containing a linker histone at each nucleosome are stiffer compared to those without the linker histone. The simulated persistence lengths and elastic moduli agree with experimental data. Finally, we show that the chromatin fiber does not behave as an isotropic elastic rod, but its rigidity depends on the direction of deformation: Chromatin is much more resistant to stretching than to bending. PMID:16711856

  18. Monte Carlo simulation of chromatin stretching

    NASA Astrophysics Data System (ADS)

    Aumann, Frank; Lankas, Filip; Caudron, Maïwen; Langowski, Jörg

    2006-04-01

    We present Monte Carlo (MC) simulations of the stretching of a single 30nm chromatin fiber. The model approximates the DNA by a flexible polymer chain with Debye-Hückel electrostatics and uses a two-angle zigzag model for the geometry of the linker DNA connecting the nucleosomes. The latter are represented by flat disks interacting via an attractive Gay-Berne potential. Our results show that the stiffness of the chromatin fiber strongly depends on the linker DNA length. Furthermore, changing the twisting angle between nucleosomes from 90° to 130° increases the stiffness significantly. An increase in the opening angle from 22° to 34° leads to softer fibers for small linker lengths. We observe that fibers containing a linker histone at each nucleosome are stiffer compared to those without the linker histone. The simulated persistence lengths and elastic moduli agree with experimental data. Finally, we show that the chromatin fiber does not behave as an isotropic elastic rod, but its rigidity depends on the direction of deformation: Chromatin is much more resistant to stretching than to bending.

  19. EBV latency types adopt alternative chromatin conformations.

    PubMed

    Tempera, Italo; Klichinsky, Michael; Lieberman, Paul M

    2011-07-01

    Epstein-Barr Virus (EBV) can establish latent infections with distinct gene expression patterns referred to as latency types. These different latency types are epigenetically stable and correspond to different promoter utilization. Here we explore the three-dimensional conformations of the EBV genome in different latency types. We employed Chromosome Conformation Capture (3C) assay to investigate chromatin loop formation between the OriP enhancer and the promoters that determine type I (Qp) or type III (Cp) gene expression. We show that OriP is in close physical proximity to Qp in type I latency, and to Cp in type III latency. The cellular chromatin insulator and boundary factor CTCF was implicated in EBV chromatin loop formation. Combining 3C and ChIP assays we found that CTCF is physically associated with OriP-Qp loop formation in type I and OriP-Cp loop formation in type III latency. Mutations in the CTCF binding site located at Qp disrupt loop formation between Qp and OriP, and lead to the activation of Cp transcription. Mutation of the CTCF binding site at Cp, as well as siRNA depletion of CTCF eliminates both OriP-associated loops, indicating that CTCF plays an integral role in loop formation. These data indicate that epigenetically stable EBV latency types adopt distinct chromatin architectures that depend on CTCF and mediate alternative promoter targeting by the OriP enhancer. PMID:21829357

  20. Chromatin organization of gammaherpesvirus latent genomes.

    PubMed

    Tempera, Italo; Lieberman, Paul M

    2010-01-01

    The gammaherpesviruses are a subclass of the herpesvirus family that establish stable latent infections in proliferating lymphoid and epithelial cells. The latent genomes are maintained as multicopy chromatinized episomes that replicate in synchrony with the cellular genome. Importantly, most of the episomes do not integrate into the host chromosome. Therefore, it is essential that the viral "minichromosome" establish a chromatin structure that is suitable for gene expression, DNA replication, and chromosome segregation. Evidence suggests that chromatin organization is important for each of these functions and plays a regulatory role in the establishment and maintenance of latent infection. Here, we review recent studies on the chromatin organization of the human gammaherpesviruses, Epstein-Barr virus (EBV) and Kaposi's sarcoma-associated herpesvirus (KSHV). We discuss the potential role of viral origins of DNA replication and viral encoded origin-binding proteins like EBNA1 and LANA in establishment of viral chromosome organization during latent infection. We also discuss the roles of host cell factors, like CTCF and cohesins, that contribute to higher-order chromosome structures that may be important for stable gene expression programs during latent infection in proliferating cells. PMID:19853673

  1. 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.

  2. Chromatin remodeling effects on enhancer activity.

    PubMed

    García-González, Estela; Escamilla-Del-Arenal, Martín; Arzate-Mejía, Rodrigo; Recillas-Targa, Félix

    2016-08-01

    During organism development, a diversity of cell types emerges with disparate, yet stable profiles of gene expression with distinctive cellular functions. In addition to gene promoters, the genome contains enhancer regulatory sequences, which are implicated in cellular specialization by facilitating cell-type and tissue-specific gene expression. Enhancers are DNA binding elements characterized by highly sophisticated and various mechanisms of action allowing for the specific interaction of general and tissue-specific transcription factors (TFs). However, eukaryotic organisms package their genetic material into chromatin, generating a physical barrier for TFs to interact with their cognate sequences. The ability of TFs to bind DNA regulatory elements is also modulated by changes in the chromatin structure, including histone modifications, histone variants, ATP-dependent chromatin remodeling, and the methylation status of DNA. Furthermore, it has recently been revealed that enhancer sequences are also transcribed into a set of enhancer RNAs with regulatory potential. These interdependent processes act in the context of a complex network of chromatin interactions, which together contributes to a renewed vision of how gene activation is coordinated in a cell-type-dependent manner. In this review, we describe the interplay between genetic and epigenetic aspects associated with enhancers and discuss their possible roles on enhancer function. PMID:27026300

  3. 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

  4. Dynamic creation of a light-induced terahertz guided-wave resonator.

    PubMed

    Gingras, Lauren; Blanchard, François; Georgin, Marcel; Cooke, David G

    2016-02-01

    We demonstrate a dynamic light-induced resonator for terahertz (THz) frequency light created on ultrashort time scales inside a planar waveguide. The resonator is created by patterned femtosecond photoexcitation of a one-dimensional array of photoconductive regions inside a silicon-filled parallel plate waveguide. The metal-dielectric photonic crystal is created on a 2 ps time scale, ten times faster than the 20 ps transit time of the THz light through the array. The resonance reveals itself through narrowband THz transmission enhancement with accompanying phase modulation producing an induced group delay of up to 10.8 ps near resonance. PMID:26906824

  5. 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.

  6. 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.

  7. 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.

  8. 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

  9. 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.

  10. Visible-Light-Induced Decarboxylative Functionalization of Carboxylic Acids and Their Derivatives.

    PubMed

    Xuan, Jun; Zhang, Zhao-Guo; Xiao, Wen-Jing

    2015-12-21

    Visible-light-induced radical decarboxylative functionalization of carboxylic acids and their derivatives has recently received considerable attention as a novel and efficient method to create CC and CX bonds. Generally, this visible-light-promoted decarboxylation process can smoothly occur under mild reaction conditions with a broad range of substrates and an excellent functional-group tolerance. The radical species formed from the decarboxylation step can participate in not only single photocatalytic transformations, but also dual-catalytic cross-coupling reactions by combining photoredox catalysis with other catalytic processes. Recent advances in this research area are discussed herein. PMID:26509837

  11. Robust measurement of thin-film photovoltaic modules exhibiting light-induced transients

    NASA Astrophysics Data System (ADS)

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

    2015-09-01

    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.

  12. Guiding and confinement of light induced by optical vortex solitons in a cubic-quintic medium.

    PubMed

    Reyna, Albert S; de Araújo, Cid B

    2016-01-01

    The observation of confinement and guiding of light induced by an optical vortex soliton (OVS) in a cubic-quintic (defocusing-focusing) medium is reported. The waveguide effect induced by the bright region of the vortex beam, is mainly due to the defocusing nonlinearity that allows the guiding of a probe beam propagating inside of the OVS dark region. The experimental results are corroborated by numerical simulations based on the cubic-quintic nonlinear Schrödinger equation, showing excellent agreement. PMID:26696191

  13. 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.

  14. 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

  15. 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

  16. 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

  17. Inferential modeling of 3D chromatin structure

    PubMed Central

    Wang, Siyu; Xu, Jinbo; Zeng, Jianyang

    2015-01-01

    For eukaryotic cells, the biological processes involving regulatory DNA elements play an important role in cell cycle. Understanding 3D spatial arrangements of chromosomes and revealing long-range chromatin interactions are critical to decipher these biological processes. In recent years, chromosome conformation capture (3C) related techniques have been developed to measure the interaction frequencies between long-range genome loci, which have provided a great opportunity to decode the 3D organization of the genome. In this paper, we develop a new Bayesian framework to derive the 3D architecture of a chromosome from 3C-based data. By modeling each chromosome as a polymer chain, we define the conformational energy based on our current knowledge on polymer physics and use it as prior information in the Bayesian framework. We also propose an expectation-maximization (EM) based algorithm to estimate the unknown parameters of the Bayesian model and infer an ensemble of chromatin structures based on interaction frequency data. We have validated our Bayesian inference approach through cross-validation and verified the computed chromatin conformations using the geometric constraints derived from fluorescence in situ hybridization (FISH) experiments. We have further confirmed the inferred chromatin structures using the known genetic interactions derived from other studies in the literature. Our test results have indicated that our Bayesian framework can compute an accurate ensemble of 3D chromatin conformations that best interpret the distance constraints derived from 3C-based data and also agree with other sources of geometric constraints derived from experimental evidence in the previous studies. The source code of our approach can be found in https://github.com/wangsy11/InfMod3DGen. PMID:25690896

  18. 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

  19. 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

  20. Light-Induced Infrared Difference Spectroscopy in the Investigation of Light Harvesting Complexes.

    PubMed

    Mezzetti, Alberto

    2015-01-01

    Light-induced infrared difference spectroscopy (IR-DS) has been used, especially in the last decade, to investigate early photophysics, energy transfer and photoprotection mechanisms in isolated and membrane-bound light harvesting complexes (LHCs). The technique has the definite advantage to give information on how the pigments and the other constituents of the biological system (proteins, membranes, etc.) evolve during a given photoreaction. Different static and time-resolved approaches have been used. Compared to the application of IR-DS to photosynthetic Reaction Centers (RCs), however, IR-DS applied to LHCs is still in an almost pioneering age: very often sophisticated techniques (step-scan FTIR, ultrafast IR) or data analysis strategies (global analysis, target analysis, multivariate curve resolution) are needed. In addition, band assignment is usually more complicated than in RCs. The results obtained on the studied systems (chromatophores and RC-LHC supercomplexes from purple bacteria; Peridinin-Chlorophyll-a-Proteins from dinoflagellates; isolated LHCII from plants; thylakoids; Orange Carotenoid Protein from cyanobacteria) are summarized. A description of the different IR-DS techniques used is also provided, and the most stimulating perspectives are also described. Especially if used synergically with other biophysical techniques, light-induced IR-DS represents an important tool in the investigation of photophysical/photochemical reactions in LHCs and LHC-containing systems. PMID:26151118

  1. 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

  2. A light-induced spin crossover actuated single-chain magnet

    NASA Astrophysics Data System (ADS)

    Liu, Tao; Zheng, Hui; Kang, Soonchul; Shiota, Yoshihito; Hayami, Shinya; Mito, Masaki; Sato, Osamu; Yoshizawa, Kazunari; Kanegawa, Shinji; Duan, Chunying

    2013-11-01

    Both spin-crossover complexes and molecular nanomagnets display bistable magnetic states, potentially behaving as elementary binary units for information storage. It is a challenge to introduce spin-crossover units into molecular nanomagnets to switch the bistable state of the nanomagnets through external stimuli-tuned spin crossover. Here we report an iron(II) spin-crossover unit and paramagnetic iron(III) ions that are incorporated into a well-isolated double-zigzag chain. The chain exhibits thermally induced reversible spin-crossover and light-induced excited spin-state trapping at the iron(II) sites. Single-chain magnet behaviour is actuated accompanying the synergy between light-induced excited spin-state trapping at the iron(II) sites and ferromagnetic interactions between the photoinduced high-spin iron(II) and low-spin iron(III) ions in the chain. The result provides a strategy to switch the bistable state of molecular nanomagnets using external stimuli such as light and heat, with the potential to erase and write information at a molecular level.

  3. 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

  4. Light induced effects in a-Si:H films alloyed with sulfur

    SciTech Connect

    Yoon, J.H.; Taylor, P.C.; Yan, B.; Lee, C.H.

    1997-07-01

    Light-induced effects are studied in hydrogenated amorphous silicon-sulfur alloys (a-SiS{sub x}:H) and compared to those that exist in a-Si:H. The A-SiS{sub x}:H films were grown by decomposition of pre-mixtures of SiH{sub 4} and H{sub 2}S. The light-induced effects were monitored using electrical (dark conductivity and photoconductivity, including the constant photocurrent method [CPM]) and optical (photoluminescence) measurements and electron spin resonance. It is found that sulfur alloying results in a significant reduction in the degradation in the dark- and photo-conductivity. For an a-SiS{sub x}:H film grown with a gas mixture of H{sub 2}S/SiH{sub 4} = 0.02, there is an increase of over an order of magnitude in the dark conductivity and a small decrease in the photoconductivity after 50 hours of light soaking. The subgap deep defect density as measured by CPM increases with illumination time, following a stretched exponential to saturation. The saturated defect density is an order of magnitude higher than that observed in the annealed state.

  5. 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

  6. Light-induced degradation of perfluorocarboxylic acids in the presence of titanium dioxide.

    PubMed

    Dillert, Ralf; Bahnemann, Detlef; Hidaka, Hisao

    2007-03-01

    The UV-photon-induced degradation of heptafluorobutanoic acid was investigated in acidic aqueous solutions in the presence of titanium dioxide. Heptafluorobutanoic acid could be degraded with this photocatalyst in a light-induced reaction generating carbon dioxide and fluoride anions. Carbon dioxide evolution in a significant amount occurred only in the presence of molecular oxygen and the photocatalyst. The light-induced degradation of trifluoroacetic acid, pentafluoropropanoic acid, nonafluorobutanoic acid, pentadecafluorooctanoic acid, nonafluorobutanesulfonic acid, and heptadecafluorooctanesulfonic acid in the presence of titanium dioxide was also studied. The perfluorocarboxylic acids under investigation are degraded to generate CO(2) and fluoride anions while both perfluorinated sulfonic acids are persistent under the experimental conditions employed in this study. For all compounds photonic efficiencies of the mineralization reaction were estimated to be smaller than 1x10(-5). To increase the photocatalytic activity mixed systems containing homogeneous phosphotungstic acid and heterogeneous titanium dioxide catalysts were also investigated. In the mixtures of these two photocatalysts, the formation rate of CO(2) increased with illumination time. PMID:17126882

  7. 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

  8. Histone acetylation: a switch between repressive and permissive chromatin

    PubMed Central

    Eberharter, Anton; Becker, Peter B.

    2002-01-01

    The organization of eukaryotic chromatin has a major impact on all nuclear processes involving DNA substrates. Gene expression is affected by the positioning of individual nucleosomes relative to regulatory sequence elements, by the folding of the nucleosomal fiber into higher-order structures and by the compartmentalization of functional domains within the nucleus. Because site-specific acetylation of nucleosomal histones influences all three aspects of chromatin organization, it is central to the switch between permissive and repressive chromatin structure. The targeting of enzymes that modulate the histone acetylation status of chromatin, in synergy with the effects mediated by other chromatin remodeling factors, is central to gene regulation. PMID:11882541

  9. 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

  10. Mass Spectrometry-Based Proteomics for the Analysis of Chromatin Structure and Dynamics

    PubMed Central

    Soldi, Monica; Cuomo, Alessandro; Bremang, Michael; Bonaldi, Tiziana

    2013-01-01

    Chromatin is a highly structured nucleoprotein complex made of histone proteins and DNA that controls nearly all DNA-dependent processes. Chromatin plasticity is regulated by different associated proteins, post-translational modifications on histones (hPTMs) and DNA methylation, which act in a concerted manner to enforce a specific “chromatin landscape”, with a regulatory effect on gene expression. Mass Spectrometry (MS) has emerged as a powerful analytical strategy to detect histone PTMs, revealing interplays between neighbouring PTMs and enabling screens for their readers in a comprehensive and quantitative fashion. Here we provide an overview of the recent achievements of state-of-the-art mass spectrometry-based proteomics for the detailed qualitative and quantitative characterization of histone post-translational modifications, histone variants, and global interactomes at specific chromatin regions. This synopsis emphasizes how the advances in high resolution MS, from “Bottom Up” to “Top Down” analysis, together with the uptake of quantitative proteomics methods by chromatin biologists, have made MS a well-established method in the epigenetics field, enabling the acquisition of original information, highly complementary to that offered by more conventional, antibody-based, assays. PMID:23466885

  11. 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

  12. Chromatin signature discovery via histone modification profile alignments

    PubMed Central

    Wang, Jianrong; Lunyak, Victoria V.; Jordan, I. King

    2012-01-01

    We report on the development of an unsupervised algorithm for the genome-wide discovery and analysis of chromatin signatures. Our Chromatin-profile Alignment followed by Tree-clustering algorithm (ChAT) employs dynamic programming of combinatorial histone modification profiles to identify locally similar chromatin sub-regions and provides complementary utility with respect to existing methods. We applied ChAT to genomic maps of 39 histone modifications in human CD4+ T cells to identify both known and novel chromatin signatures. ChAT was able to detect chromatin signatures previously associated with transcription start sites and enhancers as well as novel signatures associated with a variety of regulatory elements. Promoter-associated signatures discovered with ChAT indicate that complex chromatin signatures, made up of numerous co-located histone modifications, facilitate cell-type specific gene expression. The discovery of novel L1 retrotransposon-associated bivalent chromatin signatures suggests that these elements influence the mono-allelic expression of human genes by shaping the chromatin environment of imprinted genomic regions. Analysis of long gene-associated chromatin signatures point to a role for the H4K20me1 and H3K79me3 histone modifications in transcriptional pause release. The novel chromatin signatures and functional associations uncovered by ChAT underscore the ability of the algorithm to yield novel insight on chromatin-based regulatory mechanisms. PMID:22989711

  13. Physical properties of unacetylated chromatin as examined by magnetic tweezers

    NASA Astrophysics Data System (ADS)

    McGill, Kerry; Dunlap, David; Lucchesi, John

    2011-10-01

    As the source of genetic material, DNA is involved in a variety of biological processes like transcription, cell replication, and more. In these processes, DNA is manipulated into different structures and is subjected to different levels of physical force on a molecular scale. When tension is applied to one hierarchical structure called chromatin, it appears to behave like a Hookian spring. The base component of chromatin is a nucleosome, which is constructed when DNA coils around octamers of histone proteins. The histones can become acetylated---a chemical process in which an acetyl functional group attaches to amino acids of the histones, often lysines. Acetylation may loosen chromatin's coils and therefore lower the amount of tension required to stretch the chromatin. Comparing the levels of tension required to stretch acetylated chromatin could reveal, directly, physical differences in the chromatin fiber that bear ion the function of the DNA molecule. Work presented will be the investigation of unacetylated chromatin.

  14. 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

  15. Intergenic Locations of Rice Centromeric Chromatin

    PubMed Central

    Yan, Huihuang; Talbert, Paul B; Lee, Hye-Ran; Jett, Jamie; Henikoff, Steven; Chen, Feng; Jiang, Jiming

    2008-01-01

    Centromeres are sites for assembly of the chromosomal structures that mediate faithful segregation at mitosis and meiosis. Plant and animal centromeres are typically located in megabase-sized arrays of tandem satellite repeats, making their precise mapping difficult. However, some rice centromeres are largely embedded in nonsatellite DNA, providing an excellent model to study centromere structure and evolution. We used chromatin immunoprecipitation and 454 sequencing to define the boundaries of nine of the 12 centromeres of rice. Centromere regions from chromosomes 8 and 9 were found to share synteny, most likely reflecting an ancient genome duplication. For four centromeres, we mapped discrete subdomains of binding by the centromeric histone variant CENH3. These subdomains were depleted in both intact and nonfunctional genes relative to interspersed subdomains lacking CENH3. The intergenic location of rice centromeric chromatin resembles the situation for human neocentromeres and supports a model of the evolution of centromeres from gene-poor regions. PMID:19067486

  16. 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

  17. On the topology of chromatin fibres

    PubMed Central

    Barbi, Maria; Mozziconacci, Julien; Victor, Jean-Marc; Wong, Hua; Lavelle, Christophe

    2012-01-01

    The ability of cells to pack, use and duplicate DNA remains one of the most fascinating questions in biology. To understand DNA organization and dynamics, it is important to consider the physical and topological constraints acting on it. In the eukaryotic cell nucleus, DNA is organized by proteins acting as spools on which DNA can be wrapped. These proteins can subsequently interact and form a structure called the chromatin fibre. Using a simple geometric model, we propose a general method for computing topological properties (twist, writhe and linking number) of the DNA embedded in those fibres. The relevance of the method is reviewed through the analysis of magnetic tweezers single molecule experiments that revealed unexpected properties of the chromatin fibre. Possible biological implications of these results are discussed. PMID:24098838

  18. [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

  19. Inducible DamID systems for genomic mapping of chromatin proteins in Drosophila

    PubMed Central

    Pindyurin, Alexey V.; Pagie, Ludo; Kozhevnikova, Elena N.; van Arensbergen, Joris; van Steensel, Bas

    2016-01-01

    Dam identification (DamID) is a powerful technique to generate genome-wide maps of chromatin protein binding. Due to its high sensitivity, it is particularly suited to study the genome interactions of chromatin proteins in small tissue samples in model organisms such as Drosophila. Here, we report an intein-based approach to tune the expression level of Dam and Dam-fusion proteins in Drosophila by addition of a ligand to fly food. This helps to suppress possible toxic effects of Dam. In addition, we describe a strategy for genetically controlled expression of Dam in a specific cell type in complex tissues. We demonstrate the utility of the latter by generating a glia-specific map of Polycomb in small samples of brain tissue. These new DamID tools will be valuable for the mapping of binding patterns of chromatin proteins in Drosophila tissues and especially in cell lineages. PMID:27001518

  20. Small acidic peptides from wheat germ chromatin. I. Isolation and biochemical characterization.

    PubMed

    Mancinelli, L; Castigli, E; Qualadrucci, P; Gianfranceschi, G L; Bramucci, M; Miano, A; Amici, D

    1992-01-01

    RNA synthesis in cell and cell-free systems is inhibited by a family of acidic, low molecular weight chromatin peptides (CPs). These peptides were extracted from deproteinized DNA of prokaryotic and eukaryotic cells, but the low yield of purified material by this procedure hinders efforts aimed at understanding their action mechanism in gene regulation. In this report we describe two purification methods of CPs from an easily available source, wheat germ. A comparison is made between the method starting from deproteinized DNA and the method from purified chromatin. The biological effects (inhibition of L1210 cell growth and DNA in vitro transcription) of CPs from wheat germ together with their chemical characteristics (molecular weight, amino acid composition and presence of phosphoserine) show strong homology with those of CPs from other sources. These results suggest a possible role of these chromatin peptides in controlling gene expression. PMID:1508994

  1. Inducible DamID systems for genomic mapping of chromatin proteins in Drosophila.

    PubMed

    Pindyurin, Alexey V; Pagie, Ludo; Kozhevnikova, Elena N; van Arensbergen, Joris; van Steensel, Bas

    2016-07-01

    Dam identification (DamID) is a powerful technique to generate genome-wide maps of chromatin protein binding. Due to its high sensitivity, it is particularly suited to study the genome interactions of chromatin proteins in small tissue samples in model organisms such as Drosophila Here, we report an intein-based approach to tune the expression level of Dam and Dam-fusion proteins in Drosophila by addition of a ligand to fly food. This helps to suppress possible toxic effects of Dam. In addition, we describe a strategy for genetically controlled expression of Dam in a specific cell type in complex tissues. We demonstrate the utility of the latter by generating a glia-specific map of Polycomb in small samples of brain tissue. These new DamID tools will be valuable for the mapping of binding patterns of chromatin proteins in Drosophila tissues and especially in cell lineages. PMID:27001518

  2. Epigenetic Regulation by ATP-Dependent Chromatin-Remodeling Enzymes: SNF-ing Out Crosstalk.

    PubMed

    Runge, John S; Raab, Jesse R; Magnuson, Terry

    2016-01-01

    Cells utilize precise mechanisms to access genomic DNA with spatiotemporal accuracy. ATP-dependent chromatin-remodeling enzymes (also known simply as "remodelers") comprise a specialized class of enzymes that is intimately involved in genomic organization and accessibility. Remodelers selectively position nucleosomes to either alleviate chromatin compaction or achieve genomic condensation locally, based on a multitude of cellular signals. By dictating nucleosome position, remodelers control local euchromatic and heterochromatic states. These activities govern the accessibility of regulatory regions like promoters and enhancers to transcription factors, RNA polymerases, and coactivators or -repressors. As studies unravel the complexities of epigenetic topography, evidence points to a chromatin-based interactome where regulators interact competitively, cooperatively, and/or codependently through physical and functional means. These types of interactions, or crosstalk, between remodelers raise important questions for tissue development. Here, we briefly review the evidence for remodeler interactions and argue for additional studies examining crosstalk. PMID:26969969

  3. Light-induced Ca2+ release in the visible cones of the zebrafish.

    PubMed

    Cilluffo, Marianne C; Matthews, Hugh R; Brockerhoff, Susan E; Fain, Gordon L

    2004-01-01

    We used suction-pipette recording and fluo-4 fluorescence to study light-induced Ca2+ release from the visible double cones of zebrafish. In Ringer, light produces a slow decrease in fluorescence which can be fitted by the sum of two decaying exponentials with time constants of 0.5 and 3.8 s. In 0Ca2+-0Na+ solution, for which fluxes of Ca2+ across the outer segment plasma membrane are greatly reduced, light produces a slow increase in fluorescence. Both the decrease and increase are delayed after incorporation of the Ca2+ chelator BAPTA, indicating that both are produced by a change in Ca2+. If the Ca2+ pool is first released by bright light in 0Ca2+-0Na+ solution and the cone returned to Ringer, the time course of Ca2+ decline is much faster than in Ringer without previous light exposure. This indicates that the time constants of 0.5 and 3.8 s actually reflect a sum of Na+/Ca2+-K+ exchange and light-induced release of Ca2+. The Ca2+ released by light appears to come from at least two sites, the first comprising 66% of the total pool and half-released by bleaching 4.8% of the pigment. Release of the remaining Ca2+ from the second site requires the bleaching of nearly all of the pigment. If, after release, the cone is maintained in darkness, a substantial fraction of the Ca2+ returns to the release pool even in the absence of pigment regeneration. The light-induced release of Ca2+ can produce a modulation of the dark current as large as 0.75 pA independently of the normal transduction cascade, though the rise time of the current is considerably slower than the normal light response. These experiments show that Ca2+ can be released within the cone outer segment by light intensities within the physiological range of photopic vision. The role this Ca2+ release plays remains unresolved. PMID:15579223

  4. Titration and hysteresis in epigenetic chromatin silencing

    NASA Astrophysics Data System (ADS)

    Dayarian, Adel; Sengupta, Anirvan M.

    2013-06-01

    Epigenetic mechanisms of silencing via heritable chromatin modifications play a major role in gene regulation and cell fate specification. We consider a model of epigenetic chromatin silencing in budding yeast and study the bifurcation diagram and characterize the bistable and the monostable regimes. The main focus of this paper is to examine how the perturbations altering the activity of histone modifying enzymes affect the epigenetic states. We analyze the implications of having the total number of silencing proteins, given by the sum of proteins bound to the nucleosomes and the ones available in the ambient, to be constant. This constraint couples different regions of chromatin through the shared reservoir of ambient silencing proteins. We show that the response of the system to perturbations depends dramatically on the titration effect caused by the above constraint. In particular, for a certain range of overall abundance of silencing proteins, the hysteresis loop changes qualitatively with certain jump replaced by continuous merger of different states. In addition, we find a nonmonotonic dependence of gene expression on the rate of histone deacetylation activity of Sir2. We discuss how these qualitative predictions of our model could be compared with experimental studies of the yeast system under anti-silencing drugs.

  5. 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.

  6. 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...

  7. 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. PMID:26400310

  8. Probing the impact of chromatin conformation on genome editing tools.

    PubMed

    Chen, Xiaoyu; Rinsma, Marrit; Janssen, Josephine M; Liu, Jin; Maggio, Ignazio; Gonçalves, Manuel A F V

    2016-07-27

    Transcription activator-like effector nucleases (TALENs) and RNA-guided nucleases derived from clustered, regularly interspaced, short palindromic repeats (CRISPR)-Cas9 systems have become ubiquitous genome editing tools. Despite this, the impact that distinct high-order chromatin conformations have on these sequence-specific designer nucleases is, presently, ill-defined. The same applies to the relative performance of TALENs and CRISPR/Cas9 nucleases at isogenic target sequences subjected to different epigenetic modifications. Here, to address these gaps in our knowledge, we have implemented quantitative cellular systems based on genetic reporters in which the euchromatic and heterochromatic statuses of designer nuclease target sites are stringently controlled by small-molecule drug availability. By using these systems, we demonstrate that TALENs and CRISPR/Cas9 nucleases are both significantly affected by the high-order epigenetic context of their target sequences. In addition, this outcome could also be ascertained for S. pyogenes CRISPR/Cas9 complexes harbouring Cas9 variants whose DNA cleaving specificities are superior to that of the wild-type Cas9 protein. Thus, the herein investigated cellular models will serve as valuable functional readouts for screening and assessing the role of chromatin on designer nucleases based on different platforms or with different architectures or compositions. PMID:27280977

  9. Preparation and Analysis of Native Chromatin-Modifying Complexes.

    PubMed

    Doyon, Y; Côté, J

    2016-01-01

    Nucleosomes, the basic units of chromatin, are decorated with a myriad of posttranslational modifications (PTMs) by the action of chromatin modifiers. These enzymes function almost exclusively as part of stable protein complexes that assist their recruitment to specific genomic loci, specify their substrate, and provide allosteric control. By altering the interactions within nucleosomes or with neighboring nucleosomes and serving as a platform to engage effector proteins, PTMs deposited by histone-modifying complexes influence virtually every nuclear process and are at the heart of the epigenetic mechanisms. Hence, it is critical to identify their components, define their structures, and characterize their biochemical activities. Here we describe protocols for tandem affinity purification (TAP) of native histone acetyltransferase (HAT) and methyltransferase (HMT) complexes from human cells engineered to express bait proteins from a genomic safe harbor or their endogenous chromosomal genes, using zinc-finger nucleases (ZFNs), TAL effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 systems. The approaches presented aim to preserve natural transcriptional and posttranscriptional regulation and minimize biochemical artifacts due to ectopic expression. Near homogenous preparations of native complexes are obtained in sufficient amounts to perform biochemical assays and characterize their components. PMID:27372759

  10. 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. PMID:25363760

  11. Photo-sensible (thymine containing) azo-polysiloxanes: synthesis and light induced effects

    NASA Astrophysics Data System (ADS)

    Enea, R.; Apostol, I.; Damian, V.; Hurduc, N.; Iordache, I.

    2008-03-01

    . The paper presents the possibility to obtain azo-polysiloxanes modified with thymine and their light induced processing with potential interest in opto-electronics or biomolecules nanomanipulation. The presence of the thymine group in the polymeric structure can confer to material biological properties, in the same time the capacity of tymine to generate H-bonds being useful to the relief geometry stabilization in time. The investigated polymers were obtained in a two step reaction, starting from a polysiloxane containing chlorobenzyl groups in the side chain. The azopolysiloxanes' photochromic behaviour was investigated in solid state, using thin films etalated on the surface of a quartz slide. The effect of surface relief structuration process under the action of UV (355 nm) laser radiation was studied. Laser induced effects on the material surface depends on the incident laser fluence and number of pulses.

  12. 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

  13. 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.

  14. Retinol Dehydrogenase (RDH12) Protects Photoreceptors from Light-induced Degeneration in Mice*S

    PubMed Central

    Maeda, Akiko; Maeda, Tadao; Imanishi, Yoshikazu; Sun, Wenyu; Jastrzebska, Beata; Hatala, Denise A.; Winkens, Huub J.; Hofmann, Klaus Peter; Janssen, Jacques J.; Baehr, Wolfgang; Driessen, Carola A.; Palczewski, Krzysztof

    2014-01-01

    RDH12 has been suggested to be one of the retinol dehydrogenases (RDH) involved in the vitamin A recycling system (visual cycle) in the eye. Loss of function mutations in the RDH12 gene were recently reported to be associated with autosomal recessive childhood-onset severe retinal dystrophy. Here we show that RDH12 localizes to the photoreceptor inner segments and that deletion of this gene in mice slows the kinetics of all-trans-retinal reduction, delaying dark adaptation. However, accelerated 11-cis-retinal production and increased susceptibility to light-induced photoreceptor apoptosis were also observed in Rdh12−/− mice, suggesting that RDH12 plays a unique, nonredundant role in the photoreceptor inner segments to regulate the flow of retinoids in the eye. Thus, severe visual impairments of individuals with null mutations in RDH12 may likely be caused by light damage1. PMID:17032653

  15. 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.

  16. Light-Induced Exciton Spin Hall Effect in van der Waals Heterostructures.

    PubMed

    Li, Yun-Mei; Li, Jian; Shi, Li-Kun; Zhang, Dong; Yang, Wen; Chang, Kai

    2015-10-16

    We propose a light-induced spin Hall effect for interlayer exciton gas in monolayer MoSe2-WSe2 van der Waals heterostructure. By applying two infrared, spatially varying laser beams coupled to the exciton internal states, a spin-dependent gauge potential on the exciton center-of-mass motion is induced. This gauge potential deflects excitons in different spin states towards opposite directions, leading to a finite spin current but vanishing mass current. In the Hall bar geometry, the spin-dependent deflection gives rise to spin-dependent chiral edge states with spin-velocity locking. The spin current and chiral edge states of the excitons can be detected by spatially resolved photoluminescence spectroscopy. PMID:26550894

  17. Tuning and Erasing Surface Wrinkles by Reversible Visible-Light-Induced Photoisomerization.

    PubMed

    Zong, Chuanyong; Zhao, Yan; Ji, Haipeng; Han, Xue; Xie, Jixun; Wang, Juanjuan; Cao, Yanping; Jiang, Shichun; Lu, Conghua

    2016-03-14

    Periodic wrinkling across different scales has received considerable attention because it not only represents structure failure but also finds wide applications. How to prevent wrinkling or create desired wrinkling patterns is non-trivial because the dynamic evolution of wrinkles is a highly nonlinear problem. Herein, we report a simple yet powerful method to dynamically tune and/or erase wrinkling patterns with visible light. The light-induced photoisomerization of azobenzene units in azopolymer films leads to stress release and consequently to the erasure of the wrinkles. The wrinkles in unexposed regions are also affected and oriented perpendicular to the exposed boundary during the stress reorganization. Theoretical models were developed to understand the dynamics of the reversible photoisomerization-induced wrinkle evolution. This method can be applied for designing functional materials/devices, for example, for the reversible optical writing/erasure of information as demonstrated here. PMID:26894439

  18. A tunable azine covalent organic framework platform for visible light-induced hydrogen generation

    NASA Astrophysics Data System (ADS)

    Vyas, Vijay S.; Haase, Frederik; Stegbauer, Linus; Savasci, Gökcen; Podjaski, Filip; Ochsenfeld, Christian; Lotsch, Bettina V.

    2015-09-01

    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.

  19. 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.

  20. Light-induced effects-impacts to module performance measurements and reliability testing: An overview

    NASA Technical Reports Server (NTRS)

    Wronski, C. R.

    1985-01-01

    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.

  1. High efficiency light-induced dielectrophoresis biochip prepared using CVD techniques.

    PubMed

    Wu, Hung-Wei; Huang, Yao-Sheng; Lee, Hsin-Ying; Tsai, Wu-Han; Chen, Kuan-Yu; Jian, Li-Yi

    2016-10-01

    This article describes a high-efficiency light-induced dielectrophoresis biochip containing a thin film prepared through inductively coupled plasma chemical vapor deposition (ICPCVD). The biochip comprises two ITO glass substrates and a photoconductive amorphous silicon thin film. The biochip can effectively sort particular particles (or cells) by projecting visible light onto the surface of the silicon thin film. The sorting efficiency of biochips is highly associated with the quality of the deposited amorphous silicon thin films; therefore, the choice of deposition technique is extremely critical. However, no study has examined this problem. Hence, the current study thoroughly compared the efficiency of the biochip when films produced through plasma-enhanced chemical vapor deposition and ICPCVD are used. PMID:27530346

  2. Enhanced recovery of light-induced degradation on the micromorph solar cells by electric field

    NASA Astrophysics Data System (ADS)

    Sun, H.-C.; Yang, Y.-J.; Chen, J. Y.; Chao, T.-M.; Liu, C. W.; Lin, W.-Y.; Bi, C.-C.; Yeh, C.-H.

    2012-09-01

    The recovery of light-induced degradation of the tandem micromorph solar cell by applying reverse bias is compared with the single-junction amorphous silicon solar cell. The illuminated current density-voltage characteristics and external quantum efficiency show that the degradation of both the micromorph and the amorphous silicon cells can be recovered by applying sufficient reverse bias. The micromorph cell was recovered at smaller reverse bias than amorphous silicon cell. The abundant H in the microcrystalline silicon bottom cell of the micromorph cell can act as a reservoir to repair the defects in the amorphous silicon top cell at the reverse bias. This is responsible for small recovery bias of tandem cells.

  3. Photosynthetic Independence of Light-induced Anthocyanin Formation in Zea Seedlings 1

    PubMed Central

    Duke, Stephen O.; Fox, Sue B.; Naylor, Aubrey W.

    1976-01-01

    Results are reported which support the view that the photosynthetic photosystems are not involved in the high irradiance response (HIR) phenomenon of light-dependent anthocyanin biosynthesis in dark-grown Zea mays L. seedlings. A negative correlation between change in greening rates and change in light-dependent anthocyanin accumulation rates with age was demonstrated. Lack of chlorophyll synthesis in a strain of maize possessing a temperature-sensitive lesion for chlorophyll synthesis could not be correlated with light-induced anthocyanin accumulation. Furthermore, seedlings totally lacking photosynthetic capabilities, either due to a genetic lesion or to excision of all photosynthetic tissue, had an enhanced rate of photoinduced anthocyanin formation. This evidence indicates that the HIR results in the initiation of processes that are in competition with chloroplast development for substrate in normal, intact seedlings. PMID:16659449

  4. Light-induced atomic desorption for loading a sodium magneto-optical trap

    SciTech Connect

    Telles, Gustavo; Ishikawa, Tetsuya; Gibbs, Matthew; Raman, Chandra

    2010-03-15

    We report studies of photon-stimulated desorption, also known as light-induced atomic desorption, of sodium atoms from a vacuum-cell glass surface used for loading a magneto-optical trap (MOT). Fluorescence detection was used to record the trapped atom number and the desorption rate. We observed a steep wavelength dependence of the desorption process above 2.6 eV photon energy, a result significant for estimations of sodium vapor density in the lunar atmosphere. Our data fit well to a simple model for the loading of the MOT dependent only on the sodium desorption rate and residual gas density. Up to 3.7x10{sup 7} Na atoms were confined under ultrahigh-vacuum conditions, creating promising loading conditions for a vapor-cell-based atomic Bose-Einstein condensate of sodium.

  5. 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

  6. 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.

  7. Light-induced surface graft polymerizations initiated by an anthraquinone dye on cotton fibers.

    PubMed

    Zhuo, Jingyuan; Sun, Gang

    2014-11-01

    Anthraquinone and its derivatives could serve as photo-sensitizers and generate radicals and reactive oxygen species in polymers under exposure of UVA or day light. Such a property was utilized in development of novel light-induced surface radical graft polymerizations on cotton fibers that were dyed with an anthraquinone derivative, 2-ethylanthraquinone. Several functional monomers were directly grafted onto the dyed cotton fibers upon UVA exposure. The chemical and morphological structures and thermal properties of the grafted fibers were confirmed and characterized by Fourier transform infrared spectrometer (FTIR), scanning electron microscope (SEM) and thermal gravimetric analysis (TGA). Reaction conditions including concentrations of the photosensitizer, the amount of monomers, as well as UVA irradiation time could influence grafting efficiencies. More interestingly, the surface graft polymerization did not significantly change the light active functions of the agent, evidenced by the light-active antimicrobial functions of the grafted fibers. PMID:25129730

  8. Light-induced point defect reactions of residual iron in crystalline silicon after aluminum gettering

    SciTech Connect

    Abdelbarey, D.; Kveder, V.; Schroeter, W.; Seibt, M.

    2010-08-15

    Deep level transient spectroscopy is used to study light-induced reactions of residual iron impurities after aluminum gettering (AlG) in crystalline silicon. White-light illumination at room temperature leads to the formation of a defect which is associated with a donor level at 0.33 eV above the valence band. This defect is stable up to about 175 deg. C where it dissociates reversibly in case of small iron concentrations and irreversibly for high iron concentrations. Since marker experiments using gold and platinum diffusion show a high vacancy concentration after AlG a tentative identification of the new defect as the metastable iron-vacancy pair is proposed.

  9. 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

  10. 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

  11. Low-intensity light induces vasorelaxation: a study for possible mechanism

    NASA Astrophysics Data System (ADS)

    Morimoto, Yuji; Matsuo, Hirotaka; Arai, Tsunenori; Kikuchi, Makoto

    1996-05-01

    To investigate the mechanism of light induced vasorelaxation, vascular tension change in normal buffer solution was compared with that in the buffer containing either the following drug: (1) guanylate cyclase inhibitor; (2) nitric oxide synthetase inhibitors and the optical isomers; and (3) vasodilating agent. The vasorelaxation caused by ultraviolet light irradiation was independent of the presence of an intact endothelium. It was inhibited by methyleneblue, but not influenced by either L-NMMA or D-NMMA. On the other hand, this vasorelaxation was enhanced by the agents containing nitro group (L-NAME, D-NAME) or sodium nitrite. These results show that the light activates guanylate cyclase, which results in the vasorelaxation. This activation was reinforced by the agents containing nitro group. We conclude that primary photochemical product, which is probably nitric oxide originated from photodissociation of nitro groups, may produce the vasorelaxation. The preliminary investigation suggests that ultraviolet irradiation may be benefit in the treatment for vasospasm.

  12. 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.

  13. Light-Induced Solubility Modulation of Polyfluorene To Enhance the Performance of OLEDs.

    PubMed

    Schelkle, Korwin M; Bender, Markus; Jeltsch, Krischan; Buckup, Tiago; Müllen, Klaus; Hamburger, Manuel; Bunz, Uwe H F

    2015-11-23

    Liquid-phase processing is a key prerequisite for the cost-efficient fabrication of organic electronic devices. We report an approach for light-induced modulation of the solubility of π-conjugated polymers (polyfluorene) with side chains functionalized with hydroxycinnamic acid. Irradiation with light cleaves the solubilizing side chains and renders the thin films of the polyfluorene insoluble. In a proof of concept device, polyfluorenes were applied as emissive layers in OLEDs. Photoirradiation of the emission layer leads to an increase in OLED performance combined with a modulation of the solubility of the thin film. These results offer the possibility for further development in terms of manipulating the solubility and emissive parameters of an important class of functional materials. PMID:26463263

  14. Light-induced fluorescence endoscopy (LIFE) imaging system for early cancer detection

    NASA Astrophysics Data System (ADS)

    Zeng, Haishan; MacAulay, Calum E.; Lam, Stephen; Palcic, Branko

    1999-09-01

    This paper summarizes our experiences on the development of a Light Induced Fluorescence Endoscopy (LIFE) imaging system for early cancer detection in the respiratory and gastrointestinal tract. The system utilizes tissue autofluorescence to provide real time video imaging of the examined organ. No exogenous fluorescent tumor markers are needed. It is used by a physician in adjunct to conventional white-light endoscopy. Suspicious areas are identified in pseudo color to guide biopsy. A multi- center clinical trial has demonstrated that in the lung, the relative sensitivity of white-light imaging + LIFE imaging vs. white-light imaging alone was 6.3 for intraepithelial neoplastic lesion detection and 2.71 when invasive carcinomas were also included. The following issues will be discussed: (1) spectroscopy study design for imaging system development; (2) architecture of the imaging systems; (3) different imaging modalities (white-light imaging, dual channel fluorescence imaging, and combined fluorescence/reflectance imaging); and (4) clinical applications.

  15. 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

  16. 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

  17. 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. PMID:26351155

  18. 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

  19. 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

    2016-01-01

    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. PMID:27240733

  20. 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.

  1. A tunable azine covalent organic framework platform for visible light-induced hydrogen generation.

    PubMed

    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

  2. Theory of light-induced deformation of azobenzene elastomers: Influence of network structure

    NASA Astrophysics Data System (ADS)

    Toshchevikov, V. P.; Saphiannikova, M.; Heinrich, G.

    2012-07-01

    Azobenzene elastomers have been extensively explored in the last decade as photo-deformable smart materials which are able to transform light energy into mechanical stress. Presently, there is a great need for theoretical approaches to accurately predict the quantitative response of these materials based on their microscopic structure. Recently, we proposed a theory of light-induced deformation of azobenzene elastomers using a simple regular cubic network model [V. Toshchevikov, M. Saphiannikova, and G. Heinrich, J. Phys. Chem. B 116, 913 (2012), 10.1021/jp206323h]. In the present study, we extend the previous theory using more realistic network models which take into account the random orientation of end-to-end vectors of network strands as well as the molecular weight distribution of the strands. Interaction of the chromophores with the linearly polarized light is described by an effective orientation potential which orients the chromophores perpendicular to the polarization direction. We show that both monodisperse and polydisperse azobenzene elastomers can demonstrate either a uniaxial expansion or contraction along the polarization direction. The sign of deformation (expansion/contraction) depends on the orientation distribution of chromophores with respect to the main chains which is defined by the chemical structure and by the lengths of spacers. The degree of cross-linking and the polydispersity of network strands do not affect the sign of deformation but influence the magnitude of light-induced deformation. We demonstrate that photo-mechanical properties of mono- and poly-disperse azobenzene elastomers with random spatial distribution of network strands can be described in a very good approximation by a regular cubic network model with an appropriately chosen length of the strands.

  3. Rapamycin attenuates visible light-induced injury in retinal photoreceptor cells via inhibiting endoplasmic reticulum stress.

    PubMed

    Li, Guang-Yu; Fan, Bin; Jiao, Ying-Ying

    2014-05-14

    An extended exposure of the retina to visible light may lead to photochemical damage in retinal photoreceptor cells. The exact mechanism of retinal light damage remains unknown, and an effective therapy is still unavailable. Here, we demonstrated that rapamycin, an inhibitor of the mammalian target of rapamycin (mTOR), markedly protected 661W photoreceptor cells from visible light exposure-induced damage at the nanomolar level. We also observed by transmission electron microscopy that light exposure led to severe endoplasmic reticulum (ER) stress in 661W cells as well as abnormal endomembranes and ER membranes. In addition, obvious upregulated ER stress markers were monitored by western blot at the protein level and by quantitative reverse transcription-polymerase chain reaction (RT-PCR) at the mRNA level. Interestingly, rapamycin pretreatment significantly suppressed light-induced ER stress and all three major branches of the unfolded protein response (UPR), including the RNA-dependent protein kinase-like ER kinase (PERK), inositol-requiring enzyme 1 (IRE1), and activating transcription factor 6 (ATF6) pathways both at the protein and mRNA levels. Additionally, the inhibition of ER stress by rapamycin was further confirmed with a dithiothreitol (DTT; a classical ER stress inducer)-damaged 661W cell model. Meanwhile, our results also revealed that rapamycin was able to remarkably inhibit the activation of mTOR and its downstream factors eukaryotic translation initiation factor 4E-binding protein 1 (4EBP1), p-4EBP1, p70, p-p70, and phosphorylated ribosomal protein S6 kinase (p-S6K) in the light-injured 661W cells. Thus, these data indicate that visible light induces ER stress in 661W cells; whereas the mTOR inhibitor, rapamycin, effectively protects 661W cells from light injury through suppressing the ER stress pathway. PMID:24607296

  4. Coherent spin-light-induced mechanisms in the semirelativistic limit of the self-consistent Dirac-Maxwell equations

    NASA Astrophysics Data System (ADS)

    Hinschberger, Y.; Manfredi, G.; Hervieux, P.-A.

    2016-04-01

    We present a self-consistent mean-field model based on a two-component Pauli-like equation that incorporates quantum and relativistic effects (up to second order in 1 /c ) for both external and internal electromagnetic fields. By taking the semirelativistic limit of the Dirac-Maxwell equations in the presence of an external electromagnetic field we obtain an analytical expression of a coherent light-induced mean-field Hamiltonian. The latter exhibits several mechanisms that involve the internal mean fields created by all the electrons and the external electromagnetic field (laser). The role played by the light-induced current density and the light-induced second-order charge density acting as sources in Maxwell's equations are clarified. In particular, we identify clearly four different mechanisms involving the spins that may play an important role in coherent ultrafast spin dynamics.

  5. Snf2h-mediated chromatin organization and histone H1 dynamics govern cerebellar morphogenesis and neural maturation

    PubMed Central

    Alvarez-Saavedra, Matías; De Repentigny, Yves; Lagali, Pamela S.; Raghu Ram, Edupuganti V. S.; Yan, Keqin; Hashem, Emile; Ivanochko, Danton; Huh, Michael S.; Yang, Doo; Mears, Alan J.; Todd, Matthew A. M.; Corcoran, Chelsea P.; Bassett, Erin A.; Tokarew, Nicholas J. A.; Kokavec, Juraj; Majumder, Romit; Ioshikhes, Ilya; Wallace, Valerie A.; Kothary, Rashmi; Meshorer, Eran; Stopka, Tomas; Skoultchi, Arthur I.; Picketts, David J.

    2014-01-01

    Chromatin compaction mediates progenitor to post-mitotic cell transitions and modulates gene expression programs, yet the mechanisms are poorly defined. Snf2h and Snf2l are ATP-dependent chromatin remodelling proteins that assemble, reposition and space nucleosomes, and are robustly expressed in the brain. Here we show that mice conditionally inactivated for Snf2h in neural progenitors have reduced levels of histone H1 and H2A variants that compromise chromatin fluidity and transcriptional programs within the developing cerebellum. Disorganized chromatin limits Purkinje and granule neuron progenitor expansion, resulting in abnormal post-natal foliation, while deregulated transcriptional programs contribute to altered neural maturation, motor dysfunction and death. However, mice survive to young adulthood, in part from Snf2l compensation that restores Engrailed-1 expression. Similarly, Purkinje-specific Snf2h ablation affects chromatin ultrastructure and dendritic arborization, but alters cognitive skills rather than motor control. Our studies reveal that Snf2h controls chromatin organization and histone H1 dynamics for the establishment of gene expression programs underlying cerebellar morphogenesis and neural maturation. PMID:24946904

  6. Role of space charges on light-induced effects in nematic liquid crystals doped by methyl red

    NASA Astrophysics Data System (ADS)

    Lucchetti, L.; Simoni, F.

    2014-03-01

    We show that both the extraordinarily large nonlinear response and the light-induced permanent reorientation in liquid crystals doped by the azo dye methyl red originates from the same phenomenon of modification of the charge density on the irradiated surface. The demonstration is done by applying ac voltage to the samples, showing that in this case no permanent anchoring is possible. The measurements confirm the role of photoisomerization that gives a transient contribution to the actual reorientation process only in the high dose regime. This result allows us to draw a picture for light-induced effects that might be applied to a large class of compounds.

  7. 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.

  8. 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.

  9. Anterior-posterior differences in HoxD chromatin topology in limb development

    PubMed Central

    Williamson, Iain; Eskeland, Ragnhild; Lettice, Laura A.; Hill, Alison E.; Boyle, Shelagh; Grimes, Graeme R.; Hill, Robert E.; Bickmore, Wendy A.

    2012-01-01

    A late phase of HoxD activation is crucial for the patterning and growth of distal structures across the anterior-posterior (A-P) limb axis of mammals. Polycomb complexes and chromatin compaction have been shown to regulate Hox loci along the main body axis in embryonic development, but the extent to which they have a role in limb-specific HoxD expression, an evolutionary adaptation defined by the activity of distal enhancer elements that drive expression of 5′ Hoxd genes, has yet to be fully elucidated. We reveal two levels of chromatin topology that differentiate distal limb A-P HoxD activity. Using both immortalised cell lines derived from posterior and anterior regions of distal E10.5 mouse limb buds, and analysis in E10.5 dissected limb buds themselves, we show that there is a loss of polycomb-catalysed H3K27me3 histone modification and a chromatin decompaction over HoxD in the distal posterior limb compared with anterior. Moreover, we show that the global control region (GCR) long-range enhancer spatially colocalises with the 5′ HoxD genomic region specifically in the distal posterior limb. This is consistent with the formation of a chromatin loop between 5′ HoxD and the GCR regulatory module at the time and place of distal limb bud development when the GCR participates in initiating Hoxd gene quantitative collinearity and Hoxd13 expression. This is the first example of A-P differences in chromatin compaction and chromatin looping in the development of the mammalian secondary body axis (limb). PMID:22872084

  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. The role of chromatin structure in cell migration

    PubMed Central

    Gerlitz, Gabi; Bustin, Michael

    2010-01-01

    Chromatin dynamics play a major role in regulating genetic processes. Now, accumulating data suggest that chromatin structure may also affect the mechanical properties of the nucleus and cell migration. Global chromatin organization seems to modulate the shape, the size and the stiffness of the nucleus. Directed-cell migration, which often requires nuclear reshaping to allow cellular passage through narrow openings, is dependent not only on changes in cytoskeletal elements, but also on the global chromatin condensation. Conceivably, during cell migration a physical link between the chromatin and the cytoskeleton facilitates coordinated structural changes in these two components. Thus, in addition to regulating genetic processes, we suggest that alterations in chromatin structure may facilitate cellular reorganizations necessary for efficient migration. PMID:20951589

  12. Role of histone modifications in defining chromatin structure and function.

    PubMed

    Gelato, Kathy A; Fischle, Wolfgang

    2008-04-01

    Chromosomes in eukaryotic cell nuclei are not uniformly organized, but rather contain distinct chromatin elements, with each state having a defined biochemical structure and biological function. These are recognizable by their distinct architectures and molecular components, which can change in response to cellular stimuli or metabolic requirements. Chromatin elements are characterized by the fundamental histone and DNA components, as well as other associated non-histone proteins and factors. Post-translational modifications of histone proteins in particular often correlate with a specific chromatin structure and function. Patterns of histone modifications are implicated as having a role in directing the level of chromatin compaction, as well as playing roles in multiple functional pathways directing the readout of distinct regions of the genome. We review the properties of various chromatin elements and the apparent links of histone modifications with chromatin organization and functional output. PMID:18225984

  13. 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

  14. In Brief: Picturing the complex world of chromatin remodelling families.

    PubMed

    Witkowski, Leora; Foulkes, William D

    2015-12-01

    Over the past decade, chromatin remodelling emerged as one of the most important causes of both abnormal development and cancer. Although much has been written about one or another of the complexes, no recent concise summary of the chromatin remodelling families as a whole is available. In this short review, we introduce the family members, briefly summarize their role in developmental abnormalities and neoplasia, and outline the different ways in which these families remodel chromatin. PMID:26174723

  15. 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.

  16. 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

  17. Chromatin insulators: regulatory mechanisms and epigenetic inheritance

    PubMed Central

    Bushey, Ashley M.; Dorman, Elizabeth R.; Corces, Victor G.

    2008-01-01

    Enhancer-blocking insulators are DNA elements that disrupt the communication between a regulatory sequence, such as an enhancer or a silencer, and a promoter. Insulators participate in both transcriptional regulation and global nuclear organization, two features of chromatin that are thought to be maintained from one generation to the next through epigenetic mechanisms. Furthermore, there are many regulatory mechanisms in place that enhance or hinder insulator activity. These modes of regulation could be used to establish cell-type specific insulator activity that is epigenetically inherited along a cell and/or organismal lineage. This review will discuss the evidence for epigenetic inheritance and regulation of insulator function. PMID:18851828

  18. Hydrogen peroxide mediates higher order chromatin degradation.

    PubMed

    Bai, H; Konat, G W

    2003-01-01

    Although a large body of evidence supports a causative link between oxidative stress and neurodegeneration, the mechanisms are still elusive. We have recently demonstrated that hydrogen peroxide (H(2)O(2)), the major mediator of oxidative stress triggers higher order chromatin degradation (HOCD), i.e. excision of chromatin loops at the matrix attachment regions (MARs). The present study was designed to determine the specificity of H(2)O(2) in respect to HOCD induction. Rat glioma C6 cells were exposed to H(2)O(2) and other oxidants, and the fragmentation of genomic DNA was assessed by field inversion gel electrophoresis (FIGE). S1 digestion before FIGE was used to detect single strand fragmentation. The exposure of C6 cells to H(2)O(2) induced a rapid and extensive HOCD. Thus, within 30 min, total chromatin was single strandedly digested into 50 kb fragments. Evident HOCD was elicited by H(2)O(2) at concentrations as low as 5 micro M. HOCD was mostly reversible during 4-8h following the removal of H(2)O(2) from the medium indicating an efficient relegation of the chromatin fragments. No HOCD was induced by H(2)O(2) in isolated nuclei indicating that HOCD-endonuclease is activated indirectly by cytoplasmic signal pathways triggered by H(2)O(2). The exposure of cells to a synthetic peroxide, i.e. tert-butyrylhydroperoxide (tBH) also induced HOCD, but to a lesser extent than H(2)O(2). Contrary to the peroxides, the exposure of cells to equitoxic concentration of hypochlorite and spermine NONOate, a nitric oxide generator, failed to induce rapid HOCD. These results indicate that rapid HOCD is not a result of oxidative stress per se, but is rather triggered by signaling cascades initiated specifically by H(2)O(2). Furthermore, the rapid and extensive HOCD was observed in several rat and human cell lines challenged with H(2)O(2), indicating that the process is not restricted to glial cells, but rather represents a general response of cells to H(2)O(2). PMID:12421592

  19. The Effect of Internucleosomal Interaction on Folding of the Chromatin Fiber

    PubMed Central

    Stehr, René; Kepper, Nick; Rippe, Karsten; Wedemann, Gero

    2008-01-01

    The folding of the nucleosome chain into a chromatin fiber modulates DNA accessibility and is therefore an important factor for the control of gene expression. The fiber conformation depends crucially on the interaction between individual nucleosomes. However, this parameter has not been accurately determined experimentally, and it is affected by posttranslational histone modifications and binding of chromosomal proteins. Here, the effect of different internucleosomal interaction strengths on the fiber conformation was investigated by Monte Carlo computer simulations. The fiber geometry was modeled to fit that of chicken erythrocyte chromatin, which has been examined in numerous experimental studies. In the Monte Carlo simulation, the nucleosome shape was described as an oblate spherocylinder, and a replica exchange protocol was developed to reach thermal equilibrium for a broad range of internucleosomal interaction energies. The simulations revealed the large impact of the nucleosome geometry and the nucleosome repeat length on the compaction of the chromatin fiber. At high internucleosomal interaction energies, a lateral self-association of distant fiber parts and an interdigitation of nucleosomes were apparent. These results identify key factors for the control of the compaction and higher order folding of the chromatin fiber. PMID:18658212

  20. Kinase-mediated changes in nucleosome conformation trigger chromatin decondensation via poly-ADP-ribosylation

    PubMed Central

    Thomas, Colin J.; Kotova, Elena; Andrake, Mark; Adolf-Bryfogle, Jared; Glaser, Robert; Regnard, Catherine; Tulin, Alexei V.

    2014-01-01

    SUMMARY Dynamically controlled post-translational modifications of nucleosomal histones alter chromatin condensation to regulate transcriptional activation. We report that a nuclear tandem kinase, JIL-1, controls gene expression by activating Poly(ADP-ribose) Polymerase 1 (PARP-1). JIL-1 phosphorylates the C-terminus of the H2Av histone variant, which stimulates PARP-1 enzymatic activity in the surrounding chromatin, leading to further modification of histones and chromatin loosening. The H2Av nucleosome has a higher surface representation of PARP-1 binding patch consisting of H3 and H4 epitopes. Phosphorylation of H2Av by JIL-1 restructures this surface patch leading to activation of PARP-1. Exposure of Val61 and Leu23 of the H4 histone is critical for PARP-1 binding on nucleosome and PARP-1 activation following H2Av phosphorylation. We propose that chromatin loosening and associated initiation of gene expression is activated by phosphorylation of H2Av in a nucleosome positioned in promoter regions of PARP-1 dependent genes. PMID:24508391

  1. The Centromere: Chromatin Foundation for the Kinetochore Machinery

    PubMed Central

    Fukagawa, Tatsuo; Earnshaw, William C.

    2014-01-01

    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

  2. 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

  3. 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

  4. 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

  5. Is there a relationship between the chromatin status and DNA fragmentation of boar spermatozoa following freezing-thawing?

    PubMed

    Fraser, L; Strzezek, J

    2007-07-15

    In this study a radioisotope method, which is based on the quantitative measurements of tritiated-labeled actinomycin D ((3)H-AMD) incorporation into the sperm nuclei ((3)H-AMD incorporation assay), was used to assess the chromatin status of frozen-thawed boar spermatozoa. This study also tested the hypothesis that frozen-thawed spermatozoa with altered chromatin were susceptible to DNA fragmentation measured with the neutral comet assay (NCA). Boar semen was diluted in lactose-hen egg yolk-glycerol extender (L-HEY) or lactose ostrich egg yolk lipoprotein fractions-glycerol extender (L-LPFo), packaged into aluminum tubes or plastic straws and frozen in a controlled programmable freezer. In Experiment 1, the chromatin status and DNA fragmentation were measured in fresh and frozen-thawed spermatozoa from the same ejaculates. There was a significant increase in sperm chromatin destabilization and DNA fragmentation in frozen-thawed semen as compared with fresh semen. The proportions of spermatozoa labeled with (3)H-AMD were concurrent with elevated levels of sperm DNA fragmentation in K-3 extender, without cryoprotective substances, compared with L-HEY or L-LPFo extender. Regression analysis revealed that the results of the (3)H-AMD incorporation assay and NCA for frozen-thawed spermatozoa were correlated. Boars differed significantly in terms of post-thaw sperm DNA damage. In Experiment 2, the susceptibility of sperm chromatin to decondensation was assessed using a low concentration of heparin. Treatment of frozen-thawed spermatozoa with heparin revealed enhanced (3)H-AMD binding, suggesting nuclear chromatin decondensation. The deterioration in post-thaw sperm viability, such as motility, mitochondrial function and plasma membrane integrity, was concurrent with increased chromatin instability and DNA fragmentation. This is the first report to show that freezing-thawing procedure facilitated destabilization in the chromatin structure of boar spermatozoa, resulting in

  6. 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.

  7. The ubiquitin-dependent targeting pathway in Saccharomyces cerevisiae plays a critical role in multiple chromatin assembly regulatory steps.

    PubMed Central

    Harkness, Troy A A; Davies, Gerald F; Ramaswamy, Vijay; Arnason, Terra G

    2002-01-01

    In a screen designed to isolate Saccharomyces cerevisiae strains defective for in vitro chromatin assembly, two temperature-sensitive (ts) mutants were obtained: rmc1 and rmc3 (remodeling of chromatin). Cloning of RMC1 and RMC3 revealed a broad role for the ubiquitin-dependent targeting cascade as the ubiquitin-protein ligases (E3s), the anaphase promoting complex (APC; RMC1 encodes APC5) and Rsp5p, respectively, were identified. Genetic studies linked the rmc1/apc5 chromatin assembly defect to APC function: rmc1/apc5 genetically interacted with apc9Delta, apc10Delta, and cdc26Delta mutants. Furthermore, phenotypes associated with the rmc1/apc5 allele were consistent with defects in chromatin metabolism and in APC function: (i) UV sensitivity, (ii) plasmid loss, (iii) accumulation of G2/M cells, and (iv) suppression of the ts defect by growth on glucose-free media and by expression of ubiquitin. On the other hand, the multifunctional E3, Rsp5p, was shown to be required for both in vitro and in vivo chromatin assembly, as well as for the proper transcriptional and translational control of at least histone H3. The finding that the distinctly different E3 enzymes, APC and Rsp5p, both play roles in regulating chromatin assembly highlight the depth of the regulatory networks at play. The significance of these findings will be discussed. PMID:12399376

  8. 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

  9. 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

  10. 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.

  11. 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

  12. 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

  13. LIGHT SCATTERING: Observation of multiple scattering of laser radiation from a light-induced jet of microparticles in suspension

    NASA Astrophysics Data System (ADS)

    Kondrat'ev, Andrei V.

    2004-06-01

    Variation in the correlation function of light multiply scattered by a random medium was observed with increasing the incident beam power. The light-induced motion of microparticles in suspension, caused by a high-power laser radiation, serves as an additional factor in the decorrelation of the scattered light. The experimental data are in good agreement with the results of theoretical analysis.

  14. Visible Light-Induced Radical Rearrangement to Construct C-C Bonds via an Intramolecular Aryl Migration/Desulfonylation Process.

    PubMed

    Li, Yuyuan; Hu, Bei; Dong, Wuheng; Xie, Xiaomin; Wan, Jun; Zhang, Zhaoguo

    2016-08-19

    A highly efficient intramolecular selective aryl migration/desulfonylation of 2-bromo-N-aryl-N-(arenesulfonyl)amide via visible light-induced photoredox catalysis has been accomplished. This approach allows for the construction of a variety of multisubstituted N,2-diarylacetamide under mild reaction conditions. PMID:27351977

  15. 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. PMID:25955879

  16. 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

  17. Sarpogrelate, a 5-HT2A Receptor Antagonist, Protects the Retina From Light-Induced Retinopathy

    PubMed Central

    Tullis, Brandon E.; Ryals, Renee C.; Coyner, Aaron S.; Gale, Michael J.; Nicholson, Alex,; Ku, Cristy,; Regis, Dain,; Sinha, Wrik,; Datta, Shreya,; Wen, Yuquan,; Yang, Paul,; Pennesi, Mark E.

    2015-01-01

    Purpose To determine if sarpogrelate, a selective 5-HT2A receptor antagonist, is protective against light-induced retinopathy in BALB/c mice. Methods BALB/c mice were dosed intraperitoneally with 5, 15, 30, 40, or 50 mg/kg sarpogrelate 48, 24, and 0 hours prior to bright light exposure (10,000 lux) as well as 24 and 48 hours after exposure. Additionally, a single injection regimen was evaluated by injecting mice with 50 mg/kg sarpogrelate once immediately prior to light exposure. To investigate the potential for additive effects of serotonin receptor agents, a combination therapy consisting of sarpogrelate (15 mg/kg) and 8-OH-DPAT (1 mg/kg) was evaluated with the 5-day treatment regimen. Neuroprotection was characterized by the preservation of retinal thickness and function, measured by spectral-domain optical coherence tomography (SD-OCT) and electroretinography (ERG), respectively. Results Mice that were light damaged and injected with saline had significantly reduced outer retinal thickness, total retinal thickness, and ERG amplitudes compared with naïve mice. A 5-day administration of 15, 30, or 40 mg/kg of sarpogrelate was able to partially protect retinal morphology and full protection of retinal morphology was achieved with a 50 mg/kg dose. Both 15 and 30 mg/kg doses of sarpogrelate partially preserved retinal function measured by ERG, whereas 40 and 50 mg/kg doses fully preserved retinal function. Additionally, a single administration of 50 mg/kg sarpogrelate was able to fully preserve both retinal morphology and function. Administration of 15 mg/kg of sarpogrelate and 1 mg/kg of 8-OH-DPAT together demonstrated an additive effect and fully preserved retinal morphology. Conclusions A 5- or 1-day treatment with 50 mg/kg sarpogrelate can completely protect the retina of BALB/c mice from light-induced retinopathy. Partial protection can be achieved with lower doses starting at 15 mg/kg and protection increases in a dose-dependent manner. Treatment with low

  18. 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

  19. Assembly of telomeric chromatin to create ALTernative endings.

    PubMed

    O'Sullivan, Roderick J; Almouzni, Genevieve

    2014-11-01

    Circumvention of the telomere length-dependent mechanisms that control the upper boundaries of cellular proliferation is necessary for the unlimited growth of cancer. Most cancer cells achieve cellular immortality by up-regulating the expression of telomerase to extend and maintain their telomere length. However, a small but significant number of cancers do so via the exchange of telomeric DNA between chromosomes in a pathway termed alternative lengthening of telomeres, or ALT. Although it remains to be clarified why a cell chooses the ALT pathway and how ALT is initiated, recently identified mutations in factors that shape the chromatin and epigenetic landscape of ALT telomeres are shedding light on these mechanisms. In this review, we examine these recent findings and integrate them into the current models of the ALT mechanism. PMID:25172551

  20. Chromatin-modifying enzymes as therapeutic targets – Part 2

    PubMed Central

    Keppler, Brian R; Archer, Trevor K

    2009-01-01

    Background Part 1 of this review described the importance of histone acetylases, deacetylases, methylases and demethylases in transcriptional control and their potential as therapeutic targets. However, precise gene regulation requires the involvement of more than just the addition or removal of acetyl and methyl groups on histones. Histone phosphorylation, ubiquitylation, SUMOylation and poly-ADP-ribosylation, as well as ATP-dependent nucleosome remodeling complexes, play equally pivotal roles in the maintenance of transcriptional fidelity. Accordingly, the enzymes responsible for these modifications are also misregulated in various disease states. Objective To review the complex roles of chromatin-modifying enzymes in gene regulation and to highlight their potential as therapeutic targets. Methods This review is based on recent published literature and online resources. Results/conclusion In this second and final part of the review, we discuss the importance of these other histone and nucleosome modifying enzymes in gene transcription as well as their therapeutic potential. PMID:18851700

  1. ARTEMIS nuclease facilitates apoptotic chromatin cleavage.

    PubMed

    Britton, Sébastien; Frit, Philippe; Biard, Denis; Salles, Bernard; Calsou, Patrick

    2009-10-15

    One hallmark of apoptosis is DNA degradation that first appears as high molecular weight fragments followed by extensive internucleosomal fragmentation. During apoptosis, the DNA-dependent protein kinase (DNA-PK) is activated. DNA-PK is involved in the repair of DNA double-strand breaks (DSB) and its catalytic subunit is associated with the nuclease ARTEMIS. Here, we report that, on initiation of apoptosis in human cells by agents causing DNA DSB or by staurosporine or other agents, ARTEMIS binds to apoptotic chromatin together with DNA-PK and other DSB repair proteins. ARTEMIS recruitment to chromatin showed a time and dose dependency. It required DNA-PK protein kinase activity and was blocked by antagonizing the onset of apoptosis with a pan-caspase inhibitor or on overexpression of the antiapoptotic BCL2 protein. In the absence of ARTEMIS, no defect in caspase-3, poly(ADP-ribose) polymerase-1, and XRCC4 cleavage or in H2AX phosphorylation was observed and DNA-PK catalytic subunit was still phosphorylated on S2056 in response to staurosporine. However, DNA fragmentation including high molecular weight fragmentation was delayed in ARTEMIS-deficient cells compared with cells expressing ARTEMIS. In addition, ARTEMIS enhanced the kinetics of MLL gene cleavage at a breakage cluster breakpoint that is frequently translocated in acute or therapy-related leukemias. These results show a facilitating role for ARTEMIS at least in early, site-specific chromosome breakage during apoptosis. PMID:19808974

  2. Histone modification and chromatin remodeling during NER.

    PubMed

    Waters, Raymond; van Eijk, Patrick; Reed, Simon

    2015-12-01

    Here we review our developments of and results with high resolution studies on global genome nucleotide excision repair (GG-NER) in Saccharomyces cerevisiae. Technologies were developed to examine NER at nucleotide resolution in yeast sequences of choice and to determine how these related to local changes in chromatin. We focused on how GG-NER relates to histone acetylation for its functioning and we identified the histone acetyltransferase Gcn5 and acetylation at lysines 9/14 of histone H3 as a major factor in enabling efficient repair. Factors influencing this Gcn5-mediated event are considered which include Rad16, a GG-NER specific SWI/SNF factor and the yeast histone variant of H2AZ (Htz1). We describe results employing primarily MFA2 as a model gene, but also those with URA3 located at subtelomeric sequences. In the latter case we also see a role for acetylation at histone H4. We then consider the development of a high resolution genome-wide approach that enables one to examine correlations between histone modifications and the NER of UV-induced cyclobutane pyrimidine dimers throughout entire yeast genome. This is an approach that will enable rapid advances in understanding the complexities of how compacted chromatin in chromosomes is processed to access DNA damage before it is returned to its pre-damaged status to maintain epigenetic codes. PMID:26422133

  3. Facioscapulohumeral muscular dystrophy: consequences of chromatin relaxation

    PubMed Central

    van der Maarel, Silvère M.; Miller, Daniel G.; Tawil, Rabi; Filippova, Galina N.; Tapscott, Stephen J.

    2013-01-01

    Purpose of review In recent years we have seen remarkable progress in our understanding of the disease mechanism underlying facioscapulohumeral muscular dystrophy (FSHD). The purpose of this review is to provide a comprehensive overview of our current understanding of the disease mechanism and to discuss the observations supporting the possibility of a developmental defect in this disorder. Recent findings In the majority of cases FSHD is caused by contraction of the D4Z4 repeat array (FSHD1). This results in local chromatin relaxation and stable expression of the DUX4 retrogene in skeletal muscle, but only when a polymorphic DUX4 polyadenylation signal is present. In some cases (FSHD2), D4Z4 chromatin relaxation and stable DUX4 expression occurs in the absence of D4Z4 array contraction. DUX4 is a germline transcription factor and its expression in skeletal muscle leads to activation of early stem cell and germline programs and transcriptional activation of retroelements. Summary Recent studies have provided a plausible disease mechanism for FSHD where FSHD results from inappropriate expression of the germline transcription factor DUX4. The genes regulated by DUX4 suggest several mechanisms of muscle damage, and provide potential biomarkers and therapeutic targets that should be investigated in future studies. PMID:22892954

  4. The light-induced transcriptome of the zebrafish pineal gland reveals complex regulation of the circadian clockwork by light

    PubMed Central

    Ben-Moshe, Zohar; Alon, Shahar; Mracek, Philipp; Faigenbloom, Lior; Tovin, Adi; Vatine, Gad D.; Eisenberg, Eli; Foulkes, Nicholas S.; Gothilf, Yoav

    2014-01-01

    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

  5. 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

  6. Global chromatin fibre compaction in response to DNA damage

    SciTech Connect

    Hamilton, Charlotte; Hayward, Richard L.; Gilbert, Nick

    2011-11-04

    Highlights: Black-Right-Pointing-Pointer Robust KAP1 phosphorylation in response to DNA damage in HCT116 cells. Black-Right-Pointing-Pointer DNA repair foci are found in soluble chromatin. Black-Right-Pointing-Pointer Biophysical analysis reveals global chromatin fibre compaction after DNA damage. Black-Right-Pointing-Pointer DNA damage is accompanied by rapid linker histone dephosphorylation. -- Abstract: DNA is protected by packaging it into higher order chromatin fibres, but this can impede nuclear processes like DNA repair. Despite considerable research into the factors required for signalling and repairing DNA damage, it is unclear if there are concomitant changes in global chromatin fibre structure. In human cells DNA double strand break (DSB) formation triggers a signalling cascade resulting in H2AX phosphorylation ({gamma}H2AX), the rapid recruitment of chromatin associated proteins and the subsequent repair of damaged sites. KAP1 is a transcriptional corepressor and in HCT116 cells we found that after DSB formation by chemicals or ionising radiation there was a wave of, predominantly ATM dependent, KAP1 phosphorylation. Both KAP1 and phosphorylated KAP1 were readily extracted from cells indicating they do not have a structural role and {gamma}H2AX was extracted in soluble chromatin indicating that sites of damage are not attached to an underlying structural matrix. After DSB formation we did not find a concomitant change in the sensitivity of chromatin fibres to micrococcal nuclease digestion. Therefore to directly investigate higher order chromatin fibre structures we used a biophysical sedimentation technique based on sucrose gradient centrifugation to compare the conformation of chromatin fibres isolated from cells before and after DNA DSB formation. After damage we found global chromatin fibre compaction, accompanied by rapid linker histone dephosphorylation, consistent with fibres being more regularly folded or fibre deformation being stabilized by

  7. Light-induced lipid oxidation in sheep milk: effects of dietary grape seed and linseed, alone or in combination, on milk oxidative stability.

    PubMed

    Correddu, Fabio; Nudda, Anna; Manca, Maria G; Pulina, Giuseppe; Dalsgaard, Trine K

    2015-04-22

    The present work aimed to investigate the milk oxidative stability when the sheep diet includes a source of polyphenols (grape seed, (GS)) and a source of polyunsaturated fatty acids (linseed, (LIN)), alone or in combination (MIX) compared to a control group (CON). For this purpose light-induced oxidation in milk was studied. After 24 h of light exposure the lipid hydroperoxides increased in milk in the LIN and MIX groups. The calculated ratio between the level of lipid hydroperoxides and unsaturated fatty acids (UFAs) in milk was lower in the GS and MIX than in the LIN group. At the same time the level of the ratio between hexanal/linoleic acid in milk was lower in the GS and MIX than in the CON group. Although the dietary inclusion of grape seed did not reduce the level of lipid oxidation products in sheep milk, it effectively reduced the extent of oxidation of UFA. PMID:25828384

  8. 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

  9. Light induced suppression of sulfur in a cesium sputter ion source.

    PubMed

    Martschini, Martin; Rohlén, Johan; Andersson, Pontus; Golser, Robin; Hanstorp, Dag; Lindahl, Anton O; Priller, Alfred; Steier, Peter; Forstner, Oliver

    2012-04-01

    New techniques for suppression of atomic isobars in negative ion beams are of great interest for accelerator mass spectrometry (AMS). Especially small and medium-sized facilities can significantly extend their measurement capabilities to new interesting isotopes with a technique independent of terminal voltage. In a new approach, the effect of continuous wave laser light directed towards the cathode surface in a cesium sputter ion source of the Middleton type was studied. The laser light induced a significant change in oxygen, sulfur and chlorine negative ion production from a AgCl target. Approximately 100 mW of laser light reduced the sulfur to chlorine ratio by one order of magnitude. The effect was found to depend on laser power and ion source parameters but not on the laser wavelength. The time constant of the effect varied from a few seconds up to several minutes. Experiments were first performed at the ion beam facility GUNILLA at University of Gothenburg with macroscopic amounts of sulfur. The results were then reproduced at the VERA AMS facility with chemically cleaned AgCl targets containing ∼1 ppm sulfur. The physical explanation behind the effect is still unclear. Nevertheless, the technique has been successfully applied during a regular AMS measurement of (36)Cl. PMID:23576897

  10. Molecular models predict light-induced glutamine tautomerization in BLUF photoreceptors.

    PubMed

    Domratcheva, Tatiana; Grigorenko, Bella L; Schlichting, Ilme; Nemukhin, Alexander V

    2008-05-15

    The recently discovered photoreceptor proteins containing BLUF (sensor of blue light using FAD) domains mediate physiological responses to blue light in bacteria and euglena. In BLUF domains, blue light activates the flavin chromophore yielding a signaling state characterized by a approximately 10 nm red-shifted absorption. We developed molecular models for the dark and light states of the BLUF domain of the Rhodobacter sphaeroides AppA protein, which are based on the crystal structures and quantum-mechanical simulations. According to these models, photon absorption by the flavin results in a tautomerization and 180 degree rotation of the Gln side chain that interacts with the flavin cofactor. This chemical modification of the Gln residue induces alterations in the hydrogen bond network in the core of the photoreceptor domain, which were observed in numerous spectroscopic experiments. The calculated electronic transition energies and vibrational frequencies of the proposed dark and light states are consistent with the optical and IR spectral changes observed during the photocycle. Light-induced isomerization of an amino acid residue instead of a chromophore represents a feature that has not been described previously in photoreceptors. PMID:18263659

  11. 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

  12. Modeling light-induced currents in the eye of Chlamydomonas reinhardtii.

    PubMed

    Gradmann, D; Ehlenbeck, S; Hegemann, P

    2002-09-15

    Rhodopsin-mediated electrical events in green algae have been recorded in the past from the eyes of numerous micro-algae like Haematococcus pluvialis, Chlamydomonas reinhardtii and Volvox carteri. However, the electrical data gathered by suction-pipette techniques could be interpreted in qualitative terms only. Here we present two models that allow a quantitative analysis of such results: First, an electrical analog circuit for the cell in suction pipette configuration is established. Applying this model to experimental data from unilluminated cells of C. reinhardtii yields a membrane conductance of about 3 Sm(-2). Furthermore, an analog circuit allows the determination of the photocurrent fraction that is recorded under experimental conditions. Second, a reaction scheme of a rhodopsin-type photocycle with an early Ca(2+) conductance and a later H(+) conductance is presented. The combination of both models provides good fits to light-induced currents recorded from C. reinhardtii. Finally, it allowed the calculation of the impact of each model parameter on the time courses of observable photocurrent and of inferred transmembrane voltage. The reduction of the flash-to-peak times at increasing light intensities are explained by superposition of two kinetically distinct rhodopsins and by assuming that the Ca(2+)-conducting state decays faster at more positive membrane voltages. PMID:12235485

  13. Biomimetic Water-Collecting Fabric with Light-Induced Superhydrophilic Bumps.

    PubMed

    Wang, Yuanfeng; Wang, Xiaowen; Lai, Chuilin; Hu, Huawen; Kong, Yeeyee; Fei, Bin; Xin, John H

    2016-02-10

    To develop an efficient water-collecting surface that integrates both fast water-capturing and easy drainage properties is of high current interest for addressing global water issues. In this work, a superhydrophobic surface was fabricated on cotton fabric via manipulation of both the surface roughness and surface energy. This was followed by a subsequent spray coating of TiO2 nanosol that created light-induced superhydrophilic bumps with a unique raised structure as a result of the interfacial tension of the TiO2 nanosol sprayed on the superhydrophobic fiber surface. These raised TiO2 bumps induce both a wettability gradient and a shape gradient, synergistically accelerating water coalescence and water collection. The in-depth study revealed that the quantity and the distribution of the TiO2 had a significant impact on the final water collection efficiency. This inexpensive and facilely fabricated fabric biomimicks the desert beetle's back and spider silk, which are capable of fog harvesting without additional energy consumption. PMID:26652924

  14. 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.

  15. 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.

  16. Compartmentalization and Ca2+ buffering are essential for prevention of light induced retinal degeneration

    PubMed Central

    Weiss, Shirley; Kohn, Elkana; Dadon, Daniela; Katz, Ben; Peters, Maximilian; Lebendiker, Mario; Kosloff, Mickey; Jo Colley, Nansi; Minke, Baruch

    2012-01-01

    Fly photoreceptors are polarized cells, which have an extended interface between their cell body and the light signaling compartment, the rhabdomere. Upon intense illumination, rhabdomeric calcium concentration reaches millimolar levels that would be toxic if Ca2+ diffusion between the rhabdomere and cell body was not robustly attenuated. Yet, it is not clear how such effective attenuation is obtained. Here we show that Ca2+ homeostasis in the photoreceptor cell relies on the protein calphotin. This unique protein functions as an immobile Ca2+ buffer, which is localized along the base of the rhabdomere, separating the signaling compartment from the cell body. Generation and analyses of transgenic Drosophila strains, in which calphotin expression levels were reduced in a graded manner, showed that moderately reduced calphotin expression impaired Ca2+ homeostasis while calphotin elimination resulted in severe light dependent photoreceptor degeneration. Electron microscopy, electrophysiology and optical methods revealed that the degeneration was rescued by prevention of Ca2+ overload via overexpression of CalX, the Na+-Ca2+ exchanger. In addition, Ca2+ imaging experiments showed that reduced calphotin levels resulted in abnormally fast kinetics of Ca2+elevation in photoreceptor cells. Together, the data suggest that calphotin functions as a Ca2+ buffer; a possibility which we directly demonstrate by expressing calphotin in a heterologous expression system. We propose that calphotin-mediated compartmentalization and Ca2+ buffering constitute an effective strategy to protect cells from Ca2+ overload and light induced degeneration. PMID:23077055

  17. Visible light induced photoelectrochemical biosensing based on oxygen-sensitive quantum dots.

    PubMed

    Wang, Wenjing; Bao, Lei; Lei, Jianping; Tu, Wenwen; Ju, Huangxian

    2012-09-26

    A visible light induced photoelectrochemical biosensing platform based on oxygen-sensitive near-infrared quantum dots (NIR QDs) was developed for detection of glucose. The NIR QDs were synthesized in an aqueous solution, and characterized with scanning electron microscopy and X-ray photoelectron spectroscopy. The as-prepared NIR QDs were employed to construct oxygen-sensitive photoelectrochemical biosensor on a fluorine-doped tin oxide (FTO) electrode. The oxygen dependency of the photocurrent was investigated at as-prepared electrode, which demonstrated the signal of photocurrent is suppressed with the decreasing of oxygen. Coupling with the consumption of oxygen during enzymatic reaction, a photoelectrochemical strategy was proposed for the detection of substrate. Using glucose oxidase (GOx) as a model enzyme, that is, GOx was covalently attached to the surface of CdTe QDs, the resulting biosensor showed the sensitive response to glucose. Under the irradiation of visible light of a wavelength at 505 nm, the proposed photoelectrochemical method could detect glucose ranging from 0.1 mM to 11 mM with a detection limit of 0.04 mM. The photoelectrochemical biosensor showed a good performance with high upper detection limit, acceptable stability and accuracy, providing an alternative method for monitoring biomolecules and extending the application of near-infrared QDs. PMID:22935371

  18. 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.

  19. Model for the light-induced magnetization in singly charged quantum dots

    NASA Astrophysics Data System (ADS)

    Henriques, A. B.; Cordeiro, R. C.; Koenraad, P. M.; Otten, F. W. M.; Bayer, M.

    2015-02-01

    Magnetization is induced in an ensemble of quantum dots, each charged with a single electron, when it is illuminated with a short circularly polarized light pulse that is resonant with the fundamental energy gap of the quantum dots. In this investigation, a quantum-mechanical model for the light-induced magnetization is presented. The phase of the magnetization precession as a function of the strength of the magnetic field in a Voigt geometry is in excellent agreement with experimental data measured on (In,Ga)As singly charged quantum dot ensembles. It is demonstrated that the precession of the hole in the trion plays a vital role because it determines the amplitude and phase of the magnetization precession. The model could also be easily extended to describe positively charged quantum dots. We also suggest that our theory, combined with measurements of the phase as a function of magnetic field, can be used as a technique to measure the resonant trion lifetime as a function of QD emission energy.

  20. Evolution of light-induced vapor generation at a liquid-immersed metallic nanoparticle

    PubMed Central

    Zhen, Yu-Rong; Neumann, Oara; Polman, Albert; García de Abajo, F. Javier

    2013-01-01

    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 micron 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. PMID:23517407

  1. 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

  2. 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

  3. 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.

  4. 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. PMID:26341017

  5. Use of quantitative light-induced fluorescence to monitor tooth whitening

    NASA Astrophysics Data System (ADS)

    Amaechi, Bennett T.; Higham, Susan M.

    2001-04-01

    The changing of tooth shade by whitening agents occurs gradually. Apart from being subjective and affected by the conditions of the surroundings, visual observation cannot detect a very slight change in tooth color. An electronic method, which can communicate the color change quantitatively, would be more reliable. Quantitative Light- induced Fluorescence (QLF) was developed to detect and assess dental caries based on the phenomenon of change of autofluorescence of a tooth by demineralization. However, stains on the tooth surface exhibit the same phenomenon, and therefore QLF can be used to measure the percentage fluorescence change of stained enamel with respect to surrounding unstained enamel. The present study described a technique of assessing the effect of a tooth-whitening agent using QLF. This was demonstrated in two experiments in which either wholly or partially stained teeth were whitened by intermittent immersion in sodium hypochlorite. Following each immersion, the integrated fluorescence change due to the stain was quantified using QLF. In either situation, the value of (Delta) Q decreased linearly as the tooth regained its natural shade. It was concluded that gradual changing of the shade of discolored teeth by a whitening agent could be quantified using QLF.

  6. 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.

  7. 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.

  8. 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

  9. 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.

  10. 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

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. Kinetic and Thermodynamic Analysis of the Light-induced Processes in Plant and Cyanobacterial Phytochromes

    PubMed Central

    Chizhov, Igor; Zorn, Björn; Manstein, Dietmar J.; Gärtner, Wolfgang

    2013-01-01

    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

  17. Light induced suppression of sulfur in a cesium sputter ion source

    PubMed Central

    Martschini, Martin; Rohlén, Johan; Andersson, Pontus; Golser, Robin; Hanstorp, Dag; Lindahl, Anton O.; Priller, Alfred; Steier, Peter; Forstner, Oliver

    2012-01-01

    New techniques for suppression of atomic isobars in negative ion beams are of great interest for accelerator mass spectrometry (AMS). Especially small and medium-sized facilities can significantly extend their measurement capabilities to new interesting isotopes with a technique independent of terminal voltage. In a new approach, the effect of continuous wave laser light directed towards the cathode surface in a cesium sputter ion source of the Middleton type was studied. The laser light induced a significant change in oxygen, sulfur and chlorine negative ion production from a AgCl target. Approximately 100 mW of laser light reduced the sulfur to chlorine ratio by one order of magnitude. The effect was found to depend on laser power and ion source parameters but not on the laser wavelength. The time constant of the effect varied from a few seconds up to several minutes. Experiments were first performed at the ion beam facility GUNILLA at University of Gothenburg with macroscopic amounts of sulfur. The results were then reproduced at the VERA AMS facility with chemically cleaned AgCl targets containing ∼1 ppm sulfur. The physical explanation behind the effect is still unclear. Nevertheless, the technique has been successfully applied during a regular AMS measurement of 36Cl. PMID:23576897

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

    PubMed

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

    2016-01-01

    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

  19. Light-induced autofluorescence of animal skin used in tissue optical modeling

    NASA Astrophysics Data System (ADS)

    Borisova, E.; Bliznakova, I.; Troyanova, P.; Avramov, L.

    2007-07-01

    Light-induced autofluorescence spectroscopy provides many possibilities for medical diagnostics needs for differentiation of tissue pathologies including cancer. For the needs of clinical practice scientists collect spectral data from patients in vivo or they study different tumor models to obtain objective information for fluorescent properties of every kind of normal and diseased tissue. Therefore it is very important to find the most appropriate and close to the human skin samples from the point of view of laser-induced fluorescence spectroscopy, which will give the possibility for easier transfer of data obtained in animal models to spectroscopic medical diagnostics in humans. In this study are presented some results for in vitro detection of the autofluorescence signals of the animal skin (pig and chicken) with using of LEDs as excitation sources (maximum emission at 365, 375, 385 and 400 nm). The autofluorescence signals from in vivo human skin were also detected for comparison with the models' results. Specific features of the spectra measured are discussed and there are proposed some of the origins of the fluorescence signals obtained. Fluorescence maxima detected are addressed to the typical fluorophores existing in the cutaneous tissues. Influence of main skin absorbers, namely melanin and hemoglobin, is also discussed.

  20. Light-induced defects in hydrogenated amorphous silicon studied by the constant-photocurrent method

    NASA Astrophysics Data System (ADS)

    Schmidt, J. A.; Arce, R.; Buitrago, R. H.; Koropecki, R. R.

    1997-04-01

    The light-induced creation of metastable defects in undoped hydrogenated amorphous silicon has been followed using photoconductivity and absorption coefficient measurements. The density of states in the gap was obtained from the deconvolution of the subgap absorption coefficient measured by the constant-photocurrent method. We found that the decay of the photoconductivity and the evolution of the integrated density of subgap states follow the dependence on illumination time (till) predicted by the ``bond-breaking'' model. The density of occupied states obtained from the deconvolution procedure shows the presence of two peaks within the gap. After subtracting the valence band-tail contribution, these peaks can be well fitted with two Gaussians. The areas of both Gaussians increase as t1/3ill while their positions and widths remain unchanged. According to the energy position of these peaks, they are ascribed to the neutral and negatively charged silicon dangling bonds D0 and D-. We found that in this intrinsic sample the density of charged defects exceeds that of neutral defects, their ratio D-/D0 being approximately 2.6. This ratio is independent of the illumination time.