WorldWideScience

Sample records for alternative chromatin tethers

  1. Nuclear Fractionation Reveals Thousands of Chromatin-Tethered Noncoding RNAs Adjacent to Active Genes

    Directory of Open Access Journals (Sweden)

    Michael S. Werner

    2015-08-01

    Full Text Available A number of long noncoding RNAs (lncRNAs have been reported to regulate transcription via recruitment of chromatin modifiers or bridging distal enhancer elements to gene promoters. However, the generality of these modes of regulation and the mechanisms of chromatin attachment for thousands of unstudied human lncRNAs remain unclear. To address these questions, we performed stringent nuclear fractionation coupled to RNA sequencing. We provide genome-wide identification of human chromatin-associated lncRNAs and demonstrate tethering of RNA to chromatin by RNAPII is a pervasive mechanism of attachment. We also uncovered thousands of chromatin-enriched RNAs (cheRNAs that share molecular properties with known lncRNAs. Although distinct from eRNAs derived from active prototypical enhancers, the production of cheRNAs is strongly correlated with the expression of neighboring protein-coding genes. This work provides an updated framework for nuclear RNA organization that includes a large chromatin-associated transcript population correlated with active genes and may prove useful in de novo enhancer annotation.

  2. EBV Latency Types Adopt Alternative Chromatin Conformations

    Science.gov (United States)

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

    2011-01-01

    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

  3. EBV latency types adopt alternative chromatin conformations.

    Directory of Open Access Journals (Sweden)

    Italo Tempera

    2011-07-01

    Full Text Available 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.

  4. LEM-3 is a midbody-tethered DNA nuclease that resolves chromatin bridges during late mitosis.

    Science.gov (United States)

    Hong, Ye; Sonneville, Remi; Wang, Bin; Scheidt, Viktor; Meier, Bettina; Woglar, Alexander; Demetriou, Sarah; Labib, Karim; Jantsch, Verena; Gartner, Anton

    2018-02-20

    Faithful chromosome segregation and genome maintenance requires the removal of all DNA bridges that physically link chromosomes before cells divide. Using C. elegans embryos we show that the LEM-3/Ankle1 nuclease defines a previously undescribed genome integrity mechanism by processing DNA bridges right before cells divide. LEM-3 acts at the midbody, the structure where abscission occurs at the end of cytokinesis. LEM-3 localization depends on factors needed for midbody assembly, and LEM-3 accumulation is increased and prolonged when chromatin bridges are trapped at the cleavage plane. LEM-3 locally processes chromatin bridges that arise from incomplete DNA replication, unresolved recombination intermediates, or the perturbance of chromosome structure. Proper LEM-3 midbody localization and function is regulated by AIR-2/Aurora B kinase. Strikingly, LEM-3 acts cooperatively with the BRC-1/BRCA1 homologous recombination factor to promote genome integrity. These findings provide a molecular basis for the suspected role of the LEM-3 orthologue Ankle1 in human breast cancer.

  5. Non-farnesylated B-type lamin can tether chromatin inside the nucleus and its chromatin interaction requires the Ig-fold region.

    Science.gov (United States)

    Uchino, Ryo; Sugiyama, Shin; Katagiri, Motoi; Chuman, Yoshiro; Furukawa, Kazuhiro

    2017-02-01

    Lamins are thought to direct heterochromatin to the nuclear lamina (NL); however, this function of lamin has not been clearly demonstrated in vivo. To address this, we analyzed polytene chromosome morphology when artificial lamin variants were expressed in Drosophila endoreplicating cells. We found that the CaaX-motif-deleted B-type lamin Dm 0 , but not A-type lamin C, was able to form a nuclear envelope-independent layer that was closely associated with chromatin. Other nuclear envelope proteins were not detected in this "ectopic lamina," and the associated chromatin showed a repressive histone modification maker but not a permissive histone modification marker nor RNA polymerase II proteins. Furthermore, deletion of the C-terminal lamin-Ig-fold domain prevents chromatin association with this ectopic lamina. Thus, non-farnesylated B-type lamin Dm 0 can form an ectopic lamina and induce changes to chromatin structure and status inside the interphase nucleus.

  6. The selector gene Pax7 dictates alternate pituitary cell fates through its pioneer action on chromatin remodeling

    NARCIS (Netherlands)

    Budry, L.; Balsalobre, A.; Gauthier, Y.; Khetchoumian, K.; L'Honore, A.; Vallette-Kasic, S.; Brue, T; Figarella-Branger, D.; Meij, B.P.|info:eu-repo/dai/nl/164045805; Drouin, J.

    2012-01-01

    Genes Dev. 2012 Oct 15;26(20):2299-310. doi: 10.1101/gad.200436.112. The selector gene Pax7 dictates alternate pituitary cell fates through its pioneer action on chromatin remodeling. Budry L, Balsalobre A, Gauthier Y, Khetchoumian K, L'honoré A, Vallette S, Brue T, Figarella-Branger D, Meij B,

  7. Noncoding transcription by alternative rna polymerases dynamically regulates an auxin-driven chromatin loop

    KAUST Repository

    Ariel, Federico D.

    2014-08-01

    The eukaryotic epigenome is shaped by the genome topology in three-dimensional space. Dynamic reversible variations in this epigenome structure directly influence the transcriptional responses to developmental cues. Here, we show that the Arabidopsis long intergenic noncoding RNA (lincRNA) APOLO is transcribed by RNA polymerases II and V in response to auxin, a phytohormone controlling numerous facets of plant development. This dual APOLO transcription regulates the formation of a chromatin loop encompassing the promoter of its neighboring gene PID, a key regulator of polar auxin transport. Altering APOLO expression affects chromatin loop formation, whereas RNA-dependent DNA methylation, active DNA demethylation, and Polycomb complexes control loop dynamics. This dynamic chromatin topology determines PID expression patterns. Hence, the dual transcription of a lincRNA influences local chromatin topology and directs dynamic auxin-controlled developmental outputs on neighboring genes. This mechanism likely underscores the adaptive success of plants in diverse environments and may be widespread in eukaryotes. © 2014 Elsevier Inc.

  8. The C-terminal domain of Brd2 is important for chromatin interaction and regulation of transcription and alternative splicing

    Czech Academy of Sciences Publication Activity Database

    Hnilicová, Jarmila; Hozeifi, Samira; Stejskalová, Eva; Dušková, Eva; Poser, I.; Humpolíčková, Jana; Hof, Martin; Staněk, David

    2013-01-01

    Roč. 24, č. 22 (2013), s. 3557-3568 ISSN 1059-1524 R&D Projects: GA AV ČR KAN200520801; GA ČR GAP305/10/0424; GA ČR GBP208/12/G016; GA ČR(CZ) GBP305/12/G034 Institutional support: RVO:68378050 ; RVO:61388955 Keywords : Brd2 * alternative splicing * chromatin Subject RIV: EB - Genetics ; Molecular Biology; CF - Physical ; Theoretical Chemistry (UFCH-W) Impact factor: 4.548, year: 2013

  9. Reprogramming chromatin

    DEFF Research Database (Denmark)

    Ehrensberger, Andreas Hasso; Svejstrup, Jesper Qualmann

    2012-01-01

    attributed to high kinetic barriers that affect all cells equally and can only be overcome by rare stochastic events. The barriers to reprogramming are likely to involve transformations of chromatin state because (i) inhibitors of chromatin-modifying enzymes can enhance the efficiency of reprogramming...... and (ii) knockdown or knock-out of chromatin-modifying enzymes can lower the efficiency of reprogramming. Here, we review the relationship between chromatin state transformations (chromatin reprogramming) and cellular reprogramming, with an emphasis on transcription factors, chromatin remodeling factors...

  10. Tethered Lubricants

    Energy Technology Data Exchange (ETDEWEB)

    Archer, Lynden

    2010-09-15

    We have performed extensive experimental and theoretical studies of interfacial friction, relaxation dynamics, and thermodynamics of polymer chains tethered to points, planes, and particles. A key result from our tribology studies using lateral force microscopy (LFM) measurements of polydisperse brushes of linear and branched chains densely grafted to planar substrates is that there are exceedingly low friction coefficients for these systems. Specific project achievements include: (1) Synthesis of three-tiered lubricant films containing controlled amounts of free and pendent PDMS chains, and investigated the effect of their molecular weight and volume fraction on interfacial friction. (2.) Detailed studies of a family of hairy particles termed nanoscale organic hybrid materials (NOHMs) and demonstration of their use as lubricants.

  11. Vertical Exploration Using Tethers

    Science.gov (United States)

    Bartlett, P. W.; Heys, S.; Drozdowski, Z.; Kennedy, T.; Wagner, M.

    2009-03-01

    Unobserved geologic features and epochs on multiple planetary bodies could be accessed using robotic tethers. Recent technology development shows the promise of tethers enabling steep slope mobility, downhole measurements and in situ sensing from aerial platforms.

  12. Where splicing joins chromatin

    Czech Academy of Sciences Publication Activity Database

    Hnilicová, Jarmila; Staněk, David

    2011-01-01

    Roč. 2, č. 3 (2011), s. 182-188 ISSN 1949-1034 R&D Projects: GA ČR GAP305/10/0424; GA AV ČR KAN200520801 Institutional research plan: CEZ:AV0Z50520514 Keywords : chromatin * exon * alternative splicing * transcription * snRNP Subject RIV: EB - Genetics ; Molecular Biology

  13. Two-Way Tether Gun

    Science.gov (United States)

    Sanger, George F.

    1994-01-01

    Safety-tether device enables crewmembers on spacecraft to retrieve crewmember drifting away from spacecraft. Alternatively, drifting crewmember who carries device uses it to grasp and return to spacecraft. Also used on Earth. For example, rescuer on vessel or pier uses it to retrieve and haul drowning or unconscious person to safety; drifting person or rescuer in water uses it to grasp and hold onto support.

  14. A Tether Is a Tether Is a Tether: Tethering at Membrane Contact Sites.

    Science.gov (United States)

    Eisenberg-Bord, Michal; Shai, Nadav; Schuldiner, Maya; Bohnert, Maria

    2016-11-21

    Membrane contact sites enable interorganelle communication by positioning organelles in close proximity using molecular "tethers." With a growing understanding of the importance of contact sites, the hunt for new contact sites and their tethers is in full swing. Determining just what is a tether has proven challenging. Here, we aim to delineate guidelines that define the prerequisites for categorizing a protein as a tether. Setting this gold standard now, while groups from different disciplines are beginning to explore membrane contact sites, will enable efficient cooperation in the growing field and help to realize a great collaborative opportunity to boost its development. Copyright © 2016 Elsevier Inc. All rights reserved.

  15. lysosome tethering and fusion

    Indian Academy of Sciences (India)

    AMIT TULI

    Molecular mechanisms regulating endosome- lysosome tethering and fusion. Mahak Sharma. Assistant Professor & Wellcome Trust-DBT Intermediate Fellow. Department of Biological Sciences. IISER-Mohali ...

  16. The investigation of tethered satellite system dynamics

    Science.gov (United States)

    Lorenzini, E. C.

    1986-01-01

    The analysis of the rotational dynamics of the satellite was focused on the rotational amplitude increase of the satellite, with respect to the tether, during retrieval. The dependence of the rotational amplitude upon the tether tension variation to the power 1/4 was thoroughly investigated. The damping of rotational oscillations achievable by reel control was also quantified while an alternative solution that makes use of a lever arm attached with a universal joint to the satellite was proposed. Comparison simulations between the Smithsonian Astrophysical Observatory and the Martin Marietta (MMA) computer code of reteival maneuvers were also carried out. The agreement between the two, completely independent, codes was extremely close, demonstrating the reliability of the models. The slack tether dynamics during reel jams was analytically investigated in order to identify the limits of applicability of the SLACK3 computer code to this particular case. Test runs with SLACK3 were also carried out.

  17. Proteomics of a fuzzy organelle: interphase chromatin

    Science.gov (United States)

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

    2014-01-01

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

  18. GRASP: A multitasking tether

    Directory of Open Access Journals (Sweden)

    Catherine eRabouille

    2016-01-01

    Full Text Available Originally identified as Golgi stacking factors in vitro, the Golgi reassembly stacking protein (GRASP family has been shown to act as membrane tethers with multiple cellular roles. As an update to previous comprehensive reviews of the GRASP family (Vinke et al., 2011 (Giuliani et al., 2011;Jarvela and Linstedt, 2012, we outline here the latest findings concerning their diverse roles. New insights into the mechanics of GRASP-mediated tethering come from recent crystal structures. The models of how GRASP65 and GRASP55 tether membranes relate directly to their role in Golgi ribbon formation in mammalian cells and the unlinking of the ribbon at the onset of mitosis. However, it is also clear that GRASPs act outside the Golgi with roles at the ER and ER exit sites (ERES. Furthermore, the proteins of this family display other roles upon cellular stress, especially in mediating unconventional secretion of both transmembrane proteins (Golgi bypass and cytoplasmic proteins (through secretory autophagosomes.

  19. Proposed Mechanisms of Tethered Antimicrobial Peptide Chrysophsin-1 as a Function of Tether Length Using QCM-D.

    Science.gov (United States)

    Lozeau, Lindsay D; Alexander, Todd E; Camesano, Terri A

    2015-10-15

    Rising antibiotic resistance has led to a call for the development of alternative antibiotics. Antimicrobial peptides (AMPs) are promising, but their potential has not been fully explored because of toxicity and lack of stability in vivo. Multiple recent studies have focused on surface immobilization of AMPs to maximize antimicrobial activity and stability while mitigating toxicity. We covalently tethered cysteine-modified chrysophsin-1 (C-CHY1) via PEG of three molecular weights, 866, 2000, and 7500. Quartz crystal microbalance with dissipation (QCM-D) was used to characterize thickness and grafting density of tethered C-CHY1, which were related to its activity against Staphylococcus aureus and Escherichia coli and found to be important in determining mechanisms leading to activity. The PEG 866 tether promoted an antimicrobial mechanism that caused displacement of positive cations from bacterial membranes. The PEG 7500 tether maintained C-CHY1's ability to effectively form membrane pores, promoting the highest activity. When AMP was tethered with PEG 2000, antimicrobial activity was limited, apparently because neither mechanism of AMP activity was able to occur with this tether. Using QCM-D, we calculated thickness and density of PEG-tethered C-CHY1 and correlated it with antimicrobial effectiveness to determine the mechanisms by which tethered C-CHY1 acts against bacteria.

  20. Modelling Tethered Enzymatic Reactions

    Science.gov (United States)

    Solis Salas, Citlali; Goyette, Jesse; Coker-Gordon, Nicola; Bridge, Marcus; Isaacson, Samuel; Allard, Jun; Maini, Philip; Dushek, Omer

    Enzymatic reactions are key to cell functioning, and whilst much work has been done in protein interaction in cases where diffusion is possible, interactions of tethered proteins are poorly understood. Yet, because of the large role cell membranes play in enzymatic reactions, several reactions may take place where one of the proteins is bound to a fixed point in space. We develop a model to characterize tethered signalling between the phosphatase SHP-1 interacting with a tethered, phosphorylated protein. We compare our model to experimental data obtained using surface plasmon resonance (SPR). We show that a single SPR experiment recovers 5 independent biophysical/biochemical constants. We also compare the results between a three dimensional model and a two dimensional model. The work gives the opportunity to use known techniques to learn more about signalling processes, and new insights into how enzyme tethering alters cellular signalling. With support from the Mexican Council for Science and Technology (CONACyT), the Public Education Secretariat (SEP), and the Mexican National Autonomous University's Foundation (Fundacion UNAM).

  1. Nuclear Matrix protein SMAR1 represses HIV-1 LTR mediated transcription through chromatin remodeling

    International Nuclear Information System (INIS)

    Sreenath, Kadreppa; Pavithra, Lakshminarasimhan; Singh, Sandeep; Sinha, Surajit; Dash, Prasanta K.; Siddappa, Nagadenahalli B.; Ranga, Udaykumar; Mitra, Debashis; Chattopadhyay, Samit

    2010-01-01

    Nuclear Matrix and MARs have been implicated in the transcriptional regulation of host as well as viral genes but their precise role in HIV-1 transcription remains unclear. Here, we show that > 98% of HIV sequences contain consensus MAR element in their promoter. We show that SMAR1 binds to the LTR MAR and reinforces transcriptional silencing by tethering the LTR MAR to nuclear matrix. SMAR1 associated HDAC1-mSin3 corepressor complex is dislodged from the LTR upon cellular activation by PMA/TNFα leading to an increase in the acetylation and a reduction in the trimethylation of histones, associated with the recruitment of RNA Polymerase II on the LTR. Overexpression of SMAR1 lead to reduction in LTR mediated transcription, both in a Tat dependent and independent manner, resulting in a decreased virion production. These results demonstrate the role of SMAR1 in regulating viral transcription by alternative compartmentalization of LTR between the nuclear matrix and chromatin.

  2. Chromatin is wonderful stuff.

    NARCIS (Netherlands)

    van Driel, R.

    2007-01-01

    Chromatin molecules have properties that set them aside from all other biomacromolecules in the cell. (i) Chromosomes, which are single chromatin molecules, are the largest macromolecules in eukaryotic cells. (ii) Chromatin molecules carry the cell's genetic and epigenetic information and all

  3. Assessing tether anchor labeling and usability in pickup trucks.

    Science.gov (United States)

    Klinich, Kathleen D; Manary, Miriam A; Malik, Laura A; Flannagan, Carol A; Jermakian, Jessica S

    2018-04-03

    reviewing the vehicle manuals. Current implementations of tether anchors among pickup trucks are not intuitive for child restraint installations, and alternate designs should be explored. Several different labeling interventions were ineffective at achieving correct tether use in pickup trucks.

  4. Electrodynamic Tethers for Jovian Exploration

    Science.gov (United States)

    2004-01-01

    This is an artist's concept of an orbiting space vehicle in the Jovian system using an electrodynamic tether propellantless propulsion system. Electrodynamic tethers offer the potential to greatly extend and enhance future scientific missions to Jupiter and the Jovian system. Like Earth, Jupiter posses a strong magnetic field and a significant magnetosphere. This may make it feasible to operate electrodynamic tethers for propulsion and power generation.

  5. Space tether dynamics: an introduction

    Science.gov (United States)

    Denny, Mark

    2018-05-01

    The dynamics of orbiting tethers (space elevators and skyhooks) is developed from an unusual direction: Lagrangian rather than Newtonian mechanics. These basic results are derived among others: space elevator required length with and without counterweight, location and magnitude of maximum tether tension, skyhook orbital parameters and tether tension. These conceptual devices are being increasingly discussed as technologically feasible; here they make an interesting pedagogical application of Lagrangian mechanics suitable for undergraduate physics students.

  6. Chromatin Structure and Function

    CERN Document Server

    Wolffe, Alan P

    1999-01-01

    The Third Edition of Chromatin: Structure and Function brings the reader up-to-date with the remarkable progress in chromatin research over the past three years. It has been extensively rewritten to cover new material on chromatin remodeling, histone modification, nuclear compartmentalization, DNA methylation, and transcriptional co-activators and co-repressors. The book is written in a clear and concise fashion, with 60 new illustrations. Chromatin: Structure and Function provides the reader with a concise and coherent account of the nature, structure, and assembly of chromatin and its active

  7. Space Station tethered elevator system

    Science.gov (United States)

    Haddock, Michael H.; Anderson, Loren A.; Hosterman, K.; Decresie, E.; Miranda, P.; Hamilton, R.

    1989-01-01

    The optimized conceptual engineering design of a space station tethered elevator is presented. The tethered elevator is an unmanned, mobile structure which operates on a ten-kilometer tether spanning the distance between Space Station Freedom and a platform. Its capabilities include providing access to residual gravity levels, remote servicing, and transportation to any point along a tether. The report discusses the potential uses, parameters, and evolution of the spacecraft design. Emphasis is placed on the elevator's structural configuration and three major subsystem designs. First, the design of elevator robotics used to aid in elevator operations and tethered experimentation is presented. Second, the design of drive mechanisms used to propel the vehicle is discussed. Third, the design of an onboard self-sufficient power generation and transmission system is addressed.

  8. The physics of chromatin

    OpenAIRE

    Schiessel, Helmut

    2003-01-01

    Recent progress has been made in the understanding of the physical properties of chromatin -- the dense complex of DNA and histone proteins that occupies the nuclei of plant and animal cells. Here I will focus on the two lowest levels of the hierarchy of DNA folding into the chromatin complex: (i) the nucleosome, the chromatin repeating unit consisting of a globular aggregate of eight histone proteins with the DNA wrapped around: its overcharging, the DNA unwrapping transition, the ''sliding'...

  9. Dynamic analysis of the tether transportation system using absolute nodal coordinate formulation

    Science.gov (United States)

    Sun, Xin; Xu, Ming; Zhong, Rui

    2017-10-01

    Long space tethers are becoming a rising concern as an alternate way for transportation in space. It benefits from fuel economizing. This paper focuses on the dynamics of the tether transportation system, which consists of two end satellites connected by a flexible tether, and a movable vehicle driven by the actuator carried by itself. The Absolute Nodal Coordinate Formulation is applied to the establishment of the equation of motion, so that the influence caused by the distributed mass and elasticity of the tether is introduced. Moreover, an approximated method for accelerating the calculation of the generalized gravitational forces on the tether is proposed by substituting the volume integral every step into summation of finite terms. Afterwards, dynamic evolutions of such a system in different configurations are illustrated using numerical simulations. The deflection of the tether and the trajectory of the crawler during the transportation is investigated. Finally, the effect on the orbit of the system due to the crawler is revealed.

  10. SUMO and Chromatin Remodeling.

    Science.gov (United States)

    Wotton, David; Pemberton, Lucy F; Merrill-Schools, Jacqueline

    2017-01-01

    Many of the known SUMO substrates are nuclear proteins, which regulate gene expression and chromatin dynamics. Sumoylation, in general, appears to correlate with decreased transcriptional activity, and in many cases modulation of the chromatin template is implicated. Sumoylation of the core histones is associated with transcriptional silencing, and transcription factor sumoylation can decrease gene expression by promoting recruitment of chromatin modifying enzymes. Additionally, sumoylation of transcriptional corepressors and chromatin remodeling enzymes can influence interactions with other transcriptional regulators, and alter their enzymatic activity. In some cases, proteins that are components of transcriptional corepressor complexes have been shown to be SUMO E3 ligases, further emphasizing the integration of sumoylation with the regulation of chromatin remodeling. Despite the evidence suggesting that sumoylation is primarily repressive for access to chromatin, recent analyses suggest that protein sumoylation on the chromatin template may play important roles at highly expressed genes. Elucidating the dynamic interplay of sumoylation with other post-translational modifications of histones and chromatin associated proteins will be key to fully understanding the regulation of access to the chromatin template.

  11. Tether Elevator Crawler Systems (TECS)

    Science.gov (United States)

    Swenson, Frank R.

    1987-01-01

    One of the needs of the experimenters on the space station is access to steady and controlled-variation microgravity environments. A method of providing these environments is to place the experiment on a tether attached to the space station. This provides a high degree of isolation from structural oscillations and vibrations. Crawlers can move these experiments along the tethers to preferred locations, much like an elevator. This report describes the motion control laws developed for these crawlers and the testing of laboratory models of these tether elevator crawlers.

  12. Stability of DNA-tethered lipid membranes with mobile tethers.

    Science.gov (United States)

    Chung, Minsub; Boxer, Steven G

    2011-05-03

    We recently introduced two approaches for tethering planar lipid bilayers as membrane patches to either a supported lipid bilayer or DNA-functionalized surface using DNA hybridization (Chung, M.; Lowe, R. D.; Chan, Y-H. M.; Ganesan, P. V.; Boxer, S. G. J. Struct. Biol.2009, 168, 190-9). When mobile DNA tethers are used, the tethered bilayer patches become unstable, while they are stable if the tethers are fixed on the surface. Because the mobile tethers between a patch and a supported lipid bilayer offer a particularly interesting architecture for studying the dynamics of membrane-membrane interactions, we have investigated the sources of instability, focusing on membrane composition. The most stable patches were made with a mixture of saturated lipids and cholesterol, suggesting an important role for membrane stiffness. Other factors such as the effect of tether length, lateral mobility, and patch membrane edge were also investigated. On the basis of these results, a model for the mechanism of patch destruction is developed.

  13. Dense chromatin plates in metaphase chromosomes.

    Science.gov (United States)

    Gállego, Isaac; Castro-Hartmann, Pablo; Caravaca, Juan Manuel; Caño, Silvia; Daban, Joan-Ramon

    2009-04-01

    In a previous work we observed multilayered plate-like structures surrounding partially denatured HeLa chromosomes at metaphase ionic conditions. This unexpected finding has led us to carry out an extensive investigation of these structures. Our results show that plates can also be found in metaphase chromosomes from chicken lymphocytes. We have used atomic force microscopy (AFM) to image and investigate the mechanical properties of plates in aqueous solution. Plates are thin (approximately 6.5 nm each layer) but compact and resistant to penetration by the AFM tip: their Young's modulus is approximately 0.2 GPa and the stress required for surface penetration is approximately 0.03 GPa in the presence of Mg(2+) (5-20 mM). Low-ionic strength conditions produce emanation of chromatin fibers from the edges of uncrosslinked plates. These observations and AFM results obtained applying high forces indicate that the chromatin filament is tightly tethered inside the plates. Images of metal-shadowed plates and cryo-electron microscopy images of frozen-hydrated plates suggest that nucleosomes are tilted with respect to the plate surface to allow an interdigitation between the successive layers and a thickness reduction compatible with the observed plate height. The similarities between denatured plates from chicken chromosomes and aggregates of purified chromatin from chicken erythrocytes suggest that chromatin has intrinsic structural properties leading to plate formation. Scanning electron micrographs and images obtained with the 200-kV transmission microscope show that plates are the dominant component of compact chromatids. We propose that metaphase chromosomes are formed by many stacked plates perpendicular to the chromatid axis.

  14. Experiments and Numerical Simulations of Electrodynamic Tether

    Science.gov (United States)

    Iki, Kentaro; Kawamoto, Satomi; Takahashi, Ayaka; Ishimoto, Tomori; Yanagida, Atsushi; Toda, Susumu

    As an effective means of suppressing space debris growth, the Aerospace Research and Development Directorate of the Japan Aerospace Exploration Agency (JAXA) has been investigating an active space debris removal system that employs highly efficient electrodynamic tether (EDT) technology for orbital transfer. This study investigates tether deployment dynamics by means of on-ground experiments and numerical simulations of an electrodynamic tether system. Some key parameters used in the numerical simulations, such as the elastic modulus and damping ratio of the tether, the spring constant of the coiling of the tether, and deployment friction, must be estimated, and various experiments are conducted to determine these values. As a result, the following values were obtained: The elastic modulus of the tether was 40 GPa, and the damping ratio of the tether was 0.02. The spring constant and the damping ratio of the tether coiling were 10-4 N/m and 0.025 respectively. The deployment friction was 0.038ν + 0.005 N. In numerical simulations using a multiple mass tether model, tethers with lengths of several kilometers are deployed and the attitude dynamics of satellites attached to the end of the tether and tether libration are calculated. As a result, the simulations confirmed successful deployment of the tether with a length of 500 m using the electrodynamic tether system.

  15. Tethered Pyrotechnic Apparatus for Acquiring a Ground Sample

    Science.gov (United States)

    Jones, Jack; Zimmerman, Wayne; Wu, Jiunn Jenq; Badescu, Mircea; Sherrit, Stewart

    2009-01-01

    A proposed alternative design for the balloon-borne ground-sampling system described in the immediately preceding article would not rely on free fall to drive a harpoonlike sample-collecting device into the ground. Instead, the harpoon-like sample-collecting device would be a pyrotechnically driven, tethered projectile. The apparatus would include a tripod that would be tethered to the gondola. A gun for shooting the projectile into the ground would be mounted at the apex of the tripod. The gun would include an electronic trigger circuit, a chamber at the breech end containing a pyrotechnic charge, and a barrel. A sabot would be placed in the barrel just below the pyrotechnic charge, and the tethered projectile would be placed in the barrel just below the sabot. The tripod feet would be equipped with contact sensors connected to the trigger circuit. In operation, the tripod would be lowered to the ground on its tether. Once contact with the ground was detected by the sensors on all three tripod feet, the trigger circuit would fire the pyrotechnic charge to drive the projectile into the ground. (Requiring contact among all three tripod feet and the ground would ensure that the projectile would be fired into the ground, rather than up toward the gondola or the balloon.) The tethered projectile would then be reeled back up to the gondola for analysis of the sample.

  16. Chromatin stiffening underlies enhanced locus mobility after DNA damage in budding yeast.

    Science.gov (United States)

    Herbert, Sébastien; Brion, Alice; Arbona, Jean-Michel; Lelek, Mickaël; Veillet, Adeline; Lelandais, Benoît; Parmar, Jyotsana; Fernández, Fabiola García; Almayrac, Etienne; Khalil, Yasmine; Birgy, Eleonore; Fabre, Emmanuelle; Zimmer, Christophe

    2017-09-01

    DNA double-strand breaks (DSBs) induce a cellular response that involves histone modifications and chromatin remodeling at the damaged site and increases chromosome dynamics both locally at the damaged site and globally in the nucleus. In parallel, it has become clear that the spatial organization and dynamics of chromosomes can be largely explained by the statistical properties of tethered, but randomly moving, polymer chains, characterized mainly by their rigidity and compaction. How these properties of chromatin are affected during DNA damage remains, however, unclear. Here, we use live cell microscopy to track chromatin loci and measure distances between loci on yeast chromosome IV in thousands of cells, in the presence or absence of genotoxic stress. We confirm that DSBs result in enhanced chromatin subdiffusion and show that intrachromosomal distances increase with DNA damage all along the chromosome. Our data can be explained by an increase in chromatin rigidity, but not by chromatin decondensation or centromeric untethering only. We provide evidence that chromatin stiffening is mediated in part by histone H2A phosphorylation. Our results support a genome-wide stiffening of the chromatin fiber as a consequence of DNA damage and as a novel mechanism underlying increased chromatin mobility. © 2017 The Authors.

  17. High-throughput assessment of context-dependent effects of chromatin proteins.

    Science.gov (United States)

    Brueckner, Laura; van Arensbergen, Joris; Akhtar, Waseem; Pagie, Ludo; van Steensel, Bas

    2016-01-01

    Chromatin proteins control gene activity in a concerted manner. We developed a high-throughput assay to study the effects of the local chromatin environment on the regulatory activity of a protein of interest. The assay combines a previously reported multiplexing strategy based on barcoded randomly integrated reporters with Gal4-mediated tethering. We applied the assay to Drosophila heterochromatin protein 1a (HP1a), which is mostly known as a repressive protein but has also been linked to transcriptional activation. Recruitment to over 1000 genomic locations revealed that HP1a is a potent repressor able to silence even highly expressing reporter genes. However, the local chromatin context can modulate HP1a function. In pericentromeric regions, HP1a-induced repression was enhanced by twofold. In regions marked by a H3K36me3-rich chromatin signature, HP1a-dependent silencing was significantly decreased. We found no evidence for an activating function of HP1a in our experimental system. Furthermore, we did not observe stable transmission of repression over mitotic divisions after loss of targeted HP1a. The multiplexed tethered reporter assay should be applicable to a large number of chromatin proteins and will be a useful tool to dissect combinatorial regulatory interactions in chromatin.

  18. Enabling Tethered Exploration on Mars, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — Strong science motivations exist for exploring hard to reach terrain on Mars and the leading systems proposed to do so require tethers. While tethers are used...

  19. The Tethered Moon

    Science.gov (United States)

    Zahnle, Kevin; Lupu, Roxana Elena; Dubrovolskis, A. R.

    2014-01-01

    that the Moon's orbit evolves is limited by the modest radiative cooling rate of Earth's atmosphere, which in effect tethers the Moon to the Earth. Consequently the Moon's orbit evolves orders of magnitude more slowly than in conventional models. Slow orbital evolution promotes capture by orbital resonances that may have been important in the Earth-Moon system

  20. Chromatin replication and histone dynamics

    DEFF Research Database (Denmark)

    Alabert, Constance; Jasencakova, Zuzana; Groth, Anja

    2017-01-01

    organization into chromatin. We reveal how specialized replication-coupled mechanisms rapidly assemble newly synthesized DNA into nucleosomes, while the complete restoration of chromatin organization including histone marks is a continuous process taking place throughout the cell cycle. Because failure...

  1. Analysis of Chromatin Organisation

    Science.gov (United States)

    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,…

  2. The chromatin regulatory code: Beyond a histone code

    Science.gov (United States)

    Lesne, A.

    2006-03-01

    In this commentary on the contribution by Arndt Benecke in this issue, I discuss why the notion of “chromatin code” introduced and elaborated in this paper is to be preferred to that of “histone code”. Speaking of a code as regards nucleosome conformation and histone tail post-translational modifications only makes sense within the chromatin fiber, where their physico-chemical features can be translated into regulatory programs at the genome level, by means of a complex, multi-level interplay with the fiber architecture and dynamics settled in the course of Evolution. In particular, this chromatin code presumably exploits allosteric transitions of the chromatin fiber. The chromatin structure dependence of its translation suggests two alternative modes of transcription initiation regulation, also proposed in the paper by A. Benecke in this issue for interpreting strikingly bimodal micro-array data.

  3. Proteomic interrogation of human chromatin.

    Directory of Open Access Journals (Sweden)

    Mariana P Torrente

    Full Text Available Chromatin proteins provide a scaffold for DNA packaging and a basis for epigenetic regulation and genomic maintenance. Despite understanding its functional roles, mapping the chromatin proteome (i.e. the "Chromatome" is still a continuing process. Here, we assess the biological specificity and proteomic extent of three distinct chromatin preparations by identifying proteins in selected chromatin-enriched fractions using mass spectrometry-based proteomics. These experiments allowed us to produce a chromatin catalog, including several proteins ranging from highly abundant histone proteins to less abundant members of different chromatin machinery complexes. Using a Normalized Spectral Abundance Factor approach, we quantified relative abundances of the proteins across the chromatin enriched fractions giving a glimpse into their chromosomal abundance. The large-scale data sets also allowed for the discovery of a variety of novel post-translational modifications on the identified chromatin proteins. With these comparisons, we find one of the probed methods to be qualitatively superior in specificity for chromatin proteins, but inferior in proteomic extent, evidencing a compromise that must be made between biological specificity and broadness of characterization. Additionally, we attempt to identify proteins in eu- and heterochromatin, verifying the enrichments by characterizing the post-translational modifications detected on histone proteins from these chromatin regions. In summary, our results provide insights into the value of different methods to extract chromatin-associated proteins and provide starting points to study the factors that may be involved in directing gene expression and other chromatin-related processes.

  4. Position Control of an X4-Flyer Using a Tether

    Directory of Open Access Journals (Sweden)

    , Keigo Watanabe

    2014-10-01

    Full Text Available In Japan, aging of infrastructures, such as roads, bridges, and water and sewer services, etc. poses a problem, and it is required to extend the life-span of such infrastructures by maintenance. Among infrastructures, especially bridges are periodically inspected by short range visual observations, which check the damage and deterioration of the surface. However, since there are some cases where the short range visual observation is difficult, an alternative method is required so as to replace the short range visual observation with it. So, "X4-Flyer" is very attractive because of realizing a movement at high altitude easily. The objective of this study is to develop a tethered X4- Flyer, so that the conventional short range visual observation of bridges is replaced by it. In this paper, a method for the measurement and control of the position is described by using a tether for controlling the position of the X4-Flyer. In addition, it is checked whether the tethered X4-Flyer can control the position using the proposed method or not, letting it fly in a state in which a tether is being attached.

  5. Effects of fast neutrons on chromatin: dependence on chromatin structure

    Energy Technology Data Exchange (ETDEWEB)

    Radu, L. [Dept. of Molecular Genetics, V. Babes National Inst., Bd. Timisoara, Bucharest (Romania); Constantinescu, B. [Dept. of Cyclotron, H. Hulubei National Inst., Bucharest (Romania); Gazdaru, D. [Dept. of Biophysics, Physics Faculty, Univ. of Bucharest (Romania)

    2002-07-01

    The effects of fast neutrons (10-100 Gy) on chromatin extracted from normal (liver of Wistar rats) and tumor (Walker carcinosarcoma maintained on Wistar rats) tissues were compared. The spectroscopic assays used were (i) chromatin intrinsic fluorescence, (ii) time-resolved fluorescence of chromatin-proflavine complexes, and (iii) fluorescence resonance energy transfer (FRET) between dansyl chloride and acridine orange coupled to chromatin. For both normal and tumor chromatin, the intensity of intrinsic fluorescence specific for acidic and basic proteins decreased with increasing dose. The relative contributions of the excited-state lifetime of proflavine bound to chromatin were reduced upon fast-neutron irradiation, indicating a decrease in the proportion of chromatin DNA available for ligand binding. The Forster energy transfer efficiencies were also modified by irradiation. These effects were larger for chromatin from tumor tissue. In the range 0-100 Gy, fast neutrons induced alterations in DNA and acidic and basic proteins, as well as in global chromatin structure. The radiosensitivity of chromatin extracted from tumor tissue seems to be higher than that of chromatin extracted from normal tissue, probably because of its higher euchromatin (loose)-heterochromatin (compact) ratio. (author)

  6. Tethered Satellite System Contingency Investigation Board

    Science.gov (United States)

    1992-11-01

    The Tethered Satellite System (TSS-1) was launched aboard the Space Shuttle Atlantis (STS-46) on July 31, 1992. During the attempted on-orbit operations, the Tethered Satellite System failed to deploy successfully beyond 256 meters. The satellite was retrieved successfully and was returned on August 6, 1992. The National Aeronautics and Space Administration (NASA) Associate Administrator for Space Flight formed the Tethered Satellite System (TSS-1) Contingency Investigation Board on August 12, 1992. The TSS-1 Contingency Investigation Board was asked to review the anomalies which occurred, to determine the probable cause, and to recommend corrective measures to prevent recurrence. The board was supported by the TSS Systems Working group as identified in MSFC-TSS-11-90, 'Tethered Satellite System (TSS) Contingency Plan'. The board identified five anomalies for investigation: initial failure to retract the U2 umbilical; initial failure to flyaway; unplanned tether deployment stop at 179 meters; unplanned tether deployment stop at 256 meters; and failure to move tether in either direction at 224 meters. Initial observations of the returned flight hardware revealed evidence of mechanical interference by a bolt with the level wind mechanism travel as well as a helical shaped wrap of tether which indicated that the tether had been unwound from the reel beyond the travel by the level wind mechanism. Examination of the detailed mission events from flight data and mission logs related to the initial failure to flyaway and the failure to move in either direction at 224 meters, together with known preflight concerns regarding slack tether, focused the assessment of these anomalies on the upper tether control mechanism. After the second meeting, the board requested the working group to complete and validate a detailed integrated mission sequence to focus the fault tree analysis on a stuck U2 umbilical, level wind mechanical interference, and slack tether in upper tether

  7. Chromatin replication and epigenome maintenance

    DEFF Research Database (Denmark)

    Alabert, Constance; Groth, Anja

    2012-01-01

    Stability and function of eukaryotic genomes are closely linked to chromatin structure and organization. During cell division the entire genome must be accurately replicated and the chromatin landscape reproduced on new DNA. Chromatin and nuclear structure influence where and when DNA replication...... initiates, whereas the replication process itself disrupts chromatin and challenges established patterns of genome regulation. Specialized replication-coupled mechanisms assemble new DNA into chromatin, but epigenome maintenance is a continuous process taking place throughout the cell cycle. If DNA...... synthesis is perturbed, cells can suffer loss of both genome and epigenome integrity with severe consequences for the organism....

  8. Membrane tethering complexes in the endosomal system

    Directory of Open Access Journals (Sweden)

    Anne eSpang

    2016-05-01

    Full Text Available Vesicles that are generated by endocytic events at the plasma membrane are destined to early endosomes. A prerequisite for proper fusion is the tethering of two membrane entities. Tethering of vesicles to early endosomes is mediated by the CORVET complex, while fusion of late endosomes with lysosomes depends on the HOPS complex. Recycling through the TGN and to the plasma membrane is facilitated by the GARP and EARP complexes, respectively. However, there are other tethering functions in the endosomal system as there are multiple pathways through which proteins can be delivered from endosomes to either the TGN or the plasma membrane. Furthermore, complexes that may be part of novel tethering complexes have been recently identified. Thus it is likely that more tethering factors exist. In this review, I will provide an overview of different tethering complexes of the endosomal system and discuss how they may provide specificity in membrane traffic.

  9. Numerical modelling of elastic space tethers

    DEFF Research Database (Denmark)

    Kristiansen, Kristian Uldall; Palmer, P. L.; Roberts, R. M.

    2012-01-01

    In this paper the importance of the ill-posedness of the classical, non-dissipative massive tether model on an orbiting tether system is studied numerically. The computations document that via the regularisation of bending resistance a more reliable numerical integrator can be produced. Furthermore......, the numerical experiments of an orbiting tether system show that bending may introduce significant forces in some regions of phase space. Finally, numerical evidence for the existence of an almost invariant slow manifold of the singularly perturbed, regularised, non-dissipative massive tether model is provided...

  10. T-Rex: A Japanese Space Tether Experiment

    Science.gov (United States)

    Johnson, Les

    2009-01-01

    Electrodynamic tether (EDT) thrusters work by virtue of the force a magnetic field exerts on a wire carrying an electrical current. The force, which acts on any charged particle moving through a magnetic field (including the electrons moving in a current-carrying wire), were concisely expressed by Lorentz in 1895 in an equation that now bears his name. The force acts in a direction perpendicular to both the direction of current flow and the magnetic field vector. Electric motors make use of this force: a wire loop in a magnetic field is made to rotate by the torque the Lorentz Force exerts on it due to an alternating current in the loop times so as to keep the torque acting in the same sense. The motion of the loop is transmitted to a shaft, thus providing work. Although the working principle of EDT thrusters is not new, its application to space transportation may be significant. In essence, an EDT thruster is just a clever way of getting an electrical current to flow in a long orbiting wire (the tether) so that the Earth s magnetic field will accelerate the wire and, consequently the payload attached to the wire. The direction of current flow in the tether, either toward or away from the Earth along the local vertical, determines whether the magnetic force will raise or lower the orbit. The bias voltage of a vertically deployed metal tether, which results just from its orbital motion (assumed eastward) through Earth s magnetic field, is positive with respect to the ambient plasma at the top and negative at the bottom. This polarization is due to the action of the Lorentz force on the electrons in the tether. Thus, the natural current flow is the result of negative electrons being attracted to the upper end and then returned to the plasma at the lower end. The magnetic force in this case has a component opposite to the direction of motion, and thus leads to a lowering of the orbit and eventually to re-entry. In this generator mode of operation the Lorentz Force

  11. Chromatin dynamics in genome stability

    DEFF Research Database (Denmark)

    Nair, Nidhi; Shoaib, Muhammad; Sørensen, Claus Storgaard

    2017-01-01

    Genomic DNA is compacted into chromatin through packaging with histone and non-histone proteins. Importantly, DNA accessibility is dynamically regulated to ensure genome stability. This is exemplified in the response to DNA damage where chromatin relaxation near genomic lesions serves to promote ...... of chromatin structure regulation in maintaining genome integrity by multiple mechanisms including facilitating DNA repair and directly suppressing endogenous DNA damage.......Genomic DNA is compacted into chromatin through packaging with histone and non-histone proteins. Importantly, DNA accessibility is dynamically regulated to ensure genome stability. This is exemplified in the response to DNA damage where chromatin relaxation near genomic lesions serves to promote...... access of relevant enzymes to specific DNA regions for signaling and repair. Furthermore, recent data highlight genome maintenance roles of chromatin through the regulation of endogenous DNA-templated processes including transcription and replication. Here, we review research that shows the importance...

  12. The ATPases of cohesin interface with regulators to modulate cohesin-mediated DNA tethering

    Science.gov (United States)

    Çamdere, Gamze; Guacci, Vincent; Stricklin, Jeremiah; Koshland, Douglas

    2015-01-01

    Cohesin tethers together regions of DNA, thereby mediating higher order chromatin organization that is critical for sister chromatid cohesion, DNA repair and transcriptional regulation. Cohesin contains a heterodimeric ATP-binding Cassette (ABC) ATPase comprised of Smc1 and Smc3 ATPase active sites. These ATPases are required for cohesin to bind DNA. Cohesin’s DNA binding activity is also promoted by the Eco1 acetyltransferase and inhibited by Wpl1. Recently we showed that after cohesin stably binds DNA, a second step is required for DNA tethering. This second step is also controlled by Eco1 acetylation. Here, we use genetic and biochemical analyses to show that this second DNA tethering step is regulated by cohesin ATPase. Furthermore, our results also suggest that Eco1 promotes cohesion by modulating the ATPase cycle of DNA-bound cohesin in a state that is permissive for DNA tethering and refractory to Wpl1 inhibition. DOI: http://dx.doi.org/10.7554/eLife.11315.001 PMID:26583750

  13. Characteristics of thymine dimer excision from xeroderma pigmentosum chromatin

    International Nuclear Information System (INIS)

    Fujiwara, Y.; Kano, Y.

    1983-01-01

    We investigated thymine dimer excision from xeroderma pigmentosum (XP) chromatin in the cell-free reconstruction system. The normal-cell extract performed specific dimer excision from native chromatin and DNA isolated from 100 J/m 2 -irradiated cells. Such an excision in vitro was rapid and required high concentrations of extract. The extracts of XP group A, C and G cells were unable to excise from their own native-chromatin, but capable of excising from chromatin deprived of loosely bound nonhistone proteins with 0.35 M NaCl, as were from purified DNA. Thus, group A, C and G cells are most likely to be defective in the specific XP factors facilitating the excising activity under multicomponent regulation at the chromatin level. Further, either of group A, C and G extracts successfully complemented the native chromatin of the alternative groups. Uniquely, the XP group D extract excised dimers from native chromatin in the normal fashion under the condition. These results suggest that XP group A, C, D and G cells examined may not be defective in the dimer specific endonuclease and exonuclease per se. 19 references, 3 figures, 2 tables

  14. Mobile tethering: Overview, perspectives and challengess

    NARCIS (Netherlands)

    Constantinescu, M.; Onur, E.; Durmus, Y.; Nikou, S.; Reuver, M. de; Bouwman, H.; Djurica, M.; Glatz, P.M.

    2014-01-01

    Purpose: The purpose of this paper is to analyze mobile tethering from technological and social perspectives. Mobile tethering allows us to share cellular data connection with others over WiFi, Bluetooth or USB. Although the technology is ready and has promising outcomes, service providers and the

  15. Chromatin Flavors: Chromatin composition and domain organization in Drosophila melanogaster

    NARCIS (Netherlands)

    J.G. van Bemmel (Joke)

    2012-01-01

    textabstractChromatin was originally identified by W. Flemming in 1882 as not much more than the stainable substance of the cell nucleus. Flemming named this substance according to the Greek word “chroma”, meaning color. In 1911 chromatin was characterized as proteins, named histones, that

  16. Optical tweezers stretching of chromatin

    NARCIS (Netherlands)

    Pope, L.H.; Bennink, Martin L.; Greve, Jan

    2003-01-01

    Recently significant success has emerged from exciting research involving chromatin stretching using optical tweezers. These experiments, in which a single chromatin fibre is attached by one end to a micron-sized bead held in an optical trap and to a solid surface or second bead via the other end,

  17. Position Control of an X4-Flyer Using a Tether

    Directory of Open Access Journals (Sweden)

    Yusuke Ouchi

    2016-05-01

    Full Text Available In Japan, aging of infrastructures, such as roads,bridges, and water and sewer services, etc. poses a problem, andit is required to extend the life-span of such infrastructures bymaintenance. Among infrastructures, especially bridges areperiodically inspected by short range visual observations, whichcheck the damage and deterioration of the surface. However,since there are some cases where the short range visualobservation is difficult, an alternative method is required so as toreplace the short range visual observation with it. So, "X4-Flyer"is very attractive because of realizing a movement at high altitudeeasily. The objective of this study is to develop a tethered X4-Flyer, so that the conventional short range visual observation ofbridges is replaced by it. In this paper, a method for themeasurement and control of the position is described by using atether for controlling the position of the X4-Flyer. In addition, itis checked whether the tethered X4-Flyer can control the positionusing the proposed method or not, letting it fly in a state in whicha tether is being attached

  18. The Human Protein PRR14 Tethers Heterochromatin to the Nuclear Lamina during Interphase and Mitotic Exit

    Directory of Open Access Journals (Sweden)

    Andrey Poleshko

    2013-10-01

    Full Text Available The nuclear lamina is a protein meshwork that lies under the inner nuclear membrane of metazoan cells. One function of the nuclear lamina is to organize heterochromatin at the inner nuclear periphery. However, very little is known about how heterochromatin attaches to the nuclear lamina and how such attachments are restored at mitotic exit. Here, we show that a previously unstudied human protein, PRR14, functions to tether heterochromatin to the nuclear periphery during interphase, through associations with heterochromatin protein 1 (HP1 and the nuclear lamina. During early mitosis, PRR14 is released from the nuclear lamina and chromatin and remains soluble. Strikingly, at the onset of anaphase, PRR14 is incorporated rapidly into chromatin through HP1 binding. Finally, in telophase, PRR14 relocalizes to the reforming nuclear lamina. This stepwise reassembly of PRR14 suggests a function in the selection of HP1-bound heterochromatin for reattachment to the nuclear lamina as cells exit mitosis.

  19. Tethered Lubricants for Small Systems

    Energy Technology Data Exchange (ETDEWEB)

    Lynden A. Archer

    2006-01-09

    The objective of this research project is two-fold. First, to fundamentally understand friction and relaxation dynamics of polymer chains near surfaces; and second, to develop novel self-lubricated substrates suitable for MEMS devices. During the three-year performance period of this study the PI and his students have shown using theory and experiments that systematic introduction of disorder into tethered lubricant coatings (e.g. by using self-assembled monolayer (SAM) mixtures or SAMs with nonlinear, branched architectures) can be used to significantly reduce the friction coefficient of a surface. They have also developed a simple procedure based on dielectric spectroscopy for quantifying the effect of surface disorder on molecular relaxation in lubricant coatings. Details of research accomplishments in each area of the project are described in the body of the report.

  20. Optimal Control of Electrodynamic Tethers

    Science.gov (United States)

    2008-06-01

    axis of the orbit td = tether diameter e = orbit eccentricity f = state vector time derivative h = altitude of system center of mass (COM...2 2 2 2 2 1 ˆ cot sin1 1 ˆ ˆ1 sin 1 cos cos ˆ sin ˆ sin de a r dt rna e r id dt nae e na rdi dt na rd dt na i ν ωω ν ν ν ω ν ω...πη να 2 2 2 0 0 1 cos 2 cos sin sin cos sin sin cos cos a d nae e r nna na e k e i c s n i c η ν νν ν ν α α

  1. Theseus: tethered distributed robotics (TDR)

    Science.gov (United States)

    Digney, Bruce L.; Penzes, Steven G.

    2003-09-01

    The Defence Research and Development Canada's (DRDC) Autonomous Intelligent System's program conducts research to increase the independence and effectiveness of military vehicles and systems. DRDC-Suffield's Autonomous Land Systems (ALS) is creating new concept vehicles and autonomous control systems for use in outdoor areas, urban streets, urban interiors and urban subspaces. This paper will first give an overview of the ALS program and then give a specific description of the work being done for mobility in urban subspaces. Discussed will be the Theseus: Thethered Distributed Robotics (TDR) system, which will not only manage an unavoidable tether but exploit it for mobility and navigation. Also discussed will be the prototype robot called the Hedgehog, which uses conformal 3D mobility in ducts, sewer pipes, collapsed rubble voids and chimneys.

  2. The space station tethered elevator system

    Science.gov (United States)

    Anderson, Loren A.

    1989-01-01

    The optimized conceptual engineering design of a space station tethered elevator is presented. The elevator is an unmanned mobile structure which operates on a ten kilometer tether spanning the distance between the Space Station and a tethered platform. Elevator capabilities include providing access to residual gravity levels, remote servicing, and transportation to any point along a tether. The potential uses, parameters, and evolution of the spacecraft design are discussed. Engineering development of the tethered elevator is the result of work conducted in the following areas: structural configurations; robotics, drive mechanisms; and power generation and transmission systems. The structural configuration of the elevator is presented. The structure supports, houses, and protects all systems on board the elevator. The implementation of robotics on board the elevator is discussed. Elevator robotics allow for the deployment, retrieval, and manipulation of tethered objects. Robotic manipulators also aid in hooking the elevator on a tether. Critical to the operation of the tethered elevator is the design of its drive mechanisms, which are discussed. Two drivers, located internal to the elevator, propel the vehicle along a tether. These modular components consist of endless toothed belts, shunt-wound motors, regenerative power braking, and computer controlled linear actuators. The designs of self-sufficient power generation and transmission systems are reviewed. Thorough research indicates all components of the elevator will operate under power provided by fuel cells. The fuel cell systems will power the vehicle at seven kilowatts continuously and twelve kilowatts maximally. A set of secondary fuel cells provides redundancy in the unlikely event of a primary system failure. Power storage exists in the form of Nickel-Hydrogen batteries capable of powering the elevator under maximum loads.

  3. Golgi GRASPs: moonlighting membrane tethers

    Directory of Open Access Journals (Sweden)

    Jarvela T

    2012-05-01

    Full Text Available Timothy Jarvela, Adam D LinstedtDepartment of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USAAbstract: The identification of mammalian Golgi reassembly stacking proteins (GRASPs 15 years ago was followed by experiments implicating them in diverse functions, including two differing structural roles in Golgi biogenesis and at least two distinct roles in the secretion of proteins. GRASP55 and GRASP65 are localized to cis and medial/trans Golgi cisternae, respectively. They are both required for stacking of Golgi membranes in a Golgi reassembly assay. Depletion of either GRASP from cultured cells prevents the linking of Golgi membranes into their normal ribbon-like network. While GRASPs are not required for transport of secretory cargo per se, they are required for ER-to-Golgi transport of certain specific cargo, such as those containing a C-terminal valine motif. Surprisingly, GRASPs also promote secretion of cargo by the so-called unconventional secretory pathway, which bypasses the Golgi apparatus where the GRASPs reside. Furthermore, regulation of GRASP activity is now recognized for its connections to cell cycle control, development, and disease. Underlying these diverse activities is the structurally conserved N-terminal GRASP domain whose crystal structure was recently determined. It consists of a tandem array of atypical PSD95–DlgA–Zo–1 (PDZ domains, which are well-known protein–protein interaction motifs. The GRASP PDZ domains are used to localize the proteins to the Golgi as well as GRASP-mediated membrane tethering and cargo interactions. These activities are regulated, in part, by phosphorylation of the large unstructured C-terminal domain.Keywords: GRASP, review, membrane, tether, PDZ domain, secretory chaperone, unconventional secretion

  4. Biomechanical simulations of costo-vertebral and anterior vertebral body tethers for the fusionless treatment of pediatric scoliosis.

    Science.gov (United States)

    Aubin, Carl-Éric; Clin, Julien; Rawlinson, Jeremy

    2018-01-01

    Compression-based fusionless tethers are an alternative to conventional surgical treatments of pediatric scoliosis. Anterior approaches place an anterior (ANT) tether on the anterolateral convexity of the deformed spine to modify growth. Posterior, or costo-vertebral (CV), approaches have not been assessed for biomechanical and corrective effectiveness. The objective was to biomechanically assess CV and ANT tethers using six patient-specific, finite element models of adolescent scoliotic patients (11.9 ± 0.7 years, Cobb 34° ± 10°). A validated algorithm simulated the growth and Hueter-Volkmann growth modulation over a period of 2 years with the CV and ANT tethers at two initial tensions (100, 200 N). The models without tethering also simulated deformity progression with Cobb angle increasing from 34° to 56°, axial rotation 11° to 13°, and kyphosis 28° to 32° (mean values). With the CV tether, the Cobb angle was reduced to 27° and 20° for tensions of 100 and 200 N, respectively, kyphosis to 21° and 19°, and no change in axial rotation. With the ANT tether, Cobb was reduced to 32° and 9° for 100 and 200 N, respectively, kyphosis unchanged, and axial rotation to 3° and 0°. While the CV tether mildly corrected the coronal curve over a 2-year growth period, it had sagittal lordosing effect, particularly with increasing initial axial rotation (>15°). The ANT tether achieved coronal correction, maintained kyphosis, and reduced the axial rotation, but over-correction was simulated at higher initial tensions. This biomechanical study captured the differences between a CV and ANT tether and indicated the variability arising from the patient-specific characteristics. © 2017 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 36:254-264, 2018. © 2017 Orthopaedic Research Society. Published by Wiley Periodicals, Inc.

  5. SATB1 tethers multiple gene loci to reprogram expression profiledriving breast cancer metastasis

    Energy Technology Data Exchange (ETDEWEB)

    Han, Hye-Jung; Kohwi, Yoshinori; Kohwi-Shigematsu, Terumi

    2006-07-13

    Global changes in gene expression occur during tumor progression, as indicated by expression profiling of metastatic tumors. How this occurs is poorly understood. SATB1 functions as a genome organizer by folding chromatin via tethering multiple genomic loci and recruiting chromatin remodeling enzymes to regulate chromatin structure and expression of a large number of genes. Here we show that SATB1 is expressed at high levels in aggressive breast cancer cells, and is undetectable in non-malignant breast epithelial cells. Importantly, RNAi-mediated removal of SATB1 from highly-aggressive MDA-MB-231 cells altered the expression levels of over 1200 genes, restored breast-like acinar polarity in three-dimensional cultures, and prevented the metastastic phenotype in vivo. Conversely, overexpression of SATB1 in the less-aggressive breast cancer cell line Hs578T altered the gene expression profile and increased metastasis dramatically in vivo. Thus, SATB1 is a global regulator of gene expression in breast cancer cells, directly regulating crucial metastasis-associated genes, including ERRB2 (HER2/NEU), TGF-{beta}1, matrix metalloproteinase 3, and metastasin. The identification of SATB1 as a protein that re-programs chromatin organization and transcription profiles to promote breast cancer metastasis suggests a new model for metastasis and may provide means of therapeutic intervention.

  6. Chromatin and Transcription in Yeast

    Science.gov (United States)

    Rando, Oliver J.; Winston, Fred

    2012-01-01

    Understanding the mechanisms by which chromatin structure controls eukaryotic transcription has been an intense area of investigation for the past 25 years. Many of the key discoveries that created the foundation for this field came from studies of Saccharomyces cerevisiae, including the discovery of the role of chromatin in transcriptional silencing, as well as the discovery of chromatin-remodeling factors and histone modification activities. Since that time, studies in yeast have continued to contribute in leading ways. This review article summarizes the large body of yeast studies in this field. PMID:22345607

  7. Dynamics analysis of electrodynamic satellite tethers. Equations of motion and numerical solution algorithms for the tether

    Science.gov (United States)

    Nacozy, P. E.

    1984-01-01

    The equations of motion are developed for a perfectly flexible, inelastic tether with a satellite at its extremity. The tether is attached to a space vehicle in orbit. The tether is allowed to possess electrical conductivity. A numerical solution algorithm to provide the motion of the tether and satellite system is presented. The resulting differential equations can be solved by various existing standard numerical integration computer programs. The resulting differential equations allow the introduction of approximations that can lead to analytical, approximate general solutions. The differential equations allow more dynamical insight of the motion.

  8. TETHERED-BEAD, IMMUNE SANDWICH ASSAY

    Science.gov (United States)

    Silver, Jonathan; Li, Zhenyu; Neuman, Keir

    2014-01-01

    We describe a proof-of-principal, immune sandwich assay in which immune complexes link micron-size beads via DNA tethers to a sensor surface. The number of tethered beads, counted using low-magnification microscopy, provides a measure of the concentration of analyte. The prototype assay was sensitive to pM concentration of analyte. In theory, the assay could be sensitive to sub-fM analyte because beads attached via single-immune complexes and DNA strands form tethers, and tether formation in the absence of analyte is extremely rare. The limiting step at present is binding of streptavidin at the end of DNA to biotin on capture beads. Potential advantages of this type of sensor are discussed. PMID:25064819

  9. Phobos L1 Operational Tether Experiment (PHLOTE)

    Data.gov (United States)

    National Aeronautics and Space Administration — A sensor package that “floats” just above the surface of Phobos, suspended by a tether from a small spacecraft operating at the Mars/Phobos Lagrange 1 (L1) Point...

  10. Wave attenuation charcteristics of tethered float system

    Digital Repository Service at National Institute of Oceanography (India)

    Vethamony, P.

    that the system performs well when it is just submerged. As float velocity decreases with increase in float size, transmission coefficient increases with increase in float size. The influence of wave period on wave attenuation is remarkable compared to other... characteristics of floating breakwaters. Seymour and Isaacs (1974), Agerton et al. (1976) and Seymour and Hanes (1979) studied the performance of a tethered float breakwater (tethered float system), assuming that drag is the major contributor-factor for wave...

  11. Brownian motion of tethered nanowires.

    Science.gov (United States)

    Ota, Sadao; Li, Tongcang; Li, Yimin; Ye, Ziliang; Labno, Anna; Yin, Xiaobo; Alam, Mohammad-Reza; Zhang, Xiang

    2014-05-01

    Brownian motion of slender particles near a boundary is ubiquitous in biological systems and in nanomaterial assembly, but the complex hydrodynamic interaction in those systems is still poorly understood. Here, we report experimental and computational studies of the Brownian motion of silicon nanowires tethered on a substrate. An optical interference method enabled direct observation of microscopic rotations of the slender bodies in three dimensions with high angular and temporal resolutions. This quantitative observation revealed anisotropic and angle-dependent hydrodynamic wall effects: rotational diffusivity in inclined and azimuth directions follows different power laws as a function of the length, ∼ L(-2.5) and ∼ L(-3), respectively, and is more hindered for smaller inclined angles. In parallel, we developed an implicit simulation technique that takes the complex wire-wall hydrodynamic interactions into account efficiently, the result of which agreed well with the experimentally observed angle-dependent diffusion. The demonstrated techniques provide a platform for studying the microrheology of soft condensed matters, such as colloidal and biological systems near interfaces, and exploring the optimal self-assembly conditions of nanostructures.

  12. Quantitative Proteomic Analysis of Replicative and Nonreplicative Forms Reveals Important Insights into Chromatin Biology of Trypanosoma cruzi*

    Science.gov (United States)

    Leandro de Jesus, Teresa Cristina; Calderano, Simone Guedes; Vitorino, Francisca Nathalia de Luna; Llanos, Ricardo Pariona; Lopes, Mariana de Camargo; de Araújo, Christiane Bezerra; Thiemann, Otavio Henrique; Reis, Marcelo da Silva; Elias, Maria Carolina

    2017-01-01

    Chromatin associated proteins are key regulators of many important processes in the cell. Trypanosoma cruzi, a protozoa flagellate that causes Chagas disease, alternates between replicative and nonreplicative forms accompanied by a shift on global transcription levels and by changes in its chromatin architecture. Here, we investigated the T. cruzi chromatin proteome using three different protocols and compared it between replicative (epimastigote) and nonreplicative (trypomastigote) forms by high-resolution mass spectrometry. More than 2000 proteins were identified and quantified both in chromatin and nonchromatin extracts. Besides histones and other known nuclear proteins, trypanosomes chromatin also contains metabolic (mainly from carbohydrate pathway), cytoskeleton and many other proteins with unknown functions. Strikingly, the two parasite forms differ greatly regarding their chromatin-associated factors composition and amount. Although the nucleosome content is the same for both life forms (as seen by MNase digestion), the remaining proteins were much less detected in nonreplicative forms, suggesting that they have a naked chromatin. Proteins associated to DNA proliferation, such as PCNA, RPA, and DNA topoisomerases were exclusively found in the chromatin of replicative stages. On the other hand, the nonreplicative stages have an enrichment of a histone H2B variant. Furthermore, almost 20% of replicative stages chromatin-associated proteins are expressed in nonreplicative forms, but located at nonchromatin space. We identified different classes of proteins including phosphatases and a Ran-binding protein, that may shuttle between chromatin and nonchromatin space during differentiation. Seven proteins, including those with unknown functions, were selected for further validation. We confirmed their location in chromatin and their differential expression, using Western blotting assays and chromatin immunoprecipitation (ChIP). Our results indicate that the

  13. Thrust Control During Towing of Space Debris using an Elastic Tether

    Directory of Open Access Journals (Sweden)

    A. D. Ledkov

    2014-01-01

    Full Text Available The paper considers a maneuver for deorbiting the large space debris using an active spacecraft connected with the debris by an elastic tether. Tether slacking during the maneuver can lead to the tether rupture, kinking, and winding on the descending object. Therefore it is important to prevent slacking. The objective of this work is to find the law of thrust force control of the active spacecraft to ensure a continuously strained tether during the maneuver.Using Lagrange formalism a mathematical model to describe the system plane motion is developed. This model considers the active spacecraft as a mass point, the space debris as a rigid body, and the tether as a weightless elastic rod. A thrust force is directed along the local horizon of the spacecraft. Linearization of nonlinear differential equation describing longitudinal oscillations of the tether length is performed. Its phase portrait is analyzed. An approximate expression describing the position of the center on the phase portrait is obtained. A time-optimal control with full feedback to ensure that the tether is in the strained state is found by solving the Bellman equation. To use the obtained optimal law it is necessary to set the measuring equipment on the spacecraft, which is capable of accurate measuring a distance to the space debris and its relative velocity. An alternative control law, which is simpler in terms of the practical implementation, is proposed. As an example, the descent from an orbit of nonfunctioning Soviet satellite Meteor-2 is considered. It is shown that both proposed laws provide continuous strain of the tether during deorbiting of the satellite. Moreover, slack does not occur even at the first period of oscillation of the tether length. It is shown that the use of the proposed control laws leads to slight increase of deorbiting time as compared to the case of using the constant thrust.The results can be used to develop the control systems of small spacecrafts

  14. Chromatin challenges during DNA replication and repair

    DEFF Research Database (Denmark)

    Groth, Anja; Rocha, Walter; Verreault, Alain

    2007-01-01

    Inheritance and maintenance of the DNA sequence and its organization into chromatin are central for eukaryotic life. To orchestrate DNA-replication and -repair processes in the context of chromatin is a challenge, both in terms of accessibility and maintenance of chromatin organization. To meet...... the challenge of maintenance, cells have evolved efficient nucleosome-assembly pathways and chromatin-maturation mechanisms that reproduce chromatin organization in the wake of DNA replication and repair. The aim of this Review is to describe how these pathways operate and to highlight how the epigenetic...... landscape may be stably maintained even in the face of dramatic changes in chromatin structure....

  15. Tension waves in tethered satellite cables

    Science.gov (United States)

    Lallman, F. J.

    1984-01-01

    A one-degree-of-freedom simulation of the Tethered Satellite System (TSS) was programmed using a distributed system model of the tether based on the one-dimensional wave equation. This model represents the time varying tension profile along the tether as the sum of two traveling waves of tension moving in opposite directions. A control loop was devised which combines a deployment rate command with the measured tension at the deployer to produce a smooth, stable rate of deployment of the subsatellite. Simulation results show a buildup of periodic bursts of high frequency oscillation in tension. This report covers the mathematical modelling and simulation results and explains the reason for the observed oscillations. The design of a possible vibration damping device is discussed.

  16. A Child with Tethered Cord Syndrome

    Directory of Open Access Journals (Sweden)

    Bekti Safarini

    2012-06-01

    Full Text Available Tethered Cord Syndome (TCS refers to a group of neurological disorders related to malformations of the spinal cord, pulling of the spinal cord at the base of spinal canal. Tethered cord syndrome can be seen at any age but most often during childhood. A few children complain of diffuse pain in lower extremitiesor urological symptoms, 20% - 30 % of the patients will have a neurogenic bladder. A 9 years old girl, complained to have a flank pain and eneuresis. A mass is palpable at right flank. Ultrasound revealed duplex hydronephrosis and hydroureter with trabeculated bladder. Voiding Cystouretrography showed grade V vesicoureteral reflux (VUR and neurogenic bladder appearance. Lumbosacral MRI demonstrated tethered cord with adjacent lipoma and spina bifida (Sains Medika, 4(1:89-96.

  17. Miniaturized Interrogation System for Marsupial Rover Sensing Tether, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — Luna proposes to continue development of its marsupial rover sensing tether (MaRS Tether) technology by miniaturizing the sensor's interrogation system. Luna is...

  18. Extended Length Marsupial Rover Sensing Tether, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — Luna proposes to continue development of its marsupial rover sensing tether (MaRS Tether) technology by extending the length of the sensing technology out to nearly...

  19. 75 FR 47316 - Centennial Challenges 2010 Strong Tether Challenge

    Science.gov (United States)

    2010-08-05

    ..., 2010. ADDRESSES: 2010 Strong Tether Challenge will be conducted at the 2010 Space Elevator Conference... NATIONAL AERONAUTICS AND SPACE ADMINISTRATION Centennial Challenges 2010 Strong Tether Challenge AGENCY: National Aeronautics and Space Administration (NASA). ACTION: Notice. SUMMARY: This notice is...

  20. Chromatin remodeling in mammalian embryos.

    Science.gov (United States)

    Cabot, Birgit; Cabot, Ryan A

    2018-03-01

    The mammalian embryo undergoes a dramatic amount of epigenetic remodeling during the first week of development. In this review, we discuss several epigenetic changes that happen over the course of cleavage development, focusing on covalent marks (e.g., histone methylation and acetylation) and non-covalent remodeling (chromatin remodeling via remodeling complexes; e.g., SWI/SNF-mediated chromatin remodeling). Comparisons are also drawn between remodeling events that occur in embryos from a variety of mammalian species. © 2018 Society for Reproduction and Fertility.

  1. Global Quantitative Modeling of Chromatin Factor Interactions

    Science.gov (United States)

    Zhou, Jian; Troyanskaya, Olga G.

    2014-01-01

    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

  2. A Systematic Analysis of Factors Localized to Damaged Chromatin Reveals PARP-Dependent Recruitment of Transcription Factors

    Directory of Open Access Journals (Sweden)

    Lior Izhar

    2015-06-01

    Full Text Available Localization to sites of DNA damage is a hallmark of DNA damage response (DDR proteins. To identify DDR factors, we screened epitope-tagged proteins for localization to sites of chromatin damaged by UV laser microirradiation and found >120 proteins that localize to damaged chromatin. These include the BAF tumor suppressor complex and the amyotrophic lateral sclerosis (ALS candidate protein TAF15. TAF15 contains multiple domains that bind damaged chromatin in a poly-(ADP-ribose polymerase (PARP-dependent manner, suggesting a possible role as glue that tethers multiple PAR chains together. Many positives were transcription factors; > 70% of randomly tested transcription factors localized to sites of DNA damage, and of these, ∼90% were PARP dependent for localization. Mutational analyses showed that localization to damaged chromatin is DNA-binding-domain dependent. By examining Hoechst staining patterns at damage sites, we see evidence of chromatin decompaction that is PARP dependent. We propose that PARP-regulated chromatin remodeling at sites of damage allows transient accessibility of DNA-binding proteins.

  3. Spine-shortening vertebral osteotomy for tethered cord syndrome: report of three cases.

    Science.gov (United States)

    Miyakoshi, Naohisa; Abe, Eiji; Suzuki, Tetsuya; Kido, Tadato; Chiba, Mitsuho; Shimada, Yoichi

    2009-10-15

    Retrospective case series. To review findings from 3 patients who underwent spine-shortening vertebral osteotomy for tethered cord syndrome with a minimum follow-up of 3 years. Surgical detethering is the gold standard for symptomatic tethered cord syndrome. However, complications such as cerebrospinal fluid leakage and neurologic deterioration are common. Spine-shortening vertebral osteotomy, proposed by Kokubun, is an alternative surgical technique to reduce neural tension indirectly. However, case series of this novel procedure for tethered cord syndrome have not been reported in the English literature. Three patients aged 13, 22, and 27 years presented with progressive pain and/or neurologic dysfunction. They underwent spine-shortening vertebral osteotomy of L1 with a pedicle screw and rod system. Their clinical and radiologic outcomes are reviewed. All patients got relief from their preoperative symptoms after surgery, and no complications occurred. Complete bone union was obtained in all patients without correction loss. Spine-shortening vertebral osteotomy can be a safe and alternative surgical technique for tethered cord syndrome.

  4. A Long-Distance Chromatin Affair

    NARCIS (Netherlands)

    Denker, Annette; de Laat, Wouter

    2015-01-01

    Changes in transcription factor binding sequences result in correlated changes in chromatin composition locally and at sites hundreds of kilobases away. New studies demonstrate that this concordance is mediated via spatial chromatin interactions that constitute regulatory modules of the human

  5. Guarding against Collateral Damage during Chromatin Transactions

    DEFF Research Database (Denmark)

    Altmeyer, Matthias; Lukas, Jiri

    2013-01-01

    Signal amplifications are vital for chromatin function, yet they also bear the risk of transforming into unrestrained, self-escalating, and potentially harmful responses. Examples of inbuilt limitations are emerging, revealing how chromatin transactions are confined within physiological boundaries....

  6. Transcription Through Chromatin - Dynamic Organization of Genes

    Indian Academy of Sciences (India)

    In this article, we discuss the dynamic organization of eukaryotic genes into chromatin. Remodeling of chromatin confers it the ability for dynamic change. Remodeling is essential for transcriptional regulation, the first step of gene expression. Chromatin Structure and Gene Expression. Transcription is the first step of gene ...

  7. STICS: surface-tethered iterative carbohydrate synthesis.

    Science.gov (United States)

    Pornsuriyasak, Papapida; Ranade, Sneha C; Li, Aixiao; Parlato, M Cristina; Sims, Charles R; Shulga, Olga V; Stine, Keith J; Demchenko, Alexei V

    2009-04-14

    A new surface-tethered iterative carbohydrate synthesis (STICS) technology is presented in which a surface functionalized 'stick' made of chemically stable high surface area porous gold allows one to perform cost efficient and simple synthesis of oligosaccharide chains; at the end of the synthesis, the oligosaccharide can be cleaved off and the stick reused for subsequent syntheses.

  8. Tethered "kiteplane" design for the Laddermill project

    NARCIS (Netherlands)

    Breukels, J.; Ockels, W.

    2005-01-01

    The Laddermill is an innovative concept for generating energy from wind using large kite-like wings on a tether. The wings are able to fly in both the regime of airplanes and kites. We therefore call these structures "kiteplanes". By providing a recurring motion with a large lift during ascending

  9. Ionic-Liquid-Tethered Nanoparticles: Hybrid Electrolytes

    KAUST Repository

    Moganty, Surya S.

    2010-10-22

    A new class of solventless electrolytes was created by tethering ionic liquids to hard inorganic ZrO2 nanostructures (see picture; NIM=nanoscale ionic material). These hybrid fluids exhibit exceptional redox stability windows, excellent thermal stability, good lithium transference numbers, long-term interfacial stability in the presence of a lithium anode and, when doped with lithium salt, reasonable ionic conductivities.

  10. Tethered Aerostat Effects on Nearby Seismometers

    Energy Technology Data Exchange (ETDEWEB)

    Bowman, Daniel [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

    2017-12-01

    This report assesses seismic interference generated by a tethered aerostat. The study was motivated by a planned aerostat deployment within the footprint of the Dry Alluvium Geology seismic network. No evidence was found for seismic interference generated by the aerostat, and thus the e ects on the Dry Alluvium Geology sensors will be negligible.

  11. Coordinated coupling control of tethered space robot using releasing characteristics of space tether

    Science.gov (United States)

    Huang, Panfeng; Zhang, Fan; Xu, Xiudong; Meng, Zhongjie; Liu, Zhengxiong; Hu, Yongxin

    2016-04-01

    Tethered space robot (TSR) is a new concept of space robot, which is released from the platform satellite, and retrieved via connected tether after space debris capture. In this paper, we propose a new coordinate control scheme for optimal trajectory and attitude tracking, and use releasing motor torque to instead the tension force, since it is difficult to track in practical. Firstly, the 6-DOF dynamics model of TSR is derived, in which the dynamics of tether releasing system is taken into account. Then, we propose and design the coordinated coupled controller, which is composed of a 6-DOF sliding mode controller and a PD controller tether's releasing. Thrust is treated as control input of the 6-DOF sliding mode controller to control the in-plane and out-of-plane angle of the tether and attitude angles of the TSR. The torque of releasing motor is used as input of PD controller, which controls the length rate of space tether. After the verification of the control scheme, finally, the simulation experiment is presented in order to validate the effectiveness of this control method. The results show that TSR can track the optimal approaching trajectory accurately. Simultaneously, the attitude angles can be changed to the desired attitude angles in control period, and the terminal accuracy is ±0.3°.

  12. Transitions of tethered chain molecules under tension.

    Science.gov (United States)

    Luettmer-Strathmann, Jutta; Binder, Kurt

    2014-09-21

    An applied tension force changes the equilibrium conformations of a polymer chain tethered to a planar substrate and thus affects the adsorption transition as well as the coil-globule and crystallization transitions. Conversely, solvent quality and surface attraction are reflected in equilibrium force-extension curves that can be measured in experiments. To investigate these effects theoretically, we study tethered chains under tension with Wang-Landau simulations of a bond-fluctuation lattice model. Applying our model to pulling experiments on biological molecules we obtain a good description of experimental data in the intermediate force range, where universal features dominate and finite size effects are small. For tethered chains in poor solvent, we observe the predicted two-phase coexistence at transitions from the globule to stretched conformations and also discover direct transitions from crystalline to stretched conformations. A phase portrait for finite chains constructed by evaluating the density of states for a broad range of solvent conditions and tensions shows how increasing tension leads to a disappearance of the globular phase. For chains in good solvents tethered to hard and attractive surfaces we find the predicted scaling with the chain length in the low-force regime and show that our results are well described by an analytical, independent-bond approximation for the bond-fluctuation model for the highest tensions. Finally, for a hard or slightly attractive surface the stretching of a tethered chain is a conformational change that does not correspond to a phase transition. However, when the surface attraction is sufficient to adsorb a chain it will undergo a desorption transition at a critical value of the applied force. Our results for force-induced desorption show the transition to be discontinuous with partially desorbed conformations in the coexistence region.

  13. Optimal control of electrodynamic tether satellites

    Science.gov (United States)

    Stevens, Robert E.

    Low thrust propulsion systems offer a fuel-efficient means to maneuver satellites to new orbits, however they can only perform such maneuvers when they are continuously operated for a long time. Such long-term maneuvers occur over many orbital revolutions often rendering short time scale trajectory optimization methods ineffective. An approach to multirevolution, long time scale optimal control of an electrodynamic tether is investigated for a tethered satellite system in Low Earth Orbit with atmospheric drag. Control is assumed to be periodic over several orbits since under the assumptions of a nearly circular orbit, periodic control yields the only solution that significantly contributes to secular changes in the orbital parameters. The optimal control problem is constructed in such a way as to maneuver the satellite to a new orbit while minimizing a cost function subject to the constraints of the time-averaged equations of motion by controlling current in the tether. To accurately capture the tether orbital dynamics, libration is modeled and controlled over long time scales in a similar manner to the orbital states. Libration is addressed in two parts; equilibrium and stability analysis, and control. Libration equations of motion are derived and analyzed to provide equilibrium and stability criteria that define the constraints of the design. A new libration mean square state is introduced and constrained to maintain libration within an acceptable envelope throughout a given maneuver. Optimal control solutions are achieved using a pseudospectral method that maneuver an electrodynamic tether to new orbits over long time scales while managing librational motion using only current in a wire.

  14. The physical size of transcription factors is key to transcriptional regulation in chromatin domains

    Science.gov (United States)

    Maeshima, Kazuhiro; Kaizu, Kazunari; Tamura, Sachiko; Nozaki, Tadasu; Kokubo, Tetsuro; Takahashi, Koichi

    2015-02-01

    Genetic information, which is stored in the long strand of genomic DNA as chromatin, must be scanned and read out by various transcription factors. First, gene-specific transcription factors, which are relatively small (˜50 kDa), scan the genome and bind regulatory elements. Such factors then recruit general transcription factors, Mediators, RNA polymerases, nucleosome remodellers, and histone modifiers, most of which are large protein complexes of 1-3 MDa in size. Here, we propose a new model for the functional significance of the size of transcription factors (or complexes) for gene regulation of chromatin domains. Recent findings suggest that chromatin consists of irregularly folded nucleosome fibres (10 nm fibres) and forms numerous condensed domains (e.g., topologically associating domains). Although the flexibility and dynamics of chromatin allow repositioning of genes within the condensed domains, the size exclusion effect of the domain may limit accessibility of DNA sequences by transcription factors. We used Monte Carlo computer simulations to determine the physical size limit of transcription factors that can enter condensed chromatin domains. Small gene-specific transcription factors can penetrate into the chromatin domains and search their target sequences, whereas large transcription complexes cannot enter the domain. Due to this property, once a large complex binds its target site via gene-specific factors it can act as a ‘buoy’ to keep the target region on the surface of the condensed domain and maintain transcriptional competency. This size-dependent specialization of target-scanning and surface-tethering functions could provide novel insight into the mechanisms of various DNA transactions, such as DNA replication and repair/recombination.

  15. Research on the material and structure of space electrodynamic tether

    Science.gov (United States)

    Dong, Xiaolin; Li, Yongpeng; Zhang, Zhanzhi; Kong, Lingchao; Wang, Xiaoding

    In order to reduce the number of space debris efficiently, many approaches have been developed, such as: initiative propulsion, space robot removal system, electrodynamic tether system and etc. The principle of electrodynamic tether system is as following: Firstly, release the tether from the obsolete satellites or upper stages. Then produce the tether current by collecting and emitting electrons. Finally, when the tether moves through the earth’s magnetic field, the Lorentz Force will be generated by the electrodynamic tether, which could move the whole system away from the orbit. Due to the system should be in orbit for several months or even years, the tether need survive the space environment and the collision from the micro orbital debris for a long time. It requires the tether to be lightweight, high tensile strength and long life-span. Meanwhile, the tether should be conductive, even have the ability of collecting electrons. To satisfy these requirements, the research on material and structure of space electrodynamic tether should be focused on, which is also one of the key technologies of the whole system. This paper summarized the development on the material and structure of space electrodynamic tether, which will contribute to the whole system design.

  16. Current Collection Experiment of Bare Electrodynamic Tether Using Sounding Rocket

    Science.gov (United States)

    Yamagiwa, Yoshiki; Kanbe, Atsushi; Wakatsuki, Masaru; Tanaka, Kouji; Sumino, Makoto; Watanabe, Takeo; Sahara, Hironori; Fujii, Hironori A.

    Three innovative tether technologies, tape tether deployment, attitude control by tether robot, and current collection by bare tether, will be verified in the Tether Experiment (T-REx) by using JAXA's sounding rocket S-520 in 2010. In the experiments, the current collection experiment by bare tether is the first experiment in space in the world, and it is expected that this experiment not only will give the new knowledge in plasma physics but also will be very important for the understanding of the charging phenomenon of spaceship and the design of the electrodynamic tether system in the future. The detail and the state of preparation of the experiment are shown in this paper.

  17. Altering surface fluctuations by blending tethered and untethered chains.

    Science.gov (United States)

    Lee, J K; Akgun, B; Jiang, Z; Narayanan, S; Foster, M D

    2017-11-15

    "Partially tethering" a thin film of a polymer melt by covalently attaching to the substrate a fraction of the chains in an unentangled melt dramatically increases the relaxation time of the surface height fluctuations. This phenomenon is observed even when the film thickness, h, is 20 times the unperturbed chain radius, R g,tethered , of the tethered chains, indicating that partial tethering is more influential than any physical attraction with the substrate. Furthermore, a partially tethered layer of a low average molecular weight of 5k showed much slower surface fluctuations than did a reference layer of pure untethered chains of much greater molecular weight (48k), so the partial tethering effect is stronger than the effects of entanglement and increase in glass transition temperature, T g , with molecular weight. Partial tethering offers a means of tailoring these fluctuations which influence wetting, adhesion, and tribology of the surface.

  18. Bromodomain proteins: repairing DNA damage within chromatin.

    Science.gov (United States)

    Chiu, Li-Ya; Gong, Fade; Miller, Kyle M

    2017-10-05

    Genome surveillance and repair, termed the DNA damage response (DDR), functions within chromatin. Chromatin-based DDR mechanisms sustain genome and epigenome integrity, defects that can disrupt cellular homeostasis and contribute to human diseases. An important chromatin DDR pathway is acetylation signalling which is controlled by histone acetyltransferase (HAT) and histone deacetylase (HDAC) enzymes, which regulate acetylated lysines within proteins. Acetylated proteins, including histones, can modulate chromatin structure and provide molecular signals that are bound by acetyl-lysine binders, including bromodomain (BRD) proteins. Acetylation signalling regulates several DDR pathways, as exemplified by the preponderance of HATs, HDACs and BRD proteins that localize at DNA breaks to modify chromatin for lesion repair. Here, we explore the involvement of acetylation signalling in the DDR, focusing on the involvement of BRD proteins in promoting chromatin remodelling to repair DNA double-strand breaks. BRD proteins have widespread DDR functions including chromatin remodelling, chromatin modification and transcriptional regulation. We discuss mechanistically how BRD proteins read acetylation signals within chromatin to trigger DDR and chromatin activities to facilitate genome-epigenome maintenance. Thus, DDR pathways involving BRD proteins represent key participants in pathways that preserve genome-epigenome integrity to safeguard normal genome and cellular functions.This article is part of the themed issue 'Chromatin modifiers and remodellers in DNA repair and signalling'. © 2017 The Author(s).

  19. In-plane adaptive retrieval control for a noncooperative target by tethered space robots

    OpenAIRE

    Zhongjie Meng; Bingheng Wang; Panfeng Huang; Zhengxiong Liu

    2016-01-01

    Using tether to replace rigid arms, the tethered space robot has more flexibility and security than the traditional space robot, which gives it a wide application prospect in the satellite retrieval. After a noncooperative satellite is captured by the tethered space robot, the tethered space robot and the satellite compose a combination with uncertain mass, inertia, and tether junction position. The tether length, tether deflection, and combination attitude are coupled seriously and control i...

  20. Open chromatin in plant genomes.

    Science.gov (United States)

    Zhang, Wenli; Zhang, Tao; Wu, Yufeng; Jiang, Jiming

    2014-01-01

    Sensitivity to DNase I digestion is an indicator of the accessibility and configuration of chromatin in eukaryotic genomes. Open chromatin exhibits high sensitivity to DNase I cleavage. DNase I hypersensitive sites (DHSs) in eukaryotic genomes can be identified through DNase I treatment followed by sequencing (DNase-seq). DHSs are most frequently associated with various cis-regulatory DNA elements, including promoters, enhancers, and silencers in both animal and plant genomes. Genome-wide identification of DHSs provides an efficient method to interpret previously un-annotated regulatory DNA sequences. In this review, we provide an overview of the historical perspective of DHS research in eukaryotes. We summarize the main achievements of DHS research in model animal species and review the recent progress of DHS research in plants. We finally discuss possible future directions of using DHS as a tool in plant genomics research. © 2014 S. Karger AG, Basel.

  1. Nuclear phosphoinositide regulation of chromatin.

    Science.gov (United States)

    Hamann, Bree L; Blind, Raymond D

    2018-01-01

    Phospholipid signaling has clear connections to a wide array of cellular processes, particularly in gene expression and in controlling the chromatin biology of cells. However, most of the work elucidating how phospholipid signaling pathways contribute to cellular physiology have studied cytoplasmic membranes, while relatively little attention has been paid to the role of phospholipid signaling in the nucleus. Recent work from several labs has shown that nuclear phospholipid signaling can have important roles that are specific to this cellular compartment. This review focuses on the nuclear phospholipid functions and the activities of phospholipid signaling enzymes that regulate metazoan chromatin and gene expression. In particular, we highlight the roles that nuclear phosphoinositides play in several nuclear-driven physiological processes, such as differentiation, proliferation, and gene expression. Taken together, the recent discovery of several specifically nuclear phospholipid functions could have dramatic impact on our understanding of the fundamental mechanisms that enable tight control of cellular physiology. © 2017 Wiley Periodicals, Inc.

  2. Coordinated control of tethered space robot using mobile tether attachment point in approaching phase

    Science.gov (United States)

    Wang, Dongke; Huang, Panfeng; Cai, Jia; Meng, Zhongjie

    2014-09-01

    Tethered space robots (TSRs) have wide applications in future on-orbit service owing to its flexibility and great workspace. However, the control problem is quite complex and difficult in the phase of approaching target, and the fuel consumption must also be taken into account. Hence, we present a novel scheme of achieving coordinated orbit and attitude control simultaneously for the TSR. Space tether, which can provide greater force compared with the thruster force, is used in the design of the orbit and attitude coordinated controller. A coordinated control mechanism is designed to provide attitude control torques of the pitch and yaw motions by adjusting the position of the mobile tether attachment point, while the roll motion is stabilized by the thruster. In order to guarantee this mechanism to work properly, constant tether tension strategies are utilized to plan an optimal approaching trajectory which is tracked by the coordinated controller of tether force and thruster force. Numerical simulation validates the feasibility of our proposed coordinated control scheme for TSR in the approaching phase. Furthermore, fuel consumption of the orbit and attitude control are both significantly reduced compared with traditional thruster control.

  3. Tethered Forth system for FPGA applications

    Science.gov (United States)

    Goździkowski, Paweł; Zabołotny, Wojciech M.

    2013-10-01

    This paper presents the tethered Forth system dedicated for testing and debugging of FPGA based electronic systems. Use of the Forth language allows to interactively develop and run complex testing or debugging routines. The solution is based on a small, 16-bit soft core CPU, used to implement the Forth Virtual Machine. Thanks to the use of the tethered Forth model it is possible to minimize usage of the internal RAM memory in the FPGA. The function of the intelligent terminal, which is an essential part of the tethered Forth system, may be fulfilled by the standard PC computer or by the smartphone. System is implemented in Python (the software for intelligent terminal), and in VHDL (the IP core for FPGA), so it can be easily ported to different hardware platforms. The connection between the terminal and FPGA may be established and disconnected many times without disturbing the state of the FPGA based system. The presented system has been verified in the hardware, and may be used as a tool for debugging, testing and even implementing of control algorithms for FPGA based systems.

  4. Aerobic and anaerobic performances in tethered swimming.

    Science.gov (United States)

    Papoti, M; da Silva, A S R; Araujo, G G; Santiago, V; Martins, L E B; Cunha, S A; Gobatto, C A

    2013-08-01

    The purpose of this study was to investigate whether the critical force (CritF) and anaerobic impulse capacity (AIC) - estimated by tethered swimming - reflect the aerobic and anaerobic performance of swimmers. 12 swimmers performed incremental test in tethered swimming to determine lactate anaerobic threshold (AnTLAC), maximal oxygen uptake ( ˙VO2MAX) and force associated with the ˙VO2MAX (i ˙VO2MAX). The swimmers performed 4 exhaustive (tlim) exercise bouts (100, 110, 120 and 130% i ˙VO2MAX) to compute the CritF and AIC (F vs. 1/tlim model); a 30-s all-out tethered swimming bout to determine their anaerobic fitness (ANF); 100, 200, and 400-m time-trials to determine the swimming performance. CritF (57.09±11.77 N) did not differ from AnTLAC (53.96±11.52 N, (P>0.05) but was significantly lower than i ˙VO2MAX (71.02±8.36 N). In addition, CritF presented significant correlation with AnTLAC (r=0.76; Pswimming. © Georg Thieme Verlag KG Stuttgart · New York.

  5. Models of dynamic extraction of lipid tethers from cell membranes

    International Nuclear Information System (INIS)

    Nowak, Sarah A; Chou, Tom

    2010-01-01

    When a ligand that is bound to an integral membrane receptor is pulled, the membrane and the underlying cytoskeleton can deform before either the membrane delaminates from the cytoskeleton or the ligand detaches from the receptor. If the membrane delaminates from the cytoskeleton, it may be further extruded and form a membrane tether. We develop a phenomenological model for this process by assuming that deformations obey Hooke's law up to a critical force at which the cell membrane locally detaches from the cytoskeleton and a membrane tether forms. We compute the probability of tether formation and show that tethers can be extruded only within an intermediate range of force loading rates and pulling velocities. The mean tether length that arises at the moment of ligand detachment is computed as are the force loading rates and pulling velocities that yield the longest tethers

  6. Review of deployment technology for tethered satellite systems

    Science.gov (United States)

    Yu, B. S.; Wen, H.; Jin, D. P.

    2018-03-01

    Tethered satellite systems (TSSs) have attracted significant attention due to their potential and valuable applications for scientific research. With the development of various launched on-orbit missions, the deployment of tethers is considered a crucial technology for operation of a TSS. Both past orbiting experiments and numerical results have shown that oscillations of the deployed tether due to the Coriolis force and environmental perturbations are inevitable and that the impact between the space tether and end-body at the end of the deployment process leads to complicated nonlinear phenomena. Hence, a set of suitable control methods plays a fundamental role in tether deployment. This review article summarizes previous work on aspects of the dynamics, control, and ground-based experiments of tether deployment. The relevant basic principles, analytical expressions, simulation cases, and experimental results are presented as well.

  7. Coat/tether interactions – exceptions or rule?

    Directory of Open Access Journals (Sweden)

    Saskia eSchroeter

    2016-05-01

    Full Text Available Coat complexes are important for cargo selection and vesicle formation. Recent evidence suggests that they may also be involved in vesicle targeting. Tethering factors, which form an initial bridge between vesicles and the target membrane, may bind to coat complexes. In this review, we ask whether these coat/tether interactions share some common mechanisms, or whether they are special adaptations to the needs of very specific transport steps. We compare recent findings in two multisubunit tethering complexes, the Dsl1 complex and the HOPS complex, and put them into context with the TRAPP I complex as a prominent example for coat/tether interactions. We explore where coat/tether interactions are found, compare their function and structure, and comment on a possible evolution from a common ancestor of coats and tethers.

  8. Orbital oscillations of an elastic vertically-tethered satellite

    Science.gov (United States)

    Aslanov, V. S.

    2011-10-01

    The motion of a satellite in a circular orbit with respect to its center of mass is considered. The satellite bears an elastic tether system unrolled along the local vertical. The load at the end of the tether oscillates harmonically. The satellite motion under the action of the gravitational moment and the moment due to the tether tension force is studied. The bifurcation diagram is constructed and the hetero- and homoclinic separatrix trajectories are determined. Mel'nikov's method is used to study the satellite chaotic behavior near separatrices under the action of the periodic tether tension force. The results of the present paper can be used to analyze tether systems of gravitational stabilization and to study the orbital behavior of a satellite with an unrolled tether system with respect to the satellite center of mass.

  9. UV-induced structural changes in chromatin

    International Nuclear Information System (INIS)

    Lang, H.; Zimmer, C.; Vengerov, Yu.Yu.

    1985-01-01

    UV-induced structural alterations of chromatin were studied by means of CD, electron microscopic, and gel electrophoretic measurements. The results indicate that chromatin undergoes serious structural changes after irradiation even at very low fluences. In the low fluence range the structural transitions from the higher ordered chromatin structure to the unfolded state occur without detectable changes in the content of histone H1 and of the core histones. Histone H1 disappears only at fluences above 10 kJ/m 2 . Furthermore, DNA in chromatin is much more sensitive against UV-irradiation and shows a higher degree of strand scission relative to free DNA. While fragmentation in free DNA occurs at fluences above 15 kJ/m 2 , it occurs even at 5.5 kJ/m 2 in the case of chromatin. The biological meaning of the observed UV-induced structural alterations of chromatin is discussed. (author)

  10. Tethers as Debris: Simulating Impacts of Tether Fragments on Shuttle Tiles

    Science.gov (United States)

    Evans, Steven W.

    2004-01-01

    The SPHC hydrodynamic code was used to simulate impacts of Kevlar and aluminum projectiles on a model of the LI-900 type insulating tiles used on Space Shuffle Orbiters The intent was to examine likely damage that such tiles might experience if impacted by orbital debris consisting of tether fragments. Projectile speeds ranged from 300 meters per second to 10 kilometers per second. Damage is characterized by penetration depth, tile surface-hole diameter, tile body-cavity diameter, coating fracture diameter, tether and cavity wall material phases, and deformation of the aluminum backwall.

  11. Human Genome Replication Proceeds through Four Chromatin States

    Science.gov (United States)

    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

  12. Chromatin dynamics during DSB repair

    Czech Academy of Sciences Publication Activity Database

    Falk, Martin; Lukášová, Emilie; Gabrielová, Barbora; Ondřej, Vladan; Kozubek, Stanislav

    2007-01-01

    Roč. 1773, č. 10 (2007), s. 1534-1545 ISSN 0167-4889 R&D Projects: GA ČR(CZ) GP204/06/P349; GA ČR(CZ) 1QS500040508; GA AV ČR(CZ) IAA1065203; GA MŠk(CZ) 1P05OC084 Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : chromatin structure * double- strand breaks (DSB) * DNA repair Subject RIV: BO - Biophysics Impact factor: 4.374, year: 2007

  13. Transcriptional networks and chromatin remodeling controlling adipogenesis

    DEFF Research Database (Denmark)

    Siersbæk, Rasmus; Nielsen, Ronni; Mandrup, Susanne

    2012-01-01

    Adipocyte differentiation is tightly controlled by a transcriptional cascade, which directs the extensive reprogramming of gene expression required to convert fibroblast-like precursor cells into mature lipid-laden adipocytes. Recent global analyses of transcription factor binding and chromatin...... remodeling have revealed 'snapshots' of this cascade and the chromatin landscape at specific time-points of differentiation. These studies demonstrate that multiple adipogenic transcription factors co-occupy hotspots characterized by an open chromatin structure and specific epigenetic modifications....... Such transcription factor hotspots are likely to represent key signaling nodes which integrate multiple adipogenic signals at specific chromatin sites, thereby facilitating coordinated action on gene expression....

  14. Passivity-Based Control of a Rigid Electrodynamic Tether

    DEFF Research Database (Denmark)

    Larsen, Martin Birkelund; Blanke, Mogens

    2011-01-01

    Electrodynamic tethers provide actuation for performing orbit correction of spacecrafts. When an electrodynamic tether system is orbiting the Earth in an inclined orbit, periodic changes in the magnetic field result in a family of unstable periodic solutions in the attitude motion. This paper shows...... how these periodic solutions can be stabilized by controlling only the current through the tether. A port-controlled Hamiltonian formulation is employed to describe the tethered satellite system and a passive input-output connection is utilized in the control design. The control law consists of two...

  15. Dynamic Modeling and Control of a Tethered Space Robot

    Directory of Open Access Journals (Sweden)

    M. Soltani

    2016-09-01

    Full Text Available In present study, dynamic modeling and control of a tethered space robot system in trajectory tracking of its end effector is investigated. Considering variation of the tether length in the model, dynamics of the system is modeled using Lagrange’s method. Librational motion of the tether is controlled by adjusting the tether length similar to conventional manipulators,control of the robot is performed by its motors. It is clear that, in the trajectory tracking of the end effector, the tether length should be kept more or less constant, keeping them in a stable position. Limiting the tether length variation while using it as a tool for controlling the tether librational motion, is the main challenging part of the control system. To deal with this problem, a hybrid control  system is proposed to control the system. A nonlinear model predictive control approach (NMPC is utilized to control the tether librational motion and a modified computed torque method (CTM is used to control the manipulator motion. Initially the NMPC controller is developed for a simple tethered satellite system. Then it is combined with the CTM controller. The proposed controller is employed to control motion of a space robot’s end effector on a predefined trajectory. Performance of the controller is then evaluated by numerical simulations.

  16. Lyapunov Orbits in the Jupiter System Using Electrodynamic Tethers

    Science.gov (United States)

    Bokelmann, Kevin; Russell, Ryan P.; Lantoine, Gregory

    2013-01-01

    Various researchers have proposed the use of electrodynamic tethers for power generation and capture from interplanetary transfers. The effect of tether forces on periodic orbits in Jupiter-satellite systems are investigated. A perturbation force is added to the restricted three-body problem model and a series of simplifications allows development of a conservative system that retains the Jacobi integral. Expressions are developed to find modified locations of equilibrium positions. Modified families of Lyapunov orbits are generated as functions of tether size and Jacobi integral. Zero velocity curves and stability analyses are used to evaluate the dynamical properties of tether-modified orbits.

  17. The architects of crenarchaeal chromatin : A biophysical characterization of chromatin proteins from Sulfolobus solfataricus

    NARCIS (Netherlands)

    Driessen, Rosalie Paula Catharina

    2014-01-01

    Understanding of chromatin organization and compaction in Archaea is currently limited. The genome of several megabasepairs long is folded by a set of small chromatin proteins to fit into the micron-sized cell. A first step in understanding archaeal chromatin organization is to study the action of

  18. Nascent chromatin capture proteomics determines chromatin dynamics during DNA replication and identifies unknown fork components

    DEFF Research Database (Denmark)

    Alabert, Constance; Bukowski-Wills, Jimi-Carlo; Lee, Sung-Po

    2014-01-01

    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 3,995 proteins. The replication machinery and 485 chromatin factors...

  19. Chromatin priming of genes in development: Concepts, mechanisms and consequences.

    Science.gov (United States)

    Bonifer, Constanze; Cockerill, Peter N

    2017-05-01

    During ontogeny, cells progress through multiple alternate differentiation states by activating distinct gene regulatory networks. In this review, we highlight the important role of chromatin priming in facilitating gene activation during lineage specification and in maintaining an epigenetic memory of previous gene activation. We show that chromatin priming is part of a hugely diverse repertoire of regulatory mechanisms that genes use to ensure that they are expressed at the correct time, in the correct cell type, and at the correct level, but also that they react to signals. We also emphasize how increasing our knowledge of these principles could inform our understanding of developmental failure and disease. Copyright © 2017 ISEH - International Society for Experimental Hematology. Published by Elsevier Inc. All rights reserved.

  20. Dietary polyphenols and chromatin remodeling.

    Science.gov (United States)

    Russo, Gian Luigi; Vastolo, Viviana; Ciccarelli, Marco; Albano, Luigi; Macchia, Paolo Emidio; Ungaro, Paola

    2017-08-13

    Polyphenols are the most abundant phytochemicals in fruits, vegetables, and plant-derived beverages. Recent findings suggest that polyphenols display the ability to reverse adverse epigenetic regulation involved in pathological conditions, such as obesity, metabolic disorder, cardiovascular and neurodegenerative diseases, and various forms of cancer. Epigenetics, defined as heritable changes to the transcriptome, independent from those occurring in the genome, includes DNA methylation, histone modifications, and posttranscriptional gene regulation by noncoding RNAs. Sinergistically and cooperatively, these processes regulate gene expression by changing chromatin organization and DNA accessibility. Such induced epigenetic changes can be inherited during cell division, resulting in permanent maintenance of the acquired phenotype, but they may also occur throughout an individual life-course and may ultimately influence phenotypic outcomes (health and disease risk). In the last decade, a number of studies have shown that nutrients can affect metabolic traits by altering the structure of chromatin and directly regulate both transcription and translational processes. In this context, dietary polyphenol-targeted epigenetics becomes an attractive approach for disease prevention and intervention. Here, we will review how polyphenols, including flavonoids, curcuminoids, and stilbenes, modulate the establishment and maintenance of key epigenetic marks, thereby influencing gene expression and, hence, disease risk and health.

  1. Nuclear pore complex tethers to the cytoskeleton.

    Science.gov (United States)

    Goldberg, Martin W

    2017-08-01

    The nuclear envelope is tethered to the cytoskeleton. The best known attachments of all elements of the cytoskeleton are via the so-called LINC complex. However, the nuclear pore complexes, which mediate the transport of soluble and membrane bound molecules, are also linked to the microtubule network, primarily via motor proteins (dynein and kinesins) which are linked, most importantly, to the cytoplasmic filament protein of the nuclear pore complex, Nup358, by the adaptor BicD2. The evidence for such linkages and possible roles in nuclear migration, cell cycle control, nuclear transport and cell architecture are discussed. Copyright © 2017. Published by Elsevier Ltd.

  2. Vibroimpact Dynamics of a Tethered Satellite System

    Directory of Open Access Journals (Sweden)

    B. S. Yu

    2017-01-01

    Full Text Available This paper presents the vibroimpact dynamics of an in-plane tethered subsatellite caused by sudden braking during deployment or retrieval. The full dynamics of the subsatellite are composed of its free-flight and the instantaneous impacts. At the moment of impact, the reflective angle of the subsatellite is envisioned to be equal to its incident angle such that the impact law is obtained. Then, the stability of the periodic vibroimpacts is analyzed using the composite Poincaré map. Further, the vibroimpact responses that do not exceed a specified region are numerically determined via the cell mapping method.

  3. Chromatin Remodelers: From Function to Dysfunction

    Directory of Open Access Journals (Sweden)

    Gernot Längst

    2015-06-01

    Full Text Available 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.

  4. Transcription Through Chromatin - Dynamic Organization of Genes

    Indian Academy of Sciences (India)

    Remodeling of chromatin confers it the ability for dynamic change. Remodeling is essential for transcriptional regulation, the first step of gene expression. Chromatin Structure and Gene Expression. Transcription is the first step of gene expression in which RNA synthesis occurs from the DNA (gene) template in a series of.

  5. Chromatin dynamics resolved with force spectroscopy

    NARCIS (Netherlands)

    Chien, Fan-Tso

    2011-01-01

    In eukaryotic cells, genomic DNA is organized in chromatin fibers composed of nucleosomes as structural units. A nucleosome contains 1.7 turns of DNA wrapped around a histone octamer and is connected to the adjacent nucleosomes with linker DNA. The folding of chromatin fibers effectively increases

  6. Molecular structures guide the engineering of chromatin.

    Science.gov (United States)

    Tekel, Stefan J; Haynes, Karmella A

    2017-07-27

    Chromatin is a system of proteins, RNA, and DNA that interact with each other to organize and regulate genetic information within eukaryotic nuclei. Chromatin proteins carry out essential functions: packing DNA during cell division, partitioning DNA into sub-regions within the nucleus, and controlling levels of gene expression. There is a growing interest in manipulating chromatin dynamics for applications in medicine and agriculture. Progress in this area requires the identification of design rules for the chromatin system. Here, we focus on the relationship between the physical structure and function of chromatin proteins. We discuss key research that has elucidated the intrinsic properties of chromatin proteins and how this information informs design rules for synthetic systems. Recent work demonstrates that chromatin-derived peptide motifs are portable and in some cases can be customized to alter their function. Finally, we present a workflow for fusion protein design and discuss best practices for engineering chromatin to assist scientists in advancing the field of synthetic epigenetics. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  7. Chromatin-modifying proteins in cancer

    DEFF Research Database (Denmark)

    Fog, Cathrine K; Jensen, Klaus T; Lund, Anders Henrik

    2007-01-01

    -despite the fact that all cells in the organism contain the same genetic information. A large amount of data gathered over the last decades has demonstrated that deregulation of chromatin-modifying proteins is etiologically involved in the development and progression of cancer. Here we discuss how epigenetic...... alterations influence cancer development and review known cancer-associated alterations in chromatin-modifying proteins....

  8. A microscopic analysis of Arabidopsis chromatin

    NARCIS (Netherlands)

    Willemse, J.J.

    2007-01-01

    Genetic information of eukaryotic organisms is stored as DNA in the nuclei of their cells. Nuclear DNA is associated with several proteins, which together form chromatin. The most abundant chromatin proteins arehistones,they arrange the initial packaging step of the DNA. DNA

  9. TOPICAL REVIEW: The physics of chromatin

    Science.gov (United States)

    Schiessel, Helmut

    2003-05-01

    Recent progress has been made in the understanding of the physical properties of chromatin - the dense complex of DNA and histone proteins that occupies the nuclei of plant and animal cells. Here I will focus on the two lowest levels of the hierarchy of DNA folding into the chromatin complex. (i) The nucleosome, the chromatin repeating unit consisting of a globular aggregate of eight histone proteins with the DNA wrapped around it: its overcharging, the DNA unwrapping transition, the 'sliding' of the octamer along the DNA. (ii) The 30 nm chromatin fibre, the necklace-like structure of nucleosomes connected via linker DNA: its geometry, its mechanical properties under stretching and its response to changing ionic conditions. I will stress that chromatin combines two seemingly contradictory features: (1) high compaction of DNA within the nuclear envelope and, at the same time, (2) accessibility to genes, promoter regions and gene regulatory sequences.

  10. Stress, endogenous opioids and stereotypies in tethered pigs

    NARCIS (Netherlands)

    Loijens, L.W.S.

    2002-01-01

    Tether housing of female pigs in narrow, individual boxes represents a chronic stressor for the animals. Pigs that are housed tethered often develop behavioural disturbances, such as stereotypies, and changes in physiological regulation. The results of the studies described in the present

  11. Investigation of electrodynamic stabilization and control of long orbiting tethers

    Science.gov (United States)

    Colombo, G.; Arnold, D.

    1984-01-01

    The state-of-the-art in tether modelling among participants in the Tethered Satellite System (TSS) Program, the slack tether and its behavior, and certain advanced applications of the tether to problems in orbital mechanics are identified. The features and applications of the TSS software set are reviewed. Modelling the slack tether analytically with as many as 50 mass points and the application of this new model to a study of the behavior of a broken tether near the Shuttle are described. A reel control algorithm developed by SAO and examples of its use are described, including an example which also demonstrates the use of the tether in transferring a heavy payload from a low-orbiting Shuttle to a high circular orbit. Capture of a low-orbiting payload by a Space Station in high circular orbit is described. Energy transfer within a dumbbell-type spacecraft by cyclical reeling operations or gravitational effects on the natural elasticity of the connecting tether, it is shown, can circularize the orbit of the spacecraft.

  12. Tether enabled spacecraft systems for ultra long wavelength radio astronomy

    Science.gov (United States)

    Gemmer, Thomas; Yoder, Christopher D.; Reedy, Jacob; Mazzoleni, Andre P.

    2017-09-01

    This paper describes a proposed CubeSat mission to perform unique experiments involving interferometry and tether dynamics. A 3U CubeSat is to be placed in orbit where it will separate into three 1U CubeSats connected by a total of 100 m of tether. The separation between the three units will allow for the demonstration of high resolution radio interferometry. The increased resolution will provide access to the Ultra-Long Wavelength (ULW) scale of the electromagnetic spectrum, which is largely unexplored. During and after completion of the primary experiment, the CubeSat will be able to gather data on tethered dynamics of a space vehicle. Maneuvers to be performed and studied include direct testing of tether deployment and tethered formation flying. Tether deployment is a vital area where more data is needed as this is the phase where many tethered missions have experienced complications and failures. There are a large number of complex dynamical responses predicted by the theory associated with the deployment of an orbiting tethered system. Therefore, it is imperative to conduct an experiment that provides data on what dynamic responses actually occur.

  13. Analysis of different treatment modalities of tethered cord syndrome

    NARCIS (Netherlands)

    van der Meulen, WDM; Hoving, Eelco W.; Staal - Schreinemachers, A; Begeer, Jacobus H.

    2002-01-01

    Introduction: Although MRI has improved the diagnosis of tethered cord, many controversies still exist in the treatment of tethered cord syndrome (TCS). Especially the indications for and timing of surgical release have remained topics of discussion. Materials and methods: We retrospectively

  14. Modeling and Simulation of a Tethered Harpoon for Comet Sampling

    Science.gov (United States)

    Quadrelli, Marco B.

    2014-01-01

    This paper describes the development of a dynamic model and simulation results of a tethered harpoon for comet sampling. This model and simulation was done in order to carry out an initial sensitivity analysis for key design parameters of the tethered system. The harpoon would contain a canister which would collect a sample of soil from a cometary surface. Both a spring ejected canister and a tethered canister are considered. To arrive in close proximity of the spacecraft at the end of its trajectory so it could be captured, the free-flying canister would need to be ejected at the right time and with the proper impulse, while the tethered canister must be recovered by properly retrieving the tether at a rate that would avoid an excessive amplitude of oscillatory behavior during the retrieval. The paper describes the model of the tether dynamics and harpoon penetration physics. The simulations indicate that, without the tether, the canister would still reach the spacecraft for collection, that the tether retrieval of the canister would be achievable with reasonable fuel consumption, and that the canister amplitude upon retrieval would be insensitive to variations in vertical velocity dispersion.

  15. Climber Motion Optimization for the Tethered Space Elevator

    NARCIS (Netherlands)

    Williams, P.; Ockels, W.J.

    The tethered space elevator could provide a revolutionary means for enabling cheap transportation to geostationary altitude and beyond. Assuming that such a system can be built, one of the dynamic design problems is determining a means of moving the elevator along the tether so as to minimize the

  16. Tethered Contactless Mobile Nuclear Environment Monitoring Robot

    Energy Technology Data Exchange (ETDEWEB)

    Choi, S. Y.; Lee, E. S.; Lee, Kun J.; Kim, Su H.; Rim, C. T. [Korea Advanced Institute of Science and Technology, Daejeon (Korea, Republic of)

    2013-05-15

    In fact, the nuclear environment monitoring is significantly crucial for early detection of NPP accident, radiological emergency, the estimation of radiation exposure to nearby residents as well as the long term radioactivity. In the UAE, the nuclear environment monitoring is, however, quite challenging because sampling locations are far from NPPs and the outdoor temperature and humidity are very high for NPP workers to collect soil, air, and water samples. Therefore, nuclear environment monitoring robots (Nubos) are strongly needed for the NPPs in the UAE. The Nubos can be remotely controlled to collect samples in extreme environment instead of NPP workers. Moreover, the Nubos can be unmanned ground vehicles (UGVs), unmanned aerial vehicles (UAVs) and unmanned marine vehicles (UMVs) to collect soil, air, and water samples, respectively. In this paper, the prototype development of UGV type Nubos using power cable for a long distance power delivery, called Tethered contactless mobile Nubo is introduced and validated by experiments. In this paper, the prototype development of Tethered Contactless Mobile (TeCoM) Nubo, which can be powered continuously within several km distance and avoid tangled cable, and the indoor test are finished. As further works, outdoor demonstration and a grand scale R and D proposal of practical Nubo will be proceeded.

  17. Propulsive force asymmetry during tethered-swimming.

    Science.gov (United States)

    dos Santos, K B; Pereira, G; Papoti, M; Bento, P C B; Rodacki, A

    2013-07-01

    This study aimed to determine whether: i) tethe-red-swimming can be used to identify the asymmetry during front crawl swimming style; ii) swimmers that perform unilateral breathing present greater asymmetry in comparison to others that use bilateral breathing; iii) swimmers of best performance present smaller asymmetry than their counterparts; iv) repeated front crawl swimming movements influence body asymmetry. 18 swimmers were assessed for propulsive force parameters (peak force, mean force, impulse and rate of force development) during a maximal front crawl tethered-swimming test lasting 2 min. A factorial analysis showed that propulsive forces decreased at the beginning, intermediate and end of the test (pforce parameters (p>0.05). When performance was considered (below or above mean group time), a larger asymmetry was found in the sub-group of lower performance in comparison to those of best performance (pforces can be detected using tethered-swimming. The propulsive forces decreased during the test but asymmetries did not change under testing conditions. Although breathing preference did not influence asymmetry, swimmers with best performance were less asymmetric than their counterparts. © Georg Thieme Verlag KG Stuttgart · New York.

  18. Microgravity Experiment for Attitude Control of a Tethered Space Robot

    Science.gov (United States)

    Nohmi, Masahiro

    A tethered space robot, which is connected to a mother spacecraft through a peace of tether, is a new space system proposed in the previous work. The tethered subsystem is envisioned to be a multi-body system for a robot, whose attitude can be controlled under tether tension by its own link motion. This paper discusses about microgravity experiment for a tethered space robot. Design and mechanism of the experimental device, required for the proposed attitude control, were explained. Also, link motion control algorithm was designed for the experimental device. Characteristics of the proposed attitude control were confirmed by microgravity experiment using a drop shaft, which can provide high quality microgravity condition during 4.5s.

  19. Tethering tracts in spina bifida occulta: revisiting an established nomenclature.

    Science.gov (United States)

    Rajpal, Sharad; Salamat, M Shahriar; Tubbs, R Shane; Kelly, David R; Oakes, W Jerry; Iskandar, Bermans J

    2007-09-01

    The goal of the present study goal was to systematically confirm the previously recognized nomenclature for tethering tracts that are part of the spectrum of occult spinal dysraphic lesions. The tethering tract in 20 patients with spina bifida occulta underwent histological examination with H & E staining and epithelial membrane antigen (EMA) immunolabeling, and additional selected specimens were stained with Masson trichrome. All tethering tracts contained fibrous connective tissue. Four tracts were lined with epithelial cells and either originated within a dermoid cyst, terminated at a skin dimple/sinus opening, or had both of these characteristics. No tethering tracts exhibited EMA positivity or meningeal elements. Although all tethering tracts originated in juxtaposition to the spinal cord, their termination sites were variable. Based on histological findings and presumed embryological origin, the authors broadly classified tethering tracts terminating within the dura mater, epidural space, or lamina as "short tethering tracts" (STTs). The STTs occurred mostly in conjunction with split cord malformations and had a purely fibrous composition. Tethering tracts terminating superficial to the overlying lamina were classified as "long tethering tracts" (LTTs), and the authors propose that these are embryologically distinct from STTs. The LTTs were of two varieties: epithelial and nonepithelial, the former being typically associated with a skin dimple or spinal cord (epi)dermoid cyst. In fact, analysis of the data suggested that not every tethering tract terminating in or on the skin should be classified as a dermal sinus tract without histological confirmation, and because no evidence of meningeal tissue-lined tracts was detected, the use of the term "meningocele manqué" may not be appropriate.

  20. Self-assembled FUS binds active chromatin and regulates gene transcription

    Science.gov (United States)

    Yang, Liuqing; Gal, Jozsef; Chen, Jing; Zhu, Haining

    2014-01-01

    Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease. Fused in sarcoma (FUS) is a DNA/RNA binding protein and mutations in FUS cause a subset of familial ALS. Most ALS mutations are clustered in the C-terminal nuclear localization sequence of FUS and consequently lead to the accumulation of protein inclusions in the cytoplasm. It remains debatable whether loss of FUS normal function in the nucleus or gain of toxic function in the cytoplasm plays a more critical role in the ALS etiology. Moreover, the physiological function of FUS in the nucleus remains to be fully understood. In this study, we found that a significant portion of nuclear FUS was bound to active chromatin and that the ALS mutations dramatically decreased FUS chromatin binding ability. Functionally, the chromatin binding is required for FUS transcription activation, but not for alternative splicing regulation. The N-terminal QGSY (glutamine-glycine-serine-tyrosine)-rich region (amino acids 1–164) mediates FUS self-assembly in the nucleus of mammalian cells and the self-assembly is essential for its chromatin binding and transcription activation. In addition, RNA binding is also required for FUS self-assembly and chromatin binding. Together, our results suggest a functional assembly of FUS in the nucleus under physiological conditions, which is different from the cytoplasmic inclusions. The ALS mutations can cause loss of function in the nucleus by disrupting this assembly and chromatin binding. PMID:25453086

  1. Extensive Variation in Chromatin States Across Humans

    KAUST Repository

    Kasowski, M.

    2013-10-17

    The majority of disease-associated variants lie outside protein-coding regions, suggesting a link between variation in regulatory regions and disease predisposition. We studied differences in chromatin states using five histone modifications, cohesin, and CTCF in lymphoblastoid lines from 19 individuals of diverse ancestry. We found extensive signal variation in regulatory regions, which often switch between active and repressed states across individuals. Enhancer activity is particularly diverse among individuals, whereas gene expression remains relatively stable. Chromatin variability shows genetic inheritance in trios, correlates with genetic variation and population divergence, and is associated with disruptions of transcription factor binding motifs. Overall, our results provide insights into chromatin variation among humans.

  2. Chromatin-modifying proteins in cancer

    DEFF Research Database (Denmark)

    Fog, Cathrine K; Jensen, Klaus T; Lund, Anders Henrik

    2007-01-01

    Chromatin-modifying proteins mold the genome into areas that are accessible for transcriptional activity and areas that are transcriptionally silent. This epigenetic gene regulation allows for different transcriptional programs to be conducted in different cell types at different timepoints......-despite the fact that all cells in the organism contain the same genetic information. A large amount of data gathered over the last decades has demonstrated that deregulation of chromatin-modifying proteins is etiologically involved in the development and progression of cancer. Here we discuss how epigenetic...... alterations influence cancer development and review known cancer-associated alterations in chromatin-modifying proteins....

  3. Phosphorylation-dependent regulation of plant chromatin and chromatin-associated proteins

    KAUST Repository

    Bigeard, Jean

    2014-07-10

    In eukaryotes, most of the DNA is located in the nucleus where it is organized with histone proteins in a higher order structure as chromatin. Chromatin and chromatin-associated proteins contribute to DNA-related processes such as replication and transcription as well as epigenetic regulation. Protein functions are often regulated by PTMs among which phosphorylation is one of the most abundant PTM. Phosphorylation of proteins affects important properties, such as enzyme activity, protein stability, or subcellular localization. We here describe the main specificities of protein phosphorylation in plants and review the current knowledge on phosphorylation-dependent regulation of plant chromatin and chromatin-associated proteins. We also outline some future challenges to further elucidate protein phosphorylation and chromatin regulation.

  4. Spinal column shortening for tethered cord syndrome associated with myelomeningocele, lumbosacral lipoma, and lipomyelomeningocele in children and young adults.

    Science.gov (United States)

    Aldave, Guillermo; Hansen, Daniel; Hwang, Steven W; Moreno, Amee; Briceño, Valentina; Jea, Andrew

    2017-06-01

    fusion and no instrumentation failure in all cases by the most recent follow-up. Five of 7 patients (71%) reported improvement in preoperative symptoms during the follow-up period. The mean differences in initial and most recent Scoliosis Research Society Outcomes Questionnaire and Oswestry Disability Index scores were 0.26 and -13%, respectively; minimum clinically important difference in SRS-22 and ODI were assumed to be 0.4% and -12.8%, respectively. CONCLUSIONS Spinal column shortening seems to represent a safe and efficacious alternative to traditional untethering of the spinal cord for tethered cord syndrome.

  5. Chromatin Pioneers | Center for Cancer Research

    Science.gov (United States)

    Taking advantage of their ability to explore provocative ideas, NCI investigators pioneered the study of chromatin to demonstrate its functional importance and lay the groundwork for understanding its role in cancer and other diseases.

  6. Chromatin dynamics coupled to DNA repair.

    Science.gov (United States)

    Huertas, Dori; Sendra, Ramon; Muñoz, Purificación

    2009-01-01

    In order to protect and preserve the integrity of the genome, eukaryotic cells have developed accurate DNA repair pathways involving a coordinated network of DNA repair and epigenetic factors. The DNA damage response has to proceed in the context of chromatin, a packaged and compact structure that is flexible enough to regulate the accession of the DNA repair machinery to DNA-damaged sites. Chromatin modifications and ATP-remodeling activities are both necessary to ensure efficient DNA repair. Here we review the current progress of research into the importance of chromatin modifications and the ATP-remodeling complex to the DNA damage response, with respect to the sensing and signaling of DNA lesions, DNA repair and the processes that restore chromatin structure.

  7. Tethers as Debris: Simulating Impacts of Kevlar Tethers on Shuttle Tiles

    Science.gov (United States)

    Evans, Steven W.

    2004-01-01

    In a previous paper I examined the effects of impacts of polymer tethers on aluminum plates using the SPHC hydrodynamic code. In this paper I apply tether models to a new target - models of Space Shuttle tiles developed during the STS 107 accident investigation. In this three-dimensional simulation, a short tether fragment strikes a single tile supported on an aluminum backing plate. A tile of the LI-900 material is modeled. Penetration and damage to the tile and the backwall are characterized for three normal impact velocities. The tether is modeled as a bundle of eight 1-mm strands, with the bundle having dimensions 2-mm x 4-mm x 20-cm. The bulk material properties used are those of Kevlar(TradeMark) 49, for which a Mie-Gruneisen multiphase equation of state (eos) is used. In addition, the strength model is applied in a linear sense, such that tensile loads along the strand length are supported, but there is no strength in the lateral directions. Tile models include the various layers making up the tile structure. The outermost layer is a relatively dense borosilicate glass, known as RCG, 0.5-mm thick. The RCG layer is present on the top and four sides of the tile. Below this coating is the bulk of the tile, 1.8- in thick, made of LI-900, a product consisting of rigidized fiberous silica with a density of 9 lWft3. Below the main insulating layer is a bottom layer of the same material that has been treated to increase its density by approximately 69% to improve its strength. This densified layer is bonded to a Strain Isolation Pad (SIP), modeled as a refractory felt fabric. The SIP is bonded to an aluminum 2024 wall 0.1-in thick. The tile and backwall materials use a Me-Gruneisen multiphase eos, with the exception of the SIP felt, which uses a fabric equation of state. Fabrics must be crushed to the full bulk material density before bulk material properties and a Mie-Gruneisen eos are applied. Tether fragment impact speeds of 3,7, and 10 km/s are simulated, with

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

    Science.gov (United States)

    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

  9. Novel Roaming and Stationary Tethered Aerial Robots for Continuous Mobile Missions in Nuclear Power Plants

    OpenAIRE

    Beom W. Gu; Su Y. Choi; Young Soo Choi; Guowei Cai; Lakmal Seneviratne; Chun T. Rim

    2016-01-01

    In this paper, new tethered aerial robots including roaming tethered aerial robots (RTARs) for radioactive material sampling and stationary tethered aerial robots (STARs) for environment monitoring are proposed to meet extremely-long-endurance missions of nuclear power plants. The flight of the proposed tethered aerial robots may last for a few days or even a few months as long as the tethered cable provides continuous power. A high voltage AC or DC power system was newly adopted to reduce th...

  10. Stationary Tether Device for Buoy Apparatus and System for Using

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — A rigid, neutrally buoyant hydrodynamicaly-faired tether and associated fastening hardware that loosely holds a bathymetric float at a predetermined distance from a...

  11. Fiber Optic Shape Sensing for Tethered Marsupial Rovers Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Luna Innovations Incorporated is proposing to design, build, and test a shape, length, and tension sensing tether for robotic exploration and sample-gathering...

  12. An updated review of nanotechnologies for the space elevator tether

    OpenAIRE

    Brambilla, G.

    2010-01-01

    The space elevator tether requires an extraordinary specific ultimate strength (ratio between ultimate strength and density) and carbon nanotubes (CNTs) have been identified as the ideal candidate because of their astonishing strength. This paper reviews CNT manufacture and measured strengths.

  13. FCAPD Protective Coating for Space Tethers, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — Alameda Applied Sciences Corporation (AASC) proposes to demonstrate extended service lifetime of space tethers in the Low Earth Orbit (LEO) environment by using...

  14. The tethered cord syndrome in adults with spina bifida occulta.

    Science.gov (United States)

    Lapsiwala, Samir B; Iskandar, Bermans J

    2004-10-01

    The management of adult-onset tethered cord syndrome (TCA) remains controversial, although the necessity of early surgery in children with TCS is well established. In this paper, we review the major publications that discuss the congenital tethered spinal cord (spina bifida occulta) presenting in adulthood. Data concerning acquired tethered cord from prior myelomeningocele repair were excluded. TCS in adults is an uncommon entity that can become symptomatic. The long-term surgical outcome after tethered cord release in this patient population is generally favorable, as most patients report improvement or stabilization of their symptoms. In addition, the overall post-operative complication rate is low. Although special consideration should be given to older patients with a poor general medical condition, it seems reasonable to recommend early surgical treatment in both symptomatic and asymptomatic adults.

  15. Development of a Tethered Formation Flight Testbed for ISS Project

    Data.gov (United States)

    National Aeronautics and Space Administration — The development of a testbed for the development and demonstration of technologies needed by tethered formation flying satellites is proposed. Such a testbed would...

  16. Interaction between brushes of root-tethered dendrons

    NARCIS (Netherlands)

    Borisov, O.V.; Zhulina, E.B.; Polotsky, A.A.; Leermakers, F.A.M.; Birshtein, T.M.

    2014-01-01

    Polymer molecules densely tethered to surfaces (polymer brushes) can improve the colloidal stability of dispersion by protecting particles against aggregation. We use mean field and self-consistent field theoretical models to consider repulsive interactions between brushes of branched (dendritic)

  17. Fiber Optic Shape Sensing for Tethered Marsupial Rovers, Phase II

    Data.gov (United States)

    National Aeronautics and Space Administration — Building upon the successful proof of concept work in Phase I, Luna Innovations Incorporated is proposing to design, build, and test a sensing tether for marsupial...

  18. Chromatin Dynamics during Lytic Infection with Herpes Simplex Virus 1

    Science.gov (United States)

    Conn, Kristen L.; Schang, Luis M.

    2013-01-01

    Latent HSV-1 genomes are chromatinized with silencing marks. Since 2004, however, there has been an apparent inconsistency in the studies of the chromatinization of the HSV-1 genomes in lytically infected cells. Nuclease protection and chromatin immunoprecipitation assays suggested that the genomes were not regularly chromatinized, having only low histone occupancy. However, the chromatin modifications associated with transcribed and non-transcribed HSV-1 genes were those associated with active or repressed transcription, respectively. Moreover, the three critical HSV-1 transcriptional activators all had the capability to induce chromatin remodelling, and interacted with critical chromatin modifying enzymes. Depletion or overexpression of some, but not all, chromatin modifying proteins affected HSV-1 transcription, but often in unexpected manners. Since 2010, it has become clear that both cellular and HSV-1 chromatins are highly dynamic in infected cells. These dynamics reconcile the weak interactions between HSV-1 genomes and chromatin proteins, detected by nuclease protection and chromatin immunoprecipitation, with the proposed regulation of HSV-1 gene expression by chromatin, supported by the marks in the chromatin in the viral genomes and the abilities of the HSV-1 transcription activators to modulate chromatin. It also explains the sometimes unexpected results of interventions to modulate chromatin remodelling activities in infected cells. PMID:23863878

  19. The role of hydrogen bonding in tethered polymer layers

    OpenAIRE

    Ren, C.; Nap, R. J.; Szleifer, I.

    2008-01-01

    A molecular theory to study the properties of end tethered polymer layers, in which the polymers have the ability to form hydrogen bonds with water is presented. The approach combines the ideas of the single-chain mean-field theory to treat tethered layers with the approach of Dormidontova (Macromolecules, 2002 35,987) to include hydrogen bonds. The generalization includes the consideration of position dependent polymer-water and water-water hydrogen bonds. The theory is applied to model poly...

  20. Tethered catalysts for the hydration of carbon dioxide

    Energy Technology Data Exchange (ETDEWEB)

    Valdez, Carlos A; Satcher, Jr., Joe H; Aines, Roger D; Wong, Sergio E; Baker, Sarah E; Lightstone, Felice C; Stolaroff, Joshuah K

    2014-11-04

    A system is provided that substantially increases the efficiency of CO.sub.2 capture and removal by positioning a catalyst within an optimal distance from the air-liquid interface. The catalyst is positioned within the layer determined to be the highest concentration of carbon dioxide. A hydrophobic tether is attached to the catalyst and the hydrophobic tether modulates the position of the catalyst within the liquid layer containing the highest concentration of carbon dioxide.

  1. P-Tether-Mediated, Iterative SN2'-Cuprate Alkylation Strategy to Skipped Polyol Stereotetrads: Utility of an Oxidative "Function Switch" with Phosphite-Borane Tethers.

    Science.gov (United States)

    Markley, Jana L; Hanson, Paul R

    2017-05-19

    The development of a P-tether-mediated, iterative S N 2'-cuprate alkylation protocol for the formation of 1,3-skipped polyol stereotetrads is reported. This two-directional synthetic strategy builds molecular complexity from simple, readily prepared C 2 -symmetric dienediols and unites the chemistry of both temporary phosphite-borane tethers and temporary phosphate tethers-through an oxidative "function switch" of the P-tether itself-to generate intermediates that were previously inaccessible via either method alone.

  2. Tethered lifting systems for measurements in the lower atmosphere

    Science.gov (United States)

    Jensen, Michael Lamar

    2000-10-01

    This work defines a Tethered Lifting System for measurements in the lower atmosphere, its design and development, and applications for its use. Using historical kite research and the unique capabilities of tethered lifting platforms as motivation, a complete system has been created offering the complementary benefits of parafoil kites and tethered balloons as lifting platforms. Support systems including tethers, winching systems and payload data collection and telemetry systems round out the Tethered Lifting System to provide a complete atmospheric measurement system. The kite platforms have been enhanced by the invention and development of a wind-powered Tether Rover for Atmospheric Research (WindTRAM), providing rapid profiling and precise positioning capabilities. Design of the WindTRAM and implementation of onboard feedback control are covered in detail, as they comprise the most novel contribution of this research. The breadth of possible applications for these technologies is touched upon by examination of some of the specific research applications undertaken by the researchers at the Cooperative Institute for Research in the Environmental Sciences during the last decade.

  3. The effects of tether placement on antibody stability on surfaces

    Science.gov (United States)

    Grawe, Rebecca W.; Knotts, Thomas A.

    2017-06-01

    Despite their potential benefits, antibody microarrays have fallen short of performing reliably and have not found widespread use outside of the research setting. Experimental techniques have been unable to determine what is occurring on the surface of an atomic level, so molecular simulation has emerged as the primary method of investigating protein/surface interactions. Simulations of small proteins have indicated that the stability of the protein is a function of the residue on the protein where a tether is placed. The purpose of this research is to see whether these findings also apply to antibodies, with their greater size and complexity. To determine this, 24 tethering locations were selected on the antibody Protein Data Bank (PDB) ID: 1IGT. Replica exchange simulations were run on two different surfaces, one hydrophobic and one hydrophilic, to determine the degree to which these tethering sites stabilize or destabilize the antibody. Results showed that antibodies tethered to hydrophobic surfaces were in general less stable than antibodies tethered to hydrophilic surfaces. Moreover, the stability of the antibody was a function of the tether location on hydrophobic surfaces but not hydrophilic surfaces.

  4. Flowing Plasma Interaction with an Electric Sail Tether Element

    Science.gov (United States)

    Schneider, Todd; Vaughn, Jason; Wright, Kenneth; Anderson, Allen; Stone, Nobie

    2017-01-01

    Harnessing the power of the solar wind, an Electric Sail, or E-sail, is a relatively new concept that promises to deliver high speed propellant-less propulsion. The electric sail is an invention made in 2006 at the Kumpula Space Centre in Finland by Pekka Janhunen [Janhunen and Sandroos, 2007]. At its core, an electric sail utilizes multiple positively biased tethers which exchange momentum with solar wind protons via the repelling electric field established around each tether, in other words, by reflecting the solar wind protons. Recognizing the solar wind is a plasma, the effective repelling area of each tether is increased significantly by the formation a plasma sheath around each tether. Fig. 1 shows schematically a spacecraft employing an electric sail. The positive voltage bias (greater than10kV) applied to each tether naturally results in electron collection. Therefore, the electric sail concept necessarily includes an electron source (electron gun) to return collected electrons to space and maintain the positive bias of the tether system.

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

    Science.gov (United States)

    Eirin-Lopez, Jose M.

    2013-01-01

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

  6. A computer lab exploring evolutionary aspects of chromatin structure and dynamics for an undergraduate chromatin course*.

    Science.gov (United States)

    Eirín-López, José 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 vast body of knowledge to the classroom. With this aim, the present work describes a multidisciplinary computer lab designed to introduce undergraduate students to the dynamic nature of chromatin, within the context of the one semester course "Chromatin: Structure, Function and Evolution." This exercise is organized in three parts including (a) molecular evolutionary biology of histone families (using the H1 family as example), (b) histone structure and variation across different animal groups, and (c) effect of histone diversity on nucleosome structure and chromatin dynamics. By using freely available bioinformatic tools that can be run on common computers, the concept of chromatin dynamics is interactively illustrated from a comparative/evolutionary perspective. At the end of this computer lab, students are able to translate the bioinformatic information into a biochemical context in which the relevance of histone primary structure on chromatin dynamics is exposed. During the last 8 years this exercise has proven to be a powerful approach for teaching chromatin structure and dynamics, allowing students a higher degree of independence during the processes of learning and self-assessment. Copyright © 2013 International Union of Biochemistry and Molecular Biology, Inc.

  7. Ligation-mediated PCR for chromatin-structure analysis of interphase and metaphase chromatin.

    Science.gov (United States)

    Hershkovitz, M; Riggs, A D

    1997-02-01

    Chromatin structure is becoming increasingly recognized as important for a full understanding of gene function and cell memory. With regard to cell memory, which involves the transfer of chromatin-encoded epigenetic information from one cell generation to another, the detailed structure of metaphase chromatin is of crucial importance. In this paper we describe methods for the use of dimethyl sulfate, DNase I, and potassium permanganate for in vivo footprinting and chromatin analysis, with special emphasis on studies of metaphase cells. We review the use of ligation-mediated PCR for the analysis of chromatin, including the human phosphoglycerate kinase promoter, and also report initial studies of a matrix attachment region near the human beta-interferon gene.

  8. Quantitative analysis of chromatin accessibility in mouse embryonic fibroblasts.

    Science.gov (United States)

    Zhuo, Baowen; Yu, Juan; Chang, Luyuan; Lei, Jiafan; Wen, Zengqi; Liu, Cuifang; Mao, Guankun; Wang, Kehui; Shen, Jie; Xu, Xueqing

    2017-11-04

    Genomic DNA of eukaryotic cells is hierarchically packaged into chromatin by histones. The dynamic organization of chromatin fibers plays a critical role in the regulation of gene transcription and other DNA-associated biological processes. Recently, numerous approaches have been developed to map the chromatin organization by characterizing chromatin accessibilities in genome-wide. However, reliable methods to quantitatively map chromatin accessibility are not well-established, especially not on a genome-wide scale. Here, we developed a modified MNase-seq for mouse embryonic fibroblasts, wherein chromatin was partially digested at multiple digestion times using micrococcal nuclease (MNase), allowing quantitative analysis of local yet genome-wide chromatin compaction. Our results provide strong evidence that the chromatin accessibility at promoter regions are positively correlated with gene activity. In conclusion, our assay is an ideal tool for the quantitative study of gene regulation in the perspective of chromatin accessibility. Copyright © 2017 Elsevier Inc. All rights reserved.

  9. Map of open and closed chromatin domains in Drosophila genome.

    Science.gov (United States)

    Milon, Beatrice; Sun, Yezhou; Chang, Weizhong; Creasy, Todd; Mahurkar, Anup; Shetty, Amol; Nurminsky, Dmitry; Nurminskaya, Maria

    2014-11-18

    Chromatin compactness has been considered a major determinant of gene activity and has been associated with specific chromatin modifications in studies on a few individual genetic loci. At the same time, genome-wide patterns of open and closed chromatin have been understudied, and are at present largely predicted from chromatin modification and gene expression data. However the universal applicability of such predictions is not self-evident, and requires experimental verification. We developed and implemented a high-throughput analysis for general chromatin sensitivity to DNase I which provides a comprehensive epigenomic assessment in a single assay. Contiguous domains of open and closed chromatin were identified by computational analysis of the data, and correlated to other genome annotations including predicted chromatin "states", individual chromatin modifications, nuclear lamina interactions, and gene expression. While showing that the widely trusted predictions of chromatin structure are correct in the majority of cases, we detected diverse "exceptions" from the conventional rules. We found a profound paucity of chromatin modifications in a major fraction of closed chromatin, and identified a number of loci where chromatin configuration is opposite to that expected from modification and gene expression patterns. Further, we observed that chromatin of large introns tends to be closed even when the genes are expressed, and that a significant proportion of active genes including their promoters are located in closed chromatin. These findings reveal limitations of the existing predictive models, indicate novel mechanisms of epigenetic regulation, and provide important insights into genome organization and function.

  10. Chromatin proteins: key responders to stress.

    Directory of Open Access Journals (Sweden)

    Karen T Smith

    Full Text Available Environments can be ever-changing and stresses are commonplace. In order for organisms to survive, they need to be able to respond to change and adapt to new conditions. Fortunately, many organisms have systems in place that enable dynamic adaptation to immediate stresses and changes within the environment. Much of this cellular response is coordinated by modulating the structure and accessibility of the genome. In eukaryotic cells, the genome is packaged and rolled up by histone proteins to create a series of DNA/histone core structures known as nucleosomes; these are further condensed into chromatin. The degree and nature of the condensation can in turn determine which genes are transcribed. Histones can be modified chemically by a large number of proteins that are thereby responsible for dynamic changes in gene expression. In this Primer we discuss findings from a study published in this issue of PLoS Biology by Weiner et al. that highlight how chromatin structure and chromatin binding proteins alter transcription in response to environmental changes and stresses. Their study reveals the importance of chromatin in mediating the speed and amplitude of stress responses in cells and suggests that chromatin is a critically important component of the cellular response to stress.

  11. New mitotic regulators released from chromatin

    Directory of Open Access Journals (Sweden)

    Hideki eYokoyama

    2013-12-01

    Full Text Available Faithful action of the mitotic spindle segregates duplicated chromosomes into daughter cells. Perturbations of this process result in chromosome mis-segregation, leading to chromosomal instability and cancer development. Chromosomes are not simply passengers segregated by spindle microtubules but rather play a major active role in spindle assembly. The GTP bound form of the Ran GTPase (RanGTP, produced around chromosomes, locally activates spindle assembly factors. Recent studies have uncovered that chromosomes organize mitosis beyond spindle formation. They distinctly regulate other mitotic events, such as spindle maintenance in anaphase, which is essential for chromosome segregation. Furthermore, the direct function of chromosomes is not only to produce RanGTP but, in addition, to release key mitotic regulators from chromatin. Chromatin-remodeling factors and nuclear pore complex proteins, which have established functions on chromatin in interphase, dissociate from mitotic chromatin and function in spindle assembly or maintenance. Thus, chromosomes actively organize their own segregation using chromatin-releasing mitotic regulators as well as RanGTP.

  12. Neutron-scattering studies of chromatin

    International Nuclear Information System (INIS)

    Bradbury, E.M.; Baldwin, J.P.; Carpenter, B.G.; Hjelm, R.P.; Hancock, R.; Ibel, K.

    1976-01-01

    It is clear that a knowledge of the basic molecular structure of chromatin is a prerequisite for any progress toward an understanding of chromosome organization. With a two-component system, protein and nucleic acid, neutrons have a particularly powerful application to studies of the spatial arrangements of these components because of the ability, by contrast matching with H 2 O-D 2 O mixtures, to obtain neutron-scattering data on the individual components. With this approach it has been shown that the neutron diffraction of chromatin is consistent with a ''beads on a string'' model in which the bead consists of a protein core with DNA coiled on the outside. However, because chromatin is a gel and gives limited structural data, confirmation of such a model requires extension of the neutron studies by deuteration of specific chromatin components and the isolation of chromatin subunits. Although these studies are not complete, the neutron results so far obtained support the subunit model described above

  13. Analytical investigation of the dynamics of tethered constellations in Earth orbit, phase 2

    Science.gov (United States)

    Lorenzini, Enrico C.; Gullahorn, Gordon E.; Cosmo, Mario L.; Estes, Robert D.; Grossi, Mario D.

    1994-01-01

    This final report covers nine years of research on future tether applications and on the actual flights of the Small Expendable Deployment System (SEDS). Topics covered include: (1) a description of numerical codes used to simulate the orbital and attitude dynamics of tethered systems during station keeping and deployment maneuvers; (2) a comparison of various tethered system simulators; (3) dynamics analysis, conceptual design, potential applications and propagation of disturbances and isolation from noise of a variable gravity/microgravity laboratory tethered to the Space Station; (4) stability of a tethered space centrifuge; (5) various proposed two-dimensional tethered structures for low Earth orbit for use as planar array antennas; (6) tethered high gain antennas; (7) numerical calculation of the electromagnetic wave field on the Earth's surface on an electrodynamically tethered satellite; (8) reentry of tethered capsules; (9) deployment dynamics of SEDS-1; (10) analysis of SEDS-1 flight data; and (11) dynamics and control of SEDS-2.

  14. Discovery and annotation of functional chromatin signatures in the human genome.

    Directory of Open Access Journals (Sweden)

    Gary Hon

    2009-11-01

    Full Text Available Transcriptional regulation in human cells is a complex process involving a multitude of regulatory elements encoded by the genome. Recent studies have shown that distinct chromatin signatures mark a variety of functional genomic elements and that subtle variations of these signatures mark elements with different functions. To identify novel chromatin signatures in the human genome, we apply a de novo pattern-finding algorithm to genome-wide maps of histone modifications. We recover previously known chromatin signatures associated with promoters and enhancers. We also observe several chromatin signatures with strong enrichment of H3K36me3 marking exons. Closer examination reveals that H3K36me3 is found on well-positioned nucleosomes at exon 5' ends, and that this modification is a global mark of exon expression that also correlates with alternative splicing. Additionally, we observe strong enrichment of H2BK5me1 and H4K20me1 at highly expressed exons near the 5' end, in contrast to the opposite distribution of H3K36me3-marked exons. Finally, we also recover frequently occurring chromatin signatures displaying enrichment of repressive histone modifications. These signatures mark distinct repeat sequences and are associated with distinct modes of gene repression. Together, these results highlight the rich information embedded in the human epigenome and underscore its value in studying gene regulation.

  15. Chromatin and nucleosome dynamics in DNA damage and repair.

    Science.gov (United States)

    Hauer, Michael H; Gasser, Susan M

    2017-11-15

    Chromatin is organized into higher-order structures that form subcompartments in interphase nuclei. Different categories of specialized enzymes act on chromatin and regulate its compaction and biophysical characteristics in response to physiological conditions. We present an overview of the function of chromatin structure and its dynamic changes in response to genotoxic stress, focusing on both subnuclear organization and the physical mobility of DNA. We review the requirements and mechanisms that cause chromatin relocation, enhanced mobility, and chromatin unfolding as a consequence of genotoxic lesions. An intriguing link has been established recently between enhanced chromatin dynamics and histone loss. © 2017 Hauer and Gasser; Published by Cold Spring Harbor Laboratory Press.

  16. Autism genes keep turning up chromatin.

    Science.gov (United States)

    Lasalle, Janine M

    2013-06-19

    Autism-spectrum disorders (ASD) are complex genetic disorders collectively characterized by impaired social interactions and language as well as repetitive and restrictive behaviors. Of the hundreds of genes implicated in ASD, those encoding proteins acting at neuronal synapses have been most characterized by candidate gene studies. However, recent unbiased genome-wide analyses have turned up a multitude of novel candidate genes encoding nuclear factors implicated in chromatin remodeling, histone demethylation, histone variants, and the recognition of DNA methylation. Furthermore, the chromatin landscape of the human genome has been shown to influence the location of de novo mutations observed in ASD as well as the landscape of DNA methylation underlying neurodevelopmental and synaptic processes. Understanding the interactions of nuclear chromatin proteins and DNA with signal transduction pathways and environmental influences in the developing brain will be critical to understanding the relevance of these ASD candidate genes and continued uncovering of the "roots" of autism etiology.

  17. Sonography compared with MR imaging in the evaluation of card tethering following myelomeningocele repair

    International Nuclear Information System (INIS)

    Newman, B.; Bowen, A.; Albright, L.

    1989-01-01

    This paper reports on MR imaging and videotaped US spine examinations to evaluate cord tethering were retrospectively compared in 12 children with prior myelomeningocele repair and correlated with clinical and surgical findings. Although US did not delineate normal or abnormal anatomy as well as MR imaging, both types of studies confirmed the presence of tethering in 10 patients. One child with a normal US examination and abnormal MR images had tethering confirmed surgically. A second child had a US study suggestive of tethering with equivocal MR images. Postoperative studies in eight patients correlated less well; US suggested persistent tethering in five patients and MR imaging indicated tethering in two

  18. The dynamics of chromatin remodeling at promoters.

    Science.gov (United States)

    Mellor, Jane

    2005-07-22

    The nucleosome, the structural unit of chromatin, is known to play a central role in regulating gene transcription from promoters. The last seven years have spawned a vast amount of data on the enzymes that remodel and modify nucleosomes and the rules governing how transcription factors interact with the epigenetic code on histones. Yet despite this effort, there has yet to emerge a unifying mechanism by which nucleosomes are remodeled during gene regulation. Recent advances have allowed nucleosome dynamics on promoters to be studied in real time, dramatically changing how we think about gene regulation on chromatin templates.

  19. Dynamics of Histone Tails within Chromatin

    Science.gov (United States)

    Bernier, Morgan; North, Justin; Page, Michael; Jaroniec, Christopher; Hammel, Christopher; Poirier, Michael

    2012-02-01

    Genetic information in humans is encoded within DNA molecules that is wrapped around histone octamer proteins and compacted into a highly conserved structural polymer, chromatin. The physical and material properties of chromatin appear to influence gene expression by altering the accessibility of proteins to the DNA. The tails of the histones are flexible domains that are thought to play a role in regulating DNA accessibility and compaction; however the molecular mechanisms for these phenomena are not understood. I will present CW-EPR studies on site directed spin labeled nucleosomes that probe the structure and dynamics of these histone tails within nucleosomes.

  20. Proteome Characterization of a Chromatin Locus Using the Proteomics of Isolated Chromatin Segments Approach.

    Science.gov (United States)

    Kan, Sophie L; Saksouk, Nehmé; Déjardin, Jérome

    2017-01-01

    The biological functions of given genomic regions are ruled by the local chromatin composition. The Proteomics of Isolated Chromatin segments approach (PICh) is a powerful and unbiased method to analyze the composition of chosen chromatin segments, provided they are abundant (repeated) or that the organism studied has a small genome. PICh can be used to identify novel and unexpected regulatory factors, or when combined with quantitative mass spectrometric approaches, to characterize the function of a defined factor at the chosen locus, by quantifying composition changes at the locus upon removal/addition of that factor.

  1. Tethered Nanoparticle–Polymer Composites: Phase Stability and Curvature

    KAUST Repository

    Srivastava, Samanvaya

    2012-04-17

    Phase behavior of poly(ethylene glycol) (PEG) tethered silica nanoparticles dispersed in PEG hosts is investigated using small-angle X-ray scattering. Phase separation in dispersions of densely grafted nanoparticles is found to display strikingly different small-angle X-ray scattering signatures in comparison to phase-separated composites comprised of bare or sparsely grafted nanoparticles. A general diagram for the dispersion state and phase stability of polymer tethered nanoparticle-polymer composites incorporating results from this as well as various other contemporary studies is presented. We show that in the range of moderate to high grafting densities the dispersion state of nanoparticles in composites is largely insensitive to the grafting density of the tethered chains and chemistry of the polymer host. Instead, the ratio of the particle diameter to the size of the tethered chain and the ratio of the molecular weights of the host and tethered polymer chains (P/N) are shown to play a dominant role. Additionally, we find that well-functionalized nanoparticles form stable dispersions in their polymer host beyond the P/N limit that demarcates the wetting/dewetting transition in polymer brushes on flat substrates interacting with polymer melts. A general strategy for achieving uniform nanoparticle dispersion in polymers is proposed. © 2012 American Chemical Society.

  2. Clinical and MR findings of tethered cord syndrome

    International Nuclear Information System (INIS)

    Chung, Ho In; Kim, Hyae Young; Chung, Eun Chul; Suh, Jeong Soo; Lim, Hyo Keun; Lee, Seoung Ro; Lee, Young Seok

    1994-01-01

    Tethered cord syndrome(TCS)is defined as low position of the conus medullaris by the abnormally fixed spinal cord with progressive neurologic deficit. To evaluate the findings of TCS at MRI and its diagnostic value, we performed a retrospective analysis of MRI of 30 patients with emphasis on clinical manifestation, level of conus medullaris, cause of tethering, and associated findings. Clinical presentation included back mass(26 cases), neurogenic bladder(5 cases), urinary incontinences(5 cases), progressive constipation(2 cases), skin dimpling(1 case), gait disturbance(1 case) and club foot (1 case). Neurologic deficit was developed 11 cases(40%) and mean age of these patients at the time of diagnosis was 8.6 years. The most common cause of tethering was lipoma(63%). The tips of conus medullaris were below the level of the second lumbar spine ia all patients. The causes of tethering were lipomatous components(spinal lipoma and lipomyelomenigocele) in 67% myelomeningocele in 20%, presacral mass in 7%, thickened filum terminale in 3% and postoperative change in 3%. Associated anomalies included syringomyelia(20%) and hydrocephalus was associated in 3 out 5 patients who underwent brain MRI. MRI clearly delineated the location of conus, tethering of the filum terminate with their causes and associated abnormalities. MRI examination is a very useful diagnostic tool for the early evaluation of TCS and the postoperative follow up

  3. Classical and Nonclassical Estrogen Receptor Action on Chromatin Templates

    National Research Council Canada - National Science Library

    Nordeen, Steven

    2000-01-01

    .... Using newly-developed approaches, I investigated mechanisms of estrogen/estrogen receptor action on chromatin templates in vitro in order to better understand the role of chromatin in steroid-regulated gene expression...

  4. Chromatin Repressive Complexes in Stem Cells, Development, and Cancer

    DEFF Research Database (Denmark)

    Laugesen, Anne; Helin, Kristian

    2014-01-01

    The chromatin environment is essential for the correct specification and preservation of cell identity through modulation and maintenance of transcription patterns. Many chromatin regulators are required for development, stem cell maintenance, and differentiation. Here, we review the roles...

  5. Classical and Nonclassical Estrogen Receptor Action on Chromatin Templaces

    National Research Council Canada - National Science Library

    Nordeen, Steve

    2001-01-01

    .... Using newly-developed approaches, I investigated mechanisms of estrogen/estrogen receptor action on chromatin templates in vitro in order to better understand the role of chromatin in steroid-regulated gene expression...

  6. Chromatin as an expansive canvas for chemical biology.

    Science.gov (United States)

    Fierz, Beat; Muir, Tom W

    2012-04-17

    Chromatin is extensively chemically modified and thereby acts as a dynamic signaling platform controlling gene function. Chromatin regulation is integral to cell differentiation, lineage commitment and organism development, whereas chromatin dysregulation can lead to age-related and neurodegenerative disorders as well as cancer. Investigating chromatin biology presents a unique challenge, as the issue spans many disciplines, including cell and systems biology, biochemistry and molecular biophysics. In recent years, the application of chemical biology methods for investigating chromatin processes has gained considerable traction. Indeed, chemical biologists now have at their disposal powerful chemical tools that allow chromatin biology to be scrutinized at the level of the cell all the way down to the single chromatin fiber. Here we present recent examples of how this rapidly expanding palette of chemical tools is being used to paint a detailed picture of chromatin function in organism development and disease.

  7. Effects of perinuclear chromosome tethers in the telomeric URA3/5FOA system reflect changes to gene silencing and not nucleotide metabolism

    Directory of Open Access Journals (Sweden)

    Betty Po Kei Poon

    2012-08-01

    Full Text Available Telomeres are repetitive DNA sequences that protect the ends of linear chromosomes. Telomeres also recruit histone deacetylase complexes that can then spread along chromosome arms and repress the expression of subtelomeric genes in a process known as telomere position effect (TPE. In the budding yeast Saccharomyces cerevisiae, association of telomeres with the nuclear envelope is thought to promote TPE by increasing the local concentration of histone deacetylase complexes at chromosome ends. Importantly, our understanding of TPE stems primarily from studies that employed marker genes inserted within yeast subtelomeres. In particular, the prototrophic marker URA3 is commonly used to assay TPE by negative selection on media supplemented with 5-fluoro-orotic acid (5FOA. Recent findings suggested that decreased growth on 5FOA-containing media may not always indicate increased expression of a telomeric URA3 reporter, but can rather reflect an increase in ribonucleotide reductase (RNR function and nucleotide metabolism. Thus, we set out to test if the 5FOA sensitivity of subtelomeric URA3-harbouring cells in which we deleted various factors implicated in perinuclear telomere tethering reflects changes to TPE and/or RNR. We report that RNR inhibition restores 5FOA resistance to cells lacking RNR regulatory factors but not any of the major telomere tethering and silencing factors, including Sir2, Cohibin, Mps3, Heh1, and Esc1. In addition, we find that the disruption of tethering pathways in which these factors participate increases the level of URA3 transcripts originating from the telomeric reporter gene and abrogates silencing of subtelomeric HIS3 reporter genes without altering RNR gene expression. Thus, increased 5FOA sensitivity of telomeric URA3-harbouring cells deficient in telomere tethers reflects the dysregulation of TPE but not RNR. This is key to understanding relationships between telomere positioning, chromatin silencing, and lifespan.

  8. Fibronectin: a chromatin-associated protein?

    Science.gov (United States)

    Zardi, L; Siri, A; Carnemolla, B; Santi, L; Gardner, W D; Hoch, S O

    1979-11-01

    We have previously reported that chromatin preparations from human cultured fibroblasts contain a single homologous serum protein. In this paper we present evidence, based on immunological identity and physicochemical properties, that this serum protein is fibronectin. Furthermore, using a radioimmunoassay system, we have estimated that fibronectin represents about 0.7% of the total protein in both chromatin preparations and whole fibroblasts. Using a nitrocellulose filter assay system, we also show that fibronectin is a DNA-binding protein having an equilibrium constant of 4.6 x 10(-6) M. Equilibrium competition experiments have demonstrated that fibronectin has the ability to differentiate among nucleotides, indicating that fibronectin-DNA interaction is at least partially specific, and that a minimum polymer length of 12-18 nucleotides is required for effective binding to occur. Fibronectin has been isolated readily from plasma using DNA-affinity chromatography. We do not have direct evidence that fibronectin is an actual nonhistone chromosomal protein, but fibronectin is a DNA-binding protein (at least under in vitro assay conditions) and appears to be a normal constituent of chromatin as chromatin is currently isolated from cell nuclei.

  9. Chromatin conformation capture strategies in molecular diagnostics

    NARCIS (Netherlands)

    de Vree, Pauline J.P.

    2015-01-01

    In this thesis I have explored the clinical potential of the 4C-technology and worked on development of a novel chromatin conformation capture based technology, called TLA. In chapter 2 I describe how the 4C-technology can be applied as a targeted strategy to identify putative fusion-genes or

  10. Keystone Symposia on Epigenomics and Chromatin Dynamics

    DEFF Research Database (Denmark)

    Ravnskjær, Kim

    2012-01-01

    Keystone Symposia kicked off the start of 2012 with two joint meetings on Epigenomics and Chromatin Dynamics and a star-studded list of speakers. Held in Keystone, CO, January 17-22, and organized by Steven Jacobsen and Steven Henikoff and by Bradley Cairns and Geneviève Almouzni, respectively...

  11. Chromatin proteins and modifications as drug targets

    DEFF Research Database (Denmark)

    Helin, Kristian; Dhanak, Dashyant

    2013-01-01

    is a frequent event in disease, and the first epigenetic-based therapies for cancer treatment have been approved. A generation of new classes of potent and specific inhibitors for several chromatin-associated proteins have shown promise in preclinical trials. Although the biology of epigenetic regulation...

  12. Single Chromatin Fibre Assembly Using Optical Tweezers

    NARCIS (Netherlands)

    Bennink, Martin L.; Pope, L.H.; Leuba, S.H.; de Grooth, B.G.; Greve, Jan

    2001-01-01

    Here we observe the formation of a single chromatin fibre using optical tweezers. A single -DNA molecule was suspended between two micron-sized beads, one held by a micropipette and the other in an optical trap. The constrained DNA molecule was incubated with Xenopus laevis egg extract in order to

  13. Chromatin remodeling effects on enhancer activity.

    Science.gov (United States)

    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.

  14. The Latest Twists in Chromatin Remodeling.

    Science.gov (United States)

    Blossey, Ralf; Schiessel, Helmut

    2018-01-05

    In its most restrictive interpretation, the notion of chromatin remodeling refers to the action of chromatin-remodeling enzymes on nucleosomes with the aim of displacing and removing them from the chromatin fiber (the effective polymer formed by a DNA molecule and proteins). This local modification of the fiber structure can have consequences for the initiation and repression of the transcription process, and when the remodeling process spreads along the fiber, it also results in long-range effects essential for fiber condensation. There are three regulatory levels of relevance that can be distinguished for this process: the intrinsic sequence preference of the histone octamer, which rules the positioning of the nucleosome along the DNA, notably in relation to the genetic information coded in DNA; the recognition or selection of nucleosomal substrates by remodeling complexes; and, finally, the motor action on the nucleosome exerted by the chromatin remodeler. Recent work has been able to provide crucial insights at each of these three levels that add new twists to this exciting and unfinished story, which we highlight in this perspective. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  15. The Chromatin Scaffold Protein SAFB1 Renders Chromatin Permissive for DNA Damage Signaling

    DEFF Research Database (Denmark)

    Altmeyer, Matthias; Toledo Lazaro, Luis Ignacio; Gudjonsson, Thorkell

    2013-01-01

    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......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...... barriers by making chromatin permissive for DNA damage signaling, whereas the ensuing exclusion of SAFB1 may help prevent excessive signaling....

  16. Reliability of tethered swimming evaluation in age group swimmers.

    Science.gov (United States)

    Amaro, Nuno; Marinho, Daniel A; Batalha, Nuno; Marques, Mário C; Morouço, Pedro

    2014-06-28

    The aim of the present study was to examine the reliability of tethered swimming in the evaluation of age group swimmers. The sample was composed of 8 male national level swimmers with at least 4 years of experience in competitive swimming. Each swimmer performed two 30 second maximal intensity tethered swimming tests, on separate days. Individual force-time curves were registered to assess maximum force, mean force and the mean impulse of force. Both consistency and reliability were very strong, with Cronbach's Alpha values ranging from 0.970 to 0.995. All the applied metrics presented a very high agreement between tests, with the mean impulse of force presenting the highest. These results indicate that tethered swimming can be used to evaluate age group swimmers. Furthermore, better comprehension of the swimmers ability to effectively exert force in the water can be obtained using the impulse of force.

  17. Reliability of Tethered Swimming Evaluation in Age Group Swimmers

    Directory of Open Access Journals (Sweden)

    Amaro Nuno

    2014-07-01

    Full Text Available The aim of the present study was to examine the reliability of tethered swimming in the evaluation of age group swimmers. The sample was composed of 8 male national level swimmers with at least 4 years of experience in competitive swimming. Each swimmer performed two 30 second maximal intensity tethered swimming tests, on separate days. Individual force-time curves were registered to assess maximum force, mean force and the mean impulse of force. Both consistency and reliability were very strong, with Cronbach's Alpha values ranging from 0.970 to 0.995. All the applied metrics presented a very high agreement between tests, with the mean impulse of force presenting the highest. These results indicate that tethered swimming can be used to evaluate age group swimmers. Furthermore, better comprehension of the swimmers ability to effectively exert force in the water can be obtained using the impulse of force.

  18. Spatially confined folding of chromatin in the interphase nucleus

    NARCIS (Netherlands)

    Mateos-Langerak, J.; Bohn, M.; de Leeuw, W.; Giromus, O.; Manders, E.M.M.; Verschure, P.J.; Indemans, M.H.G.; Gierman, H.J.; Heermann, D.W.; van Driel, R.; Goetze, S.

    2009-01-01

    Genome function in higher eukaryotes involves major changes in the spatial organization of the chromatin fiber. Nevertheless, our understanding of chromatin folding is remarkably limited. Polymer models have been used to describe chromatin folding. However, none of the proposed models gives a

  19. Chromatin Dynamics of the mouse β-globin locus

    NARCIS (Netherlands)

    M.P.C. van de Corput (Mariëtte); E. de Boer (Ernie); T.A. Knoch (Tobias); W.A. van Cappellen (Gert); M. Lesnussa (Michael); H.J.F.M.M. Eussen (Bert)

    2010-01-01

    textabstractLately it has become more clear that (subtle) changes in 3D organization of chromatin can either trigger transcription or silence genes or gene clusters. It has also been postulated that due to changes in chromatin structure, a change in chromatin accessibility of transcription factors

  20. Dynamic reorganization of open chromatin underlies diverse transcriptomes during spermatogenesis

    Science.gov (United States)

    Maezawa, So; Yukawa, Masashi; Alavattam, Kris G; Barski, Artem

    2018-01-01

    Abstract During spermatogenesis, germ cells undergo massive cellular reconstruction and dynamic chromatin remodeling to facilitate highly diverse transcriptomes, which are required for the production of functional sperm. However, it remains unknown how germline chromatin is organized to promote the dynamic, complex transcriptomes of spermatogenesis. Here, using ATAC-seq, we establish the varied landscape of open chromatin during spermatogenesis. We identify the reorganization of accessible chromatin in intergenic and intronic regions during the mitosis-to-meiosis transition. During the transition, mitotic-type open chromatin is closed while the de novo formation of meiotic-type open chromatin takes place. Contrastingly, differentiation processes such as spermatogonial differentiation and the meiosis-to-postmeiosis transition involve chromatin closure without the de novo formation of accessible chromatin. In spermiogenesis, the germline-specific Polycomb protein SCML2 promotes the closure of open chromatin at autosomes for gene suppression. Paradoxically, we identify the massive de novo formation of accessible chromatin when the sex chromosomes undergo meiotic sex chromosome inactivation, and this is also mediated by SCML2. These results reveal meiotic sex chromosome inactivation as an active process for chromatin organization. Together, our results unravel the genome-wide, dynamic reorganization of open chromatin and reveal mechanisms that underlie diverse transcriptomes during spermatogenesis. PMID:29126117

  1. Synthesis and insertion chemistry of mixed tether uranium metallocene complexes.

    Science.gov (United States)

    Siladke, Nathan A; LeDuc, Jennifer; Ziller, Joseph W; Evans, William J

    2012-11-12

    The synthesis of mixed tethered alkyl uranium metallocenes has been investigated by examining the reactivity of the bis(tethered alkyl) metallocene [(η(5)-C(5)Me(4)SiMe(2)CH(2)-κC)(2)U] (1) with substrates that react with only one of the U-C linkages. The effect of these mixed tether coordination environments on the reactivity of the remaining U-C bond has been studied by using CO insertion chemistry. One equivalent of azidoadamantane (AdN(3)) reacts with 1 to yield the mixed tethered alkyl triazenido complex [(η(5)-C(5)Me(4)SiMe(2)CH(2)-κC)U(η(5)-C(5)Me(4)SiMe(2)-CH(2)NNN-Ad-κ(2)N(1,3))]. Similarly, a single equivalent of CS(2) reacts with 1 to form the mixed tethered alkyl dithiocarboxylate complex [(η(5)-C(5)Me(4)SiMe(2)CH(2)-κC)U(η(5)-C(5)Me(4)SiMe(2)-CH(2)C(S)(2)-κ(2)S,S')], a reaction that constitutes the first example of CS(2) insertion into a U(4+)-C bond. Complex 1 reacts with one equivalent of pyridine N-oxide by C-H bond activation of the pyridine ring to form a mixed tethered alkyl cyclometalated pyridine N-oxide complex [(η(5)-C(5)Me(4)SiMe(2)CH(2)-κC)(η(5)-C(5)Me(4)SiMe(3))U(C(6)H(4)NO-κ(2)C,O)]. The remaining (η(5)-C(5)Me(4)SiMe(2)CH(2)-κC)(2-) ligand in each of these mixed tethered species show reactivity towards CO and tethered enolate ligands form by insertion. Subsequent rearrangement have been identified in [(η(5)-C(5)Me(4)SiMe(3))U(C(5)H(4)NO-κ(2)C,O)(η(5)-C(5)Me(4)SiMe(2)C(=CH(2))O-κO)] and [(η(5)-C(5)Me(4)SiMe(2)CH(2)NNN-Ad-κ(2)N(1,3))U(η(5)-C(5)Me(4)SiMe(2)C(=CH(2))O-κO)]. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Synthesis and insertion chemistry of mixed tether uranium metallocene complexes

    International Nuclear Information System (INIS)

    Siladke, Nathan A.; LeDuc, Jennifer; Ziller, Joseph W.; Evans, William J.

    2012-01-01

    The synthesis of mixed tethered alkyl uranium metallocenes has been investigated by examining the reactivity of the bis(tethered alkyl) metallocene [(η 5 -C 5 Me 4 SiMe 2 CH 2 -κC) 2 U] (1) with substrates that react with only one of the U-C linkages. The effect of these mixed tether coordination environments on the reactivity of the remaining U-C bond has been studied by using CO insertion chemistry. One equivalent of azidoadamantane (AdN 3 ) reacts with 1 to yield the mixed tethered alkyl triazenido complex [(η 5 -C 5 Me 4 SiMe 2 CH 2 -κC)U(η 5 -C 5 Me 4 SiMe 2 -CH 2 NNN-Ad-κ 2 N 1,3 )]. Similarly, a single equivalent of CS 2 reacts with 1 to form the mixed tethered alkyl dithiocarboxylate complex [(η 5 -C 5 Me 4 SiMe 2 CH 2 -κC)U(η 5 -C 5 Me 4 SiMe 2 - CH 2 C(S) 2 -κ 2 S,S ' )], a reaction that constitutes the first example of CS 2 insertion into a U 4+ -C bond. Complex 1 reacts with one equivalent of pyridine N-oxide by C-H bond activation of the pyridine ring to form a mixed tethered alkyl cyclometalated pyridine N-oxide complex [(η 5 -C 5 Me 4 SiMe 2 CH 2 -κC)(η 5 -C 5 Me 4 SiMe 3 )U(C 6 H 4 NO-κ 2 C,O)]. The remaining (η 5 -C 5 Me 4 SiMe 2 CH 2 -κC) 2- ligand in each of these mixed tethered species show reactivity towards CO and tethered enolate ligands form by insertion. Subsequent rearrangement have been identified in [(η 5 -C 5 Me 4 SiMe 3 )U(C 5 H 4 NO-κ 2 C,O)(η 5 -C 5 Me 4 SiMe 2 C(=CH 2 )O- κO)] and [(η 5 -C 5 Me 4 SiMe 2 CH 2 NNN-Ad-κ 2 N 1,3 )U(η 5 -C 5 Me 4 SiMe 2 C(=CH 2 )O-κO)]. (Copyright copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  3. An Effective Approach Control Scheme for the Tethered Space Robot System

    OpenAIRE

    Meng, Zhongjie; Huang, Panfeng

    2014-01-01

    The tethered space robot system (TSR), which is composed of a platform, a gripper and a space tether, has great potential in future space missions. Given the relative motion among the platform, tether, gripper and the target, an integrated approach model is derived. Then, a novel coordinated approach control scheme is presented, in which the tether tension, thrusters and the reaction wheel are all utilized. It contains the open-loop trajectory optimization, the feedback trajectory control and...

  4. H2Av facilitates H3S10 phosphorylation but is not required for heat shock-induced chromatin decondensation or transcriptional elongation.

    Science.gov (United States)

    Li, Yeran; Wang, Chao; Cai, Weili; Sengupta, Saheli; Zavortink, Michael; Deng, Huai; Girton, Jack; Johansen, Jørgen; Johansen, Kristen M

    2017-09-15

    A model has been proposed in which JIL-1 kinase-mediated H3S10 and H2Av phosphorylation is required for transcriptional elongation and heat shock-induced chromatin decondensation. However, here we show that although H3S10 phosphorylation is indeed compromised in the H2Av null mutant, chromatin decondensation at heat shock loci is unaffected in the absence of JIL-1 as well as of H2Av and that there is no discernable decrease in the elongating form of RNA polymerase II in either mutant. Furthermore, mRNA for the major heat shock protein Hsp70 is transcribed at robust levels in both H2Av and JIL-1 null mutants. Using a different chromatin remodeling paradigm that is JIL-1 dependent, we provide evidence that ectopic tethering of JIL-1 and subsequent H3S10 phosphorylation recruits PARP-1 to the remodeling site independently of H2Av phosphorylation. These data strongly suggest that H2Av or H3S10 phosphorylation by JIL-1 is not required for chromatin decondensation or transcriptional elongation in Drosophila . © 2017. Published by The Company of Biologists Ltd.

  5. Optimal Trajectories for Tethered Kite Mounted on a Vertical Axis Generator

    NARCIS (Netherlands)

    Williams, P.; Lansdorp, B.; Ockels, W.

    2007-01-01

    Tethered kite technology promises the enable the efficient extraction of energy from high altitude winds. One possible concept for converting the wind energy into electricity is to generate useful work at the ground by using a tether. The tether is able to drive a generator in one of two ways:

  6. Genome-wide identification of chromatin-enriched RNA reveals that unspliced dentin matrix protein-1 mRNA regulates cell proliferation in squamous cell carcinoma.

    Science.gov (United States)

    Suzuki, Shigeki; Hoshino, Hiroaki; Yoshida, Kazuma; Nakanishi, Jun; Tsuchiya-Hirata, Shizu; Kobuke, Seiji; Haruyama, Naoto; Nishimura, Fusanori; Shiba, Hideki

    2018-01-15

    Chromatin-enriched noncoding RNAs (ncRNAs) have emerged as key molecules in epigenetic processes by interacting with chromatin-associated proteins. Recently, protein-coding mRNA genes have been reported to be chromatin-tethered, similar with ncRNA. However, very little is known about whether chromatin-enriched mRNA is involved in the chromatin modification process. Here, we comprehensively examined chromatin-enriched RNA in squamous cell carcinoma (SQCC) cells by RNA subcellular localization analysis, which was a combination of RNA fractionation and RNA-seq. We identified 11 mRNAs as highly chromatin-enriched RNAs. Among these, we focused on the dentin matrix protein-1 (DMP-1) gene because its expression in SQCC cells has not been reported. Furthermore, we clarified that DMP-1 mRNA was retained in chromatin in its unspliced form in SQCC in vitro and in vivo. As the inhibition of the unspliced DMP-1 mRNA (unspDMP-1) expression resulted in decreased cellular proliferation in SQCC cells, we performed ChIP-qPCR to identify cell cycle-related genes whose expression was epigenetically modified by unspDMP-1, and found that the CDKN1B promoter became active in SQCC cells by inhibiting unspDMP-1 expression. This result was further validated by the increased CDKN1B gene expression in the cells treated with siRNA for unspDMP-1 and by restoration of the decreased cellular proliferation rate by simultaneously inhibiting CDKN1B expression in SQCC cells. Further, to examine whether unspDMP-1 was able to associate with the CDKN1B promoter region, SQCC cells stably expressing PP7-mCherry fusion protein were transiently transfected with the unspDMP-1 fused to 24 repeats of the PP7 RNA stem loop (unspDMP-1-24xPP7) and we found that unspDMP-1-24xPP7 was efficiently precipitated with the antibody against mCherry and was significantly enriched in the CDKN1B promoter region. Thus, unspDMP-1 is a novel chromatin-enriched RNA that epigenetically regulates cellular proliferation of SQCC

  7. Quantification of chromatin condensation level by image processing.

    Science.gov (United States)

    Irianto, Jerome; Lee, David A; Knight, Martin M

    2014-03-01

    The level of chromatin condensation is related to the silencing/activation of chromosomal territories and therefore impacts on gene expression. Chromatin condensation changes during cell cycle, progression and differentiation, and is influenced by various physicochemical and epigenetic factors. This study describes a validated experimental technique to quantify chromatin condensation. A novel image processing procedure is developed using Sobel edge detection to quantify the level of chromatin condensation from nuclei images taken by confocal microscopy. The algorithm was developed in MATLAB and used to quantify different levels of chromatin condensation in chondrocyte nuclei achieved through alteration in osmotic pressure. The resulting chromatin condensation parameter (CCP) is in good agreement with independent multi-observer qualitative visual assessment. This image processing technique thereby provides a validated unbiased parameter for rapid and highly reproducible quantification of the level of chromatin condensation. Copyright © 2013 IPEM. Published by Elsevier Ltd. All rights reserved.

  8. [Special Issue of In-Space Flight Experiments of Electrodynamic Tether]Experiment for Attitude Control of a Tethered Space Robot on the Sounding Rocket

    Science.gov (United States)

    Nohmi, Masahiro; Tanikawa, Jun; Hosoda, Takayuki

    This paper describes the space experimental result for the Tethered Space Robot -S (TSR-S) on the sounding rocket “S-520-25.” A tethered space robot is a new type of space robot connected to tether. The major advantage of the tethered space robot is that its attitude can be controlled under tether tension by its own link motion. The S-520-25 was launched on August 31. The TSR-S experiment was started at 285 seconds after the launch. The launch lock was unlocked and the robot was deployed by the springs. The tether was extended and kept its tension, and the attitude control of the robot was performed. The disturbed vibration of attitude was suppressed, and also the desired attitude was controlled by link motion of the robot.

  9. 76 FR 41526 - Centennial Challenges 2011 Strong Tether Challenge

    Science.gov (United States)

    2011-07-14

    .... 2451 (314)(d). The 2011 Strong Tether Challenge is scheduled and teams that wish to compete may... prize competitors must (1) Register and comply with all requirements in the rules and team agreement; (2... the United States, and in the case of an individual, whether participating singly or in a group, shall...

  10. Dynamic analysis and trajectory tracking of a tethered space robot

    Science.gov (United States)

    Soltani, Mehrzad; Keshmiri, Mehdi; Misra, Arun K.

    2016-11-01

    Dynamic analysis and trajectory tracking of a Tethered Space Robot (TSR) is investigated in this paper. A hybrid controller is used to perform the control task. It consists of two components, the first one deals with librational motion of the tether, while the second one takes care of the manipulator motion. A Nonlinear Model Predictive Control (NMPC) approach is used to control the tether libration; for this purpose, the libration is described by a single degree of freedom and the tether length rate is employed as the input to suppress the librational motion. A modified Computed Torque Method (CTM) is used to control the manipulator motion. The dynamic interaction between the manipulator motion and the librational motion is considered both in the system dynamics and control of the system. Using numerical simulations, performance of the proposed control system is evaluated for end-effector positioning as well as for trajectory tracking for two cases: a Low Earth Orbit (LEO) and the Geostationary Earth Orbit (GEO).

  11. Effects tethering feeding management system on carcass, organ ...

    African Journals Online (AJOL)

    The albumin, globulin and cholesterol values did not vary significantly (p< 0.05) between the treatment groups. The results of this study showed that periodic tethering feeding management system was not detrimental to the carcass, organ weight characteristics and serum metabolites of growing West African dwarf goats.

  12. Hierarchical Structure in Semicrystalline Polymers Tethered to Nanospheres

    KAUST Repository

    Kim, Sung A

    2014-01-28

    We report on structural and dynamic transitions of polymers tethered to nanoparticles. In particular, we use X-ray diffraction, vibrational spectroscopy, and thermal measurements to investigate multiscale structure and dynamic transitions of poly(ethylene glycol) (PEG) chains densely grafted to SiO2 nanoparticles. The approach used for synthesizing these hybrid particles leads to homogeneous SiO2-PEG composites with polymer grafting densities as high as 1.5 chains/nm2, which allows the hybrid materials to exist as self-suspended suspensions with distinct hierarchical structure and thermal properties. On angstrom and nanometer length scales, the tethered PEG chains exhibit more dominant TTG conformations and helix unit cell structure, in comparison to the untethered polymer. The nanoparticle tethered PEG chains are also reported to form extended crystallites on tens of nanometers length scales and to exhibit more stable crystalline structure on small dimensions. On length scales comparable to the size of each hybrid SiO 2-PEG unit, the materials are amorphous presumably as a result of the difficulty fitting the nanoparticle anchors into the PEG crystal lattice. This structural change produces large effects on the thermal transitions of PEG molecules tethered to nanoparticles. © 2014 American Chemical Society.

  13. Three dimensional dynamics of a flexible Motorised Momentum Exchange Tether

    Science.gov (United States)

    Ismail, N. A.; Cartmell, M. P.

    2016-03-01

    This paper presents a new flexural model for the three dimensional dynamics of the Motorised Momentum Exchange Tether (MMET) concept. This study has uncovered the relationships between planar and nonplanar motions, and the effect of the coupling between these two parameters on pragmatic circular and elliptical orbits. The tether sub-spans are modelled as stiffened strings governed by partial differential equations of motion, with specific boundary conditions. The tether sub-spans are flexible and elastic, thereby allowing three dimensional displacements. The boundary conditions lead to a specific frequency equation and the eigenvalues from this provide the natural frequencies of the orbiting flexible motorised tether when static, accelerating in monotonic spin, and at terminal angular velocity. A rotation transformation matrix has been utilised to get the position vectors of the system's components in an assumed inertial frame. Spatio-temporal coordinates are transformed to modal coordinates before applying Lagrange's equations, and pre-selected linear modes are included to generate the equations of motion. The equations of motion contain inertial nonlinearities which are essentially of cubic order, and these show the potential for intricate intermodal coupling effects. A simulation of planar and non-planar motions has been undertaken and the differences in the modal responses, for both motions, and between the rigid body and flexible models are highlighted and discussed.

  14. Flight control and stability of a multiple kites tethered system

    NARCIS (Netherlands)

    Podgaets, A.R.; Ockels, W.J.

    2006-01-01

    One of novel concepts to use the energy of high altitude winds is by launching a series of kite on a long rope and let them pull the rope thus driving the generator. A mathematical model of tethered kites system has been developed consisting of models of kites and of the cable that links them

  15. Tether-mission design for multiple flybys of moon Europa

    OpenAIRE

    Sanmartín Losada, Juan Ramón; Charro, Mario; Sánchez-Arriaga, Gonzalo; Sánchez-Torres, Antonio

    2015-01-01

    Electrodynamic tape-tethers are shown to allow a cheap, light, fast mission to Jupiter for multiple flybys of moon Europa and close exploration of the Jovian interior. As regards flybys, this mission is similar to the Clipper mission presently considered by NASA, the basic difference (periapsis location) arising from mission-challenge metrics.

  16. Hamiltonian Switch Metropolis Monte Carlo Simulations for Improved Conformational Sampling of Intrinsically Disordered Regions Tethered to Ordered Domains of Proteins.

    Science.gov (United States)

    Mittal, Anuradha; Lyle, Nicholas; Harmon, Tyler S; Pappu, Rohit V

    2014-08-12

    There is growing interest in the topic of intrinsically disordered proteins (IDPs). Atomistic Metropolis Monte Carlo (MMC) simulations based on novel implicit solvation models have yielded useful insights regarding sequence-ensemble relationships for IDPs modeled as autonomous units. However, a majority of naturally occurring IDPs are tethered to ordered domains. Tethering introduces additional energy scales and this creates the challenge of broken ergodicity for standard MMC sampling or molecular dynamics that cannot be readily alleviated by using generalized tempering methods. We have designed, deployed, and tested our adaptation of the Nested Markov Chain Monte Carlo sampling algorithm. We refer to our adaptation as Hamiltonian Switch Metropolis Monte Carlo (HS-MMC) sampling. In this method, transitions out of energetic traps are enabled by the introduction of an auxiliary Markov chain that draws conformations for the disordered region from a Boltzmann distribution that is governed by an alternative potential function that only includes short-range steric repulsions and conformational restraints on the ordered domain. We show using multiple, independent runs that the HS-MMC method yields conformational distributions that have similar and reproducible statistical properties, which is in direct contrast to standard MMC for equivalent amounts of sampling. The method is efficient and can be deployed for simulations of a range of biologically relevant disordered regions that are tethered to ordered domains.

  17. Replicating chromatin: a tale of histones

    DEFF Research Database (Denmark)

    Groth, Anja

    2009-01-01

    framework of chromatin and carry information to specify higher-order organization and gene expression. When replication forks traverse the chromosomes, nucleosomes are transiently disrupted, allowing the replication machinery to gain access to DNA. Histone recycling, together with new deposition, ensures...... reassembly on nascent DNA strands. The aim of this review is to discuss how histones - new and old - are handled at the replication fork, highlighting new mechanistic insights and revisiting old paradigms....

  18. HMGB proteins: Interactions with DNA and chromatin

    Czech Academy of Sciences Publication Activity Database

    Štros, Michal

    2010-01-01

    Roč. 1799, 1-2 (2010), s. 101-113 ISSN 1874-9399 R&D Projects: GA ČR(CZ) GA204/08/1530; GA AV ČR(CZ) IAA400040702 Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : HMG-box * DNA-protein interaction * chromatin Subject RIV: BO - Biophysics Impact factor: 4.000, year: 2010

  19. Learning characteristics of a space-time neural network as a tether skiprope observer

    Science.gov (United States)

    Lea, Robert N.; Villarreal, James A.; Jani, Yashvant; Copeland, Charles

    1993-01-01

    The Software Technology Laboratory at the Johnson Space Center is testing a Space Time Neural Network (STNN) for observing tether oscillations present during retrieval of a tethered satellite. Proper identification of tether oscillations, known as 'skiprope' motion, is vital to safe retrieval of the tethered satellite. Our studies indicate that STNN has certain learning characteristics that must be understood properly to utilize this type of neural network for the tethered satellite problem. We present our findings on the learning characteristics including a learning rate versus momentum performance table.

  20. Capturing Structural Heterogeneity in Chromatin Fibers.

    Science.gov (United States)

    Ekundayo, Babatunde; Richmond, Timothy J; Schalch, Thomas

    2017-10-13

    Chromatin fiber organization is implicated in processes such as transcription, DNA repair and chromosome segregation, but how nucleosomes interact to form higher-order structure remains poorly understood. We solved two crystal structures of tetranucleosomes with approximately 11-bp DNA linker length at 5.8 and 6.7 Å resolution. Minimal intramolecular nucleosome-nucleosome interactions result in a fiber model resembling a flat ribbon that is compatible with a two-start helical architecture, and that exposes histone and DNA surfaces to the environment. The differences in the two structures combined with electron microscopy reveal heterogeneous structural states, and we used site-specific chemical crosslinking to assess the diversity of nucleosome-nucleosome interactions through identification of structure-sensitive crosslink sites that provide a means to characterize fibers in solution. The chromatin fiber architectures observed here provide a basis for understanding heterogeneous chromatin higher-order structures as they occur in a genomic context. Copyright © 2017 Elsevier Ltd. All rights reserved.

  1. Titration and hysteresis in epigenetic chromatin silencing

    Science.gov (United States)

    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.

  2. Titration and hysteresis in epigenetic chromatin silencing

    International Nuclear Information System (INIS)

    Dayarian, Adel; Sengupta, Anirvan M

    2013-01-01

    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. (paper)

  3. Higher order chromatin organization in cancer

    Science.gov (United States)

    Reddy, Karen L.; Feinberg, Andrew P.

    2013-01-01

    In spite of our increased understanding of how genomes are dysregulated in cancer and a plethora of molecular diagnostic tools, the front line and ‘gold standard’ detection of cancer remains the pathologist’s detection of gross changes in cellular and tissue structure, most strikingly nuclear dis-organization. In fact, for over 140 years it has been noted that nuclear morphology is often disrupted in cancer. Even today, nuclear morphology measures include nuclear size, shape, DNA content (ploidy) and ‘chromatin organization’. Given the importance of nuclear shape to diagnoses of cancer phenotypes, it is surprising and frustrating that we currently lack a detailed understanding to explain these changes and how they might arise and relate to molecular events in the cell. It is an implicit hypothesis that perturbation of chromatin and epigenetic signatures may lead to alterations in nuclear structure (or vice versa) and that these perturbations lie at the heart of cancer genesis. In this review, we attempt to synthesize research leading to our current understanding on how chromatin interactions at the nuclear lamina, epigenetic modulation and gene regulation may intersect in cancer and offer a perspective on critical experiments that would help clarify how nuclear architecture may contribute to the cancerous phenotype. We also discuss the historical understanding of nuclear structure in normal cells and as a diagnostic in cancer. PMID:23266653

  4. Modelling a tethered mammalian sperm cell undergoing hyperactivation

    KAUST Repository

    Curtis, M.P.

    2012-09-01

    The beat patterns of mammalian sperm flagella can be categorised into two different types. The first involves symmetric waves propagating down the flagellum with a net linear propulsion of the sperm cell. The second, hyperactive, waveform is classified by vigorous asymmetric waves of higher amplitude, lower wavenumber and frequency propagating down the flagellum resulting in highly curved trajectories. The latter beat pattern is part of the capacitation process whereby sperm prepare for the prospective penetration of the zona pellucida and fusion with the egg. Hyperactivation is often observed to initiate as sperm escape from epithelial and ciliary bindings formed within the isthmic regions of the female oviducts, leading to a conjecture in the literature that this waveform is mechanically important for sperm escape. Hence, we explore the mechanical effects of hyperactivation on a tethered sperm, focussing on a Newtonian fluid. Using a resistive force theory model we demonstrate that hyperactivation can indeed generate forces that pull the sperm away from a tethering point and consequently a hyperactivated sperm cell bound to an epithelial surface need not always be pushed by its flagellum. More generally, directions of the forces generated by tethered flagella are insensitive to reductions in beat frequency and the detailed flagellar responses depend on the nature of the binding at the tethering point. Furthermore, waveform asymmetry and amplitude increases enhance the tendency for a tethered flagellum to start tugging on its binding. The same is generally predicted to be true for reductions in the wavenumber of the flagellum beat, but not universally so, emphasising the dynamical complexity of flagellar force generation. Finally, qualitative observations drawn from experimental data of human sperm bound to excised female reproductive tract are also presented and are found to be consistent with the theoretical predictions. © 2012 Elsevier Ltd.

  5. Autonomous Vision-Based Tethered-Assisted Rover Docking

    Science.gov (United States)

    Tsai, Dorian; Nesnas, Issa A.D.; Zarzhitsky, Dimitri

    2013-01-01

    Many intriguing science discoveries on planetary surfaces, such as the seasonal flows on crater walls and skylight entrances to lava tubes, are at sites that are currently inaccessible to state-of-the-art rovers. The in situ exploration of such sites is likely to require a tethered platform both for mechanical support and for providing power and communication. Mother/daughter architectures have been investigated where a mother deploys a tethered daughter into extreme terrains. Deploying and retracting a tethered daughter requires undocking and re-docking of the daughter to the mother, with the latter being the challenging part. In this paper, we describe a vision-based tether-assisted algorithm for the autonomous re-docking of a daughter to its mother following an extreme terrain excursion. The algorithm uses fiducials mounted on the mother to improve the reliability and accuracy of estimating the pose of the mother relative to the daughter. The tether that is anchored by the mother helps the docking process and increases the system's tolerance to pose uncertainties by mechanically aligning the mating parts in the final docking phase. A preliminary version of the algorithm was developed and field-tested on the Axel rover in the JPL Mars Yard. The algorithm achieved an 80% success rate in 40 experiments in both firm and loose soils and starting from up to 6 m away at up to 40 deg radial angle and 20 deg relative heading. The algorithm does not rely on an initial estimate of the relative pose. The preliminary results are promising and help retire the risk associated with the autonomous docking process enabling consideration in future martian and lunar missions.

  6. Relaxation Dynamics of Nanoparticle-Tethered Polymer Chains

    KAUST Repository

    Kim, Sung A

    2015-09-08

    © 2015 American Chemical Society. Relaxation dynamics of nanoparticle-tethered cis-1,4-polyisoprene (PI) are investigated using dielectric spectroscopy and rheometry. A model system composed of polymer chains densely grafted to spherical SiO2 nanoparticles to form self-suspended suspensions facilitates detailed studies of slow global chain and fast segmental mode dynamics under surface and geometrical confinement-from experiments performed in bulk materials. We report that unentangled polymer molecules tethered to nanoparticles relax far more slowly than their tethered entangled counterparts. Specifically, at fixed grafting density we find, counterintuitively, that increasing the tethered polymer molecular weight up to values close to the entanglement molecular weight speeds up chain relaxation dynamics. Decreasing the polymer grafting density for a fixed molecular weight has the opposite effect: it dramatically slows down chain relaxation, increases interchain coupling, and leads to a transition in rheological response from simple fluid behavior to viscoelastic fluid behavior for tethered PI chains that are unentangled by conventional measures. Increasing the measurement temperature produces an even stronger elastic response and speeds up molecular relaxation at a rate that decreases with grafting density and molecular weight. These observations are discussed in terms of chain confinement driven by crowding between particles and by the existence of an entropic attractive force produced by the space-filling constraint on individual chains in a self-suspended material. Our results indicate that the entropic force between densely grafted polymer molecules couples motions of individual chains in an analogous manner to reversible cross-links in associating polymers.

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

    KAUST Repository

    Jégu, Teddy

    2015-10-12

    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.

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

    Science.gov (United States)

    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.

  9. PTEN Interacts with Histone H1 and Controls Chromatin Condensation

    Science.gov (United States)

    Chen, Zhu Hong; Zhu, Minglu; Yang, Jingyi; Liang, Hui; He, Jinxue; He, Shiming; Wang, Pan; Kang, Xi; McNutt, Michael A.; Yin, Yuxin; Shen, Wen H.

    2014-01-01

    SUMMARY Chromatin organization and dynamics are integral to global gene transcription. Histone modification influences chromatin status and gene expression. PTEN plays multiple roles in tumor suppression, development and metabolism. Here we report on the interplay of PTEN, histone H1 and chromatin. We show that loss of PTEN leads to dissociation of histone H1 from chromatin and decondensation of chromatin. PTEN deletion also results in elevation of histone H4 acetylation at lysine 16, an epigenetic marker for chromatin activation. We found that PTEN and histone H1 physically interact through their C-terminal domains. Disruption of the PTEN C-terminus promotes the chromatin association of MOF acetyltransferase and induces H4K16 acetylation. Hyperacetylation of H4K16 impairs the association of PTEN with histone H1, which constitutes regulatory feedback that may deteriorate chromatin stability. Our results demonstrate that PTEN controls chromatin condensation, thus influencing gene expression. We propose that PTEN regulates global gene transcription profiling through histones and chromatin remodeling. PMID:25199838

  10. Tether pointing platform and space elevator mechanisms analysis of the key concepts for SATP and scaled SATP

    Science.gov (United States)

    Turci, E.

    1986-01-01

    The key concepts for a scaled and full model Science and Applications Tethered Platform (SATP) are analysized. This includes a tether pointing platform and a space elevator. The mechanism concepts and technological solutions are given. The idea of the tether pointing platform mechanism is to control and stabilize the attitude of a platform by means of a movable tether. The idea of the space elevator mechanism for a scaled SATP is to drag the tether gripping it between two rotating wheels.

  11. Prevalence of X-chromatin in Jordanian women

    International Nuclear Information System (INIS)

    Bataineh, Ziad M.; Al-Azab, Mohammad A.

    2004-01-01

    This study was conducted to evaluate the distribution of X-chromatin among Jordanian women at different age groups. Results will be compared with other studies for possible racial and environmental effects on X-chromatin distribution. Blood samples were drawn from all women subjected to this study by finger prick and stained with Wright's stain. X-chromatin positive polymorphonuclear cells were counted and corrected for percentage. Samples were taken during the late 2002 and early 2003 from healthy women attending routine checkup in health centers in Northern Jordan. The number of X-chromatin was highest in the 50 and above years age group. The number of X-chromatin was 14-18% in other age groups. These results were in accordance with other studies. It seems that racial and environmental factors are ineffective on distribution of X-chromatin in Jordanian women. These data could be used as as reference for further studies. (author)

  12. A role for chromatin topology in imprinted domain regulation.

    Science.gov (United States)

    MacDonald, William A; Sachani, Saqib S; White, Carlee R; Mann, Mellissa R W

    2016-02-01

    Recently, many advancements in genome-wide chromatin topology and nuclear architecture have unveiled the complex and hidden world of the nucleus, where chromatin is organized into discrete neighbourhoods with coordinated gene expression. This includes the active and inactive X chromosomes. Using X chromosome inactivation as a working model, we utilized publicly available datasets together with a literature review to gain insight into topologically associated domains, lamin-associated domains, nucleolar-associating domains, scaffold/matrix attachment regions, and nucleoporin-associated chromatin and their role in regulating monoallelic expression. Furthermore, we comprehensively review for the first time the role of chromatin topology and nuclear architecture in the regulation of genomic imprinting. We propose that chromatin topology and nuclear architecture are important regulatory mechanisms for directing gene expression within imprinted domains. Furthermore, we predict that dynamic changes in chromatin topology and nuclear architecture play roles in tissue-specific imprint domain regulation during early development and differentiation.

  13. Capitalizing on disaster: Establishing chromatin specificity behind the replication fork.

    Science.gov (United States)

    Ramachandran, Srinivas; Ahmad, Kami; Henikoff, Steven

    2017-04-01

    Eukaryotic genomes are packaged into nucleosomal chromatin, and genomic activity requires the precise localization of transcription factors, histone modifications and nucleosomes. Classic work described the progressive reassembly and maturation of bulk chromatin behind replication forks. More recent proteomics has detailed the molecular machines that accompany the replicative polymerase to promote rapid histone deposition onto the newly replicated DNA. However, localized chromatin features are transiently obliterated by DNA replication every S phase of the cell cycle. Genomic strategies now observe the rebuilding of locus-specific chromatin features, and reveal surprising delays in transcription factor binding behind replication forks. This implies that transient chromatin disorganization during replication is a central juncture for targeted transcription factor binding within genomes. We propose that transient occlusion of regulatory elements by disorganized nucleosomes during chromatin maturation enforces specificity of factor binding. © 2017 WILEY Periodicals, Inc.

  14. Topography of the sex chromatin in vaginal histiocytes.

    Science.gov (United States)

    Cano, S; Urbiola, G; Dorantes, S; Márquez-Monter, H

    1975-01-01

    Routine vaginal smears with good numbers of histiocytes with kidney shaped morphology of their nuclei were selected for the study of sex chromatin topography. A variable distribution of the sex chromatin was found in 125 nuclei studied: polar in 57.4 percent, ventral in 21.9 percent and dorsal in 20.7 percent of the nuclei. No relationship was found between sex chromatin and cytoplasmic morphology and phagocytic activity.

  15. Stability control of a flexible maneuverable tethered space net robot

    Science.gov (United States)

    Zhang, Fan; Huang, Panfeng

    2018-04-01

    As a promising solution for active space debris capture and removal, a maneuverable Tethered Space Net Robot (TSNR) is proposed as an improved Space Tethered Net (TSN). In addition to the advantages inherit to the TSN, the TSNR's maneuverability expands the capture's potential. However, oscillations caused by the TSNR's flexibility and elasticity of make higher requests of the control scheme. Based on the dynamics model, a modified adaptive super-twisting sliding mode control scheme is proposed in this paper for TSNR stability control. The proposed continuous control force can effectively suppress oscillations. Theoretical verification and numerical simulations demonstrate that the desired trajectory can be tracked steadily and efficiently by employing the proposed control scheme.

  16. A simplified tether model for molecular motor transporting cargo

    International Nuclear Information System (INIS)

    Fang-Zhen, Li; Li-Chun, Jiang

    2010-01-01

    Molecular motors are proteins or protein complexes which function as transporting engines in biological cells. This paper models the tether between motor and its cargo as a symmetric linear potential. Different from Elston and Peskin's work for which performance of the system was discussed only in some limiting cases, this study produces analytic solutions of the problem for general cases by simplifying the transport system into two physical states, which makes it possible to discuss the dynamics of the motor–cargo system in detail. It turns out that the tether strength between motor and cargo should be greater than a threshold or the motor will fail to transport the cargo, which was not discussed by former researchers yet. Value of the threshold depends on the diffusion coefficients of cargo and motor and also on the strength of the Brownian ratchets dragging the system. The threshold approaches a finite constant when the strength of the ratchet tends to infinity. (general)

  17. Tethered elevator: A unique opportunity for space processing

    Science.gov (United States)

    Monti, R.

    1986-01-01

    The latest fluid dynamic and material science experiments in the microgravity environment have emphasized the importance of the residual gravity level and of the g-jitter on fluid physics phenomena. The tethered elevator presents the possibility of providing variable g-levels (both steady and g-jitter) around a very low steady g-level (that can be realized when the elevator is near the center of mass of the space station-tether complex). When positioning a variable periodic oscillation to the payload a clean g-jitter disturbance can be obtained that would not be otherwise obtainable by other systems. These two possibilities make the elevator a facility to help resolve a number of still open questions that are preventing wider utilization of the space environment in the microgravity area.

  18. Synthesis and insertion chemistry of mixed tether uranium metallocene complexes

    Energy Technology Data Exchange (ETDEWEB)

    Siladke, Nathan A.; LeDuc, Jennifer; Ziller, Joseph W.; Evans, William J. [Department of Chemistry, University of California, Irvine, CA (United States)

    2012-11-12

    The synthesis of mixed tethered alkyl uranium metallocenes has been investigated by examining the reactivity of the bis(tethered alkyl) metallocene [(η{sup 5}-C{sub 5}Me{sub 4}SiMe{sub 2}CH{sub 2}-κC){sub 2}U] (1) with substrates that react with only one of the U-C linkages. The effect of these mixed tether coordination environments on the reactivity of the remaining U-C bond has been studied by using CO insertion chemistry. One equivalent of azidoadamantane (AdN{sub 3}) reacts with 1 to yield the mixed tethered alkyl triazenido complex [(η{sup 5}-C{sub 5}Me{sub 4}SiMe{sub 2}CH{sub 2}-κC)U(η{sup 5}-C{sub 5}Me{sub 4}SiMe{sub 2}-CH{sub 2}NNN-Ad-κ{sup 2}N{sup 1,3})]. Similarly, a single equivalent of CS{sub 2} reacts with 1 to form the mixed tethered alkyl dithiocarboxylate complex [(η{sup 5}-C{sub 5}Me{sub 4}SiMe{sub 2}CH{sub 2}-κC)U(η{sup 5}-C{sub 5}Me{sub 4}SiMe{sub 2}- CH{sub 2}C(S){sub 2}-κ{sup 2}S,S{sup '})], a reaction that constitutes the first example of CS{sub 2} insertion into a U{sup 4+}-C bond. Complex 1 reacts with one equivalent of pyridine N-oxide by C-H bond activation of the pyridine ring to form a mixed tethered alkyl cyclometalated pyridine N-oxide complex [(η{sup 5}-C{sub 5}Me{sub 4}SiMe{sub 2}CH{sub 2}-κC)(η{sup 5}-C{sub 5}Me{sub 4}SiMe{sub 3})U(C{sub 6}H{sub 4}NO-κ{sup 2} C,O)]. The remaining (η{sup 5}-C{sub 5}Me{sub 4}SiMe{sub 2}CH{sub 2}-κC){sup 2-} ligand in each of these mixed tethered species show reactivity towards CO and tethered enolate ligands form by insertion. Subsequent rearrangement have been identified in [(η{sup 5}-C{sub 5}Me{sub 4}SiMe{sub 3})U(C{sub 5}H{sub 4}NO-κ{sup 2}C,O)(η{sup 5}-C{sub 5}Me{sub 4}SiMe{sub 2}C(=CH{sub 2})O- κO)] and [(η{sup 5}-C{sub 5}Me{sub 4}SiMe{sub 2}CH{sub 2}NNN-Ad-κ{sup 2}N{sup 1,3})U(η{sup 5}-C{sub 5}Me{sub 4}SiMe{sub 2}C(=CH{sub 2})O-κO)]. (Copyright copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  19. Chromatin Architecture Defines the Glucocorticoid Response

    Science.gov (United States)

    Burd, Craig J.; Archer, Trevor K.

    2013-01-01

    The glucocorticoid receptor (GR) functions to regulate a wide group of physiological processes through hormone inducible interaction with genomic loci and subsequent manipulation of the transcriptional output of target genes. Despite expression in a wide variety of tissues, the GR has diverse roles that are regulated tightly in a cell type specific manner. With the advent of whole genome approaches, the details of that diversity and the mechanisms regulating them are beginning to be elucidated. This review aims describe the recent advances detailing the role chromatin structure plays in dictating GR specificity. PMID:23545159

  20. Histone chaperone networks shaping chromatin function

    DEFF Research Database (Denmark)

    Hammond, Colin; Strømme, Caroline Bianchi; Huang, Hongda

    2017-01-01

    The association of histones with specific chaperone complexes is important for their folding, oligomerization, post-translational modification, nuclear import, stability, assembly and genomic localization. In this way, the chaperoning of soluble histones is a key determinant of histone availability...... and fate, which affects all chromosomal processes, including gene expression, chromosome segregation and genome replication and repair. Here, we review the distinct structural and functional properties of the expanding network of histone chaperones. We emphasize how chaperones cooperate in the histone...... chaperone network and via co-chaperone complexes to match histone supply with demand, thereby promoting proper nucleosome assembly and maintaining epigenetic information by recycling modified histones evicted from chromatin....

  1. Histone acetylation: molecular mnemonics on the chromatin.

    Science.gov (United States)

    Gräff, Johannes; Tsai, Li-Huei

    2013-02-01

    Long-lasting memories require specific gene expression programmes that are, in part, orchestrated by epigenetic mechanisms. Of the epigenetic modifications identified in cognitive processes, histone acetylation has spurred considerable interest. Whereas increments in histone acetylation have consistently been shown to favour learning and memory, a lack thereof has been causally implicated in cognitive impairments in neurodevelopmental disorders, neurodegeneration and ageing. As histone acetylation and cognitive functions can be pharmacologically restored by histone deacetylase inhibitors, this epigenetic modification might constitute a molecular memory aid on the chromatin and, by extension, a new template for therapeutic interventions against cognitive frailty.

  2. Probing Chromatin Modifications in Response to ERK Signaling.

    Science.gov (United States)

    Oksuz, Ozgur; Tee, Wee-Wei

    2017-01-01

    Chromatin immunoprecipitation (ChIP) is a technique used to determine the association of proteins or histone modifications with chromatin regions in living cells or tissues, and is used extensively in the chromatin biology field to study transcriptional and epigenetic mechanisms. Increasing evidence points to an epigenetic coordination of signaling cascades, such as ERK, that regulate key processes in development and disease, revealing novel principles of gene regulation. Here we describe a detailed protocol for performing chromatin immunoprecipitation followed by qPCR (ChIP-qPCR) for probing histone modifications regulated by ERK signaling in mouse ESCs.

  3. Effect of chromatin structure on quantitative ultrasound parameters.

    Science.gov (United States)

    Pasternak, Maurice; Doss, Lilian; Farhat, Golnaz; Al-Mahrouki, Azza; Kim, Christina Hyunjung; Kolios, Michael; Tran, William Tyler; Czarnota, Gregory J

    2017-03-21

    High-frequency ultrasound (~20 MHz) techniques were investigated using in vitro and ex vivo models to determine whether alterations in chromatin structure are responsible for ultrasound backscatter changes in biological samples. Acute myeloid leukemia (AML) cells and their isolated nuclei were exposed to various chromatin altering treatments. These included 10 different ionic environments, DNA cleaving and unfolding agents, as well as DNA condensing agents. Raw radiofrequency (RF) data was used to generate quantitative ultrasound parameters from spectral and form factor analyses. Chromatin structure was evaluated using electron microscopy. Results indicated that trends in quantitative ultrasound parameters mirrored trends in biophysical chromatin structure parameters. In general, higher ordered states of chromatin compaction resulted in increases to ultrasound paramaters of midband fit, spectral intercept, and estimated scatterer concentration, while samples with decondensed forms of chromatin followed an opposite trend. Experiments with isolated nuclei demonstrated that chromatin changes alone were sufficient to account for these observations. Experiments with ex vivo samples indicated similar effects of chromatin structure changes. The results obtained in this research provide a mechanistic explanation for ultrasound investigations studying scattering from cells and tissues undergoing biological processes affecting chromatin.

  4. Formaldehyde Crosslinking: A Tool for the Study of Chromatin Complexes*

    Science.gov (United States)

    Hoffman, Elizabeth A.; Frey, Brian L.; Smith, Lloyd M.; Auble, David T.

    2015-01-01

    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. Formaldehyde crosslinking: a tool for the study of chromatin complexes.

    Science.gov (United States)

    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. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  6. The Role of Chromatin-Associated Proteins in Cancer

    DEFF Research Database (Denmark)

    Helin, Kristian; Minucci, Saverio

    2017-01-01

    The organization of the chromatin structure is essential for maintaining cell-type-specific gene expression and therefore for cell identity. This structure is highly dynamic and is regulated by a large number of chromatin-associated proteins that are required for normal development...... and differentiation. Recurrent somatic mutations have been found with high frequency in genes coding for chromatin-associated proteins in cancer, and several of these are required for cancer maintenance. In this review, we discuss recent advances in understanding the role of chromatin-associated proteins...

  7. Chromatin SUMOylation in heat stress: To protect, pause and organise?: SUMO stress response on chromatin.

    Science.gov (United States)

    Niskanen, Einari A; Palvimo, Jorma J

    2017-06-01

    Post-translational modifications, e.g. SUMO modifications (SUMOylation), provide a mechanism for swiftly changing a protein's activity. Various stress conditions trigger a SUMO stress response (SSR) - a stress-induced rapid change in the conjugation of SUMO to multiple proteins, which predominantly targets nuclear proteins. The SSR has been postulated to protect stressed cells by preserving the functionality of crucial proteins. However, it is unclear how it exerts its protective functions. Interestingly, heat stress (HS) increases SUMOylation of proteins at active promoters and enhancers. In promoters, HS-induced SUMOylation correlates with gene transcription and stress-induced RNA polymerase II (Pol2) pausing. Conversely, a disappearance of SUMOylation in HS occurs at chromatin anchor points that maintain chromatin-looping structures and the spatial organisation of chromatin. In reviewing the literature, we hypothesise that the SSR regulates Pol2 pausing by modulating the interactions of pausing-regulating proteins, whereas deSUMOylation alters the function of chromatin anchors. © 2017 WILEY Periodicals, Inc.

  8. Modeling of tethered satellite formations using graph theory

    DEFF Research Database (Denmark)

    Larsen, Martin Birkelund; Smith, Roy S; Blanke, Mogens

    2011-01-01

    satellite formation and proposes a method to deduce the equations of motion for the attitude dynamics of the formation in a compact form. The use of graph theory and Lagrange mechanics together allows a broad class of formations to be described using the same framework. A method is stated for finding...... stationary configurations and an upper limit of their number is determined. The method is shown to be valid for general tethered satellite formations that form a tree structure....

  9. Crowded, Confined, and Frustrated: Dynamics of Molecules Tethered to Nanoparticles

    KAUST Repository

    Agarwal, Praveen

    2012-12-01

    Above a critical chemistry-dependent molecular weight, all polymer molecules entangle and, as a result, exhibit slow dynamics, enhanced viscosity, and elasticity. Herein we report on the dynamics of low molecular weight polymers tethered to nanoparticles and find that even conventionally unentangled chains manifest dynamical features similar to entangled, long-chain molecules. Our findings are shown to imply that crowding and confinement of polymers on particles produce topological constraints analogous to those in entangled systems. © 2012 American Physical Society.

  10. Deorbit efficiency assessment through numerical simulation of electromagnetic tether devices

    Directory of Open Access Journals (Sweden)

    Alexandru IONEL

    2016-03-01

    Full Text Available This paper examines the deorbit efficiency of an electromagnetic tether deorbit device when used to deorbit an upper stage at end of mission from low Earth orbit. This is done via a numerical simulation in Matlab R2013a, using ode45, taking into account perturbations on the upper stage’s trajectory. The perturbations taken into account are the atmospheric drag, the 3rd body (Sun and Moon, and Earth’s gravitational potential expanded into spherical harmonics.

  11. Applying Parallel Processing Techniques to Tether Dynamics Simulation

    Science.gov (United States)

    Wells, B. Earl

    1996-01-01

    The focus of this research has been to determine the effectiveness of applying parallel processing techniques to a sizable real-world problem, the simulation of the dynamics associated with a tether which connects two objects in low earth orbit, and to explore the degree to which the parallelization process can be automated through the creation of new software tools. The goal has been to utilize this specific application problem as a base to develop more generally applicable techniques.

  12. A Tether-Based Variable-Gravity Research Facility Concept

    Science.gov (United States)

    Sorensen, Kirk

    2006-01-01

    The recent announcement of a return to the Moon and a mission to Mars has made the question of human response to lower levels of gravity more important. Recent advances in tether technology spurred by NASA s research in MXER tethers has led to a re-examination of the concept of a variable-gravity research facility (xGRF) for human research in low Earth orbit. Breakthroughs in simplified inertial tracking have made it possible to consider eliminating the despun section of previous designs. This, in turn, improves the prospect of a facility based entirely around a tether, with the human module on one end and a countermass on the other. With such a configuration, propellantless spinup and spindown is also possible based on the conservation of angular momentum from a gravity-gradient configuration to a spinning configuration. This not only saves large amounts of propellant but vastly simplifies crew and consumable resupply operations, since these can now be done in a microgravity configuration. The importance of the science to be obtained and the performance improvements in this new design argue strongly for further investigation.

  13. Relationship between tethered forces and the four swimming techniques performance.

    Science.gov (United States)

    Morouço, Pedro; Keskinen, Kari L; Vilas-Boas, Joao Paulo; Fernandes, Ricardo Jorge

    2011-05-01

    The purpose of the current study was to identify the relationships between competitive performance and tether forces according to distance swam, in the four strokes, and to analyze if relative values of force production are better determinants of swimming performance than absolute values. The subjects (n = 32) performed a 30 s tethered swimming all-out effort. The competitive swimming velocities were obtained in the distances 50, 100 and 200 m using official chronometric values of competitions within 25 days after testing protocol. Mean force and velocity (50 m event) show significant correlations for front crawl (r = .92, p backstroke (r = .81, p < .05), breaststroke (r = .94, p < .01) and butterfly (r = .92, p < .01). The data suggests that absolute values of force production are more associated to competitive performance than relative values (normalized to body mass). Tethered swimming test seems to be a reliable protocol to evaluate the swimmer stroking force production and a helpful estimator of competitive performance in short distance competitive events.

  14. Tethering complexes in the endocytic pathway: CORVET and HOPS.

    Science.gov (United States)

    Solinger, Jachen A; Spang, Anne

    2013-06-01

    Endocytosis describes the processes by which proteins, peptides and solutes, and also pathogens, enter the cell. Endocytosed material progresses to endosomes. Genetic studies in yeast, worms, flies and mammals have identified a set of universally conserved proteins that are essential for early-to-late endosome transition and lysosome biogenesis, and for endolysosomal trafficking pathways, including autophagy. The two Vps-C complexes CORVET (class C core vacuole/endosome tethering) and HOPS (homotypic fusion and vacuole protein sorting) perform diverse biochemical functions in endocytosis: they tether membranes, interact with Rab GTPases, activate and proof-read SNARE assembly to drive membrane fusion, and possibly attach endosomes to the cytoskeleton. In addition, several of the CORVET and HOPS subunits have diversified in metazoans, and probably form additional specialized complexes to accomodate the higher complexity of trafficking pathways in these cells. Recent studies offer new insights into the complex relationships between CORVET and HOPS complexes and other factors of the endolysosomal pathway. Interactions with V-ATPase, the ESCRT machinery, phosphoinositides, the cytoskeleton and the Rab switch suggest an intricate cooperative network for endosome maturation. Accumulating evidence supports the view that endosomal tethering complexes implement a regulatory logic that governs endomembrane identity and dynamics. © 2013 The Authors Journal compilation © 2013 FEBS.

  15. High-field MR imaging of tethered cord

    International Nuclear Information System (INIS)

    Sigal, R.; Bicetre, L.; Blass, C.; Doyon, D.; Pariente, D.

    1986-01-01

    MR imaging examinations of 12 patients with tethered cord syndrome have been performed on a 1.5-T MR imaging unit. Patients ranged in age from 3 to 60 years. MR findings were compared with those of myelography and metrizamide CT in all cases. Five patients underwent surgical control and postoperative MR imaging. Sagittal and axial sections were obtained using a spin-echo multisection, multiecho technique. T1-axial weighted images (SE 600/25) were sufficient to locate the position of the tip of the conus. They also allowed identification of extraspinal and intraspinal lipomas and clear-cut demarcation form associated tethered cord. Drawbacks of MR imaging were lack of precise depiction of the bone structures and the fact that clear identification of abnormal roots was problematic. The craniovertebral junction was always checked; two asymptomatic Chiari malformations were visualized. This study leads the authors to conclude that MR imaging should be used as the examination of first choice in the management of tethered cord syndrome

  16. The Chd1 Chromatin Remodeler Shifts Nucleosomal DNA Bidirectionally as a Monomer

    Energy Technology Data Exchange (ETDEWEB)

    Qiu, Yupeng; Levendosky, Robert F.; Chakravarthy, Srinivas; Patel, Ashok; Bowman, Gregory D.; Myong, Sua

    2017-10-01

    Chromatin remodelers catalyze dynamic packaging of the genome by carrying out nucleosome assembly/disassembly, histone exchange, and nucleosome repositioning. Remodeling results in evenly spaced nucleosomes, which requires probing both sides of the nucleosome, yet the way remodelers organize sliding activity to achieve this task is not understood. Here, we show that the monomeric Chd1 remodeler shifts DNA back and forth by dynamically alternating between different segments of the nucleosome. During sliding, Chd1 generates unstable remodeling intermediates that spontaneously relax to a pre-remodeled position. We demonstrate that nucleosome sliding is tightly controlled by two regulatory domains: the DNA-binding domain, which interferes with sliding when its range is limited by a truncated linking segment, and the chromodomains, which play a key role in substrate discrimination. We propose that active interplay of the ATPase motor with the regulatory domains may promote dynamic nucleosome structures uniquely suited for histone exchange and chromatin reorganization during transcription.

  17. DNA breaks and repair in interstitial telomere sequences: Influence of chromatin structure

    International Nuclear Information System (INIS)

    Revaud, D.

    2009-06-01

    Interstitial Telomeric Sequences (ITS) are over-involved in spontaneous and radiationinduced chromosome aberrations in chinese hamster cells. We have performed a study to investigate the origin of their instability, spontaneously or after low doses irradiation. Our results demonstrate that ITS have a particular chromatin structure: short nucleotide repeat length, less compaction of the 30 nm chromatin fiber, presence of G-quadruplex structures. These features would modulate breaks production and would favour the recruitment of alternative DNA repair mechanisms, which are prone to produce chromosome aberrations. These pathways could be at the origin of chromosome aberrations in ITS whereas NHEJ and HR Double Strand Break repair pathways are rather required for a correct repair in these regions. (author)

  18. Mapping chromatin interactions with 5C technology

    Science.gov (United States)

    Ferraiuolo, Maria A.; Sanyal, Amartya; Naumova, Natalia; Dekker, Job; Dostie, Josée

    2013-01-01

    In eukaryotes, genome organization can be observed on many levels and at different scales. This organization is important not only to reduce chromosome length but also for the proper execution of various biological processes. High-resolution mapping of spatial chromatin structure was made possible by the development of the chromosome conformation capture (3C) technique. 3C uses chemical cross-linking followed by proximity-based ligation of fragmented DNA to capture frequently interacting chromatin segments in cell populations. Several 3C-related methods capable of higher chromosome conformation mapping throughput were reported afterwards. These techniques include the 3C-carbon copy (5C) approach, which offers the advantage of being highly quantitative and reproducible. We provide here a reference protocol for the production of 5C libraries analyzed by next-generation sequencing or onto microarrays. A procedure used to verify that 3C library templates bear the high quality required to produce superior 5C libraries is also described. We believe that this comprehensive detailed protocol will help guide researchers in probing spatial genome organization and its role in various biological processes. PMID:23137922

  19. Chromatin Immunoprecipitation (ChIP) using Drosophila tissue

    OpenAIRE

    Tran, Vuong; Gan, Qiang; Chen, Xin

    2012-01-01

    Epigenetics remains a rapidly developing field that studies how the chromatin state contributes to differential gene expression in distinct cell types at different developmental stages. Epigenetic regulation contributes to a broad spectrum of biological processes, including cellular differentiation during embryonic development and homeostasis in adulthood. A critical strategy in epigenetic studies is to examine how various histone modifications and chromatin factors regulate gene expression. ...

  20. Human sperm chromatin epigenetic potential: genomics, proteomics, and male infertility

    Directory of Open Access Journals (Sweden)

    Judit Castillo

    2015-01-01

    Full Text Available The classical idea about the function of the mammalian sperm chromatin is that it serves to transmit a highly protected and transcriptionally inactive paternal genome, largely condensed by protamines, to the next generation. In addition, recent sperm chromatin genome-wide dissection studies indicate the presence of a differential distribution of the genes and repetitive sequences in the protamine-condensed and histone-condensed sperm chromatin domains, which could be potentially involved in regulatory roles after fertilization. Interestingly, recent proteomic studies have shown that sperm chromatin contains many additional proteins, in addition to the abundant histones and protamines, with specific modifications and chromatin affinity features which are also delivered to the oocyte. Both gene and protein signatures seem to be altered in infertile patients and, as such, are consistent with the potential involvement of the sperm chromatin landscape in early embryo development. This present work reviews the available information on the composition of the human sperm chromatin and its epigenetic potential, with a particular focus on recent results derived from high-throughput genomic and proteomic studies. As a complement, we provide experimental evidence for the detection of phosphorylations and acetylations in human protamine 1 using a mass spectrometry approach. The available data indicate that the sperm chromatin is much more complex than what it was previously thought, raising the possibility that it could also serve to transmit crucial paternal epigenetic information to the embryo.

  1. Chromatin architecture and gene expression in Escherichia coli

    DEFF Research Database (Denmark)

    Willenbrock, Hanni; Ussery, David

    2004-01-01

    Two recent genome-scale analyses underscore the importance of DNA topology and chromatin structure in regulating transcription in Escherichia coli.......Two recent genome-scale analyses underscore the importance of DNA topology and chromatin structure in regulating transcription in Escherichia coli....

  2. Brd4 Shields Chromatin from ATM Kinase Signaling Storms

    OpenAIRE

    Choi, Serah; Bakkenist, Christopher J.

    2013-01-01

    Upon activation, ataxia telangiectasia mutated (ATM) kinase rapidly phosphorylates hundreds of proteins, setting off chaotic signaling storms from areas of damaged chromatin. Recent work by Kaidi and Jackson and Floyd et al. advance our knowledge of the mechanisms that initiate or limit ATM kinase signaling storms at chromatin.

  3. Rapid genome-scale mapping of chromatin accessibility in tissue

    DEFF Research Database (Denmark)

    Grøntved, Lars; Bandle, Russell; John, Sam

    2012-01-01

    BACKGROUND: The challenge in extracting genome-wide chromatin features from limiting clinical samples poses a significant hurdle in identification of regulatory marks that impact the physiological or pathological state. Current methods that identify nuclease accessible chromatin are reliant on la...

  4. Homoeologous chromatin exchange in a radiation-induced gene transfer

    International Nuclear Information System (INIS)

    Dvorak, J.; Knott, D.R.

    1977-01-01

    Some of the ionizing-radiation-induced translocations between alien and wheat chromosomes show no deleterious effects and are transmitted normally through the pollen. Translocations of this type will be called ''compensating''. In one such compensating translocation, designated T4, it was found that chromatin in the long arm of wheat chromosome 7D was replaced with homoeologous chromatin of the Agropyron chromosome

  5. A human morphologically normal spermatozoon may have noncondensed chromatin.

    Science.gov (United States)

    Boitrelle, F; Pagnier, M; Athiel, Y; Swierkowski-Blanchard, N; Torre, A; Alter, L; Muratorio, C; Vialard, F; Albert, M; Selva, J

    2015-10-01

    According to numerous assisted reproductive medicine practitioners, semen with normal characteristics might not require further investigation. However, on the scale of the individual spermatozoon, it is well known that normal morphology does not guarantee optimal nuclear quality. Here, for 20 patients with normal sperm characteristics and a high proportion of spermatozoa with noncondensed chromatin, we subsequently assessed chromatin condensation status (aniline blue staining) and morphology (Papanicolaou staining) of the same 3749 spermatozoa. Although the overall proportion of morphologically normal spermatozoa was not correlated with the overall proportion of spermatozoa with noncondensed chromatin, an individual spermatozoon's morphology appeared to be closely related to its chromatin condensation status. Morphologically normal spermatozoa with noncondensed chromatin were seen in all patients; the proportion averaged 23.3% [min 10.9%-max 44.4%]. Morphologically abnormal spermatozoa were more likely to have noncondensed chromatin than morphologically normal ones (P 80% for each type), and more than half the vacuolated spermatozoa also presented noncondensed chromatin. However, a morphologically normal spermatozoon may also have a noncondensed chromatin. © 2014 Blackwell Verlag GmbH.

  6. A Quantitative Proteomic Analysis of In Vitro Assembled Chromatin*

    Science.gov (United States)

    Völker-Albert, Moritz Carl; Pusch, Miriam Caroline; Fedisch, Andreas; Schilcher, Pierre; Schmidt, Andreas; Imhof, Axel

    2016-01-01

    The structure of chromatin is critical for many aspects of cellular physiology and is considered to be the primary medium to store epigenetic information. It is defined by the histone molecules that constitute the nucleosome, the positioning of the nucleosomes along the DNA and the non-histone proteins that associate with it. These factors help to establish and maintain a largely DNA sequence-independent but surprisingly stable structure. Chromatin is extensively disassembled and reassembled during DNA replication, repair, recombination or transcription in order to allow the necessary factors to gain access to their substrate. Despite such constant interference with chromatin structure, the epigenetic information is generally well maintained. Surprisingly, the mechanisms that coordinate chromatin assembly and ensure proper assembly are not particularly well understood. Here, we use label free quantitative mass spectrometry to describe the kinetics of in vitro assembled chromatin supported by an embryo extract prepared from preblastoderm Drosophila melanogaster embryos. The use of a data independent acquisition method for proteome wide quantitation allows a time resolved comparison of in vitro chromatin assembly. A comparison of our in vitro data with proteomic studies of replicative chromatin assembly in vivo reveals an extensive overlap showing that the in vitro system can be used for investigating the kinetics of chromatin assembly in a proteome-wide manner. PMID:26811354

  7. Analysis of Chromatin Dynamics during Glucocorticoid Receptor Activation

    Science.gov (United States)

    Burd, Craig J.; Ward, James M.; Crusselle-Davis, Valerie J.; Kissling, Grace E.; Phadke, Dhiral; Shah, Ruchir R.

    2012-01-01

    Steroid hormone receptors initiate a genetic program tightly regulated by the chromatin environment of the responsive regions. Using the glucocorticoid receptor (GR) as a model factor for transcriptional initiation, we classified chromatin structure through formaldehyde-assisted isolation of regulatory elements (FAIRE). We looked at dynamic changes in FAIRE signals during GR activation specifically at regions of receptor interaction. We found a distribution of GR-responsive regions with diverse responses to activation and chromatin modulation. The majority of GR binding regions demonstrate increases in FAIRE signal in response to ligand. However, the majority GR-responsive regions shared a similar FAIRE signal in the basal chromatin state, suggesting a common chromatin structure for GR recruitment. Supporting this notion, global FAIRE sequencing (seq) data indicated an enrichment of signal surrounding the GR binding site prior to activation. Brg-1 knockdown showed response element-specific effects of ATPase-dependent chromatin remodeling. FAIRE induction was universally decreased by Brg-1 depletion, but to varying degrees in a target specific manner. Taken together, these data suggest classes of nuclear receptor response regions that react to activation through different chromatin regulatory events and identify a chromatin structure that classifies the majority of response elements tested. PMID:22451486

  8. Human sperm chromatin epigenetic potential: genomics, proteomics, and male infertility.

    Science.gov (United States)

    Castillo, Judit; Estanyol, Josep Maria; Ballescá, Josep Lluis; Oliva, Rafael

    2015-01-01

    The classical idea about the function of the mammalian sperm chromatin is that it serves to transmit a highly protected and transcriptionally inactive paternal genome, largely condensed by protamines, to the next generation. In addition, recent sperm chromatin genome-wide dissection studies indicate the presence of a differential distribution of the genes and repetitive sequences in the protamine-condensed and histone-condensed sperm chromatin domains, which could be potentially involved in regulatory roles after fertilization. Interestingly, recent proteomic studies have shown that sperm chromatin contains many additional proteins, in addition to the abundant histones and protamines, with specific modifications and chromatin affinity features which are also delivered to the oocyte. Both gene and protein signatures seem to be altered in infertile patients and, as such, are consistent with the potential involvement of the sperm chromatin landscape in early embryo development. This present work reviews the available information on the composition of the human sperm chromatin and its epigenetic potential, with a particular focus on recent results derived from high-throughput genomic and proteomic studies. As a complement, we provide experimental evidence for the detection of phosphorylations and acetylations in human protamine 1 using a mass spectrometry approach. The available data indicate that the sperm chromatin is much more complex than what it was previously thought, raising the possibility that it could also serve to transmit crucial paternal epigenetic information to the embryo.

  9. Multiple modes of chromatin remodeling by Forkhead box proteins.

    Science.gov (United States)

    Lalmansingh, Avin S; Karmakar, Sudipan; Jin, Yetao; Nagaich, Akhilesh K

    2012-07-01

    Forkhead box (FOX) proteins represent a large family of transcriptional regulators unified by their DNA binding domain (DBD) known as a 'forkhead' or 'winged helix' domain. Over 40 FOX genes have been identified in the mammalian genome. FOX proteins share significant sequence similarities in the DBD which allow them to bind to a consensus DNA response element. However, their modes of action are quite diverse as they regulate gene expression by acting as pioneer factors, transcription factors, or both. This review focuses on the mechanisms of chromatin remodeling with an emphasis on three sub-classes-FOXA, FOXO, and FOXP members. FOXA proteins serve as pioneer factors to open up local chromatin structure and thereby increase accessibility of chromatin to factors regulating transcription. FOXP proteins, in contrast, function as classic transcription factors to recruit a variety of chromatin modifying enzymes to regulate gene expression. FOXO proteins represent a hybrid subclass having dual roles as pioneering factors and transcription factors. A subset of FOX proteins interacts with condensed mitotic chromatin and may function as 'bookmarking' agents to maintain transcriptional competence at specific genomic sites. The overall diversity in chromatin remodeling function by FOX proteins is related to unique structural motifs present within the DBD flanking regions that govern selective interactions with core histones and/or chromatin coregulatory proteins. This article is part of a Special Issue entitled: Chromatin in time and space. Published by Elsevier B.V.

  10. Novel Roaming and Stationary Tethered Aerial Robots for Continuous Mobile Missions in Nuclear Power Plants

    Directory of Open Access Journals (Sweden)

    Beom W. Gu

    2016-08-01

    Full Text Available In this paper, new tethered aerial robots including roaming tethered aerial robots (RTARs for radioactive material sampling and stationary tethered aerial robots (STARs for environment monitoring are proposed to meet extremely-long-endurance missions of nuclear power plants. The flight of the proposed tethered aerial robots may last for a few days or even a few months as long as the tethered cable provides continuous power. A high voltage AC or DC power system was newly adopted to reduce the mass of the tethered cable. The RTAR uses a tethered cable spooled from the aerial robot and an aerial tension control system. The aerial tension control system provides the appropriate tension to the tethered cable, which is accordingly laid down on the ground as the RTAR roams. The STAR includes a tethered cable spooled from the ground and a ground tension control system, which enables the STAR to reach high altitudes. Prototypes of the RTAR and STAR were designed and successfully demonstrated in outdoor environments, where the load power, power type, operating frequency, and flight attitude of the RTAR and STAR were: 180 W, AC 100 kHz, and 20 m; and 300 W, AC or DC 100 kHz, and 80 m, respectively.

  11. Novel roaming and stationary tethered aerial robots for continuous mobile missions in nuclear power plants

    International Nuclear Information System (INIS)

    Gu, Beom W.; Choi, Su Y.; Rim, Chun T.; Choi, Young Soo; Cai, Guowei; Seneviratne, Lakmal

    2016-01-01

    In this paper, new tethered aerial robots including roaming tethered aerial robots (RTARs) for radioactive material sampling and stationary tethered aerial robots (STARs) for environment monitoring are proposed to meet extremely-long-endurance missions of nuclear power plants. The flight of the proposed tethered aerial robots may last for a few days or even a few months as long as the tethered cable provides continuous power. A high voltage AC or DC power system was newly adopted to reduce the mass of the tethered cable. The RTAR uses a tethered cable spooled from the aerial robot and an aerial tension control system. The aerial tension control system provides the appropriate tension to the tethered cable, which is accordingly laid down on the ground as the RTAR roams. The STAR includes a tethered cable spooled from the ground and a ground tension control system, which enables the STAR to reach high altitudes. Prototypes of the RTAR and STAR were designed and successfully demonstrated in outdoor environments, where the load power, power type, operating frequency, and flight attitude of the RTAR and STAR were: 180 W, AC 100 kHz, and 20 m; and 300 W, AC or DC 100 kHz, and 80 m, respectively

  12. Dynamics Model for a Multi-Tethered Space-Based Interferometer

    National Research Council Canada - National Science Library

    Gates, Stephen

    2000-01-01

    .... Tether constitutive behavior is discussed. Prescribed motion of any system degrees of freedom is treated, and expressions for the corresponding constraint force/torque components are established.

  13. Novel roaming and stationary tethered aerial robots for continuous mobile missions in nuclear power plants

    Energy Technology Data Exchange (ETDEWEB)

    Gu, Beom W.; Choi, Su Y.; Rim, Chun T. [Dept. of Nuclear and Quantum Engineering, KAIST, Daejeon (Korea, Republic of); Choi, Young Soo [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of); Cai, Guowei; Seneviratne, Lakmal [Dept. of Aerospace Engineering, Khalifa University, Abu Dhabi (United Arab Emirates)

    2016-08-15

    In this paper, new tethered aerial robots including roaming tethered aerial robots (RTARs) for radioactive material sampling and stationary tethered aerial robots (STARs) for environment monitoring are proposed to meet extremely-long-endurance missions of nuclear power plants. The flight of the proposed tethered aerial robots may last for a few days or even a few months as long as the tethered cable provides continuous power. A high voltage AC or DC power system was newly adopted to reduce the mass of the tethered cable. The RTAR uses a tethered cable spooled from the aerial robot and an aerial tension control system. The aerial tension control system provides the appropriate tension to the tethered cable, which is accordingly laid down on the ground as the RTAR roams. The STAR includes a tethered cable spooled from the ground and a ground tension control system, which enables the STAR to reach high altitudes. Prototypes of the RTAR and STAR were designed and successfully demonstrated in outdoor environments, where the load power, power type, operating frequency, and flight attitude of the RTAR and STAR were: 180 W, AC 100 kHz, and 20 m; and 300 W, AC or DC 100 kHz, and 80 m, respectively.

  14. Tethered elevator and platforms as space station facilities: Systems studies and demonstrative experiments

    Science.gov (United States)

    1986-01-01

    Several key concepts of the science and applications tethered platforms were studied. Some conclusions reached are herein listed. Tether elevator and platform could improve the space station scientific and applicative capabilities. The space elevator presents unique characteristics as microgravity facility and as a tethered platform servicing vehicle. Pointing platforms could represent a new kind of observation facility for large class of payloads. The dynamical, control and technological complexity of these concepts advised demonstrative experiments. The on-going tethered satellite system offers the opportunity to perform such experiments. And feasibility studies are in progress.

  15. Comprehensive analysis of the chromatin landscape in Drosophila melanogaster.

    Science.gov (United States)

    Kharchenko, Peter V; Alekseyenko, Artyom A; Schwartz, Yuri B; Minoda, Aki; Riddle, Nicole C; Ernst, Jason; Sabo, Peter J; Larschan, Erica; Gorchakov, Andrey A; Gu, Tingting; Linder-Basso, Daniela; Plachetka, Annette; Shanower, Gregory; Tolstorukov, Michael Y; Luquette, Lovelace J; Xi, Ruibin; Jung, Youngsook L; Park, Richard W; Bishop, Eric P; Canfield, Theresa K; Sandstrom, Richard; Thurman, Robert E; MacAlpine, David M; Stamatoyannopoulos, John A; Kellis, Manolis; Elgin, Sarah C R; Kuroda, Mitzi I; Pirrotta, Vincenzo; Karpen, Gary H; Park, Peter J

    2011-03-24

    Chromatin is composed of DNA and a variety of modified histones and non-histone proteins, which have an impact on cell differentiation, gene regulation and other key cellular processes. Here we present a genome-wide chromatin landscape for Drosophila melanogaster based on eighteen histone modifications, summarized by nine prevalent combinatorial patterns. Integrative analysis with other data (non-histone chromatin proteins, DNase I hypersensitivity, GRO-Seq reads produced by engaged polymerase, short/long RNA products) reveals discrete characteristics of chromosomes, genes, regulatory elements and other functional domains. We find that active genes display distinct chromatin signatures that are correlated with disparate gene lengths, exon patterns, regulatory functions and genomic contexts. We also demonstrate a diversity of signatures among Polycomb targets that include a subset with paused polymerase. This systematic profiling and integrative analysis of chromatin signatures provides insights into how genomic elements are regulated, and will serve as a resource for future experimental investigations of genome structure and function.

  16. Genome maintenance in the context of 4D chromatin condensation

    Science.gov (United States)

    Yu, Sonia; Yang, Fan; Shen, Wen H.

    2016-01-01

    The eukaryotic genome is packaged in the three-dimensional nuclear space by forming loops, domains and compartments in a hierarchical manner. However, when duplicated genomes prepare for segregation, mitotic cells eliminate topologically associating domains and abandon the compartmentalized structure. Alongside chromatin architecture reorganization during the transition from interphase to mitosis, cells halt most DNA-templated processes such as transcription and repair. The intrinsically condensed chromatin serves as a sophisticated signaling module subjected to selective relaxation for programmed genomic activities. To understand the elaborate genome-epigenome interplay during cell cycle progression, the steady three-dimensional genome requires a time scale to form a dynamic four-dimensional and a more comprehensive portrait. In this review, we will dissect the functions of critical chromatin architectural components in constructing and maintaining an orderly packaged chromatin environment. We will also highlight the importance of the spatially-and-temporally-conscious orchestration of chromatin remodeling to ensure high-fidelity genetic transmission. PMID:27098512

  17. Chromatin Dynamics during Nucleotide Excision Repair: Histones on the Move

    Science.gov (United States)

    Adam, Salomé; Polo, Sophie E.

    2012-01-01

    It has been a long-standing question how DNA damage repair proceeds in a nuclear environment where DNA is packaged into chromatin. Several decades of analysis combining in vitro and in vivo studies in various model organisms ranging from yeast to human have markedly increased our understanding of the mechanisms underlying chromatin disorganization upon damage detection and re-assembly after repair. Here, we review the methods that have been developed over the years to delineate chromatin alterations in response to DNA damage by focusing on the well-characterized Nucleotide Excision Repair (NER) pathway. We also highlight how these methods have provided key mechanistic insight into histone dynamics coupled to repair in mammals, raising new issues about the maintenance of chromatin integrity. In particular, we discuss how NER factors and central players in chromatin dynamics such as histone modifiers, nucleosome remodeling factors, and histone chaperones function to mobilize histones during repair. PMID:23109890

  18. The AID-induced DNA damage response in chromatin

    DEFF Research Database (Denmark)

    Daniel, Jeremy A; Nussenzweig, André

    2013-01-01

    Chemical modifications to the DNA and histone protein components of chromatin can modulate gene expression and genome stability. Understanding the physiological impact of changes in chromatin structure remains an important question in biology. As one example, in order to generate antibody diversity...... with somatic hypermutation and class switch recombination, chromatin must be made accessible for activation-induced cytidine deaminase (AID)-mediated deamination of cytosines in DNA. These lesions are recognized and removed by various DNA repair pathways but, if not handled properly, can lead to formation...... of oncogenic chromosomal translocations. In this review, we focus the discussion on how chromatin-modifying activities and -binding proteins contribute to the native chromatin environment in which AID-induced DNA damage is targeted and repaired. Outstanding questions remain regarding the direct roles...

  19. Chromatin organisation of transgenes in Dictyostelium.

    Science.gov (United States)

    Windhof, I M; Dubin, M J; Nellen, W

    2013-07-01

    The introduction of transgenes in Dictyostelium discoideum typically results in the integration of the transformation vector into the genome at one or a few insertion sites as tandem arrays of approximately 100 copies. Exceptions are extrachromosomal vectors, which do not integrate into chromosomes, and vectors containing resistance markers such as blasticidin, which integrate as single copies at one or a few sites. Here we report that low copy number vector inserts display typical euchromatic features while high copy number insertions are enriched for modifications associate with heterochromatin. Interestingly, high copy number insertions also colocalise with heterochromatin, are enriched for the centromeric histone CenH3 and display centromere-like behaviour during mitosis. We also found that the chromatin organisation on extrachromosmal transgenes is different from those integrated into the chromosomes.

  20. The DDR at telomeres lacking intact shelterin does not require substantial chromatin decompaction.

    Science.gov (United States)

    Timashev, Leonid A; Babcock, Hazen; Zhuang, Xiaowei; de Lange, Titia

    2017-03-15

    Telomeres are protected by shelterin, a six-subunit protein complex that represses the DNA damage response (DDR) at chromosome ends. Extensive data suggest that TRF2 in shelterin remodels telomeres into the t-loop structure, thereby hiding telomere ends from double-stranded break repair and ATM signaling, whereas POT1 represses ATR signaling by excluding RPA. An alternative protection mechanism was suggested recently by which shelterin subunits TRF1, TRF2, and TIN2 mediate telomeric chromatin compaction, which was proposed to minimize access of DDR factors. We performed superresolution imaging of telomeres in mouse cells after conditional deletion of TRF1, TRF2, or both, the latter of which results in the complete loss of shelterin. Upon removal of TRF1 or TRF2, we observed only minor changes in the telomere volume in most of our experiments. Upon codeletion of TRF1 and TRF2, the telomere volume increased by varying amounts, but even those samples exhibiting small changes in telomere volume showed DDR at nearly all telomeres. Upon shelterin removal, telomeres underwent 53BP1-dependent clustering, potentially explaining at least in part the apparent increase in telomere volume. Furthermore, chromatin accessibility, as determined by ATAC-seq (assay for transposase-accessible chromatin [ATAC] with high-throughput sequencing), was not substantially altered by shelterin removal. These results suggest that the DDR induced by shelterin removal does not require substantial telomere decompaction. © 2017 Timashev et al.; Published by Cold Spring Harbor Laboratory Press.

  1. Tethered Transition Metals Promoted Photocatalytic System for Efficient Hydrogen Evolutions

    KAUST Repository

    Takanabe, Kazuhiro

    2015-03-05

    The present invention is directed, at least in part, to a process for improving the efficiency of a photocatalyst (a semiconductor photocatalyst) by tethering (depositing) a metal (e.g., metal ions of a late transition metal, such as nickel) to the semiconductor (photocatalyst) surface through the use of an organic ligand. More specifically, 1,2-ethanedithiol (EDT) functions as an excellent molecular linker (organic ligand) to attach a transition metal complex (e.g., nickel (Ni.sup.2+ ions)) to the semiconductor surface, which can be in the form of a cadmium sulfide surface. The photocatalyst has particular utility in generating hydrogen from H.sub.2S.

  2. Fullerenic structures and such structures tethered to carbon materials

    Science.gov (United States)

    Goel, Anish; Howard, Jack B.; Vander Sande, John B.

    2010-01-05

    The fullerenic structures include fullerenes having molecular weights less than that of C.sub.60 with the exception of C.sub.36 and fullerenes having molecular weights greater than C.sub.60. Examples include fullerenes C.sub.50, C.sub.58, C.sub.130, and C.sub.176. Fullerenic structure chemically bonded to a carbon surface is also disclosed along with a method for tethering fullerenes to a carbon material. The method includes adding functionalized fullerene to a liquid suspension containing carbon material, drying the suspension to produce a powder, and heat treating the powder.

  3. PREDICTION OF CHROMATIN STATES USING DNA SEQUENCE PROPERTIES

    KAUST Repository

    Bahabri, Rihab R.

    2013-06-01

    Activities of DNA are to a great extent controlled epigenetically through the internal struc- ture of chromatin. This structure is dynamic and is influenced by different modifications of histone proteins. Various combinations of epigenetic modification of histones pinpoint to different functional regions of the DNA determining the so-called chromatin states. How- ever, the characterization of chromatin states by the DNA sequence properties remains largely unknown. In this study we aim to explore whether DNA sequence patterns in the human genome can characterize different chromatin states. Using DNA sequence motifs we built binary classifiers for each chromatic state to eval- uate whether a given genomic sequence is a good candidate for belonging to a particular chromatin state. Of four classification algorithms (C4.5, Naive Bayes, Random Forest, and SVM) used for this purpose, the decision tree based classifiers (C4.5 and Random Forest) yielded best results among those we evaluated. Our results suggest that in general these models lack sufficient predictive power, although for four chromatin states (insulators, het- erochromatin, and two types of copy number variation) we found that presence of certain motifs in DNA sequences does imply an increased probability that such a sequence is one of these chromatin states.

  4. Histone redistribution and conformational effect on chromatin induced by formaldehyde.

    Science.gov (United States)

    Polacow, I; Cabasso, L; Li, H J

    1976-10-19

    Histone redistributions between endogenous DNA in calf thymus chromatin and exogenous DNA from Clostridium perfringens (69% A + T) or from Micrococcus luteus (30% A + T) induced by 0.6 M NaCl or by 2% formaldehyde were studied by thermal denaturation. The observed redistribution occurred on histone Hl when the exogenous DNA was (A + T)-richer than the DNA in chromatin, and when the mixture was exposed to 0.6 M NaCl or formaldehyde. When a (G + C)-richer DNA was added as the acceptor for histones, no substantial transfer of histones from chromatin DNA to exogenous DNA was found. Thus the activation energy of histone dissociation from chromatin DNA seems to be substantially lowered by 0.6 M NaCl or formaldehyde such that histones (mostly histone Hl) can be dissociated and bind the (A + T)-richer DNA and form a more stable complex. It is suggested that the formaldehyde effect on histones may be due to the loss of positive charges on lysine and arginin residues (probably more on lysine than on arginine) in histones after their rapid reaction with formaldehyde. Formaldehyde treatment of chromatin also distorts the DNA conformation, as revealed by circular dichroism (CD) studies. This structural effect occurs mainly on those base pairs bound by histones other than Hl, or within the chromatin subunit. Histone redistribution is treated as a thermodynamic phenomenon of histone binding to DNA. The validity of using formaldehyde to study chromatin structure is discussed.

  5. Anti-chromatin antibodies in juvenile rheumatoid arthritis

    Directory of Open Access Journals (Sweden)

    V. Gerloni

    2011-09-01

    Full Text Available Objective: to evaluate the prevalence and clinical significance of anti-chromatin antibodies (Abs in juvenile rheumatoid arthritis (JRA. Methods: IgG anti-chromatin Abs were detected by an enzyme-linked immunosorbent assay (ELISA, in sera of 94 children with JRA (10 children with systemic, 38 with polyarticular and 46 with oligoarticular disease onset. As control group, 33 age- and-sex-matched healthy children (HC were also examined. Results: Abs to chromatin were detected in 24/94 (25,5% of children suffering from JRA. Particularly, the higher prevalence of anti-chromatin Abs has been found in children with oligoarticular (30,4% and polyarticular (23,7% onset JRA. In these groups Abs titers were significantly higher compared to systemic JRA and HC (p=0.003. Anti-chromatin Abs were observed more frequently in patients with oligoarticular disease and chronic uveitis (21,7%. Furthermore, higher levels of anti-chromatin Abs has been found in all the patients treated with anti-TNFα therapy (p<0.0001. Conclusions: our results confirm previous data about the prevalence of anti-chromatin Abs in JRA. These Abs were significantly higher in the group of patients with oligoarticular onset with past or present hystory of ocular involvement and in the group with polyarticular JRA treated with biologic therapy. A long-term follow-up study could be useful to evaluate the potential utility of these autoantibodies.

  6. Chromatinization of the KSHV Genome During the KSHV Life Cycle

    International Nuclear Information System (INIS)

    Uppal, Timsy; Jha, Hem C.; Verma, Subhash C.; Robertson, Erle S.

    2015-01-01

    Kaposi’s sarcoma-associated herpesvirus (KSHV) belongs to the gamma herpesvirus family and is the causative agent of various lymphoproliferative diseases in humans. KSHV, like other herpesviruses, establishes life-long latent infection with the expression of a limited number of viral genes. Expression of these genes is tightly regulated by both the viral and cellular factors. Recent advancements in identifying the expression profiles of viral transcripts, using tilling arrays and next generation sequencing have identified additional coding and non-coding transcripts in the KSHV genome. Determining the functions of these transcripts will provide a better understanding of the mechanisms utilized by KSHV in altering cellular pathways involved in promoting cell growth and tumorigenesis. Replication of the viral genome is critical in maintaining the existing copies of the viral episomes during both latent and lytic phases of the viral life cycle. The replication of the viral episome is facilitated by viral components responsible for recruiting chromatin modifying enzymes and replication factors for altering the chromatin complexity and replication initiation functions, respectively. Importantly, chromatin modification of the viral genome plays a crucial role in determining whether the viral genome will persist as latent episome or undergo lytic reactivation. Additionally, chromatinization of the incoming virion DNA, which lacks chromatin structure, in the target cells during primary infection, helps in establishing latent infection. Here, we discuss the recent advancements on our understating of KSHV genome chromatinization and the consequences of chromatin modifications on viral life cycle

  7. Sperm-derived histones contribute to zygotic chromatin in humans

    Directory of Open Access Journals (Sweden)

    Derijck Alwin AHA

    2008-03-01

    Full Text Available Abstract Background about 15% to 30% of the DNA in human sperm is packed in nucleosomes and transmission of this fraction to the embryo potentially serves as a mechanism to facilitate paternal epigenetic programs during embryonic development. However, hitherto it has not been established whether these nucleosomes are removed like the protamines or indeed contribute to paternal zygotic chromatin, thereby potentially contributing to the epigenome of the embryo. Results to clarify the fate of sperm-derived nucleosomes we have used the deposition characteristics of histone H3 variants from which follows that H3 replication variants present in zygotic paternal chromatin prior to S-phase originate from sperm. We have performed heterologous ICSI by injecting human sperm into mouse oocytes. Probing these zygotes with an antibody highly specific for the H3.1/H3.2 replication variants showed a clear signal in the decondensed human sperm chromatin prior to S-phase. In addition, staining of human multipronuclear zygotes also showed the H3.1/H3.2 replication variants in paternal chromatin prior to DNA replication. Conclusion these findings reveal that sperm-derived nucleosomal chromatin contributes to paternal zygotic chromatin, potentially serving as a template for replication, when epigenetic information can be copied. Hence, the execution of epigenetic programs originating from transmitted paternal chromatin during subsequent embryonic development is a logical consequence of this observation.

  8. Rapid and reversible epigenome editing by endogenous chromatin regulators.

    Science.gov (United States)

    Braun, Simon M G; Kirkland, Jacob G; Chory, Emma J; Husmann, Dylan; Calarco, Joseph P; Crabtree, Gerald R

    2017-09-15

    Understanding the causal link between epigenetic marks and gene regulation remains a central question in chromatin biology. To edit the epigenome we developed the FIRE-Cas9 system for rapid and reversible recruitment of endogenous chromatin regulators to specific genomic loci. We enhanced the dCas9-MS2 anchor for genome targeting with Fkbp/Frb dimerizing fusion proteins to allow chemical-induced proximity of a desired chromatin regulator. We find that mSWI/SNF (BAF) complex recruitment is sufficient to oppose Polycomb within minutes, leading to activation of bivalent gene transcription in mouse embryonic stem cells. Furthermore, Hp1/Suv39h1 heterochromatin complex recruitment to active promoters deposits H3K9me3 domains, resulting in gene silencing that can be reversed upon washout of the chemical dimerizer. This inducible recruitment strategy provides precise kinetic information to model epigenetic memory and plasticity. It is broadly applicable to mechanistic studies of chromatin in mammalian cells and is particularly suited to the analysis of endogenous multi-subunit chromatin regulator complexes.Understanding the link between epigenetic marks and gene regulation requires the development of new tools to directly manipulate chromatin. Here the authors demonstrate a Cas9-based system to recruit chromatin remodelers to loci of interest, allowing rapid, reversible manipulation of epigenetic states.

  9. Chromatinization of the KSHV Genome During the KSHV Life Cycle

    Energy Technology Data Exchange (ETDEWEB)

    Uppal, Timsy [Department of Microbiology and Immunology, School of Medicine, University of Nevada, 1664 N Virginia Street, MS 320, Reno, NV 89557 (United States); Jha, Hem C. [Department of Microbiology and the Tumor Virology Program of the Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, 201E Johnson Pavilion, 3610 Hamilton Walk, Philadelphia, PA 19104 (United States); Verma, Subhash C. [Department of Microbiology and Immunology, School of Medicine, University of Nevada, 1664 N Virginia Street, MS 320, Reno, NV 89557 (United States); Robertson, Erle S., E-mail: erle@mail.med.upenn.edu [Department of Microbiology and the Tumor Virology Program of the Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, 201E Johnson Pavilion, 3610 Hamilton Walk, Philadelphia, PA 19104 (United States)

    2015-01-14

    Kaposi’s sarcoma-associated herpesvirus (KSHV) belongs to the gamma herpesvirus family and is the causative agent of various lymphoproliferative diseases in humans. KSHV, like other herpesviruses, establishes life-long latent infection with the expression of a limited number of viral genes. Expression of these genes is tightly regulated by both the viral and cellular factors. Recent advancements in identifying the expression profiles of viral transcripts, using tilling arrays and next generation sequencing have identified additional coding and non-coding transcripts in the KSHV genome. Determining the functions of these transcripts will provide a better understanding of the mechanisms utilized by KSHV in altering cellular pathways involved in promoting cell growth and tumorigenesis. Replication of the viral genome is critical in maintaining the existing copies of the viral episomes during both latent and lytic phases of the viral life cycle. The replication of the viral episome is facilitated by viral components responsible for recruiting chromatin modifying enzymes and replication factors for altering the chromatin complexity and replication initiation functions, respectively. Importantly, chromatin modification of the viral genome plays a crucial role in determining whether the viral genome will persist as latent episome or undergo lytic reactivation. Additionally, chromatinization of the incoming virion DNA, which lacks chromatin structure, in the target cells during primary infection, helps in establishing latent infection. Here, we discuss the recent advancements on our understating of KSHV genome chromatinization and the consequences of chromatin modifications on viral life cycle.

  10. Tracking the mechanical dynamics of human embryonic stem cell chromatin

    Directory of Open Access Journals (Sweden)

    Hinde Elizabeth

    2012-12-01

    Full Text Available Abstract Background A plastic chromatin structure has emerged as fundamental to the self-renewal and pluripotent capacity of embryonic stem (ES cells. Direct measurement of chromatin dynamics in vivo is, however, challenging as high spatiotemporal resolution is required. Here, we present a new tracking-based method which can detect high frequency chromatin movement and quantify the mechanical dynamics of chromatin in live cells. Results We use this method to study how the mechanical properties of chromatin movement in human embryonic stem cells (hESCs are modulated spatiotemporally during differentiation into cardiomyocytes (CM. Notably, we find that pluripotency is associated with a highly discrete, energy-dependent frequency of chromatin movement that we refer to as a ‘breathing’ state. We find that this ‘breathing’ state is strictly dependent on the metabolic state of the cell and is progressively silenced during differentiation. Conclusions We thus propose that the measured chromatin high frequency movements in hESCs may represent a hallmark of pluripotency and serve as a mechanism to maintain the genome in a transcriptionally accessible state. This is a result that could not have been observed without the high spatial and temporal resolution provided by this novel tracking method.

  11. Dynamics of chromatin accessibility and gene regulation by MADS-domain transcription factors in flower development.

    Science.gov (United States)

    Pajoro, Alice; Madrigal, Pedro; Muiño, Jose M; Matus, José Tomás; Jin, Jian; Mecchia, Martin A; Debernardi, Juan M; Palatnik, Javier F; Balazadeh, Salma; Arif, Muhammad; Ó'Maoiléidigh, Diarmuid S; Wellmer, Frank; Krajewski, Pawel; Riechmann, José-Luis; Angenent, Gerco C; Kaufmann, Kerstin

    2014-03-03

    Development of eukaryotic organisms is controlled by transcription factors that trigger specific and global changes in gene expression programs. In plants, MADS-domain transcription factors act as master regulators of developmental switches and organ specification. However, the mechanisms by which these factors dynamically regulate the expression of their target genes at different developmental stages are still poorly understood. We characterized the relationship of chromatin accessibility, gene expression, and DNA binding of two MADS-domain proteins at different stages of Arabidopsis flower development. Dynamic changes in APETALA1 and SEPALLATA3 DNA binding correlated with changes in gene expression, and many of the target genes could be associated with the developmental stage in which they are transcriptionally controlled. We also observe dynamic changes in chromatin accessibility during flower development. Remarkably, DNA binding of APETALA1 and SEPALLATA3 is largely independent of the accessibility status of their binding regions and it can precede increases in DNA accessibility. These results suggest that APETALA1 and SEPALLATA3 may modulate chromatin accessibility, thereby facilitating access of other transcriptional regulators to their target genes. Our findings indicate that different homeotic factors regulate partly overlapping, yet also distinctive sets of target genes in a partly stage-specific fashion. By combining the information from DNA-binding and gene expression data, we are able to propose models of stage-specific regulatory interactions, thereby addressing dynamics of regulatory networks throughout flower development. Furthermore, MADS-domain TFs may regulate gene expression by alternative strategies, one of which is modulation of chromatin accessibility.

  12. The chromatin remodeling Isw1a complex is regulated by SUMOylation.

    Science.gov (United States)

    Shen, Qingtang; Beyrouthy, Nissrine; Matabishi-Bibi, Laura; Dargemont, Catherine

    2017-10-05

    The ISWI class of proteins consists of a family of chromatin remodeling ATPases that is ubiquitous in eukaryotes and predominantly functions to slide nucleosomes laterally. The yeast Saccharomyces cerevisiae Isw1 partners with several non-essential alternative subunits - Ioc2, Ioc3, or Ioc4 - to form two distinct complexes Isw1a and Isw1b. Besides its ATPase domain, Isw1 presents a C-terminal region formed by HAND, SANT, and SLIDE domains responsible for interaction with the Ioc proteins and optimal association of Isw1 to chromatin. Despite diverse studies on the functions of the Isw1-containing complexes, molecular evidence for a regulation of this chromatin remodeling ATPase is still elusive. Results presented here indicate that Isw1 is not only ubiquitylated but also strongly SUMOylated on multiple lysine residues by the redundant Siz1/Siz2 SUMO E3 ligases. However, Isw1 is a poor substrate of the Ulp1 and Ulp2 SUMO proteases, thus resulting in a high level of modification. Extensive site-directed mutagenesis allowed us to identify the major SUMOylation sites and develop a SUMO-defective mutant of Isw1. Using this molecular tool, we show that SUMOylation of Isw1 specifically facilitates and/or stabilizes its interaction with its cofactor Ioc3 and consequently the efficient recruitment of the Isw1-Ioc3 complex onto chromatin. Together these data reveal a new regulatory mechanism for this fascinating remodeling factor. © 2017 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.

  13. Emerging insights into the roles of membrane tethers from analysis of whole organisms: The tip of an iceberg?

    Directory of Open Access Journals (Sweden)

    Wei Hong eToh

    2016-02-01

    Full Text Available Membrane tethers have been identified throughout different compartments of the endomembrane system. It is now well established that a number of membrane tethers mediate docking of membrane carriers in anterograde and retrograde transport and in regulating the organization of membrane compartments. Much of our information on membrane tethers have been obtained from the analysis of individual membrane tethers in cultured cells. In the future it will be important to better appreciate the network of interactions mediated by tethers and the potential co-ordination of their collective functions in vivo. There are now a number of studies which have analyzed membrane tethers in tissues and organisms which are providing new insights into the role of this class of membrane protein at the physiological level. Here we review recent advances in the understanding of the function of membrane tethers from knock outs (or knock downs in whole organisms and from mutations in tethers associated with disease.

  14. The Cellular DNA Helicase ChlR1 Regulates Chromatin and Nuclear Matrix Attachment of the Human Papillomavirus 16 E2 Protein and High-Copy-Number Viral Genome Establishment.

    Science.gov (United States)

    Harris, Leanne; McFarlane-Majeed, Laura; Campos-León, Karen; Roberts, Sally; Parish, Joanna L

    2017-01-01

    In papillomavirus infections, the viral genome is established as a double-stranded DNA episome. To segregate the episomes into daughter cells during mitosis, they are tethered to cellular chromatin by the viral E2 protein. We previously demonstrated that the E2 proteins of diverse papillomavirus types, including bovine papillomavirus (BPV) and human papillomavirus 16 (HPV16), associate with the cellular DNA helicase ChlR1. This virus-host interaction is important for the tethering of BPV E2 to mitotic chromatin and the stable maintenance of BPV episomes. The role of the association between E2 and ChlR1 in the HPV16 life cycle is unresolved. Here we show that an HPV16 E2 Y131A mutant (E2 Y131A ) had significantly reduced binding to ChlR1 but retained transcriptional activation and viral origin-dependent replication functions. Subcellular fractionation of keratinocytes expressing E2 Y131A showed a marked change in the localization of the protein. Compared to that of wild-type E2 (E2 WT ), the chromatin-bound pool of E2 Y131A was decreased, concomitant with an increase in nuclear matrix-associated protein. Cell cycle synchronization indicated that the shift in subcellular localization of E2 Y131A occurred in mid-S phase. A similar alteration between the subcellular pools of the E2 WT protein occurred upon ChlR1 silencing. Notably, in an HPV16 life cycle model in primary human keratinocytes, mutant E2 Y131A genomes were established as episomes, but at a markedly lower copy number than that of wild-type HPV16 genomes, and they were not maintained upon cell passage. Our studies indicate that ChlR1 is an important regulator of the chromatin association of E2 and of the establishment and maintenance of HPV16 episomes. Infections with high-risk human papillomaviruses (HPVs) are a major cause of anogenital and oropharyngeal cancers. During infection, the circular DNA genome of HPV persists within the nucleus, independently of the host cell chromatin. Persistence of infection

  15. Dynamic modeling and Super-Twisting Sliding Mode Control for Tethered Space Robot

    Science.gov (United States)

    Zhao, Yakun; Huang, Panfeng; Zhang, Fan

    2018-02-01

    Recent years, tethered space capturing systems have been considered as one of the most promising solutions for active space debris removal due to the increasing threat of space debris to spacecraft and astronauts. In this paper, one of the tethered space capturing systems, Tethered Space Robot (TSR), is investigated. TSR includes a space platform, a space tether, and a gripper as the terminal device. Based on the assumptions that the platform and the gripper are point masses and the tether is rigid, inextensible and remaining straight, the dynamic model of TSR is presented, in which the disturbances from space environment is considered. According to the previous study, the in-plane and out-of-plane angles of the tether oscillate periodically although the tether is released to the desired length. A super-twisting adaptive sliding mode control scheme is designed for TSR to eliminate the vibration of the tether to assure a successful capture in station-keeping phase. Both uncontrolled and controlled situations are simulated. The simulation results show that the proposed controller is effective. Additionally, after comparing with normal sliding mode control algorithm, it is verified that the proposed control scheme can avoid the chattering of normal sliding mode control and is robust for unknown boundary perturbations.

  16. Opioid activity in behavorial and heart rate responses of tethered pigs to acute stress

    NARCIS (Netherlands)

    Loijens, L.W.S.; Janssens, C.J.J.G.; Schouten, W.G.P.; Wiegant, V.M.

    2002-01-01

    In a longitudinal experiment, effects of long-term tether housing on heart rate and behavioral responses to an acute stressor (a 15-min challenge with a nosesling) were investigated in pigs. The animals were challenged during loose housing and again after 10–11 weeks of tether housing. To detect

  17. Modeling and Control of Electrodynamic Tethers - an Energy and Topology Approach

    DEFF Research Database (Denmark)

    Larsen, Martin Birkelund

    of the Earth for creating a Lorentz force along the tether which occur when a current carrying wire operates in a magnetic field. The use of electrodynamic tethers are interesting since they operate solely on electrical energy, which can be provided by solar panels of the spacecrafts. In this way the amount...

  18. In-plane adaptive retrieval control for a noncooperative target by tethered space robots

    Directory of Open Access Journals (Sweden)

    Zhongjie Meng

    2016-09-01

    Full Text Available Using tether to replace rigid arms, the tethered space robot has more flexibility and security than the traditional space robot, which gives it a wide application prospect in the satellite retrieval. After a noncooperative satellite is captured by the tethered space robot, the tethered space robot and the satellite compose a combination with uncertain mass, inertia, and tether junction position. The tether length, tether deflection, and combination attitude are coupled seriously and control inputs are strictly limited, which make the retrieval of tethered space robot very difficult. First, a retrieval dynamic model of in-plane motion is derived using Lagrangian method. Then, in order to solve the uncertainty problems of dynamics parameters, an adaptive controller and its parameter updating law are proposed using the dynamic inversion theory. Moreover, an anti-windup strategy with auxiliary variables is derived to compensate the limited control inputs. Simulation results validate the feasibility of the proposed adaptive anti-windup control method. The noncooperative satellite is retrieved along the desired trajectory effectively.

  19. The development and significance of abnormal stereotyped behaviours in tethered sows

    NARCIS (Netherlands)

    Cronin, G.M.

    1985-01-01

    The development and performance of abnormal stereotyped behaviours (stereotypies) by tethered sows were studied in order to investigate the consequences of the behaviours for animal welfare and sow productivity.

    In Chapter 2, the behaviour of 36 tethered sows in a commercial herd

  20. Tethered spinal cord: the effect of neurosurgery on the lower urinary tract and male sexual function

    NARCIS (Netherlands)

    Boemers, T. M.; van Gool, J. D.; de Jong, T. P.

    1995-01-01

    To determine the effect of neurosurgical untethering on the lower urinary tract and male sexual function, in patients with tethered spinal cord. Thirty-six children with tethered spinal cord due to neurospinal dysraphism were assessed clinically and urodynamically before and after surgical

  1. SUMO-2 Orchestrates Chromatin Modifiers in Response to DNA Damage

    DEFF Research Database (Denmark)

    Hendriks, Ivo A; Treffers, Louise W; Verlaan-de Vries, Matty

    2015-01-01

    dynamically SUMOylated interaction networks of chromatin modifiers, transcription factors, DNA repair factors, and nuclear body components. SUMOylated chromatin modifiers include JARID1B/KDM5B, JARID1C/KDM5C, p300, CBP, PARP1, SetDB1, and MBD1. Whereas SUMOylated JARID1B was ubiquitylated by the SUMO......-targeted ubiquitin ligase RNF4 and degraded by the proteasome in response to DNA damage, JARID1C was SUMOylated and recruited to the chromatin to demethylate histone H3K4....

  2. Chromatin regulation at the frontier of synthetic biology

    Science.gov (United States)

    Keung, Albert J.; Joung, J. Keith; Khalil, Ahmad S.; Collins, James J.

    2016-01-01

    As synthetic biology approaches are extended to diverse applications throughout medicine, biotechnology and basic biological research, there is an increasing need to engineer yeast, plant and mammalian cells. Eukaryotic genomes are regulated by the diverse biochemical and biophysical states of chromatin, which brings distinct challenges, as well as opportunities, over applications in bacteria. Recent synthetic approaches, including `epigenome editing', have allowed the direct and functional dissection of many aspects of physiological chromatin regulation. These studies lay the foundation for biomedical and biotechnological engineering applications that could take advantage of the unique combinatorial and spatiotemporal layers of chromatin regulation to create synthetic systems of unprecedented sophistication. PMID:25668787

  3. Flight mechanics applications for tethers in space: Cooperative Italian-US programs

    Science.gov (United States)

    Bevilacqua, Franco; Merlina, Pietro; Anderson, John L.

    1990-01-01

    Since the 1974 proposal by Giuseppe Colombo to fly a tethered subsatellite from the Shuttle Orbiter, the creative thinking of many scientists and engineers from Italy and U.S. has generated a broad range of potential tether applications in space. Many of these applications have promise for enabling innovative research and operational activities relating to flight mechanics in earth orbit and at suborbital altitudes. From a flight mechanics standpoint the most interesting of the currently proposed flight demonstrations are: the second Tethered Satellite System experiment which offers both the potential for aerothermodynamics and hypersonics research and for atmospheric science research; the Tethered Initiated Space Recovery System which would enable orbital deboost and recovery of a re-entry vehicle and waste removal from a space station; and the Tether Elevator/Crawler System which would provide a variable microgravity environment and space station center of mass management. The outer atmospheric and orbital flight mechanics characteristics of these proposed tether flight demonstrations are described. The second Tethered Satellite System mission will deploy the tethered satellite earthward and will bring it as low as 130 km from ground and thus into the transition region between the atmosphere (non-ionized) and the partially ionized ionosphere. The atmospheric flight mechanics of the tethered satellite is discussed and simulation results are presented. The Tether Initiated Space Recovery System experiment will demonstrate the ability of a simple tether system to deboost and recover a reentry vehicle. The main feature of this demonstration is the utilization of a Small Expendable Deployment System (SEDS) and the low-tension deployment assumed to separate the reentry vehicle from the Shuttle. This low-tension deployment maneuver is discussed and its criticalities are outlined. The Tether Elevator/Crawler System is a new space element able to move in a controlled way

  4. Closed Loop Control of a Tethered Magnetic Capsule Endoscope.

    Science.gov (United States)

    Taddese, Addisu Z; Slawinski, Piotr R; Obstein, Keith L; Valdastri, Pietro

    2016-06-01

    Magnetic field gradients have repeatedly been shown to be the most feasible mechanism for gastrointestinal capsule endoscope actuation. An inverse quartic magnetic force variation with distance results in large force gradients induced by small movements of a driving magnet; this necessitates robotic actuation of magnets to implement stable control of the device. A typical system consists of a serial robot with a permanent magnet at its end effector that actuates a capsule with an embedded permanent magnet. We present a tethered capsule system where a capsule with an embedded magnet is closed loop controlled in 2 degree-of-freedom in position and 2 degree-of-freedom in orientation. Capitalizing on the magnetic field of the external driving permanent magnet, the capsule is localized in 6-D allowing for both position and orientation feedback to be used in a control scheme. We developed a relationship between the serial robot's joint parameters and the magnetic force and torque that is exerted onto the capsule. Our methodology was validated both in a dynamic simulation environment where a custom plug-in for magnetic interaction was written, as well as on an experimental platform. The tethered capsule was demonstrated to follow desired trajectories in both position and orientation with accuracy that is acceptable for colonoscopy.

  5. Piperidinium tethered nanoparticle-hybrid electrolyte for lithium metal batteries

    KAUST Repository

    Korf, Kevin S.

    2014-06-23

    We report on the synthesis of novel piperidinium-based ionic liquid tethered nanoparticle hybrid electrolytes and investigate their physical and electrochemical properties. Hybrid electrolytes based on the ionic liquid 1-methyl-1-propylpiperidinium bis(trifluoromethanesulfone) imide covalently tethered to silica nanoparticles (SiO2-PP-TFSI) were blended with propylene carbonate-1 M lithium bis(trifluoromethanesulfone) imide (LiTFSI). We employed NMR analysis to confirm the successful creation of the hybrid material. Dielectric and rheological measurements show that these electrolytes exhibit exceptional room-temperature DC ionic conductivity (10-2 to 10 -3 S cm-1) as well as high shear mechanical moduli (105 to 106 Pa). Lithium transference numbers were found to increase with particle loading and to reach values as high as 0.22 at high particle loadings where the particle jam to form a soft glassy elastic medium. Analysis of lithium electrodeposits obtained in the hybrid electrolytes using SEM and EDX spectra show that the SiO2-PP-TFSI nanoparticles are able to smooth lithium deposition and inhibit lithium dendrite proliferation in Li metal batteries. LTOSiO2-PP-TFSI/PC in 1 M LiTFSILi half-cells based on the SiO2-PP-TFSI hybrid electrolytes exhibit attractive voltage profiles and trouble-free extended cycling behavior over more than 1000 cycles of charge and discharge. This journal is © the Partner Organisations 2014.

  6. Brownian dynamics of wall tethered polymers in shear flow

    Science.gov (United States)

    Lin, Tiras Y.; Saadat, Amir; Kushwaha, Amit; Shaqfeh, Eric S. G.

    2017-11-01

    The dynamics of a wall tethered polymer in shear flow is studied using Brownian dynamics. Simulations are performed with bead-spring chains, and the effect of hydrodynamic interactions (HI) is incorporated through Blake's tensor with a finite size bead correction. We characterize the configuration of the polymer as a function of the Weissenberg number by investigating the regions the polymer explores in both the flow-gradient and flow-vorticity planes. The fractional extension in the flow direction, the width in the vorticity direction, and the thickness in the gradient direction are reported as well, and these quantities are found to compare favorably with the experimental data of the literature. The cyclic motion of the polymer is demonstrated through analysis of the mean velocity field of the end bead. We characterize the collision process of each bead with the wall as a Poisson process and extract an average wall collision rate, which in general varies along the backbone of the chain. The inclusion of HI with the wall for a tethered polymer is found to reduce the average wall collision rate. We anticipate that results from this work will be directly applicable to, e.g., the design of polymer brushes or the use of DNA for making nanowires in molecular electronics. T.Y.L. is supported by the Department of Defense (DoD) through the National Defense Science & Engineering Graduate Fellowship (NDSEG) Program.

  7. Dynamics and stability of a tethered centrifuge in low earth orbit

    Science.gov (United States)

    Quadrelli, B. M.; Lorenzini, E. C.

    1992-01-01

    The three-dimensional attitude dynamics of a spaceborne tethered centrifuge for artificial gravity experiments in low earth orbit is analyzed using two different methods. First, the tethered centrifuge is modeled as a dumbbell with a straight viscoelastic tether, point tip-masses, and sophisticated environmental models such as nonspherical gravity, thermal perturbations, and a dynamic atmospheric model. The motion of the centrifuge during spin-up, de-spin, and steady-rotation is then simulated. Second, a continuum model of the tether is developed for analyzing the stability of lateral tether oscillations. Results indicate that the maximum fluctuation about the 1-g radial acceleration level is less than 0.001 g; the time required for spin-up and de-spin is less than one orbit; and lateral oscillations are stable for any practical values of the system parameters.

  8. Transport Vesicle Tethering at the Trans Golgi Network: Coiled Coil Proteins in Action.

    Science.gov (United States)

    Cheung, Pak-Yan P; Pfeffer, Suzanne R

    2016-01-01

    The Golgi complex is decorated with so-called Golgin proteins that share a common feature: a large proportion of their amino acid sequences are predicted to form coiled-coil structures. The possible presence of extensive coiled coils implies that these proteins are highly elongated molecules that can extend a significant distance from the Golgi surface. This property would help them to capture or trap inbound transport vesicles and to tether Golgi mini-stacks together. This review will summarize our current understanding of coiled coil tethers that are needed for the receipt of transport vesicles at the trans Golgi network (TGN). How do long tethering proteins actually catch vesicles? Golgi-associated, coiled coil tethers contain numerous binding sites for small GTPases, SNARE proteins, and vesicle coat proteins. How are these interactions coordinated and are any or all of them important for the tethering process? Progress toward understanding these questions and remaining, unresolved mysteries will be discussed.

  9. Chromatin compaction by condensin I, intra-kinetochore stretch and tension, and anaphase onset, in collective spindle assembly checkpoint interaction

    International Nuclear Information System (INIS)

    Matsson, Leif

    2014-01-01

    The control mechanism in mitosis and meiosis by which cells decide to inhibit or allow segregation, the so-called spindle assembly checkpoint (SAC), increases the fidelity of chromosome segregation. It acts like a clockwork mechanism which measures time in units of stable attachments of microtubules (MTs) to kinetochores (the order parameter). Stable MT–kinetochore attachments mediate poleward forces and ‘unstable’ attachments, acting alone or together with motor proteins on kinetochores via chromosomes, antipoleward forces. Stable and unstable attachments could be separated, and the non-equilibrium integrated MT mediated force acting on stably attached kinetochores was derived in a collective interaction (Matsson 2009 J. Phys.: Condens. Matter 21 502101), in which kinetochores were treated as rigid protein complexes. As forces and tension in that model became equally distributed in all bioriented sister chromatid (SC) pairs, segregation was inhibited without need of a ‘wait-anaphase’ signal. In this generalization, the kinetochore is divided into an inner chromatin proximal complex and an outer MT proximal complex, and the integrated MT mediated force is divided into an integrated poleward and an integrated antipoleward force. The model also describes the collective interaction of condensin I with chromatin, which together with the MT mediated dynamics yields the putative in vivo tension in kinetochores and centromeric and pericentromeric chromatin, as a non-linear function of the order parameter. Supported by the compaction force and an increased stiffness in chromatin towards the end of metaphase, the two opposing integrated MT mediated poleward forces, together with metaphase oscillations, induce a swift and synchronized anaphase onset by first increasing the intra-kinetochore stretch. This increase lowers the SAC energy threshold, making a cleavage by separase of all cohesin tethering SC pairs in anaphase energetically possible, thereby reducing the

  10. HACking the centromere chromatin code: insights from human artificial chromosomes.

    Science.gov (United States)

    Bergmann, Jan H; Martins, Nuno M C; Larionov, Vladimir; Masumoto, Hiroshi; Earnshaw, William C

    2012-07-01

    The centromere is a specialized chromosomal region that serves as the assembly site of the kinetochore. At the centromere, CENP-A nucleosomes form part of a chromatin landscape termed centrochromatin. This chromatin environment conveys epigenetic marks regulating kinetochore formation. Recent work sheds light on the intricate relationship between centrochromatin state, the CENP-A assembly pathway and the maintenance of centromere function. Here, we review the emerging picture of how chromatin affects mammalian kinetochore formation. We place particular emphasis on data obtained from Human Artificial Chromosome (HAC) biology and the targeted engineering of centrochromatin using synthetic HACs. We discuss implications of these findings, which indicate that a delicate balance of histone modifications and chromatin state dictates both de novo centromere formation and the maintenance of centromere identity in dividing cell populations.

  11. Aberrant Chromatin Modification as a Mechanism of Prostate Cancer Progression

    National Research Council Canada - National Science Library

    Chen, Hongwu

    2004-01-01

    .... However, the underlying mechanism is still unclear. The purpose of this study is to test the hypothesis that aberrant chromatin modification plays a critical role in prostate cancer progression...

  12. FACT facilitates chromatin transcription by RNA polymerases I and III

    DEFF Research Database (Denmark)

    Birch, Joanna L; Tan, Bertrand C-M; Panov, Kostya I

    2009-01-01

    Efficient transcription elongation from a chromatin template requires RNA polymerases (Pols) to negotiate nucleosomes. Our biochemical analyses demonstrate that RNA Pol I can transcribe through nucleosome templates and that this requires structural rearrangement of the nucleosomal core particle....... The subunits of the histone chaperone FACT (facilitates chromatin transcription), SSRP1 and Spt16, co-purify and co-immunoprecipitate with mammalian Pol I complexes. In cells, SSRP1 is detectable at the rRNA gene repeats. Crucially, siRNA-mediated repression of FACT subunit expression in cells results...... in a significant reduction in 47S pre-rRNA levels, whereas synthesis of the first 40 nt of the rRNA is not affected, implying that FACT is important for Pol I transcription elongation through chromatin. FACT also associates with RNA Pol III complexes, is present at the chromatin of genes transcribed by Pol III...

  13. Nascent Connections: R-Loops and Chromatin Patterning.

    Science.gov (United States)

    Chédin, Frédéric

    2016-12-01

    RNA molecules, such as long noncoding RNAs (lncRNAs), have critical roles in regulating gene expression, chromosome architecture, and the modification states of chromatin. Recent developments suggest that RNA also influences gene expression and chromatin patterns through the interaction of nascent transcripts with their DNA template via the formation of co-transcriptional R-loop structures. R-loop formation over specific, conserved, hotspots occurs at thousands of genes in mammalian genomes and represents an important and dynamic feature of mammalian chromatin. Here, focusing primarily on mammalian systems, I describe the accumulating connections and possible mechanisms linking R-loop formation and chromatin patterning. The possible contribution of aberrant R-loops to pathological conditions is also discussed. Copyright © 2016 Elsevier Ltd. All rights reserved.

  14. Probing Chromatin-modifying Enzymes with Chemical Tools

    KAUST Repository

    Fischle, Wolfgang

    2016-02-04

    Chromatin is the universal template of genetic information in all eukaryotic organisms. Chemical modifications of the DNA-packaging histone proteins and the DNA bases are crucial signaling events in directing the use and readout of eukaryotic genomes. The enzymes that install and remove these chromatin modifications as well as the proteins that bind these marks govern information that goes beyond the sequence of DNA. Therefore, these so-called epigenetic regulators are intensively studied and represent promising drug targets in modern medicine. We summarize and discuss recent advances in the field of chemical biology that have provided chromatin research with sophisticated tools for investigating the composition, activity, and target sites of chromatin modifying enzymes and reader proteins.

  15. Structure of plant nuclear and ribosomal DNA containing chromatin.

    Science.gov (United States)

    Leber, B; Hemleben, V

    1979-11-10

    Digestion of plant chromatin from Brassica pekinensis and Matthiola incana with staphylococcus nuclease leads to a DNA repeat of 175 plus or minus 8 and a core size of 140 base pairs. DNase I digestion results in multiples of 10 bases. Ribosomal RNN genes were studied as a model system for active plant chromatin because of their great redundancy and their high transcriptional activity in growing and differentiating tissues. The actively transcribed genes were identified by nascent RNA of ribosomal origin still attached to its matrix DNA. Hybridization techniques were used to demonstrate that even transcriptionally active gene sequences are present in nuclease generated chromatin subunits. Comparison of the DNase I kinetics of chromatin digestion with the amount of ribosomal RNA genes which is available for hybridization at the given times indicated that ribosomal RNA genes are digested, but not preferentially degraded by DNase I.

  16. Cytogenetic abnormality in man, wider implications of theories of sex chromatin origin.

    Science.gov (United States)

    MILES, C P

    1962-01-01

    Female nuclei may be identified by means of sex chromatin. In general the number of sex chromatin bodies is one less than the number of X chromosomes. An exception to this rule is a case of sex chromatin-positive XO Turner's syndrome. This case suggests the possibility of sex chromatin-positive XY males, and it may be evidence for chromosomal differentiation.

  17. Single-cell Hi-C bridges microscopy and genome-wide sequencing approaches to study 3D chromatin organization.

    Science.gov (United States)

    Ulianov, Sergey V; Tachibana-Konwalski, Kikue; Razin, Sergey V

    2017-10-01

    Recent years have witnessed an explosion of the single-cell biochemical toolbox including chromosome conformation capture (3C)-based methods that provide novel insights into chromatin spatial organization in individual cells. The observations made with these techniques revealed that topologically associating domains emerge from cell population averages and do not exist as static structures in individual cells. Stochastic nature of the genome folding is likely to be biologically relevant and may reflect the ability of chromatin fibers to adopt a number of alternative configurations, some of which could be transiently stabilized and serve regulatory purposes. Single-cell Hi-C approaches provide an opportunity to analyze chromatin folding in rare cell types such as stem cells, tumor progenitors, oocytes, and totipotent cells, contributing to a deeper understanding of basic mechanisms in development and disease. Here, we review key findings of single-cell Hi-C and discuss possible biological reasons and consequences of the inferred dynamic chromatin spatial organization. © 2017 WILEY Periodicals, Inc.

  18. Chromatin in 3D: progress and prospects for plants.

    Science.gov (United States)

    Liu, Chang; Weigel, Detlef

    2015-08-21

    Methods that use high-throughput sequencing have begun to reveal features of the three-dimensional structure of genomes at a resolution that goes far beyond that of traditional microscopy. Integration of these methods with other molecular tools has advanced our knowledge of both global and local chromatin packing in plants, and has revealed how patterns of chromatin packing correlate with the genomic and epigenomic landscapes. This update reports recent progress made in this area in plants, and suggests new research directions.

  19. Mechanism of chromatin degradation in thymocytes of irradiated rats

    International Nuclear Information System (INIS)

    Nikonova, L.V.; Nelipovich, P.A.; Umanskij, S.R.

    1983-01-01

    Chromatin digestion in isolated thymocyte nuclei with DNAase I, micrococcal nuclease and nuclease from Serratia marcescens was studied. It was shown that 3 h after irradiation (10 Gy), the kinetics of accumulation of acid soluble and salt soluble products of DNA degradation, caused by exogenous nucleases, remains unchanged. The administration of cycloheximide does not influence the sensitivity of chromatin to DNAase I and somewhat increases the rate of salt soluble products formation upon the nuclease from S, marcescens treatment

  20. ATP-Dependent Chromatin Remodeling Factors and Their Roles in Affecting Nucleosome Fiber Composition

    Directory of Open Access Journals (Sweden)

    Alexandra Lusser

    2011-10-01

    Full Text Available ATP-dependent chromatin remodeling factors of the SNF2 family are key components of the cellular machineries that shape and regulate chromatin structure and function. Members of this group of proteins have broad and heterogeneous functions ranging from controlling gene activity, facilitating DNA damage repair, promoting homologous recombination to maintaining genomic stability. Several chromatin remodeling factors are critical components of nucleosome assembly processes, and recent reports have identified specific functions of distinct chromatin remodeling factors in the assembly of variant histones into chromatin. In this review we will discuss the specific roles of ATP-dependent chromatin remodeling factors in determining nucleosome composition and, thus, chromatin fiber properties.

  1. Chromatin modifications and the DNA damage response to ionizing radiation

    International Nuclear Information System (INIS)

    Kumar, Rakesh; Horikoshi, Nobuo; Singh, Mayank; Gupta, Arun; Misra, Hari S.; Albuquerque, Kevin; Hunt, Clayton R.; Pandita, Tej K.

    2013-01-01

    In order to survive, cells have evolved highly effective repair mechanisms to deal with the potentially lethal DNA damage produced by exposure to endogenous as well as exogenous agents. Ionizing radiation exposure induces highly lethal DNA damage, especially DNA double-strand breaks (DSBs), that is sensed by the cellular machinery and then subsequently repaired by either of two different DSB repair mechanisms: (1) non-homologous end joining, which re-ligates the broken ends of the DNA and (2) homologous recombination, that employs an undamaged identical DNA sequence as a template, to maintain the fidelity of DNA repair. Repair of DSBs must occur within the natural context of the cellular DNA which, along with specific proteins, is organized to form chromatin, the overall structure of which can impede DNA damage site access by repair proteins. The chromatin complex is a dynamic structure and is known to change as required for ongoing cellular processes such as gene transcription or DNA replication. Similarly, during the process of DNA damage sensing and repair, chromatin needs to undergo several changes in order to facilitate accessibility of the repair machinery. Cells utilize several factors to modify the chromatin in order to locally open up the structure to reveal the underlying DNA sequence but post-translational modification of the histone components is one of the primary mechanisms. In this review, we will summarize chromatin modifications by the respective chromatin modifying factors that occur during the DNA damage response.

  2. Cytoplasmic chromatin triggers inflammation in senescence and cancer.

    Science.gov (United States)

    Dou, Zhixun; Ghosh, Kanad; Vizioli, Maria Grazia; Zhu, Jiajun; Sen, Payel; Wangensteen, Kirk J; Simithy, Johayra; Lan, Yemin; Lin, Yanping; Zhou, Zhuo; Capell, Brian C; Xu, Caiyue; Xu, Mingang; Kieckhaefer, Julia E; Jiang, Tianying; Shoshkes-Carmel, Michal; Tanim, K M Ahasan Al; Barber, Glen N; Seykora, John T; Millar, Sarah E; Kaestner, Klaus H; Garcia, Benjamin A; Adams, Peter D; Berger, Shelley L

    2017-10-19

    Chromatin is traditionally viewed as a nuclear entity that regulates gene expression and silencing. However, we recently discovered the presence of cytoplasmic chromatin fragments that pinch off from intact nuclei of primary cells during senescence, a form of terminal cell-cycle arrest associated with pro-inflammatory responses. The functional significance of chromatin in the cytoplasm is unclear. Here we show that cytoplasmic chromatin activates the innate immunity cytosolic DNA-sensing cGAS-STING (cyclic GMP-AMP synthase linked to stimulator of interferon genes) pathway, leading both to short-term inflammation to restrain activated oncogenes and to chronic inflammation that associates with tissue destruction and cancer. The cytoplasmic chromatin-cGAS-STING pathway promotes the senescence-associated secretory phenotype in primary human cells and in mice. Mice deficient in STING show impaired immuno-surveillance of oncogenic RAS and reduced tissue inflammation upon ionizing radiation. Furthermore, this pathway is activated in cancer cells, and correlates with pro-inflammatory gene expression in human cancers. Overall, our findings indicate that genomic DNA serves as a reservoir to initiate a pro-inflammatory pathway in the cytoplasm in senescence and cancer. Targeting the cytoplasmic chromatin-mediated pathway may hold promise in treating inflammation-related disorders.

  3. Characterizing the molecular architectures of chromatin-modifying complexes.

    Science.gov (United States)

    Setiaputra, Dheva T; Yip, Calvin K

    2017-11-01

    Eukaryotic cells package their genome in the form of a DNA-protein complex known as chromatin. This organization not only condenses the genome to fit within the confines of the nucleus, but also provides a platform for a cell to regulate accessibility to different gene sequences. The basic packaging element of chromatin is the nucleosome, which consists of 146 base pairs of DNA wrapped around histone proteins. One major means that a cell regulates chromatin structure is by depositing post-translational modifications on nucleosomal histone proteins, and thereby altering internucleosomal interactions and/or binding to different chromatin associated factors. These chromatin modifications are often catalyzed by multi-subunit enzyme complexes, whose large size, sophisticated composition, and inherent conformational flexibility pose significant technical challenges to their biochemical and structural characterization. Multiple structural approaches including nuclear magnetic resonance spectroscopy, X-ray crystallography, single-particle electron microscopy, and crosslinking coupled to mass spectrometry are often used synergistically to probe the overall architecture, subunit organization, and catalytic mechanisms of these macromolecular assemblies. In this review, we highlight several recent chromatin-modifying complexes studies that embodies this multipronged structural approach, and explore common themes amongst them. This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman. Copyright © 2017 Elsevier B.V. All rights reserved.

  4. A chromatin insulator driving three-dimensional Polycomb response element (PRE) contacts and Polycomb association with the chromatin fiber

    DEFF Research Database (Denmark)

    Comet, Itys; Schuettengruber, Bernd; Sexton, Tom

    2011-01-01

    Regulation of gene expression involves long-distance communication between regulatory elements and target promoters, but how this is achieved remains unknown. Insulator elements have been proposed to modulate the communication between regulatory elements and promoters due to their ability to insu...... histone mark reflect this insulator-dependent chromatin conformation, suggesting that Polycomb action at a distance can be organized by local chromatin topology.......Regulation of gene expression involves long-distance communication between regulatory elements and target promoters, but how this is achieved remains unknown. Insulator elements have been proposed to modulate the communication between regulatory elements and promoters due to their ability...... to insulate genes from regulatory elements or to take part in long-distance interactions. Using a high-resolution chromatin conformation capture (H3C) method, we show that the Drosophila gypsy insulator behaves as a conformational chromatin border that is able to prohibit contacts between a Polycomb response...

  5. Recognition imaging of chromatin and chromatin-remodeling complexes in the atomic force microscope.

    Science.gov (United States)

    Lohr, Dennis; Wang, Hongda; Bash, Ralph; Lindsay, Stuart M

    2009-01-01

    Atomic force microscopy (AFM) can directly visualize single molecules in solution, which makes it an extremely powerful technique for carrying out studies of biological complexes and the processes in which they are involved. A recent development, called Recognition Imaging, allows the identification of a specific type of protein in solution AFM images, a capability that greatly enhances the power of the AFM approach for studies of complex biological materials. In this technique, an antibody against the protein of interest is attached to an AFM tip. Scanning a sample with this tip generates a typical topographic image simultaneously and in exact spatial registration with a "recognition image." The latter identifies the locations of antibody-antigen binding events and thus the locations of the protein of interest in the image field. The recognition image can be electronically superimposed on the topographic image, providing a very accurate map of specific protein locations in the topographic image. This technique has been mainly used in in vitro studies of biological complexes and reconstituted chromatin, but has great potential for studying chromatin and protein complexes isolated from nuclei.

  6. Interphase Chromosome Conformation and Chromatin-Chromatin Interactions in Human Epithelial Cells Cultured Under Different Gravity Conditions

    Science.gov (United States)

    Zhang, Ye; Wong, Michael; Hada, Megumi; Wu, Honglu

    2015-01-01

    Microgravity has been shown to alter global gene expression patterns and protein levels both in cultured cells and animal models. It has been suggested that the packaging of chromatin fibers in the interphase nucleus is closely related to genome function, and the changes in transcriptional activity are tightly correlated with changes in chromatin folding. This study explores the changes of chromatin conformation and chromatin-chromatin interactions in the simulated microgravity environment, and investigates their correlation to the expression of genes located at different regions of the chromosome. To investigate the folding of chromatin in interphase under various culture conditions, human epithelial cells, fibroblasts, and lymphocytes were fixed in the G1 phase. Interphase chromosomes were hybridized with a multicolor banding in situ hybridization (mBAND) probe for chromosome 3 which distinguishes six regions of the chromosome as separate colors. After images were captured with a laser scanning confocal microscope, the 3-dimensional structure of interphase chromosome 3 was reconstructed at multi-mega base pair scale. In order to determine the effects of microgravity on chromosome conformation and orientation, measures such as distance between homologous pairs, relative orientation of chromosome arms about a shared midpoint, and orientation of arms within individual chromosomes were all considered as potentially impacted by simulated microgravity conditions. The studies revealed non-random folding of chromatin in interphase, and suggested an association of interphase chromatin folding with radiation-induced chromosome aberration hotspots. Interestingly, the distributions of genes with expression changes over chromosome 3 in cells cultured under microgravity environment are apparently clustered on specific loci and chromosomes. This data provides important insights into how mammalian cells respond to microgravity at molecular level.

  7. The Effect of Tethers on Artificial Cell Membranes: A Coarse-Grained Molecular Dynamics Study.

    Directory of Open Access Journals (Sweden)

    William Hoiles

    Full Text Available Tethered bilayer lipid membranes (tBLMs provide a stable platform for modeling the dynamics and order of biological membranes where the tethers mimic the cytoskeletal supports present in biological cell membranes. In this paper coarse-grained molecular dynamics (CGMD is applied to study the effects of tethers on lipid membrane properties. Using results from the CGMD model and the overdamped Fokker-Planck equation, we show that the diffusion tensor and particle density of water in the tBLM is spatially dependent. Further, it is shown that the membrane thickness, lipid diffusion, defect density, free energy of lipid flip-flop, and membrane dielectric permittivity are all dependent on the tether density. The numerically computed results from the CGMD model are in agreement with the experimentally measured results from tBLMs containing different tether densities and lipids derived from Archaebacteria. Additionally, using experimental measurements from Escherichia coli bacteria and Saccharomyces Cerevisiae yeast tethered membranes, we illustrate how previous molecular dynamics results can be combined with the proposed model to estimate the dielectric permittivity and defect density of these membranes as a function of tether density.

  8. Experimental studies on the human gait using a tethered pelvic assist device (T-PAD).

    Science.gov (United States)

    Vashista, Vineet; Mustafa, S K; Agrawal, Sunil K

    2011-01-01

    This paper presents the prototype of a novel tethered pelvic assist device (T-PAD). This is a purely passive device, consisting of a set of elastic tethers with one end attached to a hip brace worn by a subject walking on a treadmill, and the other end attached to a fixed frame surrounding the subject. T-PAD offers the flexibility of varying the assistance required on the pelvis by changing the configuration of the tether attachment locations, number of tethers and tether elasticity. Experimental studies were conducted using a full and a partial pelvic constraint configuration of T-PAD, with varying tether elasticity. The studies were aimed at observing the effect of T-PAD on the human gait. Results show that T-PAD reduced the range-of-motion for the pelvic angles with increase of tether elasticity. However, it had mixed effects on the range-of-motion of the hip angles, but negligible effect on the knee and ankle joint angles. Overall, T-PAD shows potential as a low-cost pelvic support device with pelvic motion control capabilities, and can work in tandem with existing gait trainers. © 2011 IEEE

  9. The Effect of Tethers on Artificial Cell Membranes: A Coarse-Grained Molecular Dynamics Study.

    Science.gov (United States)

    Hoiles, William; Gupta, Rini; Cornell, Bruce; Cranfield, Charles; Krishnamurthy, Vikram

    2016-01-01

    Tethered bilayer lipid membranes (tBLMs) provide a stable platform for modeling the dynamics and order of biological membranes where the tethers mimic the cytoskeletal supports present in biological cell membranes. In this paper coarse-grained molecular dynamics (CGMD) is applied to study the effects of tethers on lipid membrane properties. Using results from the CGMD model and the overdamped Fokker-Planck equation, we show that the diffusion tensor and particle density of water in the tBLM is spatially dependent. Further, it is shown that the membrane thickness, lipid diffusion, defect density, free energy of lipid flip-flop, and membrane dielectric permittivity are all dependent on the tether density. The numerically computed results from the CGMD model are in agreement with the experimentally measured results from tBLMs containing different tether densities and lipids derived from Archaebacteria. Additionally, using experimental measurements from Escherichia coli bacteria and Saccharomyces Cerevisiae yeast tethered membranes, we illustrate how previous molecular dynamics results can be combined with the proposed model to estimate the dielectric permittivity and defect density of these membranes as a function of tether density.

  10. Electromechanical effects on tether formation from lipid membranes: A theoretical analysis

    Science.gov (United States)

    Glassinger, E.; Lee, A. C.; Raphael, R. M.

    2005-10-01

    The material properties of biomembranes can be measured by forming a tether, a thin bilayer tube that extends from the membrane surface. Recent experiments have demonstrated that the force required to maintain a tether is sensitive to the transmembrane potential. As a first approach towards understanding this phenomenon, a thermodynamic analysis of the influence of electrical fields on tether formation from an aspirated lipid vesicle is developed. The analysis considers contributions from Maxwell stresses as well as two forms of electromechanical coupling: coupling between the electric field and curvature strain (flexoelectric coupling) and between the electric field and areal strain (piezoelectric coupling). Predictions of equilibrium tether conformations are obtained numerically. For expected values of the dimensionless coupling parameters, flexoelectric coupling alters the force required to form a tether of a given length, while piezoelectric coupling and Maxwell forces do not greatly change the force versus tether length behavior. The results of this analysis indicate that tether experiments have the potential to characterize electromechanical coupling in both synthetic and cellular membranes.

  11. Controlled Activation of Protein Rotational Dynamics Using Smart Hydrogel Tethering

    Energy Technology Data Exchange (ETDEWEB)

    Beech, Brenda M.; Xiong, Yijia; Boschek, Curt B.; Baird, Cheryl L.; Bigelow, Diana J.; Mcateer, Kathleen; Squier, Thomas C.

    2014-09-05

    Stimulus-responsive hydrogel materials that stabilize and control protein dynamics have the potential to enable a range of applications to take advantage of the inherent specificity and catalytic efficiencies of proteins. Here we describe the modular construction of a hydrogel using an engineered calmodulin (CaM) within a polyethylene glycol (PEG) matrix that involves the reversible tethering of proteins through an engineered CaM-binding sequence. For these measurements, maltose binding protein (MBP) was isotopically labeled with [13C] and [15N], permitting dynamic structural measurements using TROSY-HSQC NMR spectroscopy. Upon initial formation of hydrogels protein dynamics are suppressed, with concomitant increases in protein stability. Relaxation of the hydrogel matrix following transient heating results in the activation of protein dynamics and restoration of substrate-induced large-amplitude domain motions necessary for substrate binding.

  12. Physisorbed Polymer-Tethered Lipid Bilayer with Lipopolymer Gradient

    Directory of Open Access Journals (Sweden)

    Christoph A. Naumann

    2012-11-01

    Full Text Available Physisorbed polymer-tethered lipid bilayers consisting of phospholipids and lipopolymers represent an attractive planar model membrane platform, in which bilayer fluidity and membrane elastic properties can be regulated through lipopolymer molar concentration. Herein we report a method for the fabrication of such a planar model membrane system with a lateral gradient of lipopolymer density. In addition, a procedure is described, which leads to a sharp boundary between regions of low and high lipopolymer molar concentrations. Resulting gradients and sharp boundaries are visualized on the basis of membrane buckling structures at elevated lipopolymer concentrations using epifluorescence microscopy and atomic force microscopy. Furthermore, results from spot photobleaching experiments are presented, which provide insight into the lipid lateral fluidity in these model membrane architectures. The presented experimental data highlight a planar, solid-supported membrane characterized by fascinating length scale-dependent dynamics and elastic properties with remarkable parallels to those observed in cellular membranes.

  13. DOE Geothermal Data Repository - Tethering Data to Information: Preprint

    Energy Technology Data Exchange (ETDEWEB)

    Weers, J.; Anderson, A.

    2014-02-01

    Data are not inherently information. Without context, data are just numbers, figures, names, or points on a line. By assigning context to data, we can validate ideas, form opinions, and generate knowledge. This is an important distinction to information scientists, as we recognize that the context in which we keep our data plays a big part in generating its value. The mechanisms used to assign this context often include their own data, supplemental to the data being described and defining semantic relationships, commonly referred to as metadata. This paper provides the status of the DOE Geothermal Data Repository (DOE GDR), including recent efforts to tether data submissions to information, discusses the important distinction between data and information, outlines a path to generate useful knowledge from raw data, and details the steps taken in order to become a node on the National Geothermal Data System (NGDS).

  14. Kv7 channels can function without constitutive calmodulin tethering.

    Directory of Open Access Journals (Sweden)

    Juan Camilo Gómez-Posada

    Full Text Available M-channels are voltage-gated potassium channels composed of Kv7.2-7.5 subunits that serve as important regulators of neuronal excitability. Calmodulin binding is required for Kv7 channel function and mutations in Kv7.2 that disrupt calmodulin binding cause Benign Familial Neonatal Convulsions (BFNC, a dominantly inherited human epilepsy. On the basis that Kv7.2 mutants deficient in calmodulin binding are not functional, calmodulin has been defined as an auxiliary subunit of Kv7 channels. However, we have identified a presumably phosphomimetic mutation S511D that permits calmodulin-independent function. Thus, our data reveal that constitutive tethering of calmodulin is not required for Kv7 channel function.

  15. Circular Orbit Target Capture Using Space Tether-Net System

    Directory of Open Access Journals (Sweden)

    Guang Zhai

    2013-01-01

    Full Text Available The space tether-net system for on-orbit capture is proposed in this paper. In order to research the dynamic behaviors during system deployment, both free and nonfree deployment dynamics in circular orbit are developed; the system motion with respect to Local Vertical and Local Horizontal frame is also researched with analysis and simulation. The results show that in the case of free deployment, the capture net follows curve trajectories due to the relative orbit dynamic perturbation, and the initial deployment velocities are planned by state transformation equations for static and floating target captures; in the case of non-free deployment, the system undergoes an altitude libration along the Local Vertical, and the analytical solutions that describe the attitude libration are obtained by using variable separation and integration. Finally, the dynamics of postdeployment system is also proved marginally stable if the critical initial conditions are satisfied.

  16. Reconstitution of Cholesterol-Dependent Vaginolysin into Tethered Phospholipid Bilayers

    DEFF Research Database (Denmark)

    Budvytyte, Rima; Pleckaityte, M.; Zvirbliene, A.

    2013-01-01

    Functional reconstitution of the cholesterol-dependent cytolysin vaginolysin (VLY) from Gardnerella vaginalis into artificial tethered bilayer membranes (tBLMs) has been accomplished. The reconstitution of VLY was followed in real-time by electrochemical impedance spectroscopy (EIS). Changes...... of the EIS parameters of the tBLMs upon exposure to VLY solutions were consistent with the formation of water-filled pores in the membranes. It was found that reconstitution of VLY is a strictly cholesterol-dependent, irreversible process. At a constant cholesterol concentration reconstitution of VLY...... substitutions led to noticeably lesser tBLM damage. Pre-incubation of VLY with the neutralizing monoclonal antibody 9B4 inactivated the VLY membrane damage in a concentration-dependent manner, while the non-neutralizing antibody 21A5 exhibited no effect. These findings demonstrate the biological relevance...

  17. Experiments and simulation of a net closing mechanism for tether-net capture of space debris

    Science.gov (United States)

    Sharf, Inna; Thomsen, Benjamin; Botta, Eleonora M.; Misra, Arun K.

    2017-10-01

    This research addresses the design and testing of a debris containment system for use in a tether-net approach to space debris removal. The tether-net active debris removal involves the ejection of a net from a spacecraft by applying impulses to masses on the net, subsequent expansion of the net, the envelopment and capture of the debris target, and the de-orbiting of the debris via a tether to the chaser spacecraft. To ensure a debris removal mission's success, it is important that the debris be successfully captured and then, secured within the net. To this end, we present a concept for a net closing mechanism, which we believe will permit consistently successful debris capture via a simple and unobtrusive design. This net closing system functions by extending the main tether connecting the chaser spacecraft and the net vertex to the perimeter and around the perimeter of the net, allowing the tether to actuate closure of the net in a manner similar to a cinch cord. A particular embodiment of the design in a laboratory test-bed is described: the test-bed itself is comprised of a scaled-down tether-net, a supporting frame and a mock-up debris. Experiments conducted with the facility demonstrate the practicality of the net closing system. A model of the net closure concept has been integrated into the previously developed dynamics simulator of the chaser/tether-net/debris system. Simulations under tether tensioning conditions demonstrate the effectiveness of the closure concept for debris containment, in the gravity-free environment of space, for a realistic debris target. The on-ground experimental test-bed is also used to showcase its utility for validating the dynamics simulation of the net deployment, and a full-scale automated setup would make possible a range of validation studies of other aspects of a tether-net debris capture mission.

  18. Heterobifunctional crosslinkers for tethering single ligand molecules to scanning probes

    International Nuclear Information System (INIS)

    Riener, Christian K.; Kienberger, Ferry; Hahn, Christoph D.; Buchinger, Gerhard M.; Egwim, Innocent O.C.; Haselgruebler, Thomas; Ebner, Andreas; Romanin, Christoph; Klampfl, Christian; Lackner, Bernd; Prinz, Heino; Blaas, Dieter; Hinterdorfer, Peter; Gruber, Hermann J.

    2003-01-01

    Single molecule recognition force microscopy (SMRFM) is a versatile atomic force microscopy (AFM) method to probe specific interactions of cognitive molecules on the single molecule level. It allows insights to be gained into interaction potentials and kinetic barriers and is capable of mapping interaction sites with nm positional accuracy. These applications require a ligand to be attached to the AFM tip, preferably by a distensible poly(ethylene glycol) (PEG) chain between the measuring tip and the ligand molecule. The PEG chain greatly facilitates specific binding of the ligand to immobile receptor sites on the sample surface. The present study contributes to tip-PEG-ligand tethering in three ways: (i) a convenient synthetic route was found to prepare NH 2 -PEG-COOH which is the key intermediate for long heterobifunctional crosslinkers; (ii) a variety of heterobifunctional PEG derivatives for tip-PEG-ligand linking were prepared from NH 2 -PEG-COOH; (iii) in particular, a new PEG crosslinker with one thiol-reactive end and one terminal nitrilotriacetic acid (NTA) group was synthesized and successfully used to tether His 6 -tagged protein molecules to AFM tips via noncovalent NTA-Ni 2+ -His 6 bridges. The new crosslinker was applied to link a recombinant His 6 -tagged fragment of the very-low density lipoprotein receptor to the AFM tip whereupon specific docking to the capsid of human rhinovirus particles was observed by force microscopy. In a parallel study, the specific interaction of the small GTPase Ran with the nuclear import receptor importin β1 was studied in detail by SMRFM, using the new crosslinker to link His 6 -tagged Ran to the measuring tip [Nat. Struct. Biol. (2003), 10, 553-557

  19. Minimally invasive tethered cord release in children: A technical note

    Directory of Open Access Journals (Sweden)

    S. Kağan Başarslan

    2014-03-01

    Full Text Available Tethered cord release is commonly performed in pediatric neurosurgery. Nowadays, minimally invasive procedures are created growing interest due to its highly tolerable nature for surgery. It has been main purpose a minimal damaging on access route and maximum protection of normal structures in surgery. We present a surgical treatment of tethered cord syndrome, by which is provided the cord releasing unlike the many methods being applied with tissue removal. The main advantage of performing this surgery through 2 cm hole is to avoid removing ligamentum flavum and bony structure like lamina in addition to reduce the length of the incision and the related scar tissue. J Clin Exp Invest 2014; 5 (1: 115-117 Technical note: the patient was taken on the operating table in the sitting-prone position, and L5-S1 distance was determined by fluoroscopy. The skin and subcutaneous tissues was passed via a 2 cm vertical incision settled in 0.5 cm laterally from midline. L5-S1 distance and its covering ligamentum flavum are displayed by the guidance of L5 lamina. Williams’s retractor was placed in the distance after fetching microscope. The foregoing procedures are the same with microdiscectomic surgery. By a vertical incision made on the flavum, its both layer was lifted up and hanged with simple suture on the back tissue for a comfortable exposure of the Dura. Thecal sac was opened by 0.5 cm long vertical incision on the Dura after obtaining secure CSF drainage with the help of yellow-tipped syringe needle. With finding by a nerve hook, the phylum was burned and released securely. Then the Dura was sutured primarily for the closure by means of microsurgery instruments, and flavum was laid on it again.

  20. Tethered ribozyme ligation enables detection of molecular proximity in homogeneous solutions.

    Science.gov (United States)

    Katzman, Bella; Vyazmensky, Maria; Press, Olga; Volokita, Micha; Engel, Stanislav

    2015-03-01

    In contemporary drug discovery, bulk selection represents an important alternative to time consuming and expensive high-throughput screening. The selection methods, however, generally rely on affinity separation, a step that limits overall selection process efficiency. To overcome common drawbacks of conventional methods, we exploited the unique catalytic properties of an artificial enzyme, ribozyme ligase, to develop a selection methodology in which the entire detection process takes place in a homogeneous solution, thus eliminating the need for affinity separation. A molecular target is associated with the ribozyme, and library compounds are attached to a barcoded oligonucleotide that is a substrate for the ribozyme ligase. Spatial proximity resulting from specific target-compound interactions increases the probability of ribozyme ligation to the oligo-substrate, thus differentiating the interacting species from the bulk mixture. The covalent link formed between the ribozyme and target-interacting compounds diminishes the mass-action effect on the efficiency with which low-affinity and rare active species are detected. In addition, the magnitude of the detection signal associated with the interaction event renders the methodology an efficient platform for identifying inhibitors of intermolecular interactions. The proposed solution-based tethered ribozyme-ligation proximity detection method may facilitate the discovery of target-interacting compounds using both library selection and high-throughput screening approaches. Copyright © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. Cytoplasmic tethering of a RING protein RBCK1 by its splice variant lacking the RING domain

    International Nuclear Information System (INIS)

    Yoshimoto, Nobuo; Tatematsu, Kenji; Koyanagi, Tomoyoshi; Okajima, Toshihide; Tanizawa, Katsuyuki; Kuroda, Shun'ichi

    2005-01-01

    RBCC protein interacting with PKC 1 (RBCK1) is a transcription factor belonging to the RING-IBR protein family and has been shown to shuttle between the nucleus and cytoplasm, possessing both the nuclear export and localization signals within its amino acid sequence. RBCK2, lacking the C-terminal half of RBCK1 including the RING-IBR domain, has also been identified as an alternative splice variant of RBCK1. RBCK2 shows no transcriptional activity and instead it represses the transcriptional activity of RBCK1. Here, we show that RBCK2 is present usually in the cytoplasm containing two Leu-rich regions that presumably serve as a nuclear export signal (NES). Moreover, an NES-disrupted RBCK1 that is mostly localized within the nucleus is translocated to the cytoplasm when coexpressed with RBCK2, suggesting that RBCK2 serves as a cytoplasmic tethering protein for RBCK1. We propose a novel and general function of RING-lacking splice variants of RING proteins to control the intracellular localization and functions of the parental RING proteins by forming a hetero-oligomeric complex

  2. Catalyst system comprising a first catalyst system tethered to a supported catalyst

    Science.gov (United States)

    Angelici, Robert J.; Gao, Hanrong

    1998-08-04

    The present invention provides new catalyst formats which comprise a supported catalyst tethered to a second and different catalyst by a suitable tethering ligand. A preferred system comprises a heterogeneous supported metal catalyst tethered to a homogeneous catalyst. This combination of homogeneous and heterogeneous catalysts has a sufficient lifetime and unusually high catalytic activity in arene hydrogenations, and potentially many other reactions as well, including, but not limited to hydroformylation, hydrosilation, olefin oxidation, isomerization, hydrocyanation, olefin metathesis, olefin polymerization, carbonylation, enantioselective catalysis and photoduplication. These catalysts are easily separated from the products, and can be reused repeatedly, making these systems very economical.

  3. Electron Emitter for small-size Electrodynamic Space Tether using MEMS Technology

    DEFF Research Database (Denmark)

    Fleron, René A. W.; Blanke, Mogens

    2004-01-01

    system with focus on electron emitter design and manufacture using micro-electro-mechanical- system (MEMS) technology. The paper addresses the system concepts of a small size electrodynamic tether mission and shows a novel electron emitter for the 1-2 mA range where altitude can be effectively affected...... and the current flowing in the electrodynamic space tether. Applications to small spacecraft, or space debris in the 1–10 kg range, possess difficulties with electron emission technology, as low power emitting devices are needed. This paper addresses the system concepts of a small spacecraft electrodynamic tether...

  4. The protein encoded by the proto-oncogene DEK changes the topology of chromatin and reduces the efficiency of DNA replication in a chromatin-specific manner

    DEFF Research Database (Denmark)

    Alexiadis, V; Waldmann, T; Andersen, Jens S.

    2000-01-01

    The structure of chromatin regulates the genetic activity of the underlying DNA sequence. We report here that the protein encoded by the proto-oncogene DEK, which is involved in acute myelogenous leukemia, induces alterations of the superhelical density of DNA in chromatin. The change in topology...... protein substantially reduces the replication efficiency of chromatin but not of naked DNA templates....

  5. ISWI chromatin remodellers sense nucleosome modifications to determine substrate preference

    Science.gov (United States)

    Dann, Geoffrey P.; Liszczak, Glen P.; Bagert, John D.; Müller, Manuel M.; Nguyen, Uyen T. T.; Wojcik, Felix; Brown, Zachary Z.; Bos, Jeffrey; Panchenko, Tatyana; Pihl, Rasmus; Pollock, Samuel B.; Diehl, Katharine L.; Allis, C. David; Muir, Tom W.

    2018-01-01

    ATP-dependent chromatin remodellers regulate access to genetic information by controlling nucleosome positions in vivo1. However, the mechanism by which remodellers discriminate between different nucleosome substrates is poorly understood. Many chromatin remodelling proteins possess conserved protein domains that interact with nucleosomal features2. Here we used a quantitative high-throughput approach, based on the use of a DNA-barcoded mononucleosome library, to profile the biochemical activity of human ISWI family remodellers in response to a diverse set of nucleosome modifications. We show that accessory (non-ATPase) subunits of ISWI remodellers can distinguish between differentially modified nucleosomes, directing remodelling activity towards specific nucleosome substrates according to their modification state. Unexpectedly, we show that the nucleosome acidic patch3 is necessary for maximum activity of all ISWI remodellers evaluated. This dependence also extends to CHD and SWI/SNF family remodellers, suggesting that the acidic patch may be generally required for chromatin remodelling. Critically, remodelling activity can be regulated by modifications neighbouring the acidic patch, signifying that it may act as a tunable interaction hotspot for ATP-dependent chromatin remodellers and, by extension, many other chromatin effectors that engage this region of the nucleosome surface4–9. PMID:28767641

  6. Micron-scale coherence in interphase chromatin dynamics.

    Science.gov (United States)

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

    2013-09-24

    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.

  7. Parallel Evolution of Chromatin Structure Underlying Metabolic Adaptation.

    Science.gov (United States)

    Cheng, Jian; Guo, Xiaoxian; Cai, Pengli; Cheng, Xiaozhi; Piškur, Jure; Ma, Yanhe; Jiang, Huifeng; Gu, Zhenglong

    2017-11-01

    Parallel evolution occurs when a similar trait emerges in independent evolutionary lineages. Although changes in protein coding and gene transcription have been investigated as underlying mechanisms for parallel evolution, parallel changes in chromatin structure have never been reported. Here, Saccharomyces cerevisiae and a distantly related yeast species, Dekkera bruxellensis, are investigated because both species have independently evolved the capacity of aerobic fermentation. By profiling and comparing genome sequences, transcriptomic landscapes, and chromatin structures, we revealed that parallel changes in nucleosome occupancy in the promoter regions of mitochondria-localized genes led to concerted suppression of mitochondrial functions by glucose, which can explain the metabolic convergence in these two independent yeast species. Further investigation indicated that similar mutational processes in the promoter regions of these genes in the two independent evolutionary lineages underlay the parallel changes in chromatin structure. Our results indicate that, despite several hundred million years of separation, parallel changes in chromatin structure, can be an important adaptation mechanism for different organisms. Due to the important role of chromatin structure changes in regulating gene expression and organism phenotypes, the novel mechanism revealed in this study could be a general phenomenon contributing to parallel adaptation in nature. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  8. Systematic Epigenomic Analysis Reveals Chromatin States Associated with Melanoma Progression.

    Science.gov (United States)

    Fiziev, Petko; Akdemir, Kadir C; Miller, John P; Keung, Emily Z; Samant, Neha S; Sharma, Sneha; Natale, Christopher A; Terranova, Christopher J; Maitituoheti, Mayinuer; Amin, Samirkumar B; Martinez-Ledesma, Emmanuel; Dhamdhere, Mayura; Axelrad, Jacob B; Shah, Amiksha; Cheng, Christine S; Mahadeshwar, Harshad; Seth, Sahil; Barton, Michelle C; Protopopov, Alexei; Tsai, Kenneth Y; Davies, Michael A; Garcia, Benjamin A; Amit, Ido; Chin, Lynda; Ernst, Jason; Rai, Kunal

    2017-04-25

    The extent and nature of epigenomic changes associated with melanoma progression is poorly understood. Through systematic epigenomic profiling of 35 epigenetic modifications and transcriptomic analysis, we define chromatin state changes associated with melanomagenesis by using a cell phenotypic model of non-tumorigenic and tumorigenic states. Computation of specific chromatin state transitions showed loss of histone acetylations and H3K4me2/3 on regulatory regions proximal to specific cancer-regulatory genes in important melanoma-driving cell signaling pathways. Importantly, such acetylation changes were also observed between benign nevi and malignant melanoma human tissues. Intriguingly, only a small fraction of chromatin state transitions correlated with expected changes in gene expression patterns. Restoration of acetylation levels on deacetylated loci by histone deacetylase (HDAC) inhibitors selectively blocked excessive proliferation in tumorigenic cells and human melanoma cells, suggesting functional roles of observed chromatin state transitions in driving hyperproliferative phenotype. Through these results, we define functionally relevant chromatin states associated with melanoma progression. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

  9. SMC complexes orchestrate the mitotic chromatin interaction landscape.

    Science.gov (United States)

    Kakui, Yasutaka; Uhlmann, Frank

    2017-09-21

    Chromatin is a very long DNA-protein complex that controls the expression and inheritance of the genetic information. Chromatin is stored within the nucleus in interphase and further compacted into chromosomes during mitosis. This process, known as chromosome condensation, is essential for faithful segregation of genomic DNA into daughter cells. Condensin and cohesin, members of the structural maintenance of chromosomes (SMC) family, are fundamental for chromosome architecture, both for establishment of chromatin structure in the interphase nucleus and for the formation of condensed chromosomes in mitosis. These ring-shaped SMC complexes are thought to regulate the interactions between DNA strands by topologically entrapping DNA. How this activity shapes chromosomes is not yet understood. Recent high throughput chromosome conformation capture studies revealed how chromatin is reorganized during the cell cycle and have started to explore the role of SMC complexes in mitotic chromatin architecture. Here, we summarize these findings and discuss the conserved nature of chromosome condensation in eukaryotes. We highlight the unexpected finding that condensin-dependent intra-chromosomal interactions in mitosis increase within a distinctive distance range that is characteristic for an organism, while longer and shorter-range interactions are suppressed. This reveals important molecular insight into chromosome architecture.

  10. Plant programmed cell death from a chromatin point of view.

    Science.gov (United States)

    Latrasse, D; Benhamed, M; Bergounioux, C; Raynaud, C; Delarue, M

    2016-10-01

    Programmed cell death (PCD) is a ubiquitous genetically regulated process consisting of the activation of finely controlled signalling pathways that lead to cellular suicide. PCD can be part of a developmental programme (dPCD) or be triggered by environmental conditions (ePCD). In plant cells, as in animal cells, extensive chromatin condensation and degradation of the nuclear DNA are among the most conspicuous features of cells undergoing PCD. Changes in chromatin condensation could either reflect the structural changes required for internucleosomal fragmentation of nuclear DNA or relate to large-scale chromatin rearrangements associated with a major transcriptional switch occurring during cell death. The aim of this review is to give an update on plant PCD processes from a chromatin point of view. The first part will be dedicated to chromatin conformational changes associated with cell death observed in various developmental and physiological conditions, whereas the second part will be devoted to histone dynamics and DNA modifications associated with critical changes in genome expression during the cell death process. © The Author 2016. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  11. Deciphering Noncoding RNA and Chromatin Interactions: Multiplex Chromatin Interaction Analysis by Paired-End Tag Sequencing (mChIA-PET).

    Science.gov (United States)

    Choy, Jocelyn; Fullwood, Melissa J

    2017-01-01

    Genomic DNA is dynamically associated with protein factors and folded to form chromatin fibers. The 3-dimensional (3D) configuration of the chromatin will enable the distal genetic elements to come into close proximity, allowing transcriptional regulation. Noncoding RNA can mediate the 3D structure of chromatin. Chromatin Interaction Analysis by Paired-End Tag Sequencing (ChIA-PET) is a valuable and powerful technique in molecular biology which allows the study of unbiased, genome-wide de novo chromatin interactions with paired-end tags. Here, we describe the standard version of ChIA-PET and a Multiplex ChIA-PET version.

  12. Development of a Tethered Formation Flight Testbed for ISS, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — The development of a testbed for the development and demonstration of technologies needed by tethered formation flying satellites is proposed. Such a testbed would...

  13. UV-Curable Hybrid Nanocomposite Coating to Protect Tether Polymer Materials, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — To address the NASA need for coatings to protect and strengthen tether materials for Momentum-exchange Electrodynamic Reboost (MXER) technology, Luminit, LLC,...

  14. The motion and control of a complex three-body space tethered system

    Science.gov (United States)

    Shi, Gefei; Zhu, Zhanxia; Chen, Shiyu; Yuan, Jianping; Tang, Biwei

    2017-11-01

    This paper is mainly devoted to investigating the dynamics and stability control of a three body-tethered satellite system which contains a main satellite and two subsatellites connected by two straight, massless and inextensible tethers. Firstly, a detailed mathematical model is established in the central gravitational field. Then, the dynamic characteristics of the established system are investigated and analyzed. Based on the dynamic analysis, a novel sliding mode prediction model (SMPM) control strategy is proposed to suppress the motion of the built tethered system. The numerical results show that the proposed underactuated control law is highly effective in suppressing the attitude/libration motion of the underactuated three-body tethered system. Furthermore, cases of different target angles are also examined and analyzed. The simulation results reveal that even if the final equilibrium states differ from different selections of the target angles, the whole system can still be maintained in acceptable areas.

  15. An Effective Approach Control Scheme for the Tethered Space Robot System

    Directory of Open Access Journals (Sweden)

    Zhongjie Meng

    2014-09-01

    Full Text Available The tethered space robot system (TSR, which is composed of a platform, a gripper and a space tether, has great potential in future space missions. Given the relative motion among the platform, tether, gripper and the target, an integrated approach model is derived. Then, a novel coordinated approach control scheme is presented, in which the tether tension, thrusters and the reaction wheel are all utilized. It contains the open-loop trajectory optimization, the feedback trajectory control and attitude control. The numerical simulation results show that the rendezvous between TSR and the target can be realized by the proposed coordinated control scheme, and the propellant consumption is efficiently reduced. Moreover, the control scheme performs well in the presence of the initial state's perturbations, actuator characteristics and sensor errors.

  16. Advanced Particle-in-Cell (PIC) Tools for Simulation of Electrodynamic Tether Plasma Interactions, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — Electrodynamic tethers are optimally suited for use in Low-Earth-Orbit (LEO) to generate thrust or drag maneuver satellites. LEO region is polluted with space debris...

  17. Materials for advancement of MXER tether design (1000-371), Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — There exist a need to develop, identify, and classify various materials that can be used in the fabrication of electrodynamic tethers for various applications. These...

  18. UV-Curable Hybrid Nanocomposite Coating to Protect Tether Polymer Materials Project

    Data.gov (United States)

    National Aeronautics and Space Administration — To address the NASA need for coatings to protect and strengthen tether materials for Momentum-exchange Electrodynamic Reboost (MXER) technology, Luminit, LLC,...

  19. Myocardial Infarction Alters Adaptation of the Tethered Mitral Valve

    NARCIS (Netherlands)

    Dal-Bianco, Jacob P; Aikawa, Elena; Bischoff, Joyce; Guerrero, J Luis; Hjortnaes, Jesper; Beaudoin, Jonathan; Szymanski, Catherine; Bartko, Philipp E; Seybolt, Margo M; Handschumacher, Mark D; Sullivan, Suzanne; Garcia, Michael L; Mauskapf, Adam; Titus, James S; Wylie-Sears, Jill; Irvin, Whitney S; Chaput, Miguel; Messas, Emmanuel; Hagège, Albert A; Carpentier, Alain; Levine, Robert A

    2016-01-01

    BACKGROUND: In patients with myocardial infarction (MI), leaflet tethering by displaced papillary muscles induces mitral regurgitation (MR), which doubles mortality. Mitral valves (MVs) are larger in such patients but fibrosis sets in counterproductively. The investigators previously reported that

  20. Materials for Advancement of MXER Tether Design (1000-549), Phase II

    Data.gov (United States)

    National Aeronautics and Space Administration — There exist a need to develop, identify, and classify various materials that can be used in the fabrication of electrodynamic tethers for various applications. These...

  1. Significance of relative velocity in drag force or drag power estimation for a tethered float

    Digital Repository Service at National Institute of Oceanography (India)

    Vethamony, P.; Sastry, J.S.

    There is difference in opinion regarding the use of relative velocity instead of particle velocity alone in the estimation of drag force or power. In the present study, a tethered spherical float which undergoes oscillatory motion in regular waves...

  2. Investigation of electrodynamic stabilization and control of long orbiting tethers. [space shuttle payloads

    Science.gov (United States)

    Arnold, D. A.; Dobrowolny, M.

    1981-01-01

    An algorithm for using electric currents to control pendular oscillations induced by various perturbing forces on the Skyhook wire is considered. Transverse and vertical forces on the tether; tether instability modes and causes during retrieval by space shuttle; simple and spherical pendulum motion and vector damping; and current generation and control are discussed. A computer program for numerical integration of the in-plane and out-of-plane displacements of the tether vs time was developed for heuristic study. Some techniques for controlling instabilities during payload retrieval and methods for employing the tether for launching satellites from the space shuttle are considered. Derivations and analyses of a general nature used in all of the areas studied are included.

  3. The formation and modification of chromatin-like structure of human parvovirus B19 regulate viral genome replication and RNA processing.

    Science.gov (United States)

    Xu, Huanzhou; Hao, Sujuan; Zhang, Junmei; Chen, Zhen; Wang, Hanzhong; Guan, Wuxiang

    2017-03-15

    B19 virus (B19V) is a single stranded virus in the genus of Erythroparvovirus in the family of Parvoviridae. One of the limiting steps of B19V infection is the replication of viral genome which affected the alternative processing of its RNA. Minute virus of mice (MVM) and adeno-associated virus (AAV) has been reported to form chromatin-like structure within hours after infection of cells. However, the role of chromatin-like structure is unclear. In the present study, we found that B19V formed chromatin-like structure after 12h when B19V infectious clone was co-transfected with pHelper plasmid to HEK293T cells. Interestingly, the inhibitor of DNA methyl-transferase (5-Aza-2'-deoxycytidine, DAC) inhibited not only the formation of chromatin-like structure, but also the replication of the viral genomic DNA. More importantly, the splicing of the second intron at splice acceptor sites (A2-1, and A2-2) were reduced and polyadenylation at (pA)p increased when transfected HEK293T cells were treated with DAC. Our results showed that the formation and modification of chromatin-like structure are a new layer to regulate B19V gene expression and RNA processing. Copyright © 2017 Elsevier B.V. All rights reserved.

  4. Evaluation of gram stain as an alternative in the assessment of human spermatozoa quality.

    Science.gov (United States)

    Mantas, D; Msaouel, P; Angelopoulou, R

    2006-01-01

    During spermiogenesis, protaminosis and sperm chromatin condensation are important prerequisites for the preservation of DNA integrity in spermatozoa. The aim of this study is to assess Gram stain as an alternative technique for the evaluation of human sperm chromatin condensation status. Aniline blue and Gram staining were applied to semen samples from 34 donors in order to determine the relationship between sperm chromatin condensation and infertility. In addition, the possible correlation between morphology and vitality (eosin-Y staining) of spermatozoa compared with their nuclear status (aniline blue and Gram staining) was studied. Chromatin condensation and sperm vitality were significantly higher in fertile men compared to the subfertile. A significant correlation was found between chromatin condensation and (a) sperm vitality (p Gram staining may be used as a routine method in assisted reproduction laboratories and could assist in the evaluation of sperm quality as well as in the selection of the appropriate fertilization technique.

  5. Cryo?electron tomography reveals a critical role of RIM1? in synaptic vesicle tethering

    OpenAIRE

    Fern?ndez-Busnadiego, Rub?n; Asano, Shoh; Oprisoreanu, Ana-Maria; Sakata, Eri; Doengi, Michael; Kochovski, Zdravko; Z?rner, Magdalena; Stein, Valentin; Schoch, Susanne; Baumeister, Wolfgang; Lu?i?, Vladan

    2013-01-01

    Synaptic vesicles are embedded in a complex filamentous network at the presynaptic terminal. Before fusion, vesicles are linked to the active zone (AZ) by short filaments (tethers). The identity of the molecules that form and regulate tethers remains unknown, but Rab3-interacting molecule (RIM) is a prominent candidate, given its central role in AZ organization. In this paper, we analyzed presynaptic architecture of RIM1? knockout (KO) mice by cryo?electron tomography. In stark contrast to pr...

  6. Optimal Trajectory Planning and Coordinated Tracking Control Method of Tethered Space Robot Based on Velocity Impulse

    OpenAIRE

    Huang, Panfeng; Xu, Xiudong; Meng, Zhongjie

    2014-01-01

    The tethered space robot (TSR) is a new concept of space robot which consists of a robot platform, space tether and operation robot. This paper presents a multi-objective optimal trajectory planning and a coordinated tracking control scheme for TSR based on velocity impulse in the approaching phase. Both total velocity impulse and flight time are included in this optimization. The non-dominated sorting genetic algorithm is employed to obtain the optimal trajectory Pareto solution using the TS...

  7. Evaluation of Power Conversion on Heavy Payload Tethered Hexarotors: A Strategic Approach

    OpenAIRE

    Wasantha Samarathunga; Guangwei Wang

    2015-01-01

    This research article addresses the evaluation of power conversion on heavy payload tethered hexarotors where the payloads are high and hovering times are long. Modifications were added to the power conversion unit based on operation reliability perspective. Since the objective power conversion is large comparing to existing tethered UAVs today, a strategic engineering approach was proposed and tested based on partial observations on current spikes and power thresholds of DCDC swi...

  8. Simulation of a tethered microgravity robot pair and validation on a planar air bearing

    Science.gov (United States)

    Mantellato, R.; Lorenzini, E. C.; Sternberg, D.; Roascio, D.; Saenz-Otero, A.; Zachrau, H. J.

    2017-09-01

    A software model has been developed to simulate the on-orbit dynamics of a dual-mass tethered system where one or both of the tethered spacecraft are able to produce propulsive thrust. The software simulates translations and rotations of both spacecraft, with the visco-elastic tether being simulated as a lumped-mass model. Thanks to this last feature, tether longitudinal and lateral modes of vibration and tether tension can be accurately assessed. Also, the way the spacecraft motion responds to sudden tether tension spikes can be studied in detail. The code enables the simulation of different scenarios, including space tug missions for deorbit maneuvers in a debris mitigation context and general-purpose tethered formation flight missions. This study aims to validate the software through a representative test campaign performed with the MIT Synchronized Position Hold Engage and Reorient Experimental Satellites (SPHERES) planar air bearing system. Results obtained with the numerical simulator are compared with data from direct measurements in different testing setups. The studied cases take into account different initial conditions of the spacecraft velocities and relative attitudes, and thrust forces. Data analysis is presented comparing the results of the simulations with direct measurements of acceleration and Azimuth rate of the two bodies in the planar air bearing test facility using a Nylon tether. Plans for conducting a microgravity test campaign using the SPHERES satellites aboard the International Space Station are also being scheduled in the near future in order to further validate the simulation using data from the relevant operational environment of extended microgravity with full six degree of freedom (per body) motion.

  9. Alternative security

    International Nuclear Information System (INIS)

    Weston, B.H.

    1990-01-01

    This book contains the following chapters: The Military and Alternative Security: New Missions for Stable Conventional Security; Technology and Alternative Security: A Cherished Myth Expires; Law and Alternative Security: Toward a Just World Peace; Politics and Alternative Security: Toward a More Democratic, Therefore More Peaceful, World; Economics and Alternative Security: Toward a Peacekeeping International Economy; Psychology and Alternative Security: Needs, Perceptions, and Misperceptions; Religion and Alternative Security: A Prophetic Vision; and Toward Post-Nuclear Global Security: An Overview

  10. Chromatin Regulation and the Histone Code in HIV Latency
.

    Science.gov (United States)

    Turner, Anne-Marie W; Margolis, David M

    2017-06-01

    The formation of a latent reservoir of Human Immunodeficiency Virus (HIV) infection hidden from immune clearance remains a significant obstacle to approaches to eradicate HIV infection. Towards an understanding of the mechanisms of HIV persistence, there is a growing body of work implicating epigenetic regulation of chromatin in establishment and maintenance of this latent reservoir. Here we discuss recent advances in the field of chromatin regulation, specifically in our understanding of the histone code, and how these discoveries relate to our current knowledge of the chromatin mechanisms linked to HIV transcriptional repression and the reversal of latency. We also examine mechanisms unexplored in the context of HIV latency and briefly discuss current therapies aimed at the induction of proviral expression within latently infected cells. We aim to emphasize that a greater understanding of the epigenetic mechanisms which govern HIV latency could lead to new therapeutic targets for latency reversal and clearance cure strategies.

  11. Defining B Cell Chromatin: Lessons from EBF1.

    Science.gov (United States)

    Boller, Sören; Li, Rui; Grosschedl, Rudolf

    2018-04-01

    Hematopoiesis is regulated by signals from the microenvironment, transcription factor networks, and changes of the epigenetic landscape. Transcription factors interact with and shape chromatin to allow for lineage- and cell type-specific changes in gene expression. During B lymphopoiesis, epigenetic regulation is observed in multilineage progenitors in which a specific chromatin context is established, at the onset of the B cell differentiation when early B cell factor 1 (EBF1) induces lineage-specific changes in chromatin, during V(D)J recombination and after antigen-driven activation of B cells and terminal differentiation. In this review, we discuss the epigenetic changes underlying B cell differentiation, focusing on the role of transcription factor EBF1 in B cell lineage priming. Copyright © 2018 Elsevier Ltd. All rights reserved.

  12. chromswitch: A flexible method to detect chromatin state switches.

    Science.gov (United States)

    Jessa, Selin; Kleinman, Claudia L

    2018-02-09

    Chromatin state plays a major role in controlling gene expression, and comparative analysis of ChIP-seq data is key to understanding epigenetic regulation. We present chromswitch, an R/Bioconductor package to integrate epigenomic data in a defined window of interest to detect an overall switch in chromatin state. Chromswitch accurately classifies a benchmarking dataset, and when applied genome-wide, the tool successfully detects chromatin changes that result in brain-specific expression. Chromswitch is implemented as an R package available from Bioconductor at https://bioconductor.org/packages/chromswitch. claudia.kleinman@mcgill.ca. Supplementary material are available online. All data and code for the analysis presented in this paper are available at https://doi.org/10.5281/zenodo.1101260.

  13. Oxidative stress signaling to chromatin in health and disease

    KAUST Repository

    Kreuz, Sarah

    2016-06-20

    Oxidative stress has a significant impact on the development and progression of common human pathologies, including cancer, diabetes, hypertension and neurodegenerative diseases. Increasing evidence suggests that oxidative stress globally influences chromatin structure, DNA methylation, enzymatic and non-enzymatic post-translational modifications of histones and DNA-binding proteins. The effects of oxidative stress on these chromatin alterations mediate a number of cellular changes, including modulation of gene expression, cell death, cell survival and mutagenesis, which are disease-driving mechanisms in human pathologies. Targeting oxidative stress-dependent pathways is thus a promising strategy for the prevention and treatment of these diseases. We summarize recent research developments connecting oxidative stress and chromatin regulation.

  14. Calcium-induced chromatin condensation and cyclin phosphorylation during chromatin condensation cycles in ammonia-activated sea urchin eggs.

    Science.gov (United States)

    Patel, R; Twigg, J; Crossley, I; Golsteyn, R; Whitaker, M

    1989-01-01

    Ammonia-activated sea urchin eggs undergo repeated cycles of DNA synthesis, nuclear envelope breakdown (NEB) and chromatin condensation. No mitotic spindle forms, nor do the eggs undergo cytokinesis. Ammonia-activated eggs exhibit a form of the cell cycle in which the nuclear cycle proceeds without segregation of the chromatin into daughter cells. We discuss here experiments that demonstrate that intracellular free calcium concentration controls the S phase-M phase transition in ammonia-activated eggs, as it does in fertilized embryos. Cyclins are proteins that are synthesized throughout the cell cycle and destroyed abruptly during each round of chromatin condensation. We find that cycles of cyclin phosphorylation and destruction occur coincident with chromatin condensation in ammonia-activated eggs. Cyclin phosphorylation also occurs in eggs treated with the tumour promoter, phorbol myristate acetate (PMA). There is no accompanying NEB or chromatin condensation, however, and the nucleus is insensitive to exogenously-generated calcium transients. These latter data indicate that cyclin synthesis and phosphorylation is not a sufficient condition for calcium-induced NEB in sea urchin embryos. PMA must fail to induce one of the necessary cell cycle initiation signals. We suggest that the missing signal is the activation of the cell cycle control protein p34cdc2, which we have shown to be phosphorylated at fertilization and which is phosphorylated in ammonia-activated eggs.

  15. Study of dynamical stability of tethered systems during space tug maneuvers

    Science.gov (United States)

    Mantellato, R.; Olivieri, L.; Lorenzini, E. C.

    2017-09-01

    The dynamics of a space tether system composed of one active spacecraft, an uncontrolled large debris (e.g., a defunct satellite), and a visco-elastic tether connecting the two bodies are investigated in this paper. The active spacecraft is assumed to be equipped with a propulsive system for carrying out a tug maneuver that forces the orbital decay of the debris. The dynamical stability and the eigenfrequencies of the tethered system under the action of the thrust are investigated with both numerical and analytical models. A more complex numerical lumped-masses model provides the reference to validate the results hailing from the simplified models. Simplified models of orbital decay, tether, and debris attitude motions were derived using the Clohessy-Wiltshire equations. The results obtained with the simplified models fit very well with those from the lumped-masses model for a wide range of initial conditions. Thanks to the analytical models two resonance conditions were found, both of them affecting the attitude dynamics of the debris, that could represent a serious issue for the safety of the tug maneuver. Also, an instability mechanism that could induce the dual mass system to rotate around its center of mass under certain conditions was identified. These findings make it possible to pinpoint the set of initial conditions of the tethered system at the beginning of the thrust event that provides a dynamically stable tug maneuver for different configurations of the system (e.g., low/high thrust, stiff/elastic tethers).

  16. Biomimicry enhances sequential reactions of tethered glycolytic enzymes, TPI and GAPDHS.

    Science.gov (United States)

    Mukai, Chinatsu; Gao, Lizeng; Bergkvist, Magnus; Nelson, Jacquelyn L; Hinchman, Meleana M; Travis, Alexander J

    2013-01-01

    Maintaining activity of enzymes tethered to solid interfaces remains a major challenge in developing hybrid organic-inorganic devices. In nature, mammalian spermatozoa have overcome this design challenge by having glycolytic enzymes with specialized targeting domains that enable them to function while tethered to a cytoskeletal element. As a step toward designing a hybrid organic-inorganic ATP-generating system, we implemented a biomimetic site-specific immobilization strategy to tether two glycolytic enzymes representing different functional enzyme families: triose phosphoisomerase (TPI; an isomerase) and glyceraldehyde 3-phosphate dehydrogenase (GAPDHS; an oxidoreductase). We then evaluated the activities of these enzymes in comparison to when they were tethered via classical carboxyl-amine crosslinking. Both enzymes show similar surface binding regardless of immobilization method. Remarkably, specific activities for both enzymes were significantly higher when tethered using the biomimetic, site-specific immobilization approach. Using this biomimetic approach, we tethered both enzymes to a single surface and demonstrated their function in series in both forward and reverse directions. Again, the activities in series were significantly higher in both directions when the enzymes were coupled using this biomimetic approach versus carboxyl-amine binding. Our results suggest that biomimetic, site-specific immobilization can provide important functional advantages over chemically specific, but non-oriented attachment, an important strategic insight given the growing interest in recapitulating entire biological pathways on hybrid organic-inorganic devices.

  17. Biomimicry enhances sequential reactions of tethered glycolytic enzymes, TPI and GAPDHS.

    Directory of Open Access Journals (Sweden)

    Chinatsu Mukai

    Full Text Available Maintaining activity of enzymes tethered to solid interfaces remains a major challenge in developing hybrid organic-inorganic devices. In nature, mammalian spermatozoa have overcome this design challenge by having glycolytic enzymes with specialized targeting domains that enable them to function while tethered to a cytoskeletal element. As a step toward designing a hybrid organic-inorganic ATP-generating system, we implemented a biomimetic site-specific immobilization strategy to tether two glycolytic enzymes representing different functional enzyme families: triose phosphoisomerase (TPI; an isomerase and glyceraldehyde 3-phosphate dehydrogenase (GAPDHS; an oxidoreductase. We then evaluated the activities of these enzymes in comparison to when they were tethered via classical carboxyl-amine crosslinking. Both enzymes show similar surface binding regardless of immobilization method. Remarkably, specific activities for both enzymes were significantly higher when tethered using the biomimetic, site-specific immobilization approach. Using this biomimetic approach, we tethered both enzymes to a single surface and demonstrated their function in series in both forward and reverse directions. Again, the activities in series were significantly higher in both directions when the enzymes were coupled using this biomimetic approach versus carboxyl-amine binding. Our results suggest that biomimetic, site-specific immobilization can provide important functional advantages over chemically specific, but non-oriented attachment, an important strategic insight given the growing interest in recapitulating entire biological pathways on hybrid organic-inorganic devices.

  18. The mechanics of motorised momentum exchange tethers when applied to active debris removal from LEO

    International Nuclear Information System (INIS)

    Caldecott, Ralph; Kamarulzaman, Dayangku N. S.; Kirrane, James P.; Cartmell, Matthew P.; Ganilova, Olga A.

    2014-01-01

    The concept of momentum exchange when applied to space tethers for propulsion is well established, and a considerable body of literature now exists on the on-orbit modelling, the dynamics, and also the control of a large range of tether system applications. The authors consider here a new application for the Motorised Momentum Exchange Tether by highlighting three key stages of development leading to a conceptualisation that can subsequently be developed into a technology for Active Debris Removal. The paper starts with a study of the on-orbit mechanics of a full sized motorised tether in which it is shown that a laden and therefore highly massasymmetrical tether can still be forced to spin, and certainly to librate, thereby confirming its possible usefulness for active debris removal (ADR). The second part of the paper concentrates on the modelling of the centripetal deployment of a symmetrical MMET in order to get it initialized for debris removal operations, and the third and final part of the paper provides an entry into scale modelling for low cost mission design and testing. It is shown that the motorised momentum exchange tether offers a potential solution to the removal of large pieces of orbital debris, and that dynamic methodologies can be implemented to in order to optimise the emergent design

  19. Tethered swimming can be used to evaluate force contribution for short-distance swimming performance.

    Science.gov (United States)

    Morouço, Pedro G; Marinho, Daniel A; Keskinen, Kari L; Badillo, Juan J; Marques, Mário C

    2014-11-01

    The purpose of this study was two-fold: (a) to compare stroke and the physiological responses between maximal tethered and free front crawl swimming and (b) to evaluate the contribution of force exertion for swimming performance over short distances. A total of 34 male swimmers, representing various levels of competitive performance, participated in this study. Each participant was tested in both a 30-second maximal tethered swimming test and a 50-m free swimming test. The tethered force parameters, the swimming speed, stroke (stroke rate [SR]), and the physiological responses (increase in blood lactate concentration [ΔBLa], heart rate, and rate of perceived exertion) were recorded and calculated. The results showed no differences in stroke and the physiological responses between tethered and free swimming, with a high level of agreement for the SR and ΔBLa. A strong correlation was obtained between the maximum impulse of force per stroke and the speed (r = 0.91; p swimming performance. The relationship between the swimming speed and maximum force tended to be nonlinear, whereas linear relationships were observed with the maximum impulse. This study demonstrates that tethered swimming does not significantly alter stroke and the physiological responses compared with free swimming, and that the maximum impulse per stroke should be used to evaluate the balance between force and the ability to effectively apply force during sprint swimming. Consequently, coaches can rely on tethered forces to identify strength deficits and improve swimming performance over short distances.

  20. N-Butyrate alters chromatin accessibility to DNA repair enzymes

    International Nuclear Information System (INIS)

    Smith, P.J.

    1986-01-01

    Current evidence suggests that the complex nature of mammalian chromatin can result in the concealment of DNA damage from repair enzymes and their co-factors. Recently it has been proposed that the acetylation of histone proteins in chromatin may provide a surveillance system whereby damaged regions of DNA become exposed due to changes in chromatin accessibility. This hypothesis has been tested by: (i) using n-butyrate to induce hyperacetylation in human adenocarcinoma (HT29) cells; (ii) monitoring the enzymatic accessibility of chromatin in permeabilised cells; (iii) measuring u.v. repair-associated nicking of DNA in intact cells and (iv) determining the effects of n-butyrate on cellular sensitivity to DNA damaging agents. The results indicate that the accessibility of chromatin to Micrococcus luteus u.v. endonuclease is enhanced by greater than 2-fold in n-butyrate-treated cells and that there is a corresponding increase in u.v. repair incision rates in intact cells exposed to the drug. Non-toxic levels of n-butyrate induce a block to G1 phase transit and there is a significant growth delay on removal of the drug. Resistance of HT29 cells to u.v.-radiation and adriamycin is enhanced in n-butyrate-treated cells whereas X-ray sensitivity is increased. Although changes in the responses of cells to DNA damaging agents must be considered in relation to the effects of n-butyrate on growth rate and cell-cycle distribution, the results are not inconsistent with the proposal that increased enzymatic-accessibility/repair is biologically favourable for the resistance of cells to u.v.-radiation damage. Overall the results support the suggested operation of a histone acetylation-based chromatin surveillance system in human cells

  1. The telomere binding protein TRF2 induces chromatin compaction.

    Directory of Open Access Journals (Sweden)

    Asmaa M Baker

    2011-04-01

    Full Text Available Mammalian telomeres are specialized chromatin structures that require the telomere binding protein, TRF2, for maintaining chromosome stability. In addition to its ability to modulate DNA repair activities, TRF2 also has direct effects on DNA structure and topology. Given that mammalian telomeric chromatin includes nucleosomes, we investigated the effect of this protein on chromatin structure. TRF2 bound to reconstituted telomeric nucleosomal fibers through both its basic N-terminus and its C-terminal DNA binding domain. Analytical agarose gel electrophoresis (AAGE studies showed that TRF2 promoted the folding of nucleosomal arrays into more compact structures by neutralizing negative surface charge. A construct containing the N-terminal and TRFH domains together altered the charge and radius of nucleosomal arrays similarly to full-length TRF2 suggesting that TRF2-driven changes in global chromatin structure were largely due to these regions. However, the most compact chromatin structures were induced by the isolated basic N-terminal region, as judged by both AAGE and atomic force microscopy. Although the N-terminal region condensed nucleosomal array fibers, the TRFH domain, known to alter DNA topology, was required for stimulation of a strand invasion-like reaction with nucleosomal arrays. Optimal strand invasion also required the C-terminal DNA binding domain. Furthermore, the reaction was not stimulated on linear histone-free DNA. Our data suggest that nucleosomal chromatin has the ability to facilitate this activity of TRF2 which is thought to be involved in stabilizing looped telomere structures.

  2. Statistical physics of nucleosome positioning and chromatin structure

    Science.gov (United States)

    Morozov, Alexandre

    2012-02-01

    Genomic DNA is packaged into chromatin in eukaryotic cells. The fundamental building block of chromatin is the nucleosome, a 147 bp-long DNA molecule wrapped around the surface of a histone octamer. Arrays of nucleosomes are positioned along DNA according to their sequence preferences and folded into higher-order chromatin fibers whose structure is poorly understood. We have developed a framework for predicting sequence-specific histone-DNA interactions and the effective two-body potential responsible for ordering nucleosomes into regular higher-order structures. Our approach is based on the analogy between nucleosomal arrays and a one-dimensional fluid of finite-size particles with nearest-neighbor interactions. We derive simple rules which allow us to predict nucleosome occupancy solely from the dinucleotide content of the underlying DNA sequences.Dinucleotide content determines the degree of stiffness of the DNA polymer and thus defines its ability to bend into the nucleosomal superhelix. As expected, the nucleosome positioning rules are universal for chromatin assembled in vitro on genomic DNA from baker's yeast and from the nematode worm C.elegans, where nucleosome placement follows intrinsic sequence preferences and steric exclusion. However, the positioning rules inferred from in vivo C.elegans chromatin are affected by global nucleosome depletion from chromosome arms relative to central domains, likely caused by the attachment of the chromosome arms to the nuclear membrane. Furthermore, intrinsic nucleosome positioning rules are overwritten in transcribed regions, indicating that chromatin organization is actively managed by the transcriptional and splicing machinery.

  3. Chromatin structure and evolution in the human genome

    Directory of Open Access Journals (Sweden)

    Dunlop Malcolm G

    2007-05-01

    Full Text Available Abstract Background Evolutionary rates are not constant across the human genome but genes in close proximity have been shown to experience similar levels of divergence and selection. The higher-order organisation of chromosomes has often been invoked to explain such phenomena but previously there has been insufficient data on chromosome structure to investigate this rigorously. Using the results of a recent genome-wide analysis of open and closed human chromatin structures we have investigated the global association between divergence, selection and chromatin structure for the first time. Results In this study we have shown that, paradoxically, synonymous site divergence (dS at non-CpG sites is highest in regions of open chromatin, primarily as a result of an increased number of transitions, while the rates of other traditional measures of mutation (intergenic, intronic and ancient repeat divergence as well as SNP density are highest in closed regions of the genome. Analysis of human-chimpanzee divergence across intron-exon boundaries indicates that although genes in relatively open chromatin generally display little selection at their synonymous sites, those in closed regions show markedly lower divergence at their fourfold degenerate sites than in neighbouring introns and intergenic regions. Exclusion of known Exonic Splice Enhancer hexamers has little affect on the divergence observed at fourfold degenerate sites across chromatin categories; however, we show that closed chromatin is enriched with certain classes of ncRNA genes whose RNA secondary structure may be particularly important. Conclusion We conclude that, overall, non-CpG mutation rates are lowest in open regions of the genome and that regions of the genome with a closed chromatin structure have the highest background mutation rate. This might reflect lower rates of DNA damage or enhanced DNA repair processes in regions of open chromatin. Our results also indicate that dS is a poor

  4. The importance of topoisomerases for chromatin regulated genes

    DEFF Research Database (Denmark)

    Fredsøe, Jacob Christian; Pedersen, Jakob Madsen; Rødgaard, Morten Terpager

    2013-01-01

    DNA topoisomerases are enzymes, which function to relieve torsional stress in the DNA helix by introducing transient breaks into the DNA molecule. By use of Saccharomyces cerevisiae and microarray technology we have previously shown that topoisomerases are required for the activation of chromatin...... topoisomerases for optimal activation, but in contrast to the PHO5 gene, topoisomerases are not required for chromatin remodeling of the GAL1/10 promoter region, indicating a different role of the enzymes. We are currently performing a detailed investigation of the GAL genes to elucidate the precise role...

  5. Chromatin Structure of Epstein-Barr Virus Latent Episomes.

    Science.gov (United States)

    Lieberman, Paul M

    2015-01-01

    EBV latent infection is characterized by a highly restricted pattern of viral gene expression. EBV can establish latent infections in multiple different tissue types with remarkable variation and plasticity in viral transcription and replication. During latency, the viral genome persists as a multi-copy episome, a non-integrated-closed circular DNA with nucleosome structure similar to cellular chromosomes. Chromatin assembly and histone modifications contribute to the regulation of viral gene expression, DNA replication, and episome persistence during latency. This review focuses on how EBV latency is regulated by chromatin and its associated processes.

  6. Citrullination regulates pluripotency and histone H1 binding to chromatin

    DEFF Research Database (Denmark)

    Christophorou, Maria A; Castelo-Branco, Gonçalo; Halley-Stott, Richard P

    2014-01-01

    citrullination of core histones has been linked to transcriptional regulation and the DNA damage response. PADI4 (also called PAD4 or PADV), the only PADI with a nuclear localization signal, was previously shown to act in myeloid cells where it mediates profound chromatin decondensation during the innate immune...... and activating their expression. Its inhibition lowers the percentage of pluripotent cells in the early mouse embryo and significantly reduces reprogramming efficiency. Using an unbiased proteomic approach we identify linker histone H1 variants, which are involved in the generation of compact chromatin, as novel...

  7. Retention of the Native Epigenome in Purified Mammalian Chromatin.

    Directory of Open Access Journals (Sweden)

    Andreas H Ehrensberger

    Full Text Available A protocol is presented for the isolation of native mammalian chromatin as fibers of 25-250 nucleosomes under conditions that preserve the natural epigenetic signature. The material is composed almost exclusively of histones and DNA and conforms to the structure expected by electron microscopy. All sequences probed for were retained, indicating that the material is representative of the majority of the genome. DNA methylation marks and histone marks resembled the patterns observed in vivo. Importantly, nucleosome positions also remained largely unchanged, except on CpG islands, where nucleosomes were found to be unstable. The technical challenges of reconstituting biochemical reactions with native mammalian chromatin are discussed.

  8. Lipoproteins tethered dendrimeric nanoconstructs for effective targeting to cancer cells

    Energy Technology Data Exchange (ETDEWEB)

    Jain, Anupriya; Jain, Keerti, E-mail: keertijain02@gmail.com; Mehra, Neelesh Kumar, E-mail: neelesh81mph@gmail.com; Jain, N. K., E-mail: dr.jnarendr@gmail.com [Dr. H. S. Gour University, Pharmaceutics Research Laboratory, Department of Pharmaceutical Sciences (India)

    2013-10-15

    In the present investigation, poly (propylene imine) dendrimers up to fifth generation (PPI G5.0) were synthesized using ethylene diamine and acrylonitrile. Lipoproteins (high-density lipoprotein; HDL and low-density lipoprotein; LDL) were isolated from human plasma by discontinuous density gradient ultracentrifugation, characterized and tethered to G5.0 PPI dendrimers to construct LDL- and HDL-conjugated dendrimeric nanoconstructs for tumor-specific delivery of docetaxel. Developed formulations showed sustained release characteristics in in vitro drug release and in vivo pharmacokinetic studies. The cancer targeting potential of lipoprotein coupled dendrimers was investigated by ex vivo cytotoxicity and cell uptake studies using human hepatocellular carcinoma cell lines (HepG2 cells) and biodistribution studies in albino rats of Sprague-Dawley strain. Lipoprotein anchored dendrimeric nanoconstructs showed significant uptake by cancer cells as well as higher biodistribution of docetaxel to liver and spleen. It is concluded that these precisely synthesized engineered dendrimeric nanoconstructs could serve as promising drug carrier for fighting with the fatal disease, i.e., cancer, attributed to their defined targeting and therapeutic potential.

  9. Design of a lightweight, tethered, torque-controlled knee exoskeleton.

    Science.gov (United States)

    Witte, Kirby Ann; Fatschel, Andreas M; Collins, Steven H

    2017-07-01

    Lower-limb exoskeletons show promise for improving gait rehabilitation for those with chronic gait abnormalities due to injury, stroke or other illness. We designed and built a tethered knee exoskeleton with a strong lightweight frame and comfortable, four-point contact with the leg. The device is structurally compliant in select directions, instrumented to measure joint angle and applied torque, and is lightweight (0.76 kg). The exoskeleton is actuated by two off-board motors. Closed loop torque control is achieved using classical proportional feedback control with damping injection in conjunction with iterative learning. We tested torque measurement accuracy and found root mean squared (RMS) error of 0.8 Nm with a max load of 62.2 Nm. Bandwidth was measured to be phase limited at 45 Hz when tested on a rigid test stand and 23 Hz when tested on a person's leg. During bandwidth tests peak extension torques were measured up to 50 Nm. Torque tracking was tested during walking on a treadmill at 1.25 m/s with peak flexion torques of 30 Nm. RMS torque tracking error averaged over a hundred steps was 0.91 Nm. We intend to use this knee exoskeleton to investigate robotic assistance strategies to improve gait rehabilitation and enhance human athletic ability.

  10. Flow structures around a beetle in a tethered flight

    Science.gov (United States)

    Lee, Boogeon; Oh, Sehyeong; Park, Hyungmin; Choi, Haecheon

    2017-11-01

    In the present study, through a wind-tunnel experiment, we visualize the flow in a tethered flight of a rhinoceros beetle using a smoke-wire visualization technique. Measurements are done at five side planes along the wind span while varying the body angle (angle between the horizontal and the body axis) to investigate the influence of the stroke plane angle that was observed to change depending on the flight mode such as hovering, forward and takeoff flights so on. Observing that a large attached leading-edge vortex is only found on the hindwing, it is inferred that most of the aerodynamic forces would be generated by hindwings (flexible inner wings) compared to the elytra (hard outer wings). In addition, it is observed to use unsteady lift-generating mechanisms such as clap-and-fling, wing-wing interaction and wake capture. Finally, we discuss the relation between the advance ratio and Strouhal number by adjusting free-stream velocity and the body angle (i.e., angle of wake-induced flow). Supported by a Grant to Bio-Mimetic Robot Research Center Funded by Defense Acquisition Program Administration, and by ADD, Korea (UD130070ID).

  11. An electrochemical immunosensor using ferrocenyl-tethered dendrimer.

    Science.gov (United States)

    Kwon, Seong Jung; Kim, Eunkyung; Yang, Haesik; Kwak, Juhyoun

    2006-03-01

    We report here an enzyme-amplified, sandwich-type immunosensor for detecting the biospecific interaction between an antibody and antigen using redox mediation. We employed biotin/anti-biotin IgG as a model immunosensing pair. Partially ferrocenyl-tethered dendrimer (Fc-D), whose ferrocene moiety acts as a redox mediator, was immobilized to the electrode surface by covalent binding between the dendrimer amines and the carboxylic acids of a self-assembled monolayer. The unreacted amines of the immobilized Fc-D were modified with biotin groups to allow the specific binding of goat anti-biotin IgG. Rabbit anti-goat IgG-conjugated alkaline phosphatase was bound to goat anti-biotin IgG to catalyze conversion of p-aminophenyl phosphate monohydrate to p-aminophenol. This product is oxidized to quinoimide by the reduction of ferrocenium back to ferrocene, producing an electrocatalytic anodic current. Cyclic voltammograms and surface plasmon resonance experiments showed that the binding of nonspecific proteins is not significant on the biotinylated Fc-D surface. We also examined the change in peak current according to the concentration of anti-biotin IgG and found that the detection range of this immunosensing scheme is between 0.1 and 30 microg mL(-1).

  12. Glucocorticoid receptor binding to chromatin is selectively controlled by the coregulator Hic-5 and chromatin remodeling enzymes.

    Science.gov (United States)

    Lee, Brian H; Stallcup, Michael R

    2017-06-02

    The steroid hormone-activated glucocorticoid receptor (GR) regulates cellular stress pathways by binding to genomic regulatory elements of target genes and recruiting coregulator proteins to remodel chromatin and regulate transcription complex assembly. The coregulator hydrogen peroxide-inducible clone 5 (Hic-5) is required for glucocorticoid (GC) regulation of some genes but not others and blocks the regulation of a third gene set by inhibiting GR binding. How Hic-5 exerts these gene-specific effects and specifically how it blocks GR binding to some genes but not others is unclear. Here we show that site-specific blocking of GR binding is due to gene-specific requirements for ATP-dependent chromatin remodeling enzymes. By depletion of 11 different chromatin remodelers, we found that ATPases chromodomain helicase DNA-binding protein 9 (CHD9) and Brahma homologue (BRM, a product of the SMARCA2 gene) are required for GC-regulated expression of the blocked genes but not for other GC-regulated genes. Furthermore, CHD9 and BRM were required for GR occupancy and chromatin remodeling at GR-binding regions associated with blocked genes but not at GR-binding regions associated with other GC-regulated genes. Hic-5 selectively inhibits GR interaction with CHD9 and BRM, thereby blocking chromatin remodeling and robust GR binding at GR-binding sites associated with blocked genes. Thus, Hic-5 regulates GR binding site selection by a novel mechanism, exploiting gene-specific requirements for chromatin remodeling enzymes to selectively influence DNA occupancy and gene regulation by a transcription factor. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  13. Exposure to Hycanthone alters chromatin structure around specific gene functions and specific repeats in Schistosoma mansoni

    Directory of Open Access Journals (Sweden)

    David eRoquis

    2014-07-01

    Full Text Available Schistosoma mansoni is a parasitic plathyhelminth responsible for intestinal schistosomiasis (or bilharziasis, a disease affecting 67 million people worldwide and causing an important economic burden. The schistosomicides hycanthone, and its later proxy oxamniquine, were widely used for treatments in endemic areas during the 20th century. Recently, the mechanism of action, as well as the genetic origin of a stably and Mendelian inherited resistance for both drugs was elucidated in two strains. However, several observations suggested early on that alternative mechanisms might exist, by which resistance could be induced for these two drugs in sensitive lines of schistosomes. This induced resistance appeared rapidly, within the first generation, but was metastable (not stably inherited. Epigenetic inheritance could explain such a phenomenon and we therefore re-analyzed the historical data with our current knowledge of epigenetics. In addition, we performed new experiments such as ChIP-seq on hycanthone treated worms. We found distinct chromatin structure changes between sensitive worms and induced resistant worms from the same strain. No specific pathway was discovered, but genes in which chromatin structure modification were observed are mostly associated with transport and catabolism, which makes sense in the context of the elimination of the drug. Specific differences were observed in the repetitive compartment of the genome. We finally describe what types of experiments are needed to understand the complexity of heritability that can be based on genetic and/or epigenetic mechanisms for drug resistance in schistosomes.

  14. Effect of Interaction between Chromatin Loops on Cell-to-Cell Variability in Gene Expression.

    Directory of Open Access Journals (Sweden)

    Tuoqi Liu

    2016-05-01

    Full Text Available According to recent experimental evidence, the interaction between chromatin loops, which can be characterized by three factors-connection pattern, distance between regulatory elements, and communication form, play an important role in determining the level of cell-to-cell variability in gene expression. These quantitative experiments call for a corresponding modeling effect that addresses the question of how changes in these factors affect variability at the expression level in a systematic rather than case-by-case fashion. Here we make such an effort, based on a mechanic model that maps three fundamental patterns for two interacting DNA loops into a 4-state model of stochastic transcription. We first show that in contrast to side-by-side loops, nested loops enhance mRNA expression and reduce expression noise whereas alternating loops have just opposite effects. Then, we compare effects of facilitated tracking and direct looping on gene expression. We find that the former performs better than the latter in controlling mean expression and in tuning expression noise, but this control or tuning is distance-dependent, remarkable for moderate loop lengths, and there is a limit loop length such that the difference in effect between two communication forms almost disappears. Our analysis and results justify the facilitated chromatin-looping hypothesis.

  15. Testing Whether Defective Chromatin Assembly in S-Phase Contributes to Breast Cancer

    National Research Council Canada - National Science Library

    Adams, Peter

    2003-01-01

    .... We used a dominant negative mutant of (chromatin assembly factor-I) CAF1, a complex that assembles newly synthesized DNA into nucleosomes, to inhibit S-phase chromatin assembly and found that this induced S-phase arrest...

  16. Testing Whether Defective Chromatin Assembly in S-Phase Contributes to Breast Cancer

    National Research Council Canada - National Science Library

    Adams, Peter

    2004-01-01

    .... We used a dominant negative mutant of (chromatin assembly factor-I) CAF1, a complex that assembles newly synthesized DNA into nucleosomes, to inhibit S-phase chromatin assembly and found that this induced S-phase arrest...

  17. Bridging the dynamics and organization of chromatin domains by mathematical modeling.

    Science.gov (United States)

    Shinkai, Soya; Nozaki, Tadasu; Maeshima, Kazuhiro; Togashi, Yuichi

    2017-07-04

    The genome is 3-dimensionally organized in the cell, and the mammalian genome DNA is partitioned into submegabase-sized chromatin domains. Genome functions are regulated within and across the domains according to their organization, whereas the chromatin itself is highly dynamic. However, the details of such dynamic organization of chromatin domains in living cells remain unclear. To unify chromatin dynamics and organization, we recently demonstrated that structural information of chromatin domains in living human cells can be extracted from analyses of the subdiffusive nucleosome movement using mathematical modeling. Our mathematical analysis suggested that as the chromatin domain becomes smaller and more compact, nucleosome movement becomes increasingly restricted. Here, we show the implication of these results for bridging the gap between chromatin dynamics and organization, and provide physical insight into chromatin domains as efficient units to conduct genome functions in the thermal noisy environment of the cell.

  18. Alternative additives; Alternative additiver

    Energy Technology Data Exchange (ETDEWEB)

    2007-08-15

    In this project a number of industrial and agricultural waste products have been characterised and evaluated in terms of alkali-getter performance. The intended use is for biomass-fired power stations aiming at reducing corrosion or slagging related problems. The following products have been obtained, characterised and evaluated: 1) Brewery draff 2) Danish de-gassed manure 3) Paper sludge 4) Moulding sand 5) Spent bleaching earth 6) Anorthosite 7) Sand 8) Clay-sludge. Most of the above alternative additive candidates are deemed unsuitable due to insufficient chemical effect and/or expensive requirements for pre-treatment (such as drying and transportation). 3 products were selected for full-scale testing: de-gassed manure, spent bleaching earth and clay slugde. The full scale tests were undertaken at the biomass-fired power stations in Koege, Slagelse and Ensted. Spent bleaching earth (SBE) and clay sludge were the only tested additive candidates that had a proven ability to react with KCl, to thereby reduce Cl-concentrations in deposits, and reduce the deposit flux to superheater tubes. Their performance was shown to nearly as good as commercial additives. De-gassed manure, however, did not evaluate positively due to inhibiting effects of Ca in the manure. Furthermore, de-gassed manure has a high concentration of heavy metals, which imposes a financial burden with regard to proper disposal of the ash by-products. Clay-sludge is a wet clay slurring, and drying and transportation of this product entails substantial costs. Spent bleaching does not require much pre-treatment and is therefore the most promising alternative additive. On the other hand, bleaching earth contains residual plant oil which means that a range of legislation relating to waste combustion comes into play. Not least a waste combustion fee of 330 DKK/tonne. For all alternative (and commercial) additives disposal costs of the increase ash by-products represents a significant cost. This is

  19. Histone H1 regulates chromatin condensation in Leishmania parasites.

    Science.gov (United States)

    Masina, Slavica; Zangger, Haroun; Rivier, Denis; Fasel, Nicolas

    2007-05-01

    We investigated the functional role of the Leishmania histone H1 and demonstrate for the first time that addition of histone H1 has a strong effect on microccocal digestion, chromatin condensation of parasite nuclei and that its overexpression can modulate parasite infectivity in vivo.

  20. Modulation of the Chromatin Phosphoproteome by the Haspin Protein Kinase

    DEFF Research Database (Denmark)

    Maiolica, Alessio; de Medina-Redondo, Maria; Schoof, Erwin

    2014-01-01

    , histone H3 is the only confirmed Haspin substrate. We used a combination of biochemical, pharmacological, and mass spectrometric approaches to study the consequences of Haspin inhibition in mitotic cells. We quantified 3964 phosphorylation sites on chromatin- associated proteins and identified a Haspin...

  1. Interaction of maize chromatin-associated HMG proteins with mononucleosomes

    DEFF Research Database (Denmark)

    Lichota, J.; Grasser, Klaus D.

    2003-01-01

    Two groups of plant chromatin-associated high mobility group (HMG) proteins, namely the HMGA family, typically containing four A/T-hook DNA-binding motifs, and the HMGB family, containing a single HMG-box DNA-binding domain, have been identified. We have examined the interaction of recombinant...

  2. The size of the thyroid hormone receptor in chromatin

    International Nuclear Information System (INIS)

    Gruol, D.J.; Kempner, E.S.

    1982-01-01

    We have used radiation inactivation and target theory to determine the size of the functional unit for T 3 binding in rat liver chromatin. The process involves exposure of frozen chromatin samples to a beam of high energy electrons produced in a linear accelerator and subsequent measurement of the residual capacity to bind hormone. Our experiments were carried out using three forms of solubilized chromatin: 1) sonicated, containing the receptor in fragments which sedimented faster than 30 S; 2) digested by nuclease, containing the receptor in a form which sedimented at 5-6 S; 3) digested by nuclease and made 0.5 M in KCl, containing the receptor in a form which sedimented at 3.8 S. We have shown that in each sample preparation the receptor retained the ability to bind T 3 with the same capacity and affinity that had previously been measured with high molecular weith chromatin. Irradiation caused a reduction in the capacity to bind T 3 but did not change the affinity of the remaining receptors for the hormone. In each preparation, the radiation resulted in a simple exponential loss of binding capacity with dose, indicating that a single target size was detected. Within the variation of the measurements, the target size for each form of the receptor was the same, 59,000 daltons

  3. Chromatin immunoprecipitation: optimization, quantitative analysis and data normalization

    Directory of Open Access Journals (Sweden)

    Peterhansel Christoph

    2007-09-01

    Full Text Available Abstract Background Chromatin remodeling, histone modifications and other chromatin-related processes play a crucial role in gene regulation. A very useful technique to study these processes is chromatin immunoprecipitation (ChIP. ChIP is widely used for a few model systems, including Arabidopsis, but establishment of the technique for other organisms is still remarkably challenging. Furthermore, quantitative analysis of the precipitated material and normalization of the data is often underestimated, negatively affecting data quality. Results We developed a robust ChIP protocol, using maize (Zea mays as a model system, and present a general strategy to systematically optimize this protocol for any type of tissue. We propose endogenous controls for active and for repressed chromatin, and discuss various other controls that are essential for successful ChIP experiments. We experienced that the use of quantitative PCR (QPCR is crucial for obtaining high quality ChIP data and we explain why. The method of data normalization has a major impact on the quality of ChIP analyses. Therefore, we analyzed different normalization strategies, resulting in a thorough discussion of the advantages and drawbacks of the various approaches. Conclusion Here we provide a robust ChIP protocol and strategy to optimize the protocol for any type of tissue; we argue that quantitative real-time PCR (QPCR is the best method to analyze the precipitates, and present comprehensive insights into data normalization.

  4. Divide and (epigenetic) rule: Chromatin domains as functional and ...

    Indian Academy of Sciences (India)

    is put on the regulatory elements such as boundary elements, that mark the limits of chromatin domains and divide the genome into ... Firstly the composition of eukaryotic genome would suggest that excess of DNA is often, not .... ated MARs and their dynamic reorganization has recently shown to be important for gene ...

  5. Role of chromatin factors in Arabidopsis root stem cell maintenance

    NARCIS (Netherlands)

    Kornet, N.G.|info:eu-repo/dai/nl/311445713

    2008-01-01

    Stem cells replenish the cells present in an organism throughout its lifetime and sustain growth. They have unique characteristics: the capability to self-renew and the potential to differentiate into several cell types. Recently, it has become clear that chromatin factors support these unique

  6. Epigenetic regulation and chromatin remodeling in learning and memory.

    Science.gov (United States)

    Kim, Somi; Kaang, Bong-Kiun

    2017-01-13

    Understanding the underlying mechanisms of memory formation and maintenance has been a major goal in the field of neuroscience. Memory formation and maintenance are tightly controlled complex processes. Among the various processes occurring at different levels, gene expression regulation is especially crucial for proper memory processing, as some genes need to be activated while some genes must be suppressed. Epigenetic regulation of the genome involves processes such as DNA methylation and histone post-translational modifications. These processes edit genomic properties or the interactions between the genome and histone cores. They then induce structural changes in the chromatin and lead to transcriptional changes of different genes. Recent studies have focused on the concept of chromatin remodeling, which consists of 3D structural changes in chromatin in relation to gene regulation, and is an important process in learning and memory. In this review, we will introduce three major epigenetic processes involved in memory regulation: DNA methylation, histone methylation and histone acetylation. We will also discuss general mechanisms of long-term memory storage and relate the epigenetic control of learning and memory to chromatin remodeling. Finally, we will discuss how epigenetic mechanisms can contribute to the pathologies of neurological disorders and cause memory-related symptoms.

  7. Chromatin remodelers in the DNA double strand break response

    NARCIS (Netherlands)

    Smeenk, Godelieve

    2012-01-01

    During my PhD project, I studied the role of several chromatin remodelers in the DNA double strand break (DSB) response. We discovered that both CHD4 and SMARCA5 are required for ubiquitin signaling through the E3 ubiquitin ligases RNF8 and RNF168, which is a central signaling event in the response

  8. Chromatin-regulating proteins as targets for cancer therapy

    International Nuclear Information System (INIS)

    Oike, Takahiro; Ogiwara, Hideaki; Kohno, Takashi; Amornwichet, Napapat; Nakano, Takashi

    2014-01-01

    Chromatin-regulating proteins represent a large class of novel targets for cancer therapy. In the context of radiotherapy, acetylation and deacetylation of histones by histone acetyltransferases (HATs) and histone deacetylases (HDACs) play important roles in the repair of DNA double-strand breaks generated by ionizing irradiation, and are therefore attractive targets for radiosensitization. Small-molecule inhibitors of HATs (garcinol, anacardic acid and curcumin) and HDACs (vorinostat, sodium butyrate and valproic acid) have been shown to sensitize cancer cells to ionizing irradiation in preclinical models, and some of these molecules are being tested in clinical trials, either alone or in combination with radiotherapy. Meanwhile, recent large-scale genome analyses have identified frequent mutations in genes encoding chromatin-regulating proteins, especially in those encoding subunits of the SWI/SNF chromatin-remodeling complex, in various human cancers. These observations have driven researchers toward development of targeted therapies against cancers carrying these mutations. DOT1L inhibition in MLL-rearranged leukemia, EZH2 inhibition in EZH2-mutant or MLL-rearranged hematologic malignancies and SNF5-deficient tumors, BRD4 inhibition in various hematologic malignancies, and BRM inhibition in BRG1-deficient tumors have demonstrated promising anti-tumor effects in preclinical models, and these strategies are currently awaiting clinical application. Overall, the data collected so far suggest that targeting chromatin-regulating proteins is a promising strategy for tomorrow's cancer therapy, including radiotherapy and molecularly targeted chemotherapy. (author)

  9. Tethered Particle Motion: An Easy Technique for Probing DNA Topology and Interactions with Transcription Factors.

    Science.gov (United States)

    Kovari, Daniel T; Yan, Yan; Finzi, Laura; Dunlap, David

    2018-01-01

    Tethered Particle Motion (TPM) is a versatile in vitro technique for monitoring the conformations a linear macromolecule, such as DNA, can exhibit. The technique involves monitoring the diffusive motion of a particle anchored to a fixed point via the macromolecule of interest, which acts as a tether. In this chapter, we provide an overview of TPM, review the fundamental principles that determine the accuracy with which effective tether lengths can be used to distinguish different tether conformations, present software tools that assist in capturing and analyzing TPM data, and provide a protocol which uses TPM to characterize lac repressor-induced DNA looping. Critical to any TPM assay is the understanding of the timescale over which the diffusive motion of the particle must be observed to accurately distinguish tether conformations. Approximating the tether as a Hookean spring, we show how to estimate the diffusion timescale and discuss how it relates to the confidence with which tether conformations can be distinguished. Applying those estimates to a lac repressor titration assay, we describe how to perform a TPM experiment. We also provide graphically driven software which can be used to speed up data collection and analysis. Lastly, we detail how TPM data from the titration assay can be used to calculate relevant molecular descriptors such as the J factor for DNA looping and lac repressor-operator dissociation constants. While the included protocol is geared toward studying DNA looping, the technique, fundamental principles, and analytical methods are more general and can be adapted to a wide variety of molecular systems.

  10. Citrullination regulates pluripotency and histone H1 binding to chromatin

    Science.gov (United States)

    Christophorou, Maria A.; Castelo-Branco, Gonçalo; Halley-Stott, Richard P.; Oliveira, Clara Slade; Loos, Remco; Radzisheuskaya, Aliaksandra; Mowen, Kerri A.; Bertone, Paul; Silva, José C. R.; Zernicka-Goetz, Magdalena; Nielsen, Michael L.; Gurdon, John B.; Kouzarides, Tony

    2014-03-01

    Citrullination is the post-translational conversion of an arginine residue within a protein to the non-coded amino acid citrulline. This modification leads to the loss of a positive charge and reduction in hydrogen-bonding ability. It is carried out by a small family of tissue-specific vertebrate enzymes called peptidylarginine deiminases (PADIs) and is associated with the development of diverse pathological states such as autoimmunity, cancer, neurodegenerative disorders, prion diseases and thrombosis. Nevertheless, the physiological functions of citrullination remain ill-defined, although citrullination of core histones has been linked to transcriptional regulation and the DNA damage response. PADI4 (also called PAD4 or PADV), the only PADI with a nuclear localization signal, was previously shown to act in myeloid cells where it mediates profound chromatin decondensation during the innate immune response to infection. Here we show that the expression and enzymatic activity of Padi4 are also induced under conditions of ground-state pluripotency and during reprogramming in mouse. Padi4 is part of the pluripotency transcriptional network, binding to regulatory elements of key stem-cell genes and activating their expression. Its inhibition lowers the percentage of pluripotent cells in the early mouse embryo and significantly reduces reprogramming efficiency. Using an unbiased proteomic approach we identify linker histone H1 variants, which are involved in the generation of compact chromatin, as novel PADI4 substrates. Citrullination of a single arginine residue within the DNA-binding site of H1 results in its displacement from chromatin and global chromatin decondensation. Together, these results uncover a role for citrullination in the regulation of pluripotency and provide new mechanistic insights into how citrullination regulates chromatin compaction.

  11. Virus evolution reveals an exclusive role for LEDGF/p75 in chromosomal tethering of HIV.

    Directory of Open Access Journals (Sweden)

    Anneleen Hombrouck

    2007-03-01

    Full Text Available Retroviruses by definition insert their viral genome into the host cell chromosome. Although the key player of retroviral integration is viral integrase, a role for cellular cofactors has been proposed. Lentiviral integrases use the cellular protein LEDGF/p75 to tether the preintegration complex to the chromosome, although the existence of alternative host proteins substituting for the function of LEDGF/p75 in integration has been proposed. Truncation mutants of LEDGF/p75 lacking the chromosome attachment site strongly inhibit HIV replication by competition for the interaction with integrase. In an attempt to select HIV strains that can overcome the inhibition, we now have used T-cell lines that stably express a C-terminal fragment of LEDGF/p75. Despite resistance development, the affinity of integrase for LEDGF/p75 is reduced and replication kinetics in human primary T cells is impaired. Detection of the integrase mutations A128T and E170G at key positions in the LEDGF/p75-integrase interface provides in vivo evidence for previously reported crystallographic data. Moreover, the complementary inhibition by LEDGF/p75 knockdown and mutagenesis at the integrase-LEDGF/p75 interface points to the incapability of HIV to circumvent LEDGF/p75 function during proviral integration. Altogether, the data provide a striking example of the power of viral molecular evolution. The results underline the importance of the LEDGF/p75 HIV-1 interplay as target for innovative antiviral therapy. Moreover, the role of LEDGF/p75 in targeting integration will stimulate research on strategies to direct gene therapy vectors into safe landing sites.

  12. Human RNA polymerase III transcriptomes and relationships to Pol II promoter chromatin and enhancer-binding factors.

    Science.gov (United States)

    Oler, Andrew J; Alla, Ravi K; Roberts, Douglas N; Wong, Alexander; Hollenhorst, Peter C; Chandler, Katherine J; Cassiday, Patrick A; Nelson, Cassie A; Hagedorn, Curt H; Graves, Barbara J; Cairns, Bradley R

    2010-05-01

    RNA polymerase (Pol) III transcribes many noncoding RNAs (for example, transfer RNAs) important for translational capacity and other functions. We localized Pol III, alternative TFIIIB complexes (BRF1 or BRF2) and TFIIIC in HeLa cells to determine the Pol III transcriptome, define gene classes and reveal 'TFIIIC-only' sites. Pol III localization in other transformed and primary cell lines reveals previously uncharacterized and cell type-specific Pol III loci as well as one microRNA. Notably, only a fraction of the in silico-predicted Pol III loci are occupied. Many occupied Pol III genes reside within an annotated Pol II promoter. Outside of Pol II promoters, occupied Pol III genes overlap with enhancer-like chromatin and enhancer-binding proteins such as ETS1 and STAT1. Moreover, Pol III occupancy scales with the levels of nearby Pol II, active chromatin and CpG content. These results suggest that active chromatin gates Pol III accessibility to the genome.

  13. Chromatin conformation in living cells: support for a zig-zag model of the 30 nm chromatin fiber

    Science.gov (United States)

    Rydberg, B.; Holley, W. R.; Mian, I. S.; Chatterjee, A.

    1998-01-01

    A new method was used to probe the conformation of chromatin in living mammalian cells. The method employs ionizing radiation and is based on the concept that such radiation induces correlated breaks in DNA strands that are in spatial proximity. Human dermal fibroblasts in G0 phase of the cell cycle and Chinese hamster ovary cells in mitosis were irradiated by X-rays or accelerated ions. Following lysis of the cells, DNA fragments induced by correlated breaks were end-labeled and separated according to size on denaturing polyacrylamide gels. A characteristic peak was obtained for a fragment size of 78 bases, which is the size that corresponds to one turn of DNA around the nucleosome. Additional peaks between 175 and 450 bases reflect the relative position of nearest-neighbor nucleosomes. Theoretical calculations that simulate the indirect and direct effect of radiation on DNA demonstrate that the fragment size distributions are closely related to the chromatin structure model used. Comparison of the experimental data with theoretical results support a zig-zag model of the chromatin fiber rather than a simple helical model. Thus, radiation-induced damage analysis can provide information on chromatin structure in the living cell. Copyright 1998 Academic Press.

  14. Biogenic nonmethane hydrocarbon emissions estimated from tethered balloon observations

    Science.gov (United States)

    Davis, K. J.; Lenschow, D. H.; Zimmerman, P. R.

    1994-01-01

    A new technique for estimating surface fluxes of trace gases, the mixed-layer gradient technique, is used to calculate isoprene and terpene emissions from forests. The technique is applied to tethered balloon measurements made over the Amazon forest and a pine-oak forest in Alabama at altitudes up to 300 m. The observations were made during the dry season Amazon Boundary Layer Experiment (ABLE 2A) and the Rural Oxidants in the Southern Environment 1990 experiment (ROSE I). Results from large eddy simulations of scalar transport in the clear convective boundary layer are used to infer fluxes from the balloon profiles. Profiles from the Amazon give a mean daytime emission of 3630 +/- 1400 micrograms isoprene sq m/h, where the uncertainty represents the standard deviation of the mean of eight flux estimates. Twenty profiles from Alabama give emissions of 4470 +/- 3300 micrograms isoprene sq m/h, 1740 +/- 1060 micrograms alpha-pinene sq m/h, and 790 +/- 560 micrograms beta-pinene sq m/h, respectively. These results are in agreement with emissions derived from chemical budgets. The emissions may be overestimated because of uncertainty about how to incorporate the effects of the canopy on the mixed-layer gradients. The large variability in these emission estimates is probably due to the relatively short sampling times of the balloon profiles, though spatially heterogeneous emissions may also play a role. Fluxes derived using this technique are representative of an upwind footprint of several kilometers and are independent of hydrocarbon oxidation rate and mean advection.

  15. ChromNet: Learning the human chromatin network from all ENCODE ChIP-seq data.

    Science.gov (United States)

    Lundberg, Scott M; Tu, William B; Raught, Brian; Penn, Linda Z; Hoffman, Michael M; Lee, Su-In

    2016-04-30

    A cell's epigenome arises from interactions among regulatory factors-transcription factors and histone modifications-co-localized at particular genomic regions. We developed a novel statistical method, ChromNet, to infer a network of these interactions, the chromatin network, by inferring conditional-dependence relationships among a large number of ChIP-seq data sets. We applied ChromNet to all available 1451 ChIP-seq data sets from the ENCODE Project, and showed that ChromNet revealed previously known physical interactions better than alternative approaches. We experimentally validated one of the previously unreported interactions, MYC-HCFC1. An interactive visualization tool is available at http://chromnet.cs.washington.edu.

  16. A tethering complex drives the terminal stage of SNARE-dependent membrane fusion

    Science.gov (United States)

    D'Agostino, Massimo; Risselada, Herre Jelger; Lürick, Anna; Ungermann, Christian; Mayer, Andreas

    2017-11-01

    Membrane fusion in eukaryotic cells mediates the biogenesis of organelles, vesicular traffic between them, and exo- and endocytosis of important signalling molecules, such as hormones and neurotransmitters. Distinct tasks in intracellular membrane fusion have been assigned to conserved protein systems. Tethering proteins mediate the initial recognition and attachment of membranes, whereas SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) protein complexes are considered as the core fusion engine. SNARE complexes provide mechanical energy to distort membranes and drive them through a hemifusion intermediate towards the formation of a fusion pore. This last step is highly energy-demanding. Here we combine the in vivo and in vitro fusion of yeast vacuoles with molecular simulations to show that tethering proteins are critical for overcoming the final energy barrier to fusion pore formation. SNAREs alone drive vacuoles only into the hemifused state. Tethering proteins greatly increase the volume of SNARE complexes and deform the site of hemifusion, which lowers the energy barrier for pore opening and provides the driving force. Thereby, tethering proteins assume a crucial mechanical role in the terminal stage of membrane fusion that is likely to be conserved at multiple steps of vesicular traffic. We therefore propose that SNAREs and tethering proteins should be considered as a single, non-dissociable device that drives fusion. The core fusion machinery may then be larger and more complex than previously thought.

  17. Optimal Trajectory Planning and Coordinated Tracking Control Method of Tethered Space Robot Based on Velocity Impulse

    Directory of Open Access Journals (Sweden)

    Panfeng Huang

    2014-09-01

    Full Text Available The tethered space robot (TSR is a new concept of space robot which consists of a robot platform, space tether and operation robot. This paper presents a multi-objective optimal trajectory planning and a coordinated tracking control scheme for TSR based on velocity impulse in the approaching phase. Both total velocity impulse and flight time are included in this optimization. The non-dominated sorting genetic algorithm is employed to obtain the optimal trajectory Pareto solution using the TSR dynamic model and optimal trajectory planning model. The coordinated tracking control scheme utilizes optimal velocity impulse. Furthermore, the PID controller is designed in order to compensate for the distance measurement errors. The PID control force is optimized and distributed to thrusters and the space tether using a simulated annealing algorithm. The attitude interferential torque of the space tether is compensated a using time-delay algorithm through reaction wheels. The simulation results show that the multi-objective optimal trajectory planning method can reveal the relationships among flight time, fuel consumption, planar view angle and velocity impulse number. This method can provide a series of optimal trajectory according to a number of special tasks. The coordinated control scheme can significantly save thruster fuel for tracking the optimal trajectory, restrain the attitude interferential torque produced by space tether and maintain the relative attitude stability of the operation robot.

  18. Observing Formation of Flux Rope by Tether-cutting Reconnection in the Sun

    Energy Technology Data Exchange (ETDEWEB)

    Xue, Zhike; Yan, Xiaoli; Yang, Liheng; Wang, Jincheng; Zhao, Li, E-mail: zkxue@ynao.ac.cn [Yunnan Observatories, Chinese Academy of Sciences, Kunming Yunnan 650216 (China)

    2017-05-10

    Tether-cutting reconnection is considered as one mechanism for the formation of a flux rope. It has been proposed for more than 30 years; however, so far, direct observations of it are very rare. In this Letter, we present observations of the formation of a flux rope via tether-cutting reconnection in NOAA AR 11967 on 2014 February 2 by combining observations with the New Vacuum Solar Telescope and the Solar Dynamic Observatory . The tether-cutting reconnection occurs between two sets of highly sheared magnetic arcades. Comprehensive observational evidence of the reconnection is as follows: changes of the connections between the arcades, brightenings at the reconnection site, hot outflows, formation of a flux rope, slow-rise motion of the flux rope, and flux cancelation. The outflows are along three directions from the reconnection site to the footpoints with the velocities from 24 ± 1 km s{sup −1} to 69 ± 5 km s{sup −1}. Additionally, it is found that the newly formed flux rope connects far footpoints and has a left-handed twisted structure with many fine threads and a concave-up-shape structure in the middle. All the observations are in agreement with the tether-cutting model and provide evidence that tether-cutting reconnection leads to the formation of the flux rope associated with flux shear flow and cancelation.

  19. A ``Spring-mass'' model of tethered satellite systems: properties of planar periodic motions

    Science.gov (United States)

    Sidorenko, Vladislav V.; Celletti, Alessandra

    2010-06-01

    This paper is devoted to the dynamics in a central gravity field of two point masses connected by a massless tether (the so called “spring-mass” model of tethered satellite systems). Only the motions with straight strained tether are studied, while the case of “slack” tether is not considered. It is assumed that the distance between the point masses is substantially smaller than the distance between the system’s center of mass and the field center. This assumption allows us to treat the motion of the center of mass as an unperturbed Keplerian one, so to focus our study on attitude dynamics. A particular attention is given to the family of planar periodic motions in which the center of mass moves on an elliptic orbit, and the point masses never leave the orbital plane. If the eccentricity tends to zero, the corresponding family admits as a limit case the relative equilibrium in which the tether is elongated along the line joining the center of mass with the field center. We study the bifurcations and the stability of these planar periodic motions with respect to in-plane and out-of-plane perturbations. Our results show that the stable motions take place if the eccentricity of the orbit is sufficiently small.

  20. Shuttle tethered operations: The effect on orbital trajectory and inertial navigation

    Science.gov (United States)

    Lardas, Mark N.

    1989-01-01

    The first full scale test of a large tethered satellite system is planned. The Orbiter will be linked to a 500 kg payload by a 20 km tether, an action with a profound effect on the trajectory of the Orbiter. For the first time in the history of the Shuttle program, the vehicle will conduct prolonged operations with the center of mass of the orbiting system a significant distance from the center of mass of the Space Shuttle Orbiter, a violation of the fundamental assumption made in both the Orbiter ground-based and onboard navigation software. Inertial navigation of tethered operations with the Shuttle is further complicated by the presence of non-conservative forces in the system: Reaction Control System (RCS) translational effects, atmospheric drag, and electro-magnetic dynamics. These can couple with the conservative tether dynamics effects, and degrade the navigation software performance. The primary effects are examined on the Orbiter's trajectory, coupling by conservative forces during tethered operations, and the impact of both on the ability to meet inertial navigation constraints. The impact of electrodynamics, different RCS control modes, commanded attitudes, and attitude deadbands are presented. Operational guidelines which optimize successful mission navigation, and necessary navigation constraints are discussed.

  1. Determination of a quantitative parameter to evaluate swimming technique based on the maximal tethered swimming test.

    Science.gov (United States)

    Soncin, Rafael; Mezêncio, Bruno; Ferreira, Jacielle Carolina; Rodrigues, Sara Andrade; Huebner, Rudolf; Serrão, Julio Cerca; Szmuchrowski, Leszek

    2017-06-01

    The aim of this study was to propose a new force parameter, associated with swimmers' technique and performance. Twelve swimmers performed five repetitions of 25 m sprint crawl and a tethered swimming test with maximal effort. The parameters calculated were: the mean swimming velocity for crawl sprint, the mean propulsive force of the tethered swimming test as well as an oscillation parameter calculated from force fluctuation. The oscillation parameter evaluates the force variation around the mean force during the tethered test as a measure of swimming technique. Two parameters showed significant correlations with swimming velocity: the mean force during the tethered swimming (r = 0.85) and the product of the mean force square root and the oscillation (r = 0.86). However, the intercept coefficient was significantly different from zero only for the mean force, suggesting that although the correlation coefficient of the parameters was similar, part of the mean velocity magnitude that was not associated with the mean force was associated with the product of the mean force square root and the oscillation. Thus, force fluctuation during tethered swimming can be used as a quantitative index of swimmers' technique.

  2. Chromatin analyses of Zymoseptoria tritici: Methods for chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq).

    Science.gov (United States)

    Soyer, Jessica L; Möller, Mareike; Schotanus, Klaas; Connolly, Lanelle R; Galazka, Jonathan M; Freitag, Michael; Stukenbrock, Eva H

    2015-06-01

    The presence or absence of specific transcription factors, chromatin remodeling machineries, chromatin modification enzymes, post-translational histone modifications and histone variants all play crucial roles in the regulation of pathogenicity genes. Chromatin immunoprecipitation (ChIP) followed by high-throughput sequencing (ChIP-seq) provides an important tool to study genome-wide protein-DNA interactions to help understand gene regulation in the context of native chromatin. ChIP-seq is a convenient in vivo technique to identify, map and characterize occupancy of specific DNA fragments with proteins against which specific antibodies exist or which can be epitope-tagged in vivo. We optimized existing ChIP protocols for use in the wheat pathogen Zymoseptoria tritici and closely related sister species. Here, we provide a detailed method, underscoring which aspects of the technique are organism-specific. Library preparation for Illumina sequencing is described, as this is currently the most widely used ChIP-seq method. One approach for the analysis and visualization of representative sequence is described; improved tools for these analyses are constantly being developed. Using ChIP-seq with antibodies against H3K4me2, which is considered a mark for euchromatin or H3K9me3 and H3K27me3, which are considered marks for heterochromatin, the overall distribution of euchromatin and heterochromatin in the genome of Z. tritici can be determined. Our ChIP-seq protocol was also successfully applied to Z. tritici strains with high levels of melanization or aberrant colony morphology, and to different species of the genus (Z. ardabiliae and Z. pseudotritici), suggesting that our technique is robust. The methods described here provide a powerful framework to study new aspects of chromatin biology and gene regulation in this prominent wheat pathogen. Copyright © 2015 Elsevier Inc. All rights reserved.

  3. Working memory training triggers delayed chromatin remodeling in the mouse corticostriatothalamic circuit.

    Science.gov (United States)

    Cassanelli, Pablo Martín; Cladouchos, María Laura; Fernández Macedo, Georgina; Sifonios, Laura; Giaccardi, Laura Inés; Gutiérrez, María Laura; Gravielle, María Clara; Wikinski, Silvia

    2015-07-03

    Working memory is a cognitive function serving goal-oriented behavior. In the last decade, working memory training has been shown to improve performance and its efficacy for the treatment of several neuropsychiatric disorders has begun to be examined. Neuroimaging studies have contributed to elucidate the brain areas involved but little is known about the underlying cellular events. A growing body of evidence has provided a link between working memory and relatively long-lasting epigenetic changes. However, the effects elicited by working memory training at the epigenetic level remain unknown. In this study we establish an animal model of working memory training and explore the changes in histone H3 acetylation (H3K9,14Ac) and histone H3 dimethylation on lysine 27 (H3K27Me2) triggered by the procedure in the brain regions of the corticostriatothalamic circuit (prelimbic/infralimbic cortex (PrL/IL), dorsomedial striatum (DMSt) and dorsomedial thalamus (DMTh)). Mice trained on a spontaneous alternation task showed improved alternation scores when tested with a retention interval that disrupts the performance of untrained animals. We then determined the involvement of the brain areas of the corticostriatothalamic circuit in working memory training by measuring the marker of neuronal activation c-fos. We observed increased c-fos levels in PrL/IL and DMSt in trained mice 90min after training. These animals also presented lower immunoreactivity for H3K9,14Ac in DMSt 24h but not 90min after the procedure. Increases in H3K27Me2, a repressive chromatin mark, were found in the DMSt and DMTh 24h after the task. Altogether, we present a mouse model to study the cellular underpinnings of working memory training and provide evidence indicating delayed chromatin remodeling towards repression triggered by the procedure. Copyright © 2015 Elsevier Inc. All rights reserved.

  4. Measurement of calcium influx in tethered rings of rabbit aorta under tension

    International Nuclear Information System (INIS)

    Gleason, M.M.; Ratz, P.H.; Flaim, S.F.

    1985-01-01

    Calcium (Ca) influx in vascular smooth muscle is routinely measured in untethered preparations not under passive stretch, and Ca influx data are correlated with data for steady-state isometric tension obtained under parallel conditions from tethered preparations under passive stretch. The validity of this method was tested by simultaneous measurement of Ca influx and tension in tethered rings of rabbit thoracic aorta. Ca influx ( 45 Ca 3-min pulse) and tension were measured at 3 and 30 min after norepinephrine (NE) or KCl and under control (no agonist) conditions. Active tension was significantly altered by variations in passive tension. Ca influx was unaffected by passive tension under control, NE, or KCl conditions, and results were similar at 3 and 30 min. The results confirm the validity of correlating Ca influx data from untethered rings with steady-state contractile response data obtained from tethered rings under similar experimental conditions

  5. Nonlinear Control of Electrodynamic Tether in Equatorial or Somewhat Inclined Orbits

    DEFF Research Database (Denmark)

    Larsen, Martin Birkelund; Blanke, Mogens

    2007-01-01

    This paper applies different control design methods to a tethered satellite system (TSS) to investigate essential control properties of this under-actuated and nonlinear system. When the tether position in the orbit plane is controlled by the tether current, out of orbit plane motions occur...... as an unwanted side effect, due to nonlinear interaction with the Earth’s magnetic field. This paper focus on the uncontrollable out-of-plane motions and the robustness against B-field uncertainty associated with each of three popular controller design methodologies for nonlinear systems: linear quadratic...... feedback designed for the controllable subspace of the system, a feedback linearization design and a sliding mode control. The controllers are evaluated by their ability to suppress variations in the B-field and their robustness with respect to the internal dynamics....

  6. Diamond surface functionalization with biomimicry – Amine surface tether and thiol moiety for electrochemical sensors

    Energy Technology Data Exchange (ETDEWEB)

    Sund, James B., E-mail: jim@jamessund.com [Department of Electrical and Computer Engineering, Duke University, Durham, NC (United States); Causey, Corey P. [Departments of Chemistry and Biochemistry, Duke University, Durham, NC (United States); Wolter, Scott D. [Department of Physics, Elon University, Elon, NC 27244 (United States); Parker, Charles B., E-mail: charles.parker@duke.edu [Department of Electrical and Computer Engineering, Duke University, Durham, NC (United States); Stoner, Brian R. [Department of Electrical and Computer Engineering, Duke University, Durham, NC (United States); Research Triangle Institute (RTI) International, Research Triangle Park, NC (United States); Toone, Eric J. [Departments of Chemistry and Biochemistry, Duke University, Durham, NC (United States); Glass, Jeffrey T. [Department of Electrical and Computer Engineering, Duke University, Durham, NC (United States)

    2014-05-01

    Highlights: • Diamond surfaces were functionalized with organic molecules using a novel approach. • Used biomimicry to select a molecule to bind NO, similar to the human body. • Molecular orbital theory predicted the molecule-analyte oxidation behavior. • A thiol moiety was attached to an amine surface tether on the diamond surface. • XPS analysis verified each surface functionalization step. - Abstract: The surface of conducting diamond was functionalized with a terminal thiol group that is capable of binding and detecting nitrogen–oxygen species. The functionalization process employed multiple steps starting with doped diamond films grown by plasma enhanced chemical vapor deposition followed by hydrogen termination and photochemical attachment of a chemically protected amine alkene. The surface tether was deprotected to reveal the amine functionality, which enabled the tether to be extended with surface chemistry to add a terminal thiol moiety for electrochemical sensing applications. Each step of the process was validated using X-ray photoelectron spectroscopy analysis.

  7. Dynamics and control of three-body tethered system in large elliptic orbits

    Science.gov (United States)

    Shi, Gefei; Zhu, Zhanxia; Zhu, Zheng H.

    2018-03-01

    This paper investigates the dynamic characteristics a three-body tethered satellite system in large elliptic orbits and the control strategy to suppress the libration of the system in orbital transfer process. The system is modeled by a two-piece dumbbell model in the domain of true anomaly. The model consists of one main satellite and two subsatellites connected with two straight, massless and inextensible tethers. Two control strategies based on the sliding mode control are developed to control the libration to the zero state and the steady state respectively. The results of numerical simulations show that the proposed control scheme has good performance in controlling the libration motion of a three-body tethered satellite system in an elliptic orbit with large eccentricity by limited control inputs. Furthermore, Hamiltonians in both states are examined and it shows that less control input is required to control the libration motion to the steady state than that of zero state.

  8. Increased chromatin plasticity supports enhanced metastatic potential of mouse melanoma cells.

    Science.gov (United States)

    Maizels, Yael; Elbaz, Adi; Hernandez-Vicens, Rosari; Sandrusy, Oshrat; Rosenberg, Anna; Gerlitz, Gabi

    2017-08-15

    Metastasis formation is strongly dependent on the migration capabilities of tumor cells. Recently it has become apparent that nuclear structure and morphology affect the cellular ability to migrate. Previously we found that migration of melanoma cells is both associated with and dependent on global chromatin condensation. Therefore, we anticipated that tumor progression would be associated with increased chromatin condensation. Interestingly, the opposite has been reported for melanoma. In trying to resolve this contradiction, we show that during growth conditions, tumor progression is associated with global chromatin de-condensation that is beneficial for faster proliferation. However, upon induction of migration, in both low- and high-metastatic mouse melanoma cells chromatin undergoes condensation to support cell migration. Our results reveal that throughout tumor progression induction of chromatin condensation by migration signals is maintained, whereas the organization of chromatin during growth conditions is altered. Thus, tumor progression is associated with an increase in chromatin dynamics. Copyright © 2017 Elsevier Inc. All rights reserved.

  9. Widespread Chromatin Accessibility at Repetitive Elements Links Stem Cells with Human Cancer

    Directory of Open Access Journals (Sweden)

    Nicholas C. Gomez

    2016-11-01

    Full Text Available Chromatin regulation is critical for differentiation and disease. However, features linking the chromatin environment of stem cells with disease remain largely unknown. We explored chromatin accessibility in embryonic and multipotent stem cells and unexpectedly identified widespread chromatin accessibility at repetitive elements. Integrating genomic and biochemical approaches, we demonstrate that these sites of increased accessibility are associated with well-positioned nucleosomes marked by distinct histone modifications. Differentiation is accompanied by chromatin remodeling at repetitive elements associated with altered expression of genes in relevant developmental pathways. Remarkably, we found that the chromatin environment of Ewing sarcoma, a mesenchymally derived tumor, is shared with primary mesenchymal stem cells (MSCs. Accessibility at repetitive elements in MSCs offers a permissive environment that is exploited by the critical oncogene responsible for this cancer. Our data demonstrate that stem cells harbor a unique chromatin landscape characterized by accessibility at repetitive elements, a feature associated with differentiation and oncogenesis.

  10. Airborne imaging for heritage documentation using the Fotokite tethered flying camera

    Science.gov (United States)

    Verhoeven, Geert; Lupashin, Sergei; Briese, Christian; Doneus, Michael

    2014-05-01

    safe operation of these devices is still an issue, certainly when flying on locations which can be crowded (such as students on excavations or tourists walking around historic places). As the future of UAS regulation remains unclear, this talk presents an alternative approach to aerial imaging: the Fotokite. Developed at the ETH Zürich, the Fotokite is a tethered flying camera that is essentially a multi-copter connected to the ground with a taut tether to achieve controlled flight. Crucially, it relies solely on onboard IMU (Inertial Measurement Unit) measurements to fly, launches in seconds, and is classified as not a UAS (Unmanned Aerial System), e.g. in the latest FAA (Federal Aviation Administration) UAS proposal. As a result it may be used for imaging cultural heritage in a variety of environments and settings with minimal training by non-experienced pilots. Furthermore, it is subject to less extensive certification, regulation and import/export restrictions, making it a viable solution for use at a greater range of sites than traditional methods. Unlike a balloon or a kite it is not subject to particular weather conditions and, thanks to active stabilization, is capable of a variety of intelligent flight modes. Finally, it is compact and lightweight, making it easy to transport and deploy, and its lack of reliance on GNSS (Global Navigation Satellite System) makes it possible to use in urban, overbuilt areas. After outlining its operating principles, the talk will present some archaeological case studies in which the Fotokite was used, hereby assessing its capabilities compared to the conventional UAS's on the market.

  11. Differential Regulation of Synaptic Vesicle Tethering and Docking by UNC-18 and TOM-1.

    Science.gov (United States)

    Gracheva, Elena O; Maryon, Ed B; Berthelot-Grosjean, Martine; Richmond, Janet E

    2010-01-01

    The assembly of SNARE complexes between syntaxin, SNAP-25 and synaptobrevin is required to prime synaptic vesicles for fusion. Since Munc18 and tomosyn compete for syntaxin interactions, the interplay between these proteins is predicted to be important in regulating synaptic transmission. We explored this possibility, by examining genetic interactions between C. elegans unc-18(Munc18), unc-64(syntaxin) and tom-1(tomosyn). We have previously demonstrated that unc-18 mutants have reduced synaptic transmission, whereas tom-1 mutants exhibit enhanced release. Here we show that the unc-18 mutant release defect is associated with loss of two morphologically distinct vesicle pools; those tethered within 25 nm of the plasma membrane and those docked with the plasma membrane. In contrast, priming defective unc-13 mutants accumulate tethered vesicles, while docked vesicles are greatly reduced, indicating tethering is UNC-18-dependent and occurs in the absence of priming. C. elegans unc-64 mutants phenocopy unc-18 mutants, losing both tethered and docked vesicles, whereas overexpression of open syntaxin preferentially increases vesicle docking, suggesting UNC-18/closed syntaxin interactions are responsible for vesicle tethering. Given the competition between vertebrate tomosyn and Munc18, for syntaxin binding, we hypothesized that C. elegans TOM-1 may inhibit both UNC-18-dependent vesicle targeting steps. Consistent with this hypothesis, tom-1 mutants exhibit enhanced UNC-18 plasma membrane localization and a concomitant increase in both tethered and docked synaptic vesicles. Furthermore, in tom-1;unc-18 double mutants the docked, primed vesicle pool is preferentially rescued relative to unc-18 single mutants. Together these data provide evidence for the differential regulation of two vesicle targeting steps by UNC-18 and TOM-1 through competitive interactions with syntaxin.

  12. Differential regulation of synaptic vesicle tethering and docking by UNC-18 and TOM-1

    Directory of Open Access Journals (Sweden)

    Elena O Gracheva

    2010-10-01

    Full Text Available The assembly of SNARE complexes between syntaxin, SNAP-25 and synaptobrevin is required to prime synaptic vesicles for fusion. Since Munc18 and tomosyn compete for syntaxin interactions, the interplay between these proteins is predicted to be important in regulating synaptic transmission. We explored this possibility, by examining genetic interactions between C. elegans unc-18(Munc18, unc-64(syntaxin and tom-1(tomosyn. We have previously demonstrated that unc-18 mutants have reduced synaptic transmission, whereas tom-1 mutants exhibit enhanced release. Here we show that the unc-18 mutant release defect is associated with loss of two morphologically distinct vesicle pools; those tethered within 25nm of the plasma membrane and those docked with the plasma membrane. In contrast, priming defective unc-13 mutants accumulate tethered vesicles, while docked vesicles are greatly reduced, indicating tethering is UNC-18-dependent and occurs in the absence of priming. C. elegans unc-64 mutants phenocopy unc-18 mutants, losing both tethered and docked vesicles, whereas overexpression of open syntaxin preferentially increases vesicle docking, suggesting UNC-18/closed syntaxin interactions are responsible for vesicle tethering. Given the competition between vertebrate tomosyn and Munc18, for syntaxin binding, we hypothesized that C. elegans TOM-1 may inhibit both UNC-18-dependent vesicle targeting steps. Consistent with this hypothesis, tom-1 mutants exhibit enhanced UNC-18 plasma membrane localization and a concomitant increase in both tethered and docked synaptic vesicles. Furthermore, in tom-1;unc-18 double mutants the docked, primed vesicle pool is preferentially rescued relative to unc-18 single mutants. Together these data provide evidence for the differential regulation of two vesicle targeting steps by UNC-18 and TOM-1 through competitive interactions with syntaxin

  13. Conserved TCP domain of Sas-4/CPAP is essential for pericentriolar material tethering during centrosome biogenesis

    Science.gov (United States)

    Zheng, Xiangdong; Gooi, Li Ming; Wason, Arpit; Gabriel, Elke; Mehrjardi, Narges Zare; Yang, Qian; Zhang, Xingrun; Debec, Alain; Basiri, Marcus L.; Avidor-Reiss, Tomer; Pozniakovsky, Andrei; Poser, Ina; Šarić, Tomo; Hyman, Anthony A.; Li, Haitao; Gopalakrishnan, Jay

    2014-01-01

    Pericentriolar material (PCM) recruitment to centrioles forms a key step in centrosome biogenesis. Deregulation of this process leads to centrosome aberrations causing disorders, one of which is autosomal recessive primary microcephaly (MCPH), a neurodevelopmental disorder where brain size is reduced. During PCM recruitment, the conserved centrosomal protein Sas-4/CPAP/MCPH6, known to play a role in centriole formation, acts as a scaffold for cytoplasmic PCM complexes to bind and then tethers them to centrioles to form functional centrosomes. To understand Sas-4’s tethering role, we determined the crystal structure of its T complex protein 10 (TCP) domain displaying a solvent-exposed single-layer of β-sheets fold. This unique feature of the TCP domain suggests that it could provide an “extended surface-like” platform to tether the Sas-4–PCM scaffold to a centriole. Functional studies in Drosophila, human cells, and human induced pluripotent stem cell-derived neural progenitor cells were used to test this hypothesis, where point mutations within the 9–10th β-strands (β9–10 mutants including a MCPH-associated mutation) perturbed PCM tethering while allowing Sas-4/CPAP to scaffold cytoplasmic PCM complexes. Specifically, the Sas-4 β9–10 mutants displayed perturbed interactions with Ana2, a centrosome duplication factor, and Bld-10, a centriole microtubule-binding protein, suggesting a role for the β9–10 surface in mediating protein–protein interactions for efficient Sas-4–PCM scaffold centriole tethering. Hence, we provide possible insights into how centrosomal protein defects result in human MCPH and how Sas-4 proteins act as a vehicle to tether PCM complexes to centrioles independent of its well-known role in centriole duplication. PMID:24385583

  14. Alternative Fuels

    Science.gov (United States)

    Alternative fuels include gaseous fuels such as hydrogen, natural gas, and propane; alcohols such as ethanol, methanol, and butanol; vegetable and waste-derived oils; and electricity. Overview of alternative fuels is here.

  15. Chromatin Conformation Capture-Based Analysis of Nuclear Architecture.

    Science.gov (United States)

    Grob, Stefan; Grossniklaus, Ueli

    2017-01-01

    Nuclear organization and higher-order chromosome structure in interphase nuclei are thought to have important effects on fundamental biological processes, including chromosome condensation, replication, and transcription. Until recently, however, nuclear organization could only be analyzed microscopically. The development of chromatin conformation capture (3C)-based techniques now allows a detailed look at chromosomal architecture from the level of individual loci to the entire genome. Here we provide a robust Hi-C protocol, allowing the analysis of nuclear organization in nuclei from different wild-type and mutant plant tissues. This method is quantitative and provides a highly efficient and comprehensive way to study chromatin organization during plant development, in response to different environmental stimuli, and in mutants disrupting a variety of processes, including epigenetic pathways regulating gene expression.

  16. Stabilization of periodic solutions in a tethered satellite system by damping injection

    DEFF Research Database (Denmark)

    Larsen, Martin Birkelund; Blanke, Mogens

    2009-01-01

    presents a control design for stabilizing these periodic solutions. The design consists of a control law for stabilizing the open-loop equilibrium and a bias term which forces the system trajectory away from the equilibrium. The tether needs to be positioned away from open-loop equilibrium for the tether...... to affect the orbit parameters. An approximation of the periodic solutions of the closed loop system is found as a series expansion in the parameter plane spanned by the controller gain and the bias term. The stability of the solutions is investigated using linear Floquet analysis of the variational...

  17. Wall effect on fluid–structure interactions of a tethered bluff body

    Energy Technology Data Exchange (ETDEWEB)

    Sharma, Sumant; Raghav, Vrishank, E-mail: vrishank@gatech.edu; Komerath, Narayanan, E-mail: komerath@gatech.edu; Smith, Marilyn

    2013-11-01

    Wind tunnel experiments have shown an unexplained amplification of the free motion of a tethered bluff body in a small wind tunnel relative to that in a large wind tunnel. The influence of wall proximity on fluid–structure interaction is explored using a compound pendulum motion in the plane orthogonal to a steady freestream with a doublet model for aerodynamic forces. Wall proximity amplifies a purely symmetric single degree of freedom oscillation with the addition of an out-of-phase force. The success of this simple level of simulation enables progress to develop metrics for unsteady wall interference in dynamic testing of tethered bluff bodies.

  18. Calculating the electromagnetic field on the earth due to an electrodynamic tethered system in the ionosphere

    Science.gov (United States)

    Estes, Robert D.

    1989-01-01

    A method is presented for calculating the electromagnetic wave field on the earth's surface associated with the operation of an electrodynamic tethered satellite system of constant or slowly varying current in the upper ionosphere. The wave field at the ionospheric boundary and on the earth's surface is obtained by numerical integration. The results suggest that the ionospheric waves do not propagate into the atmosphere and that the image of the Alfven wings from a steady-current tether should be greatly broadened on the earth's surface.

  19. Diamond surface functionalization with biomimicry - Amine surface tether and thiol moiety for electrochemical sensors

    Science.gov (United States)

    Sund, James B.; Causey, Corey P.; Wolter, Scott D.; Parker, Charles B.; Stoner, Brian R.; Toone, Eric J.; Glass, Jeffrey T.

    2014-05-01

    The surface of conducting diamond was functionalized with a terminal thiol group that is capable of binding and detecting nitrogen-oxygen species. The functionalization process employed multiple steps starting with doped diamond films grown by plasma enhanced chemical vapor deposition followed by hydrogen termination and photochemical attachment of a chemically protected amine alkene. The surface tether was deprotected to reveal the amine functionality, which enabled the tether to be extended with surface chemistry to add a terminal thiol moiety for electrochemical sensing applications. Each step of the process was validated using X-ray photoelectron spectroscopy analysis.

  20. Stabilization of periodic solutions in a tethered satellite system by damping injection

    DEFF Research Database (Denmark)

    Larsen, Martin Birkelund; Blanke, Mogens

    2009-01-01

    A spacecraft with electrodynamic tether orbiting the Earth will be subject to a periodic forcing term induced by the variation of the magnetic field along the orbit. The periodic forcing term leads to a family of unstable periodic solutions for a tether carrying a constant current. This paper...... to affect the orbit parameters. An approximation of the periodic solutions of the closed loop system is found as a series expansion in the parameter plane spanned by the controller gain and the bias term. The stability of the solutions is investigated using linear Floquet analysis of the variational...

  1. Mono- and Bis(pyrrolo)tetrathiafulvalene Derivatives Tethered to C60

    DEFF Research Database (Denmark)

    Solano, Marta Vico; Della Pia, E. A.; Jevric, M.

    2014-01-01

    A series of mono- (MPTTF) and bis(pyrrolo) tetrathiafulvalene (BPTTF) derivatives tethered to one or two C-60 moieties was synthesized and characterized. The synthetic strategy for these dumbbell-shaped compounds was based on a 1,3-dipolar cycloaddition reaction between aldehyde-functionalized MP......A series of mono- (MPTTF) and bis(pyrrolo) tetrathiafulvalene (BPTTF) derivatives tethered to one or two C-60 moieties was synthesized and characterized. The synthetic strategy for these dumbbell-shaped compounds was based on a 1,3-dipolar cycloaddition reaction between aldehyde...

  2. Drop Tower tests in preparation of a Tethered Electromagnetic Docking space demonstration

    Science.gov (United States)

    Olivieri, Lorenzo; Francesconi, Alessandro; Antonello, Andrea; Bettiol, Laura; Branz, Francesco; Duzzi, Matteo; Mantellato, Riccardo; Sansone, Francesco; Savioli, Livia

    2016-07-01

    A group of students of the University of Padova is recently developing some technologies to implement a Tethered Electromagnetic Docking (TED) experiment, a novel system for close rendezvous and mating manoeuvres between two spacecraft, consisting in a small tethered probe ejected by the chaser and magnetically guided by a receiving electromagnet mounted on the target. Because of the generated magnetic field, automatic self-alignment and mating are possible; then, as the tether is rewinded, the chaser is able to dock with the target. This concept allows to simplify standard docking procedures, thanks to the reduction of proximity navigation and guidance requirements, as well as consequent fuel reduction. Other interesting applications are expected, from active debris removal to space tugging; in particular, the utilization of the tethered connection for detumbling operations is considered. The realization of a space demonstrator requires a preliminary verification of the critical technologies employed in TED, in particular the magnetic guidance and the probe deploy and retrieve; in the framework of ESA "Drop your Thesis!" 2014 and 2016 campaigns the experiments FELDs (Flexible Electromagnetic Leash Docking system) and STAR (System for Tether Automatic Retrieval) have been focused on the test of such critical elements in the relevant microgravity environment of ZARM Drop Tower in Bremen. In particular, FELDs consisted in a simplified model of TED with a magnetic target interface, a passive tethered probe and its launch system: the experiment allowed to assess the passive self-alignment of the probe with respect to the target and to study the effect of friction between the tether and the release system. Similarly, STAR is investigating the tether actively controlled deployment and retrieval, with the experiment campaign planned on November 2016. In addition, another microgravity experiment is in preparation for the investigation of active magnetic navigation: PACMAN

  3. Low-frequency magnetic field effect on cytoskeleton and chromatin

    Czech Academy of Sciences Publication Activity Database

    Kroupová, Jana; Bártová, Eva; Fojt, Lukáš; Strašák, Luděk; Kozubek, Stanislav; Vetterl, Vladimír

    2006-01-01

    Roč. 70, č. 1 (2006), s. 96-100 ISSN 1567-5394 R&D Projects: GA AV ČR(CZ) IBS5004107; GA AV ČR(CZ) IAA4004404; GA MŠk(CZ) ME 685 Institutional research plan: CEZ:AV0Z50040507 Keywords : magnetic field * chromatin * FISH Subject RIV: BO - Biophysics Impact factor: 1.880, year: 2006

  4. Chromatin Dynamics in Vivo: A Game of Musical Chairs

    OpenAIRE

    Melters, Daniël P.; Nye, Jonathan; Zhao, Haiqing; Dalal, Yamini

    2015-01-01

    Histones are a major component of chromatin, the nucleoprotein complex fundamental to regulating transcription, facilitating cell division, and maintaining genome integrity in almost all eukaryotes. In addition to canonical, replication-dependent histones, replication-independent histone variants exist in most eukaryotes. In recent years, steady progress has been made in understanding how histone variants assemble, their involvement in development, mitosis, transcription, and genome repair. I...

  5. Light scattering measurements supporting helical structures for chromatin in solution.

    Science.gov (United States)

    Campbell, A M; Cotter, R I; Pardon, J F

    1978-05-01

    Laser light scattering measurements have been made on a series of polynucleosomes containing from 50 to 150 nucleosomes. Radii of gyration have been determined as a function of polynucleosome length for different ionic strength solutions. The results suggest that at low ionic strength the chromatin adopts a loosely helical structure rather than a random coil. The helix becomes more regular on increasing the ionic strength, the dimension resembling those proposed by Finch and Klug for their solenoid model.

  6. Chromatin condensation of Xist genomic loci during oogenesis in mice.

    Science.gov (United States)

    Fukuda, Atsushi; Mitani, Atsushi; Miyashita, Toshiyuki; Umezawa, Akihiro; Akutsu, Hidenori

    2015-12-01

    Repression of maternal Xist (Xm-Xist) during preimplantation in mouse embryos is essential for establishing imprinted X chromosome inactivation. Nuclear transplantation (NT) studies using nuclei derived from non-growing (ng) and full-grown (fg) oocytes have indicated that maternal-specific repressive modifications are imposed on Xm-Xist during oogenesis, as well as on autosomal imprinted genes. Recent studies have revealed that histone H3 lysine 9 trimethylation (H3K9me3) enrichments on Xm-Xist promoter regions are involved in silencing at the preimplantation stages. However, whether H3K9me3 is imposed on Xm-Xist during oogenesis is not known. Here, we dissected the chromatin states in ng and fg oocytes and early preimplantation stage embryos. Chromatin immunoprecipitation experiments against H3K9me3 revealed that there was no significant enrichment within the Xm-Xist region during oogenesis. However, NT embryos with ng nuclei (ngNT) showed extensive Xm-Xist derepression and H3K9me3 hypomethylation of the promoter region at the 4-cell stage, which corresponds to the onset of paternal Xist expression. We also found that the chromatin state at the Xist genomic locus became markedly condensed as oocyte growth proceeded. Although the condensed Xm-Xist genomic locus relaxed during early preimplantation phases, the extent of the relaxation across Xm-Xist loci derived from normally developed oocytes was significantly smaller than those of paternal-Xist and ngNT-Xist genomic loci. Furthermore, Xm-Xist from 2-cell metaphase nuclei became derepressed following NT. We propose that chromatin condensation is associated with imprinted Xist repression and that skipping of the condensation step by NT leads to Xist activation during the early preimplantation phase. © 2015. Published by The Company of Biologists Ltd.

  7. Controlled DNA compaction within chromatin: the tail-bridging effect

    OpenAIRE

    Muehlbacher, Frank; Holm, Christian; Schiessel, Helmut

    2005-01-01

    We study the mechanism underlying the attraction between nucleosomes, the fundamental packaging units of DNA inside the chromatin complex. We introduce a simple model of the nucleosome, the eight-tail colloid, consisting of a charged sphere with eight oppositely charged, flexible, grafted chains that represent the terminal histone tails. We demonstrate that our complexes are attracted via the formation of chain bridges and that this attraction can be tuned by changing the fraction of charged ...

  8. Histone occurrence in chromatin from Peridinium balticum, a binucleate dinoflagellate.

    Science.gov (United States)

    Rizzo, P J; Cox, E R

    1977-12-23

    Peridinium balticum is one of two dinoflagellates known to have dissimilar nuclei together in the same cell. One nucleus (dinokaryotic) has permanently condensed chromosomes, while the other (eukaryotic) does not have morphologically distinct chromosomes. Acid extracts of chromatin prepared from a mixture of dinokaryotic and eukaryotic nuclei and purified eukaryotic nuclei give four bands that co-migrate with four of the five histones from calf thymus when analyzed in urea-containing polyacrylamide gels.

  9. Wavelet transform analysis of chromatin texture changes during heat shock.

    Science.gov (United States)

    Herbomel, G; Grichine, A; Fertin, A; Delon, A; Vourc'h, C; Souchier, C; Usson, Y

    2016-06-01

    Texture analysis can be a useful tool to investigate the organization of chromatin. Approaches based on multiscale analysis and in particular the 'à trou' wavelet analysis has already been used for microscopy (Olivo Marin). In order to analyse texture changes, the statistical properties of the wavelet coefficient images were summarized by the first four statistical orders: mean, standard deviation, skewness and kurtosis of the coefficient image histogram. The 'à trou' transform provided a representation of the wavelet coefficients and texture parameters with the same statistical robustness throughout the scale spaces. It was applied for quantifying chromatin texture and heat-induced chromatin changes in living cells. We investigated the changes by both laser scanning and spinning disk confocal microscopies and compared the texture parameters before and after increasing duration of heat shock exposure (15 min, 30 min and 1 h). Furthermore, as activation of the heat shock response also correlates with a rapid localization of HSF1 within a few nuclear structures termed nuclear stress bodies (nSBs), we compared the dynamics of nSBs formation with that of textural changes during 1 h of continuous heat shock. Next, we studied the recovery phase following a 1-h heat shock. Significant differences were observed, particularly affecting the perinucleolar region, even for the shortest heat shock time affecting mostly the skewness and standard deviation. Furthermore, progressive changes could be observed according to the duration of heat shock, mostly affecting fine details (pixel-wise changes) as revealed by the parameters, obtained from the first- and second-order wavelet coefficients. 'A trou' wavelet texture analysis provided a sensitive and efficient tool to investigate minute changes of chromatin. © 2015 The Authors Journal of Microscopy © 2015 Royal Microscopical Society.

  10. Circular chromatin complexes in human lymphocytes high-resolution autoradiography

    International Nuclear Information System (INIS)

    Becak, M.L.; Fukuda-Pizzocaro, K.; Santos, R. de C.S. dos; Brunner, O.

    1985-01-01

    Transcriptionally active chromatin fibers were observed in chromosomes presenting the loops/scaffold configuration. The active fibers showed altered nucleosomes and presented multiforked aspects which led to the formation of ring complexes. The ribonucleoprotein transcripts (RNP) appeared as networks of 0.1 μm or multiples tandemly disposed along the fiber. It is suggested that the ring complexes belong to the human genome. The possibility that these circular structures come from a prokaryote is also considered. (author) [pt

  11. Epigenetic Regulation of Higher Order Chromatin Conformations and Gene Transcription

    OpenAIRE

    Göndör, Anita

    2007-01-01

    Epigenetic states constitute heritable features of the chromatin to regulate when, where and how genes are expressed in the developing conceptus. A special case of epigenetic regulation, genomic imprinting, is defined as parent of origin-dependent monoallelic expression. The Igf2-H19 locus is considered as paradigm of genomic imprinting with a growth-promoting gene, Igf2, expressed paternally and a growth antagonist, H19 encoding a non-coding transcript, expressed only from the maternal allel...

  12. The horizontal sacrum as an indicator of the tethered spinal cord in spina bifida aperta and occulta.

    Science.gov (United States)

    Tubbs, R Shane; Bui, Cuong J; Loukas, Marios; Shoja, Mohammadali M; Oakes, W Jerry

    2007-01-01

    The authors report on symptomatic patients with myelomeningocele (MMC) and lipomyelomeningocele (LMMC) who were found to have changes in their lumbosacral angle (LSA) corresponding to the onset of symptoms indicative of a tethered spinal cord. The authors review data obtained in these two cohorts of patients and compare the LSAs measured in the perinatal period with those seen when the patients presented with symptoms of a tethered spinal cord. Children with LMMC, roughly one third of studied cases, were symptomatic due to a tethered spinal cord at their most recent follow-up. In children in whom the MMC was the closed form at birth, 20 of 30 had symptoms that could be indicative of a tethered spinal cord at their most recent follow-up. The LSA was altered in both groups with symptoms. Signs and symptoms indicative of a tethered spinal cord appear to correspond to increases in the LSA.

  13. Transcription-dependent association of HDAC2 with active chromatin.

    Science.gov (United States)

    Jahan, Sanzida; Sun, Jian-Min; He, Shihua; Davie, James R

    2018-02-01

    Histone deacetylase 2 (HDAC2) catalyzes deacetylation of histones at the promoter and coding regions of transcribed genes and regulates chromatin structure and transcription. To explore the role of HDAC2 and phosphorylated HDAC2 in gene regulation, we studied the location along transcribed genes, the mode of recruitment and the associated proteins with HDAC2 and HDAC2S394ph in chicken polychromatic erythrocytes. We show that HDAC2 and HDAC2S394ph are associated with transcriptionally active chromatin and located in the interchromatin channels. HDAC2S394ph was present primarly at the upstream promoter region of the transcribed CA2 and GAS41 genes, while total HDAC2 was also found within the coding region of the CA2 gene. Recruitment of HDAC2 to these genes was partially dependent upon on-going transcription. Unmodified HDAC2 was associated with RNA binding proteins and interacted with RNA bound to the initiating and elongating forms of RNA polymerase II. HDAC2S394ph was not associated with RNA polymerase II. These results highlight the differential properties of unmodified and phosphorylated HDAC2 and the organization of acetylated transcriptionally active chromatin in the chicken polychromatic erythrocyte. © 2017 Wiley Periodicals, Inc.

  14. Structure of centromere chromatin: from nucleosome to chromosomal architecture.

    Science.gov (United States)

    Schalch, Thomas; Steiner, Florian A

    2017-08-01

    The centromere is essential for the segregation of chromosomes, as it serves as attachment site for microtubules to mediate chromosome segregation during mitosis and meiosis. In most organisms, the centromere is restricted to one chromosomal region that appears as primary constriction on the condensed chromosome and is partitioned into two chromatin domains: The centromere core is characterized by the centromere-specific histone H3 variant CENP-A (also called cenH3) and is required for specifying the centromere and for building the kinetochore complex during mitosis. This core region is generally flanked by pericentric heterochromatin, characterized by nucleosomes containing H3 methylated on lysine 9 (H3K9me) that are bound by heterochromatin proteins. During mitosis, these two domains together form a three-dimensional structure that exposes CENP-A-containing chromatin to the surface for interaction with the kinetochore and microtubules. At the same time, this structure supports the tension generated during the segregation of sister chromatids to opposite poles. In this review, we discuss recent insight into the characteristics of the centromere, from the specialized chromatin structures at the centromere core and the pericentromere to the three-dimensional organization of these regions that make up the functional centromere.

  15. Antisense transcription-dependent chromatin signature modulates sense transcript dynamics.

    Science.gov (United States)

    Brown, Thomas; Howe, Françoise S; Murray, Struan C; Wouters, Meredith; Lorenz, Philipp; Seward, Emily; Rata, Scott; Angel, Andrew; Mellor, Jane

    2018-02-12

    Antisense transcription is widespread in genomes. Despite large differences in gene size and architecture, we find that yeast and human genes share a unique, antisense transcription-associated chromatin signature. We asked whether this signature is related to a biological function for antisense transcription. Using quantitative RNA-FISH, we observed changes in sense transcript distributions in nuclei and cytoplasm as antisense transcript levels were altered. To determine the mechanistic differences underlying these distributions, we developed a mathematical framework describing transcription from initiation to transcript degradation. At GAL1 , high levels of antisense transcription alter sense transcription dynamics, reducing rates of transcript production and processing, while increasing transcript stability. This relationship with transcript stability is also observed as a genome-wide association. Establishing the antisense transcription-associated chromatin signature through disruption of the Set3C histone deacetylase activity is sufficient to similarly change these rates even in the absence of antisense transcription. Thus, antisense transcription alters sense transcription dynamics in a chromatin-dependent manner. © 2018 The Authors. Published under the terms of the CC BY 4.0 license.

  16. The Drosophila CLAMP protein associates with diverse proteins on chromatin.

    Science.gov (United States)

    Urban, Jennifer A; Urban, John M; Kuzu, Guray; Larschan, Erica N

    2017-01-01

    Gaining new insights into gene regulation involves an in-depth understanding of protein-protein interactions on chromatin. A powerful model for studying mechanisms of gene regulation is dosage compensation, a process that targets the X-chromosome to equalize gene expression between XY males and XX females. We previously identified a zinc finger protein in Drosophila melanogaster that plays a sex-specific role in targeting the Male-specific lethal (MSL) dosage compensation complex to the male X-chromosome, called the Chromatin-Linked Adapter for MSL Proteins (CLAMP). More recently, we established that CLAMP has non-sex-specific roles as an essential protein that regulates chromatin accessibility at promoters genome-wide. To identify associations between CLAMP and other factors in both male and female cells, we used two complementary mass spectrometry approaches. We demonstrate that CLAMP associates with the transcriptional regulator complex Negative Elongation Factor (NELF) in both sexes and determine that CLAMP reduces NELF recruitment to several target genes. In sum, we have identified many new CLAMP-associated factors and provide a resource for further study of this little understood essential protein.

  17. Targeted modulation of alternative splicing by TALE-directed chromatin editing

    Czech Academy of Sciences Publication Activity Database

    Bieberstein, Nicole; Staněk, David

    2015-01-01

    Roč. 282, SI (2015), s. 210-210 ISSN 1742-464X. [40th Congress of the Federation-of-European-Biochemical-Societies (FEBS) - The Biochemical Basis of Life. 04.07.2015-09.07.2015, Berlín] R&D Projects: GA ČR(CZ) GBP305/12/G034 Institutional support: RVO:68378050 Keywords : histone methylation * pre-mRNA splicing * TALEN Subject RIV: EB - Genetics ; Molecular Biology

  18. ADP-ribose-specific chromatin-affinity purification for investigating genome-wide or locus-specific chromatin ADP-ribosylation.

    Science.gov (United States)

    Bisceglie, Lavinia; Bartolomei, Giody; Hottiger, Michael O

    2017-09-01

    Protein ADP-ribosylation is a structurally heterogeneous post-translational modification (PTM) that influences the physicochemical and biological properties of the modified protein. ADP-ribosylation of chromatin changes its structural properties, thereby regulating important nuclear functions. A lack of suitable antibodies for chromatin immunoprecipitation (ChIP) has so far prevented a comprehensive analysis of DNA-associated protein ADP-ribosylation. To analyze chromatin ADP-ribosylation, we recently developed a novel ADP-ribose-specific chromatin-affinity purification (ADPr-ChAP) methodology that uses the recently identified ADP-ribose-binding domains RNF146 WWE and Af1521. In this protocol, we describe how to use this robust and versatile method for genome-wide and loci-specific localization of chromatin ADP-ribosylation. ADPr-ChAP enables bioinformatic comparisons of ADP-ribosylation with other chromatin modifications and is useful for understanding how ADP-ribosylation regulates biologically important cellular processes. ADPr-ChAP takes 1 week and requires standard skills in molecular biology and biochemistry. Although not covered in detail here, this technique can also be combined with conventional ChIP or DNA analysis to define the histone marks specifically associated with the ADP-ribosylated chromatin fractions and dissect the molecular mechanism and functional role of chromatin ADP-ribosylation.

  19. The protein encoded by the proto-oncogene DEK changes the topology of chromatin and reduces the efficiency of DNA replication in a chromatin-specific manner

    DEFF Research Database (Denmark)

    Alexiadis, V; Waldmann, T; Andersen, Jens S.

    2000-01-01

    The structure of chromatin regulates the genetic activity of the underlying DNA sequence. We report here that the protein encoded by the proto-oncogene DEK, which is involved in acute myelogenous leukemia, induces alterations of the superhelical density of DNA in chromatin. The change in topology...

  20. 3C-digital PCR for quantification of chromatin interactions.

    Science.gov (United States)

    Du, Meijun; Wang, Liang

    2016-12-06

    Chromosome conformation capture (3C) is a powerful and widely used technique for detecting the physical interactions between chromatin regions in vivo. The principle of 3C is to convert physical chromatin interactions into specific DNA ligation products, which are then detected by quantitative polymerase chain reaction (qPCR). However, 3C-qPCR assays are often complicated by the necessity of normalization controls to correct for amplification biases. In addition, qPCR is often limited to a certain cycle number, making it difficult to detect fragment ligations with low frequency. Recently, digital PCR (dPCR) technology has become available, which allows for highly sensitive nucleic acid quantification. Main advantage of dPCR is its high precision of absolute nucleic acid quantification without requirement of normalization controls. To demonstrate the utility of dPCR in quantifying chromatin interactions, we examined two prostate cancer risk loci at 8q24 and 2p11.2 for their interaction target genes MYC and CAPG in LNCaP cell line. We designed anchor and testing primers at known regulatory element fragments and target gene regions, respectively. dPCR results showed that interaction frequency between the regulatory element and MYC gene promoter was 0.7 (95% CI 0.40-1.10) copies per 1000 genome copies while other regions showed relatively low ligation frequencies. The dPCR results also showed that the ligation frequencies between the regulatory element and two EcoRI fragments containing CAPG gene promoter were 1.9 copies (95% CI 1.41-2.47) and 1.3 copies per 1000 genome copies (95% CI 0.76-1.92), respectively, while the interaction signals were reduced on either side of the promoter region of CAPG gene. Additionally, we observed comparable results from 3C-dPCR and 3C-qPCR at 2p11.2 in another cell line (DU145). Compared to traditional 3C-qPCR, our results show that 3C-dPCR is much simpler and more sensitive to detect weak chromatin interactions. It may eliminate

  1. Exploration of Two Training Paradigms Using Forced Induced Weight Shifting With the Tethered Pelvic Assist Device to Reduce Asymmetry in Individuals After Stroke: Case Reports.

    Science.gov (United States)

    Bishop, Lauri; Khan, Moiz; Martelli, Dario; Quinn, Lori; Stein, Joel; Agrawal, Sunil

    2017-10-01

    Many robotic devices in rehabilitation incorporate an assist-as-needed haptic guidance paradigm to promote training. This error reduction model, while beneficial for skill acquisition, could be detrimental for long-term retention. Error augmentation (EA) models have been explored as alternatives. A robotic Tethered Pelvic Assist Device has been developed to study force application to the pelvis on gait and was used here to induce weight shift onto the paretic (error reduction) or nonparetic (error augmentation) limb during treadmill training. The purpose of these case reports is to examine effects of training with these two paradigms to reduce load force asymmetry during gait in two individuals after stroke (>6 mos). Participants presented with baseline gait asymmetry, although independent community ambulators. Participants underwent 1-hr trainings for 3 days using either the error reduction or error augmentation model. Outcomes included the Borg rating of perceived exertion scale for treatment tolerance and measures of force and stance symmetry. Both participants tolerated training. Force symmetry (measured on treadmill) improved from pretraining to posttraining (36.58% and 14.64% gains), however, with limited transfer to overground gait measures (stance symmetry gains of 9.74% and 16.21%). Training with the Tethered Pelvic Assist Device device proved feasible to improve force symmetry on the treadmill irrespective of training model. Future work should consider methods to increase transfer to overground gait.

  2. Linker histone partial phosphorylation: effects on secondary structure and chromatin condensation

    Science.gov (United States)

    Lopez, Rita; Sarg, Bettina; Lindner, Herbert; Bartolomé, Salvador; Ponte, Inma; Suau, Pedro; Roque, Alicia

    2015-01-01

    Linker histones are involved in chromatin higher-order structure and gene regulation. We have successfully achieved partial phosphorylation of linker histones in chicken erythrocyte soluble chromatin with CDK2, as indicated by HPCE, MALDI-TOF and Tandem MS. We have studied the effects of linker histone partial phosphorylation on secondary structure and chromatin condensation. Infrared spectroscopy analysis showed a gradual increase of β-structure in the phosphorylated samples, concomitant to a decrease in α-helix/turns, with increasing linker histone phosphorylation. This conformational change could act as the first step in the phosphorylation-induced effects on chromatin condensation. A decrease of the sedimentation rate through sucrose gradients of the phosphorylated samples was observed, indicating a global relaxation of the 30-nm fiber following linker histone phosphorylation. Analysis of specific genes, combining nuclease digestion and qPCR, showed that phosphorylated samples were more accessible than unphosphorylated samples, suggesting local chromatin relaxation. Chromatin aggregation was induced by MgCl2 and analyzed by dynamic light scattering (DLS). Phosphorylated chromatin had lower percentages in volume of aggregated molecules and the aggregates had smaller hydrodynamic diameter than unphosphorylated chromatin, indicating that linker histone phosphorylation impaired chromatin aggregation. These findings provide new insights into the effects of linker histone phosphorylation in chromatin condensation. PMID:25870416

  3. RNA is an integral component of chromatin that contributes to its structural organization.

    Directory of Open Access Journals (Sweden)

    Antonio Rodríguez-Campos

    Full Text Available Chromatin structure is influenced by multiples factors, such as pH, temperature, nature and concentration of counterions, post-translational modifications of histones and binding of structural non-histone proteins. RNA is also known to contribute to the regulation of chromatin structure as chromatin-induced gene silencing was shown to depend on the RNAi machinery in S. pombe, plants and Drosophila. Moreover, both in Drosophila and mammals, dosage compensation requires the contribution of specific non-coding RNAs. However, whether RNA itself plays a direct structural role in chromatin is not known. Here, we report results that indicate a general structural role for RNA in eukaryotic chromatin. RNA is found associated to purified chromatin prepared from chicken liver, or cultured Drosophila S2 cells, and treatment with RNase A alters the structural properties of chromatin. Our results indicate that chromatin-associated RNAs, which account for 2%-5% of total chromatin-associated nucleic acids, are polyA(- and show a size similar to that of the DNA contained in the corresponding chromatin fragments. Chromatin-associated RNA(s are not likely to correspond to nascent transcripts as they are also found bound to chromatin when cells are treated with alpha-amanitin. After treatment with RNase A, chromatin fragments of molecular weight >3.000 bp of DNA showed reduced sedimentation through sucrose gradients and increased sensitivity to micrococcal nuclease digestion. This structural transition, which is observed both at euchromatic and heterochromatic regions, proceeds without loss of histone H1 or any significant change in core-histone composition and integrity.

  4. Cryo–electron tomography reveals a critical role of RIM1α in synaptic vesicle tethering

    Science.gov (United States)

    Fernández-Busnadiego, Rubén; Asano, Shoh; Oprisoreanu, Ana-Maria; Sakata, Eri; Doengi, Michael; Kochovski, Zdravko; Zürner, Magdalena; Stein, Valentin; Schoch, Susanne; Baumeister, Wolfgang

    2013-01-01

    Synaptic vesicles are embedded in a complex filamentous network at the presynaptic terminal. Before fusion, vesicles are linked to the active zone (AZ) by short filaments (tethers). The identity of the molecules that form and regulate tethers remains unknown, but Rab3-interacting molecule (RIM) is a prominent candidate, given its central role in AZ organization. In this paper, we analyzed presynaptic architecture of RIM1α knockout (KO) mice by cryo–electron tomography. In stark contrast to previous work on dehydrated, chemically fixed samples, our data show significant alterations in vesicle distribution and AZ tethering that could provide a structural basis for the functional deficits of RIM1α KO synapses. Proteasome inhibition reversed these structural defects, suggesting a functional recovery confirmed by electrophysiological recordings. Altogether, our results not only point to the ubiquitin–proteasome system as an important regulator of presynaptic architecture and function but also show that the tethering machinery plays a critical role in exocytosis, converging into a structural model of synaptic vesicle priming by RIM1α. PMID:23712261

  5. Cryo-electron tomography reveals a critical role of RIM1α in synaptic vesicle tethering.

    Science.gov (United States)

    Fernández-Busnadiego, Rubén; Asano, Shoh; Oprisoreanu, Ana-Maria; Sakata, Eri; Doengi, Michael; Kochovski, Zdravko; Zürner, Magdalena; Stein, Valentin; Schoch, Susanne; Baumeister, Wolfgang; Lucić, Vladan

    2013-05-27

    Synaptic vesicles are embedded in a complex filamentous network at the presynaptic terminal. Before fusion, vesicles are linked to the active zone (AZ) by short filaments (tethers). The identity of the molecules that form and regulate tethers remains unknown, but Rab3-interacting molecule (RIM) is a prominent candidate, given its central role in AZ organization. In this paper, we analyzed presynaptic architecture of RIM1α knockout (KO) mice by cryo-electron tomography. In stark contrast to previous work on dehydrated, chemically fixed samples, our data show significant alterations in vesicle distribution and AZ tethering that could provide a structural basis for the functional deficits of RIM1α KO synapses. Proteasome inhibition reversed these structural defects, suggesting a functional recovery confirmed by electrophysiological recordings. Altogether, our results not only point to the ubiquitin-proteasome system as an important regulator of presynaptic architecture and function but also show that the tethering machinery plays a critical role in exocytosis, converging into a structural model of synaptic vesicle priming by RIM1α.

  6. Tethering a laminin peptide to a crosslinked collagen scaffold for biofunctionality.

    Science.gov (United States)

    Damodaran, Gopinath; Collighan, Russell; Griffin, Martin; Pandit, Abhay

    2009-06-15

    Cell adhesion peptide regulates various cellular functions like proliferation, attachment, and spreading. The cellular response to laminin peptide (PPFLMLLKGSTR), a motif of laminin-5 alpha3 chain, tethered to type I collagen, crosslinked using microbial transglutaminase (mTGase) was investigated. mTGase is an enzyme that initiates crosslinking by reacting with the glutamine and lysine residues on the collagen fibers stabilizing the molecular structure. In this study that tethering of the laminin peptide in a mTGase crosslinked collagen scaffold enhanced cell proliferation and attachment. Laminin peptide tethered crosslinked scaffold showed unaltered cell morphology of 3T3 fibroblasts when compared with collagen and crosslinked scaffold. The triple helical structure of collagen remained unaltered by the addition of laminin peptide. In addition a dose-dependent affinity of the laminin peptide towards collagen was seen. The degree of crosslinking was measured by amino acid analysis, differential scanning calorimeter and fourier transform infrared spectroscopy. Increased crosslinking was observed in mTGase crosslinked group. mTGase crosslinking showed higher shrinkage temperature. There was alteration in the fibrillar architecture due to the crosslinking activity of mTGase. Hence, the use of enzyme-mediated linking shows promise in tethering cell adhesive peptides through biodegradable scaffolds. Copyright 2008 Wiley Periodicals, Inc.

  7. Summary of Data Analysis of the YES2 Tethered SpaceMail Experiment

    NARCIS (Netherlands)

    Kruijff, M.; Van der Heide, E.J.; Ockels, W.J.; Gill, E.K.A.

    2008-01-01

    The 2nd Young Engineers' Satellite (YES2) is a 36 kg student-built experiment that piggybacked on the Foton-M3 microgravity platform in September 2007. YES2 intended to demonstrate tethered SpaceMail, a concept for frequent sample return originally proposed for the International Space Station (ISS).

  8. Tethered Cord Syndrome with Syrinx in A Nigerian Adult Female: A ...

    African Journals Online (AJOL)

    Alasia Datonye

    *Department of Radiology and **Department of Internal Medicine, University of Port. Harcourt Teaching ... 1,2 of the spinal cord . This may be secondary to any of a heterogeneous group of disorder e.g spinal lipomas, lipomatous filum,and split cord malformations. It typically .... Ratliff J, Mahoney PS, Kline DG. Tethered cord.

  9. Optimal Cross-Wind Towing and Power Generation with Tethered Kites

    NARCIS (Netherlands)

    Williams, P.; Lansdorp, B.; Ockels, W.

    2007-01-01

    Non-powered flight vehicles such as kites can provide a means of transmitting wind energy from higher altitudes to the ground via tethers. Although there have been many proposals for systems to extract wind energy from higher altitudes, this paper focuses on the use of a light lifting body at the

  10. Nonholonomic Closed-loop Velocity Control of a Soft-tethered Magnetic Capsule Endoscope

    Science.gov (United States)

    Taddese, Addisu Z.; Slawinski, Piotr R.; Obstein, Keith L.; Valdastri, Pietro

    2017-01-01

    In this paper, we demonstrate velocity-level closed-loop control of a tethered magnetic capsule endoscope that is actuated via serial manipulator with a permanent magnet at its end-effector. Closed-loop control (2 degrees-of-freedom in position, and 2 in orientation) is made possible with the use of a real-time magnetic localization algorithm that utilizes the actuating magnetic field and thus does not require additional hardware. Velocity control is implemented to create smooth motion that is clinically necessary for colorectal cancer diagnostics. Our control algorithm generates a spline that passes through a set of input points that roughly defines the shape of the desired trajectory. The velocity controller acts in the tangential direction to the path, while a secondary position controller enforces a nonholonomic constraint on capsule motion. A soft nonholonomic constraint is naturally imposed by the lumen while we enforce a strict constraint for both more accurate estimation of tether disturbance and hypothesized intuitiveness for a clinician's teleoperation. An integrating disturbance force estimation control term is introduced to predict the disturbance of the tether. This paper presents the theoretical formulations and experimental validation of our methodology. Results show the system's ability to achieve a repeatable velocity step response with low steady-state error as well as ability of the tethered capsule to maneuver around a bend. PMID:28316873

  11. Endogenous opioids are involved in abnormal stereotyped behaviour of tethered sows

    NARCIS (Netherlands)

    Cronin, G.M.; Wiepkema, P.R.; Ree, van J.M.

    1985-01-01

    Tethered sows continuously performed stereotypies during a substantial part of the day time. A single subcutaneous injection with naloxone significantly decreased the profound stereotypies, while explorative behaviours of pigs were not affected by naloxone. In addition a long-term effect of naloxone

  12. Endogenous opioids are involved in abnormal stereotyped behaviours of tethered sows

    NARCIS (Netherlands)

    Cronin, G.M.; Wiepkema, P.R.; Ree, J.M. van

    1985-01-01

    Tethered sows continuously performed stereotypies during a substantial part of the day time. A single subcutaneous injection with naloxone significantly decreased the profound stereotypies, while explorative behaviours of pigs were not affected by naloxone. In addition a long-term effect of naloxone

  13. Tethered particle analysis of supercoiled circular DNA using peptide nucleic acid handles

    DEFF Research Database (Denmark)

    Norregaard, Kamilla; Andersson, Magnus; Nielsen, Peter Eigil

    2014-01-01

    -digoxigenin-coated glass cover slide, and one conjugated with biotin for attachment to a submicron-sized streptavidin-coated polystyrene bead. Plasmids are constructed, purified and incubated with the PNA handles. The dynamics of the construct is analyzed by tracking the tethered bead using video microscopy: less...

  14. Technical and economical assessment on tethered wind-energy systems (TWES)

    Energy Technology Data Exchange (ETDEWEB)

    Furuya, O.; Maekawa, S.

    1982-06-01

    The objective of the work reported was to establish the potential of tethered wind energy systems for energy conversion in the upper atmosphere. Of the concepts investigated, the Vertical Takeoff and Landing (VTOL) lift generation concept had the highest potential as compared to balloon, wind and hybrid concepts.

  15. Tethered Cord Syndrome with Syrinx in A Nigerian Adult Female: A ...

    African Journals Online (AJOL)

    Alasia Datonye

    system did not show scoliosis. The respiratory and gastrointestinal systems were all normal. There were no cutaneous stigmata (hypertrichosis). Laboratory investigations showed normal haematogical indices. Urinalysis was also normal. An impression of transverse myelitis was made to exclude tethered cord syndrome.

  16. A Three-Compartment Model Describing Temperature Changes in Tethered Flying Blowflies

    NARCIS (Netherlands)

    Stavenga, D.G.; Schwering, P.B.W.; Tinbergen, J.

    1993-01-01

    A three-compartment model is presented that describes temperature measurements of tethered flying blowflies, obtained by thermal imaging. During rest, the body temperature is approximately equal to the ambient temperature. At the start of flight, the thorax temperature increases exponentially with a

  17. Titanium-tethered vancomycin prevents resistance to rifampicin in Staphylococcus aureus in vitro.

    Directory of Open Access Journals (Sweden)

    Martin Rottman

    Full Text Available Rifampicin is currently recognized as the most potent drug against Gram positive implant related infections. The use of rifampicin is limited by the emergence of bacterial resistance, which is often managed by coadministration of a second antibiotic. The purpose of this study was to determine the effectiveness of soluble rifampicin in combination with vancomycin tethered to titanium metal as a means to control bacterial growth and resistance in vitro. Bacterial growth was inhibited when the vancomycin-tethered titanium discs were treated with Staphylococcus aureus inocula of ≤2×10⁶ CFU, however inocula greater than 2×10⁶ CFU/disc adhered and survived. The combination of surface-tethered vancomycin with soluble rifampicin enhanced the inhibitory effect of rifampicin for an inoculum of 10⁶ CFU/cm² by one dilution (combination MIC of 0.008 mg/L versus 0.015 mg/L for rifampicin alone. Moreover, surface tethered vancomycin prevented the emergence of a rifampicin resistant population in an inoculum of 2×10⁸ CFU.

  18. Folding of multidomain proteins: biophysical consequences of tethering even in apparently independent folding.

    Science.gov (United States)

    Arviv, Oshrit; Levy, Yaakov

    2012-12-01

    Most eukaryotic and a substantial fraction of prokaryotic proteins are composed of more than one domain. The tethering of these evolutionary, structural, and functional units raises, among others, questions regarding the folding process of conjugated domains. Studying the folding of multidomain proteins in silico enables one to identify and isolate the tethering-induced biophysical determinants that govern crosstalks generated between neighboring domains. For this purpose, we carried out coarse-grained and atomistic molecular dynamics simulations of two two-domain constructs from the immunoglobulin-like β-sandwich fold. Each of these was experimentally shown to behave as the "sum of its parts," that is, the thermodynamic and kinetic folding behavior of the constituent domains of these constructs seems to occur independently, with the folding of each domain uncoupled from the folding of its partner in the two-domain construct. We show that the properties of the individual domains can be significantly affected by conjugation to another domain. The tethering may be accompanied by stabilizing as well as destabilizing factors whose magnitude depends on the size of the interface, the length, and the flexibility of the linker, and the relative stability of the domains. Accordingly, the folding of a multidomain protein should not be viewed as the sum of the folding patterns of each of its parts, but rather, it involves abrogating several effects that lead to this outcome. An imbalance between these effects may result in either stabilization or destabilization owing to the tethering. Copyright © 2012 Wiley Periodicals, Inc.

  19. Drug-induced premature chromosome condensation (PCC) protocols: cytogenetic approaches in mitotic chromosome and interphase chromatin.

    Science.gov (United States)

    Gotoh, Eisuke

    2015-01-01

    Chromosome analysis is a fundamental technique which is used in wide areas of cytogenetic study including karyotyping species, hereditary diseases diagnosis, or chromosome biology study. Chromosomes are usually prepared from mitotic cells arrested by colcemid block protocol. However, obtaining mitotic chromosomes is often hampered under several circumstances. As a result, cytogenetic analysis will be sometimes difficult or even impossible in such cases. Premature chromosome condensation (PCC) (see Note 1) is an alternative method that has proved to be a unique and useful way in chromosome analysis. Former, PCC has been achieved following cell fusion method (cell-fusion PCC) mediated either by fusogenic viruses (e.g., Sendai virus) or cell fusion chemicals (e.g., polyethylene glycol), but the cell fusion PCC has several drawbacks. The novel drug-induced PCC using protein phosphatase inhibitors was introduced about 20 years ago. This method is much simpler and easier even than the conventional mitotic chromosome preparation protocol use with colcemid block and furthermore obtained PCC index (equivalent to mitotic index for metaphase chromosome) is usually much higher than colcemid block method. Moreover, this method allows the interphase chromatin to be condensed to visualize like mitotic chromosomes. Therefore drug-induced PCC has opened the way for chromosome analysis not only in metaphase chromosomes but also in interphase chromatin. The drug-induced PCC has thus proven the usefulness in cytogenetics and other cell biology fields. For this second edition version, updated modifications/changes are supplemented in Subheadings 2, 3, and 4, and a new section describing the application of PCC in chromosome science fields is added with citation of updated references.

  20. Electrodynamic Tethers and E-Sails as Active Experiment Testbeds and Technologies in Space

    Science.gov (United States)

    Gilchrist, B. E.; Wiegmann, B.; Johnson, L.; Bilen, S. G.; Habash Krause, L.; Miars, G.; Leon, O.

    2017-12-01

    The use of small-to-large flexible structures in space such as tethers continues to be studied for scientific and technology applications. Here we will consider tether electrodynamic and electrostatic interactions with magneto-plasmas in ionospheres, magnetospheres, and interplanetary space. These systems are enabling fundamental studies of basic plasma physics phenomena, allowing direct studies of the space environment, and generating technological applications beneficial for science missions. Electrodynamic tethers can drive current through the tether based on the Lorenz force adding or extracting energy from its orbit allowing for the study of charged bodies or plasma plumes moving through meso-sonic magnetoplasmas [1]. Technologically, this also generates propulsive forces requiring no propellant and little or no consumables in any planetary system with a magnetic field and ionosphere, e.g., Jupiter [2]. Further, so called electric sails (E-sails) are being studied to provide thrust through momentum exchange with the hypersonic solar wind. The E-sail uses multiple, very long (10s of km) charged, mostly bare rotating conducting tethers to deflect solar wind protons. It is estimated that a spacecraft could achieve a velocity over 100 km/s with time [3,4]. 1. Banks, P.M., "Review of electrodynamic tethers for space plasma science," J. Spacecraft and Rockets, vol. 26, no. 4, pp. 234-239, 1989. 2. Talley, C., J. Moore, D. Gallagher, and L. Johnson, "Propulsion and power from a rotating electrodynamic tether at Jupiter," 38th AIAA Aerospace Sciences Meeting and Exhibit, January 2000. 3. Janhunen, P., "The electric sail—A new propulsion method which may enable fast missions to the outer solar system," J. British Interpl. Soc., vol. 61, no. 8, pp. 322-325, 2008. 4. Wiegman, B., T. Scheider, A. Heaton, J. Vaughn, N. Stone, and K. Wright, "The Heliopause Electrostatic Rapid Transit System (HERTS)—Design, trades, and analyses performed in a two-year NASA investigation

  1. Temporal profiling of the chromatin proteome reveals system-wide responses to replication inhibition

    DEFF Research Database (Denmark)

    Khoudoli, Guennadi A; Gillespie, Peter J; Stewart, Graeme

    2008-01-01

    Although the replication, expression, and maintenance of DNA are well-studied processes, the way that they are coordinated is poorly understood. Here, we report an analysis of the changing association of proteins with chromatin (the chromatin proteome) during progression through interphase...... of the cell cycle. Sperm nuclei were incubated in Xenopus egg extracts, and chromatin-associated proteins were analyzed by mass spectrometry at different times. Approximately 75% of the proteins varied in abundance on chromatin by more than 15%, suggesting that the chromatin proteome is highly dynamic....... Proteins were then assigned to one of 12 different clusters on the basis of their pattern of chromatin association. Each cluster contained functional groups of proteins involved in different nuclear processes related to progression through interphase. We also blocked DNA replication by inhibiting either...

  2. DNA repair goes hip-hop: SMARCA and CHD chromatin remodellers join the break dance.

    Science.gov (United States)

    Rother, Magdalena B; van Attikum, Haico

    2017-10-05

    Proper signalling and repair of DNA double-strand breaks (DSB) is critical to prevent genome instability and diseases such as cancer. The packaging of DNA into chromatin, however, has evolved as a mere obstacle to these DSB responses. Posttranslational modifications and ATP-dependent chromatin remodelling help to overcome this barrier by modulating nucleosome structures and allow signalling and repair machineries access to DSBs in chromatin. Here we recap our current knowledge on how ATP-dependent SMARCA- and CHD-type chromatin remodellers alter chromatin structure during the signalling and repair of DSBs and discuss how their dysfunction impacts genome stability and human disease.This article is part of the themed issue 'Chromatin modifiers and remodellers in DNA repair and signalling'. © 2017 The Authors.

  3. Autodigestion of chromatin in some radiosensitive and radioresistant mouse cells. Role of proteolysis and endonucleolysis

    International Nuclear Information System (INIS)

    Suciu, D.; Bojan, O.

    1981-01-01

    Evidence is presented indicating that mouse thymus, spleen, kidney, lung and heart contain a protease activity with relatively high specificity for histones. It is suggested that degradation of chromatin occurring in irradiated lymphoid tissues is produced by the action of alkaline endonuclease in association with this histone protease. The autodigestion of chromatin was assessed by determining the release of soluble chromatin from cells suspended in sucrose media of low ionic strength. It was found that the protease inhibitors, phenylmethylsulphonyl fluoride and especially NaHSO 3 , were also capable of depressing the activity of alkaline endonuclease, the fragmentation of chromatin, and the release of soluble chromatin. The results suggest that the release of histones from irradiated lymphoid tissues cannot be considered as a determinant step in the fragmentation of DNA in chromatin. (author)

  4. Contribution of Topological Domains and Loop Formation to 3D Chromatin Organization

    Directory of Open Access Journals (Sweden)

    Vuthy Ea

    2015-07-01

    Full Text Available Recent investigations on 3D chromatin folding revealed that the eukaryote genomes are both highly compartmentalized and extremely dynamic. This review presents the most recent advances in topological domains’ organization of the eukaryote genomes and discusses the relationship to chromatin loop formation. CTCF protein appears as a central factor of these two organization levels having either a strong insulating role at TAD borders, or a weaker architectural role in chromatin loop formation. TAD borders directly impact on chromatin dynamics by restricting contacts within specific genomic portions thus confining chromatin loop formation within TADs. We discuss how sub-TAD chromatin dynamics, constrained into a recently described statistical helix conformation, can produce functional interactions by contact stabilization.

  5. Front Crawl Swimming Performance and Bi-Lateral Force Asymmetry during Land-Based and Tethered Swimming Tests

    Directory of Open Access Journals (Sweden)

    Karini B. dos Santos, Paulo C. Barauce Bento, Gleber Pereira, Carl Payton, André L.F. Rodacki

    2017-12-01

    Full Text Available The aims of this study were to investigate whether land-based and tethered swimming strength tests can explain swimming performance in 200-meter front crawl and, whether these tests were able to identify bilateral symmetry in force production. In the first session, eighteen swimmers completed a maximum effort 200 m front crawl swim (swimming performance and 15 seconds maximal effort tethered front crawl swim. In the second session, participants performed the upper extremity isometric strength test. Peak force production of tethered swimming and isometric strength tests were significantly correlated for the strongest and weakest sides (r = 0.58 and r = 0.63, respectively; p < 0.05, but only peak force production during tethered swimming correlated with 200 m swimming performance time (r = -0.55, p < 0.05. Bilateral asymmetries in peak force and rate of force development were similar between the tethered swimming and isometric strength tests (peak force: 13%, p = 0.24; rate of force development: 15%, p = 0.88 However, both tests detected significant difference of peak force and rate of force development between body sides. The tethered swimming test can partially explain the 200 m front crawl swimming performance. In addition, the land-based and tethered swimming tests may be used to identify bilateral asymmetry of swimming

  6. Front Crawl Swimming Performance and Bi-Lateral Force Asymmetry during Land-Based and Tethered Swimming Tests.

    Science.gov (United States)

    Dos Santos, Karini B; Bento, Paulo C Barauce; Pereira, Gleber; Payton, Carl; Rodacki, André L F

    2017-12-01

    The aims of this study were to investigate whether land-based and tethered swimming strength tests can explain swimming performance in 200-meter front crawl and, whether these tests were able to identify bilateral symmetry in force production. In the first session, eighteen swimmers completed a maximum effort 200 m front crawl swim (swimming performance) and 15 seconds maximal effort tethered front crawl swim. In the second session, participants performed the upper extremity isometric strength test. Peak force production of tethered swimming and isometric strength tests were significantly correlated for the strongest and weakest sides (r = 0.58 and r = 0.63, respectively; p force production during tethered swimming correlated with 200 m swimming performance time (r = -0.55, p force and rate of force development were similar between the tethered swimming and isometric strength tests (peak force: 13%, p = 0.24; rate of force development: 15%, p = 0.88) However, both tests detected significant difference of peak force and rate of force development between body sides. The tethered swimming test can partially explain the 200 m front crawl swimming performance. In addition, the land-based and tethered swimming tests may be used to identify bilateral asymmetry of swimming.

  7. The chromatin landscape of Drosophila: comparisons between species, sexes, and chromosomes

    Science.gov (United States)

    Brown, Emily J.; Bachtrog, Doris

    2014-01-01

    The chromatin landscape is key for gene regulation, but little is known about how it differs between sexes or between species. Here, we study the sex-specific chromatin landscape of Drosophila miranda, a species with young sex chromosomes, and compare it with Drosophila melanogaster. We analyze six histone modifications in male and female larvae of D. miranda (H3K4me1, H3K4me3, H3K36me3, H4K16ac, H3K27me3, and H3K9me2), and define seven biologically meaningful chromatin states that show different enrichments for transcribed and silent genes, repetitive elements, housekeeping, and tissue-specific genes. The genome-wide distribution of both active and repressive chromatin states differs between males and females. In males, active chromatin is enriched on the X, relative to females, due to dosage compensation of the hemizygous X. Furthermore, a smaller fraction of the euchromatic portion of the genome is in a repressive chromatin state in males relative to females. However, sex-specific chromatin states appear not to explain sex-biased expression of genes. Overall, conservation of chromatin states between male and female D. miranda is comparable to conservation between D. miranda and D. melanogaster, which diverged >30 MY ago. Active chromatin states are more highly conserved across species, while heterochromatin shows very low levels of conservation. Divergence in chromatin profiles contributes to expression divergence between species, with ∼26% of genes in different chromatin states in the two species showing species-specific or species-biased expression, an enrichment of approximately threefold over null expectation. Our data suggest that heteromorphic sex chromosomes in males (that is, a hypertranscribed X and an inactivated Y) may contribute to global redistribution of active and repressive chromatin marks between chromosomes and sexes. PMID:24840603

  8. Salt and divalent cations affect the flexible nature of the natural beaded chromatin structure

    DEFF Research Database (Denmark)

    Christiansen, Gunna; Griffith, J

    1977-01-01

    A natural chromatin containing simian virus 40 (SV40) DNA and histone has been used to examine changes in chromatin structure caused by various physical and chemical treatments. We find that histone H1 depleted chromatin is more compact in solutions of 0.15M NaCl or 2 mM MgCl2 than in 0.01 M NaCl...

  9. Chromatin preparation and ChIP from Drosophila brain and discs tissues

    OpenAIRE

    sprotocols

    2015-01-01

    Authors: Constance Richter, Katarzyna Oktaba, Juerg Mueller & Juergen A. Knoblich ### Abstract Chromatin preparation and chromatin immunoprecipitation (ChIP) protocol as described in Oktaba et al., 2008, Dev Cell, 15, 877-89. The protocol includes description of chromatin preparation from larval tissues, ChIP and quantitative analysis of ChIP material. ### Procedure **1. First “fast” dissection**: Dissect for 20 minutes third instar larvae in ice-cold PBS and remove gut an...

  10. Novel RNA Duplex Locks HIV-1 in a Latent State via Chromatin-mediated Transcriptional Silencing

    Directory of Open Access Journals (Sweden)

    Chantelle Ahlenstiel

    2015-01-01

    Full Text Available Transcriptional gene silencing (TGS of mammalian genes can be induced by short interfering RNA (siRNA targeting promoter regions. We previously reported potent TGS of HIV-1 by siRNA (PromA, which targets tandem NF-κB motifs within the viral 5′LTR. In this study, we screened a siRNA panel with the aim of identifying novel 5′LTR targets, to provide multiplexing potential with enhanced viral silencing and application toward developing alternate therapeutic strategies. Systematic examination identified a novel siRNA target, si143, confirmed to induce TGS as the silencing mechanism. TGS was prolonged with virus suppression >12 days, despite a limited ability to induce post- TGS. Epigenetic changes associated with silencing were suggested by partial reversal by histone deacetylase inhibitors and confirmed by chromatin immunoprecipitation analyses, which showed induction of H3K27me3 and H3K9me3, reduction in H3K9Ac, and recruitment of argonaute-1, all characteristic marks of heterochromatin and TGS. Together, these epigenetic changes mimic those associated with HIV-1 latency. Further, robust resistance to reactivation was observed in the J-Lat 9.2 cell latency model, when transduced with shPromA and/or sh143. These data support si/shRNA-mediated TGS approaches to HIV-1 and provide alternate targets to pursue a functional cure, whereby the viral reservoir is locked in latency following antiretroviral therapy cessation.

  11. Analysis of Myc-induced histone modifications on target chromatin.

    Directory of Open Access Journals (Sweden)

    Francesca Martinato

    Full Text Available The c-myc proto-oncogene is induced by mitogens and is a central regulator of cell growth and differentiation. The c-myc product, Myc, is a transcription factor that binds a multitude of genomic sites, estimated to be over 10-15% of all promoter regions. Target promoters generally pre-exist in an active or poised chromatin state that is further modified by Myc, contributing to fine transcriptional regulation (activation or repression of the afferent gene. Among other mechanisms, Myc recruits histone acetyl-transferases to target chromatin and locally promotes hyper-acetylation of multiple lysines on histones H3 and H4, although the identity and combination of the modified lysines is unknown. Whether Myc dynamically regulates other histone modifications (or marks at its binding sites also remains to be addressed. Here, we used quantitative chromatin immunoprecipitation (qChIP to profile a total of 24 lysine-acetylation and -methylation marks modulated by Myc at target promoters in a human B-cell line with a regulatable c-myc transgene. Myc binding promoted acetylation of multiple lysines, primarily of H3K9, H3K14, H3K18, H4K5 and H4K12, but significantly also of H4K8, H4K91 and H2AK5. Dimethylation of H3K79 was also selectively induced at target promoters. A majority of target promoters showed co-induction of multiple marks - in various combinations - correlating with recruitment of the two HATs tested (Tip60 and HBO1, incorporation of the histone variant H2A.Z and transcriptional activation. Based on this and previous findings, we surmise that Myc recruits the Tip60/p400 complex to achieve a coordinated histone acetylation/exchange reaction at activated promoters. Our data are also consistent with the additive and redundant role of multiple acetylation events in transcriptional activation.

  12. Chromatin association of UHRF1 during the cell cycle

    KAUST Repository

    Al-Gashgari, Bothayna

    2017-05-01

    Ubiquitin-like with PHD and RING Finger domains 1 (UHRF1) is a nuclear protein that associates with chromatin. Regardless of the various functions of UHRF1 in the cell, one of its more important functions is its role in the maintenance of DNA methylation patterns by the recruitment of DNMT1. Studies on UHRF1 based on this function have revealed the importance of UHRF1 during the cell cycle. Moreover, based on different studies various factors were described to be involved in the regulation of UHRF1 with different functionalities that can control its binding affinity to different targets on chromatin. These factors are regulated differently in a cell cycle specific manner. In light of this, we propose that UHRF1 has different binding behaviors during the cell cycle in regard to its association with chromatin. In this project, we first analyzed the binding behavior of endogenous UHRF1 from different unsynchronized cell systems in pull-down assays with peptides and oligonucleotides. Moreover, to analyze UHRF1 binding behavior during the cell cycle, we used two different approaches. First we sorted Jurkat and HT1080 cells based on their cell cycle stage using FACS analysis. Additionally, we synchronized HeLa cells to different stages of the cell cycle by chemical treatments, and used extracts from cellsorting and cell synchronization experiments for pull-down assays. We observed that UHRF1 in different cell systems has different preferences in regard to its binding to H3 unmodified and H3K9me3. Moreover, we detected that UHRF1, in general, displays different patterns between different stages of cell cycle; however, we cannot draw a final model for UHRF1 binding pattern during cell cycle.

  13. Phosphorylation of the chromatin binding domain of KSHV LANA.

    Directory of Open Access Journals (Sweden)

    Crystal Woodard

    Full Text Available The Kaposi sarcoma associated herpesvirus (KSHV latency associated nuclear antigen (LANA is expressed in all KSHV associated malignancies and is essential for maintenance of KSHV genomes in infected cells. To identify kinases that are potentially capable of modifying LANA, in vitro phosphorylation assays were performed using an Epstein Barr virus plus LANA protein microarray and 268 human kinases purified in active form from yeast. Interestingly, of the Epstein-Barr virus proteins on the array, the EBNA1 protein had the most similar kinase profile to LANA. We focused on nuclear kinases and on the N-terminus of LANA (amino acids 1-329 that contains the LANA chromatin binding domain. Sixty-three nuclear kinases phosphorylated the LANA N-terminus. Twenty-four nuclear kinases phosphorylated a peptide covering the LANA chromatin binding domain (amino acids 3-21. Alanine mutations of serine 10 and threonine 14 abolish or severely diminish chromatin and histone binding by LANA. However, conversion of these residues to the phosphomimetic glutamic acid restored histone binding suggesting that phosphorylation of serine 10 and threonine 14 may modulate LANA function. Serine 10 and threonine 14 were validated as substrates of casein kinase 1, PIM1, GSK-3 and RSK3 kinases. Short-term treatment of transfected cells with inhibitors of these kinases found that only RSK inhibition reduced LANA interaction with endogenous histone H2B. Extended treatment of PEL cell cultures with RSK inhibitor caused a decrease in LANA protein levels associated with p21 induction and a loss of PEL cell viability. The data indicate that RSK phosphorylation affects both LANA accumulation and function.

  14. Tethered domains and flexible regions in tRNase Z(L, the long form of tRNase Z.

    Directory of Open Access Journals (Sweden)

    Christopher Wilson

    Full Text Available tRNase Z, a member of the metallo-β-lactamase family, endonucleolytically removes the pre-tRNA 3' trailer in a step central to tRNA maturation. The short form (tRNase Z(S is the only one found in bacteria and archaebacteria and is also present in some eukaryotes. The homologous long form (tRNase Z(L, exclusively found in eukaryotes, consists of related amino- and carboxy-domains, suggesting that tRNase Z(L arose from a tandem duplication of tRNase Z(S followed by interdependent divergence of the domains. X-ray crystallographic structures of tRNase Z(S reveal a flexible arm (FA extruded from the body of tRNase Z remote from the active site that binds tRNA far from the scissile bond. No tRNase Z(L structures have been solved; alternative biophysical studies are therefore needed to illuminate its functional characteristics. Structural analyses of tRNase Z(L performed by limited proteolysis, two dimensional gel electrophoresis and mass spectrometry establish stability of the amino and carboxy domains and flexibility of the FA and inter-domain tether, with implications for tRNase Z(L function.

  15. Evaluation of sperm chromatin structure in boar semen

    Directory of Open Access Journals (Sweden)

    Banaszewska Dorota

    2015-06-01

    Full Text Available This study was an attempt to evaluate sperm chromatin structure in the semen of insemination boars. Preparations of semen were stained with acridine orange, aniline blue, and chromomycin A3. Abnormal protamination occurred more frequently in young individuals whose sexual development was not yet complete, but may also be an individual trait. This possibility is important to factor into the decision regarding further exploitation of insemination boars. Thus a precise assessment of abnormalities in the protamination process would seem to be expedient as a tool supplementing morphological and molecular evaluation of semen. Disruptions in nucleoprotein structure can be treated as indicators of the biological value of sperm cells.

  16. Keeping it quiet: chromatin control of gammaherpesvirus latency.

    Science.gov (United States)

    Lieberman, Paul M

    2013-12-01

    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 gammaherpesviruses to establish stable latent infections that mediate viral pathogenesis.

  17. The architecture and function of the chromatin replication machinery.

    Science.gov (United States)

    Miller, Thomas Cr; Costa, Alessandro

    2017-12-01

    Genomic DNA in eukaryotic cells is packaged into nucleosome arrays. During replication, nucleosomes need to be dismantled ahead of the advancing replication fork and reassembled on duplicated DNA. The architecture and function of the core replisome machinery is now beginning to be elucidated, with recent insights shaping our view on DNA replication processes. Simultaneously, breakthroughs in our mechanistic understanding of epigenetic inheritance allow us to build new models of how histone chaperones integrate with the replisome to reshuffle nucleosomes. The emerging picture indicates that the core eukaryotic DNA replication machinery has evolved elements that handle nucleosomes to facilitate chromatin duplication. Copyright © 2017. Published by Elsevier Ltd.

  18. Chromatin structure and epigenetics of tumour cells: A review

    Czech Academy of Sciences Publication Activity Database

    Bártová, Eva; Krejčí, Jana; Hájek, R.; Harničarová, Andrea; Kozubek, Stanislav

    2009-01-01

    Roč. 9, č. 1 (2009), s. 51-61 ISSN 1871-529X R&D Projects: GA AV ČR(CZ) 1QS500040508; GA ČR(CZ) GA204/06/0978 Grant - others:GA MŠk(CZ) LC06027; GA MŠk(CZ) LC535 Program:LC; LC Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : tumour cells * chromatin * radiation Subject RIV: BO - Biophysics

  19. Mouse sperm chromatin proteins: quantitative isolation and partial characterization. [Mice

    Energy Technology Data Exchange (ETDEWEB)

    Balhorn, R.; Gledhill, B.L.; Wyrobek, A.J.

    1977-09-06

    Conditions are described that permit the quantitative extraction of chromatin proteins from the epididymal sperm of the mouse. These proteins have been isolated free of contaminating tail proteins following removal of the tails with cetyltrimethylammonium bromide (CTAB). Without this treatment, numerous acid-soluble tail proteins coextract with the nuclear proteins isolated from partially purified heads. The proteins isolated in this manner do not require prior modification with iodoacetamide and show no evidence of proteolytic degradation. In acid-urea polyacrylamide gels, 99% of the sperm protein migrates as one electrophoretic band. Evidence is presented that suggests that this single band contains two protamine-like proteins.

  20. Chromatin Dynamics in Genome Stability: Roles in Suppressing Endogenous DNA Damage and Facilitating DNA Repair

    Science.gov (United States)

    Nair, Nidhi; Shoaib, Muhammad

    2017-01-01

    Genomic DNA is compacted into chromatin through packaging with histone and non-histone proteins. Importantly, DNA accessibility is dynamically regulated to ensure genome stability. This is exemplified in the response to DNA damage where chromatin relaxation near genomic lesions serves to promote access of relevant enzymes to specific DNA regions for signaling and repair. Furthermore, recent data highlight genome maintenance roles of chromatin through the regulation of endogenous DNA-templated processes including transcription and replication. Here, we review research that shows the importance of chromatin structure regulation in maintaining genome integrity by multiple mechanisms including facilitating DNA repair and directly suppressing endogenous DNA damage. PMID:28698521