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. Identification of alternative topological domains in chromatin

    OpenAIRE

    Filippova, Darya; Patro, Rob; Duggal, Geet; Kingsford, Carl

    2014-01-01

    Chromosome conformation capture experiments have led to the discovery of dense, contiguous, megabase-sized topological domains that are similar across cell types and conserved across species. These domains are strongly correlated with a number of chromatin markers and have since been included in a number of analyses. However, functionally-relevant domains may exist at multiple length scales. We introduce a new and efficient algorithm that is able to capture persistent domains across various r...

  3. Assembly of telomeric chromatin to create ALTernative endings.

    Science.gov (United States)

    O'Sullivan, Roderick J; Almouzni, Genevieve

    2014-11-01

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

  4. Alternative Lengthening of Telomeres is characterized by reduced compaction of telomeric chromatin.

    OpenAIRE

    Episkopou, Charikleia; Draskovic, Irena; Van Beneden, Amandine; Tilman, Gaëlle; Mattiussi, Marina; Gobin, Matthieu; Arnoult, Nausica; Londoño-Vallejo, Arturo; Decottignies, Anabelle

    2014-01-01

    International audience Proper telomeric chromatin configuration is thought to be essential for telomere homeostasis and stability. Previous studies in mouse suggested that loss of heterochromatin marks at telomeres might favor onset of Alternative Lengthening of Telomeres (ALT) pathway, by promoting homologous recombination. However, analysis of chromatin status at human ALT telomeres has never been reported. Here, using isogenic human cell lines and cellular hybrids, which rely either on ...

  5. Suppression of the alternative lengthening of telomere pathway by the chromatin remodelling factor ATRX.

    Science.gov (United States)

    Clynes, David; Jelinska, Clare; Xella, Barbara; Ayyub, Helena; Scott, Caroline; Mitson, Matthew; Taylor, Stephen; Higgs, Douglas R; Gibbons, Richard J

    2015-01-01

    Fifteen per cent of cancers maintain telomere length independently of telomerase by the homologous recombination (HR)-associated alternative lengthening of telomeres (ALT) pathway. A unifying feature of these tumours are mutations in ATRX. Here we show that expression of ectopic ATRX triggers a suppression of the pathway and telomere shortening. Importantly ATRX-mediated ALT suppression is dependent on the histone chaperone DAXX. Re-expression of ATRX is associated with a reduction in replication fork stalling, a known trigger for HR and loss of MRN from telomeres. A G-quadruplex stabilizer partially reverses the effect of ATRX, inferring ATRX may normally facilitate replication through these sequences that, if they persist, promote ALT. We propose that defective telomere chromatinization through loss of ATRX promotes the persistence of aberrant DNA secondary structures, which in turn present a barrier to DNA replication, leading to replication fork stalling, collapse, HR and subsequent recombination-mediated telomere synthesis in ALT cancers. PMID:26143912

  6. 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.

  7. Dynamic regulation of alternative splicing and chromatin structure in Drosophila gonads revealed by RNA-seq

    OpenAIRE

    Gan, Qiang; Chepelev, Iouri; Wei, Gang; Tarayrah, Lama; Cui, Kairong; Zhao, Keji; Chen, Xin

    2010-01-01

    Both transcription and post-transcriptional processes, such as alternative splicing, play crucial roles in controlling developmental programs in metazoans. Recently emerged RNA-seq method has brought our understandings of eukaryotic transcriptomes to a new level, because it can resolve both gene expression level and alternative splicing events simultaneously.

  8. Suppression of the alternative lengthening of telomere pathway by the chromatin remodelling factor ATRX

    OpenAIRE

    Clynes, David; Jelinska, Clare; Xella, Barbara; Ayyub, Helena; Scott, Caroline; Mitson, Matthew; Taylor, Stephen; Higgs, Douglas R.; Gibbons, Richard J.

    2015-01-01

    Fifteen per cent of cancers maintain telomere length independently of telomerase by the homologous recombination (HR)-associated alternative lengthening of telomeres (ALT) pathway. A unifying feature of these tumours are mutations in ATRX. Here we show that expression of ectopic ATRX triggers a suppression of the pathway and telomere shortening. Importantly ATRX-mediated ALT suppression is dependent on the histone chaperone DAXX. Re-expression of ATRX is associated with a reduction in replica...

  9. Dynamics of the Space Tug System with a Short Tether

    OpenAIRE

    Jiafu Liu; Naigang Cui; Fan Shen; Siyuan Rong

    2015-01-01

    The dynamics of the space tug system with a short tether similar to the ROGER system during deorbiting is presented. The kinematical characteristic of this system is significantly different from the traditional tethered system as the tether is tensional and tensionless alternately during the deorbiting process. The dynamics obtained based on the methods for the traditional tethered system is not suitable for the space tug system. Therefore, a novel method for deriving dynamics for the deorbit...

  10. Conductive Tether Coating for Electrodynamic Tethers

    Science.gov (United States)

    Vaughn, Jason A.; Schuler, Pete

    2000-01-01

    The Propulsive Small Expendable Deployer System (ProSEDS), which is an on-orbit demonstration of the propulsion capabilities of electrodynamic tethers in space, is a secondary payload on a Delta 11 unmanned expendable booster. The ProSEDS tether consists of a 5 km bare electrodynamic tether and a 1 0-km non-conductive leader tether. Near the Delta 11, 160 m of the conductive tether is insulated to prevent plasma electron collection from the plasma contactor and for other science requirements. The remainder of the 5-km conductive tether is coated with a new conductive coating to collect plasma electrons. A bare metal tether easily collects electrons from the plasma, but thermal concerns preclude this design. A highly emissive conductive polymer developed by Triton Systems, Inc. has been optimized for both conductivity and thermo-optical properties. The current design for the ProSEDS conductive tether is seven individually coated strands of 28 AWG aluminum wire, coated with an atomic oxygen-resistant conductive polymer composed of a mixture of COR (Colorless Oxygen Resistant) and polyanaline (PANI) known as C-COR (Conductive-Colorless Oxygen Resistant). The conductive-coated wire strands are cold-welded to individually coated strands of the insulated tether. The insulated tether is coated with 1 mil of polyimide and an atomic oxygen resistant polymer TOR-BP. The insulated tether must stand off the entire voltage of the tether (1 200 V) at various times during the mission. All seven wires are twisted around a Kevlar-29 core using the Hi-wire design. Extensive testing has been performed at the Marshall Space Flight Center to qualify both the conductive coating and insulating coating for use on the ProSEDS tether. The conductive coating has been exposed to a plasma to verify the coatings ability to collect electrons from the space plasma from 0 to 1500 V, and to verify the coatings ability to collect electrons after atomic oxygen exposure. The insulated coating has been

  11. 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

  12. 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.

  13. A critical role for alternative polyadenylation factor CPSF6 in targeting HIV-1 integration to transcriptionally active chromatin.

    Science.gov (United States)

    Sowd, Gregory A; Serrao, Erik; Wang, Hao; Wang, Weifeng; Fadel, Hind J; Poeschla, Eric M; Engelman, Alan N

    2016-02-23

    Integration is vital to retroviral replication and influences the establishment of the latent HIV reservoir. HIV-1 integration favors active genes, which is in part determined by the interaction between integrase and lens epithelium-derived growth factor (LEDGF)/p75. Because gene targeting remains significantly enriched, relative to random in LEDGF/p75 deficient cells, other host factors likely contribute to gene-tropic integration. Nucleoporins 153 and 358, which bind HIV-1 capsid, play comparatively minor roles in integration targeting, but the influence of another capsid binding protein, cleavage and polyadenylation specificity factor 6 (CPSF6), has not been reported. In this study we knocked down or knocked out CPSF6 in parallel or in tandem with LEDGF/p75. CPSF6 knockout changed viral infectivity kinetics, decreased proviral formation, and preferentially decreased integration into transcriptionally active genes, spliced genes, and regions of chromatin enriched in genes and activating histone modifications. LEDGF/p75 depletion by contrast preferentially altered positional integration targeting within gene bodies. Dual factor knockout reduced integration into genes to below the levels observed with either single knockout and revealed that CPSF6 played a more dominant role than LEDGF/p75 in directing integration to euchromatin. CPSF6 complementation rescued HIV-1 integration site distribution in CPSF6 knockout cells, but complementation with a capsid binding mutant of CPSF6 did not. We conclude that integration targeting proceeds via two distinct mechanisms: capsid-CPSF6 binding directs HIV-1 to actively transcribed euchromatin, where the integrase-LEDGF/p75 interaction drives integration into gene bodies. PMID:26858452

  14. Tether Deployer And Brake

    Science.gov (United States)

    Carroll, Joseph A.; Alexander, Charles M.

    1993-01-01

    Design concept promises speed, control, and reliability. Scheme for deploying tether provides for fast, free, and snagless payout and fast, dependable braking. Developed for small, expendable tethers in outer space, scheme also useful in laying transoceanic cables, deploying guidance wires to torpedoes and missiles, paying out rescue lines from ship to ship via rockets, deploying antenna wires, releasing communication and power cables to sonobuoys and expendable bathythermographs, and in reeling out lines from fishing rods.

  15. 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.

  16. Direct Measurement of Local Chromatin Fluidity Using Optical Trap Modulation Force Spectroscopy

    OpenAIRE

    Roopa, T.; Shivashankar, G. V.

    2006-01-01

    Chromatin assembly is condensed by histone tail-tail interactions and other nuclear proteins into a highly compact structure. Using an optical trap modulation force spectroscopy, we probe the effect of tail interactions on local chromatin fluidity. Chromatin fibers, purified from mammalian cells, are tethered between a microscope coverslip and a glass micropipette. Mechanical unzipping of tail interactions, using the micropipette, lead to the enhancement of local fluidity. This is measured us...

  17. GRASP: A Multitasking Tether.

    Science.gov (United States)

    Rabouille, Catherine; Linstedt, Adam D

    2016-01-01

    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 (Giuliani et al., 2011; Vinke 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). PMID:26858948

  18. Anchoring a Leviathan: How the Nuclear Membrane Tethers the Genome

    Directory of Open Access Journals (Sweden)

    Rafal eCzapiewski

    2016-05-01

    Full Text Available It is well established that the nuclear envelope has many distinct direct connections to chromatin that contribute to genome organization. The functional consequences of genome organization on gene regulation are less clear. Even less understood is how interactions of lamins and nuclear envelope transmembrane proteins (NETs with chromatin can produce anchoring tethers that can withstand the physical forces of and on the genome. Chromosomes are the largest molecules in the cell, making megadalton protein structures like the nuclear pore complexes and ribosomes seem small by comparison. Thus to withstand strong forces from chromosome dynamics an anchoring tether is likely to be much more complex than a single protein-protein or protein-DNA interaction. Here we will briefly review known NE-genome interactions that likely contribute to spatial genome organization, postulate in the context of experimental data how these anchoring tethers contribute to gene regulation, and posit several hypotheses for the physical nature of these tethers that need to be investigated experimentally. Significantly, disruption of these anchoring tethers and the subsequent consequences for gene regulation could explain how mutations in nuclear envelope proteins cause diseases ranging from muscular dystrophy to lipodystrophy to premature ageing progeroid syndromes. The two favored hypotheses for nuclear envelope protein involvement in disease are 1 weakening nuclear and cellular mechanical stability, and 2 disrupting genome organization and gene regulation. Considerable experimental support has been obtained for both. The integration of both mechanical and gene expression defects in the disruption of anchoring tethers could provide a unifying hypothesis consistent with both.

  19. 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

  20. Tethered float liquid level sensor

    Energy Technology Data Exchange (ETDEWEB)

    Daily, III, William Dean

    2016-09-06

    An apparatus for sensing the level of a liquid includes a float, a tether attached to the float, a pulley attached to the tether, a rotation sensor connected to the pulley that senses vertical movement of said float and senses the level of the liquid.

  1. 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.

  2. Dynamics of the Space Tug System with a Short Tether

    Directory of Open Access Journals (Sweden)

    Jiafu Liu

    2015-01-01

    Full Text Available The dynamics of the space tug system with a short tether similar to the ROGER system during deorbiting is presented. The kinematical characteristic of this system is significantly different from the traditional tethered system as the tether is tensional and tensionless alternately during the deorbiting process. The dynamics obtained based on the methods for the traditional tethered system is not suitable for the space tug system. Therefore, a novel method for deriving dynamics for the deorbiting system similar to the ROGER system is proposed by adopting the orbital coordinates of the two spacecraft and the Euler angles of ROGER spacecraft as the generalized coordinates instead of in- and out-plane librations and the length of the tether and so forth. Then, the librations of the system are equivalently obtained using the orbital positions of the two spacecraft. At last, the geostationary orbit (GEO and the orbit whose apogee is 300 km above GEO are chosen as the initial and target orbits, respectively, to perform the numerical simulations. The simulation results indicate that the dynamics can describe the characteristic of the tether-net system conveniently and accurately, and the deorbiting results are deeply affected by the initial conditions and parameters.

  3. Where splicing joins chromatin

    OpenAIRE

    Hnilicová, Jarmila; Staněk, David

    2011-01-01

    There are numerous data suggesting that two key steps in gene expression—transcription and splicing influence each other closely. For a long time it was known that chromatin modifications regulate transcription, but only recently it was shown that chromatin and histone modifications play a significant role in pre-mRNA splicing. Here we summarize interactions between splicing machinery and chromatin and discuss their potential functional significance. We focus mainly on histone acetylation and...

  4. Tethered cord syndrome: case report

    International Nuclear Information System (INIS)

    Tethered cord syndrome is one of the filum terminale congenital defects. It can coexist with anomalies of the spinal canal and column, as well as with anorectal defects. The authors present a case of tethered cord syndrome diagnosed in a 45-year-old woman. She showed typical lumbo-sacral radicular syndrome with no neurological deficits and no bowel/bladder dysfunction. The anomaly coexisted with fibrolipoma, spina bifida and Tarlov cyst. Magnetic resonance imaging is the method of choice in diagnostics of tethered cord syndrome. It provides crucial information, which is necessary for planning surgical treatment of the anomaly. (author)

  5. 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.

  6. 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.

  7. Effect of chromosome tethering on nuclear organization in yeast.

    Directory of Open Access Journals (Sweden)

    Barış Avşaroğlu

    Full Text Available Interphase chromosomes in Saccharomyces cerevisiae are tethered to the nuclear envelope at their telomeres and to the spindle pole body (SPB at their centromeres. Using a polymer model of yeast chromosomes that includes these interactions, we show theoretically that telomere attachment to the nuclear envelope is a major determinant of gene positioning within the nucleus only for genes within 10 kb of the telomeres. We test this prediction by measuring the distance between the SPB and the silent mating locus (HML on chromosome III in wild-type and mutant yeast strains that contain altered chromosome-tethering interactions. In wild-type yeast cells we find that disruption of the telomere tether does not dramatically change the position of HML with respect to the SPB, in agreement with theoretical predictions. Alternatively, using a mutant strain with a synthetic tether that localizes an HML-proximal site to the nuclear envelope, we find a significant change in the SPB-HML distance, again as predicted by theory. Our study quantifies the importance of tethering at telomeres on the organization of interphase chromosomes in yeast, which has been shown to play a significant role in determining chromosome function such as gene expression and recombination.

  8. Prenucleosomes and Active Chromatin

    Science.gov (United States)

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

    2016-01-01

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

  9. TIN2-tethered TPP1 recruits human telomerase to telomeres in vivo.

    OpenAIRE

    Abreu, E.; Aritonovska, E.; Reichenbach, P.; Cristofari, G.; Culp, B.; Terns, R. M.; Lingner, J; Terns, M P

    2010-01-01

    Recruitment to telomeres is a pivotal step in the function and regulation of human telomerase; however, the molecular basis for recruitment is not known. Here, we have directly investigated the process of telomerase recruitment via fluorescence in situ hybridization (FISH) and chromatin immunoprecipitation (ChIP). We find that depletion of two components of the shelterin complex that is found at telomeres--TPP1 and the protein that tethers TPP1 to the complex, TIN2--results in a loss of telom...

  10. Chromatin deregulation in disease.

    Science.gov (United States)

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

    2016-03-01

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

  11. Enabling Tethered Exploration on Mars Project

    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...

  12. 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...

  13. 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

  14. Polymeric Coatings for Electrodynamic Tethers

    Science.gov (United States)

    Vaughn, Jason A.; Kamenetzky, Rachel R.; Finckenor, Miria M.; Schuler, Peter

    2000-01-01

    Two polymeric coatings have been developed for the Propulsive Small Expendable Deployer System (ProSEDS) mission. ProSEDS is designed to provide an on-orbit demonstration of the electrodynamic propulsion capabilities of tethers in space. The ProSEDS experiment will be a secondary payload on a Delta II unmanned expendable booster scheduled for launch in August 2000. A 5-km conductive tether is attached to the Delta 11 second stage and collects current from the low Earth orbit (LEO) plasma to facilitate de-orbit of the spent stage. The conductive tether is attached to a 10-km non-conductive tether, the other end of which is attached to an endmass containing several scientific instruments. A bare metal tether would have the best conductivity but thermal concerns preclude this design. A conductive polymer developed by Triton Systems has been optimized for conductivity and thermo-optical properties. The current design for the ProSEDS conductive tether is seven strands of 28 AWG aluminum wire individually coated with 8.7 micrometers (0.35 mil) of an atomic oxygen-resistant conductive polymer composed of a mixture of 87% Clear Oxygen-Resistant polymer (COR) and 13% polyanaline (PANi), wrapped around a braided Kevlar (TM) 49 core. Extensive testing has been performed at the Marshall Space Flight Center (MSFC) to qualify this material for flight on ProSEDS. Atomic oxygen exposure was performed, with solar absorptance and infrared emittance measured before and after exposure. Conductivity was measured before and after atomic oxygen exposure. High voltage tests, up to 1500 V, of the current collecting ability of the COR/PANi have been completed. Approximately 160 meters of the conductive tether closest to the Delta 11 second stage is insulated to prevent any electron reconnection to the tether from the plasma contactor. The insulation is composed of polyimide overcoated with TOR-BP, another polymeric coating developed by Triton for this mission. TOR-BP acts as both insulator

  15. Short, high current electrodynamic tether

    OpenAIRE

    Savich, N.A.; Sanmartín Losada, Juan Ramón

    1994-01-01

    An electrodynamic tether experiment, to be carried out in the Russian spacecraft Almaz, is proposed. A 10 km tether would be deployed downwards; the lower 8 km would be nonconductive, the upper 2 km would be conductive, bare, and 2.2 mm in diameter, and would act as a thruster, with power supply at the top. This hybrid arrangement allows for other, onelectrodynamic experiments,reducing costs; it also limits the induced electromotive force, reducing the power to be handled. The current-volt...

  16. Nucleosome dynamics during chromatin remodeling in vivo.

    Science.gov (United States)

    Ramachandran, Srinivas; Henikoff, Steven

    2016-01-01

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

  17. Long Noncoding RNAs, Chromatin, and Development

    Directory of Open Access Journals (Sweden)

    Daniel P. Caley

    2010-01-01

    Full Text Available The way in which the genome of a multicellular organism can orchestrate the differentiation of trillions of cells and many organs, all from a single fertilized egg, is the subject of intense study. Different cell types can be defined by the networks of genes they express. This differential expression is regulated at the epigenetic level by chromatin modifications, such as DNA and histone methylation, which interact with structural and enzymatic proteins, resulting in the activation or silencing of any given gene. While detailed mechanisms are emerging on the role of different chromatin modifications and how these functions are effected at the molecular level, it is still unclear how their deposition across the epigenomic landscape is regulated in different cells. A raft of recent evidence is accumulating that implicates long noncoding RNAs (lncRNAs in these processes. Most genomes studied to date undergo widespread transcription, the majority of which is not translated into proteins. In this review, we will describe recent work suggesting that lncRNAs are more than transcriptional "noise", but instead play a functional role by acting as tethers and guides to bind proteins responsible for modifying chromatin and mediating their deposition at specific genomic locations. We suggest that lncRNAs are at the heart of developmental regulation, determining the epigenetic status and transcriptional network in any given cell type, and that they provide a means to integrate external differentiation cues with dynamic nuclear responses through the regulation of a metastable epigenome. Better characterization of the lncRNA-protein "interactome" may eventually lead to a new molecular toolkit, allowing researchers and clinicians to modulate the genome at the epigenetic level to treat conditions such as cancer.

  18. Sliding mode control of electromagnetic tethered satellite formation

    Science.gov (United States)

    Hallaj, Mohammad Amin Alandi; Assadian, Nima

    2016-08-01

    This paper investigates the control of tethered satellite formation actuated by electromagnetic dipoles and reaction wheels using the robust sliding mode control technique. Generating electromagnetic forces and moments by electric current coils provides an attractive control actuation alternative for tethered satellite system due to the advantages of no propellant consumption and no obligatory rotational motion. Based on a dumbbell model of tethered satellite in which the flexibility and mass of the tether is neglected, the equations of motion in Cartesian coordinate are derived. In this model, the J2 perturbation is taken into account. The far-field and mid-field models of electromagnetic forces and moments of two satellites on each other and the effect of the Earth's magnetic field are presented. A robust sliding mode controller is designed for precise trajectory tracking purposes and to deal with the electromagnetic force and moment uncertainties and external disturbances due to the Earth's gravitational and magnetic fields inaccuracy. Numerical simulation results are presented to validate the effectiveness of the developed controller and its superiority over the linear controller.

  19. 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.

  20. Chromatin chemistry goes cellular.

    OpenAIRE

    W. Fischle; D. Schwarzer; Mootz, H.

    2015-01-01

    Analysing post-translational modifications of histone proteins as they occur within chromatin is challenging due to their large number and chemical diversity. A major step forward has now been achieved by using split intein chemistry to engineer functionalized histones within cells.

  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. 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.

  3. 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

  4. Artificial Gravity: Tethers and Containers

    Science.gov (United States)

    Criswell, D. R.

    1985-01-01

    Tethers used in conjunction with containers offer a means of enhanced control of basic variables such as local acceleration, pointing and orientation, and protected or controlled environments against particle or electromagnetic radiation. Permanent occupancy of space will require the rapid exploration of the short and long term responses of many living organisms to the space environment or separated components of that environment. Tethers and ET facilities could provide the rapid establishment of laboratories in LEO within which to study living systems in a wide range of separate controlled environments for long periods of time, support large optical arrays; provide orbiting laboratories; and provide controlled environments within which the application of advanced manufacturing, assembly, control, and robotics could be developed to aid off-Earth industry and science and the conduct of more complex space operations.

  5. On the survivability of tethers in space

    OpenAIRE

    Anselmo, Luciano; Pardini, Carmen

    2000-01-01

    Tethers have been proposed for several space applications, like satellite de-orbiting or re-boost, electric energy generation, scientific research and so on. However, they may be vulnerable to orbital debris and meteoroid impacts. The problem was assessed, to assist tether systems design, by detailed numerical computations of the average impact rate of artificial debris, taking into account the specific geometric properties of tethers as debris targets, when compared to typical satellites. Th...

  6. Early Results of the Multi-Application Survivable Tether (MAST) Space Tether Experiment

    OpenAIRE

    Hoyt, Robert; Voronka, Nestor; Newton, Tyrel; Barnes, Ian; Shepherd, Jack; Frank, S. Scott; Slostad, Jeff; Jaroux, Belgacem; Twiggs, Robert

    2007-01-01

    The Multi-Application Survivable Tether (MAST) Experiment utilizes three tethered picosatellites to study the survivability of space tether structures and materials in the low Earth orbit environment. The MAST picosatellites initially deployed as a single body from a CubeSat PPOD deployer were designed to subsequently deploy a 1,000 meter long multi-line "Hoytether" between two of the picosatellites. The third picosatellite will then slowly crawl up and down the tether photographing it and tr...

  7. Get-Away tether experiment - Experimental plans

    Science.gov (United States)

    Greene, Michael; Walls, Justin; Carter, J. Theron; Rupp, Charles C.

    1988-01-01

    The experimental capabilities of the Get-Away Tether Experiment (GATE) are presented and a series of demonstration mission are proposed. The GATE is a free-flying tether system that will develop or demonstrate technology in the areas of tether dynamics (deployment and stabilization, retrieval, stationkeeping, and severance), tether electrodynamics, micrometeor hazards to tethers, and disturbance rejection. The system consists of two subsatellites connected by 1 km of tether. The free-flying system is ejected from the Orbiter via a Getaway Special (GAS) canister. Two dynamics missions are profiled along with a description of electrodynamic mission capabilities. The dynamic interactions of the end body and tether may be observed from the Orbiter or from an on-board video tracking system. Hence, GATE provides a unique, low cost capability to demonstrate various tether technologies, and address critical design and safety issues associated with future tether applications. An assessment of the significant measurable parameters and associated instrumentation is given. Future work and system development projection schedules are also outlined.

  8. Analysis of Chromatin Attachment and Partitioning Functions of Bovine Papillomavirus Type 1 E2 Protein

    OpenAIRE

    Abroi, Aare; Ilves, Ivar; Kivi, Sirje; Ustav, Mart

    2004-01-01

    Recent studies have suggested that the tethering of viral genomes to host cell chromosomes could provide one of the ways to achieve their nuclear retention and partitioning during extrachromosomal maintenance in dividing cells. The data we present here provide firm evidence that the partitioning of the bovine papillomavirus type 1 (BPV1) genome is dependent on the chromatin attachment process mediated by viral E2 protein and its multiple binding sites. On the other hand, the attachment of E2 ...

  9. 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

  10. Chromatin boundary elements organize genomic architecture and developmental gene regulation in Drosophila Hox clusters.

    Science.gov (United States)

    Ma, Zhibo; Li, Mo; Roy, Sharmila; Liu, Kevin J; Romine, Matthew L; Lane, Derrick C; Patel, Sapna K; Cai, Haini N

    2016-08-26

    The three-dimensional (3D) organization of the eukaryotic genome is critical for its proper function. Evidence suggests that extensive chromatin loops form the building blocks of the genomic architecture, separating genes and gene clusters into distinct functional domains. These loops are anchored in part by a special type of DNA elements called chromatin boundary elements (CBEs). CBEs were originally found to insulate neighboring genes by blocking influences of transcriptional enhancers or the spread of silent chromatin. However, recent results show that chromatin loops can also play a positive role in gene regulation by looping out intervening DNA and "delivering" remote enhancers to gene promoters. In addition, studies from human and model organisms indicate that the configuration of chromatin loops, many of which are tethered by CBEs, is dynamically regulated during cell differentiation. In particular, a recent work by Li et al has shown that the SF1 boundary, located in the Drosophila Hox cluster, regulates local genes by tethering different subsets of chromatin loops: One subset enclose a neighboring gene ftz, limiting its access by the surrounding Scr enhancers and restrict the spread of repressive histones during early embryogenesis; and the other loops subdivide the Scr regulatory region into independent domains of enhancer accessibility. The enhancer-blocking activity of these CBE elements varies greatly in strength and tissue distribution. Further, tandem pairing of SF1 and SF2 facilitate the bypass of distal enhancers in transgenic flies, providing a mechanism for endogenous enhancers to circumvent genomic interruptions resulting from chromosomal rearrangement. This study demonstrates how a network of chromatin boundaries, centrally organized by SF1, can remodel the 3D genome to facilitate gene regulation during development. PMID:27621770

  11. Chromatin boundary elements organize genomic architecture and developmental gene regulation in Drosophila Hox clusters

    Science.gov (United States)

    Ma, Zhibo; Li, Mo; Roy, Sharmila; Liu, Kevin J; Romine, Matthew L; Lane, Derrick C; Patel, Sapna K; Cai, Haini N

    2016-01-01

    The three-dimensional (3D) organization of the eukaryotic genome is critical for its proper function. Evidence suggests that extensive chromatin loops form the building blocks of the genomic architecture, separating genes and gene clusters into distinct functional domains. These loops are anchored in part by a special type of DNA elements called chromatin boundary elements (CBEs). CBEs were originally found to insulate neighboring genes by blocking influences of transcriptional enhancers or the spread of silent chromatin. However, recent results show that chromatin loops can also play a positive role in gene regulation by looping out intervening DNA and “delivering” remote enhancers to gene promoters. In addition, studies from human and model organisms indicate that the configuration of chromatin loops, many of which are tethered by CBEs, is dynamically regulated during cell differentiation. In particular, a recent work by Li et al has shown that the SF1 boundary, located in the Drosophila Hox cluster, regulates local genes by tethering different subsets of chromatin loops: One subset enclose a neighboring gene ftz, limiting its access by the surrounding Scr enhancers and restrict the spread of repressive histones during early embryogenesis; and the other loops subdivide the Scr regulatory region into independent domains of enhancer accessibility. The enhancer-blocking activity of these CBE elements varies greatly in strength and tissue distribution. Further, tandem pairing of SF1 and SF2 facilitate the bypass of distal enhancers in transgenic flies, providing a mechanism for endogenous enhancers to circumvent genomic interruptions resulting from chromosomal rearrangement. This study demonstrates how a network of chromatin boundaries, centrally organized by SF1, can remodel the 3D genome to facilitate gene regulation during development.

  12. 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 u

  13. Cas9 Functionally Opens Chromatin

    OpenAIRE

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

    2016-01-01

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

  14. Cas9 Functionally Opens Chromatin

    OpenAIRE

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

    2015-01-01

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

  15. Cas9 Functionally Opens Chromatin.

    Directory of Open Access Journals (Sweden)

    Amira A Barkal

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

  16. Cas9 Functionally Opens Chromatin

    Science.gov (United States)

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

    2016-01-01

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

  17. Seismic Response of Submerged Floating Tunnel Tether

    Institute of Scientific and Technical Information of China (English)

    SU Zhi-bin; SUN Sheng-nan

    2013-01-01

    A mathematical equation for vibration of submerged floating tunnel tether under the effects of earthquake and parametric excitation is presented.Multi-step Galerkin method is used to simplify this equation and the fourth-order Runge-Kuta integration method is used for numerical analysis.Finally,vibration response of submerged floating tunnel tether subjected to earthquake and parametric excitation is analyzed in a few numerical examples.The results show that the vibration response of tether varies with the seismic wave type; the steady maximum mid-span displacement of tether subjected to seismic wave keeps constant when parametric resonance takes place; the transient maximum mid-span displacement of tether is related to the peak value of input seismic wave acceleration.

  18. Electrodynamics of the Getaway Tether Experiment

    Science.gov (United States)

    Greene, Michael; Baginski, Michael; Wheelock, Douglas

    1989-01-01

    An electrodynamic circuit model of the interaction of a pair of small tethered satellites and the ionosphere is developed and analyzed. The system under study, the Getaway Tether Experiment (GATE), is composed of two small satellites and 1 km of insulated conducting tether. The nonlinear model has elements representing the emission, collection, and resistive flow of charge through an electrically conductive tether, plasma contactors, and the ionosphere. The circuit model is incorporated into a dynamic orbital simulation to predict mission performance. Simulation results show the feasibility to bilaterally transfer energy between stored electrical energy and orbital momentum. A transient model is also developed using the circuit model and a string of N lumped-parameter modules, each consisting of resistance, capacitance, and induced potential for the tether. Transients are shown via simulation to occur over millisecond intervals.

  19. Characteristics of thymine dimer excision from xeroderma pigmentosum chromatin

    International Nuclear Information System (INIS)

    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/m2-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

  20. Epigenetics & chromatin: Interactions and processes

    NARCIS (Netherlands)

    S. Henikoff (Steven); F.G. Grosveld (Frank)

    2013-01-01

    textabstractOn 11 to 13 March 2013, BioMed Central will be hosting its inaugural conference, Epigenetics & Chromatin: Interactions and Processes, at Harvard Medical School, Cambridge, MA, USA. Epigenetics & Chromatin has now launched a special article series based on the general themes of the confer

  1. 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.

  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. Dynamic simulation of tethered satellite systems

    International Nuclear Information System (INIS)

    The idea of connecting several spacecrafts by tethers to create mechanical systems with interesting dynamic properties was first brought up by Tsiolkovskii at the end of the nineteenth century, long before the technical means for realization were available. Today, after about 30 years of worldwide research, Tethered Satellite Systems have evolved into a promising technology with a considerable number of possible applications. These systems can be used to build large structures in orbit and provide a fuel-saving way of returning payloads from a space station. Conducting tethers interacting with the Earth's magnetic field can serve as motors or generators, transforming kinetic and electric energy into each other very efficiently. To develop this new technology seventeen experiments have been carried out in orbit since 1966 with NASA's TSS missions being the most well known. The work introduced in this thesis is part of a project carried out by the Institute of Mechanics of the Vienna University of Technology as contractor of the European Space Agency. A software package for the dynamic simulation of Tethered Satellite Systems with variable tether length has been developed to serve as a tool for the development and testing of such systems. The focus is on the deployment and retrieval of the tether, which is an important but tricky process, and has to be controlled by proper control algorithms. This can elegantly be done by a force acting on the tether at the point where it leaves the satellite. In the simulation program a mechanical model consisting of two satellites and a massive, perfectly flexible, visco-elastic tether is considered. The actual length of the tether is not given as a prescribed function of time but is an additional unknown and has to be calculated from the dynamics of the entire system and the forces acting on the tether. Hence the deployment mechanism has an important influence on the deployment dynamics. In this work the tether is considered to

  5. FCAPD Protective Coating for Space Tethers Project

    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...

  6. Tethers in space handbook, second edition

    Science.gov (United States)

    Penzo, Paul A. (Editor); Ammann, Paul W. (Editor)

    1989-01-01

    The Tethers in Space Handbook, Second Edition represents an update to the initial volume issued in September 1986. As originally intended, this handbook is designed to serve as a reference manual for policy makers, program managers, educators, engineers, and scientists alike. It contains information for the uninitiated, providing insight into the fundamental behavior of tethers in space. For those familiar with space tethers, it includes a summary of past and ongoing studies and programs, a complete bibliography of tether publications, and names, addresses, and phone numbers of workers in the field. Perhaps its most valuable asset is the brief description of nearly 50 tether applications which have been proposed and analyzed over the past 10 years. The great variety of these applications, from energy generation to boosting satellites to gravity wave detection is an indication that tethers will play a significant part in the future of space development. This edition of the handbook preserves the major characteristics of the original; however, some significant rearrangements and additions have been made. The first section on Tether Programs has been brought up to date, and now includes a description of TSS-2, the aerodynamic NASA/Italian Space Agency (ASI) mission. Tether Applications follows, and this section has been substantially rearranged. First, the index and cross-reference for the applications have been simplified. Also, the categories have changed slightly, with Technology and Test changed to Aerodynamics, and the Constellations category removed. In reality, tether constellations may be applicable to many of the other categories, since it is simply a different way of using tethers. Finally, to separate out those applications which are obviously in the future, a Concepts category has been added. A new section included here on Conference Summaries recognizes the fact that the tether community is growing internationally, and that meetings provide a means of

  7. 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.

  8. Tethered satellite system dynamics and control

    Science.gov (United States)

    Musetti, B.; Cibrario, B.; Bussolino, L.; Bodley, C. S.; Flanders, H. A.; Mowery, D. K.; Tomlin, D. D.

    1990-01-01

    The first tethered satellite system, scheduled for launch in May 1991, is reviewed. The system dynamics, dynamics control, and dynamics simulations are discussed. Particular attention is given to in-plane and out-of-plane librations; tether oscillation modes; orbiter and sub-satellite dynamics; deployer control system; the sub-satellite attitude measurement and control system; the Aeritalia Dynamics Model; the Martin-Marietta and NASA-MSFC Dynamics Model; and simulation results.

  9. Numerical modelling of elastic space tethers

    DEFF Research Database (Denmark)

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

    2012-01-01

    , 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....... It is also shown that on the slow manifold the dynamics of the satellites are well-approximated by the finite dimensional slack-spring model....

  10. Chromatin, epigenetics and stem cells.

    Science.gov (United States)

    Roloff, Tim C; Nuber, Ulrike A

    2005-03-01

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

  11. Painting a Clearer Picture of Chromatin.

    Science.gov (United States)

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

    2016-02-22

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

  12. Brain Function and Chromatin Plasticity

    OpenAIRE

    Dulac, Catherine

    2010-01-01

    The characteristics of epigenetic control, including the potential for long-lasting, stable effects on gene expression that outlive an initial transient signal, could be of singular importance for post-mitotic neurons, which are subject to changes with short- to long-lasting influence on their activity and connectivity. Persistent changes in chromatin structure are thought to contribute to mechanisms of epigenetic inheritance. Recent advances in chromatin biology offer new avenues to investig...

  13. Chromatin remodeling, development and disease

    International Nuclear Information System (INIS)

    Development is a stepwise process in which multi-potent progenitor cells undergo lineage commitment, differentiation, proliferation and maturation to produce mature cells with restricted developmental potentials. This process is directed by spatiotemporally distinct gene expression programs that allow cells to stringently orchestrate intricate transcriptional activation or silencing events. In eukaryotes, chromatin structure contributes to developmental progression as a blueprint for coordinated gene expression by actively participating in the regulation of gene expression. Changes in higher order chromatin structure or covalent modification of its components are considered to be critical events in dictating lineage-specific gene expression during development. Mammalian cells utilize multi-subunit nuclear complexes to alter chromatin structure. Histone-modifying complex catalyzes covalent modifications of histone tails including acetylation, methylation, phosphorylation and ubiquitination. ATP-dependent chromatin remodeling complex, which disrupts histone-DNA contacts and induces nucleosome mobilization, requires energy from ATP hydrolysis for its catalytic activity. Here, we discuss the diverse functions of ATP-dependent chromatin remodeling complexes during mammalian development. In particular, the roles of these complexes during embryonic and hematopoietic development are reviewed in depth. In addition, pathological conditions such as tumor development that are induced by mutation of several key subunits of the chromatin remodeling complex are discussed, together with possible mechanisms that underlie tumor suppression by the complex

  14. Comprehensive analysis of LANA interacting proteins essential for viral genome tethering and persistence.

    Directory of Open Access Journals (Sweden)

    Subhash C Verma

    Full Text Available Kaposi's sarcoma associated herpesvirus is tightly linked to multiple human malignancies including Kaposi's sarcoma (KS, Primary Effusion Lymphoma (PEL and Multicentric Castleman's Disease (MCD. KSHV like other herpesviruses establishes life-long latency in the infected host by persisting as chromatin and tethering to host chromatin through the virally encoded protein Latency Associated Nuclear Antigen (LANA. LANA, a multifunctional protein, is capable of binding to a large number of cellular proteins responsible for transcriptional regulation of various cellular and viral pathways involved in blocking cell death and promoting cell proliferation. This leads to enhanced cell division and replication of the viral genome, which segregates faithfully in the dividing tumor cells. The mechanism of genome segregation is well known and the binding of LANA to nucleosomal proteins, throughout the cell cycle, suggests that these interactions play an important role in efficient segregation. Various biochemical methods have identified a large number of LANA binding proteins, including histone H2A/H2B, histone H1, MeCP2, DEK, CENP-F, NuMA, Bub1, HP-1, and Brd4. These nucleosomal proteins may have various functions in tethering of the viral genome during specific phases of the viral life cycle. Therefore, we performed a comprehensive analysis of their interaction with LANA using a number of different assays. We show that LANA binds to core nucleosomal histones and also associates with other host chromatin proteins including histone H1 and high mobility group proteins (HMGs. We used various biochemical assays including co-immunoprecipitation and in-vivo localization by split GFP and fluorescence resonance energy transfer (FRET to demonstrate their association.

  15. Chromatin structure and DNA damage

    International Nuclear Information System (INIS)

    This dissertation examines the structure and structural transitions of chromatin in relation to DNA damage. The ability of intact and histone H1 depleted chromatin fibers to fold into higher ordered structures in vitro was examined following DNA photodamage introduced by two different agents. (1) 254-nm UV radiation and (2) trimethylpsoralen (plus near-UV radiation). Both agents are highly specific for DNA and form adducts predicted to cause different degrees of distortion in the DNA helix. The salt-induced structural transitions of intact and histone H1 depleted chromatin fibers were monitored by both analytical ultracentrifugation and light scattering. Our results show that even in the presence of extremely large, nonphysiological amounts of photodamage by either agent the ability of chromatin to fold into higher ordered structures is not affected. The compact, 30 nm fiber must therefore be able to accommodate a large amount of DNA damage without any measurable changes in the overall size or degree of compaction of this structure. The distribution of pyrimidine dimers was mapped at the single nucleotide level in nucleosome core DNA from UV-irradiated mononucleosomes, chromatin fibers, and human cells in culture using the 3' → 5' exonuclease activity of T4 DNA polymerase

  16. Single Molecule Studies of Chromatin

    Energy Technology Data Exchange (ETDEWEB)

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

    2006-02-06

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

  17. Chromatin remodelers and their roles in chromatin organization

    OpenAIRE

    Strålfors, Annelie

    2012-01-01

    The DNA in the eukaryotic nucleus is organized into a complex DNA-protein structure called chromatin. The basic repeating unit of chromatin is the nucleosome, which consists of 147 bp of DNA wrapped around a histone protein octamer. The nucleosomes form a “beads on a string” structure, which can be folded into higherorder structures that allow an extensive degree of DNA compaction. This compaction is so effective that 2 meters of DNA can fit into the human cell nucleus with a ...

  18. Tethering Complexes in the Arabidopsis Endomembrane System.

    Science.gov (United States)

    Vukašinović, Nemanja; Žárský, Viktor

    2016-01-01

    Targeting of endomembrane transport containers is of the utmost importance for proper land plant growth and development. Given the immobility of plant cells, localized membrane vesicle secretion and recycling are amongst the main processes guiding proper cell, tissue and whole plant morphogenesis. Cell wall biogenesis and modification are dependent on vectorial membrane traffic, not only during normal development, but also in stress responses and in plant defense against pathogens and/or symbiosis. It is surprising how little we know about these processes in plants, from small GTPase regulation to the tethering complexes that act as their effectors. Tethering factors are single proteins or protein complexes mediating first contact between the target membrane and arriving membrane vesicles. In this review we focus on the tethering complexes of the best-studied plant model-Arabidopsis thaliana. Genome-based predictions indicate the presence of all major tethering complexes in plants that are known from a hypothetical last eukaryotic common ancestor (LECA). The evolutionary multiplication of paralogs of plant tethering complex subunits has produced the massively expanded EXO70 family, indicating a subfunctionalization of the terminal exocytosis machinery in land plants. Interpretation of loss of function (LOF) mutant phenotypes has to consider that related, yet clearly functionally-specific complexes often share some common core subunits. It is therefore impossible to conclude with clarity which version of the complex is responsible for the phenotypic deviations observed. Experimental interest in the analysis of plant tethering complexes is growing and we hope to contribute with this review by attracting even more attention to this fascinating field of plant cell biology. PMID:27243010

  19. Passivity-Based Control of a Rigid Electrodynamic Tether

    OpenAIRE

    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 an...

  20. MR imaging evaluation of tethered spinal cord

    International Nuclear Information System (INIS)

    Seven cases of tethered cord underwent magnetic resonance imaging. The associated findings included the following: case 1: caudal regression, inperforated anus, cutaneovesical fistula, and diverticulum of the bladder; case 2: Arnold-Chiari malformation, hydromyelia, and urinary reflux; case 3; lipoma; case 4: postoperative syringomyelia and residual lipoma; case 5: diastematomyelia and spinal bifida; case 6: dysraphism, diastematomyelia, and myelomeningocele; and case 7: postoperative split cord T1-weighted axial and sagittal images are sufficient for evaluation of tethered cord and associated anomalies and are also useful for postoperative follow-up and the detection of possible complications

  1. Tethers in Space: A propellantless propulsion in-orbit demonstration

    NARCIS (Netherlands)

    Kruijff, M.

    2011-01-01

    Space tethers are cables that connect satellites or other endmasses in orbit. The emptiness of space and the near-weightlessness there make it possible to deploy very long and thin tethers. By exploiting basic principles of physics, tethers can provide propellantless propulsion and enable unique app

  2. Formation and finite element analysis of tethered bilayer lipid structures.

    Science.gov (United States)

    Kwak, Kwang Joo; Valincius, Gintaras; Liao, Wei-Ching; Hu, Xin; Wen, Xuejin; Lee, Andrew; Yu, Bo; Vanderah, David J; Lu, Wu; Lee, L James

    2010-12-01

    Rapid solvent exchange of an ethanolic solution of diphytanoyl phosphatidylcholine (DPhyPC) in the presence of a mixed self-assembled monolayer (SAM) [thiolipid/β-mercaptoethanol (βME) (3/7 mol/mol) on Au] shows a transition from densely packed tethered bilayer lipid membranes [(dp)tBLMs], to loosely packed tethered bilayer lipid membranes [(lp)tBLMs], and tethered bilayer liposome nanoparticles (tBLNs) with decreasing DPhyPC concentration. The tethered lipidic constructs in the aqueous medium were analyzed by atomic force microscopy (AFM) and electrochemical impedance spectroscopy (EIS). Finite element analysis (FEA) was applied to interpret spectral EIS features without referring to equivalent circuit modeling. Using structural data obtained earlier from neutron reflectometry and dielectric constants of lipid bilayers, we reproduced experimentally observed features of the electrochemical impedance (EI) spectra of complex surface constructs involving small pinhole defects, large membrane-free patches, and bound liposomes. We demonstrated by FEA that highly insulating (dp)tBLMs with low-defect density exhibit EI spectra in the shape of a perfect semicircle with or without low-frequency upward "tails" in the Cole-Cole representation. Such EI spectra were observed at DPhyPC concentrations of >5 × 10(-3) mol L(-1). While AFM was not able to visualize very small lateral defects in such films, EI spectra unambiguously signaled their presence by increased low frequency "tails". Using FEA we demonstrate that films with large diameter visible defects (>25 nm by AFM) produce EI spectral features consisting of two semicircles of comparable size. Such films were typically obtained at DPhyPC concentrations of FEA revealed that, to account for these EI features for bound liposome systems (50-500 nm diameter), one needs to assume much lower tBLM conductivities of the submembrane space, which separates the electrode surface and the phospholipid bilayer. Alternatively, FEA

  3. 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.

  4. 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.

  5. Electrodynamic Tethers for Novel LEO Missions

    Science.gov (United States)

    Kantner, Michael; Hoyt, Robert; Scardera, Michael; Johnson, Charles

    2011-01-01

    The exponential increase of launch system size - and cost - with deltaV makes missions requiring large total impulse cost prohibitive. Northrop Grumman and partners have matured a fundamentally different method for generating propulsion using electrodynamic tethers (EDTs) that escapes the limitations of the rocket equation. With essentially unlimited delta V, we can perform new classes of missions that are currently unaffordable or unfeasible.

  6. ATM alters the otherwise robust chromatin mobility at sites of DNA double-strand breaks (DSBs in human cells.

    Directory of Open Access Journals (Sweden)

    Annabelle Becker

    Full Text Available Ionizing radiation induces DNA double strand breaks (DSBs which can lead to the formation of chromosome rearrangements through error prone repair. In mammalian cells the positional stability of chromatin contributes to the maintenance of genome integrity. DSBs exhibit only a small, submicron scale diffusive mobility, but a slight increase in the mobility of chromatin domains by the induction of DSBs might influence repair fidelity and the formation of translocations. The radiation-induced local DNA decondensation in the vicinity of DSBs is one factor potentially enhancing the mobility of DSB-containing chromatin domains. Therefore in this study we focus on the influence of different chromatin modifying proteins, known to be activated by the DNA damage response, on the mobility of DSBs. IRIF (ionizing radiation induced foci in U2OS cells stably expressing 53BP1-GFP were used as a surrogate marker of DSBs. Low angle charged particle irradiation, known to trigger a pronounced DNA decondensation, was used for the defined induction of linear tracks of IRIF. Our results show that movement of IRIF is independent of the investigated chromatin modifying proteins like ACF1 or PARP1 and PARG. Also depletion of proteins that tether DNA strands like MRE11 and cohesin did not alter IRIF dynamics significantly. Inhibition of ATM, a key component of DNA damage response signaling, resulted in a pronounced confinement of DSB mobility, which might be attributed to a diminished radiation induced decondensation. This confinement following ATM inhibition was confirmed using X-rays, proving that this effect is not restricted to densely ionizing radiation. In conclusion, repair sites of DSBs exhibit a limited mobility on a small spatial scale that is mainly unaffected by depletion of single remodeling or DNA tethering proteins. However, it relies on functional ATM kinase which is considered to influence the chromatin structure after irradiation.

  7. 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....

  8. Conjunctions and Collision Avoidance with Electrodynamic Tethers

    Science.gov (United States)

    Levin, E.

    2013-09-01

    Electrodynamic propulsion technology is currently in development by NASA, ESA, and JAXA for the purpose of affordable removal of large debris objects from LEO. At the same time, the Naval Research Laboratory is preparing a 3U CubeSat with a 1-km electrodynamic tether for a flight demonstration of electrodynamic propulsion. This type of propulsion does not require fuel. The electrodynamic thrust is the Lorentz force acting on the electric current in a long conductor (tether) in the geomagnetic field. Electrons are collected from the ambient plasma on one end and emitted back into the plasma from the other end. The electric current loop is closed through the ionosphere, as demonstrated in two previous flights. The vehicle is solar powered. To support safe navigation of electrodynamic tethers, proper conjunction analysis and collision avoidance strategies are needed. The typical lengths of electrodynamic tethers for near-term applications are measured in kilometers, and the conjunction geometry is very different from the geometry of conjunctions between compact objects. It is commonly thought that the collision cross-section in a conjunction between a tether and a compact object is represented by the product of the tether length and the size of the object. However, rigorous analysis shows that this is not the case, and that the above assumption leads to grossly overestimated collision probabilities. The paper will present the results of a detailed mathematical analysis of the conjunction geometry and collision probabilities in close approaches between electrodynamic tethers and compact objects, such as satellites, rocket bodies, and debris fragments. Electrodynamic spacecraft will not require fuel, and therefore, can thrust constantly. Their orbit transfers can take many days, but can result in major orbit changes, including large rotations of the orbital plane, both in the inclination and the node. During these orbit transfers, the electrodynamic spacecraft will

  9. 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°.

  10. Analysis of chromatin attachment and partitioning functions of bovine papillomavirus type 1 E2 protein.

    Science.gov (United States)

    Abroi, Aare; Ilves, Ivar; Kivi, Sirje; Ustav, Mart

    2004-02-01

    Recent studies have suggested that the tethering of viral genomes to host cell chromosomes could provide one of the ways to achieve their nuclear retention and partitioning during extrachromosomal maintenance in dividing cells. The data we present here provide firm evidence that the partitioning of the bovine papillomavirus type 1 (BPV1) genome is dependent on the chromatin attachment process mediated by viral E2 protein and its multiple binding sites. On the other hand, the attachment of E2 and the E2-mediated tethering of reporter plasmids to host chromosomes are not necessarily sufficient for efficient partitioning, suggesting that additional E2-dependent activities might be involved in the latter process. The activity of E2 protein in chromatin attachment and partitioning is more sensitive to the point mutations in the N-terminal domain than its transactivation and replication initiation functions. Therefore, at least part of the interactions of the E2 N-terminal domain with its targets during the chromatin attachment and partitioning processes are likely to involve specific receptors not involved in transactivation and replication activities of the protein. The mutational analysis also indicates that the binding of E2 to chromatin is not achieved through interaction of linear N-terminal subsequences of the E2 protein with putative receptors. Instead, the composite surface elements of the N-terminal domain build up the receptor-binding surface of E2. In this regard, the interaction of BPV1 E2 with its chromosomal targets clearly differs from the interactions of LANA1 protein from Kaposi's sarcoma-associated human herpesvirus and EBNA1 from Epstein-Barr virus with their specific receptors. PMID:14747575

  11. Coming to terms with chromatin structure.

    Science.gov (United States)

    Even-Faitelson, Liron; Hassan-Zadeh, Vahideh; Baghestani, Zahra; Bazett-Jones, David P

    2016-03-01

    Chromatin, once thought to serve only as a means to package DNA, is now recognized as a major regulator of gene activity. As a result of the wide range of methods used to describe the numerous levels of chromatin organization, the terminology that has emerged to describe these organizational states is often imprecise and sometimes misleading. In this review, we discuss our current understanding of chromatin architecture and propose terms to describe the various biochemical and structural states of chromatin. PMID:26223534

  12. Chromatin state dynamics during blood formation

    OpenAIRE

    Lara-Astiaso, David; Weiner, Assaf; Lorenzo-Vivas, Erika; Zaretsky, Irina; Jaitin, Diego Adhemar; David, Eyal; Keren-Shaul, Hadas; Mildner, Alexander; Winter, Deborah; Jung, Steffen; Friedman, Nir; Amit, Ido

    2014-01-01

    Chromatin modifications are crucial for development, yet little is known about their dynamics during differentiation. Hematopoiesis provides a well-defined model to study chromatin state dynamics, however technical limitations impede profiling of homogeneous differentiation intermediates. We developed a high sensitivity indexing-first chromatin immunoprecipitation approach (iChIP) to profile the dynamics of four chromatin modifications across 16 stages of hematopoietic differentiation. We ide...

  13. Predicting chromatin organization using histone marks

    OpenAIRE

    Huang, Jialiang; Marco, Eugenio; Pinello, Luca; Yuan, Guo-Cheng

    2015-01-01

    Genome-wide mapping of three dimensional chromatin organization is an important yet technically challenging task. To aid experimental effort and to understand the determinants of long-range chromatin interactions, we have developed a computational model integrating Hi-C and histone mark ChIP-seq data to predict two important features of chromatin organization: chromatin interaction hubs and topologically associated domain (TAD) boundaries. Our model accurately and robustly predicts these feat...

  14. Impact of Chromatin on HIV Replication

    OpenAIRE

    Agosto, Luis M.; Matthew Gagne; Henderson, Andrew J.

    2015-01-01

    Chromatin influences Human Immunodeficiency Virus (HIV) integration and replication. This review highlights critical host factors that influence chromatin structure and organization and that also impact HIV integration, transcriptional regulation and latency. Furthermore, recent attempts to target chromatin associated factors to reduce the HIV proviral load are discussed.

  15. Surfactant Behavior of Amphiphilic Polymer-Tethered Nanoparticles.

    Science.gov (United States)

    Zhang, Yue; Zhao, Hanying

    2016-04-19

    In recent years, an emerging research area has been the surfactant behavior of polymer-tethered nanoparticles. In this feature article, we have provided a general introduction to the synthesis, self-assembly, and interfacial activity of polymer-tethered inorganic nanoparticles, polymer-tethered organic nanoparticles, and polymer-tethered natural nanoparticles. In addition, applications of the polymer-tethered nanoparticles in colloidal and materials science are briefly reviewed. All research demonstrates that amphiphilic polymer-tethered nanoparticles exhibit surfactant behavior and can be used as elemental building blocks for the fabrication of advanced structures by the self-assembly approach. The polymer-tethered nanoparticles provide new opportunities to engineer materials and biomaterials possessing specific functionality and physical properties. PMID:27018567

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

    Directory of Open Access Journals (Sweden)

    Grøntved Lars

    2012-06-01

    Full Text Available Abstract 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 large amounts of purified nuclei as starting material. This complicates analysis of trace clinical tissue samples that are often stored frozen. We have developed an alternative nuclease based procedure to bypass nuclear preparation to interrogate nuclease accessible regions in frozen tissue samples. Results Here we introduce a novel technique that specifically identifies Tissue Accessible Chromatin (TACh. The TACh method uses pulverized frozen tissue as starting material and employs one of the two robust endonucleases, Benzonase or Cyansase, which are fully active under a range of stringent conditions such as high levels of detergent and DTT. As a proof of principle we applied TACh to frozen mouse liver tissue. Combined with massive parallel sequencing TACh identifies accessible regions that are associated with euchromatic features and accessibility at transcriptional start sites correlates positively with levels of gene transcription. Accessible chromatin identified by TACh overlaps to a large extend with accessible chromatin identified by DNase I using nuclei purified from freshly isolated liver tissue as starting material. The similarities are most pronounced at highly accessible regions, whereas identification of less accessible regions tends to be more divergence between nucleases. Interestingly, we show that some of the differences between DNase I and Benzonase relate to their intrinsic sequence biases and accordingly accessibility of CpG islands is probed more efficiently using TACh. Conclusion The TACh methodology identifies accessible chromatin derived from frozen tissue samples. We propose that this simple, robust approach can be applied

  17. Radiation-induced XRCC4 association with chromatin DNA analyzed by biochemical fractionation

    International Nuclear Information System (INIS)

    XRCC4, in association with DNA ligase IV, is thought to play a critical role in the ligation of two DNA ends in DNA double-strand break (DSB) repair through non-homologous end-joining (NHEJ) pathway. In the present study, we captured radiation-induced chromatin-recruitment of XRCC4 by biochemical fractionation using detergent Nonidet P-40. A subpopulation of XRCC4 changed into a form that is resistant to the extraction with 0.5% Nonidet P-40-containing buffer after irradiation. This form of XRCC4 was liberated by micrococcal nuclease treatment, indicating that it had been tethered to chromatin DNA. This chromatin-recruitment of XRCC4 could be seen immediately (<0.1 hr) after irradiation and remained up to 4 hr after 20 Gy irradiation. It was seen even after irradiation of small doses, id est (i.e.), 2 Gy, but the residence of XRCC4 on chromatin was very transient after 2 Gy irradiation, returning to near normal level in 0.2-0.5 hr after irradiation. The chromatin-bound XRCC4 represented only -1% of total XRCC4 molecules even after 20 Gy irradiation and the quantitative analysis using purified protein as the reference suggested that only a few XRCC4-DNA ligase IV complexes were recruited to each DNA end. We further show that the chromatin-recruitment of XRCC4 was not attenuated by wortmannin, an inhibitor of DNA-PK, or siRNA-mediated knockdown of the DNA-PK catalytic subunit (DNA-PKcs), indicating that this process does not require DNA-PKcs. These results would provide us with useful experimental tools and important insights to understand the DNA repair process through NHEJ pathway. (author)

  18. 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...

  19. Spectroscopic study of laser irradiated chromatin

    Energy Technology Data Exchange (ETDEWEB)

    Radu, Liliana, E-mail: liliana1radu@gmail.com [V. Babes National Institute, Department of Molecular Genetics and Radiobiology (Romania); Mihailescu, I. [National Institute for Lasers, Plasma and Radiation Physics, Department of Lasers (Romania); Gazdaru, Doina [Faculty of Physics, Bucharest University, Department of Biophysics (Romania); Preoteasa, V. [V. Babes National Institute, Department of Molecular Genetics and Radiobiology (Romania)

    2013-04-15

    The effects of three UV excimer laser radiations, with wavelengths of 193, 248 and 282 nm respectively, on the structure of chromatin (the complex of deoxyribonucleic acid with proteins that exists in eukaryotic cells nuclei) were investigated. The chromatin was extracted from livers of Winstar rats. The spectroscopic methods used are: fluorescence (Foerster) resonance energy transfer (FRET), time resolved fluorescence and steady-state fluorescence. A chromatin deoxyribonucleic acid radiolysis, a chromatin proteins damage and a change of the global chromatin structure on lasers action were indicated by this study. It exists some small differences between the actions of these three laser radiations.

  20. Chromatin Dynamics of Circadian Transcription

    OpenAIRE

    Aguilar-Arnal, Lorena; Sassone-Corsi, Paolo

    2015-01-01

    The molecular circadian clock orchestrates the daily cyclical expression of thousands of genes. Disruption of this transcriptional program leads to a variety of pathologies, including insomnia, depression and metabolic disorders. Circadian rhythms in gene expression rely on specific chromatin transitions which are ultimately coordinated by the molecular clock. As a consequence, a highly plastic and dynamic circadian epigenome can be delineated across different tissues and cell types. Intrigui...

  1. A Tethering Device for Mobile Robot Guidance

    Directory of Open Access Journals (Sweden)

    Sangik Na

    2009-11-01

    Full Text Available A new human and robot interface tool, so-called Navi-Guider, which makes it easy to handle mobile robots, is presented in this paper. The Navi-Guider is easily mounted on a mobile robot and is able to detect a length and a direction of the tether pulled out by a user. Those detected factors are utilized for the robot guidance and control. This paper addresses detailed hardware and software architecture of the Navi-Guider and demonstrates the practical usability of the system through actual experimental tests. The new device, NaviGuider, is an intuitive control tool for moving mobile robots from a place to another place just by pulling the tether.

  2. Magnetic Carbon Nanotubes Tethered with Maghemite Nanoparticles

    Science.gov (United States)

    Kim, Il Tae; Nunnery, Grady; Jacob, Karl; Schwartz, Justin; Liu, Xiaotao; Tannenbaum, Rina

    2011-03-01

    We describe a novel, facile method for the synthesis of magnetic carbon nanotubes (m-CNTs) decorated with monodisperse γ - Fe 2 O3 magnetic (maghemite) nanoparticles and their aligned feature in a magnetic field. The tethering of the nanoparticles was achieved by the initial activation of the surface of the CNTs with carboxylic acid groups, followed by the attachment of the γ - Fe 2 O3 nanoparticles via a modified sol-gel process. Sodium dodecylbenzene sulfonate (NaDDBS) was introduced into the suspension to prevent the formation of an iron oxide 3D network. Various characterization methods were used to confirm the formation of well-defined maghemite nanoparticles. The tethered nanoparticles imparted magnetic characteristics to the CNTs, which became superparamagnetic. The m-CNTs were oriented parallel to the direction of a magnetic field. This has the potential of enhancing various properties, e.g. mechanical and electrical properties, in composite materials.

  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. Tethered nuclear power for the space station

    International Nuclear Information System (INIS)

    A nuclear space power system the SP-100 is being developed for future missions where large amounts of electrical power will be required. Although it is primarily intended for unmanned spacecraft, it can be adapted to a manned space platform by tethering it above the station through an electrical transmission line which isolates the reactor far away from the inhabited platform and conveys its power back to where it is needed. The transmission line, used in conjunction with an instrument rate shield, attenuates reactor radiation in the vicinity of the space station to less than one-one hundredth of the natural background which is already there. This combination of shielding and distance attenuation is less than one-tenth the mass of boom-mounted or onboard man-rated shields that are required when the reactor is mounted nearby. This paper describes how connection is made to the platform (configuration, operational requirements) and introduces a new element the coaxial transmission tube which enables efficient transmission of electrical power through long tethers in space. Design methodology for transmission tubes and tube arrays is discussed. An example conceptual design is presented that shows SP-100 at three power levels 100 kWe, 300 kWe, and 1000 kWe connected to space station via a 2 km HVDC transmission line/tether. Power system performance, mass, and radiation hazard are estimated with impacts on space station architecture and operation. 23 references

  5. Coat/Tether Interactions—Exception or Rule?

    Science.gov (United States)

    Schroeter, Saskia; Beckmann, Sabrina; Schmitt, Hans Dieter

    2016-01-01

    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. PMID:27243008

  6. Modeling of tethered satellite formations using graph theory

    DEFF Research Database (Denmark)

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

    2011-01-01

    could form stable formations in space are cumbersome when done at a case to case basis, and a common framework providing a basic model of the dynamics of tethered satellite formations can therefore be advantageous. This paper suggests the use of graph theoretical quantities to describe a tethered...... 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....

  7. Electrodynamics of long metallic tethers in the ionospheric plasma

    Science.gov (United States)

    Dobrowolny, M.

    1978-01-01

    A study is presented of the electrodynamic interactions of long metallic tethers (lengths up to 100 km) with the ionospheric plasma. The study, which is of interest in view of possible future experiments using long tethers in space, includes the derivation of current and potential distribution along the tether, taking also the effects of internal resistance into account. Electrostatic and electrodynamic drag forces are computed and compared with aerodynamic drag.

  8. 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.

  9. Dynamic analysis of tethered space system deployment process

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Discusses in detail the deploying strategies and feature of themotion of the Tethered Space System and the effects of some parameters, such as the property and initial length of the tether, the perturbation of the atmosphere, the ellipse of the orbit and the mass distribution of the system and points out the deploying strategy is based on the controlling of tension and the length of tether. And concludes from the computer simulation results of a tethered atmosphere probing satellite deployment that the deploying strategy presented does work well.

  10. A proposed bare tether experiment on board a sounding rocket

    OpenAIRE

    Fujii, Hironori; OYAMA, Kohichiro; Sasaki, Susumu; Yamagiwa, Yoshiki; Cho, Mengu; Sanmartín Losada, Juan Ramón; Charro, Mario; Heide, Erik J. van der; Kruijff, Michiel; Lebreton, Jean-Pierre; Hilgers, Alain

    2005-01-01

    A sounding rocket experiment is proposed to carry out two experiments by the conductive bare-tether; 1) the test of the OML (Orbital-Motion-Limited) theory to collect electron, and II) the test of techniques to determine (neutral) density profile in critical E-layer. The main driver of the mission is provide a space tether technology experiment in low-Earth-Orbit (LEO) deploying a long tape tether in space and verify the performance of the bare electrodynamic tape tether. The sounding rocket ...

  11. The stochastic dynamics of tethered microcantilevers in a viscous fluid

    Energy Technology Data Exchange (ETDEWEB)

    Robbins, Brian A.; Paul, Mark R. [Department of Mechanical Engineering, Virginia Tech, Blacksburg, Virginia 24061 (United States); Radiom, Milad; Ducker, William A. [Department of Chemical Engineering, Virginia Tech, Blacksburg, Virginia 24061 (United States); Walz, John Y. [Department of Chemical Engineering, University of Kentucky, Lexington, Kentucky 40506 (United States)

    2014-10-28

    We explore and quantify the coupled dynamics of a pair of micron scale cantilevers immersed in a viscous fluid that are also directly tethered to one another at their tips by a spring force. The spring force, for example, could represent the molecular stiffness or elasticity of a biomolecule or material tethered between the cantilevers. We use deterministic numerical simulations with the fluctuation-dissipation theorem to compute the stochastic dynamics of the cantilever pair for the conditions of experiment when driven only by Brownian motion. We validate our approach by comparing directly with experimental measurements in the absence of the tether which shows excellent agreement. Using numerical simulations, we quantify the correlated dynamics of the cantilever pair over a range of tether stiffness. Our results quantify the sensitivity of the auto- and cross-correlations of equilibrium fluctuations in cantilever displacement to the stiffness of the tether. We show that the tether affects the magnitude of the correlations which can be used in a measurement to probe the properties of an attached tethering substance. For the configurations of current interest using micron scale cantilevers in water, we show that the magnitude of the fluid coupling between the cantilevers is sufficiently small such that the influence of the tether can be significant. Our results show that the cross-correlation is more sensitive to tether stiffness than the auto-correlation indicating that a two-cantilever measurement has improved sensitivity when compared with a measurement using a single cantilever.

  12. The stochastic dynamics of tethered microcantilevers in a viscous fluid

    International Nuclear Information System (INIS)

    We explore and quantify the coupled dynamics of a pair of micron scale cantilevers immersed in a viscous fluid that are also directly tethered to one another at their tips by a spring force. The spring force, for example, could represent the molecular stiffness or elasticity of a biomolecule or material tethered between the cantilevers. We use deterministic numerical simulations with the fluctuation-dissipation theorem to compute the stochastic dynamics of the cantilever pair for the conditions of experiment when driven only by Brownian motion. We validate our approach by comparing directly with experimental measurements in the absence of the tether which shows excellent agreement. Using numerical simulations, we quantify the correlated dynamics of the cantilever pair over a range of tether stiffness. Our results quantify the sensitivity of the auto- and cross-correlations of equilibrium fluctuations in cantilever displacement to the stiffness of the tether. We show that the tether affects the magnitude of the correlations which can be used in a measurement to probe the properties of an attached tethering substance. For the configurations of current interest using micron scale cantilevers in water, we show that the magnitude of the fluid coupling between the cantilevers is sufficiently small such that the influence of the tether can be significant. Our results show that the cross-correlation is more sensitive to tether stiffness than the auto-correlation indicating that a two-cantilever measurement has improved sensitivity when compared with a measurement using a single cantilever.

  13. Characterization of the RNA content of chromatin

    OpenAIRE

    Mondal, Tanmoy; Rasmussen, Markus; Pandey, Gaurav Kumar; Isaksson, Anders; Kanduri, Chandrasekhar

    2010-01-01

    Noncoding RNA (ncRNA) constitutes a significant portion of the mammalian transcriptome. Emerging evidence suggests that it regulates gene expression in cis or trans by modulating the chromatin structure. To uncover the functional role of ncRNA in chromatin organization, we deep sequenced chromatin-associated RNAs (CARs) from human fibroblast (HF) cells. This resulted in the identification of 141 intronic regions and 74 intergenic regions harboring CARs. The intronic and intergenic CARs show s...

  14. Electrodynamic-tether time-domain reflectometer for analyzing tether faults and degradation

    Science.gov (United States)

    Bilén, Sven G.; Gilchrist, Brian E.

    2001-02-01

    We propose using time-domain-reflectometry (TDR) systems to locate and track faults along electrodynamic tether (EDT) systems. Inclusion of a TDR on long-duration EDT missions would facilitate tracking of the expected performance degradation due to faults caused by hazards such as micrometeors. The TDR technique has long been an effective tool for determining the location of loads and faults along common transmission lines (TLs) such as coaxial cables. Also sometimes known as pulse reflectometry, TDR works by sending an impulse down a TL and recording the reflected energy as a function of time. Measurement of the reflected TDR waveform provides insight into the physical structure of the TL and any loads, i.e., faults, along its length. In addition, the delay between launched and reflected signals determines the location of the load or fault. Hence, the TDR technique requires knowledge of the propagation characteristics of the TL under test. To examine the feasibility of extending the technique to EDTs we use a previously developed model for the tether transmission line. This model has temporal, and hence spatial, limitations, which may be overcome with enhancements to the tether TL model. We present some general parameters governing the development of such a tether TDR system as well as computer simulations of the TDR system's response. .

  15. Computational strategies to address chromatin structure problems.

    Science.gov (United States)

    Perišić, Ognjen; Schlick, Tamar

    2016-01-01

    While the genetic information is contained in double helical DNA, gene expression is a complex multilevel process that involves various functional units, from nucleosomes to fully formed chromatin fibers accompanied by a host of various chromatin binding enzymes. The chromatin fiber is a polymer composed of histone protein complexes upon which DNA wraps, like yarn upon many spools. The nature of chromatin structure has been an open question since the beginning of modern molecular biology. Many experiments have shown that the chromatin fiber is a highly dynamic entity with pronounced structural diversity that includes properties of idealized zig-zag and solenoid models, as well as other motifs. This diversity can produce a high packing ratio and thus inhibit access to a majority of the wound DNA. Despite much research, chromatin's dynamic structure has not yet been fully described. Long stretches of chromatin fibers exhibit puzzling dynamic behavior that requires interpretation in the light of gene expression patterns in various tissue and organisms. The properties of chromatin fiber can be investigated with experimental techniques, like in vitro biochemistry, in vivo imagining, and high-throughput chromosome capture technology. Those techniques provide useful insights into the fiber's structure and dynamics, but they are limited in resolution and scope, especially regarding compact fibers and chromosomes in the cellular milieu. Complementary but specialized modeling techniques are needed to handle large floppy polymers such as the chromatin fiber. In this review, we discuss current approaches in the chromatin structure field with an emphasis on modeling, such as molecular dynamics and coarse-grained computational approaches. Combinations of these computational techniques complement experiments and address many relevant biological problems, as we will illustrate with special focus on epigenetic modulation of chromatin structure. PMID:27345617

  16. 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 genome

  17. Tethered Contactless Mobile Nuclear Environment Monitoring Robot

    International Nuclear Information System (INIS)

    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

  18. Lipid Gymnastics: Tethers and Fingers in membrane

    Science.gov (United States)

    Tayebi, Lobat; Miller, Gregory; Parikh, Atul

    2009-03-01

    A significant body of evidence now links local mesoscopic structure (e.g., shape and composition) of the cell membrane with its function; the mechanisms by which cellular membranes adopt the specific shapes remain poorly understood. Among all the different structures adopted by cellular membranes, the tubular shape is one of the most surprising one. While their formation is typically attributed to the reorganization of membrane cytoskeleton, many exceptions exist. We report the instantaneous formation of tubular membrane mesophases following the hydration under specific thermal conditions. The shapes emerge in a bimodal way where we have two distinct diameter ranges for tubes, ˜20μm and ˜1μm, namely fat fingers and narrow tethers. We study the roughening of hydrated drops of 3 lipids in 3 different spontaneous curvatures at various temp. and ionic strength to figure out the dominant effect in selection of tethers and fingers. Dynamics of the tubes are of particular interest where we observe four distinct steps of birth, coiling, uncoiling and retraction with different lifetime on different thermal condition. These dynamics appear to reflect interplay between membrane elasticity, surface adhesion, and thermal or hydrodynamic gradient.

  19. Chromatin domain boundaries: insulators and beyond

    Institute of Scientific and Technical Information of China (English)

    Gong Hong WEI; De Pei LIU; Chih Chuan LIANG

    2005-01-01

    The eukaryotic genome is organized into functionally and structurally distinct domains, representing regulatory units for gene expression and chromosome behavior. DNA sequences that mark the border between adjacent domains are the insulators or boundary elements, which are required in maintenance of the function of different domains. Some insulators need others enable to play insulation activity. Chromatin domains are defined by distinct sets of post-translationally modified histones. Recent studies show that these histone modifications are also involved in establishment of sharp chromatin boundaries in order to prevent the spreading of distinct domains. Additionally, in some loci, the high-order chromatin structures for long-range looping interactions also have boundary activities, suggesting a correlation between insulators and chromatin loop domains. In this review, we will discuss recent progress in the field of chromatin domain boundaries.

  20. Computational strategies to address chromatin structure problems

    Science.gov (United States)

    Perišić, Ognjen; Schlick, Tamar

    2016-06-01

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

  1. Tethered actuator for vibration control of space structures

    Science.gov (United States)

    Fujii, H. A.; Sugimoto, Y.; Watanabe, T.; Kusagaya, T.

    2015-12-01

    Effectiveness of a micro-tension actuator for vibration control of such flexible space structures as the tethered space solar power satellites is experimentally studied on the ground. A flexible leverage is employed as the micro-tension actuator in order to control the microtension of tether. The flexible leverage is connected through a tether to the flexible beam as an experimental model of the flexible solar panel with the low first modal frequency of order 1 Hz. The nonlinearity of the flexible tether is taken into account for the vibration control since the tether becomes ineffective when it slacks, i.e., when it is tension-free. The feedback controller is designed by means of the Mission Function control algorithm. Flexural rigidity of the flexible leverage plays an important role in the vibration suppression and is studied experimentally to shed light on the effectiveness of the leverages with five different kinds of rigidity. The experimental results show not only the effect of the flexural rigidity of the flexible leverage on the control performance of the vibration suppression but also the importance of selection of the rigidity to control the vibration of tethered flexible space structures through the microtension of tethers in space.

  2. Project 'VOLCANO': Electronics of tethered satellite system

    Science.gov (United States)

    Savich, N. A.

    The main goal of the 'VOLCANO' project developed jointly by the Institute of Radio Engineering and Electronics and space concern 'ENERGIA' is experimental investigation of the current-voltage characteristics of the 'Collector-Boom-Emitter' system simulating the long Tethered Satellite System (TSS) in the real space flight conditions on the transport ship 'PROGRESS'. These measurements will allow scientists to determine the attainable current values for different combinations of collectors and emitters (passive metallic sphere, thermocathode, hollow cathodes and show up some prospects of active TSS. The report is concerned with the concept, purpose and tasks of the project, the planned set up of the measurement equipment on the 'PROGRESS' ship and in the container extended on the deployable 100 m long boom end.

  3. Airborne Internet Providing Tethered Balloon System

    Directory of Open Access Journals (Sweden)

    Suvriti Dhawan1

    2015-12-01

    Full Text Available In this paper we shall introduce a new system for providing wireless network communication over a specified area using ’lighter than air’ balloons. This technology will replace the existing fiber optic network system. This will be done by using a tethered balloon along with the payload (containing a receiver, a transmitter and a radio communication device.This payload will be suspended from the ground at an altitude (depending on the area of coverage required. Users under this area will be able to access this system directly for internet connectivity. This system can be used over large areas like universities, companies and societies to provide internet facility to their users through Wi-Fi or over an area where the user is specified (commercial purposes. Currently Google is working on similar idea called the ’Google Loon’ in which they use high altitude balloons which float at an altitude twice as high as air planes and the weather. They recently tested this system over New-Zealand by providing internet to their pilot testers on ground. Their balloons not being stationary, move with directional winds and have to be replaced one after the other to maintain consistency. This can be a huge problem over the areas where upper atmospheric winds are not in favorable direction. We can resolve this problem by using our stationary tethered balloon system which can communicate with the loon balloons to provide internet facility over a desired area. Moreover when our balloon will communicate with the loon balloon it will increase the coverage area as the loon balloon has to communicate to a point which is above the ground. Our system will not only replace the existing fiber optic system but it will also be selfsustaining i.e. It will generate its own power using solar panels.

  4. Detergent interaction with tethered bilayer lipid membranes for protein reconstitution

    Science.gov (United States)

    Broccio, Matteo; Zan Goh, Haw; Loesche, Mathias

    2009-03-01

    Tethered bilayer lipid membranes (tBLMs) are self-assembled biomimetic structures in which the membrane is separated from a solid substrate by a nm-thick hydrated submembrane space. These model systems are being used in binding studies of peripheral proteins and exotoxins. Here we aim at their application for the reconstitution of water-insoluble integral membrane proteins. As an alternative to fusion of preformed proteoliposomes we study the direct reconstitution of such proteins for applications in biosensing and pharmaceutical screening. For reconstitution, highly insulating tBLMs (R˜10^5-10^6 φ) were temporarily incubated with a detergent to screen for conditions that keep the detergent-saturated membranestable and ready to incorporate detergent-solubilized proteins. We assess the electrical characteristics, i.e. specific resistance and capacitance, by means of electrochemical impedance spectroscopy (EIS) under timed incubation with decylmaltoside and dodecylmaltoside detergents in a regime around their critical micelle concentration, 1.8 mM and 0.17 mM respectively and demonstrate the restoration of the tBLM upon detergent removal. Thereby a range of concentration and incubation times was identified, that represents optimal conditions for the subsequent membrane protein reconstitution.

  5. 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.

  6. 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...... parts, a feedback connection, which stabilizes the open-loop equilibrium, and a bias term, which is able to drive the system trajectory away from this equilibrium, a feature necessary to obtain orbit adjustment capabilities of the electrodynamic tether. It is then shown how the periodic solutions of the...

  7. 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.

  8. Pulling chromatin apart: Unstacking or Unwrapping?

    Directory of Open Access Journals (Sweden)

    Victor Jean Marc

    2012-11-01

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

  9. In vivo binding of retinol to chromatin

    International Nuclear Information System (INIS)

    The authors have previously shown that exposure of responding cells to vitamin A leads to profound modifications of chromatin structure as revealed by an increased susceptibility to DNase I digestion, modified patterns of histone acetylation, and impaired synthesis of a nonhistone chromosomal protein. The present results show that these effects are most probably due to the direct interaction between retinol and chromatin, and analysis of mononucleosomes and higher oligomers obtained from retinol-treated cells shows that retinol is indeed tightly bound to chromatin. Enzymatic digestions of vitamin A containing nucleosomes with proteinase K, phospholipase C, and phospholipase A2 support a model where the final binding of retinol to chromatin is mediated by a lipoprotein: the recognition of the binding sites on DNA being dictated by the proteic component while the hydrophobic retinol is solubilized in the fatty acid moiety

  10. The Chromatin Fiber: Multiscale Problems and Approaches

    OpenAIRE

    Ozer, Gungor; Luque, Antoni; Schlick, Tamar

    2015-01-01

    The structure of chromatin, affected by many factors from DNA linker lengths to posttranslational modifications, is crucial to the regulation of eukaryotic cells. Combined experimental and computational methods have led to new insights into its structural and dynamical features, from interactions due to the flexible core histone tails of the nucleosomes to the physical mechanism driving the formation of chromosomal domains. Here we present a perspective of recent advances in chromatin modelin...

  11. Linker Histones Incorporation Maintains Chromatin Fiber Plasticity

    OpenAIRE

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

    2011-01-01

    Genomic DNA in eukaryotic cells is organized in supercoiled chromatin fibers, which undergo dynamic changes during such DNA metabolic processes as transcription or replication. Indeed, DNA-translocating enzymes like polymerases produce physical constraints in vivo. We used single-molecule micromanipulation by magnetic tweezers to study the response of chromatin to mechanical constraints in the same range as those encountered in vivo. We had previously shown that under positive torsional const...

  12. Chromatin structure of Asparagales telomeres - old story with a new end?

    Czech Academy of Sciences Publication Activity Database

    Sýkorová, Eva; Skleničková, Marie; Lim, K. Y.; Leitch, A. R.; Fajkus, Jiří

    London: Biochemical Society, 2004. s. 17. [EMBO Workshop / Harden Conference /58./ - Telemeres and Genome Stability . 03.04.2004-07.04.2004, Cambridge] R&D Projects: GA ČR GA204/02/0027; GA ČR GP204/04/P105 Keywords : alternative telomeres in plants * chromatin * nucleosome Subject RIV: BO - Biophysics

  13. Laboratory experiments on the electrodynamic behavior of tethers in space

    Science.gov (United States)

    Stenzel, Reiner L.; Urrutia, Manuel J.

    1991-01-01

    The transient current systems between tethered plasmas in a large magnetoplasma are investigated experimentally for extrapolation to electrodynamic tethers in space. The studies measure the perturbed magnetic fields and the current density associated with pulsed currents to electrodes in three-dimensional space and time. The electrodes excite electron whistlers because they produce fields that dominantly couple to electrons, allowing pulsed currents to propagate and disperse as whistler wave packets. The wave packets evolve into force-free, flux-ropelike field configurations, and a whistler 'wedge' is formed in the plasma due to 'eddy' currents caused by insulated tethers with dc currents. Substantial radiation into the whistler mode happens with moving VLF antennas as well as tethers, and the wave spread within the ray cone is the most significant characteristic event. The wave spread widens the current channel, incites current closure, and is also associated with a 'phantom loop' phenomenon.

  14. 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...

  15. 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.

  16. Fiber Optic Shape Sensing for Tethered Marsupial Rovers Project

    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...

  17. 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...

  18. 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...

  19. Etiology and Evaluation of Sperm Chromatin Anomalies

    Directory of Open Access Journals (Sweden)

    Marziyeh Tavalaee

    2008-01-01

    Full Text Available Evidence suggests that human sperm chromatin anomalies adversely affect reproductive outcomesand infertile men possess substantially amount of sperm with chromatin anomalies than fertilemen.Routine semen analysis evaluates parameters such as sperm motility and morphology, but doesnot examine the nuclear DNA integrity of spermatozoa. It has been suggested that altered nuclearchromatin structure or damaged DNA in spermatozoa could modify the special cellular functionsof human spermatozoa, and thereby affect the fertility potential. Intra-cytoplasmic sperm injection(ICSI bypass the barriers to fertilization for such a sperm, then the effect of chromatin anomalies onthe development remains a concern. Therefore, it is essential to develop and use accurate diagnostictests, which may provide better prognostic capabilities than the standard sperm assessments. Thisreview discusses our current understanding of the structure and organization of sperm DNA,the different procedures for assessment of sperm chromatin anomalies including comet assay,Chromomycin A3 (CMA3, sperm chromatin structure assay (SCSA, acridine orange test (AOT,terminal TdT-mediated dUTP-nick-end labelling (TUNEL assay, aniline blue and sperm chromatindispersion (SCD test and the impact of chromatin anomalies on reproductive outcome.

  20. Isothermal pumping analysis for high-altitude tethered balloons

    OpenAIRE

    Kuo, Kirsty A.; Hunt, Hugh E.M.

    2015-01-01

    High-altitude tethered balloons have potential applications in communications, surveillance, meteorological observations and climate engineering. To maintain balloon buoyancy, power fuel cells and perturb atmospheric conditions, fluids could be pumped from ground level to altitude using the tether as a hose. This paper examines the pumping requirements of such a delivery system. Cases considered include delivery of hydrogen, sulfur dioxide (SO2) and powders as fluid-based slurries. Isothermal...

  1. Role of the membrane for mechanosensing by tethered channels

    CERN Document Server

    Sabass, Benedikt

    2016-01-01

    Biologically important membrane channels are gated by force at attached tethers. Here, we generically characterize the non-trivial interplay of force, membrane tension, and channel deformations that can affect gating. A central finding is that minute conical channel deformation under force leads to significant energy release during opening. We also calculate channel-channel interactions and show that they can amplify force sensitivity of tethered channels.

  2. Single-particle tracking for DNA tether length monitoring

    OpenAIRE

    Pouget, Noëlle; Dennis, Cynthia; Turlan, Catherine; Grigoriev, Mikhail; Chandler, Michaël; Salomé, Laurence

    2004-01-01

    We describe a simple single-particle tracking approach for monitoring the length of DNA molecules in tethered particle motion experiments. In this method, the trajectory of a submicroscopic bead tethered by a DNA molecule to a glass surface is determined by videomicroscopy coupled to image analysis. The amplitude of motion of the bead is measured by the standard deviation of the distribution of successive positions of the bead in a given time interval. We were able to describe theoretically t...

  3. Survival Probability of Round and Tape Tethers Against Debris Impact

    OpenAIRE

    Khan, Shaker Bayajid; Sanmartin, Juan R.

    2013-01-01

    The current space environment, consisting of manmade debris and micrometeoroids, poses a risk to safe operations in space, and the situation is continuously deteriorating due to in-orbit debris collisions and to new satellite launches. Bare electrodynamic tethers can provide an efficient mechanism for rapid deorbiting of satellites from low Earth orbit at end of life. Because of its particular geometry (length very much larger than cross-sectional dimensions), a tether may have a relatively h...

  4. Analysis of tape tether survival in LEO against orbital debris

    OpenAIRE

    Khan, Shaker Bayajid; Sanmartin, Juan R.

    2014-01-01

    The low earth orbit (LEO) environment contains a large number of artificial debris, of which a significant portion is due to dead satellites and fragments of satellites resulted from explosions and in-orbit collisions. Deorbiting defunct satellites at the end of their life can be achieved by a successful operation of an Electrodynamic Tether (EDT) system. The effectiveness of an EDT greatly depends on the survivability of the tether, which can become debris itself if cut by debris particle...

  5. Space Test of Bare-Wire Anode Tethers

    Science.gov (United States)

    Johnson, L.; Fujii, H. A.; Sanmartin, J. R.

    2007-01-01

    An international team, lead by Tokyo Metropolitan University, is developing a mission concept for a suborbital test of orbital-motion-limited (OML) bare-wire anode current collection for application to electrodynamic tether propulsion. The tether is a tape with a 50-mm width, 0.05-mm thickness, and 1-km length. This will be the first space test of the OML theory. In addition, by being an engineering demonstration (of space tethers), the mission will demonstrate electric beam generation for "sounding" determination of the neutral density profile in the ionospheric "E-layer." If selected by the Institute of Space and Astronautical Science/Japanese Aerospace Exploration Agency (JAXA), the mission will launch in early 2009 using an $520 Sounding Rocket. During ascent, and above =100 km in attitude, the 1-km tape tether will be deployed at a rate of 8 m/s. Once deployed, the tape tether will serve as an anode, collecting ionospheric electrons. The electrons will be expelled into space by a hollow cathode device, thereby completing the circuit and allowing current to flow.This paper will describe the objectives of the proposed mission, the technologies to be employed, and the application of the results to future space missions using electrodynamic tethers for propulsion or power generation.

  6. Dynamics of single-stranded DNA tethered to a solid

    Science.gov (United States)

    Radiom, Milad; Paul, Mark R.; Ducker, William A.

    2016-06-01

    Tethering is used to deliver specific biological and industrial functions. For example, single-stranded DNA (ssDNA) is tethered to polymerases and long sequences of double-stranded DNA (dsDNA) during replication, and to solids in DNA microarrays. However, tethering ssDNA to a large object limits not only the available ssDNA conformations, but also the range of time-scales over which the mechanical responses of ssDNA are important. In this work we examine the effect of tethering by measurement of the mechanical response of ssDNA that is tethered at each end to two separate atomic force microscope cantilevers in aqueous solution. Thermal motion of the cantilevers drives the ends of the ssDNA chain at frequencies near 2 kHz. The presence of a tethered molecule makes a large difference to the asymmetric cross-correlation of two cantilevers, which enables resolution of the mechanical properties in our experiments. By analysis of the correlated motion of the cantilevers we extract the friction and stiffness of the ssDNA. We find that the measured friction is much larger than the friction that is usually associated with the unencumbered motion of ssDNA. We also find that the measured relaxation time, ∼30 μs, is much greater than prior measurements of the free-molecule relaxation time. We attribute the difference to the loss of conformational possibilities as a result of constraining the ends of the ssDNA.

  7. Elastic issues and vibration reduction in a tethered deorbiting mission

    Science.gov (United States)

    Sabatini, Marco; Gasbarri, Paolo; Palmerini, Giovanni B.

    2016-05-01

    Recently proposed mission concepts involving harpoons or nets to capture and de-orbit debris represent an interesting application of the tethered systems, where the orbiting bodies are connected by a flexible link. These systems present a complex behavior, as flexible characteristics combine with orbital dynamics. The focus of the paper is on the dynamic behavior of the tethered system in the final phase of the de-orbiting mission, when a powerful apogee motor is used to change the debris orbit. The thrust action introduces significant issues, as elastic waves propagate along the tether, and the relevant oscillations couple with the orbital dynamics. Input shaping techniques are proposed to limit or cancel these oscillations. However, the performance of these techniques drops when non-ideal scenarios are considered. In particular, an initially slack tether is a serious issue that must be solved if acceptably low oscillations of the tether are to be obtained. Three strategies are proposed and discussed in this paper to remove the slack condition: a natural drift of the chaser by means of a single impulse, a controlled maneuver for precisely adjusting the relative distance between chaser spacecraft and debris, and a retrieval mechanism for changing the tether length.

  8. 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.

  9. 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.

  10. Neutron-scattering studies of chromatin

    International Nuclear Information System (INIS)

    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 H2O-D2O 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

  11. Ultrastructural organization of replicating chromatin in prematurely condensed chromosomes

    Directory of Open Access Journals (Sweden)

    Arifulin E. A.

    2015-08-01

    Full Text Available Aim. The ultrastructural aspect of replicating chromatin organization is a matter of dispute. Here, we have analyzed the ultrastructural organization of replication foci using prematurely condensed chromosomes (PCC. Methods. To investigate the ultrastructure of replicating chromatin, we have used correlative light and electron microscopy as well as immunogold staining. Results. Replication in PCC occurs in the gaps between condensed chromatin domains. Using correlative light and electron microscopy, we observed that the replication foci contain decondensed chromatin as well as 80 and 130 nm globules, those were also found in condensed non-replicating chromatin domains. Using immunogolding, we demonstrated that DNA replication in S-phase PCC occurs in loose chromatin on the periphery of dense chromatin domains. Conclusion. Replication in PCC occurred in the decondensed chromatin neighboring the condensed chromatin without formation of special structures.

  12. Linker Histones Incorporation Maintains Chromatin Fiber Plasticity

    Science.gov (United States)

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

    2011-01-01

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

  13. Bacterial chromatin: converging views at different scales.

    Science.gov (United States)

    Dame, Remus T; Tark-Dame, Mariliis

    2016-06-01

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

  14. Adult idiopathic scoliosis: the tethered spine.

    Science.gov (United States)

    Whyte Ferguson, Lucy

    2014-01-01

    This article reports on an observational and treatment study using three case histories to describe common patterns of muscle and fascial asymmetry in adults with idiopathic scoliosis (IS) who have significant scoliotic curvatures that were not surgically corrected and who have chronic pain. Rather than being located in the paraspinal muscles, the myofascial trigger points (TrPs) apparently responsible for the pain were located at some distance from the spine, yet referred pain to locations throughout the thoracolumbar spine. Asymmetries in these muscles appear to tether the spine in such a way that they contribute to scoliotic curvatures. Evaluation also showed that each of these individuals had major ligamentous laxity and this may also have contributed to development of scoliotic curvatures. Treatment focused on release of TrPs found to refer pain into the spine, release of related fascia, and correction of related joint dysfunction. Treatment resulted in substantial relief of longstanding chronic pain. Treatment thus validated the diagnostic hypothesis that myofascial and fascial asymmetries were to some extent responsible for pain in adults with significant scoliotic curvatures. Treatment of these patterns of TrPs and muscle and fascial asymmetries and related joint dysfunction was also effective in relieving pain in each of these individuals after they were injured in auto accidents. Treatment of myofascial TrPs and asymmetrical fascial tension along with treatment of accompanying joint dysfunction is proposed as an effective approach to treating both chronic and acute pain in adults with scoliosis that has not been surgically corrected. PMID:24411157

  15. Numerical Simulation of Tethered Underwater Kites for Power Generation

    Science.gov (United States)

    Ghasemi, Amirmahdi; Olinger, David; Tryggvason, Gretar

    2015-11-01

    An emerging renewable energy technology, tethered undersea kites (TUSK), which is used to extract hydrokinetic energy from ocean and tidal currents, is studied. TUSK systems consist of a rigid-winged ``kite,'' or glider, moving in an ocean current which is connected by tethers to a floating buoy on the ocean surface. The TUSK kite is a current speed enhancement device since the kite can move in high-speed, cross-current motion at 4-6 times the current velocity, thus producing more power than conventional marine turbines. A computational simulation is developed to simulate the dynamic motion of an underwater kite and extendable tether. A two-step projection method within a finite volume formulation, along with an Open MP acceleration method, is employed to solve the Navier-Stokes equations. An immersed boundary method is incorporated to model the fluid-structure interaction of the rigid kite (with NACA 0012 airfoil shape in 2D and NACA 0021 airfoil shape in 3D simulations) and the fluid flow. PID control methods are used to adjust the kite angle of attack during power (tether reel-out) and retraction (reel-in) phases. Two baseline simulations (for kite motions in two and three dimensions) are studied, and system power output, flow field vorticity, tether tension, and hydrodynamic coefficients (lift and drag) for the kite are determined. The simulated power output shows good agreement with established theoretical results for a kite moving in two-dimensions.

  16. Tethered satellite system control using electromagnetic forces and reaction wheels

    Science.gov (United States)

    Alandi Hallaj, Mohammad Amin; Assadian, Nima

    2015-12-01

    In this paper a novel non-rotating space tethered configuration is introduced which its relative positions controlled using electromagnetic forces. The attitude dynamics is controlled by three reaction wheels in the body axes. The nonlinear coupled orbital dynamics of a dumbbell tethered satellite formation flight are derived through a constrained Lagrangian approach. These equations are presented in the leader satellite orbital frame. The tether is assumed to be mass-less and straight, and the J2 perturbation is included to the analysis. The forces and the moments of the electromagnetic coils are modeled based on the far-filed model of the magnetic dipoles. A guidance scheme for generating the desired positions as a function of time in Cartesian form is presented. The satellite tethered formation with variable length is controlled utilizing a linear controller. This approach is applied to a specified scenario and it is shown that the nonlinear guidance method and the linear controller can control the nonlinear system of the tethered formation and the results are compared with optimal control approach.

  17. 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.

  18. Numerical and Experimental Approaches on the Motion of a Tethered System

    Science.gov (United States)

    Takehara, Shoichiro; Terumichi, Yoshiaki; Nohmi, Masahiro; Sogabe, Kiyoshi

    In the present paper, the motion of a tethered system with large deformation and large displacement is discussed. In general, a tether is a cable or a wire rope, and a tethered system consists of a tether and the equipment attached to the tether. A tethered subsatellite in space is an example of a tethered system. In the present study, a tethered system consisting of a very flexible body (the tether) and a rigid body at one end is considered as the analytical model. A flexible body in planer motion is described using the Absolute Nodal Coordinate Formulation. Using this formulation, the motion of a flexible body with large deformation, rotation and translation can be expressed with the accuracy of rigid body motion. The combination of the flexible body motion and the rigid body motion is performed, and their interaction is discussed. Experiments are performed to investigate the fundamental motion of the tethered system and to evaluate the validity of the numerical formulation. Experiments were conducted using a steel tether and a rubber tether in gravity space. In addition, an experiment of the motion of the tethered system with a rigid body in microgravity space was conducted.

  19. 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.......Chromatin serves structural and functional roles crucial for genome stability and correct gene expression. This organization must be reproduced on daughter strands during replication to maintain proper overlay of epigenetic fabric onto genetic sequence. Nucleosomes constitute the structural...

  20. Numerical simulation of tethered DNA in shear flow

    Energy Technology Data Exchange (ETDEWEB)

    Litvinov, S; Hu, X Y; Adams, N A [Institute of Aerodynamics, Technische Universitaet Muenchen, D-85747 Garching (Germany)

    2011-05-11

    The behavior of tethered DNA in shear flow is investigated numerically by the smoothed dissipative particle dynamics (SDPD) method. Unlike numerical methods used in previous studies, SDPD models the solvent explicitly, takes into account the fully coupled hydrodynamic interactions and is free of the numerical artifact of wall sticking. Based on numerical simulations the static and dynamic properties of a tethered DNA is studied both qualitatively and quantitatively. The observed properties are in general agreement with previous experimental, numerical and theoretical work. Furthermore, the cyclic-motion phenomenon is studied by power spectrum density and cross-correlation function analysis, which suggest that there is only a very weak coherent motion of tethered DNA for a characteristic timescale larger than the relaxation time. Cyclic motion is more likely relevant as an isolated event than a typical mode of DNA motion.

  1. Orbit Maneuver of Spinning Tether via Tidal Force

    CERN Document Server

    Baoyin, Hexi; Li, Junfeng

    2014-01-01

    Recently, the spinning tethered system is regarded as a typical and fundamental space structure attracting great interest of the aerospace engineers, and has been discussed primarily for specific space missions in past decades, including on-orbit capture and propellantless orbit transfer etc. The present work studies the dynamical behaviours of a fast spinning tethered binary system under central gravitational field, and derives principles of the basic laws of orbital maneuver. Considering the characteristics of coupled librational and orbital motions, an averaging method is introduced to deal with the slow-fast system equation, thus a definite equivalent model is derived. The general orbit motion is completely determined analytically, including the orbit geometry, periodicity, conversations and moving region etc. Since the possibility of orbit control using tether reaction has been proved by previous studies, special attention is paid to the transportation mode of angular momentum and mechanical energy betwe...

  2. The Secret Life of Tethers: The Role of Tethering Factors in SNARE Complex Regulation.

    Science.gov (United States)

    Dubuke, Michelle L; Munson, Mary

    2016-01-01

    Trafficking in eukaryotic cells is a tightly regulated process to ensure correct cargo delivery to the proper destination organelle or plasma membrane. In this review, we focus on how the vesicle fusion machinery, the SNARE complex, is regulated by the interplay of the multisubunit tethering complexes (MTC) with the SNAREs and Sec1/Munc18 (SM) proteins. Although these factors are used in different stages of membrane trafficking, e.g., Golgi to plasma membrane transport vs. vacuolar fusion, and in a variety of diverse eukaryotic cell types, many commonalities between their functions are being revealed. We explore the various protein-protein interactions and findings from functional reconstitution studies in order to highlight both their common features and the differences in their modes of regulation. These studies serve as a starting point for mechanistic explorations in other systems. PMID:27243006

  3. The Momentum-eXchange/Electrodynamic Reboost (MXER) Tether Concept

    Science.gov (United States)

    Sorenson, K. F.

    2004-12-01

    Within NASA's In-Space Propulsion Technology Projects Office exists Emerging Propulsion Technologies (EPT) Investment Area that is advancing emerging propulsion concepts that have potential to lower the cost of space transportation, enable new missions, and/or increase the payload capability. The current, primary investment of EPT is the Momentum-eXchange/Electrodynamic Reboost (MXER) tether concept. The MXER tether is a long, rotating cable in an elliptical Earth orbit whose rapid rotation allows it to catch a payload in a low Earth orbit and throw it to a high-energy orbit. The orbital energy transferred by the MXER tether to the payload is restored to the tether via electrodynamic tether propulsion. This technique uses solar power to drive electrical current collected from the ionosphere through the tether, resulting in a magnetic interaction with the terrestrial field. Since the Earth itself serves as the reaction mass, the thrust force is generated without propellant, and allows the MXER facility to be repeatedly reused without resupply. Essentially, the MXER facility is a `propellantless' upper stage that could assist nearly every mission going beyond low Earth orbit. Payloads to interplanetary destinations would especially benefit from the boost provided by the MXER facility, resulting in launch vehicle cost reductions, increased payload fractions, and more frequent mission opportunities. Some of the benefits to space exploration include: (1) Multi-use, in-space, `propellantless' infrastructure, (2) Useable by essentially all missions beyond LEO, (3) Lowers overall mission costs and/or enables larger payloads, (4) ``Panama Canal" of space transportation, (5) A spiral development for future generations, (6) Readily scales up or down, (7) Future transportation to and from Lunar surface.

  4. Painting by Numbers: Increasing the Parts List for Chromatin Domains

    Science.gov (United States)

    Chen, Hsiuyi V.; Rando, Oliver J.

    2014-01-01

    In this issue of Molecular Cell, van Bemmel and colleagues (2013) report the genome-wide mapping of 42 novel chromatin factors, systematically identifying new components of the various chromatin domains present in fly cells. PMID:23438859

  5. Dynamics of an Electrodynamic Tether System in a Varying Space-Plasma Environment

    OpenAIRE

    Janeski, John

    2013-01-01

    Electrodynamic tethers have a wide range of proposed applications in the fields of satellite propulsion and space plasma research. The fundamental purpose of this dissertation is to improve the understanding of the behavior of an electrodynamic tether (EDT) system in Earth's ionosphere. An electrodynamic tether system consists of two satellites connected by a long tether that generates current to produce either power or thrust via the system's electromagnetic interaction with the space envir...

  6. Determination of single-bond association kinetics by tethered particle motion: concept and simulations

    OpenAIRE

    Merkus, Koen E.; Prins, Menno W. J.; Storm, Cornelis

    2016-01-01

    Tethered particle motion (TPM) --- the motion of a micro- or nanoparticle tethered to a substrate by a macromolecule --- is a system that has proven extremely useful for its ability to reveal physical features of the tether, because the thermal motion of the bound particle reports sensitively on parameters like the length, the rigidity, or the folding state of its tether. In this paper, we discuss a novel application of TPM, surveying its utility in probing the kinetics of single secondary bo...

  7. Dynamics of multi-tethered pyramidal satellite formation

    Science.gov (United States)

    Alary, D.; Andreev, K.; Boyko, P.; Ivanova, E.; Pritykin, D.; Sidorenko, V.; Tourneur, C.; Yarotsky, D.

    2015-12-01

    This paper is devoted to the dynamics of a multi-tethered pyramidal satellite formation rotating about its axis of symmetry in the nominal mode. Whereas the combination of rotation and gravity-gradient forces is insufficient to maintain the mutual positions of satellites, they are assumed to be equipped with low-thrust rocket engines. We propose a control strategy that allows the stabilization of the nominal spin state and demonstrate the system's proper operation by numerically simulating its controlled motion. The discussed multi-tethered formations could be employed, for example, to provide co-location of several satellites at a slot in geostationary orbit.

  8. Single Chromatin Fibre Assembly Using Optical Tweezers

    NARCIS (Netherlands)

    Bennink, M.L.; Pope, L.H.; Leuba, S.H.; Grooth, de B.G.; Greve, J.

    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 r

  9. Chromatin and epigenetics in all their states

    NARCIS (Netherlands)

    Bey, Till; Jamge, Suraj; Klemme, Sonja; Komar, Dorota Natalia; Gall, Le Sabine; Mikulski, Pawel; Schmidt, Martin; Zicola, Johan; Berr, Alexandre

    2016-01-01

    In January 2016, the first Epigenetic and Chromatin Regulation of Plant Traits conference was held in Strasbourg, France. An all-star lineup of speakers, a packed audience of 130 participants from over 20 countries, and a friendly scientific atmosphere contributed to make this conference a meetin

  10. CTCF Binding Polarity Determines Chromatin Looping

    NARCIS (Netherlands)

    de Wit, Elzo; Vos, Erica S M; Holwerda, Sjoerd J B; Valdes-Quezada, Christian; Verstegen, Marjon J A M; Teunissen, Hans; Splinter, Erik; Wijchers, Patrick J; Krijger, Peter H L; de Laat, Wouter

    2015-01-01

    CCCTC-binding factor (CTCF) is an architectural protein involved in the three-dimensional (3D) organization of chromatin. In this study, we assayed the 3D genomic contact profiles of a large number of CTCF binding sites with high-resolution 4C-seq. As recently reported, our data also suggest that ch

  11. Chromatin proteins and modifications as drug targets

    DEFF Research Database (Denmark)

    Helin, Kristian; Dhanak, Dashyant

    2013-01-01

    A plethora of groundbreaking studies have demonstrated the importance of chromatin-associated proteins and post-translational modifications of histones, proteins and DNA (so-called epigenetic modifications) for transcriptional control and normal development. Disruption of epigenetic control is a ...

  12. Impact of chromatin structure on PR signaling

    DEFF Research Database (Denmark)

    Grøntved, Lars; Hager, Gordon L

    2012-01-01

    but also to the glucocorticoid receptor (GR), as these receptors share many similarities regarding interaction with, and remodeling of, chromatin. Both receptors can bind nucleosomal DNA and have accordingly been described as pioneering factors. However recent genomic approaches (ChIP-seq and DHS...

  13. Research Discovers Frequent Mutations of Chromatin

    Institute of Scientific and Technical Information of China (English)

    2011-01-01

    With the support of National Natural Science Foundation of China, BGI, the largest genomics organization in the world, and Peking University Shenzhen Hospital, published online in Nature Geneticsics that the study on frequent mutations of chromatin remodeling genes in transitional cell carcinoma (TCC) of thebladder on August 8th, 2011. Their study provides a valuable genetic basis for future studies on TCC,

  14. 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-despi...

  15. Factors affecting chromatin stability of bovine spermatozoa.

    Science.gov (United States)

    Khalifa, T A A; Rekkas, C A; Lymberopoulos, A G; Sioga, A; Dimitriadis, I; Papanikolaou, Th

    2008-03-01

    The structural stability of transcriptionally inert paternal chromatin is of vital importance for the fertilization process and early embryonic development. Accordingly, a series of eight experiments were conducted during a 7-month period to investigate: (1) effects of bull breed, individuality, successive ejaculations, semen quality characteristics (SQC), semen dilution rates and hypothermic storage of semen in a Tris-egg yolk extender on incidence of sperm nuclear chromatin instability (NCI), and (2) effects of the interaction between variation of NCI within a frozen ejaculate and variation of oocytes quality due to maturation time and/or season on the efficiency of in vitro embryo production (IVEP). Semen samples were collected once a week from six bulls using an AV and only ejaculates (n=220) of >0.30x10(9) sperm/ml and >or=60% motility were used. NCI was measured by: (1) detection of lysine-rich histones in sperm chromatin using aniline blue staining, (2) sperm susceptibility to acid-induced nuclear DNA denaturation in situ using acridine orange test, and (3) sperm susceptibility to nuclear chromatin decondensation (NCD). Bovine oocytes (n=695) were matured in vitro for 18 or 24 h, fertilized after sperm selection through a swim-up procedure and cultured for 72 h. The results showed that the 2nd ejaculates were superior to the 1st ones with respect to chromatin stability. Dilution of semen to 49.67+/-8.56x10(6) sperm/ml (1:19) decreased resistance of sperm to NCD. Cooling of semen had no significant effect on chromatin stability. Cryopreservation of semen augmented sperm vulnerability to DNA denaturation. Improvement of SQC (semen volume, sperm motility, velocity, viability and morphological normalcy) was generally concomitant with increase of sperm resistance to NCI. While Blonde d'Aquitaine bulls had a resistance to NCD higher than Limousine bulls in fresh semen, the former showed a greater susceptibility to DNA denaturation than the latter in cooled semen

  16. 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: eithe

  17. 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...

  18. Dynamics and control of the tether elevator/crawler system

    Science.gov (United States)

    Lorenzini, E. C.; Cosmo, M.; Vetrella, S.; Moccia, A.

    1989-01-01

    This paper investigates the dynamics and acceleration levels of a new tethered system for micro- and variable-gravity applications. The system consists of two platforms tethered on opposite sides to the Space Station. A fourth platform, the elevator, is placed in between the Space Station and the upper platform. Variable-g levels on board the elevator are obtained by moving this facility along the upper tether, while microgravity experiments are carried out on board the Space Station. By controlling the length of the lower tether the position of the system center of mass can be maintained on board the Space Station despite variations of the system's distribution of mass. The paper illustrates the mathematical model, the environmental perturbations and the control techniques which have been adopted for the simulation and control of the system dynamics. Two sets of results from two different simulation runs are shown. The first set shows the system dynamics and the acceleration spectra on board the Space Station and the elevator during station-keeping. The second set of results demonstrates the capability of the elevator to attain a preselected g-level.

  19. Sounding rocket experiment of bare electrodynamic tether system

    OpenAIRE

    Fujii, Hironori; Watanabe, Takeo; Kojima, Hirohisa; Kusagaya, Tairo; Oyama, Koh-ichiro; Yamagiwa, Yoshiki; Ohtsu, Hirotaka; Cho, Mengu; Sasaki, Susumu; Tanaka, Koji; Williams, John; Rubin, Binyamin; Les Jhonson, Charles; Khazanov, George; Sanmartín Losada, Juan Ramón

    2009-01-01

    An overview of asounding rocket S-520-25th, project on space tether technology experiment is presented.The project is prepared by an international research group consisting of Japanese,European,American,andAustralianresearchers.The sounding rocket will be assembled by the ISAS/JAXA and will be launched in the summer of 2009.

  20. Tether de-orbiting of satellites at end of mission

    Science.gov (United States)

    Sanmartin, Juan R.; Sánchez-Torres, Antonio

    2012-07-01

    The accumulation of space debris around the Earth has become critical for Space security. The BETs project, financed by the European Commission through its FP7-Space program, is focusing on preventing generation of new debris by de-orbiting satellites at end of mission. The de-orbiting system considered, involving an electrodynamic bare tape-tether, uses no propellant and no power supply, while generating power for on-board use during de-orbiting. As an example, preliminary results are here presented on a specific orbit/satellite case: 1300 km altitude and 65 degrees inclination, and 500 kg mass. Design tether dimensions are 8 km length, 1.5 cm width, and 0.05 mm thickness; subsystem masses are limited to twice tether mass. Simple calculations, using orbit-averaging, solar mid-cycle phase, and ionospheric and geomagnetic field models, yield 2.6 months time for de-orbiting down to 200 km, with a probability of about 1 percent of debris cutting the tape. References: Sanmartin, J.R., Lorenzini, E.C., and Martinez-Sanchez, M., Electrodynamic Tether Applications and Constraints, J. Space. Rockets 47, 442-456, 2010. Sanmartin, J.R. et al., A universal system to de-orbit satellites at end of life, Journal of Space Technology and Science, to appear.

  1. Balloon Launched on Multiwall Carbon Nanotube Tether in Antarctica

    Czech Academy of Sciences Publication Activity Database

    Kletetschka, Günther; McKinney, E.; Kawasumiova, D.

    Cambridge: University of Cambridge, 2011. s. 1-1. [NT international Conference on the Science and Application of Nanotubes /11./. 10.07.2011-16.07.2011, Cambridge] Institutional research plan: CEZ:AV0Z30130516 Keywords : MWCNT * fibres * tether * strength * Antarctica Subject RIV: DB - Geology ; Mineralogy

  2. 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.

  3. Fortissimo: A Japanese Space Test Of Bare Wire Anode Tethers

    Science.gov (United States)

    Johnson, Les; Fujii, H. A.; Sanmartin, J. R.

    2008-01-01

    A Japanese led international team is developing a suborbital test of orbital-motion-limited (OML) bare wire anode current collection for application to electrodynamic tether (EDT) propulsion. The tether is a tape with a width of 25 mm, thickness of 0.05 mm, and is 300 m in length. This will be the first space test of OML theory. The mission will launch in the summer of 2009 using an S520 Sounding Rocket. During ascent, and above approx. 100 km in attitude, the tape tether will be deployed at a rate of approx. 8 m/s. Once deployed, the tape tether will serve as an anode, collecting ionospheric electrons. The electrons will be expelled into space by a hollow cathode device, thereby completing the circuit and allowing current to flow. The total amount of current collected will be used to assess the validity of OML theory. This paper will describe the objectives of the proposed mission, the technologies to be employed, and the application of the results to future space missions using EDTs for propulsion or power generation.

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

    OpenAIRE

    Larsen, Martin Birkelund; Blanke, Mogens

    2010-01-01

    A space tether is a cable used to connect spacecrafts in an orbiting structure. If an electrical current is lead through the tether, it can be utilized to provide propulsion for the spacecraft. In this case the cable is referred to as an electrodynamic tether. The system utilizes the magnetic field 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 operat...

  5. The landscape of accessible chromatin in mammalian preimplantation embryos.

    Science.gov (United States)

    Wu, Jingyi; Huang, Bo; Chen, He; Yin, Qiangzong; Liu, Yang; Xiang, Yunlong; Zhang, Bingjie; Liu, Bofeng; Wang, Qiujun; Xia, Weikun; Li, Wenzhi; Li, Yuanyuan; Ma, Jing; Peng, Xu; Zheng, Hui; Ming, Jia; Zhang, Wenhao; Zhang, Jing; Tian, Geng; Xu, Feng; Chang, Zai; Na, Jie; Yang, Xuerui; Xie, Wei

    2016-06-30

    In mammals, extensive chromatin reorganization is essential for reprogramming terminally committed gametes to a totipotent state during preimplantation development. However, the global chromatin landscape and its dynamics in this period remain unexplored. Here we report a genome-wide map of accessible chromatin in mouse preimplantation embryos using an improved assay for transposase-accessible chromatin with high throughput sequencing (ATAC-seq) approach with CRISPR/Cas9-assisted mitochondrial DNA depletion. We show that despite extensive parental asymmetry in DNA methylomes, the chromatin accessibility between the parental genomes is globally comparable after major zygotic genome activation (ZGA). Accessible chromatin in early embryos is widely shaped by transposable elements and overlaps extensively with putative cis-regulatory sequences. Unexpectedly, accessible chromatin is also found near the transcription end sites of active genes. By integrating the maps of cis-regulatory elements and single-cell transcriptomes, we construct the regulatory network of early development, which helps to identify the key modulators for lineage specification. Finally, we find that the activities of cis-regulatory elements and their associated open chromatin diminished before major ZGA. Surprisingly, we observed many loci showing non-canonical, large open chromatin domains over the entire transcribed units in minor ZGA, supporting the presence of an unusually permissive chromatin state. Together, these data reveal a unique spatiotemporal chromatin configuration that accompanies early mammalian development. PMID:27309802

  6. 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.

  7. 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.

  8. 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.

  9. Diversity in the organization of centromeric chromatin.

    Science.gov (United States)

    Steiner, Florian A; Henikoff, Steven

    2015-04-01

    Centromeric chromatin is distinguished primarily by nucleosomes containing the histone variant cenH3, which organizes the kinetochore that links the chromosome to the spindle apparatus. Whereas budding yeast have simple 'point' centromeres with single cenH3 nucleosomes, and fission yeast have 'regional' centromeres without obvious sequence specificity, the centromeres of most organisms are embedded in highly repetitive 'satellite' DNA. Recent studies have revealed a remarkable diversity in centromere chromatin organization among different lineages, including some that have lost cenH3 altogether. We review recent progress in understanding point, regional and satellite centromeres, as well as less well-studied centromere types, such as holocentromeres. We also discuss the formation of neocentromeres, the role of pericentric heterochromatin, and the structure and composition of the cenH3 nucleosome. PMID:25956076

  10. On the topology of chromatin fibres

    Science.gov (United States)

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

    2012-01-01

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

  11. Determination of single-bond association kinetics by tethered particle motion: concept and simulations

    CERN Document Server

    Merkus, Koen E; Storm, Cornelis

    2016-01-01

    Tethered particle motion (TPM) --- the motion of a micro- or nanoparticle tethered to a substrate by a macromolecule --- is a system that has proven extremely useful for its ability to reveal physical features of the tether, because the thermal motion of the bound particle reports sensitively on parameters like the length, the rigidity, or the folding state of its tether. In this paper, we discuss a novel application of TPM, surveying its utility in probing the kinetics of single secondary bonds: bonds that form and break between the tethered particle and a substrate due, for instance, to receptor/ligand pairs on particle and substrate. Much like the tether itself affects the motion pattern, so do the presence and absence of such secondary connections. Keeping the tether properties constant, we demonstrate how raw positional TPM data may be parsed to generate detailed insights into the association and dissociation kinetics of single secondary bonds. We do this using coarse-grained molecular dynamics simulatio...

  12. SPHERES tethered formation flight testbed: advancements in enabling NASA's SPECS mission

    Science.gov (United States)

    Chung, Soon-Jo; Adams, Danielle; Saenz-Otero, Alvar; Kong, Edmund; Miller, David W.; Leisawitz, David; Lorenzini, Enrico; Sell, Steve

    2006-06-01

    This paper reports on efforts to control a tethered formation flight spacecraft array for NASA's SPECS mission using the SPHERES test-bed developed by the MIT Space Systems Laboratory. Specifically, advances in methodology and experimental results realized since the 2005 SPIE paper are emphasized. These include a new test-bed setup with a reaction wheel assembly, a novel relative attitude measurement system using force torque sensors, and modeling of non-ideal tethers to account for tether vibration modes. The nonlinear equations of motion of multi-vehicle tethered spacecraft with elastic flexible tethers are derived from Lagrange's equations. The controllability analysis indicates that both array resizing and spin-up are fully controllable by the reaction wheels and the tether motor, thereby saving thruster fuel consumption. Based upon this analysis, linear and nonlinear controllers have been successfully implemented on the tethered SPHERES testbed, and tested at the NASA MSFC's flat floor facility using two and three SPHERES configurations.

  13. On the topology of chromatin fibres

    OpenAIRE

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

    2012-01-01

    The ability of cells to pack, use and duplicate DNA remains one of the most fascinating questions in biology. To understand DNA organization and dynamics, it is important to consider the physical and topological constraints acting on it. In the eukaryotic cell nucleus, DNA is organized by proteins acting as spools on which DNA can be wrapped. These proteins can subsequently interact and form a structure called the chromatin fibre. Using a simple geometric model, we propose a general method fo...

  14. Chromatin regulation in drug addiction and depression

    OpenAIRE

    Renthal, William; Nestler, Eric J.

    2009-01-01

    Alterations in gene expression are implicated in the pathogenesis of several neuropsychiatrie disorders, including drug addiction and depression, increasing evidence indicates that changes in gene expression in neurons, in the context of animal models of addiction and depression, are mediated in part by epigenetic mechanisms that alter chromatin structure on specific gene promoters. This review discusses recent findings from behavioral, molecular, and bioinformatic approaches that are being u...

  15. Multiscale Identification of Topological Domains in Chromatin

    OpenAIRE

    Filippova, Darya; Patro, Rob; Duggal, Geet; Kingsford, Carl

    2013-01-01

    Recent chromosome conformation capture experiments have led to the discovery of dense, contiguous, megabase-sized topological domains that are similar across cell types and conserved across species. These domains are strongly correlated with a number of chromatin markers and have since been included in a number of analyses. However, functionally-relevant domains may exist at multiple length scales. We introduce a new and efficient algorithm that is able to capture persistent domains across va...

  16. Titration and hysteresis in epigenetic chromatin silencing

    International Nuclear Information System (INIS)

    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)

  17. Controlled cooling versus rapid freezing of teratozoospermic semen samples: Impact on sperm chromatin integrity

    Directory of Open Access Journals (Sweden)

    Shivananda N Kalludi

    2011-01-01

    Full Text Available Aim: The present study evaluates the impact of controlled slow cooling and rapid freezing techniques on the sperm chromatin integrity in teratozoospermic and normozoospermic samples. Setting: The study was done in a university infertility clinic, which is a tertiary healthcare center serving the general population. Design: It was a prospective study designed in vitro. Materials and Methods: Semen samples from normozoospermic (N=16 and teratozoospermic (N=13 infertile men were cryopreserved using controlled cooling and rapid freezing techniques. The sperm chromatin integrity was analyzed in fresh and frozen-thawed samples. Statistical Analysis Used: Data were reported as mean and standard error (mean ± SEM of mean. The difference between two techniques was determined by a paired t-test. Results: The freeze-thaw induced chromatin denaturation was significantly (P<0.01 elevated in the post-thaw samples of normozoospermic and teratozoospermic groups. Compared to rapid freezing, there was no difference in the number of red sperms (with DNA damage by the controlled slow cooling method in both normozoospermic and teratozoospermic groups. Freeze-thaw induced sperm chromatin denaturation in teratozoospermic samples did not vary between controlled slow cooling and rapid freezing techniques. Conclusions: Since the controlled slow cooling technique involves the use of expensive instrument and is a time consuming protocol, rapid freezing can be a good alternative technique for teratozoospermic and normozoospermic samples when sperm DNA damage is a concern.

  18. 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.

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

    Science.gov (United States)

    Sanmartin, J. R. S.; Charro, M. C.; Sanchez-Arriaga, G. S. A.; Sanchez-Torres, A. S. T.

    2015-10-01

    A tether mission to carry out multiple flybys of Jovian moon Europa is here presented. There is general agreement on elliptic-orbit flybys of Europa resulting in cost to attain given scientific goals lower than if actually orbiting the moon, tethers being naturally fit to fly-by rather than orbit moons1. The present mission is similar in this respect to the Clipper mission considered by NASA, the basic difference lying in location of periapsis, due to different emphasis on mission-challenge metrics. Clipper minimizes damaging radiation-dose by avoiding the Jupiter neighborhood and its very harsh environment; periapsis would be at Europa, apoapsis as far as moon Callisto. As in all past outer-planet missions, Clipper faces, however, critical power and propulsion needs. On the other hand, tethers can provide both propulsion and power, but must reach near the planet to find high plasma density and magnetic field values, leading to high induced tether current, and Lorentz drag and power. The bottom line is a strong radiation dose under the very intense Radiation Belts of Jupiter. Mission design focuses on limiting dose. Perijove would be near Jupiter, at about 1.2-1.3 Jovian radius, apojove about moon Ganymede, corresponding to 1:1 resonance with Europa, so as to keep dose down: setting apojove at Europa, for convenient parallel flybys, would require two perijove passes per flyby (the Ganymede apojove, resulting in high eccentricity, about 0.86, is also less requiring on tether operations). Mission is designed to attain reductions in eccentricity per perijove pass as high as Δe ≈ - 0.04. Due the low gravity-gradient, tether spinning is necessary to keep it straight, plasma contactors placed at both ends taking active turns at being cathodic. Efficiency of capture of the incoming S/C by the tether is gauged by the ratio of S/C mass to tether mass; efficiency is higher for higher tape-tether length and lower thickness and perijove. Low tether bowing due to the Lorentz

  20. The chromatin remodeler SPLAYED regulates specific stress signaling pathways.

    Directory of Open Access Journals (Sweden)

    Justin W Walley

    2008-12-01

    Full Text Available Organisms are continuously exposed to a myriad of environmental stresses. Central to an organism's survival is the ability to mount a robust transcriptional response to the imposed stress. An emerging mechanism of transcriptional control involves dynamic changes in chromatin structure. Alterations in chromatin structure are brought about by a number of different mechanisms, including chromatin modifications, which covalently modify histone proteins; incorporation of histone variants; and chromatin remodeling, which utilizes ATP hydrolysis to alter histone-DNA contacts. While considerable insight into the mechanisms of chromatin remodeling has been gained, the biological role of chromatin remodeling complexes beyond their function as regulators of cellular differentiation and development has remained poorly understood. Here, we provide genetic, biochemical, and biological evidence for the critical role of chromatin remodeling in mediating plant defense against specific biotic stresses. We found that the Arabidopsis SWI/SNF class chromatin remodeling ATPase SPLAYED (SYD is required for the expression of selected genes downstream of the jasmonate (JA and ethylene (ET signaling pathways. SYD is also directly recruited to the promoters of several of these genes. Furthermore, we show that SYD is required for resistance against the necrotrophic pathogen Botrytis cinerea but not the biotrophic pathogen Pseudomonas syringae. These findings demonstrate not only that chromatin remodeling is required for selective pathogen resistance, but also that chromatin remodelers such as SYD can regulate specific pathways within biotic stress signaling networks.

  1. PTEN Interacts with Histone H1 and Controls Chromatin Condensation

    Directory of Open Access Journals (Sweden)

    Zhu Hong Chen

    2014-09-01

    Full Text Available 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 reduce 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.

  2. Preliminary Orbit Determination of a Tethered Satellite Using the p-Iteration Method

    Science.gov (United States)

    Cicci, D. A.; Qualls, C.

    2016-04-01

    The possibility of the future deployment of tethered satellites has created a need for a preliminary orbit determination method capable of determining whether or not a satellite is tethered to another satellite. Classical preliminary orbit determination methods, which are used for untethered satellites, typically require two or more position vectors along with their respective observation times in order to determine a preliminary orbital element set. However, these conventional methods can't distinguish between an untethered satellite and a tethered one, whose motion is modified due to the presence of a tether force. The use of conventional methods on a satellite which is part of a tethered satellite system will result in the calculation of inaccurate orbital elements. Modifications have been made to the p-iteration preliminary orbit determination method in order to allow for the identification of these tethered satellites. The modifications allow for the calculation of a modified gravitational parameter, which can be used to distinguish between a tethered satellite and an untethered one. This paper applies this modified p-iteration method to the problem of the quick identification of a tethered satellite. The performance of this method is evaluated through scenarios of differing tether lengths, levels of observation error, and orbital eccentricities. Due to the need for the preliminary orbit determination to be achieved quickly, only short time intervals between observations were considered. The manner in which this preliminary orbit information can be used to obtain tether parameters for the subsequent differential correction process is also described.

  3. Advances in dynamics and control of tethered satellite systems

    Institute of Scientific and Technical Information of China (English)

    Hao Wen; Dongping P. Jin; Haiyan Y. Hu

    2008-01-01

    The concept of tethered satellite system (TSS) promises to revolutionize many aspects of space exploration and exploitation. It provides not only numerous possible and valuable applications, but also challenging and interesting problems related to their dynamics, control, and physical implementation. Over the past decades, this exciting topic has attracted significant attention from many researchers and gained a vast number of analytical, numerical and experimental achievements with a focus on the two essential aspects of both dynamics and control. This review article presents the historic background and recent hot topics for the space tethers, and introduces the dynamics and control of TSSs in a progressive manner, from basic operating principles to the state-of-the-art achievements.

  4. 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.

  5. Inverstigation of chromatin folding patterns by atomic force microscopy

    Institute of Scientific and Technical Information of China (English)

    ZHANGYi; OUYANGZhenqian; 等

    1999-01-01

    The chromatin folding patterns in air and liquid were studied by atomic force microscopy(AFM),A gentle water-air interface method was adopted to spread chromatin from interphase nucleus of chicken erythrocyte.The chromatin was absorbed on APS-mica surface and studied with AFM,Beads-on a-string were observed and many higher-order structrues such as superbeads with dimensions 40-60nm in diameter and 4-7nm in height were found to string together to make chromation fibers.When sample spreading and absorbing time were shortened.higher-order chromatin fibers with 60-120nm in width were observed in air as well as under water environment.These chromatin structures may reflect chromatin folding patterns in the living cells.

  6. Prevalence of X-chromatin in Jordanian women

    International Nuclear Information System (INIS)

    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)

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

    Science.gov (United States)

    Gelato, Kathy A; Fischle, Wolfgang

    2008-04-01

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

  8. Electrodynamic tethers for exploration of jupiter and its icy moons

    OpenAIRE

    Sanmartín Losada, Juan Ramón

    2006-01-01

    Use of electrodynamic bare tethers in exploring the Jovian system by tapping its rotational energy for power and propulsion is studied. The position of perijove and apojove in elliptical orbits, relative to the synchronous orbit at 2.24 times Jupiter’s radius, is exploited to conveniently make the induced Lorentz force to be drag or thrust, while generating power, and navigating the system. Capture and evolution to a low elliptical orbit near Jupiter, and capture into low circular orbits at m...

  9. Chemical tethering of motile bacteria to silicon surfaces

    OpenAIRE

    Bearinger, Jane P.; Dugan, Lawrence C.; Wu, Ligang; Hill, Haley; Christian, Allen T.; Hubbell, Jeffrey A.

    2009-01-01

    We chemically immobilized live, motile Escherichia coli on micrometer-scale, photocatalytically patterned silicon surfaces via amine- and carboxylic acid–based chemistries. Immobilization facilitated (i) controlled positioning; (ii) high resolution cell wall imaging via atomic force microscopy (AFM); and (iii) chemical analysis with time-of-flight-secondary ion mass spectrometry (ToF-SIMS). Spinning motion of tethered bacteria, captured with fast-acquisition video, proved microbe viability. W...

  10. Effect of Chromosome Tethering on Nuclear Organization in Yeast

    OpenAIRE

    Avşaroğlu, Barış; Bronk, Gabriel; Gordon-Messer, Susannah; Ham, Jungoh; Bressan, Debra A.; Haber, James E; Kondev, Jane

    2014-01-01

    Interphase chromosomes in Saccharomyces cerevisiae are tethered to the nuclear envelope at their telomeres and to the spindle pole body (SPB) at their centromeres. Using a polymer model of yeast chromosomes that includes these interactions, we show theoretically that telomere attachment to the nuclear envelope is a major determinant of gene positioning within the nucleus only for genes within 10 kb of the telomeres. We test this prediction by measuring the distance between the SPB and the sil...

  11. 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.

  12. Investigation of force approximations in tethered cells simulations

    CERN Document Server

    Zakrisson, Johan; Axner, Ove; Andersson, Magnus

    2015-01-01

    Simulations of tethered cells in viscous sub-layers are frequently performed using the Stokes drag force, but without taking into account contributions from surface corrections, lift forces, buoyancy, the Basset force, the cells finite inertia, or added mass. In this work, we investigate to which extent such contributions influence, under a variety of hydrodynamic conditions, the force at the anchor point of a tethered cell and the survival probability of a bacterium that is attached to a host by either a slip or a catch bond via a tether with a few different biomechanical properties. We show that a consequence of not including some of these contributions is that the force to which a bond is exposed can be significantly underestimated; in general by ~32-46 %, where the influence of the surface corrections dominate (the parallel and normal correction coefficients contribute with ~5-8 or 23-26 %, respectively). The Basset force is a major contributor, up to 20 %, for larger cells and shear rates. The lift force...

  13. Surfactant mediated morphological tethering of Cu2O nanoparticles

    International Nuclear Information System (INIS)

    This communication describes a very simple and reproducible methodology to study the self-assembly of nanoparticles functionalized with a non-ionic tethering agent attached to the surface of the nanoparticle seeds. The synthesis starts with the [Cu(OH)4]2− species acting as a template, with varying concentration of the tethering agent Triton X-100 (TX100). The morphological alteration is systematically investigated. The effect of surfactant micelles, growth reaction time, and solution temperature has a tremendous impact on the morphology of the nanocrystals that govern the controlled synthesis of different shapes of nanostructures. The initial morphology of the nanocrystals is polyhedron in the absence of a tethering additive. The addition of TX100 suppresses the polymorph phase morphology and enhances the non-uniform spherical morphology of the nanocrystals. The surface modification effect enhances the morphological alteration, which potentially makes it applicable to various industrial uses such as water cleaning, hydrogen production, and third-generation solar cells. (paper)

  14. Ultrastructural organization of replicating chromatin in prematurely condensed chromosomes

    OpenAIRE

    Arifulin E. A.

    2015-01-01

    Aim. The ultrastructural aspect of replicating chromatin organization is a matter of dispute. Here, we have analyzed the ultrastructural organization of replication foci using prematurely condensed chromosomes (PCC). Methods. To investigate the ultrastructure of replicating chromatin, we have used correlative light and electron microscopy as well as immunogold staining. Results. Replication in PCC occurs in the gaps between condensed chromatin domains. Using correlative light and electron mic...

  15. Combinatorial epigenetic patterns as quantitative predictors of chromatin biology

    OpenAIRE

    Cieślik, Marcin; Bekiranov, Stefan

    2014-01-01

    Background Chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) is the most widely used method for characterizing the epigenetic states of chromatin on a genomic scale. With the recent availability of large genome-wide data sets, often comprising several epigenetic marks, novel approaches are required to explore functionally relevant interactions between histone modifications. Computational discovery of "chromatin states" defined by such combinatorial interactions enabled desc...

  16. Single-epitope recognition imaging of native chromatin

    OpenAIRE

    Wang Hongda; Dalal Yamini; Henikoff Steven; Lindsay Stuart

    2008-01-01

    Abstract Background Direct visualization of chromatin has the potential to provide important insights into epigenetic processes. In particular, atomic force microscopy (AFM) can visualize single nucleosomes under physiological ionic conditions. However, AFM has mostly been applied to chromatin that has been reconstituted in vitro, and its potential as a tool for the dissection of native nucleosomes has not been explored. Recently we applied AFM to native Drosophila chromatin containing the ce...

  17. Hydrogen peroxide mediates higher order chromatin degradation.

    Science.gov (United States)

    Bai, H; Konat, G W

    2003-01-01

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

  18. Method of Deployment of a Space Tethered System Aligned to the Local Vertical

    Science.gov (United States)

    Zakrzhevskii, A. E.

    2016-04-01

    The object of this research is a space tether of two bodies connected by a flexible massless string. The research objective is the development and theoretical justification of a novel approach to the solution of the problem of deployment of the space tether in a circular orbit with its alignment to the local vertical. The approach is based on use of the theorem on the angular momentum change. It allows developing the open-loop control of the tether length that provides desired change of the angular momentum of the tether under the effect of the gravitational torque to the value, which corresponds to the angular momentum of the deployed tether aligned to the local vertical. The given example of application of the approach to a case of deployment of a tether demonstrates the simplicity of use of the method in practice, and also the method of validation of the mathematical model.

  19. Modeling of induced currents from electrodynamic tethers in a laboratory plasma

    Science.gov (United States)

    Urrutia, J. M.; Stenzel, R. L.

    1990-01-01

    The presently accepted picture of the current path for electrodynamic tethers envisions a quasi-dc current flow in a 'phantom loop' consisting of the tether, two field-aligned current channels into the ionosphere and a cross-field closing current in the E-layer. Predictions are made on the establishment and maintenance of a current loop in space based on observations of time-dependent currents between tethered electrodes in a large laboratory magnetoplasma. In addition to radiation from the contactors ('whistler wings'), the insulated tether is observed to emit waves (a 'whistler wedge'). The 'wedge' provides closure during loop formation by carrying cross-field polarization currents. Whistler spread within the ray cone leads to overlapping of the current wings not far from the tether hence minimizing the role of the ionospheric closure. Maintenance of the loop requires the continuous emission of whistler waves by the entire tether thereby providing severe radiation losses.

  20. Membrane tether formation from voltage-clamped outer hair cells using optical tweezers

    Science.gov (United States)

    Qian, Feng; Ermilov, Sergey A.; Murdock, David R.; Brownell, William E.; Anvari, Bahman

    2004-06-01

    Outer hair cells contribute an active mechanical feedback to the vibrations of the cochlear structures resulting in the high sensitivity and frequency selectivity of normal hearing. We have designed and implemented a novel experimental setup that combines optical tweezers with patch-clamp apparatus to investigate the electromechanical properties of cellular plasma membranes. A micron-size bead trapped by the optical tweezers is brought in contact with the membrane of a voltage-clamped cell, and subsequently moved away to form a plasma membrane tether. Bead displacement during tether elongation is monitored by a quadrant photodetector to obtain time-resolved measurements of the tethering force. Salient information associated with the mechanical properties of the membrane tether can thus be obtained. Tethers can be pulled from the cell membrane at different holding potentials, and the tether force response can be measured while changing transmembrane potential. Experimental results from outer hair cells and human embryonic kidney cells are presented.

  1. Dynamics of a Tether System Connected to an Irregularly Shaped Celestial Body

    Science.gov (United States)

    Jalali Mashayekhi, Mohammad; K. Misra, Arun; Keshmiri, Mehdi

    2016-04-01

    The problem of pendular oscillations of a tether attached to an irregularly shaped celestial body is studied in this paper. The dynamic analysis of the system is performed by examining the phase plane trajectories. The effect of the tether length as well as the higher order terms in the gravitational potential of the celestial body on the tether dynamics is investigated. It is demonstrated that consideration of the finite size of the celestial body can have significant effects on the tether dynamics, while the effect of the asphericity of the celestial body on the tether dynamics is negligible. This study is of practical relevance for asteroid deflection using tethers, as well as for the development of space elevators on small planets/moons.

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

    International Nuclear Information System (INIS)

    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)

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

    Science.gov (United States)

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

    2002-01-01

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

  4. Biomimicry Enhances Sequential Reactions of Tethered Glycolytic Enzymes, TPI and GAPDHS

    OpenAIRE

    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 g...

  5. Interaction of the Betapapillomavirus E2 Tethering Protein with Mitotic Chromosomes▿

    OpenAIRE

    Sekhar, Vandana; Reed, Shawna C.; Alison A McBride

    2009-01-01

    During persistent papillomavirus infection, the viral E2 protein tethers the viral genome to the host cell chromosomes, ensuring maintenance and segregation of the viral genome during cell division. However, E2 proteins from different papillomaviruses interact with distinct chromosomal regions and targets. The tethering mechanism has been best characterized for bovine papillomavirus type 1 (BPV1), where the E2 protein tethers the viral genome to mitotic chromosomes in complex with the cellula...

  6. Nonlinear Control of Electrodynamic Tether in Equatorial or Somewhat Inclined Orbits

    OpenAIRE

    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 associat...

  7. The design conception of multipurpose underwater tethered systems with centralized data exchange

    OpenAIRE

    Блінцов, Олександр Володимирович

    2013-01-01

    The structure and design features of a typical tethered underwater system are given. The design complexity, limitations on the installation of additional equipment and the need for the creation of multi-purpose tethered underwater systems are shown.Logic modules, of which almost all tethered underwater systems consist: actuating mechanisms and sensors of the underwater robotic vehicle, control and display devices of the control station, documenting devices, are singled out.The concept of crea...

  8. Complex crystal structures formed by the self assembly of di-tethered nanospheres

    OpenAIRE

    Iacovella, Christopher R.; Glotzer, Sharon C.

    2009-01-01

    We report the results from a computational study of the self-assembly of amphiphilic di-tethered nanospheres using molecular simulation. As a function of the interaction strength and directionality of the tether-tether interactions, we predict the formation of four highly ordered phases not previously reported for nanoparticle systems. We find a double diamond structure comprised of a zincblende (binary diamond) arrangement of spherical micelles with a complementary diamond network of nanopar...

  9. 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.

  10. A proposed bare-tether experiment on board a sounding rocket

    OpenAIRE

    Fujii, Hironori A.; OYAMA, Koichiro; Sasaki, Susumu; Yamagiwa, Yoshiki; 藤井 裕矩; 小山 孝一郎; 佐々木 進; 山極 芳樹; Cho, Mengu; Sanmartin, Juan R.; Charro, Mario; VanderHeide, Erick J.; Kruijff, Michiel; Lebreton, Jean-Pierre

    2005-01-01

    A sounding rocket experiment is proposed to carry out two experiments by the conductive bare-tether; (1) the test of the OML (Orbital-Motion-Limited) theory to collect electron, and (2) the test of techniques to determine (neutral) density profile in critical E-layer. The main driver of the mission is provide a space tether technology experiment in Low-Earth-Orbit (LEO) deploying a long tape tether in space and verify the performance of the bare electrodynamic tape tether. The sounding rocket...

  11. Microfluidics-based side view flow chamber reveals tether-to-sling transition in rolling neutrophils.

    Science.gov (United States)

    Marki, Alex; Gutierrez, Edgar; Mikulski, Zbigniew; Groisman, Alex; Ley, Klaus

    2016-01-01

    Neutrophils rolling at high shear stress (above 6 dyn/cm(2)) form tethers in the rear and slings in the front. Here, we developed a novel photo-lithographically fabricated, silicone(PDMS)-based side-view flow chamber to dynamically visualize tether and sling formation. Fluorescently membrane-labeled mouse neutrophils rolled on P-selectin substrate at 10 dyn/cm(2). Most rolling cells formed 5 tethers that were 2-30 μm long. Breaking of a single tether caused a reproducible forward microjump of the cell, showing that the tether was load-bearing. About 15% of all tether-breaking events resulted in slings. The tether-to-sling transition was fast (rolling cell, suggesting a very low bending modulus of the tether. The sling downstream of the rolling cell aligned according to the streamlines before landing on the flow chamber. These new observations explain how slings form from tethers and provide insight into their biomechanical properties. PMID:27357741

  12. Configuration maintaining control of three-body ring tethered system based on thrust compensation

    Science.gov (United States)

    Huang, Panfeng; Liu, Binbin; Zhang, Fan

    2016-06-01

    Space multi-tethered systems have shown broad prospects in remote observation missions. This paper mainly focuses on the dynamics and configuration maintaining control of space spinning three-body ring tethered system for such mission. Firstly, we establish the spinning dynamic model of the three-body ring tethered system considering the elasticity of the tether using Newton-Euler method, and then validate the suitability of this model by numerical simulation. Subsequently, LP (Likins-Pringle) initial equilibrium conditions for the tethered system are derived based on rigid body's equilibrium theory. Simulation results show that tether slack, snapping and interaction between the tethers exist in the three-body ring system, and its' configuration can not be maintained without control. Finally, a control strategy based on thrust compensation, namely thrust to simulate tether compression under LP initial equilibrium conditions is designed to solve the configuration maintaining control problem. Control effects are verified by numerical simulation compared with uncontrolled situation. Simulation results show that the configuration of the three-body ring tethered system could maintain under this active control strategy.

  13. Microfluidics-based side view flow chamber reveals tether-to-sling transition in rolling neutrophils

    Science.gov (United States)

    Marki, Alex; Gutierrez, Edgar; Mikulski, Zbigniew; Groisman, Alex; Ley, Klaus

    2016-01-01

    Neutrophils rolling at high shear stress (above 6 dyn/cm2) form tethers in the rear and slings in the front. Here, we developed a novel photo-lithographically fabricated, silicone(PDMS)-based side-view flow chamber to dynamically visualize tether and sling formation. Fluorescently membrane-labeled mouse neutrophils rolled on P-selectin substrate at 10 dyn/cm2. Most rolling cells formed 5 tethers that were 2–30 μm long. Breaking of a single tether caused a reproducible forward microjump of the cell, showing that the tether was load-bearing. About 15% of all tether-breaking events resulted in slings. The tether-to-sling transition was fast (<100 ms) with no visible material extending above the rolling cell, suggesting a very low bending modulus of the tether. The sling downstream of the rolling cell aligned according to the streamlines before landing on the flow chamber. These new observations explain how slings form from tethers and provide insight into their biomechanical properties. PMID:27357741

  14. Nonlinear dynamics and coupling effect of libration and vibration of tethered space robot in deorbiting process

    Institute of Scientific and Technical Information of China (English)

    王班; 郭吉丰; 冯吉根; 王剑

    2016-01-01

    In order to control the growth of space debris, a novel tethered space robot (TSR) was put forward. After capture,the platform, tether, and target constituted a tethered combination system. General nonlinear dynamics of the tethered combination system in the post-capture phase was established with the consideration of the attitudes of two spacecrafts and the quadratic nonlinear elasticity of the tether. The motion law of the tethered combination in the deorbiting process with different disturbances was simulated and discussed on the premise that the platform was only controlled by a constant thrust force. It is known that the four motion freedoms of the tethered combination are coupled with each other in the deorbiting process from the simulation results. A noticeable phenomenon is that the tether longitudinal vibration does not decay to vanish even under the large tether damping with initial attitude disturbances due to the coupling effect. The approximate analytical solutions of the dynamics for a simplified model are obtained through the perturbation method. The condition of the inter resonance phenomenon is the frequency ratioλ1=2. The case study shows good accordance between the analytical solutions and numerical results, indicating the effectiveness and correctness of approximate analytical solutions.

  15. KAT7/HBO1/MYST2 Regulates CENP-A Chromatin Assembly by Antagonizing Suv39h1-Mediated Centromere Inactivation.

    Science.gov (United States)

    Ohzeki, Jun-Ichirou; Shono, Nobuaki; Otake, Koichiro; Martins, Nuno M C; Kugou, Kazuto; Kimura, Hiroshi; Nagase, Takahiro; Larionov, Vladimir; Earnshaw, William C; Masumoto, Hiroshi

    2016-06-01

    Centromere chromatin containing histone H3 variant CENP-A is required for accurate chromosome segregation as a foundation for kinetochore assembly. Human centromere chromatin assembles on a part of the long α-satellite (alphoid) DNA array, where it is flanked by pericentric heterochromatin. Heterochromatin spreads into adjacent chromatin and represses gene expression, and it can antagonize centromere function or CENP-A assembly. Here, we demonstrate an interaction between CENP-A assembly factor M18BP1 and acetyltransferase KAT7/HBO1/MYST2. Knocking out KAT7 in HeLa cells reduced centromeric CENP-A assembly. Mitotic chromosome misalignment and micronuclei formation increased in the knockout cells and were enhanced when the histone H3-K9 trimethylase Suv39h1 was overproduced. Tethering KAT7 to an ectopic alphoid DNA integration site removed heterochromatic H3K9me3 modification and was sufficient to stimulate new CENP-A or histone H3.3 assembly. Thus, KAT7-containing acetyltransferases associating with the Mis18 complex provides competence for histone turnover/exchange activity on alphoid DNA and prevents Suv39h1-mediated heterochromatin invasion into centromeres. PMID:27270040

  16. The AID-induced DNA damage response in chromatin

    DEFF Research Database (Denmark)

    Daniel, Jeremy A; Nussenzweig, André

    2013-01-01

    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...

  17. 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...

  18. 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....

  19. Analysis of chromatin integrity and DNA damage of buffalo spermatozoa.

    Science.gov (United States)

    Mahmoud, K Gh M; El-Sokary, A A E; Abdel-Ghaffar, A E; Abou El-Roos, M E A; Ahmed, Y F

    2015-01-01

    This study was conducted to determine chromatin integrity and DNA damage by DNA electrophoresis and comet assays of buffalo fresh and frozen semen. Semen samples were collected from four buffalo bulls and evaluated after freezing for semen motility, viability, sperm abnormalities, chromatin integrity and DNA damage. A significant variation was found in semen parameters after thawing. Highly significant differences (Partificial insemination. PMID:27175169

  20. Lessons from Anaplasma phagocytophilum: Chromatin Remodeling by Bacterial Effectors

    OpenAIRE

    Rennoll-Bankert, Kristen E.; Dumler, J. Stephen

    2012-01-01

    Bacterial pathogens can alter global host gene expression via histone modifications and chromatin remodeling in order to subvert host responses, including those involved with innate immunity, allowing for bacterial survival. Shigella flexneri, Listeria monocytogenes, Chlamydia trachomatis, and Anaplasma phagocytophilum express effector proteins that modify host histones and chromatin structure. A. phagocytophilum modulates granulocyte respiratory burst in part by dampening transcription of se...

  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; Olsen, Jesper V; Vertegaal, Alfred C O

    2015-01-01

    identified 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...

  2. Nuclear visions enhanced: chromatin structure, organization and dynamics

    OpenAIRE

    Meshorer, Eran; Herrmann, Harald; Raška, Ivan

    2011-01-01

    The EMBO Workshop on ‘Chromatin Structure, Organization and Dynamics' took place in April 2011 in Prague, Czech Republic. Participants presented data on the generation of models of the genome, working to correlate changes in the organization of chromatin with the functional state of the genome.

  3. Phosphorylation of histone variant regions in chromatin: unlocking the linker?

    Science.gov (United States)

    Green, G R

    2001-01-01

    Histone variants illuminate the behavior of chromatin through their unique structures and patterns of postsynthetic modification. This review examines the literature on heteromorphous histone structures in chromatin, structures that are primary targets for histone kinases and phosphatases in vivo. Special attention is paid to certain well-studied experimental systems: mammalian culture cells, chicken erythrocytes, sea urchin sperm, wheat sprouts, Tetrahymena, and budding yeast. A common theme emerges from these studies. Specialized, highly basic structures in histone variants promote chromatin condensation in a variety of developmental situations. Before, and sometimes after condensed chromatin is formed, the chromatin is rendered soluble by phosphorylation of the heteromorphous regions, preventing their interaction with linker DNA. A simple structural model accounting for histone variation and phosphorylation is presented. PMID:11467741

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

    Science.gov (United States)

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

    2016-08-01

    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

  5. Data on the kinetics of in vitro assembled chromatin.

    Science.gov (United States)

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

    2016-09-01

    Here, we use LC-MS/MS and SWATH-MS to describe the kinetics of in vitro assembled chromatin supported by an embryo extract prepared from preblastoderm Drosophila melanogaster embryos (DREX). This system allows easy manipulation of distinct aspects of chromatin assembly such as post-translational histone modifications, the levels of histone chaperones and the concentration of distinct DNA binding factors. In total, 480 proteins have been quantified as chromatin enriched factors and their binding kinetics have been monitored in the time course of 15 min, 1 h and 4 h of chromatin assembly. The data accompanying the manuscript on this approach, Völker-Albert et al., 2016 "A quantitative proteomic analysis of in vitro assembled chromatin" [1], has been deposited to the ProteomeXchange Consortium (http://www.proteomexchange.org) via the PRIDE partner repository with the dataset identifier submission number PRIDE: PXD002537 and PRIDE: PXD003445. PMID:27331114

  6. Maneuver analysis for spinning thrusting spacecraft and spinning tethered spacecraft

    Science.gov (United States)

    Martin, Kaela M.

    During axial thrusting of a spin-stabilized spacecraft undergoing orbital injections or control maneuvers, misalignments and center-of-mass offset create undesired body-fixed torques. The effects of the body-fixed torques, which in turn cause velocity pointing errors, can be reduced by ramping up (and then ramping down) the thruster. The first topic discussed in this thesis derives closed-form solutions for the angular velocity, Euler angles, inertial velocity, and inertial displacement solutions with nonzero initial conditions. Using the closed-form solutions, the effect of variations in the spin-axis moment of inertia and spin-rate on the spacecraft velocity pointing error are shown. The analytical solutions closely match numerical simulations. The next topic considers various ramp-up profiles (including parabolic, cosine, logarithmic, exponential, and cubic) to heuristically find a suboptimal solution to reduce the velocity pointing error. Some of the considered cosine, logarithmic, exponential, parabolic, and cubic profiles drive the velocity pointing error to nearly zero and hence qualify as effective solutions. The third topic examines a large tethered spacecraft that produces artificial gravity with the propulsion system on one end of the tether. Instead of thrusting through the center of mass, the offset thrust occurs at an angle to the tether which is held in the desired direction by changing the spin rate to compensate for decreasing propellant mass. The dynamics and control laws of the system are derived for constant, time-varying, planar, and non-planar thrust as well as spin-up maneuvers. The final topic discusses how the Bodewadt solution of a self-excited rigid body is unable to accurately predict the motion compared to a numerical integration of the equations of motion.

  7. On the mechanochemical machinery underlying chromatin remodeling

    Science.gov (United States)

    Yusufaly, Tahir I.

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

  8. Chromatin structure near transcriptionally active genes

    International Nuclear Information System (INIS)

    Hypersensitive domains are the most prominent features of transcriptionally active chromatin. In the case of the β/sup A/-globin gene, it seems likely that two or more protein factors are capable of binding to the DNA so tightly that the nucleosome is prevented from binding. We have shown that nucleosomes, once bound in the assembly process in vitro, cannot be displaced. The interaction of the 5S gene transcription factor TFIIIA with its target DNA also is blocked by histones, and it has been suggested that the activation of the gene must occur during replication, before histones are reassembled on the DNA. We suppose that a similar mechanism may govern the binding of the hypersensitivity factors. It should be noted that nucleosomes are excluded not only from the sites to which the factors bind, but also from the regions between the two domains and at either side. 12 refs., 6 figs

  9. Histone modifications and lamin A regulate chromatin protein dynamics in early embryonic stem cell differentiation

    OpenAIRE

    Melcer, Shai; Hezroni, Hadas; Rand, Eyal; Nissim-Rafinia, Malka; Skoultchi, Arthur; Stewart, Colin L.; Bustin, Michael; Meshorer, Eran

    2012-01-01

    Embryonic stem cells are characterized by unique epigenetic features including decondensed chromatin and hyperdynamic association of chromatin proteins with chromatin. Here we investigate the potential mechanisms that regulate chromatin plasticity in embryonic stem cells. Using epigenetic drugs and mutant embryonic stem cells lacking various chromatin proteins, we find that histone acetylation, G9a-mediated histone H3 lysine 9 (H3K9) methylation and lamin A expression, all affect chromatin pr...

  10. Gene Expression and Chromatin Modifications Associated with Maize Centromeres

    Directory of Open Access Journals (Sweden)

    Hainan Zhao

    2016-01-01

    Full Text Available Centromeres are defined by the presence of CENH3, a variant of histone H3. Centromeres in most plant species contain exclusively highly repetitive DNA sequences, which has hindered research on structure and function of centromeric chromatin. Several maize centromeres have been nearly completely sequenced, providing a sequence-based platform for genomic and epigenomic research of plant centromeres. Here we report a high resolution map of CENH3 nucleosomes in the maize genome. Although CENH3 nucleosomes are spaced ∼190 bp on average, CENH3 nucleosomes that occupied CentC, a 156-bp centromeric satellite repeat, showed clear positioning aligning with CentC monomers. Maize centromeres contain alternating CENH3-enriched and CENH3-depleted subdomains, which account for 87% and 13% of the centromeres, respectively. A number of annotated genes were identified in the centromeres, including 11 active genes that were located exclusively in CENH3-depleted subdomains. The euchromatic histone modification marks, including H3K4me3, H3K36me3 and H3K9ac, detected in maize centromeres were associated mainly with the active genes. Interestingly, maize centromeres also have lower levels of the heterochromatin histone modification mark H3K27me2 relative to pericentromeric regions. We conclude that neither H3K27me2 nor the three euchromatic histone modifications are likely to serve as functionally important epigenetic marks of centromere identity in maize.

  11. Gene Expression and Chromatin Modifications Associated with Maize Centromeres.

    Science.gov (United States)

    Zhao, Hainan; Zhu, Xiaobiao; Wang, Kai; Gent, Jonathan I; Zhang, Wenli; Dawe, R Kelly; Jiang, Jiming

    2016-01-01

    Centromeres are defined by the presence of CENH3, a variant of histone H3. Centromeres in most plant species contain exclusively highly repetitive DNA sequences, which has hindered research on structure and function of centromeric chromatin. Several maize centromeres have been nearly completely sequenced, providing a sequence-based platform for genomic and epigenomic research of plant centromeres. Here we report a high resolution map of CENH3 nucleosomes in the maize genome. Although CENH3 nucleosomes are spaced ∼190 bp on average, CENH3 nucleosomes that occupied CentC, a 156-bp centromeric satellite repeat, showed clear positioning aligning with CentC monomers. Maize centromeres contain alternating CENH3-enriched and CENH3-depleted subdomains, which account for 87% and 13% of the centromeres, respectively. A number of annotated genes were identified in the centromeres, including 11 active genes that were located exclusively in CENH3-depleted subdomains. The euchromatic histone modification marks, including H3K4me3, H3K36me3 and H3K9ac, detected in maize centromeres were associated mainly with the active genes. Interestingly, maize centromeres also have lower levels of the heterochromatin histone modification mark H3K27me2 relative to pericentromeric regions. We conclude that neither H3K27me2 nor the three euchromatic histone modifications are likely to serve as functionally important epigenetic marks of centromere identity in maize. PMID:26564952

  12. 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.

  13. 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...... platform for the detection of the activity of VLY and possibly other cholesterol-dependent cytolysins....

  14. Solvation force between tethered polyelectrolyte layers. A density functional approach

    Directory of Open Access Journals (Sweden)

    O. Pizio

    2012-10-01

    Full Text Available We use a version of the density functional theory to study the solvation force between two plates modified with a tethered layer of chains. The chains are built of tangentially jointed charged spherical segments. The plates are immersed in an electrolyte solution that involves cations, anions and solvent molecules. The latter molecules are modelled as hard spheres. We study the dependence of the solvation force and the structure of chains and of solute molecules on the grafting density, length of chains, architecture of the chains and on concentration of the solute.

  15. 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.

  16. Tethered spinal cord syndrome with symptomatic onset in adulthood

    Institute of Scientific and Technical Information of China (English)

    HE Shi-sheng; ZHAO Ying-chuan; SHI Zhi-cai; LI Ming; HOU Tie-sheng; ZHANG Ye; WU Yun-gang

    2009-01-01

    @@ Tethered spinal cord syndrome(TCS)is a condition of overstretching or compression of the caudal part of the spinal cord caused by various spinal lesions,such as a tight filum terminale or an intraspinal lipoma.~(1-9) Though it is a well-recognized cause of neurological deterioration in childhood,its symptomatic onset in adulthood is uncommon.~(10-23) Eleven cases of TCS are presented here.In addition,their related clinical features,surgical procedures and outcomes are investigated.

  17. 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

    such as CAF-1, DNMT1 and SUV39h1 are enriched in nascent chromatin, whereas 170 factors including histone H1, DNMT3, MBD1-3 and PRC1 show delayed association. This correlates with H4K5K12diAc removal and H3K9me1 accumulation, whereas H3K27me3 and H3K9me3 remain unchanged. Finally, we combine NCC...

  18. Three-Dimensional, Live-Cell Imaging of Chromatin Dynamics in Plant Nuclei Using Chromatin Tagging Systems.

    Science.gov (United States)

    Hirakawa, Takeshi; Matsunaga, Sachihiro

    2016-01-01

    In plants, chromatin dynamics spatiotemporally change in response to various environmental stimuli. However, little is known about chromatin dynamics in the nuclei of plants. Here, we introduce a three-dimensional, live-cell imaging method that can monitor chromatin dynamics in nuclei via a chromatin tagging system that can visualize specific genomic loci in living plant cells. The chromatin tagging system is based on a bacterial operator/repressor system in which the repressor is fused to fluorescent proteins. A recent refinement of promoters for the system solved the problem of gene silencing and abnormal pairing frequencies between operators. Using this system, we can detect the spatiotemporal dynamics of two homologous loci as two fluorescent signals within a nucleus and monitor the distance between homologous loci. These live-cell imaging methods will provide new insights into genome organization, development processes, and subnuclear responses to environmental stimuli in plants. PMID:27557696

  19. Analytical investigation of the dynamics of tethered constellations in earth orbit

    Science.gov (United States)

    Lorenzini, Enrico C.; Gullahorn, Gordon E.; Estes, Robert D.

    1988-01-01

    This Quarterly Report on Tethering in Earth Orbit deals with three topics: (1) Investigation of the propagation of longitudinal and transverse waves along the upper tether. Specifically, the upper tether is modeled as three massive platforms connected by two perfectly elastic continua (tether segments). The tether attachment point to the station is assumed to vibrate both longitudinally and transversely at a given frequency. Longitudinal and transverse waves propagate along the tethers affecting the acceleration levels at the elevator and at the upper platform. The displacement and acceleration frequency-response functions at the elevator and at the upper platform are computed for both longitudinal and transverse waves. An analysis to optimize the damping time of the longitudinal dampers is also carried out in order to select optimal parameters. The analytical evaluation of the performance of tuned vs. detuned longitudinal dampers is also part of this analysis. (2) The use of the Shuttle primary Reaction Control System (RCS) thrusters for blowing away a recoiling broken tether is discussed. A microcomputer system was set up to support this operation. (3) Most of the effort in the tether plasma physics study was devoted to software development. A particle simulation code has been integrated into the Macintosh II computer system and will be utilized for studying the physics of hollow cathodes.

  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...

  1. Control by damping Injection of Electrodynamic Tether System in an Inclined Orbit

    DEFF Research Database (Denmark)

    Larsen, Martin Birkelund; Blanke, Mogens

    2009-01-01

    Control of a satellite system with an electrodynamic tether as actuator is a time-periodic and underactuated control problem. This paper considers the tethered satellite in a Hamiltonian framework and determines a port-controlled Hamiltonian formulation that adequately describes the nonlinear...

  2. Minireview: role of kinases and chromatin remodeling in progesterone signaling to chromatin.

    Science.gov (United States)

    Vicent, Guillermo P; Nacht, A Silvina; Zaurín, Roser; Ballaré, Cecilia; Clausell, Jaime; Beato, Miguel

    2010-11-01

    Steroid hormones regulate gene expression by interaction of their receptors with hormone-responsive elements on DNA or with other transcription factors, but they can also activate cytoplasmic signaling cascades. Rapid activation of Erk by progestins via an interaction of the progesterone receptor (PR) with the estrogen receptor is critical for transcriptional activation of the mouse mammary tumor virus (MMTV) promoter and other progesterone target genes. Erk activation leads to the phosphorylation of PR, activation of mitogen- and stress-activated protein kinase 1, and the recruitment of a complex of the three activated proteins and of P300/CBP-associated factor (PCAF) to a single nucleosome, resulting in the phosphoacetylation of histone H3 and the displacement of heterochromatin protein 1γ. Hormone-dependent gene expression requires ATP-dependent chromatin remodeling complexes. Two switch/sucrose nonfermentable-like complexes, Brahma-related gene 1-associated factor (BAF) and polybromo-BAF are present in breast cancer cells, but only BAF is recruited to the MMTV promoter and cooperates with PCAF during activation of hormone-responsive promoters. PCAF acetylates histone H3 at K14, an epigenetic mark recognized by BAF subunits, thus anchoring the complex to chromatin. BAF catalyzes localized displacement of histones H2A and H2B, facilitating access of nuclear factor 1 and additional PR complexes to the hidden hormone-responsive elements on the MMTV promoter. The linker histone H1 is a structural component of chromatin generally regarded as a general repressor of transcription. However, it contributes to a better regulation of the MMTV promoter by favoring a more homogeneous nucleosome positioning, thus reducing basal transcription and actually enhancing hormone induced transcription. During transcriptional activation, H1 is phosphorylated and displaced from the promoter. The kinase cyclin-dependent kinase 2 is activated after progesterone treatment and could

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

    DEFF Research Database (Denmark)

    Larsen, Martin Birkelund

    only be generated perpendicular to the instantaneous magnetic field. Furthermore, the control problem is complicated by the time variations in the magnetic field. This thesis solves these problems by utilizing an energy-based system description and a passivity-based control design. An advantage of the...... 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 of propellant a spacecraft need to bring from Earth can be reduced. In this thesis the modeling and control of electrodynamic tethers are investigated, both when a single tether is used to connect two spacecrafts, and when the tethers are used i more general formations of spacecrafts. One of the...

  5. Shortest Path Planning for a Tethered Robot or an Anchored Cable

    Energy Technology Data Exchange (ETDEWEB)

    Xavier, P.G.

    1999-02-22

    We consider the problem of planning shortest paths for a tethered robot with a finite length tether in a 2D environment with polygonal obstacles. We present an algorithm that runs in time O((k{sub 1} + 1){sup 2}n{sup 4}) and finds the shortest path or correctly determines that none exists that obeys the constraints; here n is the number obstacle vertices, and k{sub 1} is the number loops in the initial configuration of the tether. The robot may cross its tether but nothing can cross obstacles, which cause the tether to bend. The algorithm applies as well for planning a shortest path for the free end of an anchored cable.

  6. Cholesterol tethered bioresponsive polycation as a candidate for gene delivery

    International Nuclear Information System (INIS)

    The efficient unpacking of viral protein shell gave the inspiration for the synthesized vectors. In this research, novel cholesterol tethered bioresponsive polyethylenimine (PEI) was specially designed via disulfide-containing cross-linker. The cholesterol lipid had proved to increase the permeability of gene vector through cell membrane. The acid-base titration indicated that the synthesized polycation possessed efficient proton sponge effect, which was suggested to increase endosomal release of pDNA complexes into the cytoplasm. The cholesterol tethered polycation could effectively induce DNA condensation and form spherical particles with diameter about 200 nm at N/P ratio of 10. At glutathione concentration of 3 mM, the polyplexes were unpacked due to the bioresponsive cleavage of the disulfide bonds. The in-vitro experiment indicated that the polyplexes showed efficient transfection efficiency to HEK293T cells. All the results indicated that the bioresponsive polycation could be served as an effective trigger to control the release of DNA at the intracellular environment. The novel bioresponsive polycation might have great potential in non-viral gene delivery research and application.

  7. Cellulose Microfibril Formation by Surface-Tethered Cellulose Synthase Enzymes.

    Science.gov (United States)

    Basu, Snehasish; Omadjela, Okako; Gaddes, David; Tadigadapa, Srinivas; Zimmer, Jochen; Catchmark, Jeffrey M

    2016-02-23

    Cellulose microfibrils are pseudocrystalline arrays of cellulose chains that are synthesized by cellulose synthases. The enzymes are organized into large membrane-embedded complexes in which each enzyme likely synthesizes and secretes a β-(1→4) glucan. The relationship between the organization of the enzymes in these complexes and cellulose crystallization has not been explored. To better understand this relationship, we used atomic force microscopy to visualize cellulose microfibril formation from nickel-film-immobilized bacterial cellulose synthase enzymes (BcsA-Bs), which in standard solution only form amorphous cellulose from monomeric BcsA-B complexes. Fourier transform infrared spectroscopy and X-ray diffraction techniques show that surface-tethered BcsA-Bs synthesize highly crystalline cellulose II in the presence of UDP-Glc, the allosteric activator cyclic-di-GMP, as well as magnesium. The cellulose II cross section/diameter and the crystal size and crystallinity depend on the surface density of tethered enzymes as well as the overall concentration of substrates. Our results provide the correlation between cellulose microfibril formation and the spatial organization of cellulose synthases. PMID:26799780

  8. Cholesterol tethered bioresponsive polycation as a candidate for gene delivery

    Energy Technology Data Exchange (ETDEWEB)

    Zhu Ying [Second Affiliated Hospital, Medical College, Zhejiang University, Hangzhou 310009 (China); Wang Youxiang, E-mail: yx_wang@zju.edu.cn [Department of Polymer Science and Engineering, Zhejiang University, Hangzhou 310027 (China); Key Laboratory of Macromolecular Synthesis and Functionalization, Ministry of Education, Zhejiang University, Hangzhou 310027 (China); Hu Qiaoling; Shen Jiacong [Department of Polymer Science and Engineering, Zhejiang University, Hangzhou 310027 (China); Key Laboratory of Macromolecular Synthesis and Functionalization, Ministry of Education, Zhejiang University, Hangzhou 310027 (China)

    2009-04-30

    The efficient unpacking of viral protein shell gave the inspiration for the synthesized vectors. In this research, novel cholesterol tethered bioresponsive polyethylenimine (PEI) was specially designed via disulfide-containing cross-linker. The cholesterol lipid had proved to increase the permeability of gene vector through cell membrane. The acid-base titration indicated that the synthesized polycation possessed efficient proton sponge effect, which was suggested to increase endosomal release of pDNA complexes into the cytoplasm. The cholesterol tethered polycation could effectively induce DNA condensation and form spherical particles with diameter about 200 nm at N/P ratio of 10. At glutathione concentration of 3 mM, the polyplexes were unpacked due to the bioresponsive cleavage of the disulfide bonds. The in-vitro experiment indicated that the polyplexes showed efficient transfection efficiency to HEK293T cells. All the results indicated that the bioresponsive polycation could be served as an effective trigger to control the release of DNA at the intracellular environment. The novel bioresponsive polycation might have great potential in non-viral gene delivery research and application.

  9. Forcing adsorption of a tethered polymer by pulling

    International Nuclear Information System (INIS)

    We present an analysis of a partially directed walk model of a polymer which at one end is tethered to a sticky surface and at the other end is subjected to a pulling force at fixed angle away from the point of tethering. Using the kernel method, we derive the full generating function for this model in two and three dimensions and obtain the respective phase diagrams. We observe adsorbed and desorbed phases with a thermodynamic phase transition in between. In the absence of a pulling force this model has a second-order thermal desorption transition which merely gets shifted by the presence of a lateral pulling force. On the other hand, if the pulling force contains a non-zero vertical component this transition becomes first order. Strikingly, we find that, if the angle between the pulling force and the surface is below a critical value, a sufficiently strong force will induce polymer adsorption, no matter how large the temperature of the system. Our findings are similar in two and three dimensions, an additional feature in three dimensions being the occurrence of a re-entrance transition at constant pulling force for low temperature, which has been observed previously for this model in the presence of pure vertical pulling. Interestingly, the re-entrance phenomenon vanishes under certain pulling angles, with details depending on how the three-dimensional polymer is modeled

  10. 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.

  11. 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.

  12. 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.

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

    Directory of Open Access Journals (Sweden)

    Timsy Uppal

    2015-01-01

    Full Text Available 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.

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

    International Nuclear Information System (INIS)

    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

  15. CTCF-Mediated Functional Chromatin Interactome in Pluripotent Cells

    Science.gov (United States)

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

    2011-01-01

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

  16. 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.

  17. 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.

  18. Nucleosome positioning and composition modulate in silico chromatin flexibility

    Science.gov (United States)

    Clauvelin, N.; Lo, P.; Kulaeva, O. I.; Nizovtseva, E. V.; Diaz-Montes, J.; Zola, J.; Parashar, M.; Studitsky, V. M.; Olson, W. K.

    2015-02-01

    The dynamic organization of chromatin plays an essential role in the regulation of gene expression and in other fundamental cellular processes. The underlying physical basis of these activities lies in the sequential positioning, chemical composition, and intermolecular interactions of the nucleosomes—the familiar assemblies of ˜150 DNA base pairs and eight histone proteins—found on chromatin fibers. Here we introduce a mesoscale model of short nucleosomal arrays and a computational framework that make it possible to incorporate detailed structural features of DNA and histones in simulations of short chromatin constructs. We explore the effects of nucleosome positioning and the presence or absence of cationic N-terminal histone tails on the ‘local’ inter-nucleosomal interactions and the global deformations of the simulated chains. The correspondence between the predicted and observed effects of nucleosome composition and numbers on the long-range communication between the ends of designed nucleosome arrays lends credence to the model and to the molecular insights gleaned from the simulated structures. We also extract effective nucleosome-nucleosome potentials from the simulations and implement the potentials in a larger-scale computational treatment of regularly repeating chromatin fibers. Our results reveal a remarkable effect of nucleosome spacing on chromatin flexibility, with small changes in DNA linker length significantly altering the interactions of nucleosomes and the dimensions of the fiber as a whole. In addition, we find that these changes in nucleosome positioning influence the statistical properties of long chromatin constructs. That is, simulated chromatin fibers with the same number of nucleosomes exhibit polymeric behaviors ranging from Gaussian to worm-like, depending upon nucleosome spacing. These findings suggest that the physical and mechanical properties of chromatin can span a wide range of behaviors, depending on nucleosome

  19. Power Generation for a JUNO-type Mission using Electrodynamic Tethers

    Science.gov (United States)

    Bombardelli, C.; Lorenzini, E. C.; Sanmartin, J. R.

    2008-09-01

    Electrodynamic tethers are known to exhibit high performance in the Jupiter environment , both as propellantless propulsion devices and as power generating systems. In spite of the considerable amount of research work of electrodynamic tethers in the Jupiter environment the case involving high inclination orbit has never been addressed so far. We present a power generation scheme for rotating electrodynamic tethers which can be applied to a generic Jupiter science missions employing polar orbits. We show that when the orbit inclination reaches 90 degrees and the tether rotates in the orbital plane the effect of the tether electrodynamic force does not impact orbital energy but orbit inclination. Thanks to favorable environmental conditions at Jupiter (i.e. strong magnetic field and fast rotating plasmasphere) relatively high power levels can be obtained with tethers of modest length when the tether transits the low altitude regions around the planet. In addition the impact on orbit inclination is minimal thanks to the high specific angular momentum of jovian orbits. As a numerical example we consider an electrodynamic tether subsystem consisting of two 3- km-long 5-cm wide and 0.05-mm-thick tape tether arms deployed radially from a main central spacecraft whose orbit has the characteristic of the current baseline JUNO orbit. The tether subsystem, whose total mass is less than 50 kg, can provide kW level average power along a 120 degrees orbital arc around the equatorial plane crossing. The inclination variation induced by the Lorentz force in this case is below 1/1000 of a degree per orbit. Applications of the concept to future Jupiter exploration missions are discussed.

  20. Interaction and conformational changes of chromatin with divalent ions.

    OpenAIRE

    Borochov, N; Ausio, J; Eisenberg, H

    1984-01-01

    We have investigated the interaction of divalent ions with chromatin towards a closer understanding of the role of metal ions in the cell nucleus. The first row transition metal ion chlorides MnCl2, CoCl2, NiCl2 and CuCl2 lead to precipitation of chicken erythrocyte chromatin at a significantly lower concentration than the alkali earth metal chlorides MgCl2, CaCl2 and BaCl2. A similar distinction can be made for the compaction of chromatin to the "30 nm" solenoid higher order structure which ...

  1. Lamin C and chromatin organization in Drosophila

    Indian Academy of Sciences (India)

    B. V. Gurudatta; L. S. Shashidhara; Veena K. Parnaik

    2010-04-01

    Drosophila lamin C (LamC) is a developmentally regulated component of the nuclear lamina. The lamC gene is situated in the fifth intron of the essential gene tout velu (ttv). We carried out genetic analysis of lamC during development. Phenotypic analyses of RNAi-mediated downregulation of lamC expression as well as targeted misexpression of lamin C suggest a role for lamC in cell survival. Of particular interest in the context of laminopathies is the caspase-dependent apoptosis induced by the overexpression of lamin C. Interestingly, misexpression of lamin C in the central nervous system, where it is not normally expressed, did not affect organization of the nuclear lamina. lamC mutant alleles suppressed position effect variegation normally displayed at near-centromeric and telomeric regions. Further, both downregulation and misexpression of lamin C affected the distribution of heterochromatin protein 1. Our results suggest that Drosophila lamC has a tissue-specific role during development and is required for chromatin organization.

  2. Centromeric chromatin and its dynamics in plants.

    Science.gov (United States)

    Lermontova, Inna; Sandmann, Michael; Mascher, Martin; Schmit, Anne-Catherine; Chabouté, Marie-Edith

    2015-07-01

    Centromeres are chromatin structures that are required for proper separation of chromosomes during mitosis and meiosis. The centromere is composed of centromeric DNA, often enriched in satellite repeats, and kinetochore complex proteins. To date, over 100 kinetochore components have been identified in various eukaryotes. Kinetochore assembly begins with incorporation of centromeric histone H3 variant CENH3 into centromeric nucleosomes. Protein components of the kinetochore are either present at centromeres throughout the cell cycle or localize to centromeres transiently, prior to attachment of microtubules to each kinetochore in prometaphase of mitotic cells. This is the case for the spindle assembly checkpoint (SAC) proteins in animal cells. The SAC complex ensures equal separation of chromosomes between daughter nuclei by preventing anaphase onset before metaphase is complete, i.e. the sister kinetochores of all chromosomes are attached to spindle fibers from opposite poles. In this review, we focus on the organization of centromeric DNA and the kinetochore assembly in plants. We summarize recent advances regarding loading of CENH3 into the centromere, and the subcellular localization and protein-protein interactions of Arabidopsis thaliana proteins involved in kinetochore assembly and function. We describe the transcriptional activity of corresponding genes based on in silico analysis of their promoters and cell cycle-dependent expression. Additionally, barley homologs of all selected A. thaliana proteins have been identified in silico, and their sequences and domain structures are presented. PMID:25976696

  3. DNA-Protein interactions in nucleosomes and in Chromatin

    International Nuclear Information System (INIS)

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

  4. 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.

  5. Shelterin Protects Chromosome Ends by Compacting Telomeric Chromatin.

    Science.gov (United States)

    Bandaria, Jigar N; Qin, Peiwu; Berk, Veysel; Chu, Steven; Yildiz, Ahmet

    2016-02-11

    Telomeres, repetitive DNA sequences at chromosome ends, are shielded against the DNA damage response (DDR) by the shelterin complex. To understand how shelterin protects telomere ends, we investigated the structural organization of telomeric chromatin in human cells using super-resolution microscopy. We found that telomeres form compact globular structures through a complex network of interactions between shelterin subunits and telomeric DNA, but not by DNA methylation, histone deacetylation, or histone trimethylation at telomeres and subtelomeric regions. Mutations that abrogate shelterin assembly or removal of individual subunits from telomeres cause up to a 10-fold increase in telomere volume. Decompacted telomeres accumulate DDR signals and become more accessible to telomere-associated proteins. Recompaction of telomeric chromatin using an orthogonal method displaces DDR signals from telomeres. These results reveal the chromatin remodeling activity of shelterin and demonstrate that shelterin-mediated compaction of telomeric chromatin provides robust protection of chromosome ends against the DDR machinery. PMID:26871633

  6. Neutron scattering studies on chromatin higher-order structure

    Energy Technology Data Exchange (ETDEWEB)

    Graziano, V.; Gerchman, S.E.; Schneider, D.K.; Ramakrishnan, V. [Brookhaven National Laboratory, Upton, NY (United States)

    1994-12-31

    We have been engaged in studies of the structure and condensation of chromatin into the 30nm filament using small-angle neutron scattering. We have also used deuterated histone H1 to determine its location in the chromatin 30nm filament. Our studies indicate that chromatin condenses with increasing ionic strength to a limiting structure that has a mass per unit length of 6-7 nucleosomes/11 nm. They also show that the linker histone H1/H5 is located in the interior of the chromatin filament, in a position compatible with its binding to the inner face of the nucleosome. Analysis of the mass per unit length as a function of H5 stoichiometry suggests that 5-7 contiguous nucleosomes need to have H5 bound before a stable higher order structure can exist.

  7. Insights into Chromatin Structure and Dynamics in Plants

    Directory of Open Access Journals (Sweden)

    Stefanie Rosa

    2013-11-01

    Full Text Available The packaging of chromatin into the nucleus of a eukaryotic cell requires an extraordinary degree of compaction and physical organization. In recent years, it has been shown that this organization is dynamically orchestrated to regulate responses to exogenous stimuli as well as to guide complex cell-type-specific developmental programs. Gene expression is regulated by the compartmentalization of functional domains within the nucleus, by distinct nucleosome compositions accomplished via differential modifications on the histone tails and through the replacement of core histones by histone variants. In this review, we focus on these aspects of chromatin organization and discuss novel approaches such as live cell imaging and photobleaching as important tools likely to give significant insights into our understanding of the very dynamic nature of chromatin and chromatin regulatory processes. We highlight the contribution plant studies have made in this area showing the potential advantages of plants as models in understanding this fundamental aspect of biology.

  8. Does seminal fluid viscosity influence sperm chromatin integrity?

    Science.gov (United States)

    Gopalkrishnan, K; Padwal, V; Balaiah, D

    2000-01-01

    A retrospective study was undertaken to investigate whether viscosity alters sperm chromatin integrity. Semen samples were obtained from 269 men attending the infertility clinic. The viscosity was measured quantitatively by needle and syringe method and the viscosity ratio was calculated against distilled water. The chromatin integrity was evaluated by in vitro decondensation test using 1% SDS and 6 mM EDTA. According to the viscosity ratios the samples were divided into 2 groups: I, normal (ratio 9, n = 30) viscosity. Chromatin integrity was significantly lower in the group with higher viscosity. Significant decrease in sperm count and motility were seen in group II as compared to group I. Thus, hyperviscosity of seminal fluid alters the sperm chromatin integrity. PMID:11028927

  9. Nuclear envelope and chromatin, lock and key of genome integrity.

    Science.gov (United States)

    Gay, Sophie; Foiani, Marco

    2015-01-01

    More than as an inert separation between the inside and outside of the nucleus, the nuclear envelope (NE) constitutes an active toll, which controls the import and export of molecules, and also a hub for a diversity of genomic processes, such as transcription, DNA repair, and chromatin dynamics. Proteins localized at the inner surface of the NE (such as lamins, nuclear pore proteins, lamin-associated proteins) interact with chromatin in a dynamic manner, contributing to the establishment of topological domains. In this review, we address the complex interplay between chromatin and NE. We discuss the divergence of this cross talk during evolution and comment both on the current established models and the most recent findings. In particular, we focus our attention on how the NE cooperates with chromatin in protecting the genome integrity. PMID:26008788

  10. Chromatin structure modulates DNA repair by photolyase in vivo.

    OpenAIRE

    Suter, B.; Livingstone-Zatchej, M; Thoma, F

    1997-01-01

    Yeast and many other organisms use nucleotide excision repair (NER) and photolyase in the presence of light (photoreactivation) to repair cyclobutane pyrimidine dimers (CPDs), a major class of DNA lesions generated by UV light. To study the role of photoreactivation at the chromatin level in vivo, we used yeast strains which contained minichromosomes (YRpTRURAP, YRpCS1) with well-characterized chromatin structures. The strains were either proficient (RAD1) or deficient (rad1 delta) in NER. In...

  11. Unsupervised pattern discovery in human chromatin structure through genomic segmentation.

    Science.gov (United States)

    Hoffman, Michael M; Buske, Orion J; Wang, Jie; Weng, Zhiping; Bilmes, Jeff A; Noble, William Stafford

    2012-05-01

    We trained Segway, a dynamic Bayesian network method, simultaneously on chromatin data from multiple experiments, including positions of histone modifications, transcription-factor binding and open chromatin, all derived from a human chronic myeloid leukemia cell line. In an unsupervised fashion, we identified patterns associated with transcription start sites, gene ends, enhancers, transcriptional regulator CTCF-binding regions and repressed regions. Software and genome browser tracks are at http://noble.gs.washington.edu/proj/segway/. PMID:22426492

  12. Higher order chromatin structure: bridging physics and biology

    OpenAIRE

    Fudenberg, Geoffrey; Mirny, Leonid A.

    2012-01-01

    Recent advances in microscopy and genomic techniques have provided new insight into spatial chromatin organization inside of the nucleus. In particular, chromosome conformation capture data has highlighted the relevance of polymer physics for high-order chromatin organization. In this context, we review basic polymer states, discuss how an appropriate polymer model can be determined from experimental data, and examine the success and limitations of various polymer models of high-order interph...

  13. How does the chromatin fiber deal with topological constraints?

    OpenAIRE

    Barbi, Maria; Mozziconacci, Julien; Victor, Jean-Marc

    2004-01-01

    In the nuclei of eukaryotic cells, DNA is packaged through several levels of compaction in an orderly retrievable way that enables the correct regulation of gene expression. The functional dynamics of this assembly involves the unwinding of the so-called 30 nm chromatin fiber and accordingly imposes strong topological constraints. We present a general method for computing both the twist and the writhe of any winding pattern. An explicit derivation is implemented for the chromatin fiber which ...

  14. Design Concept for a Reusable/Propellantless MXER Tether Space Transportation System

    Science.gov (United States)

    McCandless, B., II; Kustas, F. m.; Marshall, L. S.; Lytle, W. B.; Hansen, N. P.

    2005-01-01

    The Momentum Exchange/Electrodynamic Reboost (MXER) tether facility is a transformational concept that significantly reduces the fuel requirements (and associated costs) in transferring payloads above low earth orbit (LEO). Facility reboost is accomplished without propellant by driving current against a voltage created by a conducting tether's interaction with the Earth's magnetic field (electrodynamic reboost). This system can be used for transferring a variety of payloads (scientific, cargo, and human space vehicles) to multiple destinations including geosynchronous transfer orbit, the Moon or Mars. MXER technology advancement requires development in two key areas: survivable, high tensile strength non-conducting tethers and reliable, lightweight payload catch/release mechanisms. Fundamental requirements associated with the MXER non-conducting strength tether and catch mechanism designs will be presented. Key requirements for the tether design include high specific-strength (tensile strength/material density), material survivability to the space environment (atomic oxygen and ultraviolet radiation), and structural survivability to micrometeoroid/orbital debris (MM/OD) impacts. The driving mechanism key,gequirements include low mass-to-capture-volume ratio, positional and velocity error tolerance, and operational reliability. Preliminary tether and catch mechanism design criteria are presented, which have been used as guidelines to "screen" and down-select initial concepts. Candidate tether materials and protective coatings are summarized along with their performance in simulated space environments (e.g., oxygen plasma, thermal cycling). A candidate catch mechanism design concept is presented along with examples of demonstration hardware.

  15. 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.

  16. Minor groove binder distamycin remodels chromatin but inhibits transcription.

    Directory of Open Access Journals (Sweden)

    Parijat Majumder

    Full Text Available The condensed structure of chromatin limits access of cellular machinery towards template DNA. This in turn represses essential processes like transcription, replication, repair and recombination. The repression is alleviated by a variety of energy dependent processes, collectively known as "chromatin remodeling". In a eukaryotic cell, a fine balance between condensed and de-condensed states of chromatin helps to maintain an optimum level of gene expression. DNA binding small molecules have the potential to perturb such equilibrium. We present herein the study of an oligopeptide antibiotic distamycin, which binds to the minor groove of B-DNA. Chromatin mobility assays and circular dichroism spectroscopy have been employed to study the effect of distamycin on chromatosomes, isolated from the liver of Sprague-Dawley rats. Our results show that distamycin is capable of remodeling both chromatosomes and reconstituted nucleosomes, and the remodeling takes place in an ATP-independent manner. Binding of distamycin to the linker and nucleosomal DNA culminates in eviction of the linker histone and the formation of a population of off-centered nucleosomes. This hints at a possible corkscrew type motion of the DNA with respect to the histone octamer. Our results indicate that distamycin in spite of remodeling chromatin, inhibits transcription from both DNA and chromatin templates. Therefore, the DNA that is made accessible due to remodeling is either structurally incompetent for transcription, or bound distamycin poses a roadblock for the transcription machinery to advance.

  17. Inactivation of chromatin remodeling factors sensitizes cells to selective cytotoxic stress

    Directory of Open Access Journals (Sweden)

    Freeman MD

    2014-11-01

    Full Text Available Miles D Freeman, Tryphon Mazu, Jana S Miles, Selina Darling-Reed, Hernan Flores-Rozas College of Pharmacy and Pharmaceutical Sciences, Florida A&M University, Tallahassee, FL, USA Abstract: The SWI/SNF chromatin-remodeling complex plays an essential role in several cellular processes including cell proliferation, differentiation, and DNA repair. Loss of normal function of the SWI/SNF complex because of mutations in its subunits correlates with tumorigenesis in humans. For many of these cancers, cytotoxic chemotherapy is the primary, and sometimes the only, therapeutic alternative. Among the antineoplastic agents, anthracyclines are a common treatment option. Although effective, resistance to these agents usually develops and serious dose-related toxicity, namely, chronic cardiotoxicity, limits its use. Previous work from our laboratory showed that a deletion of the SWI/SNF factor SNF2 resulted in hypersensitivity to doxorubicin. We further investigated the contribution of other chromatin remodeling complex components in the response to cytotoxic chemotherapy. Our results indicate that, of the eight SWI/SNF strains tested, snf2, taf14, and swi3 were the most sensitive and displayed distinct sensitivity to different cytotoxic agents, while snf5 displayed resistance. Our experimental results indicate that the SWI/SNF complex plays a critical role in protecting cells from exposure to cytotoxic chemotherapy and other cytotoxic agents. Our findings may prove useful in the development of a strategy aimed at targeting these genes to provide an alternative by hypersensitizing cancer cells to chemotherapeutic agents. Keywords: chromatin remodeling, cancer, DNA damage/repair, heat-shock response, oxidative stress

  18. 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).

  19. Tethered and Polymer Supported Bilayer Lipid Membranes: Structure and Function

    Directory of Open Access Journals (Sweden)

    Jakob Andersson

    2016-05-01

    Full Text Available Solid supported bilayer lipid membranes are model systems to mimic natural cell membranes in order to understand structural and functional properties of such systems. The use of a model system allows for the use of a wide variety of analytical tools including atomic force microscopy, impedance spectroscopy, neutron reflectometry, and surface plasmon resonance spectroscopy. Among the large number of different types of model membranes polymer-supported and tethered lipid bilayers have been shown to be versatile and useful systems. Both systems consist of a lipid bilayer, which is de-coupled from an underlying support by a spacer cushion. Both systems will be reviewed, with an emphasis on the effect that the spacer moiety has on the bilayer properties.

  20. 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.

  1. 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.

  2. The HOPS/class C Vps complex tethers membranes by binding to one Rab GTPase in each apposed membrane.

    Science.gov (United States)

    Ho, Ruoya; Stroupe, Christopher

    2015-07-15

    Many Rab GTPase effectors are membrane-tethering factors, that is, they physically link two apposed membranes before intracellular membrane fusion. In this study, we investigate the distinct binding factors needed on apposed membranes for Rab effector-dependent tethering. We show that the homotypic fusion and protein-sorting/class C vacuole protein-sorting (HOPS/class C Vps) complex can tether low-curvature membranes, that is, liposomes with a diameter of ∼100 nm, only when the yeast vacuolar Rab GTPase Ypt7p is present in both tethered membranes. When HOPS is phosphorylated by the vacuolar casein kinase I, Yck3p, tethering only takes place when GTP-bound Ypt7p is present in both tethered membranes. When HOPS is not phosphorylated, however, its tethering activity shows little specificity for the nucleotide-binding state of Ypt7p. These results suggest a model for HOPS-mediated tethering in which HOPS tethers membranes by binding to Ypt7p in each of the two tethered membranes. Moreover, because vacuole-associated HOPS is presumably phosphorylated by Yck3p, our results suggest that nucleotide exchange of Ypt7p on multivesicular bodies (MVBs)/late endosomes must take place before HOPS can mediate tethering at vacuoles. PMID:25995379

  3. 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.

  4. 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.

  5. First-principles calculation of DNA looping in tethered particle experiments

    International Nuclear Information System (INIS)

    We calculate the probability of DNA loop formation mediated by regulatory proteins such as Lac repressor (LacI), using a mathematical model of DNA elasticity. Our model is adapted to calculating quantities directly observable in tethered particle motion (TPM) experiments, and it accounts for all the entropic forces present in such experiments. Our model has no free parameters; it characterizes DNA elasticity using information obtained in other kinds of experiments. It assumes a harmonic elastic energy function (or wormlike chain type elasticity), but our Monte Carlo calculation scheme is flexible enough to accommodate arbitrary elastic energy functions. We show how to compute both the 'looping J factor' (or equivalently, the looping free energy) for various DNA construct geometries and LacI concentrations, as well as the detailed probability density function of bead excursions. We also show how to extract the same quantities from recent experimental data on TPM, and then compare to our model's predictions. In particular, we present a new method to correct observed data for finite camera shutter time and other experimental effects. Although the currently available experimental data give large uncertainties, our first-principles predictions for the looping free energy change are confirmed to within about 1 kBT, for loops of length around 300 basepairs. More significantly, our model successfully reproduces the detailed distributions of bead excursion, including their surprising three-peak structure, without any fit parameters and without invoking any alternative conformation of the LacI tetramer. Indeed, the model qualitatively reproduces the observed dependence of these distributions on tether length (e.g., phasing) and on LacI concentration (titration). However, for short DNA loops (around 95 basepairs) the experiments show more looping than is predicted by the harmonic-elasticity model, echoing other recent experimental results. Because the experiments we study are

  6. Cluster filtering/control of bending/torsional vibrations of a tape tether using smart-film sensors/actuators

    Science.gov (United States)

    Kojima, Hirohisa; Kunugi, Kouta; Trivailo, Pavel M.

    2016-06-01

    Tape tethers show great promise for application in space debris removal because they possess a large collecting area, which is crucial for the collection of electrons from a plasma environment in space. Tape tethers are therefore preferred over string tethers in electrodynamic tethered systems (EDTS), which operate based on the Lorentz force derived from the interaction between the electric current on the tether and the Earth's magnetic field. Vibrations of the tether may disturb the attitude of the mother satellite and the subsatellite, and are difficult to damp in space because the damping would be minimal owing to the almost zero drag force in space. Due to their relatively large width, tape tethers experience torsional deformation and therefore cannot be treated as a string tether. If torsional deformation of tape tethers is not avoided, the advantage of tape tethers as the materials for EDT systems will be deteriorated. Point-type sensors and actuators are usually used to sense and control vibrations. However, it is difficult to apply such sensors and actuators to tape tethers because of the substantial length of the tether as well as the need for a deployment mechanism, such as a reel. In order to overcome the difficulties related to vibrations, the use of smart-film sensors and actuators for sensing and controlling vibrations of tape tethers is considered in this study. In a previous study, we presented an application of smart film for sensing vibrations of tape tethers, but the actuation of tape tethers using smart-film actuators has not yet been reported. In the present paper, we mathematically derive suitable configurations of smart-film attachment to a tape tether for cluster filtering and actuation of bending and torsional vibrations of the tape tether, and carried out cluster actuation experiments. The experimental results reveal that the bending and torsional vibrations of a tape tether can be reduced by cluster actuation control based on direct

  7. Chromatin perturbations during the DNA damage response in higher eukaryotes.

    Science.gov (United States)

    Bakkenist, Christopher J; Kastan, Michael B

    2015-12-01

    The DNA damage response is a widely used term that encompasses all signaling initiated at DNA lesions and damaged replication forks as it extends to orchestrate DNA repair, cell cycle checkpoints, cell death and senescence. ATM, an apical DNA damage signaling kinase, is virtually instantaneously activated following the introduction of DNA double-strand breaks (DSBs). The MRE11-RAD50-NBS1 (MRN) complex, which has a catalytic role in DNA repair, and the KAT5 (Tip60) acetyltransferase are required for maximal ATM kinase activation in cells exposed to low doses of ionizing radiation. The sensing of DNA lesions occurs within a highly complex and heterogeneous chromatin environment. Chromatin decondensation and histone eviction at DSBs may be permissive for KAT5 binding to H3K9me3 and H3K36me3, ATM kinase acetylation and activation. Furthermore, chromatin perturbation may be a prerequisite for most DNA repair. Nucleosome disassembly during DNA repair was first reported in the 1970s by Smerdon and colleagues when nucleosome rearrangement was noted during the process of nucleotide excision repair of UV-induced DNA damage in human cells. Recently, the multi-functional protein nucleolin was identified as the relevant histone chaperone required for partial nucleosome disruption at DBSs, the recruitment of repair enzymes and for DNA repair. Notably, ATM kinase is activated by chromatin perturbations induced by a variety of treatments that do not directly cause DSBs, including treatment with histone deacetylase inhibitors. Central to the mechanisms that activate ATR, the second apical DNA damage signaling kinase, outside of a stalled and collapsed replication fork in S-phase, is chromatin decondensation and histone eviction associated with DNA end resection at DSBs. Thus, a stress that is common to both ATM and ATR kinase activation is chromatin perturbations, and we argue that chromatin perturbations are both sufficient and required for induction of the DNA damage response

  8. Structural Fluctuations of the Chromatin Fiber within Topologically Associating Domains.

    Science.gov (United States)

    Tiana, Guido; Amitai, Assaf; Pollex, Tim; Piolot, Tristan; Holcman, David; Heard, Edith; Giorgetti, Luca

    2016-03-29

    Experiments based on chromosome conformation capture have shown that mammalian genomes are partitioned into topologically associating domains (TADs), within which the chromatin fiber preferentially interacts. TADs may provide three-dimensional scaffolds allowing genes to contact their appropriate distal regulatory DNA sequences (e.g., enhancers) and thus to be properly regulated. Understanding the cell-to-cell and temporal variability of the chromatin fiber within TADs, and what determines them, is thus of great importance to better understand transcriptional regulation. We recently described an equilibrium polymer model that can accurately predict cell-to-cell variation of chromosome conformation within single TADs, from chromosome conformation capture-based data. Here we further analyze the conformational and energetic properties of our model. We show that the chromatin fiber within TADs can easily fluctuate between several conformational states, which are hierarchically organized and are not separated by important free energy barriers, and that this is facilitated by the fact that the chromatin fiber within TADs is close to the onset of the coil-globule transition. We further show that in this dynamic state the properties of the chromatin fiber, and its contact probabilities in particular, are determined in a nontrivial manner not only by site-specific interactions between strongly interacting loci along the fiber, but also by nonlocal correlations between pairs of contacts. Finally, we use live-cell experiments to measure the dynamics of the chromatin fiber in mouse embryonic stem cells, in combination with dynamical simulations, and predict that conformational changes within one TAD are likely to occur on timescales that are much shorter than the duration of one cell cycle. This suggests that genes and their regulatory elements may come together and disassociate several times during a cell cycle. These results have important implications for transcriptional

  9. Computational study of small molecule binding for both tethered and free conditions

    CERN Document Server

    Ytreberg, F Marty

    2009-01-01

    Using a calix[4]arene-benzene complex as a test system we compare the potential of mean force for when the calix[4]arene is tethered versus free. When the complex is in vacuum our results show that the difference between tethered and free is primarily due to the entropic contribution to the potential of mean force resulting in a binding free energy difference of 6.5 kJ/mol. By contrast, when the complex is in water our results suggest that the difference between tethered and free is due to the enthalpic contribution resulting in a binding free energy difference of 1.6 kJ/mol. This study elucidates the roles of entropy and enthalpy for this small molecule system and emphasizes the point that tethering the receptor has the potential to dramatically impact the binding properties. These findings should be taken into consideration when using calixarene molecules in nanosensor design.

  10. Advanced Particle-in-Cell (PIC) Tools for Simulation of Electrodynamic Tether Plasma Interactions Project

    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...

  11. 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...

  12. 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,...

  13. Enzymatic activity of soluble and membrane tethered peptide pro-hormone convertase 1.

    Science.gov (United States)

    Bruzzaniti, Angela; Mains, Richard E

    2002-05-01

    Pro-hormone convertases PC1 and PC2 perform endoproteolytic cleavages of precursors in peptide-containing secretory granules. PC1 and PC2 are soluble, secreted with bioactive peptides. Evolutionarily related PCs have membrane tethers, not secreted. We tethered PC1 to the transmembrane-cytoplasmic domains (CD) of a granule enzyme (peptidylglycine-alpha-amidating monooxygenase; PAM) and Golgi-localized PC8. The tethered PC1 is far more stable to elevated temperature and denaturants than soluble PC1, and more active. Both tethers allow PC1 to visit the cell surface transiently, cleaving soluble molecules outside the cell. Both membrane-bound PC1 chimeras cleave membrane PAM into soluble active fragments when PAM is expressed on adjacent cells. PMID:12084516

  14. Materials for advancement of MXER tether design (1000-371) Project

    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....

  15. Materials for Advancement of MXER Tether Design (1000-549) Project

    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....

  16. Construction and Structural Analysis of Tethered Lipid Bilayer Containing Photosynthetic Antenna Proteins for Functional Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Sumino, Ayumi; Dewa, Takehisa; Takeuchi, Toshikazu; Sugiura, Ryuta; Sasaki, Nobuaki; Misawa, Nobuo; Tero, Ryugo; Urisu, Tsuneo; Gardiner, Alastair T; Cogdell, Richard J; Hashimoto, Hideki; Nango, Mamoru

    2011-07-11

    The construction and structural analysis of a tethered planar lipid bilayer containing bacterial photosynthetic membrane proteins, light-harvesting complex 2 (LH2), and light-harvesting core complex (LH1-RC) is described and establishes this system as an experimental platform for their functional analysis. The planar lipid bilayer containing LH2 and/or LH1-RC complexes was successfully formed on an avidin-immobilized coverglass via an avidin-biotin linkage. Atomic force microscopy (AFM) showed that a smooth continuous membrane was formed there. Lateral diffusion of these membrane proteins, observed by a fluorescence recovery after photobleaching (FRAY), is discussed in terms of the membrane architecture. Energy transfer from LH2 to LH1-RC within the tethered membrane architecture. Energy transfer from LH2 to LH1-RC within the tethered membrane was observed by steady-state fluorescence spectroscopy, indicating that the tethered membrane can mimic the natural situation.

  17. Attitude stabilization of electrodynamic tethers in elliptic orbits by time-delay feedback control

    Science.gov (United States)

    Iñarrea, Manuel; Lanchares, Víctor; Pascual, Ana Isabel; Salas, José Pablo

    2014-03-01

    It is well known that libration motion of electrodynamic tethers operating in inclined orbits is affected by dynamic instability due to the electromagnetic interaction between the tether and the geomagnetic field. We study the application of two feedback control methods in order to stabilize the periodic attitude motions of electrodynamic tethers in elliptic inclined orbits. Both control schemes are based on the time-delayed autosynchronization of the system. Numerical simulations of the controlled libration motion show that both control techniques are able to transform the uncontrolled unstable periodic motions into asymptotically stable ones. Such stabilized periodic attitude motions can be taken as starting points for the operation of the tether. The control domains of both methods have been computed for different values of the system parameters, as functions of the two control parameters shared by both control schemes. The relative effectiveness of the two techniques in the stabilization of the periodic attitude motion has also been studied.

  18. Polydopamine tethered enzyme/metal-organic framework composites with high stability and reusability

    Science.gov (United States)

    Wu, Xiaoling; Yang, Cheng; Ge, Jun; Liu, Zheng

    2015-11-01

    An enzyme/metal-organic framework (MOF) composite with both highly stable and easily reusable features was prepared via tethering enzyme/MOF nanocrystals with polydopamine (PDA). The micrometer-sized PDA tethered enzyme/MOF composite can be easily repeatedly used without obvious activity loss, promising for efficient enzymatic catalysis at low cost with long-term operational stability under harsh conditions.An enzyme/metal-organic framework (MOF) composite with both highly stable and easily reusable features was prepared via tethering enzyme/MOF nanocrystals with polydopamine (PDA). The micrometer-sized PDA tethered enzyme/MOF composite can be easily repeatedly used without obvious activity loss, promising for efficient enzymatic catalysis at low cost with long-term operational stability under harsh conditions. Electronic supplementary information (ESI) available: Synthesis of enzyme-MOF nanocrystals, SEM, TEM, CLSM characterization and measurements of enzymatic performances. See DOI: 10.1039/c5nr05190h

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

    DEFF Research Database (Denmark)

    Fleron, René A. W.; Blanke, Mogens

    2004-01-01

    Adjustment of the orbit of a spacecraft using the forces created by an electro-dynamic space-tether has been shown as a theoretic possibility in recent literature. Practical implementation is being pursued for larger scale missions where a hot filament device controls electron emission 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...... 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...

  20. Alternative security

    International Nuclear Information System (INIS)

    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

  1. Validation, reliability, and complications of a tethering scoliosis model in the rabbit.

    Science.gov (United States)

    Kallemeier, Patricia M; Buttermann, Glenn R; Beaubien, Brian P; Chen, Xinqian; Polga, David J; Lew, William D; Wood, Kirkham B

    2006-04-01

    This study was conducted to refine a small animal model of scoliosis, and to quantify the deformities throughout its growth period. Subcutaneous scapula-to-contralateral pelvis tethering surgery was selected due to its minimally invasive nature and potential applicability for a large animal model. The procedure was performed in 7-week-old New Zealand white rabbits. Group A animals (n=9) underwent the tethering procedure with a suture that spontaneously released. Group B animals (n=17) had the identical procedure with a robust tether and pelvic fixation, which was maintained for 2 months during growth. All animals developed immediate post-operative scoliosis with a Cobb angle of 23 degrees (range, 6-39 degrees) in group A and 59 degrees (range, 24-90 degrees) in group B animals. During the 2 month post-tethering, group A animals lost their tether and scoliosis resolved, whereas all animals in group B maintained their tether until scheduled release at which time the mean scoliosis was 62 degrees. Immediately after tether release, group B scoliosis decreased to a mean 53 degrees. Over the following 4 months of adolescent growth, the scoliosis decreased to a mean of 43 degrees at skeletal maturity; the decrease usually occurred in animals with less than 45 degrees curves at tether release. Radiographs revealed apical vertebral wedging (mean 19 degrees ) in all group B animals. Sagittal spinal alignment was also assessed, and for group B animals, the scoliotic segment developed mild to moderate kyphosis (mean 28 degrees) and torsional deformity, but the kyphosis resolved by 4 months after tether-release. Complications specific to this technique included a high rate of transient scapulothoracic dissociation and cases of cor pulmonale. In conclusion, this tethering technique in immature rabbits consistently produced scoliosis with vertebral wedging when the tether was intact through the first 2 months of the protocol. The transient exaggeration of kyphosis suggests that

  2. Effect of Temperature on Tether Extraction, Surface Protrusion, and Cortical Tension of Human Neutrophils

    OpenAIRE

    Liu, Baoyu; Goergen, Craig J.; Shao, Jin-Yu

    2007-01-01

    Neutrophil rolling on endothelial cells, the initial stage of its migrational journey to a site of inflammation, is facilitated by tether extraction and surface protrusion. Both phenomena have been studied extensively at room temperature, which is considerably lower than human body temperature. It is known that temperature greatly affects cellular mechanical properties such as viscosity. Therefore, we carried out tether extraction, surface protrusion, and cortical tension experiments at 37°C ...

  3. Low work-function coating for an entirely propellantless bare electrodynamic tether

    OpenAIRE

    Williams, John D.; Sanmartin, Juan R.; Rand, Lauren P.

    2012-01-01

    We present the possibility of a low work-function material, calcium aluminate electride, being used for a coating on a bare electrodynamic tether system. Analyses suggest that the coating would eliminate the need for an active cathodic device like a hollow cathode and, consequently, eliminate the need for an expellant to the hollow cathode, thus resulting in an electrodynamic tether system that requires no consumables. Applications include on-orbit power generation and deorbiting debris fr...

  4. Tether Extrusion from Red Blood Cells: Integral Proteins Unbinding from Cytoskeleton

    OpenAIRE

    Borghi, N.; Brochard-Wyart, F.

    2007-01-01

    We investigate the mechanical strength of adhesion and the dynamics of detachment of the membrane from the cytoskeleton of red blood cells (RBCs). Using hydrodynamical flows, we extract membrane tethers from RBCs locally attached to the tip of a microneedle. We monitor their extrusion and retraction dynamics versus flow velocity (i.e., extrusion force) over successive extrusion-retraction cycles. Membrane tether extrusion is carried out on healthy RBCs and ATP-depleted or -inhibited RBCs. For...

  5. Validation, reliability, and complications of a tethering scoliosis model in the rabbit

    OpenAIRE

    Kallemeier, Patricia M.; Buttermann, Glenn R.; Beaubien, Brian P.; Chen, Xinqian; Polga, David J.; Lew, William D; Wood, Kirkham B.

    2005-01-01

    This study was conducted to refine a small animal model of scoliosis, and to quantify the deformities throughout its growth period. Subcutaneous scapula-to-contralateral pelvis tethering surgery was selected due to its minimally invasive nature and potential applicability for a large animal model. The procedure was performed in 7-week-old New Zealand white rabbits. Group A animals (n=9) underwent the tethering procedure with a suture that spontaneously released. Group B animals (n=17) had the...

  6. CDC28 phosphorylates Cac1p and regulates the association of chromatin assembly factor I with chromatin.

    Science.gov (United States)

    Jeffery, Daniel C B; Kakusho, Naoko; You, Zhiying; Gharib, Marlene; Wyse, Brandon; Drury, Erin; Weinreich, Michael; Thibault, Pierre; Verreault, Alain; Masai, Hisao; Yankulov, Krassimir

    2015-01-01

    Chromatin Assembly Factor I (CAF-I) plays a key role in the replication-coupled assembly of nucleosomes. It is expected that its function is linked to the regulation of the cell cycle, but little detail is available. Current models suggest that CAF-I is recruited to replication forks and to chromatin via an interaction between its Cac1p subunit and the replication sliding clamp, PCNA, and that this interaction is stimulated by the kinase CDC7. Here we show that another kinase, CDC28, phosphorylates Cac1p on serines 94 and 515 in early S phase and regulates its association with chromatin, but not its association with PCNA. Mutations in the Cac1p-phosphorylation sites of CDC28 but not of CDC7 substantially reduce the in vivo phosphorylation of Cac1p. However, mutations in the putative CDC7 target sites on Cac1p reduce its stability. The association of CAF-I with chromatin is impaired in a cdc28-1 mutant and to a lesser extent in a cdc7-1 mutant. In addition, mutations in the Cac1p-phosphorylation sites by both CDC28 and CDC7 reduce gene silencing at the telomeres. We propose that this phosphorylation represents a regulatory step in the recruitment of CAF-I to chromatin in early S phase that is distinct from the association of CAF-I with PCNA. Hence, we implicate CDC28 in the regulation of chromatin reassembly during DNA replication. These findings provide novel mechanistic insights on the links between cell-cycle regulation, DNA replication and chromatin reassembly. PMID:25602519

  7. Internal and higher-order structure of chromatin nu bodies

    Energy Technology Data Exchange (ETDEWEB)

    Olins, D E

    1977-01-01

    Based upon current biophysical data (including recent laser-Raman studies) of isolated nu bodies and inner histones, we have proposed that the chromatin subunit consists of a DNA-rich outer domain surrounding a protein core composed of ..cap alpha..-helical-rich histone globular regions, close-packed with dihedral point-group symmetry. Analysis of the effects of urea on isolated nu bodies suggest that these two domains respond differently: the DNA-rich shell exhibits noncooperative destabilization; the protein core undergoes cooperative destabilization. This differential response of the two regions of a nu body to a simple chemical perturbant (i.e., urea) may furnish a model for the conformational differences in nu bodies postulated for active chromatin. Nu bodies are believed to organize into 20-30 nm higher-order fibers in condensed regions of chromatin. However, the integrity of subunits in these thick fibers has recently been seriously challenged. Evidence from our laboratory, presented here, confirms that the 20-30 nm chromatin fibers consists of a close-packing of nu bodies. The chromatin subunits, therefore, retain their integrity within the higher-order fibers.

  8. Chromatin: a tunable spring at work inside chromosomes.

    Science.gov (United States)

    Ben-Haïm, E; Lesne, A; Victor, J M

    2001-11-01

    This paper focuses on mechanical aspects of chromatin biological functioning. Within a basic geometric modeling of the chromatin assembly, we give a complete set of elastic constants (twist and bend persistence lengths, stretch modulus and twist-stretch coupling constant) of the so-called 30-nm chromatin fiber, in terms of DNA elastic properties and geometric properties of the fiber assembly. The computation naturally embeds the fiber within a current analytical model known as the "extensible wormlike rope," allowing a straightforward prediction of the force-extension curves. We show that these elastic constants are strongly sensitive to the linker length, up to 1 bp, or equivalently to its twist, and might locally reach very low values, yielding a highly flexible and extensible domain in the fiber. In particular, the twist-stretch coupling constant, reflecting the chirality of the chromatin fiber, exhibits steep variations, and sign changes when the linker length is varied. We argue that this tunable elasticity might be a key feature for chromatin function, for instance, in the initiation and regulation of transcription. PMID:11735982

  9. 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.

  10. Off-set control of the tethered systems using a graph theoretic approach

    Science.gov (United States)

    Modi, V. J.; Pradhan, S.; Misra, A. K.

    1995-03-01

    A mathematical model is developed to study the dynamics and control of the tethered satellite systems undergoing planar motion in a Keplerian orbit. The system consists of a rigid platform from which a point mass subsatellite can be deployed or retrieved by a flexible tether. The model incorporates off-set of the tether attachment point from the platform centre of mass and its time-dependent variation. The governing equations of motion are obtained using the Lagrangian formulation. The effect of system parameters is analysed numerically. The off-set control strategy, which involves movement of the attachment point, is used to regulate the tether swing and the platform dynamics is controlled by a momentum gyro. The off-set control strategy can be implemented using a manipulator which moves the tether attachment point as required. It is shown that the control of only the rigid degrees of freedom is not sufficient as the flexible dynamics of the tether becomes unstable, particularly during retrieval. In the present study, passive dampers are proposed to control the flexible dynamics. The simulation results show that the control procedure regulates the system dynamics quite successfully. The state feedback controller for the system is designed using graph theoretic approach which has computational advantage particularly for higher order systems.

  11. 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. PMID:23626684

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

    International Nuclear Information System (INIS)

    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

  13. The effects of DNA intercalators on chromatin of chicken red blood cells——differential extraction on nonhistone proteins

    Institute of Scientific and Technical Information of China (English)

    WangFan; ZhuJingde

    1990-01-01

    Taking advantage of the effects on DNA secondary structure of two DNA-intercalators,ethidium bromide and chloroquine,we used each of them to treat nuclei from both mature erythrocytes and reticulocytes of chicken,as an alternative approach to study the relationships between DNA secondary structure,nuclear proteins and chromatin structure.We presented results of differential extraction of nuclear proteins from nuclei with DNA-intercalators,as well as preliminary characterization of these proteins.A 45kd protein is the major component in fractions extracted by both intercalators from nuclei from either mature erythrocytes or reticulocytes and seems to be a DNA-binding protein.Furthermore,from current concepts of functional aspects of DNA conformation and structural heterogeneity in chromatin and nuclear proteins,we have discussed both the significance of our results as well as technical aspects of this approach.

  14. Specific requirement of the chromatin modifier mSin3B in cell cycle exit and cellular differentiation.

    Science.gov (United States)

    David, Gregory; Grandinetti, Kathryn B; Finnerty, Patricia M; Simpson, Natalie; Chu, Gerald C; Depinho, Ronald A

    2008-03-18

    The Sin3-histone deacetylase (HDAC) corepressor complex is conserved from yeast to humans. Mammals possess two highly related Sin3 proteins, mSin3A and mSin3B, which serve as scaffolds tethering HDAC enzymatic activity, and numerous sequence-specific transcription factors to enable local chromatin regulation at specific gene targets. Despite broad overlapping expression of mSin3A and mSin3B, mSin3A is cell-essential and vital for early embryonic development. Here, genetic disruption of mSin3B reveals a very different phenotype characterized by the survival of cultured cells and lethality at late stages of embryonic development with defective differentiation of multiple lineages-phenotypes that are strikingly reminiscent of those associated with loss of retinoblastoma family members or E2F transcriptional repressors. Additionally, we observe that, whereas mSin3B(-/-) cells cycle normally under standard growth conditions, they show an impaired ability to exit the cell cycle with limiting growth factors. Correspondingly, mSin3B interacts physically with the promoters of known E2F target genes, and its deficiency is associated with derepression of these gene targets in vivo. Together, these results reveal a critical role for mSin3B in the control of cell cycle exit and terminal differentiation in mammals and establish contrasting roles for the mSin3 proteins in the growth and development of specific lineages. PMID:18332431

  15. 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.

  16. Sliding and peeling of histone during chromatin remodelling

    CERN Document Server

    Garai, Ashok; Chowdhury, Debashish

    2011-01-01

    ATP-dependent chromatin remodeling enzymes (CRE) are bio-molecular motors in eukaryotic cells. These are driven by a chemical fuel, namely, adenosine triphosphate (ATP). CREs actively participate in many cellular processes that require accessibility of specific stretches of DNA which are packaged as chromatin. The basic unit of chromatin is a nucleosome where 146 bp $\\sim$ 50 nm of a double stranded DNA (dsDNA) is wrapped around a spool formed by histone proteins. We investigate the mechanism of peeling of the histone spool, and its complete detachment, from the dsDNA by a CRE. Our two-state model of a CRE captures effectively two distinct chemical (or conformational) states in the mechano-chemical cycle of each ATP-dependent CRE. We calculate the mean times for histone detachment. Our predictions on the ATP-dependence of the measurable quantities can be tested by carrying out {\\it in-vitro} experiments.

  17. H4K44 Acetylation Facilitates Chromatin Accessibility during Meiosis

    Directory of Open Access Journals (Sweden)

    Jialei Hu

    2015-12-01

    Full Text Available Meiotic recombination hotspots are associated with histone post-translational modifications and open chromatin. However, it remains unclear how histone modifications and chromatin structure regulate meiotic recombination. Here, we identify acetylation of histone H4 at Lys44 (H4K44ac occurring on the nucleosomal lateral surface. We show that H4K44 is acetylated at pre-meiosis and meiosis and displays genome-wide enrichment at recombination hotspots in meiosis. Acetylation at H4K44 is required for normal meiotic recombination, normal levels of double-strand breaks (DSBs during meiosis, and optimal sporulation. Non-modifiable H4K44R results in increased nucleosomal occupancy around DSB hotspots. Our results indicate that H4K44ac functions to facilitate chromatin accessibility favorable for normal DSB formation and meiotic recombination.

  18. MNase titration reveals differences between nucleosome occupancy and chromatin accessibility.

    Science.gov (United States)

    Mieczkowski, Jakub; Cook, April; Bowman, Sarah K; Mueller, Britta; Alver, Burak H; Kundu, Sharmistha; Deaton, Aimee M; Urban, Jennifer A; Larschan, Erica; Park, Peter J; Kingston, Robert E; Tolstorukov, Michael Y

    2016-01-01

    Chromatin accessibility plays a fundamental role in gene regulation. Nucleosome placement, usually measured by quantifying protection of DNA from enzymatic digestion, can regulate accessibility. We introduce a metric that uses micrococcal nuclease (MNase) digestion in a novel manner to measure chromatin accessibility by combining information from several digests of increasing depths. This metric, MACC (MNase accessibility), quantifies the inherent heterogeneity of nucleosome accessibility in which some nucleosomes are seen preferentially at high MNase and some at low MNase. MACC interrogates each genomic locus, measuring both nucleosome location and accessibility in the same assay. MACC can be performed either with or without a histone immunoprecipitation step, and thereby compares histone and non-histone protection. We find that changes in accessibility at enhancers, promoters and other regulatory regions do not correlate with changes in nucleosome occupancy. Moreover, high nucleosome occupancy does not necessarily preclude high accessibility, which reveals novel principles of chromatin regulation. PMID:27151365

  19. Structural plasticity of single chromatin fibers revealed by torsional manipulation

    CERN Document Server

    Bancaud, Aurelien; Barbi, Maria; Wagner, Gaudeline; Allemand, Jean-Francois; Mozziconacci, Julien; Lavelle, Christophe; Croquette, Vincent; Victor, Jean-Marc; Prunell, Ariel; Viovy, Jean-Louis

    2006-01-01

    Magnetic tweezers are used to study the mechanical response under torsion of single nucleosome arrays reconstituted on tandem repeats of 5S positioning sequences. Regular arrays are extremely resilient and can reversibly accommodate a large amount of supercoiling without much change in length. This behavior is quantitatively described by a molecular model of the chromatin 3-D architecture. In this model, we assume the existence of a dynamic equilibrium between three conformations of the nucleosome, which are determined by the crossing status of the entry/exit DNAs (positive, null or negative). Torsional strain, in displacing that equilibrium, extensively reorganizes the fiber architecture. The model explains a number of long-standing topological questions regarding DNA in chromatin, and may provide the ground to better understand the dynamic binding of most chromatin-associated proteins.

  20. Single-epitope recognition imaging of native chromatin

    Directory of Open Access Journals (Sweden)

    Wang Hongda

    2008-12-01

    Full Text Available Abstract Background Direct visualization of chromatin has the potential to provide important insights into epigenetic processes. In particular, atomic force microscopy (AFM can visualize single nucleosomes under physiological ionic conditions. However, AFM has mostly been applied to chromatin that has been reconstituted in vitro, and its potential as a tool for the dissection of native nucleosomes has not been explored. Recently we applied AFM to native Drosophila chromatin containing the centromere-specific histone 3 (CenH3, showing that it is greatly enriched in smaller particles. Taken together with biochemical analyses of CenH3 nucleosomes, we propose that centromeric nucleosomes are hemisomes, with one turn of DNA wrapped around a particle consisting of one molecule each of centromere-specific CenH3, H4, H2A and H2B. Results Here we apply a recognition mode of AFM imaging to directly identify CenH3 within histone core particles released from native centromeric chromatin. More than 90% of these particles were found to be tetrameric in height. The specificity of recognition was confirmed by blocking with a CenH3 peptide, and the strength of the interaction was quantified by force measurements. These results imply that the particles imaged by AFM are indeed mature CenH3-containing hemisomes. Conclusion Efficient and highly specific recognition of CenH3 in histone core particles isolated from native centromeric chromatin demonstrates that tetramers are the predominant form of centromeric nucleosomes in mature tetramers. Our findings provide proof of principle that this approach can yield insights into chromatin biology using direct and rapid detection of native nucleosomes in physiological salt concentrations.

  1. 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.

  2. Critical adsorption of copolymer tethered on selective surfaces

    Science.gov (United States)

    Li, Hong; Qian, Chang-Ji; Luo, Meng-Bo

    2016-04-01

    Critical adsorption behaviors of flexible copolymer chains tethered to a flat homogeneous surface are studied by using Monte Carlo simulations. We have compared the critical adsorption temperature Tc, estimated by a finite-size scaling method, for different AB copolymer sequences with A the attractive monomer and B the inert monomer. We find that Tc increases with an increase in the fraction of monomers A, fA, in copolymers, and it increases with an increase in the length of block A for the same fA. In particular, Tc of copolymer (AnBn)r can be expressed as a function of the block length, n, and Tc of copolymer (AnB)r and (ABm)r can be expressed as a linear function of fA. Tc of random copolymer chains also can be expressed as a linear function of fA and it can be estimated by using weight-average of Tc of different diblocks in the random copolymer. However, the crossover exponent is roughly independent of AB sequence distributions either for block copolymers or for random copolymers.

  3. Using tethered triblock copolymers to mediate the interaction between substrates

    International Nuclear Information System (INIS)

    Using scaling analysis and a self-consistent field (SCF) theory, we compress two copolymer-coated surfaces and isolate conditions that yield multiple, distinct minima in the interaction profile. We focus on planar surfaces that are coated with ABC triblock copolymers. Tethered to the surface by the last monomer in the C block, the copolymers are grafted at relatively low densities. The surrounding solution is a poor solvent for both the A and C blocks, and is a good solvent for the B blocks. Through scaling theory, we pinpoint the parameters that yield two minima in the interaction profile. The SCF calculations reveal the changes in the morphology of the polymers as the layers are compressed. Through both studies, we determine how the morphological changes give rise to the observed surface interactions. The results provide guidelines for creating polymer-coated colloidal systems that can form two stable crystal structures. Such systems could be used for bistable, optical switches. The findings also yield a prescription for creating systems that exhibit additional minima in the free energy of interaction. copyright 1998 American Institute of Physics

  4. SURFACE MODIFICATION OF POLYPROPYLENE MICROPOROUS MEMBRANE BY TETHERING POLYPEPTIDES

    Institute of Scientific and Technical Information of China (English)

    Zhen-mei Liu; Zhi-kang Xu; Mathias Ulbricht

    2006-01-01

    Two kinds of polypeptides were tethered onto the surface of polypropylene microporous membrane (PPMM)through a ring opening polymerization of L-glutamate N-carboxyanhydride initiated by amino groups which were introduced by ammonia plasma and γ-aminopropyl triethanoxysilane treatments. X-ray photoelectron spectroscopy (XPS), attenuated total reflectance Fourier transform infrared spectroscopy (FT-IR/ATR), scanning electron microscopy (SEM), together with water contact angle measurements were used to characterize the modified membranes. XPS analyses and FT-IR/ATR spectra demonstrated that polypeptides are actually grafted onto the membrane surface. The wettability of the membrane surface increases at first and then decreases with the increase in grafting degrees of polypeptide. Platelet adhesion and murine macrophage attachment experiments reveal an enhanced hemocompatibility for the polypeptide modified PPMMs. All these results give evidence that polypeptide grafting can simultaneously improve the hemocompatibility as well as reserve the hydrophobicity for the membrane, which will provide a potential approach to improve the performance of polypropylene hollow fiber microporous membrane used in artificial oxygenator.

  5. 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

  6. Modulation of chromatin modifying complexes by noncoding RNAs in trans

    OpenAIRE

    Názer, Ezequiel; Lei, Elissa P.

    2014-01-01

    Increasing evidence supports a central role for ncRNA in numerous aspects of chromatin function. For instance, ncRNAs can act as a scaffold for the recruitment of certain chromatin modifying complexes to specific sites within the genome. It is easily imaginable how this can occur in cis, but examples also exist whereby targeting of complexes by ncRNA occurs in trans to the site of transcription. Moreover, association of an ncRNA with a particular locus can trigger localization of the gene to ...

  7. 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 of the...... polycomb repressive complexes, PRC1 and PRC2, and the HDAC1- and HDAC2-containing complexes, NuRD, Sin3, and CoREST, in stem cells, development, and cancer, as well as the ongoing efforts to develop therapies targeting these complexes in human cancer. Furthermore, we discuss the role of repressive...... complexes in modulating thresholds for gene activation and their importance for specification and maintenance of cell fate....

  8. ATRX represses alternative lengthening of telomeres

    OpenAIRE

    Napier, Christine E.; Huschtscha, Lily I.; Harvey, Adam; Bower, Kylie; Noble, Jane R.; Hendrickson, Eric A.; Reddel, Roger R

    2015-01-01

    The unlimited proliferation of cancer cells requires a mechanism to prevent telomere shortening. Alternative Lengthening of Telomeres (ALT) is an homologous recombination-mediated mechanism of telomere elongation used in tumors, including osteosarcomas, soft tissue sarcoma subtypes, and glial brain tumors. Mutations in the ATRX/DAXX chromatin remodeling complex have been reported in tumors and cell lines that use the ALT mechanism, suggesting that ATRX may be an ALT repressor. We show here th...

  9. Unwinding Protein Complexes in ALTernative Telomere Maintenance

    OpenAIRE

    Bhattacharyya, Saumitri; Sandy, April; Groden, Joanna

    2010-01-01

    Telomeres are composed of specialized chromatin that includes DNA repair/recombination proteins, telomere DNA-binding proteins and a number of three dimensional nucleic acid structures including G-quartets and D-loops. A number of studies suggest that the BLM and WRN recQ-like helicases play important roles in recombination-mediated mechanisms of telomere elongation or Alternative Lengthening of Telomeres (ALT), processes that maintain/elongate telomeres in the absence of telomerase. BLM and ...

  10. Space demostration of bare electrodynamic tape-tether technology on the sounding rocket S520-25

    OpenAIRE

    Fujii, Hironori; Watanabe, Takeo; Sahara, Hironori; Kojima, Hirohisa; Takehara, Shoichiro; Yamagiwa, Yoshiki; Sasaki, Susumu; Abe, Takumi; Tanaka, Koji; Oyama, Khoichiro; Jhonson, Les; Khazanov, V.; Sanmartín Losada, Juan Ramón; Charro, Mario; Kruijff, Michiel

    2011-01-01

    A spaceflight validation of bare electro dynamic tape tether technology was conducted. A S520-25 sounding rocket was launched successfully at 05:00am on 31 August 2010 and successfully deployed 132.6m of tape tether over 120 seconds in a ballistic flight. The electrodynamic performance of the bare tape tether employed as an atmospheric probe was measured. Flight results are introduced through the present progressive report of the demonstration and the results of flight experiment are ex...

  11. T-REX: Bare electro-dynamic tape-tether technology experimetn on sounding rocket S520

    OpenAIRE

    Watanabe, Takeo; Fujii, Hironori; Kusagaya, Tairo; Sahara, Hironori; Kojima, Hirohisa; Takehara, Shoichiro; Yamagiwa, Yoshiki; Sasaki, Susumu; Abe, Takumi; Tanaka, Koji; Oyama, Khoichiro; Ebinuma, Takuji; Johson, Les; Khazanov, George; Sanmartín Losada, Juan Ramón

    2012-01-01

    The project to verify the performance of space tether technology was successfully demonstrated by the launch of the sounding rocket S520 the 25tu. The project is the space demonstration of science and engineering technologies of a bare tape electrodynamic tether (EDT) in the international campaign between Japan, USA, Europe and Australia. Method of "Inverse ORIGAMI (Tape tether folding)" was employed in order to deploy the bare tape EDT in a short period time of the suborbital flight. The ...

  12. Tethered swimming and dry land force parameters: useful tools to characterize front crawl performance in both genders

    OpenAIRE

    Morouço, Pedro Gil Frade

    2012-01-01

    The major purpose of this work was to examine possible relationships between tethered forces and dry-land exercises with swimming performance, for both males and female swimmers. Additionally, it was intended to verify if tethered swimming could be an easy, operative and accurate methodology for the biophysical evaluation of swimmers. For the accomplishment of these purposes the following sequence was used: (i) reviewing available literature; (ii) comparison of tethered swimming w...

  13. 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.

  14. 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.

  15. Chromatin Proteomics Reveals Variable Histone Modifications during the Life Cycle of Trypanosoma cruzi.

    Science.gov (United States)

    de Jesus, Teresa Cristina Leandro; Nunes, Vinícius Santana; Lopes, Mariana de Camargo; Martil, Daiana Evelin; Iwai, Leo Kei; Moretti, Nilmar Silvio; Machado, Fabrício Castro; de Lima-Stein, Mariana L; Thiemann, Otavio Henrique; Elias, Maria Carolina; Janzen, Christian; Schenkman, Sergio; da Cunha, Julia Pinheiro Chagas

    2016-06-01

    Histones are well-conserved proteins that form the basic structure of chromatin in eukaryotes and undergo several post-translational modifications, which are important for the control of transcription, replication, DNA damage repair, and chromosome condensation. In early branched organisms, histones are less conserved and appear to contain alternative sites for modifications, which could reveal evolutionary unique functions of histone modifications in gene expression and other chromatin-based processes. Here, by using high-resolution mass spectrometry, we identified and quantified histone post-translational modifications in two life cycle stages of Trypanosoma cruzi, the protozoan parasite that causes Chagas disease. We detected 44 new modifications, namely: 18 acetylations, seven monomethylations, seven dimethylations, seven trimethylations, and four phosphorylations. We found that replicative (epimastigote stage) contains more histone modifications than nonreplicative and infective parasites (trypomastigote stage). Acetylations of lysines at the C-terminus of histone H2A and methylations of lysine 23 of histone H3 were found to be enriched in trypomastigotes. In contrast, phosphorylation in serine 23 of H2B and methylations of lysine 76 of histone H3 predominates in proliferative states. The presence of one or two methylations in the lysine 76 was found in cells undergoing mitosis and cytokinesis, typical of proliferating parasites. Our findings provide new insights into the role of histone modifications related to the control of gene expression and cell-cycle regulation in an early divergent organism. PMID:27108550

  16. Application of the NASCAP Spacecraft Simulation Tool to Investigate Electrodynamic Tether Current Collection in LEO

    Science.gov (United States)

    Adams, Mitzi; HabashKrause, Linda

    2012-01-01

    Recent interest in using electrodynamic tethers (EDTs) for orbital maneuvering in Low Earth Orbit (LEO) has prompted the development of the Marshall ElectroDynamic Tether Orbit Propagator (MEDTOP) model. The model is comprised of several modules which address various aspects of EDT propulsion, including calculation of state vectors using a standard orbit propagator (e.g., J2), an atmospheric drag model, realistic ionospheric and magnetic field models, space weather effects, and tether librations. The natural electromotive force (EMF) attained during a radially-aligned conductive tether results in electrons flowing down the tether and accumulating on the lower-altitude spacecraft. The energy that drives this EMF is sourced from the orbital energy of the system; thus, EDTs are often proposed as de-orbiting systems. However, when the current is reversed using satellite charged particle sources, then propulsion is possible. One of the most difficult challenges of the modeling effort is to ascertain the equivalent circuit between the spacecraft and the ionospheric plasma. The present study investigates the use of the NASA Charging Analyzer Program (NASCAP) to calculate currents to and from the tethered satellites and the ionospheric plasma. NASCAP is a sophisticated set of computational tools to model the surface charging of three-dimensional (3D) spacecraft surfaces in a time-varying space environment. The model's surface is tessellated into a collection of facets, and NASCAP calculates currents and potentials for each one. Additionally, NASCAP provides for the construction of one or more nested grids to calculate space potential and time-varying electric fields. This provides for the capability to track individual particles orbits, to model charged particle wakes, and to incorporate external charged particle sources. With this study, we have developed a model of calculating currents incident onto an electrodynamic tethered satellite system, and first results are shown

  17. CDC28 phosphorylates Cac1p and regulates the association of chromatin assembly factor i with chromatin

    OpenAIRE

    Jeffery, Daniel CB; Kakusho, Naoko; You, Zhiying; Gharib, Marlene; Wyse, Brandon; Drury, Erin; Weinreich, Michael; Thibault, Pierre; Verreault, Alain; Masai, Hisao; Yankulov, Krassimir

    2015-01-01

    Chromatin Assembly Factor I (CAF-I) plays a key role in the replication-coupled assembly of nucleosomes. It is expected that its function is linked to the regulation of the cell cycle, but little detail is available. Current models suggest that CAF-I is recruited to replication forks and to chromatin via an interaction between its Cac1p subunit and the replication sliding clamp, PCNA, and that this interaction is stimulated by the kinase CDC7. Here we show that another kinase, ...

  18. 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.

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

    DEFF Research Database (Denmark)

    Lichota, J.; Grasser, Klaus D.

    2003-01-01

    maize HMGA and five different HMGB proteins with mononucleosomes (containing approx. 165 bp of DNA) purified from micrococcal nuclease-digested maize chromatin. The HMGB proteins interacted with the nucleosomes independent of the presence of the linker histone H1, while the binding of HMGA in the...

  20. Linking Morphogen and Chromatin in the Hair Follicle

    OpenAIRE

    Mesa, Kailin R; Greco, Valentina

    2013-01-01

    In this issue of Developmental Cell, Xiong et al. (2013) identify a critical role for the chromatin remodeler, Brg1, in hair follicle stem cell maintenance and epidermal repair. Brg1 interacts with the Shh9 signaling pathway to create a positive feedback loop that fuels hair follicle growth.

  1. ATP independent and ATP dependent chromatin remodeling in wheat

    International Nuclear Information System (INIS)

    Unraveling the biochemistry of chromatin dynamics during DNA replication, repair, recombination as well as transcription is the current challenge in biology. The nucleosomes containing histone octamer are the crucial elements responsible for winding and unwinding eukaryotic DNA. During DNA centric events, these nucleosomes translocate along the DNA with concomitant covalent modifications of histones. We explored these mechanisms in wheat seedlings after irradiation with survivable dose of 60Co-γ radiations. The histones isolated from irradiated seedlings showed that global acetylation of H3 decreased and H4 increased in dose depend manner till 100 grays. Time course of individual modifications showed that for H3K4 and H3K9 acetylation decreased, whereas H3S10, phosphorylation increased. There were fluctuations in acetylation of H4K5, H4K12 and H4K16, whereas H4K8 showed hyperacetylation. We found ATP-dependent chromatin remodeling activity as trans-transfer of the nucleosomes from wheat native donor chromatin on a labeled nucleosome positioning sequence and cis-transfer of the mononucleosomes in vitro. However, there was no significant change in this activity in extracts obtained from irradiated wheat seedlings. This is the first report on, demonstration of ATP-dependent chromatin remodeling activity and site specific H3 and H4 modifications in response to exposure to ionizing radiation in case of plants. (author)

  2. 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

  3. Generation of bivalent chromatin domains during cell fate decisions

    Directory of Open Access Journals (Sweden)

    De Gobbi Marco

    2011-06-01

    Full Text Available Abstract Background In self-renewing, pluripotent cells, bivalent chromatin modification is thought to silence (H3K27me3 lineage control genes while 'poising' (H3K4me3 them for subsequent activation during differentiation, implying an important role for epigenetic modification in directing cell fate decisions. However, rather than representing an equivalently balanced epigenetic mark, the patterns and levels of histone modifications at bivalent genes can vary widely and the criteria for identifying this chromatin signature are poorly defined. Results Here, we initially show how chromatin status alters during lineage commitment and differentiation at a single well characterised bivalent locus. In addition we have determined how chromatin modifications at this locus change with gene expression in both ensemble and single cell analyses. We also show, on a global scale, how mRNA expression may be reflected in the ratio of H3K4me3/H3K27me3. Conclusions While truly 'poised' bivalently modified genes may exist, the original hypothesis that all bivalent genes are epigenetically premarked for subsequent expression might be oversimplistic. In fact, from the data presented in the present work, it is equally possible that many genes that appear to be bivalent in pluripotent and multipotent cells may simply be stochastically expressed at low levels in the process of multilineage priming. Although both situations could be considered to be forms of 'poising', the underlying mechanisms and the associated implications are clearly different.

  4. Chromatin-regulating proteins as targets for cancer therapy

    International Nuclear Information System (INIS)

    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)

  5. Chromatin-regulating proteins as targets for cancer therapy.

    Science.gov (United States)

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

    2014-07-01

    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. PMID:24522270

  6. Rearrangement of chromatin domains during development in Xenopus.

    Science.gov (United States)

    Vassetzky, Y; Hair, A; Méchali, M

    2000-06-15

    A dynamic change in the organization of different gene domains transcribed by RNA polymerase I, II, or III occurs during the progression from quiescent [pre-midblastula transition (pre-MBT)] to active (post-MBT) embryos during Xenopus development. In the rDNA, c-myc, and somatic 5S gene domains, a transition from random to specific anchorage to the nuclear matrix occurs when chromatin domains become active. The keratin gene domain was also randomly associated to the nuclear matrix before MBT, whereas a defined attachment site was found in keratinocytes. In agreement with this specification, ligation-mediated (LM)-PCR genomic footprinting carried out on the subpopulation of 5S domains specifically attached to the matrix reveals the hallmarks of determined chromatin after the midblastula transition. In contrast, the same analysis performed on the total 5S gene population does not reveal specific chromatin organization, validating the use of nuclear matrix fractionation to unveil active chromatin domains. These data provide a means for the determination of active chromosomal territories in the embryo and emphasize the role of nuclear architecture in regulated gene expression during development. PMID:10859171

  7. Effect of triiodothyronine on rat liver chromatin protein kinase

    International Nuclear Information System (INIS)

    1) Injection of triiodothyronine to rats stimulates protein kinase activity in liver chromatin nonhistone proteins. A significant increase was found after two daily injections. A 4-fold increase was observed with the purified enzyme after eight daily injections of the hormone. No variations were observed in cytosol protein kinase activity. Electrophoretic pattern, effect of heat denaturation, effect of p-hydroxymercuribenzoate seem to indicate that the enzyme present in treated rats is not identical to the enzyme in control animals, which suggests that thyroid hormone has induced nuclear protein kinase. Diiodothyronine, 3, 3', 5'-triiodothyronine have no effect on protein kinase. 2) Chromatin non-histone proteins isolated from rats injected with triiodothyronine incorporated more 32P when incubated with [γ-32P]ATP than the chromatin proteins from untreated rats. Thyroidectomy reduced the in vitro 32P incorporation. It is suggested that some of the biological activity of thyroid hormone could be mediated through its effect on chromatin non-histone proteins. (orig.)

  8. Control of the Transition to Flowering by Chromatin Modifications

    Institute of Scientific and Technical Information of China (English)

    Yuehui He

    2009-01-01

    The timing of floral transition is critical to reproductive success in angiosperms and is genetically controlled by a network of flowering genes.In Arabidopsis,expression of certain flowering genes is regulated by various chromatin modifications,among which are two central regulators of flowering,namely FLOWERING LOCUS C(FLC) and FLOWERING LOCUS T(FT).Recent studies have revealed that a number of chromatin-modifying components are involved in activation or repression of FLC expression.Activation of FLC expression is associated with various 'active' chromatin modifications including acetylation of core histone tails,histone H3 lysine-4 (H3K4) methylation,H2B monoubiquitination,H3 lysine-36 (H3K36) di- and tri-methylation and deposition of the histone variant H2A.Z,whereas various 'repressive' histone modifications are associated with FLC repression,including histone deacetylation,H3K4 demethylation,histone H3 lysine-9(H3Kg) and H3 lysine-27 (H3K27) methylation,and histone arginine methylation.In addition,recent studies have revealed that Polycomb group gene-mediated transcriptional-silencing mechanism not only represses FLC expression,but also directly represses FT expression.Regulation of FLC expression provides a paradigm for control of the expression of other developmental genes in plants through chromatin mechanisms.

  9. The epigenetic regulation of cell cycle and chromatin dynamic by sirtuins

    OpenAIRE

    Martínez Redondo, Paloma

    2014-01-01

    Tesi realitzada a l'Institut d'Investigació Biomèdica de Bellvitge (IDIBELL) The chromatin consists of a hierarchical and dynamical structure that is modulated during the different cell cycle stages in order to maintain genome integrity and preserve the genetic information coded in the DNA. The dynamic structure of the chromatin depends on the coordination of the different chromatin remodeling processes: histone modifications, chromatin remodeling enzymes/complexes, DNA methylation and chr...

  10. A model of surfactant-induced surface tension effects on the parenchymal tethering of pulmonary airways.

    Science.gov (United States)

    Fujioka, Hideki; Halpern, David; Gaver, Donald P

    2013-01-18

    We developed a computational model of lung parenchyma, which is comprised of individual alveolar chamber models. Each alveolus is modeled by a truncated octahedron. Considering the force balance between the elastin and collagen fibers laying on the alveolar membrane and the pressures acting on the membrane, we computed the deformations of the parenchyma with a finite element method. We focused on the effect of surfactant on the force of parenchymal tethering an airway. As the lung inflates, the parenchyma becomes stiffer and the tethering force becomes stronger. As the alveolar surfactant concentration is reduced, the lung volume at a fixed alveolar pressure decreases, and thus, the tethering force becomes weaker. The distortion of parenchyma caused by the deformation of an airway extends widely around the airway. The displacement of parenchyma decays with distance from the airway wall, but deviates from the prediction based on a theory for a continuum material. Using results obtained from the present lung parenchyma model, we also developed a simple 1-dimensional model for parenchyma tethering force on an airway, which could be utilized for the analysis of liquid/gas transports in an axis-symmetric elastic airway. The effective shear modulus was calculated from the pressure-volume relation of parenchyma. By manipulating the pressure-volume curve, this simple model may be used to predict the parenchyma tethering force in diseased lungs. PMID:23235110

  11. 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.

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

    Science.gov (United States)

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

    1991-10-01

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

  13. 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

    2016-01-01

    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. PMID:27139377

  14. 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.

  15. Exploration of the Galilean Moons using Electrodynamic Tethers for Propellantless Maneuvers and Self-Powering

    Science.gov (United States)

    Lorenzini, E. C.; Curreli, D.; Zanutto, D.

    2010-01-01

    Recent studies have demonstrated the benefits of using electrodynamic tethers (EDT) for the exploration of the inner region of the Jovian system. Intense planetary magnetic field and reasonable environmental plasma density make the electrodynamic interaction of the conductive tether with the plasmasphere strong. The interaction is responsible for a Lorentz force that can be conveniently used for propellantless maneuvers and extraction of electrical power for on board use. Jupiter and the four Galilean Moons represent an exceptional gravitational environment for the study of the orbital dynamics of an EDT. The dynamics of such a system was analyzed using a 3-body model, consisting of the planet plus one of its moons (Io in this work) and the EDT itself. New and interesting features appear, like for example the possibility to place the tether in equilibrium with respect to a frame co-rotating with the moon at points that do not coincide with the classical Lagrangian points for non-null electrodynamic forces.

  16. Diamond surface functionalization with biomimicry – Amine surface tether and thiol moiety for electrochemical sensors

    International Nuclear Information System (INIS)

    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

  17. Sliding tethered ligands add topological interactions to the toolbox of ligand-receptor design

    Science.gov (United States)

    Bauer, Martin; Kékicheff, Patrick; Iss, Jean; Fajolles, Christophe; Charitat, Thierry; Daillant, Jean; Marques, Carlos M.

    2015-09-01

    Adhesion in the biological realm is mediated by specific lock-and-key interactions between ligand-receptor pairs. These complementary moieties are ubiquitously anchored to substrates by tethers that control the interaction range and the mobility of the ligands and receptors, thus tuning the kinetics and strength of the binding events. Here we add sliding anchoring to the toolbox of ligand-receptor design by developing a family of tethered ligands for which the spacer can slide at the anchoring point. Our results show that this additional sliding degree of freedom changes the nature of the adhesive contact by extending the spatial range over which binding may sustain a significant force. By introducing sliding tethered ligands with self-regulating length, this work paves the way for the development of versatile and reusable bio-adhesive substrates with potential applications for drug delivery and tissue engineering.

  18. Low density aerothermodynamics studies performed by means of the tethered satellite system

    Science.gov (United States)

    Carlomagno, Giovanni M.; De Luca, Luigi; Siemers, Paul M.; Wood, George M., Jr.

    1986-01-01

    Low density gas flow modeling and current ground wind-tunnel technologies are not presently able to produce fully reliable data concerning low density flow regimes. In order to answer some of these issues, the Shuttle Continuous Open Wind Tunnel (SCOWT) program has been proposed, which makes use of the tethered satellite system (TSS). SCOWT's objective is to investigate the energy and momentum transfer between the tethered satellite and its environmental medium within the range of the thermofluid-dynamic conditions experienced by TSS during its atmospheric flights. The feasibility and capability of SCOWT to perform low density aerothermodynamics studies are investigated. Some of the results, obtained by means of a tether simulation program, and the instrumentation and TSS design main requirements to meet SCOWT objectives are described.

  19. Numerical study of rocket upper stage deorbiting using passive electrodynamic tether drag

    Directory of Open Access Journals (Sweden)

    Alexandru IONEL

    2014-12-01

    Full Text Available The purpose of this article is a numerical study of the possibility of deorbiting a rocket upper stage from low Earth orbit at EOM (end of mission by means of passive electrodynamic tether drag. The article is structured as follows: the introduction presents the space debris problem in low Earth orbit and the possible methods of deorbiting spacecraft. The next part of the article describes summarily some space tether applications. The third part of the article presents the principle of operation behind passive electrodynamic tether drag. In the fourth part, this principle is detailed so as to represent the input for a numerical study for the deorbit time when using the passive electrodynamic drag concept as deorbiting application. Lastly, the results are presented and conclusions are drawn.

  20. Modeling and simulations of orbital capture with space tether-net system

    Institute of Scientific and Technical Information of China (English)

    ZHAI Guang; QIU Yue; LIANG Bin; LI Cheng

    2009-01-01

    A new flexible tether-net space robotic system used to capture, space debris is presented in this paper. With a mass point assumption, a dynamic model of the tether-net system was established in orbital frame by applying Lagrange Equations. In order to investigate the net in-plane trajectories after being cast, the noncontrolled R-bar and V-bar captures were simulated with ignoring the out-of-plane libration, and the effect of inplane libration on the trajectories of the capture net was demonstrated by simulation results. With an effort to damp the in-plane libration, the control scheme based on tether tension was investigated, then an integrated control scheme was proposed by introducing thrusters into the system, and the nonlinear close-loop dynamics was linearised by feedforward strategy. Simulation results show that the feedforward controller is effective for inplane libration damping and enables the capture net to track an expected trajectory.

  1. 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.

  2. 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

  3. The Disulfide Bonds within BST-2 Enhance Tensile Strength during Viral Tethering.

    Science.gov (United States)

    Du Pont, Kelly E; McKenzie, Aidan M; Kokhan, Oleksandr; Sumner, Isaiah; Berndsen, Christopher E

    2016-02-16

    Human BST-2/tetherin is a host factor that inhibits the release of enveloped viruses, including HIV-1, HIV-2, and SIV, from the cell surface by tethering viruses to the host cell membrane. BST-2 has an α-helical ectodomain that forms disulfide-linked dimers between two monomers forming a coiled coil. The ectodomain contains three cysteine residues that can participate in disulfide bond formation and are critical for viral tethering. The role of the disulfides in viral tethering is unknown but proposed to be for maintaining the dimer. We explored the role of the disulfides in the structure of BST-2 using experimental, biophysical methods. To understand the role of the disulfides in viral tethering, we used a new approach in viral tethering, steered molecular dynamics. We find that the disulfides coordinate the unfolding of the BST-2 monomers, which adds tensile strength to the coiled coil. Structural differences between oxidized and reduced BST-2 are apparent during unfolding, showing the monomers slide past each other in the absence of the disulfides. We found no evidence to support dissociation of the dimer upon reduction of the disulfide bonds. Moreover, the structure of BST-2 in the absence of the disulfides is similar to that of the oxidized form of BST-2, supporting previous X-ray crystallography and cellular work that showed the disulfides are not required for expression of BST-2. These data provide new insights into viral tethering by using novel techniques in the analysis of BST-2 to give amino acid level insight into functions of BST-2. PMID:26789136

  4. 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 Na...... therefore contains more DNA than the 140 base pair "core particle". The natural variation in the bridge length is consistent with the broad bands observed after nuclease digestion of chromatin. Chromatin prepared for EM without fixation containing long 20A to 30A fibers possibly complexed with protein....

  5. Determination of Force Coresponding to Maximal Lactate Steady State in Tethered Swimming

    OpenAIRE

    PAPOTI, MARCELO; VITÓRIO, RICARDO; de Araújo, Gustavo G.; Adelino S R da Silva; SANTHIAGO, VANESSA; MARTINS, LUIZ E. B.; CUNHA, SÉRGIO A.; Gobatto, Claudio A.

    2009-01-01

    The main aim of the present investigation was to verify if the aerobic capacity (AC) measured in tethered swimming corresponds to the maximal lactate steady state (MLSS) and its correlation with 30 min and 400m free style swimming. Twenty-five swimmers were submitted to an incremental tethered swimming test (ITS) with an initial load of 20N and increments of 10N each 3min. After each stage of 3min, the athletes had 30s of interval to blood sample collections that were used to measure blood la...

  6. 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

  7. Tethered satellite system dynamics and control review panel and related activities, phase 3

    Science.gov (United States)

    1991-01-01

    Two major tests of the Tethered Satellite System (TSS) engineering and flight units were conducted to demonstrate the functionality of the hardware and software. Deficiencies in the hardware/software integration tests (HSIT) led to a recommendation for more testing to be performed. Selected problem areas of tether dynamics were analyzed, including verification of the severity of skip rope oscillations, verification or comparison runs to explore dynamic phenomena observed in other simulations, and data generation runs to explore the performance of the time domain and frequency domain skip rope observers.

  8. 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.

  9. 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.

  10. Integrated test rig for tether hardware, real-time simulator and control algorithms: Robust momentum transfer validated

    Science.gov (United States)

    Kruijff, Michiel; van der Heide, Erik Jan

    2001-02-01

    In preparation of the ESA demonstration mission for a tethered sample return capability from ISS, a breadboard test has been performed to validate the robust StarTrack tether dynamics control algorithms in conjunction with the constructed hardware. The proposed mission will use hardware inherited from the YES mission (Kruijff, 1999). A tether spool is holding a 7 kg, 35 km Dyneema tether. A 45 kg re-entry capsule will be ejected by springs and then deployed by gravity gradient. The dynamics are solely controlled by a barberpole type friction brake, similar to the SEDS hardware. This hardware is integrated in a test rig, based on the TMM&M stand, that has been upgraded to accommodate both a Space Part (abruptly applied initial tether deployment speed, fine tensiometer, real-time space tether simulator using the tensiometer measurements as input, take-up roller deploying the tether at a simulator-controlled speed) and a Satellite Part (infra-red beams inside the tether canister, control computer estimating deployed length and required extra braking from the IRED interrupts, `barberpole' friction brake). So the set-up allows for a tether deployment with closed loop control, all governed by a real-time comprehensive tether dynamics simulation. The tether deployment is based on the two-stage StarTrack deployment. This scheme stabilizes the tether at an intermediate vertical stage (with 3 km deployed). When the orbit and landing site have synchronized, a high-speed deployment follows to a large angle. When the fully deployed 35-km tether swings to the vertical at approximately 40 m/s, it is cut at a prefixed time optimized for landing site accuracy. The paper discusses the tests performed to characterize the designed hardware, maturing of the developed algorithms with respect to the hardware noise levels and the difficulties and limitations of the test rig. It is found that the set-up can be applied to a variety of tether pre-mission tests. It is shown that the performed

  11. Chromatin structure analysis based on a hierarchic texture model.

    Science.gov (United States)

    Wolf, G; Beil, M; Guski, H

    1995-02-01

    The quantification of chromatin structures is an important part of nuclear grading of malignant and premalignant lesions. In order to achieve high accuracy, computerized image analysis systems have been applied in this process. Chromatin texture analysis of cell nuclei requires a suitable texture model. A hierarchic model seemed to be most compatible for this purpose. It assumes that texture consists of homogeneous regions (textons). Based on this model, two approaches to texture segmentation and feature extraction were investigated using sections of cervical tissue. We examined the reproducibility of the measurement under changing optical conditions. The coefficients of variations of the texture features ranged from 2.1% to 16.9%. The features were tested for their discriminating capability in a pilot study including 30 cases of cervical dysplasia and carcinoma. The overall classification accuracy reached 65%. This study presents an automated technique for texture analysis that is similar to human perception. PMID:7766266

  12. Proteomics and the genetics of sperm chromatin condensation

    Institute of Scientific and Technical Information of China (English)

    Rafael Oliva; Judit Castillo

    2011-01-01

    Spermatogenesis involves extremely marked cellular, genetic and chromatin changes resulting in the generation of the highly specialized sperm cell. Proteomics allows the identification of the proteins that compose the spermatogenic cells and the study of their function. The recent developments in mass spectrometry (MS) have markedly increased the throughput to identify and to study the sperm proteins. Catalogs of thousands of testis and spermatozoan proteins in human and different model species are becoming available, setting up the basis for subsequent research, diagnostic applications and possibly the future development of specific treatments. The present review intends to summarize the key genetic and chromatin changes at the different stages of spermatogenesis and in the mature sperm cell and to comment on the presently available proteomic studies.

  13. Integrative annotation of chromatin elements from ENCODE data

    OpenAIRE

    Hoffman, Michael M.; Ernst, Jason; Wilder, Steven P.; Kundaje, Anshul; Harris, Robert S.; Libbrecht, Max; Giardine, Belinda; Ellenbogen, Paul M.; Bilmes, Jeffrey A.; Birney, Ewan; Hardison, Ross C.; Dunham, Ian; Kellis, Manolis; Noble, William Stafford

    2012-01-01

    The ENCODE Project has generated a wealth of experimental information mapping diverse chromatin properties in several human cell lines. Although each such data track is independently informative toward the annotation of regulatory elements, their interrelations contain much richer information for the systematic annotation of regulatory elements. To uncover these interrelations and to generate an interpretable summary of the massive datasets of the ENCODE Project, we apply unsupervised learnin...

  14. Unsupervised pattern discovery in human chromatin structure through genomic segmentation

    OpenAIRE

    Hoffman, Michael M.; Buske, Orion J; Wang, Jie; Weng, Zhiping; Bilmes, Jeff A.; Noble, William Stafford

    2012-01-01

    We applied a dynamic Bayesian network method that identifies joint patterns from multiple functional genomics experiments to ChIP-seq histone modification and transcription factor data, and DNaseI-seq and FAIRE-seq open chromatin readouts from the human cell line K562. In an unsupervised fashion, we identified patterns associated with transcription start sites, gene ends, enhancers, CTCF elements, and repressed regions. Software and genome browser tracks are at http://noble.gs.washington.edu/...

  15. Effect of saffron on rat sperm chromatin integrity

    OpenAIRE

    Mohammad Mardani; Ahmad Vaez; Shahnaz Razavi

    2014-01-01

    Background: Currently, relation between reactive oxygen species (ROS) ROS concentration and semen quality was indicated. Saffron has traditionally been not only considered as a food additive but also as a medicinal herb, which has a good antioxidant properties. Objective: The aim of this study was to evaluate the protection potency of saffron and vitamin E on sperm chromatin integrity. Materials and Methods: Thirty adult male Wistar rats divided equally into saffron (100 mg/kg), vitamin E (10...

  16. 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. PMID:26459223

  17. Nucleosome conformational flexibility in experiments with single chromatin fibers

    OpenAIRE

    Sivolob A. V.

    2010-01-01

    Studies on the chromatin nucleosome organization play an ever increasing role in our comprehension of mechanisms of the gene activity regulation. This minireview describes the results on the nucleosome conformational flexibility, which were obtained using magnetic tweezers to apply torsion to oligonucleosome fibers reconstituted on single DNA molecules. Such an approach revealed a new structural form of the nucleosome, the reversome, in which DNA is wrapped in a right-handed superhelix around...

  18. Chromatin-regulating proteins as targets for cancer therapy

    OpenAIRE

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

  19. Chaperone-mediated assembly of centromeric chromatin in vitro

    OpenAIRE

    Furuyama, Takehito; Dalal, Yamini; Henikoff, Steven

    2006-01-01

    Every eukaryotic chromosome requires a centromere for attachment to spindle microtubules for chromosome segregation. Although centromeric DNA sequences vary greatly among species, centromeres are universally marked by the presence of a centromeric histone variant, centromeric histone 3 (CenH3), which replaces canonical histone H3 in centromeric nucleosomes. Conventional chromatin is maintained in part by histone chaperone complexes, which deposit the S phase-limited (H3) and constitutive (H3....

  20. 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 ostatní: GA MŠk(CZ) LC06027; GA MŠk(CZ) LC535 Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : tumour cells * chromatin * radiation Subject RIV: BO - Biophysics

  1. Spermine-induced aggregation of DNA, nucleosome, and chromatin.

    OpenAIRE

    Raspaud, E.; Chaperon, I; Leforestier, A; Livolant, F

    1999-01-01

    We have analyzed the conditions of aggregation or precipitation of DNA in four different states: double-stranded DNA (dsDNA), single-stranded DNA (ssDNA), mononucleosome core particles (NCP), and H1-depleted chromatin fragments (ChF) in the presence of the multivalent cation spermine (4+). In an intermediate regime of DNA concentration, these conditions are identical for the four states. This result demonstrates that the mechanism involved is general from flexible chains to rigid rods and qua...

  2. Chromatin structure in relation to telomere length maintenance in plants

    Czech Academy of Sciences Publication Activity Database

    Fajkus, Jiří; Mozgová, I.; Procházková Schrumpfová, P.; Majerová, E.; Fojtová, M.

    Zürich, 2009. s. 1. [European Workshop on Plant Chromatin. 03.09.2009-04.09.2009, Zürich] R&D Projects: GA ČR(CZ) GD204/08/H054; GA ČR(CZ) GA204/08/1530; GA MŠk(CZ) LC06004 Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : telomere * HMGB1 protein * DNA methylation Subject RIV: BO - Biophysics

  3. Transcription within Condensed Chromatin: Steric Hindrance Facilitates Elongation

    OpenAIRE

    Bécavin, Christophe; Barbi, Maria; Victor, Jean-Marc; Lesne, Annick

    2010-01-01

    During eukaryotic transcription, RNA-polymerase activity generates torsional stress in DNA, having a negative impact on the elongation process. Using our previous studies of chromatin fiber structure and conformational transitions, we suggest that this torsional stress can be alleviated, thanks to a tradeoff between the fiber twist and nucleosome conformational transitions into an activated state named “reversome”. Our model enlightens the origin of polymerase pauses, and leads to the counter...

  4. Structural plasticity of single chromatin fibers revealed by torsional manipulation

    OpenAIRE

    Bancaud, Aurelien; Silva, Natalia Conde e; Barbi, Maria; Wagner, Gaudeline; Allemand, Jean-Francois; Mozziconacci, Julien; Lavelle, Christophe; Croquette, Vincent; Victor, Jean-Marc; Prunell, Ariel; Viovy, Jean-Louis

    2007-01-01

    Magnetic tweezers are used to study the mechanical response under torsion of single nucleosome arrays reconstituted on tandem repeats of 5S positioning sequences. Regular arrays are extremely resilient and can reversibly accommodate a large amount of supercoiling without much change in length. This behavior is quantitatively described by a molecular model of the chromatin 3-D architecture. In this model, we assume the existence of a dynamic equilibrium between three conformations of the nucle...

  5. Quality of histone modification antibodies undermines chromatin biology research

    OpenAIRE

    Goran Kungulovski; Albert Jeltsch

    2015-01-01

    Histone post-translational modification (PTM) antibodies are essential research reagents in chromatin biology. However, they suffer from variable properties and insufficient documentation of quality. Antibody manufacturers and vendors should provide detailed lot-specific documentation of quality, rendering further quality checks by end-customers unnecessary. A shift from polyclonal antibodies towards sustainable reagents like monoclonal or recombinant antibodies or histone binding domains wou...

  6. Chromatin Loops as Allosteric Modulators of Enhancer-Promoter Interactions

    OpenAIRE

    Fudenberg, Geoffrey; Mirny, Leonid A.; Doyle, Boryana G.; Imakaev, Maksim Viktorovich

    2014-01-01

    The classic model of eukaryotic gene expression requires direct spatial contact between a distal enhancer and a proximal promoter. Recent Chromosome Conformation Capture (3C) studies show that enhancers and promoters are embedded in a complex network of looping interactions. Here we use a polymer model of chromatin fiber to investigate whether, and to what extent, looping interactions between elements in the vicinity of an enhancer-promoter pair can influence their contact frequency. Our equi...

  7. Changes in chromatin state in donors subjected to physical stress

    OpenAIRE

    Shckorbatov, Yuriy; Samokhvalov, Valeriy; Bevziuk, Dariya; Kovaliov, Maxim

    2009-01-01

    The purpose of the present study is to evaluate changes in chromatin of human buccal epithelium under the influence of stressing factor - dosed physical activity. Investigations were performed in a group of students (13 men) of age 19-23. Cells were stained on a slide by a 2% orcein solution in 45% acetic acid during 1 h. The following physiological indexes were determined: arterial blood pressure, pulse frequency, and frequency of breathing. The physical stress produced by the dosed physical...

  8. 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. PMID:662693

  9. Radiosensitivity: a role of ATM in chromatin modification

    International Nuclear Information System (INIS)

    Chromatin architecture plays an important role in DNA-template based processes, including transcription, DNA damage repair, replication, and apoptosis. Post-translational modification of histones and non-histone proteins through actions of histone acetyltransferase (HAT) and histone deacetylase (HDAC) regulates chromatin conformation, resulting in the control of accessibility of proteins to target sites. Some of these proteins are involved in cell cycle regulation and DNA damage repair process (ie. Rb, E2F1, p21, p53 and BRCA 1 and 2). However, the mechanism underlying the role of chromatin modification on cellular intrinsic radiation sensitivity is poorly understood. Ataxia-telangiectasia mutated (ATM), the product of the gene mutated in cells from patients with the radiation sensitivity syndrome of ataxia-telangiectasia, has been shown to be involved in multiple DNA damage-induced signal transduction pathways. Previously, we have observed that ATM interacts with histone deacetylase HDAC1 both in vivo and in vitro and its complex exhibits deacetylase activity in response to ionizing radiation. Further studies have suggested that ATM is involved in the regulation of p53 via post-translational modification. Using isogenic AT cell lines, which show radiation sensitivity differences (Do 0.7 and 1.4 Gy), we performed microarray analyses of gene expression at various intervals following irradiation. These data provide evidence for distinctive ATM-dependent or -independent radiation-mediated gene regulation patterns

  10. Novel chromatin texture features for the classification of pap smears

    Science.gov (United States)

    Bejnordi, Babak E.; Moshavegh, Ramin; Sujathan, K.; Malm, Patrik; Bengtsson, Ewert; Mehnert, Andrew

    2013-03-01

    This paper presents a set of novel structural texture features for quantifying nuclear chromatin patterns in cells on a conventional Pap smear. The features are derived from an initial segmentation of the chromatin into bloblike texture primitives. The results of a comprehensive feature selection experiment, including the set of proposed structural texture features and a range of different cytology features drawn from the literature, show that two of the four top ranking features are structural texture features. They also show that a combination of structural and conventional features yields a classification performance of 0.954±0.019 (AUC±SE) for the discrimination of normal (NILM) and abnormal (LSIL and HSIL) slides. The results of a second classification experiment, using only normal-appearing cells from both normal and abnormal slides, demonstrates that a single structural texture feature measuring chromatin margination yields a classification performance of 0.815±0.019. Overall the results demonstrate the efficacy of the proposed structural approach and that it is possible to detect malignancy associated changes (MACs) in Papanicoloau stain.

  11. High sperm chromatin stability in semen with high viscosity.

    Science.gov (United States)

    Gonzales, G F; Sánchez, A

    1994-01-01

    This study was designed to determine the effects of high semen viscosity on sperm chromatin stability. Semen samples obtained from men with normal and high viscosity were studied. Sperm chromatin stability was tested by exposure to sodium dodecyl sulfate (SDS) only and SDS together with a zinc-chelating agent, disodium ethylene diamine tetraacetate (SDS+EDTA). After SDS incubation, stable sperm was 61.36 +/- 3.0 and 54.71 +/- 3.42% for normal and high semen viscosity, respectively (P:NS), and after SDS+EDTA, it was further reduced to 12.48 +/- 0.99% in semen samples with normal consistency and in a less magnitude in semen samples with high viscosity (25.6 +/- 5.2). Comparing values obtained in SDS+EDTA, a high sperm stability was observed in samples with hyperviscosity (p hyperviscosity is associated with a high sperm chromatin stability in situations when a zinc-chelating agent is present. PMID:8122934

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

    Directory of Open Access Journals (Sweden)

    Ivo A. Hendriks

    2015-03-01

    Full Text Available Small ubiquitin-like modifiers play critical roles in the DNA damage response (DDR. To increase our understanding of SUMOylation in the mammalian DDR, we employed a quantitative proteomics approach in order to identify dynamically regulated SUMO-2 conjugates and modification sites upon treatment with the DNA damaging agent methyl methanesulfonate (MMS. We have uncovered a dynamic set of 20 upregulated and 33 downregulated SUMO-2 conjugates, and 755 SUMO-2 sites, of which 362 were dynamic in response to MMS. In contrast to yeast, where a response is centered on homologous recombination, we identified 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.

  13. 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

  14. 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.; Mann, M; Knippers, R; Gruss, C

    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...

  15. Rupture force of cell adhesion ligand tethers modulates biological activities of a cell-laden hydrogel.

    Science.gov (United States)

    Lee, Min Kyung; Park, Jooyeon; Wang, Xuefeng; Roein-Peikar, Mehdi; Ko, Eunkyung; Qin, Ellen; Lee, Jonghwi; Ha, Taekjip; Kong, Hyunjoon

    2016-04-01

    Recent efforts to design a synthetic extracellular matrix for cell culture, engineering, and therapies greatly contributed to addressing biological roles of types and spatial organization of cell adhesion ligands. It is often suggested that ligand-matrix bond strength is another path to regulate cell adhesion and activities; however tools are lacking. To this end, this study demonstrates that a hydrogel coupled with integrin-binding deoxyribonucleic acid (DNA) tethers with pre-defined rupture forces can modulate cell adhesion, differentiation, and secretion activities due to the changes in the number and, likely, force of cells adhered to a gel. The rupture force of DNA tethers was tuned by altering the spatial arrangement of matrix-binding biotin groups. The DNA tethers were immobilized on a hydrogel of alginate grafted with biotin using avidin. Mesenchymal stem cells showed enhanced adhesion, neural differentiation, and paracrine secretion when cultured on the gel coupled with DNA tethers with higher rupture forces. Such innovative cell-matrix interface engineering would be broadly useful for a series of materials used for fundamental and applied studies on biological cells. PMID:26912186

  16. Activation and routing of membrane-tethered prohormone convertases 1 and 2.

    Science.gov (United States)

    Bruzzaniti, A; Marx, R; Mains, R E

    1999-08-27

    Many peptide hormones and neuropeptides are processed by members of the subtilisin-like family of prohormone convertases (PCs), which are either soluble or integral membrane proteins. PC1 and PC2 are soluble PCs that are primarily localized to large dense core vesicles in neurons and endocrine cells. We examined whether PC1 and PC2 were active when expressed as membrane-tethered proteins, and how tethering to membranes alters the biosynthesis, enzymatic activity, and intracellular routing of these PCs. PC1 and PC2 chimeras were constructed using the transmembrane domain and cytoplasmic domain of the amidating enzyme, peptidylglycine alpha-amidating monooxygenase (PAM). The membrane-tethered PCs were rerouted from large dense core vesicles to the Golgi region. In addition, the chimeras were transiently expressed at the cell surface and rapidly internalized to the Golgi region in a fashion similar to PAM. Membrane-tethered PC1 and PC2 exhibited changes in pro-domain maturation rates, N-glycosylation, and in the pH and calcium optima required for maximal enzymatic activity against a fluorogenic substrate. In addition, the PC chimeras efficiently cleaved endogenous pro-opiomelanocortin to the correct bioactive peptides. The PAM transmembrane domain/cytoplasmic domain also prevented stimulated secretion of pro-opiomelanocortin products in AtT-20 cells. PMID:10455138

  17. 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...

  18. 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.

  19. Interplay between native topology and non-native interactions in the folding of tethered proteins

    International Nuclear Information System (INIS)

    We assessed the interplay of native topology and non-native interactions on surface-tethered protein folding via extensive Monte Carlo simulations of a simple lattice model. In particular, we investigated the thermodynamics and kinetics of protein-like sequences enclosing different amounts of non-native interactions to protein energetics, and which were designed to fold to distinct native topologies. Our results show that the high-contact order (CO) structure renders a folding transition that is robust to (external) steric constraints and non-native interactions. On the other hand, the folding process of the simple low-CO topology can be easily hampered by the presence of a nearby chemically inert plane. In this case, if non-native interactions are highly conspicuous during folding they can actually drive chain collapse into a very native-like trapped state, which impedes the formation of the native structure. The analysis of folding kinetics reveals that the empirical correlation between folding rate and CO may not apply to surface-tethered protein folding. Indeed, results reported here show that depending on the native environment of the tethered chain terminus the folding rate of a low-CO topology can become so drastically small that the high-CO topology actually folds faster under the same conditions. We predict that complex topologies are more likely to conserve their bulk folding mechanism upon surface tethering. (paper)

  20. Curvature sorting of proteins on a cylindrical lipid membrane tether connected to a reservoir

    Science.gov (United States)

    Singh, Pankaj; Mahata, Paritosh; Baumgart, Tobias; Das, Sovan Lal

    2012-05-01

    Membrane curvature of a biological cell is actively involved in various fundamental cell biological functions. It has been discovered that membrane curvature and binding of peripheral membrane proteins follow a symbiotic relationship. The exact mechanism behind this interplay of protein binding and membrane curvature has not yet been properly understood. To improve understanding of the mechanism, we study curvature sorting of proteins in a model system consisting of a tether pulled from a giant unilamellar vesicle using mechanical-thermodynamic models. The concentration of proteins bound to the membrane changes significantly due to curvature. This has also been observed in experiments by other researchers. We also find that there is a phase transition based on protein concentration and we discuss the coexistence of phases and stability of solutions. Furthermore, when sorting is favorable, the increase in protein concentration stabilizes the tether in the sense that less pulling force is required to maintain the tether. A similar mechanism may be in place, when motor proteins pull tethers from donor membranes.

  1. New amidines from intramolecular cyclization in triflic acid of nitroketene aminals with a tethered phenyl ring

    Indian Academy of Sciences (India)

    Soro Yaya; Bamba Fanté; Siaka Sorho; Coustard Jean-Marie; Adima A Augustin

    2007-05-01

    Nitroketene aminals with a tethered phenyl group underwent an intramolecular cyclization in trifluoromethanesulfonic acid to afford the corresponding N-(3-ethyl-hydrohydroxyiminobenzocycloalkenylidene) methylamine trifluoromethanesulfonate. The yields were fair to good excepted for the starting compound 1-[N-ethyl-N-(2-phenylethyl)amino]-1-methylamino-2-nitroethene.

  2. Mono- and bis(pyrrolo)tetrathiafulvalene derivatives tethered to C60

    DEFF Research Database (Denmark)

    Vico Solano, Marta; Della Pia, Eduardo Antonio; Jevric, Martyn; Schubert, Christina; Wang, Xintai; van der Pol, Cornelia; Kadziola, Anders; Nørgaard, Kasper; Guldi, Dirk M.; Nielsen, Mogens Brøndsted; Jeppesen, Jan Oskar

    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...

  3. High-Voltage Tethers For Enhanced Particle Scattering In Van Allen Belts

    Science.gov (United States)

    Mirnov, Vladimir; Ü, Defne; Danilov, Valentin

    1996-11-01

    New applications of space tethers (HVTSS) are discussed in relation with the ideafootnote Yu.V.Vasilyev, V.V.Danilov, Physics-Doklady, (1995) 342, 5. of an active experiment at the Earth's radiation belts. Two conducting strings are supposed to be tethered between the main satellite and two small subsatellites flying through the ERB. A large potential difference ~1MV is applied between the tethers by means of a generator carried on the main satellite. The tethers effectively scatter the high energy particles into loss cone, providing a control of particle life time in ERB. The rigorous theory of the sheath layer formed by relatively cold plasma is developed for both DC and AC regimes yielding an electric field profile, which is then used for the treatment of the scattering problem. With the help of the Fokker-Planck equation, the average rate of particle losses, normalized per 1 km of the theter's length is found to be: (2.5 div 14)× 10^16 sec-1km-1 for electron belts and 1.8× 10^14div 2.5× 10^20 sec-1km-1 for proton belts. New active experiments in ERB become possible under the joint realization of HVTSS and HAARPfootnote D.Papadopoulos, P.Bernhardt et al. A Joint Program of Phillips Lab and the Office of Naval Research, June, 1995 projects.

  4. Synthetic Studies to Lyngbouilloside: A Phosphate Tether-Mediated Synthesis of the Macrolactone Core

    Science.gov (United States)

    Chegondi, Rambabu

    2015-01-01

    A concise synthetic pathway to the originally assigned structure of lyngbouilloside macrolactone (3) is reported. The core macrocycle 3 was synthesized via a phosphate tether-mediated, one-pot, sequential RCM/CM/chemoselective hydrogenation reaction, Roskamp homologation, and a high yielding Boeckman acylketene cyclization. PMID:26388654

  5. 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.

  6. Vascular gene transfer from metallic stent surfaces using adenoviral vectors tethered through hydrolysable cross-linkers.

    Science.gov (United States)

    Fishbein, Ilia; Forbes, Scott P; Adamo, Richard F; Chorny, Michael; Levy, Robert J; Alferiev, Ivan S

    2014-01-01

    In-stent restenosis presents a major complication of stent-based revascularization procedures widely used to re-establish blood flow through critically narrowed segments of coronary and peripheral arteries. Endovascular stents capable of tunable release of genes with anti-restenotic activity may present an alternative strategy to presently used drug-eluting stents. In order to attain clinical translation, gene-eluting stents must exhibit predictable kinetics of stent-immobilized gene vector release and site-specific transduction of vasculature, while avoiding an excessive inflammatory response typically associated with the polymer coatings used for physical entrapment of the vector. This paper describes a detailed methodology for coatless tethering of adenoviral gene vectors to stents based on a reversible binding of the adenoviral particles to polyallylamine bisphosphonate (PABT)-modified stainless steel surface via hydrolysable cross-linkers (HC). A family of bifunctional (amine- and thiol-reactive) HC with an average t1/2 of the in-chain ester hydrolysis ranging between 5 and 50 days were used to link the vector with the stent. The vector immobilization procedure is typically carried out within 9 hr and consists of several steps: 1) incubation of the metal samples in an aqueous solution of PABT (4 hr); 2) deprotection of thiol groups installed in PABT with tris(2-carboxyethyl) phosphine (20 min); 3) expansion of thiol reactive capacity of the metal surface by reacting the samples with polyethyleneimine derivatized with pyridyldithio (PDT) groups (2 hr); 4) conversion of PDT groups to thiols with dithiothreitol (10 min); 5) modification of adenoviruses with HC (1 hr); 6) purification of modified adenoviral particles by size-exclusion column chromatography (15 min) and 7) immobilization of thiol-reactive adenoviral particles on the thiolated steel surface (1 hr). This technique has wide potential applicability beyond stents, by facilitating surface engineering of

  7. Dynamics and Power Generation Potential from a Tethered Kite Moving in a Horizontal Flightpath

    Science.gov (United States)

    Gavi, Glenn Romo

    Tethered-wing power systems are a viable possibility for collecting energy from stronger, more consistent winds found in the upper regions of the atmosphere where conventional wind turbines are incapable of reaching. To date, all of the tethered-wing systems fly with the tether oriented down-wind of the ground attachment point. Examined here are the dynamics and performance of a novel system where the tether is oriented both upwind and downwind of the ground attachment point during normal operation of the device. Certain prototypes built by Makani and Ampyx Power are considered to have motions analogous to the motions of the blade tips on conventional horizontal-axis wind turbines. If true, this system has motions that are analogous to conventional vertical-axis wind turbines. The system has a ground-based generator which is mechanical coupled to the aircraft and energy is generated on the reel-out phase of each cycle while a smaller amount of energy is consumed during the reel-in phase of each cycle. A simple model was developed which captures the dominant dynamics of this system and shows, via simulation, that the proposed system is viable and capable of stable and unstable periodic motions with a simulated closed-loop tether tension controller or a simple open loop reel-rate controller. In addition, it is capable of motions which produce net positive power. The small system examined, where parameter optimization was not performed, predicts an average cycle power of more than 500 watts in a 10 m/s wind.

  8. Dynamics of a flexible tethered satellite system utilising various materials for coplanar and non-coplanar models

    Science.gov (United States)

    Hong, Aaron Aw Teik; Varatharajoo, Renuganth

    2015-08-01

    This paper discusses the development of mathematical models for a flexible tethered satellite system (TSS) in both planar and co-planar states. The flexible tethered satellite system consists of three rigid bodies with two flexible tethers, each connecting two rigid bodies with one located in the centre and serving as the mothership. The TSS motion includes tether deformations, rotational dynamics, and orbital mechanics. The three materials that are possible to be used for a space tether are tungsten wire, Spectra-2000, and diamond; it should be noted that the diamond used here is in a form of a nanotube thread. The tether will undergo a spinning motion as well in the motorised option. In addition, the air drag perturbation is also considered since the entire TSS is flown around the Low Earth Orbit (LEO), where the air-drag perturbation is dominant. A survival analysis was then performed for planar and non-coplanar models in order to establish a dynamic performance envelope with respect to the tether's tension at different altitudes under the air-drag perturbation. The proposed models were treated numerically and analysed accordingly. Then a comparison study between the coplanar and non-coplanar models were conducted and the difference in their performances was observed and discussed. Although all materials have their own safe operation boundaries, the flexible TSS using tungsten shows a better dynamic performance than the other TSS options in a non-coplanar model.

  9. Complexity of chromatin folding is captured by the strings and binders switch model.

    Science.gov (United States)

    Barbieri, Mariano; Chotalia, Mita; Fraser, James; Lavitas, Liron-Mark; Dostie, Josée; Pombo, Ana; Nicodemi, Mario

    2012-10-01

    Chromatin has a complex spatial organization in the cell nucleus that serves vital functional purposes. A variety of chromatin folding conformations has been detected by single-cell imaging and chromosome conformation capture-based approaches. However, a unified quantitative framework describing spatial chromatin organization is still lacking. Here, we explore the "strings and binders switch" model to explain the origin and variety of chromatin behaviors that coexist and dynamically change within living cells. This simple polymer model recapitulates the scaling properties of chromatin folding reported experimentally in different cellular systems, the fractal state of chromatin, the processes of domain formation, and looping out. Additionally, the strings and binders switch model reproduces the recently proposed "fractal-globule" model, but only as one of many possible transient conformations. PMID:22988072

  10. 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.

  11. Dynamics of an Electrodynamic Tether System in a Varying Space-Plasma Environment

    Science.gov (United States)

    Janeski, John A.

    Electrodynamic tethers have a wide range of proposed applications in the fields of satellite propulsion and space plasma research. The fundamental purpose of this dissertation is to improve the understanding of the behavior of an electrodynamic tether (EDT) system in Earth's ionosphere. An electrodynamic tether system consists of two satellites connected by a long tether that generates current to produce either power or thrust via the system's electromagnetic interaction with the space environment. Previous electrodynamic tether investigations decouple the interaction between the tether and the constantly changing plasma environment. The limiting factor inhibiting the development of a full system model that has an accurate characterization of the tether/plasma interaction is that the understanding of that interaction is not well developed over a wide range of system parameters. The EDT system model developed in this study uses a high fidelity dynamics model that includes a tether current described by an analytical current collection model whose plasma parameters are determine by the International Reference Ionosphere. It is first shown that new instabilities are induced in the system dynamics under a basic analytical current model versus a constant current model. A 2-D3v Particle-in-Cell (PIC) code has been developed to study the plasma dynamics near a positively charged EDT system end-body and their impact on the current collected. Simulations are run over a range of system parameters that occur throughout a LEO orbit. The azimuthal current structures observed during the TSS-1R mission are found to enhance the current collected by the satellite when the magnetic field is slightly off of perpendicular to the orbital velocity. When the in-plane component of the magnetic field becomes large, the electrons are not able to easily cross the field lines causing plasma lobes form above and below the satellite. The lobes limit the current arriving to the satellite and also

  12. 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 gu...

  13. The Proteomic Investigation of Chromatin Functional Domains Reveals Novel Synergisms among Distinct Heterochromatin Components*

    OpenAIRE

    Soldi, Monica; Bonaldi, Tiziana

    2013-01-01

    Chromatin is a highly dynamic, well-structured nucleoprotein complex of DNA and proteins that controls virtually all DNA transactions. Chromatin dynamicity is regulated at specific loci by the presence of various associated proteins, histones, post-translational modifications, histone variants, and DNA methylation. Until now the characterization of the proteomic component of chromatin domains has been held back by the challenge of enriching distinguishable, homogeneous regions for subsequent ...

  14. A chromatin activity based chemoproteomic approach reveals a transcriptional repressome for gene-specific silencing

    OpenAIRE

    Liu, Cui; Yu, Yanbao; Liu, Feng; Wei, Xin; Wrobel, John A; Gunawardena, Harsha P.; Zhou, Li; Jin, Jian; Chen, Xian

    2014-01-01

    Immune cells develop endotoxin tolerance (ET) after prolonged stimulation. ET increases the level of a repression mark H3K9me2 in the transcriptional-silent chromatin specifically associated with pro-inflammatory genes. However, it is not clear what proteins are functionally involved in this process. Here we show that a novel chromatin activity based chemoproteomic (ChaC) approach can dissect the functional chromatin protein complexes that regulate ET-associated inflammation. Using UNC0638 th...

  15. A critical role for chromatin in mounting a synergistic transcriptional response to GAL4-VP16.

    OpenAIRE

    Chang, C; Gralla, J D

    1994-01-01

    The role of chromatin in mounting a synergistic transcriptional response to GAL4-VP16 was investigated. Strong synergy was observed when chromatin templates were used in vitro. The synergy was severely reduced when naked DNA templates were transcribed. In vivo synergy was strong when nonreplicating templates were used. However, the use of replicating templates, which involved transient disruptions of chromatin, led to strong reductions in synergy. In both of these low-synergy responses, trans...

  16. Chromatin immunoprecipitation cloning reveals rapid evolutionary patterns of centromeric DNA in Oryza species

    OpenAIRE

    Lee, Hye-Ran; Zhang, Wenli; Langdon, Tim; Jin, Weiwei; Yan, Huihuang; Cheng, Zhukuan; Jiang, Jiming

    2005-01-01

    The functional centromeres of rice (Oryza sativa, AA genome) chromosomes contain two key DNA components: the CRR centromeric retrotransposons and a 155-bp satellite repeat, CentO. However, several wild Oryza species lack the CentO repeat. We developed a chromatin immunoprecipitation-based technique to clone DNA fragments derived from chromatin containing the centromeric histone H3 variant CenH3. Chromatin immunoprecipitation cloning was carried out in the CentO-less species Oryza rhizomatis (...

  17. Biochemical and structural characterization of Cren7, a novel chromatin protein conserved among Crenarchaea

    OpenAIRE

    Guo, Li; Feng, Yingang; Zhang, Zhenfeng; Yao, Hongwei; Luo, Yuanming; Wang, Jinfeng; Huang, Li

    2007-01-01

    Archaea contain a variety of chromatin proteins consistent with the evolution of different genome packaging mechanisms. Among the two main kingdoms in the Archaea, Euryarchaeota synthesize histone homologs, whereas Crenarchaeota have not been shown to possess a chromatin protein conserved at the kingdom level. We report the identification of Cren7, a novel family of chromatin proteins highly conserved in the Crenarchaeota. A small, basic, methylated and abundant protein, Cren7 displays a high...

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

    OpenAIRE

    Monica Soldi; Alessandro Cuomo; Michael Bremang; Tiziana Bonaldi

    2013-01-01

    Chromatin is a highly structured nucleoprotein complex made of histone proteins and DNA that controls nearly all DNA-dependent processes. Chromatin plasticity is regulated by different associated proteins, post-translational modifications on histones (hPTMs) and DNA methylation, which act in a concerted manner to enforce a specific “chromatin landscape”, with a regulatory effect on gene expression. Mass Spectrometry (MS) has emerged as a powerful analytical strategy to detect histone PTMs, re...

  19. Evolution of histone 2A for chromatin compaction in eukaryotes

    OpenAIRE

    Macadangdang, Benjamin R; Oberai, Amit; Spektor, Tanya; Campos, Oscar A; Sheng, Fang; Carey, Michael F.; Vogelauer, Maria; Kurdistani, Siavash K

    2014-01-01

    eLife digest There are up to three meters of DNA in a human cell. To fit this length into the cell's nucleus in an organized manner, DNA is wrapped around proteins called histones and then tightly packaged to form a structure called chromatin. The interaction between the histones and the DNA is helped by certain amino acids on the surface of the histones fitting snugly into the DNA molecule. Plants and animals have genomes that are significantly larger than those of single-celled organisms. H...

  20. Effects of nuclear isolation on psoralen affinity for chromatin

    International Nuclear Information System (INIS)

    We have tested the effects of nuclear isolation on intercalation of TMP (a psoralen) at specific sequences and in total DNA of cultured human cells. DNA in nuclei photobound about 20% more TMP than in cells and about 10% as much as purified DNA. In contrast, a transcribed ras gene and a randomly selected polymorphic sequence each bound about 20% more TMP than total DNA in cells. However, in nuclei, as in purified DNA, both sequences were just as sensitive as total DNA. Apparently, chromatin in cells exists within diverse TMP-binding environments and some of this diversity was lost upon nuclear isolation

  1. Chromatin immunoselection defines a TAL-1 target gene.

    OpenAIRE

    Cohen-Kaminsky, S; Maouche-Chrétien, L; Vitelli, L; Vinit, M A; Blanchard, I; M. Yamamoto; Peschle, C; Roméo, P H

    1998-01-01

    Despite the major functions of the basic helix-loop-helix transcription factor TAL-1 in hematopoiesis and T-cell leukemogenesis, no TAL-1 target gene has been identified. Using immunoprecipitation of genomic fragments bound to TAL-1 in the chromatin of murine erythro-leukemia (MEL) cells, we found that 10% of the immunoselected fragments contained a CAGATG or a CAGGTG E-box, followed by a GATA site. We studied one of these fragments containing two E-boxes, CAGATG and CAGGTC, followed by a GAT...

  2. 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.

  3. Condensation of interphase chromatin in nuclei of synchronized chinese hamster ovary (CHO-K1) cells.

    Science.gov (United States)

    Gacsi, Mariann; Nagy, Gabor; Pinter, Gabor; Basnakian, Alexei G; Banfalvi, Gaspar

    2005-01-01

    Reversibly permeabilized cells have been used to visualize interphase chromatin structures in the presence and absence of biotinylated nucleotides. By reversing permeabilization, it was possible to confirm the existence of a flexible chromatin folding pattern through a series of transient geometric forms such as supercoiled, circular forms, chromatin bodies, thin and thick fibers, and elongated chromosomes. Our results show that the incorporation of biotin-11-dUTP interferes with chromatin condensation, leading to the accumulation of decondensed chromatin structures. Chromatin condensation without nucleotide incorporation was also studied in cell populations synchronized by centrifugal elutriation. After reversal of permeabilization, nuclei were isolated and chromatin structures were visualized after DAPI staining by fluorescent microscopy. Decondensed veil-like structures were observed in the early S phase (at an average C-value of 2.21), supercoiled chromatin later in the early S (2, 55 C), fibrous structures in the early mid S phase (2, 76 C), ribboned structures in the mid-S phase (2, 98 C), continuous chromatin strings later in the mid-S phase (3,28), elongated prechromosomes in the late S-phase (3, 72 C), precondensed chromosomes at the end and after the S phase (3, 99 C). Fluorescent microscopy revealed that neither interphase nor metaphase chromosomes are separate entities but form a linear array arranged in a semicircle. Linear arrangement was confirmed by computer image analysis. PMID:15684719

  4. Erythroid-specific gene chromatin has an altered association with linker histones.

    OpenAIRE

    Ridsdale, J A; Rattner, J.B.; Davie, J R

    1988-01-01

    The chromatin of several genes was assayed for sensitivity to DNAase I and for solubility as polynucleosomes in 0.15 M NaCl. The degree of solubility of chromatin fragments as polynucleosomes in 0.15 M NaCl correlates well with the sensitivity to DNAase I for several genes. Chromatin of repressed, housekeeping and erythroid-specific genes can be distinguished as distinct groups by the degree to which they display these properties. NaCl precipitation of chromatin fragments stripped and then re...

  5. Identification of potential nuclear reprogramming and differentiation factors by a novel selection method for cloning chromatin-binding proteins

    Institute of Scientific and Technical Information of China (English)

    LiuWang; AihuaZheng; LingYi; ChongrenXu; MingxiaoDing; HongkuiDeng

    2005-01-01

    Nuclear reprogramming is critical for animal cloning and stem cell creation through nuclear transfer, which requires extensive remodeling of chromosomal architecture involving dramatic changes in chromatin-binding proteins. To understand the mechanism of nuclear reprogramming, it is critical to identify chromatin-binding factors specify the reprogramming process. In this report, we have developed a high-throughput selection method, based on T7 phage display and chromatin immunoprecipitation, to isolate chromatin-binding factors expressed in mouse embryonic stem cells using primary mouse embryonic fibroblast chromatin. Seven chromatin-binding proteins have been isolated by this method. We have also isolated several chromatin-binding proteins involved in hepatocyte differentiation. Our method provides a powerful tool to rapidly and selectively identify chromatin-binding proteins. The method can be used to study epigenetic modification of chromatin during nuclear reprogramming, cell differentiation, and transdifferentiation.

  6. Multibody dynamics driving GNC and system design in tethered nets for active debris removal

    Science.gov (United States)

    Benvenuto, Riccardo; Lavagna, Michèle; Salvi, Samuele

    2016-07-01

    Debris removal in Earth orbits is an urgent issue to be faced for space exploitation durability. Among different techniques, tethered-nets present appealing benefits and some open points to fix. Former and latter are discussed in the paper, supported by the exploitation of a multibody dynamics tool. With respect to other proposed capture mechanisms, tethered-net solutions are characterised by a safer capturing distance, a passive angular momentum damping effect and the highest flexibility to unknown shape, material and attitude of the target to interface with. They also allow not considering the centre of gravity alignment with thrust axis as a constraint, as it is for any rigid link solution. Furthermore, the introduction of a closing thread around the net perimeter ensures safer and more reliable grasping and holding. In the paper, a six degrees of freedom multibody dynamics simulator is presented: it was developed at Politecnico di Milano - Department of Aerospace Science and Technologies - and it is able to describe the orbital and attitude dynamics of tethered-nets systems and end-bodies during different phases, with great flexibility in dealing with different topologies and configurations. Critical phases as impact and wrapping are analysed by simulation to address the tethered-stack controllability. It is shown how the role of contact modelling is fundamental to describe the coupled dynamics: it is demonstrated, as a major novel contribution, how friction between the net and a tumbling target allows reducing its angular motion, stabilizing the system and allowing safer towing operations. Moreover, the so-called tethered space tug is analysed: after capture, the two objects, one passive and one active, are connected by the tethered-net flexible link, the motion of the system being excited by the active spacecraft thrusters. The critical modes prevention during this phase, by means of a closed-loop control synthesis is shown. Finally, the connection between

  7. Alternative Treatments

    Science.gov (United States)

    ... Find your chapter: search by state Home > Alzheimer's Disease > Treatments > Alternative Treatments Overview What Is Dementia? What Is Alzheimer's? Younger/Early Onset Facts and Figures Know the 10 Signs Stages Inside the Brain: ...

  8. Estimation of added-mass and damping coefficients of a tethered spherical float using potential flow theory

    Digital Repository Service at National Institute of Oceanography (India)

    Vethamony, P.; Chandramohan, P.; Sastry, J.S.; Narasimhan, S.

    Added-mass (alpha) and damping coefficients (beta) of a tethered spherical float, undergoing oscillatory motion in sinusoidal waves, have been derived from the motion generated velocity potential for one degree-of-freedom (surge) using potential...

  9. H2B ubiquitylation is part of chromatin architecture that marks exon-intron structure in budding yeast

    LENUS (Irish Health Repository)

    Shieh, Grace S.

    2011-12-22

    Abstract Background The packaging of DNA into chromatin regulates transcription from initiation through 3\\' end processing. One aspect of transcription in which chromatin plays a poorly understood role is the co-transcriptional splicing of pre-mRNA. Results Here we provide evidence that H2B monoubiquitylation (H2BK123ub1) marks introns in Saccharomyces cerevisiae. A genome-wide map of H2BK123ub1 in this organism reveals that this modification is enriched in coding regions and that its levels peak at the transcribed regions of two characteristic subgroups of genes. First, long genes are more likely to have higher levels of H2BK123ub1, correlating with the postulated role of this modification in preventing cryptic transcription initiation in ORFs. Second, genes that are highly transcribed also have high levels of H2BK123ub1, including the ribosomal protein genes, which comprise the majority of intron-containing genes in yeast. H2BK123ub1 is also a feature of introns in the yeast genome, and the disruption of this modification alters the intragenic distribution of H3 trimethylation on lysine 36 (H3K36me3), which functionally correlates with alternative RNA splicing in humans. In addition, the deletion of genes encoding the U2 snRNP subunits, Lea1 or Msl1, in combination with an htb-K123R mutation, leads to synthetic lethality. Conclusion These data suggest that H2BK123ub1 facilitates cross talk between chromatin and pre-mRNA splicing by modulating the distribution of intronic and exonic histone modifications.

  10. Chromatin Assembly at Kinetochores Is Uncoupled from DNA Replication

    Science.gov (United States)

    Shelby, Richard D.; Monier, Karine; Sullivan, Kevin F.

    2000-01-01

    The specification of metazoan centromeres does not depend strictly on centromeric DNA sequences, but also requires epigenetic factors. The mechanistic basis for establishing a centromeric “state” on the DNA remains unclear. In this work, we have directly examined replication timing of the prekinetochore domain of human chromosomes. Kinetochores were labeled by expression of epitope-tagged CENP-A, which stably marks prekinetochore domains in human cells. By immunoprecipitating CENP-A mononucleosomes from synchronized cells pulsed with [3H]thymidine we demonstrate that CENP-A–associated DNA is replicated in mid-to-late S phase. Cytological analysis of DNA replication further demonstrated that centromeres replicate asynchronously in parallel with numerous other genomic regions. In contrast, quantitative Western blot analysis demonstrates that CENP-A protein synthesis occurs later, in G2. Quantitative fluorescence microscopy and transient transfection in the presence of aphidicolin, an inhibitor of DNA replication, show that CENP-A can assemble into centromeres in the absence of DNA replication. Thus, unlike most genomic chromatin, histone synthesis and assembly are uncoupled from DNA replication at the kinetochore. Uncoupling DNA replication from CENP-A synthesis suggests that regulated chromatin assembly or remodeling could play a role in epigenetic centromere propagation. PMID:11086012

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

    Science.gov (United States)

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

    2014-11-13

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

  12. Chromatin factors affecting DNA repair in mammalian cell nuclei

    International Nuclear Information System (INIS)

    We are investigating chromatin factors that participate in the incision step of DNA repair in eukaryotic cells. Localization of repair activity within nuclei, the stability and extractability of activity, the specificity for recognizing damage in chromatin or purified DNA as substrates are of interest in this investigation of human cells, CHO cells, and their radiation sensitive mutants. We have developed procedures that provide nuclei in which their DNA behaves as a collection of circular molecules. The integrity of the DNA in human nuclei can be maintained during incubation in appropriate buffers for as long as 60 minutes. When cells or nuclei are exposed to uv light prior to incubation, incisions presumably associated with DNA repair can be demonstrated. Incision activity is stable to prior extraction of nuclei with 0.6 M NaCl, which removes many nonhistone proteins. Our studies are consistent with an hypothesis that factors responsible for initiating DNA repair are localized in the nuclear matrix. 18 references, 3 figures

  13. SF3B1 Association with Chromatin Determines Splicing Outcomes

    Directory of Open Access Journals (Sweden)

    Nir Kfir

    2015-04-01

    Full Text Available Much remains unknown concerning the mechanism by which the splicing machinery pinpoints short exons within intronic sequences and how splicing factors are directed to their pre-mRNA targets. One probable explanation lies in differences in chromatin organization between exons and introns. Proteomic, co-immunoprecipitation, and sedimentation analyses described here indicate that SF3B1, an essential splicing component of the U2 snRNP complex, is strongly associated with nucleosomes. ChIP-seq and RNA-seq analyses reveal that SF3B1 specifically binds nucleosomes located at exonic positions. SF3B1 binding is enriched at nucleosomes positioned over short exons flanked by long introns that are also characterized by differential GC content between exons and introns. Disruption of SF3B1 binding to such nucleosomes affects splicing of these exons similarly to SF3B1 knockdown. Our findings suggest that the association of SF3B1 with nucleosomes is functionally important for splice-site recognition and that SF3B1 conveys splicing-relevant information embedded in chromatin structure.

  14. Structure of the Membrane-tethering GRASP Domain Reveals a Unique PDZ Ligand Interaction That Mediates Golgi Biogenesis*

    OpenAIRE

    Truschel, Steven T.; Sengupta, Debrup; Foote, Adam; Heroux, Annie; Macbeth, Mark R.; Linstedt, Adam D.

    2011-01-01

    Biogenesis of the ribbon-like membrane network of the mammalian Golgi requires membrane tethering by the conserved GRASP domain in GRASP65 and GRASP55, yet the tethering mechanism is not fully understood. Here, we report the crystal structure of the GRASP55 GRASP domain, which revealed an unusual arrangement of two tandem PDZ folds that more closely resemble prokaryotic PDZ domains. Biochemical and functional data indicated that the interaction between the ligand-binding pocket of PDZ1 and an...

  15. Differential affinity of mammalian histone H1 somatic subtypes for DNA and chromatin

    Directory of Open Access Journals (Sweden)

    Mora Xavier

    2007-05-01

    Full Text Available Abstract Background Histone H1 is involved in the formation and maintenance of chromatin higher order structure. H1 has multiple isoforms; the subtypes differ in timing of expression, extent of phosphorylation and turnover rate. In vertebrates, the amino acid substitution rates differ among subtypes by almost one order of magnitude, suggesting that each subtype might have acquired a unique function. We have devised a competitive assay to estimate the relative binding affinities of histone H1 mammalian somatic subtypes H1a-e and H1° for long chromatin fragments (30–35 nucleosomes in physiological salt (0.14 M NaCl at constant stoichiometry. Results The H1 complement of native chromatin was perturbed by adding an additional amount of one of the subtypes. A certain amount of SAR (scaffold-associated region DNA was present in the mixture to avoid precipitation of chromatin by excess H1. SAR DNA also provided a set of reference relative affinities, which were needed to estimate the relative affinities of the subtypes for chromatin from the distribution of the subtypes between the SAR and the chromatin. The amounts of chromatin, SAR and additional H1 were adjusted so as to keep the stoichiometry of perturbed chromatin similar to that of native chromatin. H1 molecules freely exchanged between the chromatin and SAR binding sites. In conditions of free exchange, H1a was the subtype of lowest affinity, H1b and H1c had intermediate affinities and H1d, H1e and H1° the highest affinities. Subtype affinities for chromatin differed by up to 19-fold. The relative affinities of the subtypes for chromatin were equivalent to those estimated for a SAR DNA fragment and a pUC19 fragment of similar length. Avian H5 had an affinity ~12-fold higher than H1e for both DNA and chromatin. Conclusion H1 subtypes freely exchange in vitro between chromatin binding sites in physiological salt (0.14 M NaCl. The large differences in relative affinity of the H1 subtypes for

  16. An electronic interface for a fiber optic tethered unmanned underwater vehicle

    Science.gov (United States)

    Sheakoski, J. R.

    1994-04-01

    As the sophistication of acoustic sensor and communication systems related to unmanned underwater vehicles (UUV) has increased, the requirement for greater volume and higher speed data transfers has emerged. Fiber optic technology provides an effective means for high bandwidth communications with a UUV while minimizing weight and space criteria aboard the UUV. Increase in data transmission speed has permitted real time processing of data on the launch platform when using large high powered computing systems. Maximum system reliability at advanced performance levels can also be realized. By designing and developing a full scale system comprised of the UUV, remote control and command platform, and data handling and routing electronics, fiber optic tethered UUV technology was demonstrated in lab field tests. This three year venture culminated in a series of successful in-water tests that proved the feasibility of fiber optic tethered UUV's and warranted the continuation of research on remotely operated UUV's.

  17. Experimental verification of chaotic control of an underactuated tethered satellite system

    Science.gov (United States)

    Pang, Zhaojun; Jin, Dongping

    2016-03-01

    This paper studies chaotic control of a tethered satellite system (TSS) driven only by a momentum-exchange device during its attitude adjustment. In dealing with such the underactuated system, an extended time-delay autosynchronization (ETDAS) is employed to stabilize the chaotic motion to a periodic motion. To obtain the control domains of the ETDAS method, a stability analysis of the controlled tethered satellite system in elliptical orbit is implemented. According to the principle of dynamic similarity, then, ground-based experiment setups are proposed and designed to emulate the in-plane motions of the TSS. Representative experiments are presented to demonstrate the effectiveness of the ETDAS scheme in controlling the chaotic motion of the underactuated TSS.

  18. In Vivo Quantification of Peroxisome Tethering to Chloroplasts in Tobacco Epidermal Cells Using Optical Tweezers.

    Science.gov (United States)

    Gao, Hongbo; Metz, Jeremy; Teanby, Nick A; Ward, Andy D; Botchway, Stanley W; Coles, Benjamin; Pollard, Mark R; Sparkes, Imogen

    2016-01-01

    Peroxisomes are highly motile organelles that display a range of motions within a short time frame. In static snapshots, they can be juxtaposed to chloroplasts, which has led to the hypothesis that they are physically interacting. Here, using optical tweezers, we tested the dynamic physical interaction in vivo. Using near-infrared optical tweezers combined with TIRF microscopy, we were able to trap peroxisomes and approximate the forces involved in chloroplast association in vivo in tobacco (Nicotiana tabacum) and observed weaker tethering to additional unknown structures within the cell. We show that chloroplasts and peroxisomes are physically tethered through peroxules, a poorly described structure in plant cells. We suggest that peroxules have a novel role in maintaining peroxisome-organelle interactions in the dynamic environment. This could be important for fatty acid mobilization and photorespiration through the interaction with oil bodies and chloroplasts, highlighting a fundamentally important role for organelle interactions for essential biochemistry and physiological processes. PMID:26518344

  19. The motion of tethered tug-debris system with fuel residuals

    Science.gov (United States)

    Aslanov, Vladimir S.; Yudintsev, Vadim V.

    2015-10-01

    Active debris removal using a space tug with a tether is one of the promising techniques to decrease the population of large non-functional satellites and orbital stages in near Earth orbits. Properties of debris should be taken into account in the development of the space tugs. In this paper we consider the motion of a debris objects with fuel residuals that can affect the safety of the debris transportation process. The equations of the attitude motion of the tug-debris system in a central gravitational field are derived. Stationary solutions of the equations are found. The system of linearized equations are introduced that can be used for short term analysis. The numerical simulation results are provided that show good accuracy of the linearized equations. Proposed equations can be used to analyze the attitude motion of the tug-debris system and to determine the conventional parameters for safe tethered transportation of space debris.

  20. Multi-mass dynamic model of a variable-length tether used in a high altitude wind energy system

    International Nuclear Information System (INIS)

    Highlights: • A multi-mass dynamics model of a variable length tether has been developed. • The modelling approach enables straightforward description of the aerodynamic drag. • The model is used in high altitude wind energy system control-oriented simulations. • The model accurately describes the shape, forces and vibrations of the tether. - Abstract: This paper presents a multibody approach to dynamics modelling of a variable-length tether moving through air, in a system where an airborne module generates aerodynamic lift and uses the tether to cyclically drive the winch-generator unit fixed on the ground. The rope is modelled as a series of straight, massless, elastic segments with the rope mass fragments lumped to the segment joints. Individual segment length is constant, with the exception of segment being wound out from the winch, while the number of segments is variable. For the segment being wound out, a special modelling approach is derived. The forces acting on the rope are also concentrated at the joints, thus simplifying computations and facilitating rope aerodynamic drag modelling. The proposed tether dynamics model is integrated into the overall model of controlled power production system and verified by computer simulation. The model is compared with two simpler tether dynamics models also proposed in the paper

  1. Tethered Aminohydroxylation: Synthesis of the β-Amino Acid of Microsclerodermins A and B

    OpenAIRE

    Pullin, Robert D. C.; Rathi, Akshat H.; Melikhova, Ekaterina Y.; Winter, Christian; Thompson, Amber L.; Donohoe, Timothy J.

    2013-01-01

    The utility of the tethered aminohydroxylation (TA) has been demonstrated by synthesis of the complex β-amino acid residue of microsclerodermins A and B. The TA provided a regio- and stereoselective functionalization of a complex homoallylic alcohol. The route includes late-stage introduction of the aliphatic side chain via a cuprate addition and cross metathesis, a tactic designed to render the synthesis applicable to other microsclerodermins.

  2. Quantifying interspecific variation in dispersal ability of noctuid moths using an advanced tethered flight technique

    OpenAIRE

    Jones, Hayley B. C.; Lim, Ka S.; Bell, James R.; Hill, Jane K.; Chapman, Jason W.

    2015-01-01

    Abstract Dispersal plays a crucial role in many aspects of species' life histories, yet is often difficult to measure directly. This is particularly true for many insects, especially nocturnal species (e.g. moths) that cannot be easily observed under natural field conditions. Consequently, over the past five decades, laboratory tethered flight techniques have been developed as a means of measuring insect flight duration and speed. However, these previous designs have tended to focus on single...

  3. Tethered capsule endomicroscopy enables less-invasive imaging of gastrointestinal tract microstructure

    OpenAIRE

    Gora, Michalina J.; Sauk, Jenny S.; Carruth, Robert W.; Gallagher, Kevin A.; Suter, Melissa J.; Nishioka, Norman S.; Kava, Lauren E.; Rosenberg, Mireille; Bouma, Brett E.; Tearney, Guillermo J.

    2013-01-01

    Here, we introduce “tethered capsule endomicroscopy,” that involves swallowing an optomechanically-engineered pill that captures cross-sectional, 30 μm (lateral) × 7 μm (axial) resolution, microscopic images of the gut wall as it travels through the digestive tract. Results in human subjects show that this technique rapidly provides three-dimensional, microstructural images of the upper gastrointestinal tract in a simple and painless procedure, opening up new opportunities for screening for i...

  4. Simulation of tethered oligomers in nanochannels using multi-particle collision dynamics

    OpenAIRE

    Raghu, Riyad; Schofield, Jeremy

    2012-01-01

    The effect of a high Reynold's number, pressure-driven flow of a compressible gas on the conformation of an oligomer tethered to the wall of a square-channel is studied under both ideal solvent and poor solvent conditions using a hybrid multiparticle collision dynamics and molecular dynamics algorithm. Unlike previous studies, the flow field contains an elongational component in addition to a shear component as well as fluid slip near the walls and results in a Schmidt number for the polymer ...

  5. Template-Tethered Collagen Mimetic Peptides for Studying Heterotrimeric Triple-Helical Interactions

    OpenAIRE

    Li, Yang; Mo, Xiao; Kim, Daniel; Yu, S. Michael

    2010-01-01

    Collagen mimetic peptides (CMPs) have been used to elucidate the structure and stability of the triple helical conformation of collagen molecules. Although CMP homotrimers have been widely studied, very little work has been reported regarding CMP heterotrimers because of synthetic difficulties. Here we present the synthesis and characterization of homotrimers and ABB type heterotrimers comprising natural and synthetic CMP sequences that are covalently tethered to a template, a tris(2-aminoeth...

  6. Analysis of a tethered stabilized Schmidt telescope asserved to the Space Station

    Science.gov (United States)

    Bertola, F.; Rafanelli, P.; Angrilli, F.; Bianchini, G.; da Forno, R.

    The concept of a Schmidt telescope connected to the Space Station by a 2-10 km long tether is discussed. A mission scenario and the optical characteristics of the telescope are described. A linearized mathematical model is used to study the dynamic behavior of the telescope platform in space. Simulations are conducted to account for environmental perturbations, thermal effects, atmospheric drag, micrometeor impact, and the dynamical response to slewing motion.

  7. Tether radiation in Juno-type and circular-equatorial Jovian orbits

    OpenAIRE

    Sánchez-Torres, Antonio; Sanmartín Losada, Juan Ramón

    2011-01-01

    Wave radiation by a conductor carrying a steady current in both a polar, highly eccentric, low perijove orbit, as in NASA's planned Juno mission, and an equatorial low Jovian orbit (LJO) mission below the intense radiation belts, is considered. Both missions will need electric power generation for scientific instruments and communication systems. Tethers generate power more efficiently than solar panels or radioisotope power systems (RPS). The radiation impedance is required to determin...

  8. Virtual migration in tethered flying monarch butterflies reveals their orientation mechanisms

    OpenAIRE

    Mouritsen, Henrik; Frost, Barrie J.

    2002-01-01

    A newly developed flight simulator allows monarch butterflies to fly actively for up to several hours in any horizontal direction while their fall migratory flight direction can be continuously recorded. From these data, long segments of virtual flight paths of tethered, flying, migratory monarch butterflies were reconstructed, and by advancing or retarding the butterflies' circadian clocks, we have shown that they possess a time-compensated sun compass. Control monarchs on local time fly app...

  9. Bacterial Tethering Analysis Reveals a “Run-Reverse-Turn” Mechanism for Pseudomonas Species Motility

    OpenAIRE

    Qian, Chen; Wong, Chui Ching; SWARUP, SANJAY; Chiam, Keng-Hwee

    2013-01-01

    We have developed a program that can accurately analyze the dynamic properties of tethered bacterial cells. The program works especially well with cells that tend to give rise to unstable rotations, such as polar-flagellated bacteria. The program has two novel components. The first dynamically adjusts the center of the cell's rotational trajectories. The second applies piecewise linear approximation to the accumulated rotation curve to reduce noise and separate the motion of bacteria into pha...

  10. Bordetella pertussis adenylate cyclase toxin translocation across a tethered lipid bilayer

    OpenAIRE

    Veneziano, Rémi; Rossi, Claire; Chenal, Alexandre; Devoisselle, Jean-Marie; Ladant, Daniel; Chopineau, Joel

    2013-01-01

    Many bacterial toxins can cross biological membranes to reach the cytosol of mammalian cells, although how they pass through a lipid bilayer remains largely unknown. Bordetella pertussis adenylate cyclase (CyaA) toxin delivers its catalytic domain directly across the cell membrane. To characterize this unique translocation process, we designed an in vitro assay based on a tethered lipid bilayer assembled over a biosensor surface derivatized with calmodulin, a natural activator of the toxin. C...

  11. Space-Based Tethered Array Radar (STAR) - A Distributed Small Satellite Network

    OpenAIRE

    Tomlinson, Philip; Brown, Thomas; Chakraborty, Dayamoy

    1988-01-01

    The Space-Based Tethered Array Radar (STAR) concept evolved from the DoD need for an affordable, launchable, survivable, and expandable Space-Based Radar for wide-area surveillance of airborne targets and for ballistic missile defense applications. Because low-observable threats can undermine conventional large monolithic Space-Based Radar satellite designs by forcing power-aperture products (inversely proportional to target radar cross-section) so high that the resulting heavy and expensive ...

  12. Optimum sizing of bare-tape tethers for de-orbiting satellites at end of mission

    Science.gov (United States)

    Sanmartín, J. R.; Sánchez-Torres, A.; Khan, S. B.; Sánchez-Arriaga, G.; Charro, M.

    2015-10-01

    De-orbiting satellites at end of mission would prevent generation of new space debris. A proposed de-orbit technology involves a bare conductive tape-tether, which uses neither propellant nor power supply while generating power for on-board use during de-orbiting. The present work shows how to select tape dimensions for a generic mission so as to satisfy requirements of very small tether-to-satellite mass ratio mt/MS and probability Nf of tether cut by small debris, while keeping de-orbit time tf short and product tf × tether length low to reduce maneuvers in avoiding collisions with large debris. Design is here discussed for particular missions (initial orbit of 720 km altitude and 63° and 92° inclinations, and 3 disparate MS values, 37.5, 375, and 3750 kg), proving it scalable. At mid-inclination and a mass-ratio of a few percent, de-orbit time takes about 2 weeks and Nf is a small fraction of 1%, with tape dimensions ranging from 1 to 6 cm, 10 to 54 μ m, and 2.8 to 8.6 km. Performance drop from middle to high inclination proved moderate: if allowing for twice as large mt/MS, increases are reduced to a factor of 4 in tf and a slight one in Nf, except for multi-ton satellites, somewhat more requiring because efficient orbital-motion-limited electron collection restricts tape-width values, resulting in tape length (slightly) increasing too.

  13. Dynamics, Control, and Estimation for Aerial Robots Tethered by Cables or Bars

    OpenAIRE

    Tognon, Marco; Franchi, Antonio

    2016-01-01

    The problem of controlling an aerial robot connected by a passive tether or a passive rigid link to the ground is considered here. We provide a thorough characterization of this nonlinear dynamical robotic system in terms of fundamental properties such as differential flatness, controllability, and observability. We prove that the robotic system is differentially flat with respect to two possible output pairs: elevation of the link and attitude of the vehicle; elevation of the link and longit...

  14. Controlled-surface-wettability-based fabrication of hydrogel substrates with matrix tethering density variations

    Science.gov (United States)

    Rahman, Md. Mahmudur; Lee, Donghee; Bhagirath, Divya; Zhao, Xiangshan; Band, Vimla; Ryu, Sangjin

    2014-03-01

    It is widely accepted that cells behave differently responding to the stiffness of extracellular matrix (ECM). Such observations were made by culturing cells on hydrogel substrates of tunable stiffness. However, it was recently proposed that cells actually sense how strongly they are tethered to ECM, not the local stiffness of ECM. To investigate the hypothesis, we develop constant-stiffness hydrogel substrates with varying matrix tethering density (the number of anchoring sites between the gel and the ECM protein molecules). We fabricate polyacrylamide gel of static stiffness and conjugate ECM proteins to the gel using a cross-linker. When treating the gel with the cross-linker, we control positioning of cross-linker solutions with different concentrations using superhydrophobic barriers on glass, functionalize the gel by pressing it to the aligned cross-linker solutions, and conjugate an ECM protein of constant concentration to the gel. We expect that the gel will be functionalized to different degrees depending on the concentration distribution of the cross-linker and thus the gel will have variations of matrix tethering density even with constant ECM protein concentration. We acknowledge support from Bioengineering for Human Health grant of UNL-UNMC.

  15. Biodegradable, Tethered Lipid Bilayer-Microsphere Systems with Membrane-Integrated α-Helical Peptide Anchors.

    Science.gov (United States)

    Fried, Eric S; Luchan, Joshua; Gilchrist, M Lane

    2016-04-12

    Supported lipid bilayers (SLBs) are ideally suited for the study of biomembrane-biomembrane interactions and for the biomimicry of cell-to-cell communication, allowing for surface ligand displays that contain laterally mobile elements. However, the SLB paradigm does not include three-dimensionality and biocompatibility. As a way to bypass these limitations, we have developed a biodegradable form of microsphere SLBs, also known as proteolipobeads (PLBs), using PLGA microspheres. Microspheres were synthesized using solvent evaporation and size selected with fluorescence activated cell sorting (FACS). Biomembranes were covalently tethered upon fusion to microsphere supports via short-chain PEG spacers connecting membrane-integrated α-helical peptides and the microsphere surface, affecting membrane diffusivity and mobility as indicated by confocal FRAP analysis. Membrane heterogeneities, which are attributed to PLGA hydrophobicity and rough surface topography, are curtailed by the addition of PEG tethers. This method allows for the presentation of tethered, laterally mobile biomembranes in three dimensions with functionally embedded attachment peptides for mobile ligand displays. PMID:26972467

  16. History of the current understanding and management of tethered spinal cord.

    Science.gov (United States)

    Safavi-Abbasi, Sam; Mapstone, Timothy B; Archer, Jacob B; Wilson, Christopher; Theodore, Nicholas; Spetzler, Robert F; Preul, Mark C

    2016-07-01

    An understanding of the underlying pathophysiology of tethered cord syndrome (TCS) and modern management strategies have only developed within the past few decades. Current understanding of this entity first began with the understanding and management of spina bifida; this later led to the gradual recognition of spina bifida occulta and the symptoms associated with tethering of the filum terminale. In the 17th century, Dutch anatomists provided the first descriptions and initiated surgical management efforts for spina bifida. In the 19th century, the term "spina bifida occulta" was coined and various presentations of spinal dysraphism were appreciated. The association of urinary, cutaneous, and skeletal abnormalities with spinal dysraphism was recognized in the 20th century. Early in the 20th century, some physicians began to suspect that traction on the conus medullaris caused myelodysplasia-related symptoms and that prophylactic surgical management could prevent the occurrence of clinical manifestations. It was not, however, until later in the 20th century that the term "tethered spinal cord" and the modern management of TCS were introduced. This gradual advancement in understanding at a time before the development of modern imaging modalities illustrates how, over the centuries, anatomists, pathologists, neurologists, and surgeons used clinical examination, a high level of suspicion, and interest in the subtle and overt clinical appearances of spinal dysraphism and TCS to advance understanding of pathophysiology, clinical appearance, and treatment of this entity. With the availability of modern imaging, spinal dysraphism can now be diagnosed and treated as early as the intrauterine stage. PMID:26967990

  17. The Atg1-kinase complex tethers Atg9-vesicles to initiate autophagy

    Science.gov (United States)

    Rao, Yijian; Perna, Marco G.; Hofmann, Benjamin; Beier, Viola; Wollert, Thomas

    2016-01-01

    Autophagosomes are double-membrane vesicles that sequester cytoplasmic material for lysosomal degradation. Their biogenesis is initiated by recruitment of Atg9-vesicles to the phagophore assembly site. This process depends on the regulated activation of the Atg1-kinase complex. However, the underlying molecular mechanism remains unclear. Here we reconstitute this early step in autophagy from purified components in vitro. We find that on assembly from its cytoplasmic subcomplexes, the Atg1-kinase complex becomes activated, enabling it to recruit and tether Atg9-vesicles. The scaffolding protein Atg17 targets the Atg1-kinase complex to autophagic membranes by specifically recognizing the membrane protein Atg9. This interaction is inhibited by the two regulatory subunits Atg31 and Atg29. Engagement of the Atg1-Atg13 subcomplex restores the Atg9-binding and membrane-tethering activity of Atg17. Our data help to unravel the mechanism that controls Atg17-mediated tethering of Atg9-vesicles, providing the molecular basis to understand initiation of autophagosome-biogenesis.

  18. Clustering of tethered satellite system simulation data by an adaptive neuro-fuzzy algorithm

    Science.gov (United States)

    Mitra, Sunanda; Pemmaraju, Surya

    1992-01-01

    Recent developments in neuro-fuzzy systems indicate that the concepts of adaptive pattern recognition, when used to identify appropriate control actions corresponding to clusters of patterns representing system states in dynamic nonlinear control systems, may result in innovative designs. A modular, unsupervised neural network architecture, in which fuzzy learning rules have been embedded is used for on-line identification of similar states. The architecture and control rules involved in Adaptive Fuzzy Leader Clustering (AFLC) allow this system to be incorporated in control systems for identification of system states corresponding to specific control actions. We have used this algorithm to cluster the simulation data of Tethered Satellite System (TSS) to estimate the range of delta voltages necessary to maintain the desired length rate of the tether. The AFLC algorithm is capable of on-line estimation of the appropriate control voltages from the corresponding length error and length rate error without a priori knowledge of their membership functions and familarity with the behavior of the Tethered Satellite System.

  19. From the Rocket Equation to Maxwell's Equations: Electrodynamic Tether Propulsion Nears Space Test

    Science.gov (United States)

    Johnson, Les; Estes, Robert

    1999-01-01

    The US space program is facing a growing challenge to its decades-long, global leadership position, as current launch costs consume valuable resources and limit achievements in science, exploration, and commercial development. More than 40% of projected launches over the next 10 years have payloads with intended destinations beyond low-Earth orbit. Therefore, more cost-effective upper stages and on-board propulsion systems are critical elements in reducing total space transportation costs. A new type of space propulsion, using electrodynamic tethers, may be capable of performing multiple sequential missions without resupply and have a potential usable lifetime of several years. They may provide an in-space infrastructure that has a very low life cycle cost and greatly enhanced mission flexibility, thus supporting the goal of reducing the cost of access to space. Electrodynamic tether thrusters work by virtue of the force the Earth's magnetic field exerts on a wire carrying an electrical current. The effect is the basis for electric motors and generators. The Propulsive Small Expendable Deployer System (ProSEDS) experiment, planned for launch in the summer of 2000, will demonstrate the use electrodynamic tether thrust by lowering the altitude of a Delta-H rocket's upper stage on which it will be flying. Applications of the technology include a passive deorbit system for spacecraft at their end-of-life, reusable Orbit Transfer Vehicles, propellantless reboost of the International Space Station, and propulsion and power generation for future missions to Jupiter.

  20. Postoperative epidural hematoma contributes to delayed upper cord tethering after decompression of Chiari malformation type I

    Directory of Open Access Journals (Sweden)

    Antonio Lopez-Gonzalez

    2014-01-01

    Full Text Available Background: Symptomatic arachnoiditis after posterior fossa surgical procedures such as decompression of Chiari malformation is a possible complication. Clinical presentation is generally insidious and delayed by months or years. It causes disturbances in the normal flow of cerebrospinal fluid and enlargement of a syrinx cavity in the upper spinal cord. Surgical de-tethering has favorable results with progressive collapse of the syrinx and relief of the associated symptoms. Case Description: A 30-year-old male with Chiari malformation type I was treated by performing posterior fossa bone decompression, dura opening and closure with a suturable bovine pericardium dural graft. Postoperative period was uneventful until the fifth day in which the patient suffered intense headache and progressive loose of consciousness caused by an acute posterior fossa epidural hematoma. It was quickly removed with complete clinical recovering. One year later, the patient experienced progressive worsened of his symptoms. Upper spinal cord tethering was diagnosed and a new surgery for debridement was required. Conclusions: The epidural hematoma compressing the dural graft against the neural structures contributes to the upper spinal cord tethering and represents a nondescribed cause of postoperative fibrosis, adhesion formation, and subsequent recurrent hindbrain compression.

  1. Shuttle-tethered satellite system definition study. Volume 1: Executive study

    Science.gov (United States)

    1979-01-01

    The Tethered Satellite System has great prospects for extending orbital operations capability of the Space Transportation System to science, applications, and technology projects not otherwise attainable. The system will installed in the Shuttle Orbiter and will have the capability to deploy a captive satellite up to 100 km away from the Orbiter. Control and retrieval of the satellite are accomplished by means of a tether line connecting the satellite and the cargo bay mounted equipment in the Orbiter. At low satellite altitudes, the system will permit investigations of a duration that could not be pursued with sounding rockets of free-flying spacecraft. The propose of the Shuttle/Tethered Satellite System Definition Study was to produce the preliminary design, preliminary specifications, gross program plans, and program cost estimate for a 1982 operational verification flight. This was accomplished during a fifteen month effort under by the NASA George C. Marshall Space Flight Center (MSFC). The MSFC Phase 1 and related studies demonstrated the feasibility of the system and served as a starting point for the Phase 2 definition study.

  2. A Structure-Based Mechanism for Vesicle Capture by the Multisubunit Tethering Complex Dsl1

    Energy Technology Data Exchange (ETDEWEB)

    Ren, Y.; Yip, C; Tripathi, A; Huie, D; Jeffrey, P; Walz, T; Hughson, F

    2009-01-01

    Vesicle trafficking requires membrane fusion, mediated by SNARE proteins, and upstream events that probably include tethering, an initial long-range attachment between a vesicle and its target organelle. Among the factors proposed to mediate tethering are a set of multisubunit tethering complexes (MTCs). The Dsl1 complex, with only three subunits, is the simplest known MTC and is essential for the retrograde traffic of COPI-coated vesicles from the Golgi to the ER. To elucidate structural principles underlying MTC function, we have determined the structure of the Dsl1 complex, revealing a tower containing at its base the binding sites for two ER SNAREs and at its tip a flexible lasso for capturing vesicles. The Dsl1 complex binds to individual SNAREs via their N-terminal regulatory domains and also to assembled SNARE complexes; moreover, it is capable of accelerating SNARE complex assembly. Our results suggest that even the simplest MTC may be capable of orchestrating vesicle capture, uncoating, and fusion.

  3. TI tether rig for solving secular spinrate change problem of electric sail

    CERN Document Server

    Janhunen, Pekka

    2016-01-01

    The electric solar wind sail (E-sail) is a way to propel a spacecraft by using the natural solar wind as a thrust source. The problem of secular spinrate change was identified earlier which is due to the orbital Coriolis effect and tends to slowly increase or decrease the sail's spinrate, depending on which way the sail is inclined with respect to the solar wind. Here we present an E-sail design and its associated control algorithm which enable spinrate control during propulsive flight by the E-sail effect itself. In the design, every other maintether ("T-tether") is galvanically connected through the remote unit with the two adjacent auxtethers, while the other maintethers ("I-tethers") are insulated from the tethers. This enables one to effectively control the maintether and auxtether voltages separately, which in turn enables spinrate control. We use a detailed numerical simulation to show that the algorithm can fully control the E-sail's spin state in real solar wind. The simulation includes a simple and ...

  4. System Dynamics and Feedforward Control for Tether-Net Space Robot System

    Directory of Open Access Journals (Sweden)

    Bin Liang

    2009-11-01

    Full Text Available A new concept using flexible tether-net system to capture space debris is presented in this paper. With a mass point assumption the tether-net system dynamic model is established in orbital frame by applying Lagrange Equations. In order to investigate the net in-plane trajectories during after cast, the non-control R-bar and V-bar captures are simulated with ignoring the out-of-plane libration, the effect of in-plane libration on the trajectories of the capture net is demonstrated by simulation results. With an effort to damp the in-plane libration, the control scheme based on tether tension is investigated firstly, after that an integrated control scheme is proposed by introduced the thrusters into the system, the nonlinear close-loop dynamics is linearised by feedforward strategy, the simulation results show that feedforward controllor is effective for in-plane libration damping and enable the capture net to track an expected trajectory.

  5. Out-of-Plane Translational PZT Bimorph Actuator with Archimedes’ Spiral Actuating Tethers

    Science.gov (United States)

    Yang, Chenye; Liu, Sanwei; Livermore, Carol

    2015-12-01

    The design, finite element analysis (FEA), and experimental characterization of a MEMS out-of-plane (vertical) translational lead-zirconate-titanate (PZT) bimorph actuator supported on Archimedes’ spiral tethers are presented. Two types of bimorph actuators with different electrode patterns (with spiral tethers half actuated or fully actuated) are designed and fabricated. Both designs are fabricated by commercial processes and are compatible with integration into more complex MEMS systems. Finite element analysis (FEA) was used to analyze and predict the displacements of both types of actuators. The deflections of both fully- actuated and half-actuated devices were measured experimentally to validate the design. At an applied voltage of 110V, the out-of-plane deflections of the actuators with half-actuated and fully-actuated tethers were measured at about 17 μm and 29 μm respectively, in good agreement with FEA predictions of 17.1 μm and 25.8 μm. The corresponding blocking forces are predicted as 10 mN and 17 mN by FEA.

  6. Chromatin and epigenetics in all their states: Meeting report of the first conference on Epigenetic and Chromatin Regulation of Plant Traits - January 14 - 15, 2016 - Strasbourg, France.

    Science.gov (United States)

    Bey, Till; Jamge, Suraj; Klemme, Sonja; Komar, Dorota Natalia; Le Gall, Sabine; Mikulski, Pawel; Schmidt, Martin; Zicola, Johan; Berr, Alexandre

    2016-08-01

    In January 2016, the first Epigenetic and Chromatin Regulation of Plant Traits conference was held in Strasbourg, France. An all-star lineup of speakers, a packed audience of 130 participants from over 20 countries, and a friendly scientific atmosphere contributed to make this conference a meeting to remember. In this article we summarize some of the new insights into chromatin, epigenetics, and epigenomics research and highlight nascent ideas and emerging concepts in this exciting area of research. PMID:27184433

  7. Cosmic alternatives?

    Science.gov (United States)

    Gregory, Ruth

    2009-04-01

    "Cosmologists are often in error but never in doubt." This pithy characterization by the Soviet physicist Lev Landau sums up the raison d'être of Facts and Speculations in Cosmology. Authors Jayant Narlikar and Geoffrey Burbidge are proponents of a "steady state" theory of cosmology, and they argue that the cosmological community has become fixated on a "Big Bang" dogma, suppressing alternative viewpoints. This book very much does what it says on the tin: it sets out what is known in cosmology, and puts forward the authors' point of view on an alternative to the Big Bang.

  8. Genome-wide analysis of interactions between ATP-dependent chromatin remodeling and histone modifications

    Directory of Open Access Journals (Sweden)

    Wang Jiang

    2009-07-01

    Full Text Available Abstract Background ATP-dependent chromatin remodeling and the covalent modification of histones play central roles in determining chromatin structure and function. Although several specific interactions between these two activities have been elaborated, the global landscape remains to be elucidated. Results In this paper, we have developed a computational method to generate the first genome-wide landscape of interactions between ATP-dependent chromatin remodeling and the covalent modification of histones in Saccharomyces cerevisiae. Our method succeeds in identifying known interactions and uncovers many previously unknown interactions between these two activities. Analysis of the genome-wide picture revealed that transcription-related modifications tend to interact with more chromatin remodelers. Our results also demonstrate that most chromatin remodeling-modification interactions act via interactions of remodelers with both histone-modifying enzymes and histone residues. We also found that the co-occurrence of both modification and remodeling has significantly different influences on multiple gene features (e.g. nucleosome occupancy compared with the presence of either one. Conclusion We gave the first genome-wide picture of ATP-dependent chromatin remodeling-histone modification interactions. We also revealed how these two activities work together to regulate chromatin structure and function. Our results suggest that distinct strategies for regulating chromatin activity are selectively employed by genes with different properties.

  9. Radiolysis of chromatin extracted from cultured mammalian cells: formation of DNA-protein cross links

    International Nuclear Information System (INIS)

    Chromatin extracted from Chinese hamster lung fibroblasts has been examined for the formation of radiation-induced DNA-protein cross links, using a membrane filter assay. The relative efficiencies of the aqueous radical intermediates, 0H., esub(aq)- and 02-, were investigated. Cross links were found in gamma-irradiated isolated chromatin and in chromatin irradiated in the cell before isolation. When isolated chromatin was irradiated under conditions in which the chromosomal proteins were dissociated from the DNA, no cross links were detectable. The most efficient radical for the production of cross links in irradiated, isolated chromatin was found to be the hydroxyl radical, whereas, the superoxide radical was essentially ineffective. For chromatin irradiated in the cell before isolation, the greatest effect was seen for cells irradiated in an atmosphere of nitrous oxide, suggesting the hydroxyl radical may be involved in the formation of cross links in intact cells also. The formation of cross links in chromatin irradiated in cells before isolation was considerably less efficient than in irradiated, isolated chromatin. (author)

  10. Induction of stable protein-deoxyribonucleic acid adducts in Chinese hamster cell chromatin by ultraviolet light

    International Nuclear Information System (INIS)

    Ultraviolet (uv)-light-mediated formation of protein-DNA adducts in Chinese hamster cell chromatin was investigated in an attempt to compare chromatin alterations induced in vitro with those observed in vivo. Three independent methods of analysis indicated stable protein-DNA associations: a membrane filter assay which retained DNA on the filter in the presence of high salt-detergent; a Sepharose 4B column assay in which protein eluted coincident with DNA; and a CsCl density gradient equilibrium assay which showed both protein and DNA banding at densities other than their respective native densities. Treatment of the irradiated chromatin with DNase provided further evidence that protein--DNA and not protein-protein adducts were being observed in the column assay. There is a fluence-dependent response of protein-DNA adduct formation when the chromatin is irradiated at low ionic strength and is linear for protein over the range studied. When the chromatin is exposed to differing conditions of pH, ionic strength, or divalent metal ion concentration, the quantity of adduct formed upon uv irradiation varies. Susceptibility to adduct formation can be partially explained in terms of the condensation state of the chromatin and other factors such as rearrangement, denaturation, and dissociation of the chromatin components. Besides providing information on the biological significance of these types of uv-induced lesions, this technique may be useful as a probe of chromatin structure

  11. Transcriptional activation by the thyroid hormone receptor through ligand-dependent receptor recruitment and chromatin remodelling

    DEFF Research Database (Denmark)

    Grøntved, Lars; Waterfall, Joshua J; Kim, Dong Wook;

    2015-01-01

    facilitates recruitment of co-activators to activate transcription. Here we show that in addition to hormone-independent TR occupancy, ChIP-seq against endogenous TR in mouse liver tissue demonstrates considerable hormone-induced TR recruitment to chromatin associated with chromatin remodelling and activated...

  12. Chd1 remodelers maintain open chromatin and regulate the epigenetics of differentiation

    Energy Technology Data Exchange (ETDEWEB)

    Persson, Jenna [Department of Biosciences and Nutrition, Center for Biosciences, Karolinska Institutet (Sweden); Ekwall, Karl, E-mail: karl.ekwall@ki.se [Department of Biosciences and Nutrition, Center for Biosciences, Karolinska Institutet (Sweden); School of Life Sciences, University College Sodertorn, NOVUM, Huddinge (Sweden)

    2010-05-01

    Eukaryotic DNA is packaged around octamers of histone proteins into nucleosomes, the basic unit of chromatin. In addition to enabling meters of DNA to fit within the confines of a nucleus, the structure of chromatin has functional implications for cell identity. Covalent chemical modifications to the DNA and to histones, histone variants, ATP-dependent chromatin remodelers, small noncoding RNAs and the level of chromatin compaction all contribute to chromosomal structure and to the activity or silencing of genes. These chromatin-level alterations are defined as epigenetic when they are heritable from mother to daughter cell. The great diversity of epigenomes that can arise from a single genome permits a single, totipotent cell to generate the hundreds of distinct cell types found in humans. Two recent studies in mouse and in fly have highlighted the importance of Chd1 chromatin remodelers for maintaining an open, active chromatin state. Based on evidence from fission yeast as a model system, we speculate that Chd1 remodelers are involved in the disassembly of nucleosomes at promoter regions, thus promoting active transcription and open chromatin. It is likely that these nucleosomes are specifically marked for disassembly by the histone variant H2A.Z.

  13. A Testis-Specific Chaperone and the Chromatin Remodeler ISWI Mediate Repackaging of the Paternal Genome

    Directory of Open Access Journals (Sweden)

    Cécile M. Doyen

    2015-11-01

    Full Text Available During spermatogenesis, the paternal genome is repackaged into a non-nucleosomal, highly compacted chromatin structure. Bioinformatic analysis revealed that Drosophila sperm chromatin proteins are characterized by a motif related to the high-mobility group (HMG box, which we termed male-specific transcript (MST-HMG box. MST77F is a MST-HMG-box protein that forms an essential component of sperm chromatin. The deposition of MST77F onto the paternal genome requires the chaperone function of tNAP, a testis-specific NAP protein. MST77F, in turn, enables the stable incorporation of MST35Ba and MST35Bb into sperm chromatin. Following MST-HMG-box protein deposition, the ATP-dependent chromatin remodeler ISWI mediates the appropriate organization of sperm chromatin. Conversely, at fertilization, maternal ISWI targets the paternal genome and drives its repackaging into de-condensed nucleosomal chromatin. Failure of this transition in ISWI mutant embryos is followed by mitotic defects, aneuploidy, and haploid embryonic divisions. Thus, ISWI enables bi-directional transitions between two fundamentally different forms of chromatin.

  14. A Model of Repetitive-DNA-Organized Chromatin Network of Interphase Chromosomes

    Directory of Open Access Journals (Sweden)

    Shao-Jun Tang

    2012-03-01

    Full Text Available During interphase, chromosomes are relatively de-condensed in the nuclear space. Interphase chromosomes are known to occupy nuclear space in a non-random manner (chromosome territory; however, their internal structures are poorly defined. In particular, little is understood about the molecular mechanisms that govern the internal organization of interphase chromosomes. The author recently proposed that pairing (or interaction of repetitive DNA-containing chromatin regions is a critical driving force that specifies the higher-order organization of eukaryotic chromosomes. Guided by this theoretical framework and published experimental data on the structure of interphase chromosomes and the spatial distribution of repetitive DNA in interphase nuclei, I postulate here a molecular structure of chromatin organization in interphase chromosomes. According to this model, an interphase chromosome is a chromatin mesh (or lattice that is formed by repeat pairing (RP. The mesh consists of two types of structural components: chromosome nodes and loose chromatin fibers. Chromosome nodes are DNA repeat assemblies (RAs that are formed via RP, while loose fibers include chromatin loops that radiate from the nodes. Different loops crosslink by RPs and form a large integrated chromatin network. I suggest that the organization of the chromatin network of a given interphase chromosome is intrinsically specified by the distribution of repetitive DNA elements on the linear chromatin. The stability of the organization is governed by the collection of RA-formed nodes, and the dynamics of the organization is driven by the assembling and disassembling of the nodes.

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

    International Nuclear Information System (INIS)

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

  16. Restoring chromatin after replication: How new and old histone marks come together

    DEFF Research Database (Denmark)

    Jasencakova, Zusana; Groth, Anja

    2010-01-01

    In dividing cells genome stability and function rely on faithful transmission of both DNA sequence and its organization into chromatin. In the course of DNA replication chromatin undergoes transient genome-wide disruption followed by restoration on new DNA. This involves tight coordination of DNA...

  17. Assembly of Two Transgenes in an Artificial Chromatin Domain Gives Highly Coordinated Expression in Tobacco

    NARCIS (Netherlands)

    Mlynárová, Ludmila; Loonen, Annelies; Mietkiewska, Elzbieta; Jansen, Ritsert C.; Nap, Jan-Peter

    2002-01-01

    The chromatin loop model predicts that genes within the same chromatin domain exhibit coordinated regulation. We here present the first direct experimental support for this model in plants. Two reporter genes, the E. coli β-glucuronidase gene and the firefly luciferase gene, driven by different prom

  18. Selection on a Subunit of the NURF Chromatin Remodeler Modifies Life History Traits in a Domesticated Strain of Caenorhabditis elegans

    Science.gov (United States)

    Large, Edward E.; Zhao, Yuehui; Long, Lijiang; Butcher, Rebecca A.; Andersen, Erik C.; McGrath, Patrick T.

    2016-01-01

    Evolutionary life history theory seeks to explain how reproductive and survival traits are shaped by selection through allocations of an individual’s resources to competing life functions. Although life-history traits evolve rapidly, little is known about the genetic and cellular mechanisms that control and couple these tradeoffs. Here, we find that two laboratory-adapted strains of C. elegans descended from a single common ancestor that lived in the 1950s have differences in a number of life-history traits, including reproductive timing, lifespan, dauer formation, growth rate, and offspring number. We identified a quantitative trait locus (QTL) of large effect that controls 24%–75% of the total trait variance in reproductive timing at various timepoints. Using CRISPR/Cas9-induced genome editing, we show this QTL is due in part to a 60 bp deletion in the 3’ end of the nurf-1 gene, which is orthologous to the human gene encoding the BPTF component of the NURF chromatin remodeling complex. Besides reproduction, nurf-1 also regulates growth rate, lifespan, and dauer formation. The fitness consequences of this deletion are environment specific—it increases fitness in the growth conditions where it was fixed but decreases fitness in alternative laboratory growth conditions. We propose that chromatin remodeling, acting through nurf-1, is a pleiotropic regulator of life history trade-offs underlying the evolution of multiple traits across different species. PMID:27467070

  19. Combined chromatin and expression analysis reveals specific regulatory mechanisms within cytokine genes in the macrophage early immune response.

    Directory of Open Access Journals (Sweden)

    Maria Jesus Iglesias

    Full Text Available Macrophages play a critical role in innate immunity, and the expression of early response genes orchestrate much of the initial response of the immune system. Macrophages undergo extensive transcriptional reprogramming in response to inflammatory stimuli such as Lipopolysaccharide (LPS.To identify gene transcription regulation patterns involved in early innate immune responses, we used two genome-wide approaches--gene expression profiling and chromatin immunoprecipitation-sequencing (ChIP-seq analysis. We examined the effect of 2 hrs LPS stimulation on early gene expression and its relation to chromatin remodeling (H3 acetylation; H3Ac and promoter binding of Sp1 and RNA polymerase II phosphorylated at serine 5 (S5P RNAPII, which is a marker for transcriptional initiation. Our results indicate novel and alternative gene regulatory mechanisms for certain proinflammatory genes. We identified two groups of up-regulated inflammatory genes with respect to chromatin modification and promoter features. One group, including highly up-regulated genes such as tumor necrosis factor (TNF, was characterized by H3Ac, high CpG content and lack of TATA boxes. The second group, containing inflammatory mediators (interleukins and CCL chemokines, was up-regulated upon LPS stimulation despite lacking H3Ac in their annotated promoters, which were low in CpG content but did contain TATA boxes. Genome-wide analysis showed that few H3Ac peaks were unique to either +/-LPS condition. However, within these, an unpacking/expansion of already existing H3Ac peaks was observed upon LPS stimulation. In contrast, a significant proportion of S5P RNAPII peaks (approx 40% was unique to either condition. Furthermore, data indicated a large portion of previously unannotated TSSs, particularly in LPS-stimulated macrophages, where only 28% of unique S5P RNAPII peaks overlap annotated promoters. The regulation of the inflammatory response appears to occur in a very specific manner at

  20. Alternative Splicing of G9a Regulates Neuronal Differentiation

    OpenAIRE

    Ana Fiszbein; Luciana E. Giono; Ana Quaglino; Bruno G. Berardino; Lorena Sigaut; Catalina von Bilderling; Ignacio E. Schor; Juliana H. Enriqué Steinberg; Mario Rossi; Lía I. Pietrasanta; Julio J. Caramelo; Anabella Srebrow; Alberto R. Kornblihtt

    2016-01-01

    Chromatin modifications are critical for the establishment and maintenance of differentiation programs. G9a, the enzyme responsible for histone H3 lysine 9 dimethylation in mammalian euchromatin, exists as two isoforms with differential inclusion of exon 10 (E10) through alternative splicing. We find that the G9a methyltransferase is required for differentiation of the mouse neuronal cell line N2a and that E10 inclusion increases during neuronal differentiation of cultured cells, as well as i...