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Sample records for dependent dna conductivity

  1. Conformational gating of DNA conductance

    PubMed Central

    Artés, Juan Manuel; Li, Yuanhui; Qi, Jianqing; Anantram, M. P.; Hihath, Joshua

    2015-01-01

    DNA is a promising molecule for applications in molecular electronics because of its unique electronic and self-assembly properties. Here we report that the conductance of DNA duplexes increases by approximately one order of magnitude when its conformation is changed from the B-form to the A-form. This large conductance increase is fully reversible, and by controlling the chemical environment, the conductance can be repeatedly switched between the two values. The conductance of the two conformations displays weak length dependencies, as is expected for guanine-rich sequences, and can be fit with a coherence-corrected hopping model. These results are supported by ab initio electronic structure calculations that indicate that the highest occupied molecular orbital is more disperse in the A-form DNA case. These results demonstrate that DNA can behave as a promising molecular switch for molecular electronics applications and also provide additional insights into the huge dispersion of DNA conductance values found in the literature. PMID:26648400

  2. Conformational gating of DNA conductance.

    PubMed

    Artés, Juan Manuel; Li, Yuanhui; Qi, Jianqing; Anantram, M P; Hihath, Joshua

    2015-01-01

    DNA is a promising molecule for applications in molecular electronics because of its unique electronic and self-assembly properties. Here we report that the conductance of DNA duplexes increases by approximately one order of magnitude when its conformation is changed from the B-form to the A-form. This large conductance increase is fully reversible, and by controlling the chemical environment, the conductance can be repeatedly switched between the two values. The conductance of the two conformations displays weak length dependencies, as is expected for guanine-rich sequences, and can be fit with a coherence-corrected hopping model. These results are supported by ab initio electronic structure calculations that indicate that the highest occupied molecular orbital is more disperse in the A-form DNA case. These results demonstrate that DNA can behave as a promising molecular switch for molecular electronics applications and also provide additional insights into the huge dispersion of DNA conductance values found in the literature. PMID:26648400

  3. First-principles transversal DNA conductance deconstructed

    SciTech Connect

    Zhang, Xiaoguang; Krstic, Predrag; Zikic, Radomir; Wells, Jack C; Fuentes-Cabrera, Miguel A

    2006-01-01

    First-principles calculation of the transverse conductance across DNA fragments placed between gold nanoelectrodes, reveals that such conductance describes electron tunneling that depends critically on geometrical rather than electronic-structure properties. By factoring the first-principles result into two simple and approximately independent tunneling factors, we show that the conductances of the A, C, G, and T fragments differ only because of their sizes: the larger is the DNA base, the smaller is the distance that separates the electrode from the corresponding molecule, and the larger is its conductance. Because the geometrical factors are difficult to control in an experiment, the DC-current measurements across DNA may not be a convenient approach to DNA sequencing.

  4. Effect of mechanical stretching on DNA conductance.

    PubMed

    Bruot, Christopher; Xiang, Limin; Palma, Julio L; Tao, Nongjian

    2015-01-27

    Studying the structural and charge transport properties in DNA is important for unraveling molecular scale processes and developing device applications of DNA molecules. Here we study the effect of mechanical stretching-induced structural changes on charge transport in single DNA molecules. The charge transport follows the hopping mechanism for DNA molecules with lengths varying from 6 to 26 base pairs, but the conductance is highly sensitive to mechanical stretching, showing an abrupt decrease at surprisingly short stretching distances and weak dependence on DNA length. We attribute this force-induced conductance decrease to the breaking of hydrogen bonds in the base pairs at the end of the sequence and describe the data with a mechanical model. PMID:25530305

  5. Heat conductivity of DNA double helix

    PubMed Central

    Savin, Alexander V.; Mazo, Mikhail A.; Kikot, Irina P.; Manevitch, Leonid I.; Onufriev, Alexey V.

    2015-01-01

    Thermal conductivity of isolated single molecule DNA fragments is of importance for nanotechnology, but has not yet been measured experimentally. Theoretical estimates based on simplified (1D) models predict anomalously high thermal conductivity. To investigate thermal properties of single molecule DNA we have developed a 3D coarse-grained (CG) model that retains the realism of the full all-atom description, but is significantly more efficient. Within the proposed model each nucleotide is represented by 6 particles or grains; the grains interact via effective potentials inferred from classical molecular dynamics (MD) trajectories based on a well-established all-atom potential function. Comparisons of 10 ns long MD trajectories between the CG and the corresponding all-atom model show similar root-mean-square deviations from the canonical B-form DNA, and similar structural fluctuations. At the same time, the CG model is 10 to 100 times faster depending on the length of the DNA fragment in the simulation. Analysis of dispersion curves derived from the CG model yields longitudinal sound velocity and torsional stiffness in close agreement with existing experiments. The computational efficiency of the CG model makes it possible to calculate thermal conductivity of a single DNA molecule not yet available experimentally. For a uniform (polyG-polyC) DNA, the estimated conductivity coefficient is 0.3 W/mK which is half the value of thermal conductivity for water. This result is in stark contrast with estimates of thermal conductivity for simplified, effectively 1D chains (”beads on a spring”) that predict anomalous (infinite) thermal conductivity. Thus, full 3D character of DNA double-helix retained in the proposed model appears to be essential for describing its thermal properties at a single molecule level. PMID:26207085

  6. Conductance of Dry DNA: Role of Environment

    NASA Technical Reports Server (NTRS)

    Anantram, M. P.; Adessi, Ch.; S. Walch

    2003-01-01

    This paper presents viewgraphs on the conductance of dry DNA and its effect on the surrounding environment. The topics include: 1) Approach; 2) Influence of Counter Ions; 3) Conductance Versus DNA Length; 4) Intrinsic Resonant Tunneling in Engineered DNA Sequence; and 5) Transmission Versus Energy.

  7. Molecular electronics: A DNA that conducts

    NASA Astrophysics Data System (ADS)

    Scheer, Elke

    2014-12-01

    Experiments with conducting atomic force microscopy provide a clear demonstration of long-range charge transport in G-quadruplex DNA molecules, and allow a hopping transport model to be developed that could also be applied to other conductive polymers.

  8. Environment and Structure Influence in DNA Conduction

    NASA Technical Reports Server (NTRS)

    Adessi, C.; Walch, S.; Anantram, M. P.; Biegel, Bryan (Technical Monitor)

    2002-01-01

    Results for transmission through the poly(G) DNA molecule are presented. We show that (i) periodically arranged sodium counter-ions in close proximity to dry DNA gives rise to a new conduction channel and aperiodicity in the counter-ion sequence can lead to a significant reduction in conduction, (ii) modification of the rise of B-DNA induces a change in the width of the transmission window, and (iii) specifically designed sequences are predicted to show intrinsic resonant tunneling behavior.

  9. Itinerant electron model and conductance of DNA

    NASA Astrophysics Data System (ADS)

    Qu, Zhen; Kang, Da-Wei; Gao, Xu-Tuan; Xie, Shi-Jie

    2008-09-01

    DNA (Deoxyribonucleic acid) has recently caught the attention of chemists and physicists. A major reason for this interest is DNA’s potential use in nanoelectronic devices, both as a template for assembling nanocircuits and as an element of such circuits. However, the electronic properties of the DNA molecule remain very controversial. Charge-transfer reactions and conductivity measurements show a large variety of possible electronic behavior, ranging from Anderson and band-gap insulators to effective molecular wires and induced superconductors. In this review article, we summarize the wide-ranging experimental and theoretical results of charge transport in DNA. An itinerant electron model is suggested and the effect of the density of itinerant electrons on the conductivity of DNA is studied. Calculations show that a DNA molecule may show conductivity from insulating to metallic, which explains the controversial and profuse electric characteristics of DNA to some extent.

  10. Structure and Environment Influence in DNA Conduction

    NASA Technical Reports Server (NTRS)

    Adessi, C.; Walch, S.; Anantram, M. P.; Biegel, Bryan A. (Technical Monitor)

    2002-01-01

    Results for transmission through a poly(G) DNA molecule are presented. We show that a modification of the rise of a B-DNA form can induce a shift of the conduction channel toward the valence one. We clearly prove that deformation of the backbone of the molecule has a significant influence on hole transport. Finally, we observe that the presence of ionic species, such Na, near the molecule can create new conduction channels.

  11. Inhomogeneous DNA: Conducting exons and insulating introns

    NASA Astrophysics Data System (ADS)

    Krokhin, A. A.; Bagci, V. M. K.; Izrailev, F. M.; Usatenko, O. V.; Yampol'Skii, V. A.

    2009-08-01

    Parts of DNA sequences known as exons and introns play very different roles in coding and storage of genetic information. Here we show that their conducting properties are also very different. Taking into account long-range correlations among four basic nucleotides that form double-stranded DNA sequence, we calculate electron localization length for exon and intron regions. Analyzing different DNA molecules, we obtain that the exons have narrow bands of extended states, unlike the introns where all the states are well localized. The band of extended states is due to a specific form of the binary correlation function of the sequence of basic DNA nucleotides.

  12. Influence of Disorder on DNA Conductance

    NASA Technical Reports Server (NTRS)

    Adessi, Christophe; Anantram, M. P.; Biegel, Bryan A. (Technical Monitor)

    2003-01-01

    Disorder along a DNA strand due to non uniformity associated with the counter ion type and location, and in rise and twist are investigated using density functional theory. We then model the conductance through a poly(G) DNA strand by including the influence of disorder. We show that the conductance drops by a few orders of magnitude between typical lengths of 10 and 100 nm. Such a decrease occurs with on-site potential disorder that is larger than 100 meV.

  13. Temperature dependence of conductivity measurement for conducting polymer

    NASA Astrophysics Data System (ADS)

    Gutierrez, Leandro; Duran, Jesus; Isah, Anne; Albers, Patrick; McDougall, Michael; Wang, Weining

    2014-03-01

    Conducting polymer-based solar cells are the newest generation solar cells. While research on this area has been progressing, the efficiency is still low because certain important parameters of the solar cell are still not well understood. It is of interest to study the temperature dependence of the solar cell parameters, such as conductivity of the polymer, open circuit voltage, and reverse saturation current to gain a better understanding on the solar cells. In this work, we report our temperature dependence of conductivity measurement using our in-house temperature-varying apparatus. In this project, we designed and built a temperature varying apparatus using a thermoelectric cooler module which gives enough temperature range as we need and costs much less than a cryostat. The set-up of the apparatus will be discussed. Temperature dependence of conductivity measurements for PEDOT:PSS films with different room-temperature conductivity will be compared and discussed. NJSGC-NASA Fellowship grant

  14. Probing radiation damage by alternated current conductivity as a method to characterize electron hopping conduction in DNA molecules

    SciTech Connect

    Gomes, Paulo J.; Coelho, Margarida; Antonio Ribeiro, Paulo; Raposo, Maria; Dionisio, Madalena

    2012-09-17

    Analysis of AC electrical conductivity of deoxyribonucleic acid (DNA) thin films, irradiated with ultraviolet (UV) light, revealed that electrical conduction arises from DNA chain electron hopping between base-pairs and phosphate groups. The hopping distance calculated from correlated barrier hopping model equals the distance between DNA base-pairs, which is consistent with the loss of conductivity with irradiation time arising from a decrease in phosphates groups. In the high frequency regime, at a given frequency, real part of conductivity strongly depends on irradiation time particularly for low dose levels suggesting the use of DNA based films for UV radiation sensors.

  15. Conductance of DNA molecules: Effects of decoherence and bonding

    NASA Astrophysics Data System (ADS)

    Zilly, Matías; Ujsághy, Orsolya; Wolf, Dietrich E.

    2010-09-01

    The influence of decoherence and bonding on the linear conductance of single double-stranded DNA molecules is examined by fitting a phenomenological statistical model developed recently [M. Zilly, O. Ujsághy, and D. E. Wolf, Eur. Phys. J. B 68, 237 (2009)10.1140/epjb/e2009-00101-0] to experimental results. The DNA molecule itself is described by a tight-binding ladder model with parameters obtained from published ab initio calculations [K. Senthilkumar, F. C. Grozema, C. F. Guerra, F. M. Bickelhaupt, F. D. Lewis, Y. A. Berlin, M. A. Ratner, and L. D. A. Siebbeles, J. Am. Chem. Soc. 127, 14894 (2005)10.1021/ja054257e]. The good agreement with the experiments on sequence and length dependence gives a hint on the nature of conduction in DNA and at the same time provides a crucial test of the model.

  16. Counterintuitive DNA Sequence Dependence in Supercoiling-Induced DNA Melting

    PubMed Central

    Vlijm, Rifka; v.d. Torre, Jaco; Dekker, Cees

    2015-01-01

    The metabolism of DNA in cells relies on the balance between hybridized double-stranded DNA (dsDNA) and local de-hybridized regions of ssDNA that provide access to binding proteins. Traditional melting experiments, in which short pieces of dsDNA are heated up until the point of melting into ssDNA, have determined that AT-rich sequences have a lower binding energy than GC-rich sequences. In cells, however, the double-stranded backbone of DNA is destabilized by negative supercoiling, and not by temperature. To investigate what the effect of GC content is on DNA melting induced by negative supercoiling, we studied DNA molecules with a GC content ranging from 38% to 77%, using single-molecule magnetic tweezer measurements in which the length of a single DNA molecule is measured as a function of applied stretching force and supercoiling density. At low force (<0.5pN), supercoiling results into twisting of the dsDNA backbone and loop formation (plectonemes), without inducing any DNA melting. This process was not influenced by the DNA sequence. When negative supercoiling is introduced at increasing force, local melting of DNA is introduced. We measured for the different DNA molecules a characteristic force Fchar, at which negative supercoiling induces local melting of the dsDNA. Surprisingly, GC-rich sequences melt at lower forces than AT-rich sequences: Fchar = 0.56pN for 77% GC but 0.73pN for 38% GC. An explanation for this counterintuitive effect is provided by the realization that supercoiling densities of a few percent only induce melting of a few percent of the base pairs. As a consequence, denaturation bubbles occur in local AT-rich regions and the sequence-dependent effect arises from an increased DNA bending/torsional energy associated with the plectonemes. This new insight indicates that an increased GC-content adjacent to AT-rich DNA regions will enhance local opening of the double-stranded DNA helix. PMID:26513573

  17. Temperature Dependent Kinetics DNA Charge Transport

    NASA Astrophysics Data System (ADS)

    Wohlgamuth, Chris; McWilliams, Marc; Slinker, Jason

    2012-10-01

    Charge transport (CT) through DNA has been extensively studied, and yet the mechanism of this process is still not yet fully understood. Besides the benefits of understanding charge transport through this fundamental molecule, further understanding of this process will elucidate the biological implications of DNA CT and advance sensing technology. Therefore, we have investigated the temperature dependence of DNA CT by measuring the electrochemistry of DNA monolayers modified with a redox-active probe. By using multiplexed electrodes on silicon chips, we compare square wave voltammetry of distinct DNA sequences under identical experimental conditions. We vary the probe length within the well matched DNA duplex in order to investigate distance dependent kinetics. This length dependent study is a necessary step to understanding the dominant mechanism behind DNA CT. Using a model put forth by O'Dea and Osteryoung and applying a nonlinear least squares analysis we are able to determine the charge transfer rates (k), transfer coefficients (α), and the total surface concentration (&*circ;) of the DNA monolayer. Arrhenius like behavior is observed for the multiple probe locations, and the results are viewed in light of and compared to the prominent charge transport mechanisms.

  18. Stimuli dependent impedance of conductive magnetorheological elastomers

    NASA Astrophysics Data System (ADS)

    Wang, Yu; Xuan, Shouhu; Dong, Bo; Xu, Feng; Gong, Xinglong

    2016-02-01

    The structure dependent impedance of conductive magnetorheological elastomers (MREs) under different loads and magnetic fields has been studied in this work. By increasing the weight fraction of iron particles, the conductivity of the MREs increased. Dynamic mechanical measurements and synchrotron radiation x-ray computed tomography (SR-CT) were used and they provided reasons for the electrical properties changing significantly under pressure and magnetic field stimulation. The high sensitivity of MREs to external stimuli renders them suitable for application in force or magnetic field sensors. The equivalent circuit model was proposed to analyze the impedance response of MREs and it fits the experimental results very well. Each circuit component reflected the change of the inner interface under different conditions, thus relative changes in the microstructure could be distinguished. This method could be used not only to detect the structural changes in the MRE but also to provide a great deal of valuable information for the further understanding of the MR mechanism.

  19. The contact area dependent interfacial thermal conductance

    SciTech Connect

    Liu, Chenhan; Wei, Zhiyong; Bi, Kedong; Yang, Juekuan; Chen, Yunfei; Wang, Jian

    2015-12-15

    The effects of the contact area on the interfacial thermal conductance σ are investigated using the atomic Green’s function method. Different from the prediction of the heat diffusion transport model, we obtain an interesting result that the interfacial thermal conductance per unit area Λ is positively dependent on the contact area as the area varies from a few atoms to several square nanometers. Through calculating the phonon transmission function, it is uncovered that the phonon transmission per unit area increases with the increased contact area. This is attributed to that each atom has more neighboring atoms in the counterpart of the interface with the increased contact area, which provides more channels for phonon transport.

  20. Temperature dependence of DNA translocations through solid-state nanopores

    PubMed Central

    Verschueren, Daniel V.; Jonsson, Magnus P.; Dekker, Cees

    2015-01-01

    In order to gain a better physical understanding of DNA translocations through solid-state nanopores, we study the temperature dependence of λ-DNA translocations through 10 nm-in-diameter silicon-nitride nanopores, both experimentally and theoretically. The measured ionic conductance G, the DNA-induced ionic-conductance blockades ΔG and the event frequency Γ all increase with increasing temperature while the DNA translocation time τ decreases. G and ΔG are accurately described when bulk and surface conductances of the nanopore are considered and access resistance is incorporated appropriately. Viscous drag on the untranslocated part of the DNA coil is found to dominate the temperature dependence of the translocation times and the event rate is well described by a balance between diffusion and electrophoretic motion. The good fit between modeled and measured properties of DNA translocations through solid-state nanopores in this first comprehensive temperature study, suggest that our model captures the relevant physics of the process. PMID:25994084

  1. Molecular conductance of double-stranded DNA evaluated by electrochemical capacitance spectroscopy.

    PubMed

    Ribeiro, W C; Gonçalves, L M; Liébana, S; Pividori, M I; Bueno, P R

    2016-04-21

    Conductance was measured in two different double stranded DNA (both with 20 bases), the more conducting poly(dG)-poly(dC) (ds-DNAc) and the less conducting poly(dA)-poly(dT) (ds-DNAi), by means of Electrochemical Capacitance Spectroscopy (ECS). The use of the ECS approach, exemplified herein with DNA nanowires, is equally a suitable and time-dependent advantageous alternative for conductance measurement of molecular systems, additionally allowing better understanding of the alignment existing between molecular scale conductance and electron transfer rate. PMID:27074378

  2. Control of electrical conduction in DNA using hole doping

    NASA Astrophysics Data System (ADS)

    Lee, Hea-Yeon; Taniguchi, Masateru; Yoo, K. H.; Otsuka, Youichi; Tanaka, Hidekazu; Kawai, Tomoji

    2002-03-01

    Control of electrical conduction in DNA using hole doping H.Y.Lee1, M.Taniguchi1, K.H.Yoo2, Y.Otsuka1 H.Tanaka1 and T.Kawai1 1The Institute of Scientific and Industrial Research(ISIR), Osaka University, Osaka, Japan. 2Department of Physics, Younsei University, Seoul, Korea Possible applications of DNA molecules in electronic devices and biosensors were suggested almost ten years ago A DNA structure containing a single type of base pair appears to be a good candidate for conduction along the \\x81E-electron clouds of the stacked bases. There have been lots of investigations on conduction mechanisms of the DNA molecules. However, it is not still clear whether the observed conductions of some DNA molecules come from motions of either ionic charges or other carriers. Although the basic mechanism for DNA-mediated charge transport should be understood for electronic applications, there have been divergent reports on its nature. And I will be present the research for the charge carrier conduction of DNA film under oxygen and iodine gas by using 10¡V100 nm gap. The doping studies using oxygen and iodine gas can provide a definite answer for the carrier conduction mechanism and also a possible method to control the carrier concentration in DNA molecules. Using oxygen and iodine adsorption experiments on the poly (dG)-poly (dC) DNA molecules, we will show that their conductance becomes increased easily by several orders of magnitudes due to the hole doping, which is a characteristic behavior of a p-type semiconductor. On the other hand, we will also show that the poly (dA) - poly (dT) DNA molecules behave as an n-type semiconductor. Our works indicate that the concentration and the type of carriers in the DNA molecules could be controlled using proper doping methods. We expect that this would be a major breakthrough in DNA-based nano-electronics, similar to the fact that the doped conductive has polyacetylene opened up a new field of electronics with exciting implications

  3. Ionic Conductivity, Structural Deformation and Programmable Anisotropy of DNA Origami in Electric Field

    PubMed Central

    Li, Chen-Yu; Hemmig, Elisa A.; Kong, Jinglin; Yoo, Jejoong; Hernández-Ainsa, Silvia

    2015-01-01

    The DNA origami technique can enable functionalization of inorganic structures for single-molecule electric current recordings. Experiments have shown that several layers of DNA molecules—a DNA origami plate— placed on top of a solid-state nanopore is permeable to ions. Here, we report a comprehensive characterization of the ionic conductivity of DNA origami plates by means of all-atom molecular dynamics (MD) simulations and nanocapillary electric current recordings. Using the MD method, we characterize the ionic conductivity of several origami constructs, revealing the local distribution of ions, the distribution of the electrostatic potential and contribution of different molecular species to the current. The simulations determine the dependence of the ionic conductivity on the applied voltage, the number of DNA layers, the nucleotide content and the lattice type of the plates. We demonstrate that increasing the concentration of Mg2+ ions makes the origami plates more compact, reducing their conductivity. The conductance of a DNA origami plate on top of a solid-state nanopore is determined by the two competing effects: bending of the DNA origami plate that reduces the current and separation of the DNA origami layers that increases the current. The latter is produced by the electro-osmotic flow and is reversible at the time scale of a hundred nanoseconds. The conductance of a DNA origami object is found to depend on its orientation, reaching maximum when the electric field aligns with the direction of the DNA helices. Our work demonstrates feasibility of programming the electrical properties of a self-assembled nanoscale object using DNA. PMID:25623807

  4. Size dependent polaronic conduction in hematite

    NASA Astrophysics Data System (ADS)

    Sharma, Monika; Banday, Azeem; Murugavel, Sevi

    2016-05-01

    Lithium Ion Batteries have been attracted as the major renewable energy source for all portable electronic devices because of its advantages like superior energy density, high theoretical capacity, high specific energy, stable cycling and less memory effects. Recently, α-Fe2O3 has been considered as a potential anode material due to high specific capacity, low cost, high abundance and environmental benignity. We have synthesized α-Fe2O3 with various sizes by using the ball milling and sol-gel procedure. Here, we report the dc conductivity measurement for the crystallite size ranging from 15 nm to 50nm. It has been observed that the enhancement in the polaronic conductivity nearly two orders in magnitude while reducing the crystallite size from bulk into nano scale level. The enhancement in the conductivity is due to the augmented to compressive strain developed in the material which leads to pronounced decrease in the hopping length of polarons. Thus, nanocrystaline α-Fe2O3 may be a better alternative anode material for lithium ion batteries than earlier reported systems.

  5. Molecular conductance of double-stranded DNA evaluated by electrochemical capacitance spectroscopy

    NASA Astrophysics Data System (ADS)

    Ribeiro, W. C.; Gonçalves, L. M.; Liébana, S.; Pividori, M. I.; Bueno, P. R.

    2016-04-01

    Conductance was measured in two different double stranded DNA (both with 20 bases), the more conducting poly(dG)-poly(dC) (ds-DNAc) and the less conducting poly(dA)-poly(dT) (ds-DNAi), by means of Electrochemical Capacitance Spectroscopy (ECS). The use of the ECS approach, exemplified herein with DNA nanowires, is equally a suitable and time-dependent advantageous alternative for conductance measurement of molecular systems, additionally allowing better understanding of the alignment existing between molecular scale conductance and electron transfer rate.Conductance was measured in two different double stranded DNA (both with 20 bases), the more conducting poly(dG)-poly(dC) (ds-DNAc) and the less conducting poly(dA)-poly(dT) (ds-DNAi), by means of Electrochemical Capacitance Spectroscopy (ECS). The use of the ECS approach, exemplified herein with DNA nanowires, is equally a suitable and time-dependent advantageous alternative for conductance measurement of molecular systems, additionally allowing better understanding of the alignment existing between molecular scale conductance and electron transfer rate. Electronic supplementary information (ESI) available. See DOI: 10.1039/c6nr01076h

  6. Temperature dependence of gramicidin channel conductance

    NASA Astrophysics Data System (ADS)

    Song, Hyundeok; Beck, Thomas

    2010-03-01

    The gramicidin channel is the smallest known biological ion channel, and it exhibits cation selectivity. Recently, Dr. John Cuppoletti's group at the University of Cincinnati has shown that the gramicidin channel can function at high temperatures with significant currents. This finding may have implications for fuel cell technologies. In order to explore the effect of temperature on channel conductance, we examined the gramicidin system at 300K, 330K, and 360K by computer simulation. Two forms of gramicidin, the head-to-head helical dimer and the intertwined double helix, were examined. Both the decrease of the free energy barrier and the increase of the diffusion of potassium ions inside the gramicidin channel at high temperatures imply an increase of current. We found that higher temperatures also affect the lifetime of hydrogen bonds, the distribution of the bending angle, the distribution of the distance between dimers, and the size of the pore radius for the helical dimer structure. These finding may be related to the gating of the gramicidin channel.

  7. Dramatic changes in DNA conductance with stretching: structural polymorphism at a critical extension.

    PubMed

    Bag, Saientan; Mogurampelly, Santosh; Goddard Iii, William A; Maiti, Prabal K

    2016-09-21

    In order to interpret recent experimental studies of the dependence of conductance of ds-DNA as the DNA is pulled from the 3'end1-3'end2 ends, which find a sharp conductance jump for a very short (4.5%) stretching length, we carried out multiscale modeling to predict the conductance of dsDNA as it is mechanically stretched to promote various structural polymorphisms. We calculate the current along the stretched DNA using a combination of molecular dynamics simulations, non-equilibrium pulling simulations, quantum mechanics calculations, and kinetic Monte Carlo simulations. For 5'end1-5'end2 attachments we find an abrupt jump in the current within a very short stretching length (6 Å or 17%) leading to a melted DNA state. In contrast, for 3'end1-3'end2 pulling it takes almost 32 Å (84%) of stretching to cause a similar jump in the current. Thus, we demonstrate that charge transport in DNA can occur over stretching lengths of several nanometers. We find that this unexpected behaviour in the B to S conformational DNA transition arises from highly inclined base pair geometries that result from this pulling protocol. We found that the dramatically different conductance behaviors for two different pulling protocols arise from how the hydrogen bonds of DNA base pairs break. PMID:27545499

  8. Sequence and Structure Dependent DNA-DNA Interactions

    NASA Astrophysics Data System (ADS)

    Kopchick, Benjamin; Qiu, Xiangyun

    Molecular forces between dsDNA strands are largely dominated by electrostatics and have been extensively studied. Quantitative knowledge has been accumulated on how DNA-DNA interactions are modulated by varied biological constituents such as ions, cationic ligands, and proteins. Despite its central role in biology, the sequence of DNA has not received substantial attention and ``random'' DNA sequences are typically used in biophysical studies. However, ~50% of human genome is composed of non-random-sequence DNAs, particularly repetitive sequences. Furthermore, covalent modifications of DNA such as methylation play key roles in gene functions. Such DNAs with specific sequences or modifications often take on structures other than the canonical B-form. Here we present series of quantitative measurements of the DNA-DNA forces with the osmotic stress method on different DNA sequences, from short repeats to the most frequent sequences in genome, and to modifications such as bromination and methylation. We observe peculiar behaviors that appear to be strongly correlated with the incurred structural changes. We speculate the causalities in terms of the differences in hydration shell and DNA surface structures.

  9. Using DNA looping to measure sequence dependent DNA elasticity

    NASA Astrophysics Data System (ADS)

    Kandinov, Alan; Raghunathan, Krishnan; Meiners, Jens-Christian

    2012-10-01

    We are using tethered particle motion (TPM) microscopy to observe protein-mediated DNA looping in the lactose repressor system in DNA constructs with varying AT / CG content. We use these data to determine the persistence length of the DNA as a function of its sequence content and compare the data to direct micromechanical measurements with constant-force axial optical tweezers. The data from the TPM experiments show a much smaller sequence effect on the persistence length than the optical tweezers experiments.

  10. Electrochemical DNA Hybridization Sensors Based on Conducting Polymers

    PubMed Central

    Rahman, Md. Mahbubur; Li, Xiao-Bo; Lopa, Nasrin Siraj; Ahn, Sang Jung; Lee, Jae-Joon

    2015-01-01

    Conducting polymers (CPs) are a group of polymeric materials that have attracted considerable attention because of their unique electronic, chemical, and biochemical properties. This is reflected in their use in a wide range of potential applications, including light-emitting diodes, anti-static coating, electrochromic materials, solar cells, chemical sensors, biosensors, and drug-release systems. Electrochemical DNA sensors based on CPs can be used in numerous areas related to human health. This review summarizes the recent progress made in the development and use of CP-based electrochemical DNA hybridization sensors. We discuss the distinct properties of CPs with respect to their use in the immobilization of probe DNA on electrode surfaces, and we describe the immobilization techniques used for developing DNA hybridization sensors together with the various transduction methods employed. In the concluding part of this review, we present some of the challenges faced in the use of CP-based DNA hybridization sensors, as well as a future perspective. PMID:25664436

  11. DNA-sensors based on functionalized conducting polymers and quantum dots

    NASA Astrophysics Data System (ADS)

    Kjällman, Tanja; Peng, Hui; Travas-Sejdic, Jadranka; Soeller, Christian

    2007-12-01

    The availability of rapid and specific biosensors is of great importance for many areas of biomedical research and modern biotechnology. This includes a need for DNA sensors where the progress of molecular biology demands routine detection of minute concentrations of specific gene fragments. A promising alternative approach to traditional DNA essays utilizes novel smart materials, including conducting polymers and nanostructured materials such as quantum dots. We have constructed a number of DNA sensors based on smart materials that allow rapid one-step detection of unlabeled DNA fragments with high specificity. These sensors are based on functionalized conducting polymers derived from polypyrrole (PPy) and poly(p-phenylenevinylene) (PPV). PPy based sensors provide intrinsic electrical readout via cyclic voltammetry and electrochemical impedance spectroscopy. The performance of these sensors is compared to a novel self-assembled monolayer-PNA construct on a gold electrode. Characterization of the novel PNA based sensor shows that it has comparable performance to the PPy based sensors and can also be read out effectively using AC cyclic voltammetry. Complementary to such solid substrate sensors we have developed a novel optical DNA essay based on a new PPV derived cationic conducting polymer. DNA detection in this essay results from sample dependent fluorescence resonance energy transfer changes between the cationic conducting polymer and Cy3 labeled probe oligonucleotides. As an alternative to such fluorochrome based sensors we discuss the use of inorganic nanocrystals ('quantum dots') and present data from water soluble CdTe quantum dots synthesized in an aqueous environment.

  12. DNA nanosensor surface grafting and salt dependence

    NASA Astrophysics Data System (ADS)

    Carvalho, B. G.; Fagundes, J.; Martin, A. A.; Raniero, L.; Favero, P. P.

    2013-02-01

    In this paper we investigated the Paracoccidoides brasiliensis fungus nanosensor by simulations of simple strand DNA grafting on gold nanoparticle. In order to improve the knowledge of nanoparticle environment, the addiction of salt solution was studied at the models proposed by us. Nanoparticle and DNA are represented by economic models validated by us in this paper. In addition, the DNA grafting and salt influences are evaluated by adsorption and bond energies calculations. This theoretical evaluation gives support to experimental diagnostics techniques of diseases.

  13. Frequency-dependent conductivity in bismuth-vanadate glassy semiconductors

    NASA Astrophysics Data System (ADS)

    Ghosh, Aswini

    1990-01-01

    The first measurements are reported for the frequency-dependent (ac) conductivity (real as well as imaginary parts) for various compositions of the bismuth-vanadate glassy semiconductors in the frequency range 102-105 Hz and in the temperature range 77-420 K. The behavior of the ac conductivity is broadly similar to what has been observed previously in many other types of amorphous semiconductors, namely, nearly linear frequency dependence and weak temperature dependence. The experimental results are analyzed with reference to various theoretical models based on quantum-mechanical tunneling and classical hopping over barriers. The analysis shows that the temperature dependence of the ac conductivity is consistent with the simple quantum-mechanical tunneling model at low temperatures; however, this model completely fails to predict the observed temperature dependence of the frequency exponent. The overlapping-large-polaron tunneling model can explain the temperature dependence of the frequency exponent at low temperatures. Fitting of this model to the low-temperature data yields a reasonable value of the wave-function decay constant. However, this model predicts the temperature dependence of the ac conductivity much higher than what actual data showed. The correlated barrier hopping model is consistent with the temperature dependence of both the ac conductivity and its frequency exponent. This model provides reasonable values of the maximum barrier heights but higher values of characteristic relaxation times.

  14. Identification of temperature-dependent thermal conductivity and experimental verification

    NASA Astrophysics Data System (ADS)

    Pan, Weizhen; Yi, Fajun; Zhu, Yanwei; Meng, Songhe

    2016-07-01

    A modified Levenberg–Marquardt method (LMM) for the identification of temperature-dependent thermal conductivity is proposed; the experiment and structure of the specimen for identification are also designed. The temperature-dependent thermal conductivities of copper C10200 and brass C28000 are identified to verify the effectiveness of the proposed identification method. The comparison between identified results and the measured data of laser flash diffusivity apparatus indicates the fine consistency and potential usage of the proposed method.

  15. ION AND TEMPERATURE DEPENDENCE OF ELECTRICAL CONDUCTANCE FOR NATURAL WATERS

    EPA Science Inventory

    Four empirical equations describing the temperature dependence of electrical conductance of aqueous solutions are compared for the case of single electrolytes. The best method uses a modified Walden product where the log of the ratio between the conductances at two temperatures i...

  16. Frequency-dependent effective hydraulic conductivity of strongly heterogeneous media.

    PubMed

    Caspari, E; Gurevich, B; Müller, T M

    2013-10-01

    The determination of the transport properties of heterogeneous porous rocks, such as an effective hydraulic conductivity, arises in a range of geoscience problems, from groundwater flow analysis to hydrocarbon reservoir modeling. In the presence of formation-scale heterogeneities, nonstationary flows, induced by pumping tests or propagating elastic waves, entail localized pressure diffusion processes with a characteristic frequency depending on the pressure diffusivity and size of the heterogeneity. Then, on a macroscale, a homogeneous equivalent medium exists, which has a frequency-dependent effective conductivity. The frequency dependence of the conductivity can be analyzed with Biot's equations of poroelasticity. In the quasistatic frequency regime of this framework, the slow compressional wave is a proxy for pressure diffusion processes. This slow compressional wave is associated with the out-of-phase motion of the fluid and solid phase, thereby creating a relative fluid-solid displacement vector field. Decoupling of the poroelasticity equations gives a diffusion equation for the fluid-solid displacement field valid in a poroelastic medium with spatial fluctuations in hydraulic conductivity. Then, an effective conductivity is found by a Green's function approach followed by a strong-contrast perturbation theory suggested earlier in the context of random dielectrics. This theory leads to closed-form expressions for the frequency-dependent effective conductivity as a function of the one- and two-point probability functions of the conductivity fluctuations. In one dimension, these expressions are consistent with exact solutions in both low- and high-frequency limits for arbitrary conductivity contrast. In 3D, the low-frequency limit depends on the details of the microstructure. However, the derived approximation for the effective conductivity is consistent with the Hashin-Shtrikman bounds. PMID:24229128

  17. Molecular Dynamics of Membrane-Spanning DNA Channels: Conductance Mechanism, Electro-Osmotic Transport, and Mechanical Gating.

    PubMed

    Yoo, Jejoong; Aksimentiev, Aleksei

    2015-12-01

    DNA self-assembly has emerged as a new paradigm for design of biomimetic membrane channels. Several experimental groups have already demonstrated assembly and insertion of DNA channels into lipid bilayer membranes; however, the structure of the channels and their conductance mechanism have remained undetermined. Here, we report the results of molecular dynamics simulations that characterized the biophysical properties of the DNA membrane channels with atomic precision. We show that, while overall remaining stable, the local structure of the channels undergoes considerable fluctuations, departing from the idealized design. The transmembrane ionic current flows both through the central pore of the channel as well as along the DNA walls and through the gaps in the DNA structure. Surprisingly, we find that the conductance of DNA channels depend on the membrane tension, making them potentially suitable for force-sensing applications. Finally, we show that electro-osmosis governs the transport of druglike molecules through the DNA channels. PMID:26551518

  18. Diversification of DnaA dependency for DNA replication in cyanobacterial evolution.

    PubMed

    Ohbayashi, Ryudo; Watanabe, Satoru; Ehira, Shigeki; Kanesaki, Yu; Chibazakura, Taku; Yoshikawa, Hirofumi

    2016-05-01

    Regulating DNA replication is essential for all living cells. The DNA replication initiation factor DnaA is highly conserved in prokaryotes and is required for accurate initiation of chromosomal replication at oriC. DnaA-independent free-living bacteria have not been identified. The dnaA gene is absent in plastids and some symbiotic bacteria, although it is not known when or how DnaA-independent mechanisms were acquired. Here, we show that the degree of dependency of DNA replication on DnaA varies among cyanobacterial species. Deletion of the dnaA gene in Synechococcus elongatus PCC 7942 shifted DNA replication from oriC to a different site as a result of the integration of an episomal plasmid. Moreover, viability during the stationary phase was higher in dnaA disruptants than in wild-type cells. Deletion of dnaA did not affect DNA replication or cell growth in Synechocystis sp. PCC 6803 or Anabaena sp. PCC 7120, indicating that functional dependency on DnaA was already lost in some nonsymbiotic cyanobacterial lineages during diversification. Therefore, we proposed that cyanobacteria acquired DnaA-independent replication mechanisms before symbiosis and such an ancestral cyanobacterium was the sole primary endosymbiont to form a plastid precursor. PMID:26517699

  19. Interplay between Ku, Artemis, and the DNA-dependent protein kinase catalytic subunit at DNA ends.

    PubMed

    Drouet, Jérôme; Frit, Philippe; Delteil, Christine; de Villartay, Jean-Pierre; Salles, Bernard; Calsou, Patrick

    2006-09-22

    Repair of DNA double strand breaks (DSB) by the nonhomologous end-joining pathway in mammals requires at least seven proteins involved in a simplified two-step process: (i) recognition and synapsis of the DNA ends dependent on the DNA-dependent protein kinase (DNA-PK) formed by the Ku70/Ku80 heterodimer and the catalytic subunit DNA-PKcs in association with Artemis; (ii) ligation dependent on the DNA ligase IV.XRCC4.Cernunnos-XLF complex. The Artemis protein exhibits exonuclease and endonuclease activities that are believed to be involved in the processing of a subclass of DSB. Here, we have analyzed the interactions of Artemis and nonhomologous end-joining pathway proteins both in a context of human nuclear cell extracts and in cells. DSB-inducing agents specifically elicit the mobilization of Artemis to damaged chromatin together with DNA-PK and XRCC4/ligase IV proteins. DNA-PKcs is necessary for the loading of Artemis on damaged DNA and is the main kinase that phosphorylates Artemis in cells damaged with highly efficient DSB producers. Under kinase-preventive conditions, both in vitro and in cells, Ku-mediated assembly of DNA-PK on DNA ends is responsible for a dissociation of the DNA-PKcs. Artemis complex. Conversely, DNA-PKcs kinase activity prevents Artemis dissociation from the DNA-PK.DNA complex. Altogether, our data allow us to propose a model in which a DNA-PKcs-mediated phosphorylation is necessary both to activate Artemis endonuclease activity and to maintain its association with the DNA end site. This tight functional coupling between the activation of both DNA-PKcs and Artemis may avoid improper processing of DNA. PMID:16857680

  20. Electrical conduction and photoresponses of gamma-ray-irradiated single-stranded DNA/single-walled carbon nanotube composite systems

    NASA Astrophysics Data System (ADS)

    Hong, W.; Lee, E. M.; Kim, D. W.; Lee, Cheol Eui

    2015-04-01

    Effects of gamma-ray irradiation on the electrical conductivity and photoresponse have been studied for single-stranded DNA (ssDNA)/single-walled carbon nanotube (SWNT) composite films. The temperature-dependent electrical conductivity of the ssDNA/SWNT composite films, well described by a fluctuation-induced tunneling model, indicated modification of the barrier for thermally activated conduction by the gamma-ray irradiation. Besides, the photoresponse measurements indicated modified photoexcited charge carrier generation and oxygen photodesorption in the composite systems due to the gamma-ray irradiation.

  1. Conformation dependent electronic transport in a DNA double-helix

    SciTech Connect

    Kundu, Sourav Karmakar, S. N.

    2015-10-15

    We present a tight-binding study of conformation dependent electronic transport properties of DNA double-helix including its helical symmetry. We have studied the changes in the localization properties of DNA as we alter the number of stacked bases within every pitch of the double-helix keeping fixed the total number of nitrogen bases within the DNA molecule. We take three DNA sequences, two of them are periodic and one is random and observe that in all the cases localization length increases as we increase the radius of DNA double-helix i.e., number of nucleobases within a pitch. We have also investigated the effect of backbone energetic on the I-V response of the system and found that in presence of helical symmetry, depending on the interplay of conformal variation and disorder, DNA can be found in either metallic, semiconducting and insulating phases, as observed experimentally.

  2. Unraveling the Complexities of DNA-Dependent Protein Kinase Autophosphorylation

    PubMed Central

    Neal, Jessica A.; Sugiman-Marangos, Seiji; VanderVere-Carozza, Pamela; Wagner, Mike; Turchi, John; Lees-Miller, Susan P.; Junop, Murray S.

    2014-01-01

    DNA-dependent protein kinase (DNA-PK) orchestrates DNA repair by regulating access to breaks through autophosphorylations within two clusters of sites (ABCDE and PQR). Blocking ABCDE phosphorylation (by alanine mutation) imparts a dominant negative effect, rendering cells hypersensitive to agents that cause DNA double-strand breaks. Here, a mutational approach is used to address the mechanistic basis of this dominant negative effect. Blocking ABCDE phosphorylation hypersensitizes cells to most types of DNA damage (base damage, cross-links, breaks, and damage induced by replication stress), suggesting that DNA-PK binds DNA ends that result from many DNA lesions and that blocking ABCDE phosphorylation sequesters these DNA ends from other repair pathways. This dominant negative effect requires DNA-PK's catalytic activity, as well as phosphorylation of multiple (non-ABCDE) DNA-PK catalytic subunit (DNA-PKcs) sites. PSIPRED analysis indicates that the ABCDE sites are located in the only contiguous extended region of this huge protein that is predicted to be disordered, suggesting a regulatory role(s) and perhaps explaining the large impact ABCDE phosphorylation has on the enzyme's function. Moreover, additional sites in this disordered region contribute to the ABCDE cluster. These data, coupled with recent structural data, suggest a model whereby early phosphorylations promote initiation of nonhomologous end joining (NHEJ), whereas ABCDE phosphorylations, potentially located in a “hinge” region between the two domains, lead to regulated conformational changes that initially promote NHEJ and eventually disengage NHEJ. PMID:24687855

  3. Functional domains of an ATP-dependent DNA ligase.

    PubMed

    Doherty, A J; Wigley, D B

    1999-01-01

    The crystal structure of an ATP-dependent DNA ligase from bacteriophage T7 revealed that the protein comprised two structural domains. In order to investigate the biochemical activities of these domains, we have overexpressed them separately and purified them to homogeneity. The larger N-terminal domain retains adenylation and ligase activities, though both at a reduced level. The adenylation activity of the large domain is stimulated by the presence of the smaller domain, suggesting that a conformational change is required for adenylation in the full length protein. The DNA binding properties of the two fragments have also been studied. The larger domain is able to band shift both single and double-stranded DNA, while the smaller fragment is only able to bind to double-stranded DNA. These data suggest that the specificity of DNA ligases for nick sites in DNA is produced by a combination of these different DNA binding activities in the intact enzyme. PMID:9878388

  4. Size Dependent Heat Conduction in One-Dimensional Diatomic Lattices

    NASA Astrophysics Data System (ADS)

    Tejal, N. Shah; P. N., Gajjar

    2016-04-01

    We study the size dependency of heat conduction in one-dimensional diatomic FPU-β lattices and establish that for low dimensional material, contribution from optical phonons is found more effective to the thermal conductivity and enhance heat transport in the thermodynamic limit N → ∞. For the finite size, thermal conductivity of 1D diatomic lattice is found to be lower than 1D monoatomic chain of the same size made up of the constituent particle of the diatomic chain. For the present 1D diatomic chain, obtained value of power divergent exponent of thermal conductivity 0.428±0.001 and diffusion exponent 1.2723 lead to the conclusions that increase in the system size, increases the thermal conductivity and existence of anomalous energy diffusion. Existing numerical data supports our findings.

  5. Xenopus transcription factor IIIA-dependent DNA renaturation.

    PubMed

    Fiser-Littell, R M; Hanas, J S

    1988-11-15

    Kinetic and titration analyses are used to elucidate the mechanism by which Xenopus transcription factor IIIA (TFIIIA), a protein required for 5 S RNA synthesis by RNA polymerase III, promotes DNA renaturation. TFIIIA promotes 50% renaturation of complementary strands (303 bases) in 45 s. Analyses of the renaturation kinetics indicate the rate-limiting step in this TFIIIA-dependent reaction is first order. TFIIIA-dependent DNA renaturation is a stoichiometric rather than a catalytic process. The renaturation rates for specific and nonspecific DNA are very similar, indicating lack of sequence specificity in this TFIIIA-dependent process. In the nanomolar concentration range of protein and DNA, renaturation occurs at a ratio of about one TFIIIA molecule/single strand (303 bases). Elevated reaction temperatures strongly stimulate TFIIIA-dependent DNA renaturation; at 45 degrees C, renaturation of the 303-base pair fragment nears completion in about 5 s. The ability of TFIIIA to rapidly promote DNA renaturation is unique when compared with Escherichia coli recA protein, single-stranded DNA binding protein, or bacteriophage T4 gene 32 protein. This mechanism by which TFIIIA promotes DNA renaturation is compatible with features of 5 S RNA gene transcription. PMID:2460459

  6. Structure of DNA-dependent protein kinase: implications for its regulation by DNA.

    PubMed

    Leuther, K K; Hammarsten, O; Kornberg, R D; Chu, G

    1999-03-01

    DNA double-strand breaks are created by ionizing radiation or during V(D)J recombination, the process that generates immunological diversity. Breaks are repaired by an end-joining reaction that requires DNA-PKCS, the catalytic subunit of DNA-dependent protein kinase. DNA-PKCS is a 460 kDa serine-threonine kinase that is activated by direct interaction with DNA. Here we report its structure at 22 A resolution, as determined by electron crystallography. The structure contains an open channel, similar to those seen in other double-stranded DNA-binding proteins, and an enclosed cavity with three openings large enough to accommodate single-stranded DNA, with one opening adjacent to the open channel. Based on these structural features, we performed biochemical experiments to examine the interactions of DNA-PKCS with different DNA molecules. Efficient kinase activation required DNA longer than 12 bp, the minimal length of the open channel. Competition experiments demonstrated that DNA-PKCS binds to double- and single-stranded DNA via separate but interacting sites. Addition of unpaired single strands to a double-stranded DNA fragment stimulated kinase activation. These results suggest that activation of the kinase involves interactions with both double- and single-stranded DNA, as suggested by the structure. A model for how the kinase is regulated by DNA is described. PMID:10064579

  7. Tight-binding approach to strain-dependent DNA electronics

    NASA Astrophysics Data System (ADS)

    Malakooti, Sadeq; Hedin, Eric; Joe, Yong

    2013-07-01

    Small mechanical strain perturbations are considered in calculations of the poly(G)-poly(C) DNA molecular electronic structure, using a tight-binding framework in conjunction with the theories of Slater-Koster and linear elasticity. Results reveal a strain-induced band gap for DNA which is linearly dependent on the induced strain. Local density of states calculations expose that the contribution of the guanine-cytosine base pairs in the charge transport mechanism is significantly enhanced relative to the backbones when DNA is compressed. Transport investigations also disclose a strain-induced metal-semiconductor transition for the DNA molecule, which suggests possible potential uses for sensing applications.

  8. Measuring the conductivity dependence of the Casimir force

    NASA Astrophysics Data System (ADS)

    Xu, Jun; Schafer, Robert; Banishev, Alexandr; Mohideen, Umar

    2015-03-01

    The strength and distance dependence of the Casimir force can be controlled through the conductivity of the material bodies, with lower conductivity in general leading to lower Casimir forces. However low conductivity, large bandgap materials which are insulating, have drawbacks as any surface electrostatic charges cannot be easily compensated. This restricts experiments to metallic or highly doped semiconductor materials. We will report on measurements of the Casimir force gradient using the frequency shift technique. Improvements in the measurement technique will be discussed. Measurements of the Casimir force gradient using low and high conductivity silicon surfaces will be reported. The authors thank G.L. Klimchitskaya and V.M. Mostepanenko for help with the theory and the US National Science Foundation for funding the research.

  9. DNA-PK is a DNA sensor for IRF-3-dependent innate immunity

    PubMed Central

    Ferguson, Brian J; Mansur, Daniel S; Peters, Nicholas E; Ren, Hongwei; Smith, Geoffrey L

    2012-01-01

    Innate immunity is the first immunological defence against pathogens. During virus infection detection of nucleic acids is crucial for the inflammatory response. Here we identify DNA-dependent protein kinase (DNA-PK) as a DNA sensor that activates innate immunity. We show that DNA-PK acts as a pattern recognition receptor, binding cytoplasmic DNA and triggering the transcription of type I interferon (IFN), cytokine and chemokine genes in a manner dependent on IFN regulatory factor 3 (IRF-3), TANK-binding kinase 1 (TBK1) and stimulator of interferon genes (STING). Both cells and mice lacking DNA-PKcs show attenuated cytokine responses to both DNA and DNA viruses but not to RNA or RNA virus infection. DNA-PK has well-established functions in the DNA repair and V(D)J recombination, hence loss of DNA-PK leads to severe combined immunodeficiency (SCID). However, we now define a novel anti-microbial function for DNA-PK, a finding with implications for host defence, vaccine development and autoimmunity. DOI: http://dx.doi.org/10.7554/eLife.00047.001 PMID:23251783

  10. Voltage-dependent conductances in Limulus ventral photoreceptors

    PubMed Central

    1982-01-01

    The voltage-dependent conductances of Limulus ventral photoreceptors have been investigated using a voltage-clamp technique. Depolarization in the dark induces inward and outward currents. The inward current is reduced by removing Na+ or Ca2+ and is abolished by removing both ions. These results suggest that both Na+ and Ca2+ carry voltage-dependent inward current. Inward current is insensitive to tetrodotoxin but is blocked by external Ni2+. The outward current has a large transient component that is followed by a smaller maintained component. Intracellular tetraethylammonium preferentially reduces the maintained component, and extracellular 4-amino pyridine preferentially reduces the transient component. Neither component is strongly affected by removal of extracellular Ca2+ or by intracellular injection of EGTA. It is concluded that the photoreceptors contain at least three separate voltage-dependent conductances: 1) a conductance giving rise to inward currents; 2) a delayed rectifier giving rise to maintained outward K+ current; and 3) a rapidly inactivating K+ conductance similar to the A current of molluscan neurons. PMID:7057161

  11. The conductivity dependence of the shear stress in electrorheological fluids

    NASA Astrophysics Data System (ADS)

    Lan, Yucheng; Xu, Xiaoyu; Men, Shouqiang; Lu, Kunquan

    1998-11-01

    A ferroelectric KNO3/silicone oil electrorheological (ER) fluid is introduced to investigate the conductivity dependence of the ER effect under dc electric fields where the ER effect is conductivity dominated. By measuring the temperature dependence of the shear stress across the Curie temperature of particles, the dependence of the ER effect on conductivity has been quantitatively obtained in experiments. There is a critical conductivity ratio Γc (or mismatch factor βc2): when Γ<Γc, the shear stress increases with Γ; when Γ>Γc, the shear stress decreases with Γ. An agreement is obtained between theory and experiment when Γ (or β2) is lower. In the higher Γ(or β2) range, the experimental data are not in agreement with the theoretical prediction and the interfacial effect should be taken into account. The experimental data are more reliable due to the same conditions, such as the chemical nature, the surfacial property of particles, and the interfacial property between particles and suspending liquid as well as the size and shape of the particles.

  12. Sequence dependent proton conduction in self-assembled peptide nanostructures

    NASA Astrophysics Data System (ADS)

    Lerner Yardeni, Jenny; Amit, Moran; Ashkenasy, Gonen; Ashkenasy, Nurit

    2016-01-01

    The advancement of diverse electrochemistry technologies depends on the development of novel proton conducting polymers. Inspired by the efficacy of proton transport through proteins, we show in this work that self-assembling peptide nanostructures may be a promising alternative for such organic proton conducting materials. We demonstrate that aromatic amino acids, which participate in charge transport in nature, unprecedentedly promote proton conduction under both high and low relative humidity conditions for d,l α-cyclic peptide nanotubes. For dehydrated networks long-range order of the assemblies, induced by the aromatic side chains, is shown to be a dominating factor for promoting conductivity. However, for hydrated networks this order of effect is less significant and conductivity can be improved by the introduction of proton donating carboxylic acid peptide side chains in addition to the aromatic side chains despite the lower order of the assemblies. Based on these observations, a novel cyclic peptide that incorporates non-natural naphthyl side chains was designed. Self-assembled nanotubes of this peptide show greatly improved dehydrated conductivity, while maintaining high conductivity under hydrated conditions. We envision that the demonstrated modularity and versatility of these bio inspired nanostructures will make them extremely attractive building blocks for the fabrication of devices for energy conversion and storage applications, as well as other applications that involve proton transport, whether dry or wet conductivity is desired.The advancement of diverse electrochemistry technologies depends on the development of novel proton conducting polymers. Inspired by the efficacy of proton transport through proteins, we show in this work that self-assembling peptide nanostructures may be a promising alternative for such organic proton conducting materials. We demonstrate that aromatic amino acids, which participate in charge transport in nature

  13. Size and dimensionality dependent phonon conductivity in nanocomposites

    NASA Astrophysics Data System (ADS)

    Al-Otaibi, Jawaher; Srivastava, G. P.

    2016-04-01

    We have studied size and dimensionality dependent phonon conductivity of PbTe-PbSe nanocomposites by considering three configurations: superlattice, embedded nanowire and embedded nanodot. Calculations have been performed in the framework of an effective medium theory. The required bulk thermal conductivities of PbTe and PbSe are evaluated by using Callaway’s effective relaxation-time theory, and by accounting for relevant scattering mechanism including three-phonon Normal and Umklapp interactions involving acoustic as well as optical branches. The thermal interface resistance is computed using the diffuse mismatch theory. It is found that the size (thickness) and volume fraction of PbSe are the two main factors that control the effective thermal conductivity in these nanocomposites. In particular, for PbSe size d  =  10 nm and volume fraction {{V}\\text{f}}=0.1 , our results predict significant reductions over the weighted average of room-temperature bulk results of 9%, 17% and 15% in the conductivity across the interfaces for the superlattice, embedded nanowire, and nanosphere structures, respectively. For a given {{V}\\text{f}} , an increase in d reduces the interface density Φ and the effective conductivity varies approximately as 1/\\sqrtΦ . It is shown that nanocompositing in any of the three configurations can beat the alloy limit for lattice thermal conductivity.

  14. Sea salt dependent electrical conduction in polar ice

    SciTech Connect

    Moore, J.; Paren, J. ); Oerter, H. )

    1992-12-10

    A 45 m length of ice core from Dolleman Island, Antarctic Peninsula has been dielectrically analyzed at 5 cm resolution using the dielectric profiling (DEP) technique. The core has also been chemically analyzed for major ionic impurities. A statistical analysis of the measurements shows that the LF (low frequency) conductivity is determined both by neutral salt and acid concentrations. The statistical relationships have been compared with results from laboratory experiments on ice doped with HF (hydrogen fluoride). Salts (probably dispersed throughout the ice fabric) determine the dielectric conductivity. The salt conduction mechanism is probably due to Bjerrum L defects alone, created by the incorporation of chloride ions in the lattice. Samples of ice from beneath the Filchner-Ronne Ice Shelf were also measured and display a similar conduction mechanism below a solubility limit of about 400 [mu]M of chloride. The temperature dependence of the neutral salt, acid and pure ice contributions to the LF conductivity of natural ice between [approximately] 70[degrees]C and 0[degrees]C is discussed. These results allow a comprehensive comparison of dielectric and chemical data from natural ice.

  15. A time dependent anatomically detailed model of cardiac conduction

    NASA Technical Reports Server (NTRS)

    Saxberg, B. E.; Grumbach, M. P.; Cohen, R. J.

    1985-01-01

    In order to understand the determinants of transitions in cardiac electrical activity from normal patterns to dysrhythmias such as ventricular fibrillation, we are constructing an anatomically and physiologically detailed finite element simulation of myocardial electrical propagation. A healthy human heart embedded in paraffin was sectioned to provide a detailed anatomical substrate for model calculations. The simulation of propagation includes anisotropy in conduction velocity due to fiber orientation as well as gradients in conduction velocities, absolute and relative refractory periods, action potential duration and electrotonic influence of nearest neighbors. The model also includes changes in the behaviour of myocardial tissue as a function of the past local activity. With this model, we can examine the significance of fiber orientation and time dependence of local propagation parameters on dysrhythmogenesis.

  16. Mode dependent lattice thermal conductivity of single layer graphene

    SciTech Connect

    Wei, Zhiyong; Yang, Juekuan; Bi, Kedong; Chen, Yunfei

    2014-10-21

    Molecular dynamics simulation is performed to extract the phonon dispersion and phonon lifetime of single layer graphene. The mode dependent thermal conductivity is calculated from the phonon kinetic theory. The predicted thermal conductivity at room temperature exhibits important quantum effects due to the high Debye temperature of graphene. But the quantum effects are reduced significantly when the simulated temperature is as high as 1000 K. Our calculations show that out-of-plane modes contribute about 41.1% to the total thermal conductivity at room temperature. The relative contribution of out-of-plane modes has a little decrease with the increase of temperature. Contact with substrate can reduce both the total thermal conductivity of graphene and the relative contribution of out-of-plane modes, in agreement with previous experiments and theories. Increasing the coupling strength between graphene and substrate can further reduce the relative contribution of out-of-plane modes. The present investigations also show that the relative contribution of different mode phonons is not sensitive to the grain size of graphene. The obtained phonon relaxation time provides useful insight for understanding the phonon mean free path and the size effects in graphene.

  17. Characterization of the tunneling conductance across DNA bases

    SciTech Connect

    Zikic, Radomir; Krstic, Predrag S; Zhang, Xiaoguang; Fuentes-Cabrera, Miguel A; Wells, Jack C; Zhao, Xiongce

    2006-01-01

    Characterization of the electrical properties of the DNA bases, Adenine, Cytosine, Guanine and Thymine, besides building the basic knowledge on these fundamental constituents of a DNA, is a crucial step in developing a DNA sequencing technology. We present a first-principles study of the current-voltage characteristics of nucleotide-like molecules of the DNA bases, placed in a 1.5 nm gap formed between gold nanoelectrodes. The quantum transport calculations in the tunneling regime are shown to vary strongly with the electrode-molecule geometry and the choice of the DFT exchangecorrelation functionals. Analysis of the results in the zero-bias limit indicates that distinguishable current-voltage characteristics of different DNA bases are dominated by the geometrical conformations of the bases and nanoelectrodes.

  18. Concentration and Length Dependence of DNA Looping in Transcriptional Regulation

    PubMed Central

    Han, Lin; Garcia, Hernan G.; Blumberg, Seth; Towles, Kevin B.; Beausang, John F.; Nelson, Philip C.; Phillips, Rob

    2009-01-01

    In many cases, transcriptional regulation involves the binding of transcription factors at sites on the DNA that are not immediately adjacent to the promoter of interest. This action at a distance is often mediated by the formation of DNA loops: Binding at two or more sites on the DNA results in the formation of a loop, which can bring the transcription factor into the immediate neighborhood of the relevant promoter. These processes are important in settings ranging from the historic bacterial examples (bacterial metabolism and the lytic-lysogeny decision in bacteriophage), to the modern concept of gene regulation to regulatory processes central to pattern formation during development of multicellular organisms. Though there have been a variety of insights into the combinatorial aspects of transcriptional control, the mechanism of DNA looping as an agent of combinatorial control in both prokaryotes and eukaryotes remains unclear. We use single-molecule techniques to dissect DNA looping in the lac operon. In particular, we measure the propensity for DNA looping by the Lac repressor as a function of the concentration of repressor protein and as a function of the distance between repressor binding sites. As with earlier single-molecule studies, we find (at least) two distinct looped states and demonstrate that the presence of these two states depends both upon the concentration of repressor protein and the distance between the two repressor binding sites. We find that loops form even at interoperator spacings considerably shorter than the DNA persistence length, without the intervention of any other proteins to prebend the DNA. The concentration measurements also permit us to use a simple statistical mechanical model of DNA loop formation to determine the free energy of DNA looping, or equivalently, the for looping. PMID:19479049

  19. Cation charge dependence of the forces driving DNA assembly.

    PubMed

    DeRouchey, Jason; Parsegian, V Adrian; Rau, Donald C

    2010-10-20

    Understanding the strength and specificity of interactions among biologically important macromolecules that control cellular functions requires quantitative knowledge of intermolecular forces. Controlled DNA condensation and assembly are particularly critical for biology, with separate repulsive and attractive intermolecular forces determining the extent of DNA compaction. How these forces depend on the charge of the condensing ion has not been determined, but such knowledge is fundamental for understanding the basis of DNA-DNA interactions. Here, we measure DNA force-distance curves for a homologous set of arginine peptides. All forces are well fit as the sum of two exponentials with 2.4- and 4.8-Å decay lengths. The shorter-decay-length force is always repulsive, with an amplitude that varies slightly with length or charge. The longer-decay-length force varies strongly with cation charge, changing from repulsion with Arg¹ to attraction with Arg². Force curves for a series of homologous polyamines and the heterogeneous protein protamine are quite similar, demonstrating the universality of these forces for DNA assembly. Repulsive amplitudes of the shorter-decay-length force are species-dependent but nearly independent of charge within each species. A striking observation was that the attractive force amplitudes for all samples collapse to a single curve, varying linearly with the inverse of the cation charge. PMID:20959102

  20. Effects of Ionic Dependence of DNA Persistence Length on the DNA Condensation at Room Temperature

    NASA Astrophysics Data System (ADS)

    Mao, Wei; Liu, Yan-Hui; Hu, Lin; Xu, Hou-Qiang

    2016-05-01

    DNA persistence length is a key parameter for quantitative interpretation of the conformational properties of DNA and related to the bending rigidity of DNA. A series of experiments pointed out that, in the DNA condensation process by multivalent cations, the condensed DNA takes elongated coil or compact globule states and the population of the compact globule states increases with an increase in ionic concentration. At the same time, single molecule experiments carried out in solution with multivalent cations (such as spermidine, spermine) indicated that DNA persistence length strongly depends on the ionic concentration. In order to revolve the effects of ionic concentration dependence of persistence length on DNA condensation, a model including the ionic concentration dependence of persistence length and strong correlation of multivalent cation on DNA is provided. The autocorrelation function of the tangent vectors is found as an effective way to detect the ionic concentration dependence of toroidal conformations. With an increase in ion concentration, the first periodic oscillation contained in the autocorrelation function shifts, the number of segment contained in the first periodic oscillation decreases gradually. According to the experiments, the average long-axis length is defined to estimate the ionic concentration dependence of condensation process further. The relation between long-axis length and ionic concentration matches the experimental results qualitatively. Supported by National Natural Science Foundation of China under Grant Nos. 11047022, 11204045, 11464004 and 31360215; The Research Foundation from Ministry of Education of China (212152), Guizhou Provincial Tracking Key Program of Social Development (SY20123089, SZ20113069); The General Financial Grant from the China Postdoctoral Science Foundation (2014M562341); The Research Foundation for Young University Teachers from Guizhou University (201311); The West Light Foundation (2015) and College

  1. A DNA enzyme with Mg(2+)-Dependent RNA Phosphoesterase Activity

    NASA Technical Reports Server (NTRS)

    Breaker, Ronald R.; Joyce, Gerald F.

    1995-01-01

    Previously we demonstrated that DNA can act as an enzyme in the Pb(2+)-dependent cleavage of an RNA phosphoester. This is a facile reaction, with an uncatalyzed rate for a typical RNA phosphoester of approx. 10(exp -4)/ min in the presence of 1 mM Pb(OAc)2 at pH 7.0 and 23 C. The Mg(2+) - dependent reaction is more difficult, with an uncatalyzed rate of approx. 10(exp -7)/ min under comparable conditions. Mg(2+) - dependent cleavage has special relevance to biology because it is compatible with intracellular conditions. Using in vitro selection, we sought to develop a family of phosphoester-cleaving DNA enzymes that operate in the presence of various divalent metals, focusing particularly on the Mg(2+) - dependent reaction. Results: We generated a population of greater than 10(exp 13) DNAs containing 40 random nucleotides and carried out repeated rounds of selective amplification, enriching for molecules that cleave a target RNA phosphoester in the presence of 1 mM Mg(2+), Mn(2+), Zn(2+) or Pb(2+). Examination of individual clones from the Mg(2+) lineage after the sixth round revealed a catalytic motif comprised of a three-stem junction.This motif was partially randomized and subjected to seven additional rounds of selective amplification, yielding catalysts with a rate of 0.01/ min. The optimized DNA catalyst was divided into separate substrate and enzyme domains and shown to have a similar level of activity under multiple turnover conditions. Conclusions: We have generated a Mg(2+) - dependent DNA enzyme that cleaves a target RNA phosphoester with a catalytic rate approx. 10(exp 5) - fold greater than that of the uncatalyzed reaction. This activity is compatible with intracellular conditions, raising the possibility that DNA enzymes might be made to operate in vivo.

  2. Interfacial Structure Dependent Spin Mixing Conductance in Cobalt Thin Films.

    PubMed

    Tokaç, M; Bunyaev, S A; Kakazei, G N; Schmool, D S; Atkinson, D; Hindmarch, A T

    2015-07-31

    Enhancement of Gilbert damping in polycrystalline cobalt thin-film multilayers of various thicknesses, overlayered with copper or iridium, was studied in order to understand the role of local interface structure in spin pumping. X-ray diffraction indicates that cobalt films less than 6 nm thick have strong fcc(111) texture while thicker films are dominated by hcp(0001) structure. The intrinsic damping for cobalt thicknesses above 6 nm is weakly dependent on cobalt thickness for both overlayer materials, and below 6 nm the iridium overlayers show higher damping enhancement compared to copper overlayers, as expected due to spin pumping. The interfacial spin mixing conductance is significantly enhanced in structures where both cobalt and iridium have fcc(111) structure in comparison to those where the cobalt layer has subtly different hcp(0001) texture at the interface. PMID:26274431

  3. Empowering Malaysian dentists to tobacco dependence treatment conduct.

    PubMed

    Nordin, Amer Siddiq Amer; Kadir, Rahimah Abdul; Yahya, Nurul Asyikin; Zakaria, Hazli; Rashid, Rusdi Abdul; Habil, Mohamed Hussain

    2014-08-01

    As a signatory to the World Health Organisation 2003 Framework Convention on Tobacco Control, Malaysia has policies in place and funded 300 public Quit clinics. Unfortunately, government dentists are not included to run tobacco dependence treatment. A cross-sectional exploratory survey was carried out to seek Malaysian dentists' opinion on their knowledge, perception and willingness to conduct tobacco dependence treatment. Participation was voluntary from those who attended a specially designed one-day, four-module workshop on tobacco cessation intervention. Data were collected using the Audience-Response-System equipment which tracked immediate responses covering four domains namely: smoking as a public health problem, smoking as an addiction, the role of dentists in the programme and confidence in conducting smoking cessation in the clinic. Sample comprised more female dentists (73.5%), mean age 33.6 (SD 8.99) years and with more than 3 years working experience. Findings indicated that the majority agreed Malaysia has a rising problem in the prevalence of smoking (71.6%) and predicted that it will affect mostly the young (81.9%). Only half of the dentists surveyed (58.9%) routinely recorded their patients' smoking habits. The majority (71.6%) believed that dentists are effective in helping their patient to stop smoking and 76.3% agreed that dentists should discuss the smoking habit with their patients; however, 60% agreed that doing so is too time consuming. In addition, only 24.7% knew of more ways to treat a smoking habit. The majority felt comfortable giving advice to patients about changing their habits (76.5%) or discussing treatment options (60.5%): 75% would opt for a combined programme of counselling and use of medication if they have to do, 15% would choose to go on counselling only, while 8% did not want to treat. In conclusion, the findings suggest that dentists have a strong potential to contribute significantly to providing smoking cessation

  4. Boundary formulations for shape sensitivity of temperature dependent conductivity problems

    NASA Technical Reports Server (NTRS)

    Kane, James H.; Wang, Hua

    1992-01-01

    Used in concert with the Kirchhoff transformation, implicit differentiation of the discretized boundary integral equations governing the conduction of heat in solids with temperature dependent thermal conductivity is shown to generate an accurate and economical approach for computation of shape sensitivities. For problems with specified temperature and heat flux boundary conditions, a linear problem results for both the analysis and sensitivity analysis. In problems with either convection or radiation boundary conditions, a nonlinear problem is generated. Several iterative strategies are presented for the solution of the resulting sets of nonlinear equations and the computational performances examined in detail. Multizone analysis and zone condensation strategies are demonstrated to provide substantive computational economies in this process for models with either localized nonlinear boundary conditions or regions of geometric insensitivity to design variables. A series of nonlinear example problems is presented that have closed form solutions. Exact analytical expressions for the shape sensitivities associated with these problems are developed and these are compared with the sensitivities computed using the boundary element formulation.

  5. High temperature electrical conductivity due to small polaron hopping motion in DNA molecules

    NASA Astrophysics Data System (ADS)

    Triberis, G. P.; Karavolas, V. C.; Simserides, C. D.

    2005-01-01

    We present a small polaron hopping model to interpret the high-temperature electrical conductivity measured along the DNA molecules. The model takes into account the one-dimensional character of the system and the presence of disorder in the DNA double helix. The experimental data for the lambda phage DNA (λ-DNA) and the poly(dA)-poly(dT) DNA follow nicely the theoretically predicted behavior leading to realistic values of the maximum hopping distances supporting the idea of multiphonon-assisted hopping of small polarons between next nearest neighbors of the DNA molecular "wire".

  6. The impact of DNA intercalators on DNA and DNA-processing enzymes elucidated through force-dependent binding kinetics

    PubMed Central

    Biebricher, Andreas S.; Heller, Iddo; Roijmans, Roel F. H.; Hoekstra, Tjalle P.; Peterman, Erwin J. G.; Wuite, Gijs J. L.

    2015-01-01

    DNA intercalators are widely used as fluorescent probes to visualize DNA and DNA transactions in vivo and in vitro. It is well known that they perturb DNA structure and stability, which can in turn influence DNA-processing by proteins. Here we elucidate this perturbation by combining single-dye fluorescence microscopy with force spectroscopy and measuring the kinetics of DNA intercalation by the mono- and bis-intercalating cyanine dyes SYTOX Orange, SYTOX Green, SYBR Gold, YO-PRO-1, YOYO-1 and POPO-3. We show that their DNA-binding affinity is mainly governed by a strongly tension-dependent dissociation rate. These rates can be tuned over a range of seven orders of magnitude by changing DNA tension, intercalating species and ionic strength. We show that optimizing these rates minimizes the impact of intercalators on strand separation and enzymatic activity. These new insights provide handles for the improved use of intercalators as DNA probes with minimal perturbation and maximal efficacy. PMID:26084388

  7. Molecular mechanics of DNA bricks: in situ structure, mechanical properties and ionic conductivity

    NASA Astrophysics Data System (ADS)

    Slone, Scott Michael; Li, Chen-Yu; Yoo, Jejoong; Aksimentiev, Aleksei

    2016-05-01

    The DNA bricks method exploits self-assembly of short DNA fragments to produce custom three-dimensional objects with subnanometer precision. In contrast to DNA origami, the DNA brick method permits a variety of different structures to be realized using the same library of DNA strands. As a consequence of their design, however, assembled DNA brick structures have fewer interhelical connections in comparison to equivalent DNA origami structures. Although the overall shape of the DNA brick objects has been characterized and found to conform to the features of the target designs, the microscopic properties of DNA brick objects remain yet to be determined. Here, we use the all-atom molecular dynamics method to directly compare the structure, mechanical properties and ionic conductivity of DNA brick and DNA origami structures different only by internal connectivity of their consistituent DNA strands. In comparison to equivalent DNA origami structures, the DNA brick structures are found to be less rigid and less dense and have a larger cross-section area normal to the DNA helix direction. At the microscopic level, the junction in the DNA brick structures are found to be right-handed, similar to the structure of individual Holliday junctions (HJ) in solution, which contrasts with the left-handed structure of HJ in DNA origami. Subject to external electric field, a DNA brick plate is more leaky to ions than an equivalent DNA origami plate because of its lower density and larger cross-section area. Overall, our results indicate that the structures produced by the DNA brick method are fairly similar in their overall appearance to those created by the DNA origami method but are more compliant when subject to external forces, which likely is a consequence of their single crossover design.

  8. DnaK-Dependent Accelerated Evolutionary Rate in Prokaryotes.

    PubMed

    Kadibalban, A Samer; Bogumil, David; Landan, Giddy; Dagan, Tal

    2016-01-01

    Many proteins depend on an interaction with molecular chaperones in order to fold into a functional tertiary structure. Previous studies showed that protein interaction with the GroEL/GroES chaperonine and Hsp90 chaperone can buffer the impact of slightly deleterious mutations in the protein sequence. This capacity of GroEL/GroES to prevent protein misfolding has been shown to accelerate the evolution of its client proteins. Whether other bacterial chaperones have a similar effect on their client proteins is currently unknown. Here, we study the impact of DnaK (Hsp70) chaperone on the evolution of its client proteins. Evolutionary parameters were derived from comparison of the Escherichia coli proteome to 1,808,565 orthologous proteins in 1,149 proteobacterial genomes. Our analysis reveals a significant positive correlation between protein binding frequency with DnaK and evolutionary rate. Proteins with high binding affinity to DnaK evolve on average 4.3-fold faster than proteins in the lowest binding affinity class at the genus resolution. Differences in evolutionary rates of DnaK interactor classes are still significant after adjusting for possible effects caused by protein expression level. Furthermore, we observe an additive effect of DnaK and GroEL chaperones on the evolutionary rates of their common interactors. Finally, we found pronounced similarities in the physicochemical profiles that characterize proteins belonging to DnaK and GroEL interactomes. Our results thus implicate DnaK-mediated folding as a major component in shaping protein evolutionary dynamics in bacteria and supply further evidence for the long-term manifestation of chaperone-mediated folding on genome evolution. PMID:27189986

  9. DnaK-Dependent Accelerated Evolutionary Rate in Prokaryotes

    PubMed Central

    Kadibalban, A. Samer; Bogumil, David; Landan, Giddy; Dagan, Tal

    2016-01-01

    Many proteins depend on an interaction with molecular chaperones in order to fold into a functional tertiary structure. Previous studies showed that protein interaction with the GroEL/GroES chaperonine and Hsp90 chaperone can buffer the impact of slightly deleterious mutations in the protein sequence. This capacity of GroEL/GroES to prevent protein misfolding has been shown to accelerate the evolution of its client proteins. Whether other bacterial chaperones have a similar effect on their client proteins is currently unknown. Here, we study the impact of DnaK (Hsp70) chaperone on the evolution of its client proteins. Evolutionary parameters were derived from comparison of the Escherichia coli proteome to 1,808,565 orthologous proteins in 1,149 proteobacterial genomes. Our analysis reveals a significant positive correlation between protein binding frequency with DnaK and evolutionary rate. Proteins with high binding affinity to DnaK evolve on average 4.3-fold faster than proteins in the lowest binding affinity class at the genus resolution. Differences in evolutionary rates of DnaK interactor classes are still significant after adjusting for possible effects caused by protein expression level. Furthermore, we observe an additive effect of DnaK and GroEL chaperones on the evolutionary rates of their common interactors. Finally, we found pronounced similarities in the physicochemical profiles that characterize proteins belonging to DnaK and GroEL interactomes. Our results thus implicate DnaK-mediated folding as a major component in shaping protein evolutionary dynamics in bacteria and supply further evidence for the long-term manifestation of chaperone-mediated folding on genome evolution. PMID:27189986

  10. pH-dependent specific binding and combing of DNA.

    PubMed Central

    Allemand, J F; Bensimon, D; Jullien, L; Bensimon, A; Croquette, V

    1997-01-01

    Recent developments in the rapid sequencing, mapping, and analysis of DNA rely on the specific binding of DNA to specially treated surfaces. We show here that specific binding of DNA via its unmodified extremities can be achieved on a great variety of surfaces by a judicious choice of the pH. On hydrophobic surfaces the best binding efficiency is reached at a pH of approximately 5.5. At that pH a approximately 40-kbp DNA is 10 times more likely to bind by an extremity than by a midsegment. A model is proposed to account for the differential adsorption of the molecule extremities and midsection as a function of pH. The pH-dependent specific binding can be used to align anchored DNA molecules by a receding meniscus, a process called molecular combing. The resulting properties of the combed molecules will be discussed. Images FIGURE 1 FIGURE 2 FIGURE 3 FIGURE 6 FIGURE 7 PMID:9336201

  11. Sequence dependence of transcription factor-mediated DNA looping

    PubMed Central

    Johnson, Stephanie; Lindén, Martin; Phillips, Rob

    2012-01-01

    DNA is subject to large deformations in a wide range of biological processes. Two key examples illustrate how such deformations influence the readout of the genetic information: the sequestering of eukaryotic genes by nucleosomes and DNA looping in transcriptional regulation in both prokaryotes and eukaryotes. These kinds of regulatory problems are now becoming amenable to systematic quantitative dissection with a powerful dialogue between theory and experiment. Here, we use a single-molecule experiment in conjunction with a statistical mechanical model to test quantitative predictions for the behavior of DNA looping at short length scales and to determine how DNA sequence affects looping at these lengths. We calculate and measure how such looping depends upon four key biological parameters: the strength of the transcription factor binding sites, the concentration of the transcription factor, and the length and sequence of the DNA loop. Our studies lead to the surprising insight that sequences that are thought to be especially favorable for nucleosome formation because of high flexibility lead to no systematically detectable effect of sequence on looping, and begin to provide a picture of the distinctions between the short length scale mechanics of nucleosome formation and looping. PMID:22718983

  12. Temperature dependence of electrical conductivity and lunar temperatures

    NASA Technical Reports Server (NTRS)

    Olhoeft, G. R.; Strangway, D. W.; Sharpe, H.; Frisillo, A. L.

    1974-01-01

    Metallic conduction mechanicsms are probably not important in lunar materials because of the small amounts of free metal and metallic oxides present. This is confirmed by the extremely low conductivities measured to date and the fact that the conductivity increases with temperature. The major conduction mechanicsm appears to be ionic. This conduction mechanism is very strongly controlled by temperature, by deviations from stoichiometry, by electric field strengths, and by oxygen fugacity.

  13. DNA methylation: conducting the orchestra from exposure to phenotype?

    PubMed

    Leenen, Fleur A D; Muller, Claude P; Turner, Jonathan D

    2016-01-01

    DNA methylation, through 5-methyl- and 5-hydroxymethylcytosine (5mC and 5hmC), is considered to be one of the principal interfaces between the genome and our environment, and it helps explain phenotypic variations in human populations. Initial reports of large differences in methylation level in genomic regulatory regions, coupled with clear gene expression data in both imprinted genes and malignant diseases, provided easily dissected molecular mechanisms for switching genes on or off. However, a more subtle process is becoming evident, where small (<10 %) changes to intermediate methylation levels are associated with complex disease phenotypes. This has resulted in two clear methylation paradigms. The latter "subtle change" paradigm is rapidly becoming the epigenetic hallmark of complex disease phenotypes, although we are currently hampered by a lack of data addressing the true biological significance and meaning of these small differences. Our initial expectation of rapidly identifying mechanisms linking environmental exposure to a disease phenotype led to numerous observational/association studies being performed. Although this expectation remains unmet, there is now a growing body of literature on specific genes, suggesting wide ranging transcriptional and translational consequences of such subtle methylation changes. Data from the glucocorticoid receptor (NR3C1) has shown that a complex interplay between DNA methylation, extensive 5'UTR splicing, and microvariability gives rise to the overall level and relative distribution of total and N-terminal protein isoforms generated. Additionally, the presence of multiple AUG translation initiation codons throughout the complete, processed mRNA enables translation variability, hereby enhancing the translational isoforms and the resulting protein isoform diversity, providing a clear link between small changes in DNA methylation and significant changes in protein isoforms and cellular locations. Methylation changes in

  14. Conductance hysteresis in the voltage-dependent anion channel.

    PubMed

    Rappaport, Shay M; Teijido, Oscar; Hoogerheide, David P; Rostovtseva, Tatiana K; Berezhkovskii, Alexander M; Bezrukov, Sergey M

    2015-09-01

    Hysteresis in the conductance of voltage-sensitive ion channels is observed when the transmembrane voltage is periodically varied with time. Although this phenomenon has been used in studies of gating of the voltage-dependent anion channel, VDAC, from the outer mitochondrial membrane for nearly four decades, full hysteresis curves have never been reported, because the focus was solely on the channel opening branches of the hysteresis loops. We studied the hysteretic response of a multichannel VDAC system to a triangular voltage ramp the frequency of which was varied over three orders of magnitude, from 0.5 mHz to 0.2 Hz. We found that in this wide frequency range the area encircled by the hysteresis curves changes by less than a factor of three, suggesting broad distribution of the characteristic times and strongly non-equilibrium behavior. At the same time, quasi-equilibrium two-state behavior is observed for hysteresis branches corresponding to VDAC opening. This enables calculation of the usual equilibrium gating parameters, gating charge and voltage of equipartitioning, which were found to be almost insensitive to the ramp frequency. To rationalize this peculiarity, we hypothesize that during voltage-induced closure and opening the system explores different regions of the complex free energy landscape, and, in the opening branch, follows quasi-equilibrium paths. PMID:26094068

  15. The conductive properties of single DNA molecules studied by torsion tunneling atomic force microscopy

    NASA Astrophysics Data System (ADS)

    Wang, W.; Niu, D. X.; Jiang, C. R.; Yang, X. J.

    2014-01-01

    The conductive properties of single natural λ-DNA molecules are studied by torsion tunneling atomic force microscopy (TR-TUNA). The currents both parallel to and perpendicular to the DNA chains are investigated, but only weak or even no current signals are detected by TR-TUNA. To improve the conductance of DNA molecules, silver and copper metallized DNAs are fabricated and their conductivities are checked by TR-TUNA. It is found that for both Cu- and Ag-DNAs, the conductivity perpendicular to the DNA chain is enhanced significantly as the metal clusters are attached to the DNA chains. But parallel to the chain the electrical transport is still weak, most probably due to the ‘beads-on-a-string’ constructions of metallized DNAs.

  16. Spectrum of complex DNA damages depends on the incident radiation

    NASA Astrophysics Data System (ADS)

    Hada, M.; Sutherland, B.

    Ionizing radiation induces clustered DNA damages in DNA-two or more abasic sites oxidized bases and strand breaks on opposite DNA strands within a few helical turns Clustered damages are considered to be difficult to repair and therefore potentially lethal and mutagenic damages Although induction of single strand breaks and isolated lesions has been studied extensively little is known of factors affecting induction of clusters other than double strand breaks DSB The aim of the present study was to determine whether the type of incident radiation could affect yield or spectra of specific clusters Genomic T7 DNA a simple 40 kbp linear blunt-ended molecule was irradiated in non-scavenging buffer conditions with Fe 970 MeV n Ti 980 MeV n C 293 MeV n Si 586 MeV n ions or protons 1 GeV n at the NASA Space Radiation Laboratory or with 100 kVp X-rays Irradiated DNA was treated with homogeneous Fpg or Nfo proteins or without enzyme treatment for DSB quantitation then electrophoresed in neutral agarose gels DSB Fpg-OxyPurine clusters and Nfo-Abasic clusters were quantified by number average length analysis The results show that the yields of all these complex damages depend on the incident radiation Although LETs are similar protons induced twice as many DSBs than did X-rays Further the spectrum of damage also depends on the radiation The yield damage Mbp Gy of all damages decreased with increasing linear energy transfer LET of the radiation The relative frequencies of DSBs to Abasic- and OxyBase clusters were higher

  17. Dnmt2-dependent methylomes lack defined DNA methylation patterns

    PubMed Central

    Raddatz, Günter; Guzzardo, Paloma M.; Olova, Nelly; Fantappié, Marcelo Rosado; Rampp, Markus; Schaefer, Matthias; Reik, Wolf; Hannon, Gregory J.; Lyko, Frank

    2013-01-01

    Several organisms have retained methyltransferase 2 (Dnmt2) as their only candidate DNA methyltransferase gene. However, information about Dnmt2-dependent methylation patterns has been limited to a few isolated loci and the results have been discussed controversially. In addition, recent studies have shown that Dnmt2 functions as a tRNA methyltransferase, which raised the possibility that Dnmt2-only genomes might be unmethylated. We have now used whole-genome bisulfite sequencing to analyze the methylomes of Dnmt2-only organisms at single-base resolution. Our results show that the genomes of Schistosoma mansoni and Drosophila melanogaster lack detectable DNA methylation patterns. Residual unconverted cytosine residues shared many attributes with bisulfite deamination artifacts and were observed at comparable levels in Dnmt2-deficient flies. Furthermore, genetically modified Dnmt2-only mouse embryonic stem cells lost the DNA methylation patterns found in wild-type cells. Our results thus uncover fundamental differences among animal methylomes and suggest that DNA methylation is dispensable for a considerable number of eukaryotic organisms. PMID:23641003

  18. Cre-dependent DNA recombination activates a STING-dependent innate immune response

    PubMed Central

    Pépin, Geneviève; Ferrand, Jonathan; Höning, Klara; Jayasekara, W. Samantha N.; Cain, Jason E.; Behlke, Mark A.; Gough, Daniel J.; G. Williams, Bryan R.; Hornung, Veit; Gantier, Michael P.

    2016-01-01

    Gene-recombinase technologies, such as Cre/loxP-mediated DNA recombination, are important tools in the study of gene function, but have potential side effects due to damaging activity on DNA. Here we show that DNA recombination by Cre instigates a robust antiviral response in mammalian cells, independent of legitimate loxP recombination. This is due to the recruitment of the cytosolic DNA sensor STING, concurrent with Cre-dependent DNA damage and the accumulation of cytoplasmic DNA. Importantly, we establish a direct interplay between this antiviral response and cell–cell interactions, indicating that low cell densities in vitro could be useful to help mitigate these effects of Cre. Taking into account the wide range of interferon stimulated genes that may be induced by the STING pathway, these results have broad implications in fields such as immunology, cancer biology, metabolism and stem cell research. Further, this study sets a precedent in the field of gene-engineering, possibly applicable to other enzymatic-based genome editing technologies. PMID:27166376

  19. Cre-dependent DNA recombination activates a STING-dependent innate immune response.

    PubMed

    Pépin, Geneviève; Ferrand, Jonathan; Höning, Klara; Jayasekara, W Samantha N; Cain, Jason E; Behlke, Mark A; Gough, Daniel J; G Williams, Bryan R; Hornung, Veit; Gantier, Michael P

    2016-06-20

    Gene-recombinase technologies, such as Cre/loxP-mediated DNA recombination, are important tools in the study of gene function, but have potential side effects due to damaging activity on DNA. Here we show that DNA recombination by Cre instigates a robust antiviral response in mammalian cells, independent of legitimate loxP recombination. This is due to the recruitment of the cytosolic DNA sensor STING, concurrent with Cre-dependent DNA damage and the accumulation of cytoplasmic DNA. Importantly, we establish a direct interplay between this antiviral response and cell-cell interactions, indicating that low cell densities in vitro could be useful to help mitigate these effects of Cre. Taking into account the wide range of interferon stimulated genes that may be induced by the STING pathway, these results have broad implications in fields such as immunology, cancer biology, metabolism and stem cell research. Further, this study sets a precedent in the field of gene-engineering, possibly applicable to other enzymatic-based genome editing technologies. PMID:27166376

  20. ATPase-Dependent Quality Control of DNA Replication Origin Licensing

    PubMed Central

    Frigola, Jordi; Remus, Dirk; Mehanna, Amina; Diffley, John F. X.

    2013-01-01

    The regulated loading of the Mcm2-7 DNA helicase into pre-replicative complexes (pre-RCs) at multiple replication origins ensures precise once per cell cycle replication in eukaryotic cells. Origin Recognition Complex (ORC), Cdc6 and Cdt1 load Mcm2-7 into a double hexamer bound around duplex DNA in an ATP-dependent reaction, but the molecular mechanism of this origin ‘licensing’ is still poorly understood. Here we show that both Mcm2-7 hexamers are recruited to origins by an essential, conserved C-terminal domain of Mcm3 which interacts with and stimulates the ATPase activity of ORC•Cdc6. ATP hydrolysis can promote Mcm2-7 loading, but can also promote Mcm2-7 release if components are missing or if ORC has been inactivated by cyclin-dependent kinase phosphorylation. Our work provides new insights into how origins are licensed and reveals a novel ATPase-dependent mechanism contributing to precise once per cell cycle replication. PMID:23474987

  1. Thioredoxin-dependent regulation of AIF-mediated DNA damage.

    PubMed

    Shelar, Sandeep B; Kaminska, Kamila K; Reddy, Shridhivya A; Kumar, Dilip; Tan, Chong-Teik; Yu, Victor C; Lu, Jun; Holmgren, Arne; Hagen, Thilo; Chew, Eng-Hui

    2015-10-01

    The thioredoxin (Trx) system is one major redox system in mammalian cells. One of its component, Trx, is involved in redox homeostasis and many cellular biological processes through participating in disulfide reduction, S-nitrosylation/S-denitrosylation reactions and protein-protein interactions. In this study, we report the identification of a novel interaction between cytosolic/nuclear Trx1 and apoptosis inducing factor (AIF), and the redox sensitivity and biological significance of the Trx-AIF interaction was characterized. Cytosolic Trx1 but not mitochondrial Trx2 was observed to interact with AIF under physiological conditions and Trx1's active site cysteines were crucial for the interaction. Under oxidative stress conditions, Trx-AIF interaction was disrupted. When the treated cells were allowed to recover from oxidative stress by means of removal of the oxidants, interaction between Trx1 and AIF was re-established time-dependently, which underpins the biological relevance of a Trx-dependent redox regulation of AIF-mediated cell death. Indeed, in times of oxidative stress, nuclear translocation of AIF was found to occur concurrently with perturbations to the Trx-AIF interaction. Once localized in the nucleus, reduced Trx1 hindered the interaction between AIF and DNA, thereby bringing about an attenuation of AIF-mediated DNA damage. In conclusion, characterization of the Trx-AIF interaction has led to an understanding of the effect of reduced Trx1 on possibly regulating AIF-dependent cell death through impeding AIF-mediated DNA damage. Importantly, identification of the novel interaction between Trx1 and AIF has provided opportunities to design and develop therapeutically relevant strategies that either promote or prevent this protein-protein interaction for the treatment of different disease states. PMID:26119781

  2. Temperature-dependent electrical conductivity of soda-lime glass

    NASA Technical Reports Server (NTRS)

    Bunnell, L. Roy; Vertrees, T. H.

    1993-01-01

    The objective of this educational exercise was to demonstrate the difference between the electrical conductivity of metals and ceramics. A list of the equipment and supplies and the procedure for the experiment are presented.

  3. Processing dependent thermal conductivity of nanoporous silica xerogel films

    NASA Astrophysics Data System (ADS)

    Jain, Anurag; Rogojevic, Svetlana; Ponoth, Shom; Gill, William N.; Plawsky, Joel L.; Simonyi, Eva; Chen, Shyng-Tsong; Ho, P. S.

    2002-03-01

    Sintered xerogel films (porous SiO2) show a much higher thermal conductivity than other low dielectric constant (low-K) materials available for the same value of K. The thermal conductivity of xerogels which we have processed using different methods is compared with that of other low-K materials such as silica hybrid (silsesquioxanes) and polymeric low-K materials. The methods used were: (1) single solvent (ethanol) method, (2) binary solvent (mixture of ethanol and ethylene glycol) method, (3) sintering. For the xerogel films, we show that process history is as important as the chemistry of the solid matrix or the porosity in determining the thermal conductivity. The thermal conductivity, measured by the 3-ω method or the photothermal deflection method, is affected by phonon scattering, which in turn is effected by the size and distribution of pores and particles and the presence of imperfections such as interfaces, substituted chemical species, impurities, microcracks, and microporosity. The thermal conductivity extrapolated to zero porosity for porous sintered xerogel films approaches that of thermally grown SiO2 indicating the least phonon scattering of all processing methods. For these films, the elastic modulus is proportional to thermal conductivity squared, in agreement with theories developed for materials with few defects and a connected matrix.

  4. DNA-conducting polymer complexes: a computational study of the hydrogen bond between building blocks.

    PubMed

    Zanuy, David; Aleman, Carlos

    2008-03-13

    Ab initio quantum mechanical calculations at the MP2 level were used for an extensive study concerning the stability of hydrogen-bonded complexes formed by pyrrole and thiophene, which are the most common building blocks of conducting polymers, and DNA bases. Results indicated that very stable complexes were formed with pyrrole, which shows a clear tendency to form specific hydrogen-bonding interactions with nucleic acid bases. Furthermore, the strength of such interactions depends significantly on the base, growing in the following order: thymine < adenine approximately equal to cytosine < guanine. On the contrary, thiophene formed complexes stabilized by nonspecific interactions between the pi-cloud of the ring and the N-H groups of the nucleic acid bases rather than specific hydrogen bonds. Overall, these results are fully consistent with experimental observations: polypyrrole is able not only to stabilize adducts with DNA but also to interact specifically, while the interactions of the latter with polythiophene and their derivatives are weaker and nonspecific. PMID:18278905

  5. Requirement for the Kinase Activity of Human DNA-Dependent Protein Kinase Catalytic Subunit in DNA Strand Break Rejoining

    PubMed Central

    Kurimasa, Akihiro; Kumano, Satoshi; Boubnov, Nikolai V.; Story, Michael D.; Tung, Chang-Shung; Peterson, Scott R.; Chen, David J.

    1999-01-01

    The catalytic subunit of DNA-dependent protein kinase (DNA-PKcs) is an enormous, 470-kDa protein serine/threonine kinase that has homology with members of the phosphatidylinositol (PI) 3-kinase superfamily. This protein contributes to the repair of DNA double-strand breaks (DSBs) by assembling broken ends of DNA molecules in combination with the DNA-binding factors Ku70 and Ku80. It may also serve as a molecular scaffold for recruiting DNA repair factors to DNA strand breaks. This study attempts to better define the role of protein kinase activity in the repair of DNA DSBs. We constructed a contiguous 14-kb human DNA-PKcs cDNA and demonstrated that it can complement the DNA DSB repair defects of two mutant cell lines known to be deficient in DNA-PKcs (M059J and V3). We then created deletion and site-directed mutations within the conserved PI 3-kinase domain of the DNA-PKcs gene to test the importance of protein kinase activity for DSB rejoining. These DNA-PKcs mutant constructs are able to express the protein but fail to complement the DNA DSB or V(D)J recombination defects of DNA-PKcs mutant cells. These results indicate that the protein kinase activity of DNA-PKcs is essential for the rejoining of DNA DSBs in mammalian cells. We have also determined a model structure for the DNA-PKcs kinase domain based on comparisons to the crystallographic structure of a cyclic AMP-dependent protein kinase. This structure gives some insight into which amino acid residues are crucial for the kinase activity in DNA-PKcs. PMID:10207111

  6. Saturation-dependent anisotropy in the Hanford subsurface hydraulic conductivity

    NASA Astrophysics Data System (ADS)

    Blank, L.; Skinner, T.; Hunt, A.

    2006-12-01

    In previous work anisotropy in a fracture network was shown to provide a possible explanation for the observed scale-effect in the hydraulic conductivity of a carbonate aquifer. Use was made of a coordinate transformation and reference made to the transverse and longitudinal electrical conductivities of thin (disordered) solid films. An analogous approach is now developed to describe the inferred anisotropy of the hydraulic conductivity as a function of saturation in the Hanford subsurface. Here different soil types play the role of fractures of different apertures, while the spatial anisotropy is generated by soils of higher silt and clay fractions. A quasi- equilibrium condition (equal matric potentials) is implemented at matric potentials believed characteristic of the Hanford subsurface (several hundred centimeters) and theoretical results for the hydraulic conductivity (modified by known values at saturation) are used to develop the distribution of K values at the appropriate potential. The results are hoped to be relevant to the dispersion of a Tc plume. Work was supported by DOE grant DE-FG02-05ER64067 and -06ER64196 and NSF grant EAR 0609884

  7. Alcohol Dependence and Domestic Violence as Sequelae of Abuse and Conduct Disorder in Childhood.

    ERIC Educational Resources Information Center

    Kunitz, Stephen J.; Levy, Jerrold E.; McCloskey, Joanne; Gabriel, K. Ruben

    1998-01-01

    This study compared 204 Navajo men and women for alcohol dependence and domestic violence as sequelae of abuse and conduct disorders in childhood. Both physical and sexual abuse were risk factors for conduct disorder. Physical abuse and conduct disorder were risk factors for alcohol dependence. Alcohol dependence and physical abuse were…

  8. Nbs1-dependent binding of Mre11 to adenovirus E4 mutant viral DNA is important for inhibiting DNA replication

    SciTech Connect

    Mathew, Shomita S.; Bridge, Eileen

    2008-04-25

    Adenovirus (Ad) infections stimulate the activation of cellular DNA damage response and repair pathways. Ad early regulatory proteins prevent activation of DNA damage responses by targeting the MRN complex, composed of the Mre11, Rad50 and Nbs1 proteins, for relocalization and degradation. In the absence of these viral proteins, Mre11 colocalizes with viral DNA replication foci. Mre11 foci formation at DNA damage induced by ionizing radiation depends on the Nbs1 component of the MRN complex and is stabilized by the mediator of DNA damage checkpoint protein 1 (Mdc1). We find that Nbs1 is required for Mre11 localization at DNA replication foci in Ad E4 mutant infections. Mre11 is important for Mdc1 foci formation in infected cells, consistent with its role as a sensor of DNA damage. Chromatin immunoprecipitation assays indicate that both Mre11 and Mdc1 are physically bound to viral DNA, which could account for their localization in viral DNA containing foci. Efficient binding of Mre11 to E4 mutant DNA depends on the presence of Nbs1, and is correlated with a significant E4 mutant DNA replication defect. Our results are consistent with a model in which physical interaction of Mre11 with viral DNA is mediated by Nbs1, and interferes with viral DNA replication.

  9. Neutron energy-dependent initial DNA damage and chromosomal exchange.

    PubMed

    Tanaka, K; Gajendiran, N; Endo, S; Komatsu, K; Hoshi, M; Kamada, N

    1999-12-01

    This study was undertaken to investigate the biological effect of monoenergetic neutrons on human lymphocyte DNA and chromosomes. Monoenergetic neutrons of 2.3, 1.0, 0.79, 0.57, 0.37 and 0.186 MeV were generated, and 252Cf neutrons and 60Co gamma-rays were also used for comparison. Biological effect was evaluated two ways. The RBE values with the comet assay were estimated as 6.3 and 5.4 at 0.37 MeV and 0.57 MeV relative to that of 60Co gamma-rays, and chromosome aberration rates were also observed in these different levels of monoenergetic neutrons. The yield of chromosome aberrations per unit dose was high at lower neutron energies with a gradual decline with 0.186 MeV neutron energy. The RBE was increased to 10.7 at 0.57 MeV from 3.9 at 252Cf neutrons and reached 16.4 as the highest RBE at 0.37 MeV, but the value decreased to 11.2 at 0.186 MeV. The response patterns of initial DNA damage and chromosome exchange were quite similar to that of LET. These results show that the intensity of DNA damage and chromosomal exchange is LET dependent. RBE of low energy neutrons is higher than that of fission neutrons. Low energy neutrons containing Hiroshima atomic bomb radiation may have created a significantly higher incidence of biological effect in atomic bomb survivors. PMID:10804992

  10. Ancestry dependent DNA methylation and influence of maternal nutrition.

    PubMed

    Mozhui, Khyobeni; Smith, Alicia K; Tylavsky, Frances A

    2015-01-01

    There is extensive variation in DNA methylation between individuals and ethnic groups. These differences arise from a combination of genetic and non-genetic influences and potential modifiers include nutritional cues, early life experience, and social and physical environments. Here we compare genome-wide DNA methylation in neonatal cord blood from African American (AA; N = 112) and European American (EA; N = 91) participants of the CANDLE Study (Conditions Affecting Neurocognitive Development and Learning in Early Childhood). Our goal is to determine if there are replicable ancestry-specific methylation patterns that may implicate risk factors for diseases that have differential prevalence between populations. To identify the most robust ancestry-specific CpG sites, we replicate our results in lymphoblastoid cell lines from Yoruba African and CEPH European panels of HapMap. We also evaluate the influence of maternal nutrition--specifically, plasma levels of vitamin D and folate during pregnancy--on methylation in newborns. We define stable ancestry-dependent methylation of genes that include tumor suppressors and cell cycle regulators (e.g., APC, BRCA1, MCC). Overall, there is lower global methylation in African ancestral groups. Plasma levels of 25-hydroxy vitamin D are also considerably lower among AA mothers and about 60% of AA and 40% of EA mothers have concentrations below 20 ng/ml. Using a weighted correlation analysis, we define a network of CpG sites that is jointly modulated by ancestry and maternal vitamin D. Our results show that differences in DNA methylation patterns are remarkably stable and maternal micronutrients can exert an influence on the child epigenome. PMID:25742137

  11. Base sequence dependence and backbone-induced effects on charge transport through DNA

    NASA Astrophysics Data System (ADS)

    Joe, Yong; Lee, Sun; Hedin, Eric

    2009-03-01

    We investigate quantum mechanical electron transmission along the long axis of the DNA molecule using a tight-binding model. Specifically, we use two different DNA models to study the charge transfer efficiency of synthetic ds-DNA. First, the generic form of a simple one-conduction channel model, called the fishbone model, is used. The sugar-phosphate backbone and the coupling amplitude between each site of the base and the backbone are incorporated into an energy-dependent on-site potential in the main DNA site. Here, individual sites represent a base-pair formed by either AT (TA) or GC (CG) pairs coupled via hydrogen bonds. Second, we employ a two-dimensional three-chain model where the backbone on-site energy, the coupling amplitude between the bases and the backbone, and a possible hopping of charge carriers between the successive backbone sites are used as key parameters. The overall transmission and the current-voltage characteristics are calculated to determine the influence of mismatch (impurity) effects in the DNA sequence. Finally, we discuss the transmission gap as a function of coupling between the bases and between the bases and the backbone. *One of the authors (E.R.H) is partially supported by a grant from the Center for Energy Research, Education, and Service (CERES) at Ball State University.

  12. Intrinsic Self-DNA Triggers Inflammatory Disease Dependent on STING

    PubMed Central

    Ahn, Jeonghyun; Ruiz, Phillip; Barber, Glen N.

    2016-01-01

    Inflammatory diseases such as Aicardi–Goutières syndrome and severe systemic lupus erythematosus are generally lethal disorders that have been traced to defects in the exonuclease TREX1 (DNase III). Mice lacking TREX1 similarly die at an early age through comparable symptoms, including inflammatory myocarditis, through chronic activation of the stimulator of IFN genes (STING) pathway. In this study, we demonstrate that phagocytes rather than myocytes are predominantly responsible for causing inflammation, an outcome that could be alleviated following adoptive transfer of normal bone marrow into TREX1−/− mice. TREX1−/− macrophages did not exhibit significant augmented ability to produce proinflammatory cytokines compared with normal macrophages following exposure to STING-dependent activators, but rather appeared chronically stimulated by genomic DNA. These results shed molecular insight into inflammation and provide concepts for the design of new therapies. PMID:25261479

  13. A Device for Performing Lateral Conductance Measurements on Individual Double-Stranded DNA Molecules

    PubMed Central

    Menard, Laurent D.; Mair, Chad E.; Woodson, Michael E.; Alarie, Jean Pierre; Ramsey, J. Michael

    2012-01-01

    A nanofluidic device is described that is capable of electrically monitoring the driven translocation of DNA molecules through a nanochannel. This is achieved by intersecting a long transport channel with a shorter orthogonal nanochannel. The ionic conductance of this transverse nanochannel is monitored while DNA is electrokinetically driven through the transport channel. When DNA passes the intersection, the transverse conductance is altered, resulting in a transient current response. In 1 M KCl solutions, this was found to be a current enhancement of 5–25%, relative to the baseline transverse ionic current. Two different device geometries were investigated. In one device, the DNA was detected after it was fully inserted into and translocating through the transport nanochannel. In the other device, the DNA was detected while it was in the process of entering the nanochannel. It was found that these two conditions are characterized by different transport dynamics. Simultaneous optical and electrical monitoring of DNA translocation confirmed that the transient events originated from DNA transport through the nanochannel intersection. PMID:22950784

  14. Neuroinflammation alters voltage-dependent conductance in striatal astrocytes

    PubMed Central

    Karpuk, Nikolay; Burkovetskaya, Maria

    2012-01-01

    Neuroinflammation has the capacity to alter normal central nervous system (CNS) homeostasis and function. The objective of the present study was to examine the effects of an inflammatory milieu on the electrophysiological properties of striatal astrocyte subpopulations with a mouse bacterial brain abscess model. Whole cell patch-clamp recordings were performed in striatal glial fibrillary acidic protein (GFAP)-green fluorescent protein (GFP)+ astrocytes neighboring abscesses at postinfection days 3 or 7 in adult mice. Cell input conductance (Gi) measurements spanning a membrane potential (Vm) surrounding resting membrane potential (RMP) revealed two prevalent astrocyte subsets. A1 and A2 astrocytes were identified by negative and positive Gi increments vs. Vm, respectively. A1 and A2 astrocytes displayed significantly different RMP, Gi, and cell membrane capacitance that were influenced by both time after bacterial exposure and astrocyte proximity to the inflammatory site. Specifically, the percentage of A1 astrocytes was decreased immediately surrounding the inflammatory lesion, whereas A2 cells were increased. These changes were particularly evident at postinfection day 7, revealing increased cell numbers with an outward current component. Furthermore, RMP was inversely modified in A1 and A2 astrocytes during neuroinflammation, and resting Gi was increased from 21 to 30 nS in the latter. In contrast, gap junction communication was significantly decreased in all astrocyte populations associated with inflamed tissues. Collectively, these findings demonstrate the heterogeneity of striatal astrocyte populations, which experience distinct electrophysiological modifications in response to CNS inflammation. PMID:22457466

  15. A robust assay to measure DNA topology-dependent protein binding affinity

    PubMed Central

    Litwin, Tamara R.; Solà, Maria; Holt, Ian J.; Neuman, Keir C.

    2015-01-01

    DNA structure and topology pervasively influence aspects of DNA metabolism including replication, transcription and segregation. However, the effects of DNA topology on DNA-protein interactions have not been systematically explored due to limitations of standard affinity assays. We developed a method to measure protein binding affinity dependence on the topology (topological linking number) of supercoiled DNA. A defined range of DNA topoisomers at equilibrium with a DNA binding protein is separated into free and protein-bound DNA populations using standard nitrocellulose filter binding techniques. Electrophoretic separation and quantification of bound and free topoisomers combined with a simple normalization procedure provide the relative affinity of the protein for the DNA as a function of linking number. Employing this assay we measured topology-dependent DNA binding of a helicase, a type IB topoisomerase, a type IIA topoisomerase, a non-specific mitochondrial DNA binding protein and a type II restriction endonuclease. Most of the proteins preferentially bind negatively supercoiled DNA but the details of the topology-dependent affinity differ among proteins in ways that expose differences in their interactions with DNA. The topology-dependent binding assay provides a robust and easily implemented method to probe topological influences on DNA-protein interactions for a wide range of DNA binding proteins. PMID:25552413

  16. The DNA-dependent protein kinase: a multifunctional protein kinase with roles in DNA double strand break repair and mitosis

    PubMed Central

    Jette, Nicholas; Lees-Miller, Susan P.

    2015-01-01

    The DNA-dependent protein kinase (DNA-PK) is a serine/threonine protein kinase composed of a large catalytic subunit (DNA-PKcs) and the Ku70/80 heterodimer. Over the past two decades, significant progress has been made in elucidating the role of DNA-PK in non-homologous end joining (NHEJ), the major pathway for repair of ionizing radiation-induced DNA double strand breaks in human cells and recently, additional roles for DNA-PK have been reported. In this review, we will describe the biochemistry, structure and function of DNA-PK, its roles in DNA double strand break repair and its newly described roles in mitosis and other cellular processes. PMID:25550082

  17. Gelatin- and DNA-based ionic conducting membranes for electrochromic devices

    NASA Astrophysics Data System (ADS)

    Pawlicka, A.; Firmino, A.; Vieira, D.; Sentanin, F.; Grote, J. G.; Kajzar, F.

    2009-09-01

    Gelatin and DNA are abundant natural products with very good biodegradation properties and can be used to obtain acetic acid or LiClO4-based gel polymer electrolytes (GPEs) with high ionic conductivity and good stability. This article presents the results of the ionic conductivity measurements of GPEs membranes based on crosslinked and plasticized gelatin and on plasticized DNA as well as on inserted/extracted charge density of electrochemical devices (ECDs) obtained with these samples. The membranes were analyzed by impedance spectroscopy, UV-Vis spectroscopy and the ECDs by charge density measurements, respectively. At room temperature the measured ionic conductivity of the membranes is in the range of 10-4-10-5 S/cm. It obeys predominantly an Arrhenius relationship in function of temperature. The ECD with red gelatin changed the color from red to deep red and the ECD with DNA-based electrolyte changes from transparent to blue. The inserted charge density values of these ECDs were of -3.0 mC/cm2 for the device with red gelatin and -6.6 mC/cm2 for the ECD with DNA-based electrolyte. The reverse potential application promoted a charge extraction and, as consequence, bleaching of the devices. Good ionic conductivity results combined with transparency and good adhesion to the electrodes and promising preliminary results of small ECDs have shown that gelatin and DNA-based GPEs are very promising materials to be used as gel polymer electrolytes in electrochromic devices.

  18. Response of the electric conductivity of double-stranded DNA on moderate mechanical stretching stresses

    NASA Astrophysics Data System (ADS)

    Wolter, Mario; Woiczikowski, P. Benjamin; Elstner, Marcus; Kubař, Tomáš

    2012-02-01

    The response of charge transport in double-stranded DNA to mechanical pulling has been studied with a multiscale computational method using classical molecular dynamics simulation, approximative density-functional theory calculations and the Landauer-Büttiker theory. The effect depends on the exact nucleobase sequence notably, and this is explained in terms of structural changes of DNA upon stretching. The results of recent single-molecule experiments are interpreted on the basis of current results. Further, recommendations for the design of DNA sequences for nanoelectronic applications are formulated.

  19. Smooth and conductive DNA-templated Cu₂O nanowires: growth morphology, spectroscopic and electrical characterization.

    PubMed

    Hassanien, Reda; Al-Said, Said A Farha; Siller, Lidija; Little, Ross; Wright, Nicholas G; Houlton, Andrew; Horrocks, Benjamin R

    2012-02-24

    DNA strands have been used as templates for the self-assembly of smooth and conductive cuprous oxide (Cu₂O) nanowires of diameter 12-23 nm and whose length is determined by the template (16 μm for λ-DNA). A combination of spectroscopic, diffraction and probe microscopy techniques showed that these nanowires comprise single crystallites of Cu₂O bound to the DNA molecules which fused together over time in a process analogous to Ostwald ripening, but driven by the free energy of interaction with the template as well as the surface tension. Electrical characterization of the nanowires by a non-contact method, scanned conductance microscopy and by contact mode conductive AFM showed the wires are electrically conductive. The conductivity estimated from the AFM cross section and the zero-bias conductance in conductive AFM experiments was 2.2-3.3 S cm⁻¹. These Cu₂O nanowires are amongst the thinnest reported and show evidence of strong quantum confinement in electronic spectra. PMID:22261265

  20. The DNA Structure-Specific Endonuclease MUS81 Mediates DNA Sensor STING-Dependent Host Rejection of Prostate Cancer Cells.

    PubMed

    Ho, Samantha S W; Zhang, Wendy Y L; Tan, Nikki Yi Jie; Khatoo, Muznah; Suter, Manuel A; Tripathi, Shubhita; Cheung, Florence S G; Lim, Weng Khong; Tan, Puay Hoon; Ngeow, Joanne; Gasser, Stephan

    2016-05-17

    Self-DNA is present in the cytosol of many cancer cells and can promote effective immune rejection of tumor cells, but the mechanisms leading to the presence of cytosolic DNA are unknown. Here, we report that the cleavage of genomic DNA by DNA structure-specific endonuclease MUS81 and PARP-dependent DNA repair pathways leads to the accumulation of cytosolic DNA in prostate cancer cells. The number of nuclear MUS81 foci and the amount of cytosolic dsDNA increased in tandem from hyperplasia to clinical stage II prostate cancers and decreased at stage III. Cytosolic DNA generated by MUS81 stimulated DNA sensor STING-dependent type I interferon (IFN) expression and promoted phagocytic and T cell responses, resulting in type I and II IFN-mediated rejection of prostate tumor cells via mechanisms that partly depended on macrophages. Our results demonstrate that the tumor suppressor MUS81 alerts the immune system to the presence of transformed host cells. PMID:27178469

  1. Quinolone-DNA Interaction: Sequence-Dependent Binding to Single-Stranded DNA Reflects the Interaction within the Gyrase-DNA Complex

    PubMed Central

    Noble, Christian G.; Barnard, Faye M.; Maxwell, Anthony

    2003-01-01

    We have investigated the interaction of quinolones with DNA by a number of methods to establish whether a particular binding mode correlates with quinolone potency. The specificities of the quinolone-mediated DNA cleavage reaction of DNA gyrase were compared for a number of quinolones. Two patterns that depended on the potency of the quinolone were identified. Binding to plasmid DNA was examined by measuring the unwinding of pBR322 by quinolones; no correlation with quinolone potency was observed. Quinolone binding to short DNA oligonucleotides was measured by surface plasmon resonance. The quinolones bound to both single- and double-stranded oligonucleotides in an Mg2+-dependent manner. Quinolones bound to single-stranded DNA with a higher affinity, and the binding exhibited sequence dependence; binding to double-stranded DNA was sequence independent. The variations in binding in the presence of metal ions showed that Mg2+ promoted tighter, more specific binding to single-stranded DNA than softer metal ions (Mn2+ and Cd2+). Single-stranded DNA binding by quinolones correlated with the in vitro quinolone potency, indicating that this mode of interaction may reflect the interaction of the quinolone with DNA in the context of the gyrase-DNA complex. PMID:12604512

  2. On-chip DNA preconcentration in different media conductivities by electrodeless dielectrophoresis.

    PubMed

    Li, Shunbo; Ye, Ziran; Hui, Yu Sanna; Gao, Yibo; Jiang, Yusheng; Wen, Weijia

    2015-09-01

    Electrodeless dielectrophoresis is the best choice to achieve preconcentration of nanoparticles and biomolecules due to its simple, robust, and easy implementation. We designed a simple chip with microchannels and nano-slits in between and then studied the trapping of DNA in high conductive medium and low conductive medium, corresponding to positive and negative dielectrophoresis (DEP), respectively. It is very important to investigate the trapping in media with different conductivities since one always has to deal with the sample solutions with different conductivities. The trapping process was analyzed by the fluorescent intensity changes. The results showed that DNA could be trapped at the nano-slit in both high and low conductive media in a lower electric field strength (10 V/cm) compared to the existing methods. This is a significant improvement to suppress the Joule heating effect in DEP related experiments. Our work may give insight to researchers for DNA trapping by a simple and low cost device in the Lab-on-a-Chip system. PMID:26487901

  3. Identification of DNA-Dependent Protein Kinase Catalytic Subunit (DNA-PKcs) as a Novel Target of Bisphenol A

    PubMed Central

    Nashimoto, Akihiro; Hase, Yasuyoshi; Sakamoto, Satoshi; Mimori, Tsuneyo; Matsumoto, Yoshihisa; Yamaguchi, Yuki; Handa, Hiroshi

    2012-01-01

    Bisphenol A (BPA) forms the backbone of plastics and epoxy resins used to produce packaging for various foods and beverages. BPA is also an estrogenic disruptor, interacting with human estrogen receptors (ER) and other related nuclear receptors. Nevertheless, the effects of BPA on human health remain unclear. The present study identified DNA-dependent protein kinase catalytic subunit (DNA-PKcs) as a novel BPA-binding protein. DNA-PKcs, in association with the Ku heterodimer (Ku70/80), is a critical enzyme involved in the repair of DNA double-strand breaks. Low levels of DNA-PK activity are previously reported to be associated with an increased risk of certain types of cancer. Although the Kd for the interaction between BPA and a drug-binding mutant of DNA-PKcs was comparatively low (137 nM), high doses of BPA were required before cellular effects were observed (100–300 μM). The results of an in vitro kinase assay showed that BPA inhibited DNA-PK kinase activity in a concentration-dependent manner. In M059K cells, BPA inhibited the phosphorylation of DNA-PKcs at Ser2056 and H2AX at Ser139 in response to ionizing radiation (IR)-irradiation. BPA also disrupted DNA-PKcs binding to Ku70/80 and increased the radiosensitivity of M059K cells, but not M059J cells (which are DNA-PKcs-deficient). Taken together, these results provide new evidence of the effects of BPA on DNA repair in mammalian cells, which are mediated via inhibition of DNA-PK activity. This study may warrant the consideration of the possible carcinogenic effects of high doses of BPA, which are mediated through its action on DNA-PK. PMID:23227178

  4. Temperature dependence of dc electrical conductivity of activated carbon-metal oxide nanocomposites. Some insight into conduction mechanisms

    NASA Astrophysics Data System (ADS)

    Barroso-Bogeat, Adrián; Alexandre-Franco, María; Fernández-González, Carmen; Sánchez-González, José; Gómez-Serrano, Vicente

    2015-12-01

    From a commercial activated carbon (AC) and six metal oxide (Al2O3, Fe2O3, SnO2, TiO2, WO3 and ZnO) precursors, two series of AC-metal oxide nanocomposites are prepared by wet impregnation, oven-drying at 120 °C, and subsequent heat treatment at 200 or 850 °C in inert atmosphere. The temperature-dependent dc electrical conductivity of AC and the as-prepared nanocomposites is measured from room temperature up to ca. 200 °C in air atmosphere by the four-probe method. The decrease in conductivity for the hybrid materials as compared to AC is the result of a complex interplay between several factors, including not only the intrinsic conductivity, crystallite size, content and chemical nature of the supported nanoparticles, which ultimately depend on the precursor and heat treatment temperature, but also the adsorption of oxygen and water from the surrounding atmosphere. The conductivity data are discussed in terms of a thermally activated process. In this regard, both AC and the prepared nanocomposites behave as semiconductors, and the temperature-dependent conductivity data have been interpreted on the basis of the classical model proposed by Mott and Davis. Because of its high content of heteroatoms, AC may be considered as a heavily doped semiconductor, so that conduction of thermally excited carriers via acceptor or donor levels is expected to be the dominant mechanism. The activation energies for the hybrid materials suggest that the supported metal oxide nanoparticles strongly modify the electronic band structure of AC by introducing new trap levels in different positions along its band gap. Furthermore, the thermally activated conduction process satisfies the Meyer-Neldel rule, which is likely connected with the shift of the Fermi level due to the introduction of the different metal oxide nanoparticles in the AC matrix.

  5. Polymeric waveguide electro-optic beam-steering device with DNA biopolymer conductive cladding layers

    NASA Astrophysics Data System (ADS)

    Aga, Roberto S.; Ouchen, Fahima; Lesko, Alyssa; Telek, Brian A.; Fehrman Cory, Emily M.; Bartsch, Carrie M.; Lombardi, Jack; Grote, James; Heckman, Emily M.

    2012-11-01

    A polymer electro-optic (EO) waveguide beam-steering device with deoxyribonucleic acid (DNA) biopolymer conductive cladding layers and a core layer of the commercially available EO polymer SEO100 is demonstrated with 100% relative poling efficiency. This demonstration device exhibits a deflection efficiency of 99 mrad/kV with a corresponding in-device EO coefficient r33 of 124 pm/V at 1550 nm. When the DNA biopolymer bottom cladding layer is replaced by the commonly used cladding polymer UV15, the deflection efficiency and in-device r33 drop to 34 mrad/kV and 43 pm/V, respectively.

  6. Interaction of Ku protein and DNA-dependent protein kinase catalytic subunit with nucleic acids.

    PubMed Central

    Dynan, W S; Yoo, S

    1998-01-01

    The Ku protein-DNA-dependent protein kinase system is one of the major pathways by which cells of higher eukaryotes respond to double-strand DNA breaks. The components of the system are evolutionarily conserved and homologs are known from a number of organisms. The Ku protein component binds directly to DNA ends and may help align them for ligation. Binding of Ku protein to DNA also nucleates formation of an active enzyme complex containing the DNA-dependent protein kinase catalytic subunit (DNA-PKcs). The interaction between Ku protein, DNA-PKcs and nucleic acids has been extensively investigated. This review summarizes the results of these biochemical investigations and relates them to recent molecular genetic studies that reveal highly characteristic repair and recombination defects in mutant cells lacking Ku protein or DNA-PKcs. PMID:9512523

  7. Simultaneous retrieval of temperature-dependent absorption coefficient and conductivity of participating media

    PubMed Central

    Ren, Yatao; Qi, Hong; Zhao, Fangzhou; Ruan, Liming; Tan, Heping

    2016-01-01

    A secondary optimization technique was proposed to estimate the temperature-dependent thermal conductivity and absorption coefficient. In the proposed method, the stochastic particle swarm optimization was applied to solve the inverse problem. The coupled radiation and conduction problem was solved in a 1D absorbing, emitting, but non-scattering slab exposed to a pulse laser. It is found that in the coupled radiation and conduction problem, the temperature response is highly sensitive to conductivity but slightly sensitive to the optical properties. On the contrary, the radiative intensity is highly sensitive to optical properties but slightly sensitive to thermal conductivity. Therefore, the optical and thermal signals should both be considered in the inverse problem to estimate the temperature-dependent properties of the transparent media. On this basis, the temperature-dependent thermal conductivity and absorption coefficient were both estimated accurately by measuring the time-dependent temperature, and radiative response at the boundary of the slab. PMID:26912418

  8. Simultaneous retrieval of temperature-dependent absorption coefficient and conductivity of participating media

    NASA Astrophysics Data System (ADS)

    Ren, Yatao; Qi, Hong; Zhao, Fangzhou; Ruan, Liming; Tan, Heping

    2016-02-01

    A secondary optimization technique was proposed to estimate the temperature-dependent thermal conductivity and absorption coefficient. In the proposed method, the stochastic particle swarm optimization was applied to solve the inverse problem. The coupled radiation and conduction problem was solved in a 1D absorbing, emitting, but non-scattering slab exposed to a pulse laser. It is found that in the coupled radiation and conduction problem, the temperature response is highly sensitive to conductivity but slightly sensitive to the optical properties. On the contrary, the radiative intensity is highly sensitive to optical properties but slightly sensitive to thermal conductivity. Therefore, the optical and thermal signals should both be considered in the inverse problem to estimate the temperature-dependent properties of the transparent media. On this basis, the temperature-dependent thermal conductivity and absorption coefficient were both estimated accurately by measuring the time-dependent temperature, and radiative response at the boundary of the slab.

  9. Simultaneous retrieval of temperature-dependent absorption coefficient and conductivity of participating media.

    PubMed

    Ren, Yatao; Qi, Hong; Zhao, Fangzhou; Ruan, Liming; Tan, Heping

    2016-01-01

    A secondary optimization technique was proposed to estimate the temperature-dependent thermal conductivity and absorption coefficient. In the proposed method, the stochastic particle swarm optimization was applied to solve the inverse problem. The coupled radiation and conduction problem was solved in a 1D absorbing, emitting, but non-scattering slab exposed to a pulse laser. It is found that in the coupled radiation and conduction problem, the temperature response is highly sensitive to conductivity but slightly sensitive to the optical properties. On the contrary, the radiative intensity is highly sensitive to optical properties but slightly sensitive to thermal conductivity. Therefore, the optical and thermal signals should both be considered in the inverse problem to estimate the temperature-dependent properties of the transparent media. On this basis, the temperature-dependent thermal conductivity and absorption coefficient were both estimated accurately by measuring the time-dependent temperature, and radiative response at the boundary of the slab. PMID:26912418

  10. DNA synthesis in yeast cell-free extracts dependent on recombinant DNA plasmids purified from Escherichia coli.

    PubMed Central

    Jong, A Y; Scott, J F

    1985-01-01

    In our attempts to establish a cell-free DNA replication system for the yeast Saccharomyces cerevisiae, we have observed that recombinant DNA plasmids purified from Escherichia coli by a common procedure (lysozyme-detergent lysis and equilibrium banding in cesium chloride ethidium bromide gradients) often serve as templates for DNA synthesis by elongation enzymes. The templates could be elongated equally well by enzymes present in the yeast cell-free extracts, by the large proteolytic fragment of E. coli DNA polymerase I or by T4 DNA polymerase. The template activity of the purified plasmids was dependent on the presence of heterologous DNA segments in the bacterial vectors. The template activity could be diminished by treatment with alkali. We propose that the ability of recombinant plasmids isolated from bacterial hosts to serve as elongation templates may lead to erroneous conclusions when these plasmids are used as templates for in vitro replication or transcription reactions. Images PMID:3889851

  11. Sequence-Dependent Photocurrent Generation through Long-Distance Excess-Electron Transfer in DNA.

    PubMed

    Lin, Shih-Hsun; Fujitsuka, Mamoru; Majima, Tetsuro

    2016-07-18

    Given its well-ordered continuous π stacking of nucleobases, DNA has been considered as a biomaterial for charge transfer in biosensors. For cathodic photocurrent generation resulting from hole transfer in DNA, sensitivity to DNA structure and base-pair stacking has been confirmed. However, such information has not been provided for anodic photocurrent generation resulting from excess-electron transfer in DNA. In the present study, we measured the anodic photocurrent of a DNA-modified Au electrode. Our results demonstrate long-distance excess-electron transfer in DNA, which is dominated by a hopping mechanism, and the photocurrent generation is sequence dependent. PMID:27243800

  12. DNA Stimulates ATP-Dependent Proteolysis and Protein-Dependent ATPase Activity of Protease La from Escherichia coli

    NASA Astrophysics Data System (ADS)

    Chung, Chin Ha; Goldberg, Alfred L.

    1982-02-01

    The product of the lon gene in Escherichia coli is an ATP-dependent protease, protease La, that also binds strongly to DNA. Addition of double-stranded or single-stranded DNA to the protease in the presence of ATP was found to stimulate the hydrolysis of casein or globin 2- to 7-fold, depending on the DNA concentration. Native DNA from several sources (plasmid pBR322, phage T7, or calf thymus) had similar effects, but after denaturation the DNA was 20-100% more effective than the native form. Although poly(rA), globin mRNA, and various tRNAs did not stimulate proteolysis, poly(rC) and poly(rU) were effective. Poly(dT) was stimulatory but (dT)10 was not. In the presence of DNA as in its absence, proteolysis required concomitant ATP hydrolysis, and the addition of DNA also enhanced ATP hydrolysis by protease La 2-fold, but only in the presence of casein. At much higher concentrations, DNA inhibited proteolysis as well as ATP cleavage. Thus, association of this enzyme with DNA may regulate the degradation of cell proteins in vivo.

  13. Modeling the electrical conduction in DNA nanowires: Charge transfer and lattice fluctuation theories

    NASA Astrophysics Data System (ADS)

    Behnia, S.; Fathizadeh, S.

    2015-02-01

    An analytical approach is proposed for the investigation of the conductivity properties of DNA. The charge mobility of DNA is studied based on an extended Peyrard-Bishop-Holstein model when the charge carrier is also subjected to an external electrical field. We have obtained the values of some of the system parameters, such as the electron-lattice coupling constant, by using the mean Lyapunov exponent method. On the other hand, the electrical current operator is calculated directly from the lattice operators. Also, we have studied Landauer resistance behavior with respect to the external field, which could serve as the interface between chaos theory tools and electronic concepts. We have examined the effect of two types of electrical fields (dc and ac) and variation of the field frequency on the current flowing through DNA. A study of the current-voltage (I -V ) characteristic diagram reveals regions with a (quasi-)Ohmic property and other regions with negative differential resistance (NDR). NDR is a phenomenon that has been observed experimentally in DNA at room temperature. We have tried to study the affected agents in charge transfer phenomena in DNA to better design nanostructures.

  14. Modeling the electrical conduction in DNA nanowires: charge transfer and lattice fluctuation theories.

    PubMed

    Behnia, S; Fathizadeh, S

    2015-02-01

    An analytical approach is proposed for the investigation of the conductivity properties of DNA. The charge mobility of DNA is studied based on an extended Peyrard-Bishop-Holstein model when the charge carrier is also subjected to an external electrical field. We have obtained the values of some of the system parameters, such as the electron-lattice coupling constant, by using the mean Lyapunov exponent method. On the other hand, the electrical current operator is calculated directly from the lattice operators. Also, we have studied Landauer resistance behavior with respect to the external field, which could serve as the interface between chaos theory tools and electronic concepts. We have examined the effect of two types of electrical fields (dc and ac) and variation of the field frequency on the current flowing through DNA. A study of the current-voltage (I-V) characteristic diagram reveals regions with a (quasi-)Ohmic property and other regions with negative differential resistance (NDR). NDR is a phenomenon that has been observed experimentally in DNA at room temperature. We have tried to study the affected agents in charge transfer phenomena in DNA to better design nanostructures. PMID:25768543

  15. Substrate-dependent millisecond domain motions in DNA polymerase β

    PubMed Central

    Berlow, Rebecca B.; Swain, Monalisa; Dalal, Shibani; Sweasy, Joann B.; Loria, J. Patrick

    2012-01-01

    DNA polymerase β (Pol β) is a 39 kDa enzyme that performs the vital cellular function of repairing damaged DNA. Mutations in Pol β have been linked to various cancers and these mutations further correlated with altered Pol β enzymatic activity. The fidelity of correct nucleotide incorporation into damaged DNA is essential for Pol β repair function and several studies have implicated conformational changes in Pol β as a determinant of this repair fidelity. In this work, the rate constants for domain motions in Pol β have been determined by solution NMR relaxation dispersion for the apo and substrate, binary forms of Pol β. In apo Pol β, molecular motions, primarily isolated to the DNA lyase domain, are observed to occur at 1400 s–1. Additional analysis suggests that these motions allow apo Pol β to sample a conformation similar to the gapped, DNA substrate bound form. Upon binding DNA, these lyase domain motions are significantly quenched whereas evidence for conformational motions in the polymerase domain become apparent. These NMR studies suggest an alteration in the dynamic landscape of Pol β due to substrate binding. Moreover, a number of the flexible residues identified in this work are also the location of residues, which upon mutation, lead to cancer phenotypes in vivo, which may be due to the intimate role of protein motions in Pol β fidelity. PMID:22446382

  16. A Novel Mutation in DNA Topoisomerase I of Yeast Causes DNA Damage and Rad9-Dependent Cell Cycle Arrest

    PubMed Central

    Levin, N. A.; Bjornsti, M. A.; Fink, G. R.

    1993-01-01

    DNA topoisomerases, enzymes that alter the superhelicity of DNA, have been implicated in such critical cellular functions as transcription, DNA replication, and recombination. In the yeast Saccharomyces cerevisiae, a null mutation in the gene encoding topoisomerase I (TOP1) causes elevated levels of mitotic recombination in the ribosomal DNA (rDNA), but has little effect on growth. We have isolated a missense mutation in TOP1 that causes mitotic hyper-recombination not only in the rDNA, but also at other loci, in addition to causing a number of other unexpected phenotypes. This topoisomerase I mutation (top1-103) causes slow growth, constitutive expression of DNA damage-inducible genes, and inviability in the absence of the double-strand break repair system. Overexpression of top1-103 causes RAD9-dependent cell cycle arrest in G(2). We show that the Top1-103 enzyme nicks DNA in vitro, suggesting that it damages DNA directly. We propose that Top1-103 mimics the action of wild-type topoisomerase I in the presence of the anti-tumor drug, camptothecin. PMID:8385050

  17. Interleukin-4 enhances PARP-dependent DNA repair activity in vitro.

    PubMed

    Ciszewski, Wojciech Michał; Wagner, Waldemar; Kania, Katarzyna Dominika; Dastych, Jarosław

    2014-09-01

    Eukaryotic cells possess several DNA repair mechanisms, including homologous recombination and the non-homologous end-joining (NHEJ) system. There are two known NHEJ systems. The major mechanism depends on the catalytic unit of DNA-dependent protein kinase (DNA-PKcs) and DNA ligase IV, and an alternative mechanism (B-NHEJ) depends on poly(ADP-ribose) polymerase (PARP). These systems are upregulated by genotoxic agents. Interleukin 4 (IL-4) is an immunoregulatory cytokine that is secreted by immune cells upon contact with certain genotoxic compounds and is known to regulate several genes encoding components of DNA repair systems in human monocytes. We have investigated the possible effects of IL-4 on the DNA repair process within murine and human cells exposed to selected genotoxic compounds. In a series of experiments, including the comet assay, cell surface annexin V staining, analysis of histone H2AX phosphorylation, and a DNA end-joining assay, we observed that IL-4 decreased DNA damage in murine fibroblasts and human glioblastoma cells exposed to genotoxic agents and increased DNA ligation activity in the nuclei of these cells in a process that depended on PARP. These observations suggest that IL-4 is capable of upregulating the alternative NHEJ DNA repair mechanism in murine and human cells. PMID:24724620

  18. Temperature dependence of conductivity enhancement induced by nanoceramic fillers in polymer electrolytes

    NASA Astrophysics Data System (ADS)

    Gao, S.; Yan, X. L.; Zhong, J.; Xue, G. B.; Wang, B.

    2013-04-01

    The microstructure and ionic conductivity of polymer nanocomposite electrolytes doped with ZnO have been systematically studied. Compared with the undoped one, a less crystalline phase, a restrained main chain movement, a reduced symmetry in the configuration of ethylene oxide/lithium ion, and an at least five-fold increase in conductivity were observed for the filler incorporated electrolyte. Lewis acid-base interactions are determining in causing these changes. The temperature dependence of conductivity is explained by the Vogel-Tammann-Fulcher equation based on the free volume theory. The mechanism of temperature dependent conductivity enhancement is interpreted by a modeling function proposed.

  19. Dependence of Thermal Conductivity on Thickness in Single-Walled Carbon Nanotube Films.

    PubMed

    Lee, Kyung-Min; Shrestha, Ramesh; Dangol, Ashesh; Chang, Won Seok; Coker, Zachary; Choi, Tae-Youl

    2016-01-01

    Herein, we report experimentally dependence of thermal conductivity on thickness of single walled carbon nanotubes (SWNTs) thin films; the measurements are based on the micropipette thermal sensor technique. Accurate and well resolved measurements of thermal conductivity made by the micropipette sensor showed a correlated behavior of thickness and thermal conductivity of CNT films that thermal conductivity decreased as thickness increased. The thickness dependence is explained by reduction of mean free path (MFP), which is induced by more intertubular junctions in more dense-packed carbon nanotube (CNT) networks; the thicker SWCNT films were revealed to have higher density. PMID:27398564

  20. Age dependency of base modification in rabbit liver DNA

    NASA Technical Reports Server (NTRS)

    Yamamoto, O.; Fuji, I.; Yoshida, T.; Cox, A. B.; Lett, J. T.

    1988-01-01

    Age-related modifications of DNA bases have been observed in the liver of the New Zealand white (NZW) rabbit (Oryctolagus cuniculus), a lagomorph with a median life span in captivity of 5-7 yr. The ages of the animals studied ranged from 6 wk to 9 yr. After the DNA had been extracted from the liver cell nuclei and hydrolyzed with acid, the bases were analyzed by column chromatography with Cellulofine gels (GC-15-m). Two peaks in the chromatogram, which eluted before the four DNA bases, contained modified bases. Those materials, which were obtained in relatively large amounts from old animals, were highly fluorescent, and were shown to be crosslinked base products by mass spectrometry. The yield of crosslinked products versus rabbit age (greater than 0.5 yr) can be fitted by an exponential function (correlation coefficient: 0.76 +/- 0.09).

  1. Heterogeneous nuclear ribonucleoprotein B1 protein impairs DNA repair mediated through the inhibition of DNA-dependent protein kinase activity

    SciTech Connect

    Iwanaga, Kentaro; Sueoka, Naoko; Sato, Akemi; Hayashi, Shinichiro; Sueoka, Eisaburo . E-mail: sueokae@post.saga-med.ac.jp

    2005-08-05

    Heterogeneous nuclear ribonucleoprotein B1, an RNA binding protein, is overexpressed from the early stage of lung cancers; it is evident even in bronchial dysplasia, a premalignant lesion. We evaluated the proteins bound with hnRNP B1 and found that hnRNP B1 interacted with DNA-dependent protein kinase (DNA-PK) complex, and recombinant hnRNP B1 protein dose-dependently inhibited DNA-PK activity in vitro. To test the effect of hnRNP B1 on DNA repair, we performed comet assay after irradiation, using normal human bronchial epithelial (HBE) cells treated with siRNA for hnRNP A2/B1: reduction of hnRNP B1 treated with siRNA for hnRNP A2/B1 induced faster DNA repair in normal HBE cells. Considering these results, we assume that overexpression of hnRNP B1 occurring in the early stage of carcinogenesis inhibits DNA-PK activity, resulting in subsequent accumulation of erroneous rejoining of DNA double-strand breaks, causing tumor progression.

  2. UV sensitivity and impaired nucleotide excision repair in DNA-dependent protein kinase mutant cells.

    PubMed Central

    Muller, C; Calsou, P; Frit, P; Cayrol, C; Carter, T; Salles, B

    1998-01-01

    DNA-dependent protein kinase (DNA-PK), a member of the phosphatidyl-inositol (PI)3-kinase family, is involved in the repair of DNA double-strand breaks. Its regulatory subunit, Ku, binds to DNA and recruits the kinase catalytic subunit (DNA-PKcs). We show here a new role of DNA-PK in the modulation of the process of nucleotide excision repair (NER) in vivo since, as compared with their respective parental cell lines, DNA-PK mutants (scid , V-3 and xrs 6 cells) exhibit sensitivity to UV-C irradiation (2.0- to 2.5-fold) and cisplatin ( approximately 3- to 4-fold) associated with a decreased activity (40-55%) of unscheduled DNA synthesis after UV-C irradiation. Moreover, we observed that wortmannin sensitized parental cells in vivo when combined with either cisplatin or UV-C light, but had no effect on the DNA-PKcs deficient scid cells. Despite a lower repair synthesis activity (approximately 2-fold) measured in vitro with nuclear cell extracts from DNA-PK mutants, a direct involvement of DNA-PK in the NER reaction in vitro has not been observed. This study establishes a regulatory function of DNA-PK in the NER process in vivo but rules out a physical role of the complex in the repair machinery at the site of the DNA lesion. PMID:9490781

  3. Length-dependent binding of human XLF to DNA and stimulation of XRCC4.DNA ligase IV activity.

    PubMed

    Lu, Haihui; Pannicke, Ulrich; Schwarz, Klaus; Lieber, Michael R

    2007-04-13

    An XRCC4-like factor, called XLF or Cernunnos, was recently identified as another important factor in the non-homologous DNA end joining (NHEJ) process. NHEJ is the major pathway for the repair of double-strand DNA breaks. The similarity in the putative secondary structures of XLF and XRCC4 as well as the association of XLF with XRCC4.DNA ligase IV in vivo suggested a role in the final ligation step of NHEJ. Here, we find that purified XLF directly interacts with purified XRCC4.DNA ligase IV complex and stimulates the ligase complex in a direct assay for ligation activity. Purified XLF has DNA binding activity, but this binding is dependent on DNA length in a manner most consistent with orientation of the C-terminal alpha helices parallel to the DNA helix. To better understand the function of XLF, we purified an XLF mutant (R57G), which was identified in patients with NHEJ deficiency and severe combined immunodeficiency. Surprisingly, the mutant protein retained its ability to stimulate XRCC4.DNA ligase IV but failed to translocate to the nucleus, and this appears to be the basis for the NHEJ defect in this patient. PMID:17317666

  4. Genomic assay reveals tolerance of DNA damage by both translesion DNA synthesis and homology-dependent repair in mammalian cells.

    PubMed

    Izhar, Lior; Ziv, Omer; Cohen, Isadora S; Geacintov, Nicholas E; Livneh, Zvi

    2013-04-16

    DNA lesions can block replication forks and lead to the formation of single-stranded gaps. These replication complications are mitigated by DNA damage tolerance mechanisms, which prevent deleterious outcomes such as cell death, genomic instability, and carcinogenesis. The two main tolerance strategies are translesion DNA synthesis (TLS), in which low-fidelity DNA polymerases bypass the blocking lesion, and homology-dependent repair (HDR; postreplication repair), which is based on the homologous sister chromatid. Here we describe a unique high-resolution method for the simultaneous analysis of TLS and HDR across defined DNA lesions in mammalian genomes. The method is based on insertion of plasmids carrying defined site-specific DNA lesions into mammalian chromosomes, using phage integrase-mediated integration. Using this method we show that mammalian cells use HDR to tolerate DNA damage in their genome. Moreover, analysis of the tolerance of the UV light-induced 6-4 photoproduct, the tobacco smoke-induced benzo[a]pyrene-guanine adduct, and an artificial trimethylene insert shows that each of these three lesions is tolerated by both TLS and HDR. We also determined the specificity of nucleotide insertion opposite these lesions during TLS in human genomes. This unique method will be useful in elucidating the mechanism of DNA damage tolerance in mammalian chromosomes and their connection to pathological processes such as carcinogenesis. PMID:23530190

  5. Structure of the adenylation domain of NAD[superscript +]-dependent DNA ligase from Staphylococcus aureus

    SciTech Connect

    Han, Seungil; Chang, Jeanne S.; Griffor, Matt; Pfizer

    2010-09-17

    DNA ligase catalyzes phosphodiester-bond formation between immediately adjacent 5'-phosphate and 3''-hydroxyl groups in double-stranded DNA and plays a central role in many cellular and biochemical processes, including DNA replication, repair and recombination. Bacterial NAD{sup +}-dependent DNA ligases have been extensively characterized as potential antibacterial targets because of their essentiality and their structural distinction from human ATP-dependent DNA ligases. The high-resolution structure of the adenylation domain of Staphylococcus aureus NAD{sup +}-dependent DNA ligase establishes the conserved domain architecture with other bacterial adenylation domains. Two apo crystal structures revealed that the active site possesses the preformed NAD{sup +}-binding pocket and the 'C2 tunnel' lined with hydrophobic residues: Leu80, Phe224, Leu287, Phe295 and Trp302. The C2 tunnel is unique to bacterial DNA ligases and the Leu80 side chain at the mouth of the tunnel points inside the tunnel and forms a narrow funnel in the S. aureus DNA ligase structure. Taken together with other DNA ligase structures, the S. aureus DNA ligase structure provides a basis for a more integrated understanding of substrate recognition and catalysis and will be also be of help in the development of small-molecule inhibitors.

  6. Temperature dependence of DNA condensation at high ionic concentration

    NASA Astrophysics Data System (ADS)

    Mao, Wei; Gao, Qingqing; Liu, Yanhui; Fan, Yangtao; Hu, Lin; Xu, Houqiang

    2016-08-01

    A series of experiments pointed out that compact states of DNA condensed by multivalent cation prefer higher temperature. The condensed DNA takes elongated coil or compact globule states and the population of the compact globule states increases with an increase in temperature. At the same time, a recent experimental work carried out in buffer solution without multivalent cation points out that DNA persistence length strongly depends on the temperature. DNA persistence length is a key parameter for quantitative interpretation of the conformational properties of DNA and related to the bending rigidity of DNA. It is necessary to revolve the effects of temperature dependence of persistence length on DNA condensation, and a model including the temperature dependence of persistence length and strong correlation of multivalent cation on DNA is provided. The autocorrelation function of the tangent vectors is found as an effective way to detect the temperature dependence of toroid conformations. With an increase in temperature, the first periodic oscillation in the autocorrelation function shifts left and the number of segments containing the first periodic oscillation decreases gradually. According to the experiments mentioned above, the long-axis length is defined to estimate the temperature dependence of condensation process further. At the temperatures defined in experiments mentioned above, the relation between long-axis length and temperature matches the experimental results.

  7. GADD45α inhibition of DNMT1 dependent DNA methylation during homology directed DNA repair

    PubMed Central

    Lee, Bongyong; Morano, Annalisa; Porcellini, Antonio; Muller, Mark T.

    2012-01-01

    In this work, we examine regulation of DNA methyltransferase 1 (DNMT1) by the DNA damage inducible protein, GADD45α. We used a system to induce homologous recombination (HR) at a unique double-strand DNA break in a GFP reporter in mammalian cells. After HR, the repaired DNA is hypermethylated in recombinant clones showing low GFP expression (HR-L expressor class), while in high expressor recombinants (HR-H clones) previous methylation patterns are erased. GADD45α, which is transiently induced by double-strand breaks, binds to chromatin undergoing HR repair. Ectopic overexpression of GADD45α during repair increases the HR-H fraction of cells (hypomethylated repaired DNA), without altering the recombination frequency. Conversely, silencing of GADD45α increases methylation of the recombined segment and amplifies the HR-L expressor (hypermethylated) population. GADD45α specifically interacts with the catalytic site of DNMT1 and inhibits methylation activity in vitro. We propose that double-strand DNA damage and the resulting HR process involves precise, strand selected DNA methylation by DNMT1 that is regulated by GADD45α. Since GADD45α binds with high avidity to hemimethylated DNA intermediates, it may also provide a barrier to spreading of methylation during or after HR repair. PMID:22135303

  8. Reply to "Comment on 'Characterization of the Tunneling Conductance Across DNA Bases'"

    SciTech Connect

    Zikic, Radomir; Krstic, Predrag S; Zhang, Xiaoguang; Fuentes-Cabrera, Miguel A; Wells, Jack C; Zhao, Xiongce

    2007-01-01

    Lagerqvist et al.'s Comment regarding the calculation of the transverse conductance of a single-strand DNA heteropolymer translocated through a nanogap between two metal electrodes fully confirms the main conclusions of our study [Phys. Rev. E 74, 011919 (2006)]. In the absence of resonant tunneling, the sensitivity to geometrical factors and the uncertainty in the density functional theory model, which is used in our study and is the basis for the parametrization of the model used by Lagerqvist et al., raises doubt about the utility of static-bias measurements for DNA sequencing. A possible scheme discussed by Lagerqvist et al., the stabilization of geometry by an applied strong transverse voltage (1 V), is outside the applicability range of the near-equilibrium theory they (and we) used. More advanced theories and precise gap measurements are needed to resolve these issues.

  9. Effects of the environment on the electric conductivity of double-stranded DNA molecules.

    PubMed

    Malyshev, A V; Díaz, E; Domínguez-Adame, F; Malyshev, V A

    2009-08-19

    We present a theoretical analysis of the effects of the environment on charge transport in double-stranded synthetic poly(G)-poly(C) DNA molecules attached to two ideal leads. Coupling of the DNA to the environment results in two effects: (i) localization of carrier functions due to static disorder and (ii) phonon-induced scattering of the carriers between the localized states, resulting in hopping conductivity. A nonlinear Pauli master equation for populations of localized states is used to describe the hopping transport and calculate the electric current as a function of the applied bias. We demonstrate that, although the electronic gap in the density of states shrinks as the disorder increases, the voltage gap in the I-V characteristics becomes wider. A simple physical explanation of this effect is provided. PMID:21828599

  10. Light sensitive memristor with bi-directional and wavelength-dependent conductance control

    NASA Astrophysics Data System (ADS)

    Maier, P.; Hartmann, F.; Rebello Sousa Dias, M.; Emmerling, M.; Schneider, C.; Castelano, L. K.; Kamp, M.; Marques, G. E.; Lopez-Richard, V.; Worschech, L.; Höfling, S.

    2016-07-01

    We report the optical control of localized charge on positioned quantum dots in an electro-photo-sensitive memristor. Interband absorption processes in the quantum dot barrier matrix lead to photo-generated electron-hole-pairs that, depending on the applied bias voltage, charge or discharge the quantum dots and hence decrease or increase the conductance. Wavelength-dependent conductance control is observed by illumination with red and infrared light, which leads to charging via interband and discharging via intraband absorption. The presented memristor enables optical conductance control and may thus be considered for sensory applications in artificial neural networks as light-sensitive synapses or optically tunable memories.

  11. First-principles study of high-conductance DNA sequencing with carbon nanotube electrodes

    NASA Astrophysics Data System (ADS)

    Chen, X.; Rungger, I.; Pemmaraju, C. D.; Schwingenschlögl, U.; Sanvito, S.

    2012-03-01

    Rapid and cost-effective DNA sequencing at the single nucleotide level might be achieved by measuring a transverse electronic current as single-stranded DNA is pulled through a nanometer-sized pore. In order to enhance the electronic coupling between the nucleotides and the electrodes and hence the current signals, we employ a pair of single-walled close-ended (6,6) carbon nanotubes (CNTs) as electrodes. We then investigate the electron transport properties of nucleotides sandwiched between such electrodes by using first-principles quantum transport theory. In particular, we consider the extreme case where the separation between the electrodes is the smallest possible that still allows the DNA translocation. The benzene-like ring at the end cap of the CNT can strongly couple with the nucleobases and therefore it can both reduce conformational fluctuations and significantly improve the conductance. As such, when the electrodes are closely spaced, the nucleobases can pass through only with their base plane parallel to the plane of CNT end caps. The optimal molecular configurations, at which the nucleotides strongly couple to the CNTs, and which yield the largest transmission, are first identified. These correspond approximately to the lowest energy configurations. Then the electronic structures and the electron transport of these optimal configurations are analyzed. The typical tunneling currents are of the order of 50 nA for voltages up to 1 V. At higher bias, where resonant transport through the molecular states is possible, the current is of the order of several μA. Below 1 V, the currents associated to the different nucleotides are consistently distinguishable, with adenine having the largest current, guanine the second largest, cytosine the third and, finally, thymine the smallest. We further calculate the transmission coefficient profiles as the nucleotides are dragged along the DNA translocation path and investigate the effects of configurational variations

  12. KU-0060648 inhibits hepatocellular carcinoma cells through DNA-PKcs-dependent and DNA-PKcs-independent mechanisms

    PubMed Central

    Wei, Mu-Xin; Tang, Min; Ruan, Ting-Yan; Xu, Jun-Ying; Zhou, Xiao-zhong; Chen, Gang; Lu, Pei-Hua

    2016-01-01

    Here we tested anti-tumor activity of KU-0060648 in preclinical hepatocellular carcinoma (HCC) models. Our results demonstrated that KU-0060648 was anti-proliferative and pro-apoptotic in established (HepG2, Huh-7 and KYN-2 lines) and primary human HCC cells, but was non-cytotoxic to non-cancerous HL-7702 hepatocytes. DNA-PKcs (DNA-activated protein kinase catalytic subunit) is an important but not exclusive target of KU-0060648. DNA-PKcs knockdown or dominant negative mutation inhibited HCC cell proliferation. On the other hand, overexpression of wild-type DNA-PKcs enhanced HepG2 cell proliferation. Importantly, KU-0060648 was still cytotoxic to DNA-PKcs-silenced or -mutated HepG2 cells, although its activity in these cells was relatively weak. Further studies showed that KU-0060648 inhibited PI3K-AKT-mTOR activation, independent of DNA-PKcs. Introduction of constitutively-active AKT1 (CA-AKT1) restored AKT-mTOR activation after KU-0060648 treatment in HepG2 cells, and alleviated subsequent cytotoxicity. In vivo, intraperitoneal (i.p.) injection of KU-0060648 significantly inhibited HepG2 xenograft growth in nude mice. AKT-mTOR activation was also inhibited in xenografted tumors. Finally, we showed that DNA-PKcs expression was significantly upregulated in human HCC tissues. Yet miRNA-101, an anti-DNA-PKcs miRNA, was downregulated. Over-expression of miR-101 in HepG2 cells inhibited DNA-PKcs expression and cell proliferation. Together, these results indicate that KU-0060648 inhibits HCC cells through DNA-PKcs-dependent and -independent mechanisms. PMID:26933997

  13. Finite Element Analysis of Hepatic Radiofrequency Ablation Probes using Temperature-Dependent Electrical Conductivity

    PubMed Central

    Chang, Isaac

    2003-01-01

    Background Few finite element models (FEM) have been developed to describe the electric field, specific absorption rate (SAR), and the temperature distribution surrounding hepatic radiofrequency ablation probes. To date, a coupled finite element model that accounts for the temperature-dependent electrical conductivity changes has not been developed for ablation type devices. While it is widely acknowledged that accounting for temperature dependent phenomena may affect the outcome of these models, the effect has not been assessed. Methods The results of four finite element models are compared: constant electrical conductivity without tissue perfusion, temperature-dependent conductivity without tissue perfusion, constant electrical conductivity with tissue perfusion, and temperature-dependent conductivity with tissue perfusion. Results The data demonstrate that significant errors are generated when constant electrical conductivity is assumed in coupled electrical-heat transfer problems that operate at high temperatures. These errors appear to be closely related to the temperature at which the ablation device operates and not to the amount of power applied by the device or the state of tissue perfusion. Conclusion Accounting for temperature-dependent phenomena may be critically important in the safe operation of radiofrequency ablation device that operate near 100°C. PMID:12780939

  14. RCC1-dependent activation of Ran accelerates cell cycle and DNA repair, inhibiting DNA damage-induced cell senescence.

    PubMed

    Cekan, Pavol; Hasegawa, Keisuke; Pan, Yu; Tubman, Emily; Odde, David; Chen, Jin-Qiu; Herrmann, Michelle A; Kumar, Sheetal; Kalab, Petr

    2016-04-15

    The coordination of cell cycle progression with the repair of DNA damage supports the genomic integrity of dividing cells. The function of many factors involved in DNA damage response (DDR) and the cell cycle depends on their Ran GTPase-regulated nuclear-cytoplasmic transport (NCT). The loading of Ran with GTP, which is mediated by RCC1, the guanine nucleotide exchange factor for Ran, is critical for NCT activity. However, the role of RCC1 or Ran⋅GTP in promoting cell proliferation or DDR is not clear. We show that RCC1 overexpression in normal cells increased cellular Ran⋅GTP levels and accelerated the cell cycle and DNA damage repair. As a result, normal cells overexpressing RCC1 evaded DNA damage-induced cell cycle arrest and senescence, mimicking colorectal carcinoma cells with high endogenous RCC1 levels. The RCC1-induced inhibition of senescence required Ran and exportin 1 and involved the activation of importin β-dependent nuclear import of 53BP1, a large NCT cargo. Our results indicate that changes in the activity of the Ran⋅GTP-regulated NCT modulate the rate of the cell cycle and the efficiency of DNA repair. Through the essential role of RCC1 in regulation of cellular Ran⋅GTP levels and NCT, RCC1 expression enables the proliferation of cells that sustain DNA damage. PMID:26864624

  15. RCC1-dependent activation of Ran accelerates cell cycle and DNA repair, inhibiting DNA damage–induced cell senescence

    PubMed Central

    Cekan, Pavol; Hasegawa, Keisuke; Pan, Yu; Tubman, Emily; Odde, David; Chen, Jin-Qiu; Herrmann, Michelle A.; Kumar, Sheetal; Kalab, Petr

    2016-01-01

    The coordination of cell cycle progression with the repair of DNA damage supports the genomic integrity of dividing cells. The function of many factors involved in DNA damage response (DDR) and the cell cycle depends on their Ran GTPase–regulated nuclear–cytoplasmic transport (NCT). The loading of Ran with GTP, which is mediated by RCC1, the guanine nucleotide exchange factor for Ran, is critical for NCT activity. However, the role of RCC1 or Ran⋅GTP in promoting cell proliferation or DDR is not clear. We show that RCC1 overexpression in normal cells increased cellular Ran⋅GTP levels and accelerated the cell cycle and DNA damage repair. As a result, normal cells overexpressing RCC1 evaded DNA damage–induced cell cycle arrest and senescence, mimicking colorectal carcinoma cells with high endogenous RCC1 levels. The RCC1-induced inhibition of senescence required Ran and exportin 1 and involved the activation of importin β–dependent nuclear import of 53BP1, a large NCT cargo. Our results indicate that changes in the activity of the Ran⋅GTP–regulated NCT modulate the rate of the cell cycle and the efficiency of DNA repair. Through the essential role of RCC1 in regulation of cellular Ran⋅GTP levels and NCT, RCC1 expression enables the proliferation of cells that sustain DNA damage. PMID:26864624

  16. Flow-Dependent Epigenetic DNA Methylation in Endothelial Gene Expression and Atherosclerosis.

    PubMed

    Dunn, Jessilyn; Thabet, Salim; Jo, Hanjoong

    2015-07-01

    Epigenetic mechanisms that regulate endothelial cell gene expression are now emerging. DNA methylation is the most stable epigenetic mark that confers persisting changes in gene expression. Not only is DNA methylation important in rendering cell identity by regulating cell type-specific gene expression throughout differentiation, but it is becoming clear that DNA methylation also plays a key role in maintaining endothelial cell homeostasis and in vascular disease development. Disturbed blood flow causes atherosclerosis, whereas stable flow protects against it by differentially regulating gene expression in endothelial cells. Recently, we and others have shown that flow-dependent gene expression and atherosclerosis development are regulated by mechanisms dependent on DNA methyltransferases (1 and 3A). Disturbed blood flow upregulates DNA methyltransferase expression both in vitro and in vivo, which leads to genome-wide DNA methylation alterations and global gene expression changes in a DNA methyltransferase-dependent manner. These studies revealed several mechanosensitive genes, such as HoxA5, Klf3, and Klf4, whose promoters were hypermethylated by disturbed blood flow, but rescued by DNA methyltransferases inhibitors such as 5Aza-2-deoxycytidine. These findings provide new insight into the mechanism by which flow controls epigenomic DNA methylation patterns, which in turn alters endothelial gene expression, regulates vascular biology, and modulates atherosclerosis development. PMID:25953647

  17. DNA sequence-dependent mechanics and protein-assisted bending in repressor-mediated loop formation

    NASA Astrophysics Data System (ADS)

    Boedicker, James Q.; Garcia, Hernan G.; Johnson, Stephanie; Phillips, Rob

    2013-12-01

    As the chief informational molecule of life, DNA is subject to extensive physical manipulations. The energy required to deform double-helical DNA depends on sequence, and this mechanical code of DNA influences gene regulation, such as through nucleosome positioning. Here we examine the sequence-dependent flexibility of DNA in bacterial transcription factor-mediated looping, a context for which the role of sequence remains poorly understood. Using a suite of synthetic constructs repressed by the Lac repressor and two well-known sequences that show large flexibility differences in vitro, we make precise statistical mechanical predictions as to how DNA sequence influences loop formation and test these predictions using in vivo transcription and in vitro single-molecule assays. Surprisingly, sequence-dependent flexibility does not affect in vivo gene regulation. By theoretically and experimentally quantifying the relative contributions of sequence and the DNA-bending protein HU to DNA mechanical properties, we reveal that bending by HU dominates DNA mechanics and masks intrinsic sequence-dependent flexibility. Such a quantitative understanding of how mechanical regulatory information is encoded in the genome will be a key step towards a predictive understanding of gene regulation at single-base pair resolution.

  18. DNA sequence-dependent mechanics and protein-assisted bending in repressor-mediated loop formation

    PubMed Central

    Boedicker, James Q.; Garcia, Hernan G.; Johnson, Stephanie; Phillips, Rob

    2014-01-01

    As the chief informational molecule of life, DNA is subject to extensive physical manipulations. The energy required to deform double-helical DNA depends on sequence, and this mechanical code of DNA influences gene regulation, such as through nucleosome positioning. Here we examine the sequence-dependent flexibility of DNA in bacterial transcription factor-mediated looping, a context for which the role of sequence remains poorly understood. Using a suite of synthetic constructs repressed by the Lac repressor and two well-known sequences that show large flexibility differences in vitro, we make precise statistical mechanical predictions as to how DNA sequence influences loop formation and test these predictions using in vivo transcription and in vitro single-molecule assays. Surprisingly, sequence-dependent flexibility does not affect in vivo gene regulation. By theoretically and experimentally quantifying the relative contributions of sequence and the DNA-bending protein HU to DNA mechanical properties, we reveal that bending by HU dominates DNA mechanics and masks intrinsic sequence-dependent flexibility. Such a quantitative understanding of how mechanical regulatory information is encoded in the genome will be a key step towards a predictive understanding of gene regulation at single-base pair resolution. PMID:24231252

  19. Atomistic Simulation of the Size and Orientation Dependences of Thermal Conductivity in GaN Nanowires

    SciTech Connect

    Wang, Zhiguo; Zu, Xiaotao; Gao, Fei; Weber, William J.; Crocombette, J.-P.

    2007-04-16

    The thermal conductivity of GaN nanowires has been determined computationally, by applying nonequilibrium atomistic simulation methods using the Stillinger-Weber [Phys. Rev. B 31, 5262 (1985)] potentials. The simulation results show that the thermal conductivity of the GaN nanowires is smaller than that of a bulk crystal and increases with increasing diameter. Surface scattering of phonons and the high surface to volume ratios of the nanowires are primarily responsible for the reduced thermal conductivity and its size dependence behavior. The thermal conductivity is also found to decrease with increasing temperature, which is due to phonon-phonon interactions at high temperatures. The thermal conductivity also exhibits a dependence on axial orientation of the nanowires.

  20. Orientation Dependent Thermal Conductance in Single-Layer MoS2

    NASA Astrophysics Data System (ADS)

    Jiang, Jin-Wu; Zhuang, Xiaoying; Rabczuk, Timon

    2013-07-01

    We investigate the thermal conductivity in the armchair and zigzag MoS2 nanoribbons, by combining the non-equilibrium Green's function approach and the first-principles method. A strong orientation dependence is observed in the thermal conductivity. Particularly, the thermal conductivity for the armchair MoS2 nanoribbon is about 673.6 Wm-1 K-1 in the armchair nanoribbon, and 841.1 Wm-1 K-1 in the zigzag nanoribbon at room temperature. By calculating the Caroli transmission, we disclose the underlying mechanism for this strong orientation dependence to be the fewer phonon transport channels in the armchair MoS2 nanoribbon in the frequency range of [150, 200] cm-1. Through the scaling of the phonon dispersion, we further illustrate that the thermal conductivity calculated for the MoS2 nanoribbon is esentially in consistent with the superior thermal conductivity found for graphene.

  1. DNA-dependent protein kinase catalytic subunit inhibitor reverses acquired radioresistance in lung adenocarcinoma by suppressing DNA repair.

    PubMed

    Li, Yong; Li, Hang; Peng, Wen; He, Xin-Yun; Huang, Min; Qiu, Dong; Xue, Ying-Bo; Lu, Liang

    2015-07-01

    The mechanisms underlying lung cancer radioresistance remain to be fully elucidated. The DNA repair pathway is a predominant target of radiotherapy, which is considered to be involved in the acquired radioresistance of cancer cells. The present study aimed to establish a radioresistant cell model using the A549 human lung cancer cell line, and to further investigate the potential mechanisms underlying the radioresistance. The A549R radioresistant lung cancer cell variant was established by exposing the parental A549 cells to repeated γ-ray irradiation at a total dose of 60 Gy. Colony formation assays were then used to determine cell survival following γ-ray exposure. The established radioresistant cells were subsequently treated with or without the NU7026 DNA-PKcs inhibitor. The levels of DNA damage were determined by counting the number of fluorescent γ-H2AX foci in the cells. The cellular capacity for DNA repair was assessed using antibodies for the detection of various DNA repair pathway proteins. The radioresistant sub-clones exhibited significantly decreased survival following NU7026 treatment, compared with the parental cells, as determined by colony formation assays (P<0.05), and this finding was found to be dose-dependent. Treatment with the DNA-dependent protein kinase (DNA-PK) inhibitor significantly reduced γ-H2AX foci formation (P<0.05) following acute radiation exposure in the radioresistant sub-clones, compared with the parental control cells. The decreased levels of γ-H2AX were accompanied by an increase in the percentage of apoptotic cells in the radioresistant cell line following post-radiation treatment with the DNA-PKcs inhibitor. The expression levels of proteins associated with the DNA repair pathway were altered markedly in the cells treated with NU7026. The results of the present study suggested that radioresistance may be associated with enhanced DNA repair following exposure to radiation, resulting in reduced apoptosis. Therefore, the

  2. Comment on "Modeling the electrical conduction in DNA nanowires: Charge transfer and lattice fluctuation theories"

    NASA Astrophysics Data System (ADS)

    Panahi, M.; Chitsazanmoghaddam, M.

    2016-04-01

    In a recent paper [S. Behnia and S. Fathizadeh, Phys. Rev. E 91, 022719 (2015), 10.1103/PhysRevE.91.022719] an analytical approach is proposed for the investigation of the conductivity properties of DNA. The authors use mean Lyapunov exponent methods as the backbone of their approach and try to interpret properties of the system based on its behavior. Their interpretation regarding the change in nature of the mean Lyapunov exponent at the denaturation temperatures and discussions of stability and instability based on the mean Lyapunov exponent method are questioned. Moreover there is misunderstanding between mean Lyapunov exponent and Lyapunov exponent.

  3. On the channel width-dependence of the thermal conductivity in ultra-narrow graphene nanoribbons

    NASA Astrophysics Data System (ADS)

    Karamitaheri, Hossein; Neophytou, Neophytos

    2016-08-01

    The thermal conductivity of low-dimensional materials and graphene nanoribbons, in particular, is limited by the strength of line-edge-roughness scattering. One way to characterize the roughness strength is the dependency of the thermal conductivity on the channel's width in the form Wβ. Although in the case of electronic transport, this dependency is very well studied, resulting in W6 for nanowires and quantum wells and W4 for nanoribbons, in the case of phonon transport it is not yet clear what this dependence is. In this work, using lattice dynamics and Non-Equilibrium Green's Function simulations, we examine the width dependence of the thermal conductivity of ultra-narrow graphene nanoribbons under the influence of line edge-roughness. We show that the exponent β is in fact not a single well-defined number, but it is different for different parts of the phonon spectrum depending on whether phonon transport is ballistic, diffusive, or localized. The exponent β takes values β < 1 for semi-ballistic phonon transport, values β ≫ 1 for sub-diffusive or localized phonons, and β = 1 only in the case where the transport is diffusive. The overall Wβ dependence of the thermal conductivity is determined by the width-dependence of the dominant phonon modes (usually the acoustic ones). We show that due to the long phonon mean-free-paths, the width-dependence of thermal conductivity becomes a channel length dependent property, because the channel length determines whether transport is ballistic, diffusive, or localized.

  4. DNA duplex length and salt concentration dependence of enthalpy-entropy compensation parameters for DNA melting.

    PubMed

    Starikov, E B; Nordén, Bengt

    2009-08-20

    Systematical differential calorimetry experiments on DNA oligomers with different lengths and placed in water solutions with various added salt concentrations may, in principle, unravel important information about the structure and dynamics of the DNA and their water-counterion surrounding. With this in mind, to reinterpret the most recent results of calorimetric experiments on DNA oligomers of such a kind, the recent enthalpy-entropy compensation theory has been used. It is demonstrated that the application of the latter could enable direct estimation of thermodynamic parameters of the microphase transitions connected to the changes in DNA dynamical regimes versus the length of the biopolymers and the ionic strengths of their water solutions, and this calls for much more systematical experimental and theoretical studies in this field. PMID:19719257

  5. Single-stranded-DNA-binding protein-dependent DNA unwinding of the yeast ARS1 region.

    PubMed Central

    Matsumoto, K; Ishimi, Y

    1994-01-01

    DNA unwinding of autonomously replicating sequence 1 (ARS1) from the yeast Saccharomyces cerevisiae was investigated. When a negatively supercoiled plasmid DNA containing ARS1 was digested with single-strand-specific mung bean nuclease, a discrete region in the vector DNA was preferentially digested. The regions containing the core consensus A domain and the 3'-flanking B domain of ARS1 were weakly digested. When the DNA was incubated with the multisubunit single-stranded DNA-binding protein (SSB, also called RPA [replication protein A]) from human and yeast cells prior to mung bean nuclease digestion, the cleavage in the A and B domains was greatly increased. Furthermore, a region corresponding to the 5'-flanking C domain of ARS1 was digested. These results indicate that three domains of ARS1, each of which is important for replication in yeast cells, closely correspond to the regions where the DNA duplex is easily unwound by torsional stress. SSB may stimulate the unwinding of the ARS1 region by its preferential binding to the destabilized three domains. Mung bean nuclease digestion of the substitution mutants with mutations of ARS1 (Y. Marahrens and B. Stillman, Science 255:817-823, 1992) revealed that the sequences in the B2 and A elements are responsible for the unwinding of the B domain and the region containing the A domain, respectively. Images PMID:8007967

  6. The Sequence-Dependent Transmission Properties Through Double Helix DNA Molecules

    NASA Astrophysics Data System (ADS)

    Dong, Rui-Xin; Yan, Xun-Ling; Yang, Bing

    In this paper, a double helix model of charge transport in a DNA molecule is presented, and the transmission spectra and I-V curves of four kinds of periodic sequences DNA are obtained. The results show that the transmission characteristics of DNA are not only related to the longitudinal transport but also to the transverse transport of the molecule. The more the composition of bases, the bigger the percent of θ-direction, and the conductive ability reduces. For a different sequence with same composition, the less the number of consecutive appearance of the same base is, the lower the conductive ability.

  7. LET dependence of DNA-protein cross-links

    SciTech Connect

    Blakely, E.A.; Chang, P.Y.; Bjornstad, K.A.

    1995-08-01

    We have preliminary data indicating a fluence-dependent yield of particle-induced protein cross-links (DPC`s) with a dependency on LET and particle residual energy. Our data indicate that the DPC yield for hamster fibroblasts in vitro irradiated at 32 keV/{mu}m is similar to that reported for hamster cells irradiated with cobalt-60 gamma rays. At 100-120 keV/{mu}m there is some evidence for an enhanced DPC yield with increasing particle fluence, but there are differences in the yields that are dependent on particle track structure.

  8. DNA-PKcs-Dependent Modulation of Cellular Radiosensitivity by a Selective Cyclooxygenase-2 Inhibitor

    SciTech Connect

    Kodym, Elisabeth; Kodym, Reinhard; Chen, Benjamin P.; Chen, David J.; Morotomi-Yano, Keiko; Choy, Hak; Saha, Debabrata

    2007-09-01

    Purpose: Inhibition of cyclooxygenase-2 has been shown to increase radiosensitivity. Recently, the suppression of radiation-induced DNA-dependant protein kinase (DNA-PK) activity by the selective cyclooxygenase-2 inhibitor celecoxib was reported. Given the importance of DNA-PK for repair of radiation-induced DNA double-strand breaks by nonhomologous end-joining and the clinical use of the substance, we investigated the relevance of the DNA-PK catalytic subunit (DNA-PKcs) for the modulation of cellular radiosensitivity by celecoxib. Methods and Materials: We used a syngeneic model of Chinese hamster ovarian cell lines: AA8, possessing a wild-type DNK-PKcs; V3, lacking a functional DNA-PKcs; and V3/WT11, V3 stably transfected with the DNA-PKcs. The cells were treated with celecoxib (50 {mu}M) for 24 h before irradiation. The modulation of radiosensitivity was determined using the colony formation assay. Results: Treatment with celecoxib increased the cellular radiosensitivity in the DNA-PKcs-deficient cell line V3 with a dose-enhancement ratio of 1.3 for a surviving fraction of 0.5. In contrast, clonogenic survival was increased in DNA-PKcs wild-type-expressing AA8 cells and in V3 cells transfected with DNA-PKcs (V3/WT11). The decrease in radiosensitivity was comparable to the radiosensitization in V3 cells, with a dose-enhancement ratio of 0.76 (AA8) and 0.80 (V3/WT11) for a survival of 0.5. Conclusions: We have demonstrated a DNA-PKcs-dependent differential modulation of cellular radiosensitivity by celecoxib. These effects might be attributed to alterations in signaling cascades downstream of DNA-PK toward cell survival. These findings offer an explanation for the poor outcomes in some recently published clinical trials.

  9. Topological symmetry-induced width dependence of thermal conductance of edge-reconstructed graphene nanoribbons

    NASA Astrophysics Data System (ADS)

    Lan, Jinghua; Cai, Yongqing; Zhang, Gang; Wang, Jian-Sheng; Zhang, Yong-Wei

    2014-07-01

    Using the nonequilibrium Green's function method, we investigate the effects of edge reconstructions on the thermal conductance of graphene nanoribbons (GNRs). For the first time, we show that the thermal conductance of edge reconstructed zigzag GNRs oscillates with the number of dimers along the width direction, N. When N is an odd or even number, the thermal conductance of edge reconstructed zigzag GNRs is about 25 or 85% that of the perfect zigzag GNRs, respectively. For edge reconstructed armchair GNRs, the thermal conductance only decreases slightly and it changes linearly with N. The significant difference in the width dependence of GNR thermal conductance may be attributed to the topological symmetry and edge reconstruction of GNRs. Our results shed light on a new approach to control the thermal conductance of GNRs by reconstructing their edges and controlling their topological symmetry.

  10. Device for dielectrophoretic separation and collection of nanoparticles and DNA under high conductance conditions.

    PubMed

    Song, Youngjun; Sonnenberg, Avery; Heaney, Yvonne; Heller, Michael J

    2015-05-01

    Most dielectrophoretic (DEP) separations of cells, nanoparticles, and other entities are carried out on microelectrode arrays or in microfluidic device formats. Less work has been directed at designing pipette-type formats that would allow dipping into and recovering specific analytes from samples in microtiter plate formats. In order to address this important area, we have fabricated micropipette tip devices containing a 2% agarose gel plug, a buffer chamber, and platinum electrode as the DEP collection device, to be used in combination with separate sample wells that contain a circular gold electrode. We demonstrated that 200 nm fluorescent nanoparticles could be isolated into DEP high-field regions and separated from 10 μm fluorescent microbeads in high conductance buffer (1× PBS) by applying an alternating current at 10 kHz with a peak-to-peak voltage (Vpp) of 160 Vpp. The collected nanoparticles were then transferred to a new buffer solution. We also demonstrated the DEP isolation and separation of genomic DNA (>50 kbps) from the 10 μm microbeads in high conductance buffer (1× PBS) with transfer of collected DNA to another solution. PMID:25780998

  11. Conducting polymer based DNA biosensor for the detection of the Bacillus cereus group species

    NASA Astrophysics Data System (ADS)

    Velusamy, Vijayalakshmi; Arshak, Khalil; Korostynska, Olga; Oliwa, Kamila; Adley, Catherine

    2009-05-01

    Biosensor designs are emerging at a significant rate and play an increasingly important role in foodborne pathogen detection. Conducting polymers are excellent tools for the fabrication of biosensors and polypyrrole has been used in the detection of biomolecules due to its unique properties. The prime intention of this paper was to pioneer the design and fabrication of a single-strand (ss) DNA biosensor for the detection of the Bacillus cereus (B.cereus) group species. Growth of B. cereus, results in production of several highly active toxins. Therefore, consumption of food containing >106 bacteria/gm may results in emetic and diarrhoeal syndromes. The most common source of this bacterium is found in liquid food products, milk powder, mixed food products and is of particular concern in the baby formula industry. The electrochemical deposition technique, such as cyclic voltammetry, was used to develop and test a model DNA-based biosensor on a gold electrode electropolymerized with polypyrrole. The electrically conducting polymer, polypyrrole is used as a platform for immobilizing DNA (1μg) on the gold electrode surface, since it can be more easily deposited from neutral pH aqueous solutions of pyrrolemonomers. The average current peak during the electrodeposition event is 288μA. There is a clear change in the current after hybridization of the complementary oligonucleotide (6.35μA) and for the noncomplementary oligonucleotide (5.77μA). The drop in current after each event was clearly noticeable and it proved to be effective.

  12. Manipulating the temperature dependence of the thermal conductivity of graphene phononic crystal

    NASA Astrophysics Data System (ADS)

    Hu, Shiqian; An, Meng; Yang, Nuo; Li, Baowen

    2016-07-01

    By using non-equilibrium molecular dynamics simulations, modulating the temperature dependence of thermal conductivity of graphene phononic crystals (GPnCs) is investigated. It is found that the temperature dependence of thermal conductivity of GPnCs follows ∼T ‑α behavior. The power exponents (α) can be efficiently tuned by changing the characteristic size of GPnCs. The phonon participation ratio spectra and dispersion relation reveal that the long-range phonon modes are more affected in GPnCs with larger holes (L 0). Our results suggest that constructing GPnCs is an effective method to manipulate the temperature dependence of thermal conductivity of graphene, which would be beneficial for developing GPnC-based thermal management and signal processing devices.

  13. Manipulating the temperature dependence of the thermal conductivity of graphene phononic crystal.

    PubMed

    Hu, Shiqian; An, Meng; Yang, Nuo; Li, Baowen

    2016-07-01

    By using non-equilibrium molecular dynamics simulations, modulating the temperature dependence of thermal conductivity of graphene phononic crystals (GPnCs) is investigated. It is found that the temperature dependence of thermal conductivity of GPnCs follows ∼T (-α) behavior. The power exponents (α) can be efficiently tuned by changing the characteristic size of GPnCs. The phonon participation ratio spectra and dispersion relation reveal that the long-range phonon modes are more affected in GPnCs with larger holes (L 0). Our results suggest that constructing GPnCs is an effective method to manipulate the temperature dependence of thermal conductivity of graphene, which would be beneficial for developing GPnC-based thermal management and signal processing devices. PMID:27196392

  14. The kinetics of force-dependent hybridization and strand-peeling of short DNA fragments

    NASA Astrophysics Data System (ADS)

    Yang, ZhouJie; Yuan, GuoHua; Zhai, WeiLi; Yan, Jie; Chen, Hu

    2016-08-01

    Deoxyribonucleic acid (DNA) carries the genetic information in all living organisms. It consists of two interwound single-stranded (ss) strands, forming a double-stranded (ds) DNA with a right-handed double-helical conformation. The two strands are held together by highly specific basepairing interactions and are further stabilized by stacking between adjacent basepairs. A transition from a dsDNA to two separated ssDNA is called melting and the reverse transition is called hybridization. Applying a tensile force to a dsDNA can result in a particular type of DNA melting, during which one ssDNA strand is peeled away from the other. In this work, we studied the kinetics of strand-peeling and hybridization of short DNA under tensile forces. Our results show that the force-dependent strand-peeling and hybridization can be described with a simple two-state model. Importantly, detailed analysis of the force-dependent transition rates revealed that the transition state consists of several basepairs dsDNA.

  15. A Review of the Role of the Sequence-Dependent Electrostatic Landscape in DNA Alkylation Patterns

    PubMed Central

    Gold, Barry; Marky, Luis M.; Stone, Michael P.; Williams, Loren D.

    2008-01-01

    Alkylating agents, including environmental and endogenous carcinogens, and DNA targeting antineoplastic agents, that adduct DNA via intermediates with significant cationic charge show a sequence selectively in their covalent bonding to nucleobases. The resulting patterns of alkylation eventually contribute to the agent-dependent distributions and types of mutations. The origin of the regioselective modification of DNA by electrophiles has been attributed to steric and/or electronic factors, but attempts to mechanistically model and predict alkylation patterns have had limited success. In this review, we present data consistent with the role of the intrinsic sequence-dependent electrostatic landscape (SDEL) in DNA that modulates the equilibrium binding of cations and the bonding of reactive charged alkylating agents to atoms that line the floor of the major groove of DNA. PMID:17112226

  16. Size-dependent electrical conductivity of indium zinc oxide deposited by RF magnetron sputtering.

    PubMed

    Heo, Young-Woo; Pearton, S J; Norton, D P

    2012-04-01

    We investigated the size-dependent electrical conductivities of indium zinc oxide stripes with different widths from 50 nm to 4 microm and with the same thickness of 50 nm deposited by RF magnetron sputtering. The size of the indium zinc oxide stripes was controlled by e-beam lithography. The distance of the two Ti/Au Ohmic electrodes along the indium zinc oxide stripes was kept constant at 25 microm. The electrical conductivity decreased as the size of the indium zinc oxide stripes decreased below a critical width (80 nm). The activation energy, derived from the electric conductivity versus temperature measurement, was dependent on the dimensions of indium zinc oxide stripes. These results can be understood as stemming from surface charge trapping from the absorption of oxygen and/or water vapor, which leads to an increase in the energy difference between the conduction energy band and the Fermi energy. PMID:22849102

  17. Thermal conductivity of simple liquids: Origin of temperature and packing fraction dependences

    NASA Astrophysics Data System (ADS)

    Ishii, Yoshiki; Sato, Keisuke; Salanne, Mathieu; Madden, Paul A.; Ohtori, Norikazu

    2014-03-01

    The origin of both weak temperature dependence and packing fraction dependence of T1/4η3/2 in the thermal conductivity of the simple Lennard-Jones (LJ) liquid is explored. In order to discuss the relative contributions from attractive or repulsive part of the interaction potential separately, the thermal conductivity of a series of Weeks-Chandler-Anderson (WCA) fluids is calculated by molecular dynamics simulations. The results show that the repulsive part plays the main role in the heat conduction, while the attractive part has no direct effect on the thermal conductivity for a given packing fraction. By investigating WCA fluids with potentials of varying softness, we explain the difference observed between the LJ liquids such as argon and Coulombic liquids such as NaCl.

  18. Electrical conduction in alkali borate glasses; a unique dependence on the concentration of modifier ions

    NASA Astrophysics Data System (ADS)

    Doweidar, H.; Moustafa, Y. M.; El-Damrawi, G. M.; Ramadan, R. M.

    2008-01-01

    The electrical conduction of Li2O-B2O3, Na2O-B2O3 and K2O-B2O3 glasses seems, at first sight, to be dominated by the activation energy. Regardless of the size of the alkali ion, there is a unique dependence of conductivity, at a certain temperature, on the alkali-alkali distance and thus on N (the number of ions per cm3). The linear dependence of logσ on N-3/2 for all types of alkali ions reveals that N is the basic parameter that determines the conductivity at a certain temperature. A derived semi-empirical relation can be used to calculate the conductivity as a function of N and temperature.

  19. Sequence-Dependent Fluorescence of Cy3- and Cy5-Labeled Double-Stranded DNA.

    PubMed

    Kretschy, Nicole; Sack, Matej; Somoza, Mark M

    2016-03-16

    The fluorescent intensity of Cy3 and Cy5 dyes is strongly dependent on the nucleobase sequence of the labeled oligonucleotides. Sequence-dependent fluorescence may significantly influence the data obtained from many common experimental methods based on fluorescence detection of nucleic acids, such as sequencing, PCR, FRET, and FISH. To quantify sequence dependent fluorescence, we have measured the fluorescence intensity of Cy3 and Cy5 bound to the 5' end of all 1024 possible double-stranded DNA 5mers. The fluorescence intensity was also determined for these dyes bound to the 5' end of fixed-sequence double-stranded DNA with a variable sequence 3' overhang adjacent to the dye. The labeled DNA oligonucleotides were made using light-directed, in situ microarray synthesis. The results indicate that the fluorescence intensity of both dyes is sensitive to all five bases or base pairs, that the sequence dependence is stronger for double- (vs single-) stranded DNA, and that the dyes are sensitive to both the adjacent dsDNA sequence and the 3'-ssDNA overhang. Purine-rich sequences result in higher fluorescence. The results can be used to estimate measurement error in experiments with fluorescent-labeled DNA, as well as to optimize the fluorescent signal by considering the nucleobase environment of the labeling cyanine dye. PMID:26895222

  20. Sequence-Dependent Fluorescence of Cy3- and Cy5-Labeled Double-Stranded DNA

    PubMed Central

    2016-01-01

    The fluorescent intensity of Cy3 and Cy5 dyes is strongly dependent on the nucleobase sequence of the labeled oligonucleotides. Sequence-dependent fluorescence may significantly influence the data obtained from many common experimental methods based on fluorescence detection of nucleic acids, such as sequencing, PCR, FRET, and FISH. To quantify sequence dependent fluorescence, we have measured the fluorescence intensity of Cy3 and Cy5 bound to the 5′ end of all 1024 possible double-stranded DNA 5mers. The fluorescence intensity was also determined for these dyes bound to the 5′ end of fixed-sequence double-stranded DNA with a variable sequence 3′ overhang adjacent to the dye. The labeled DNA oligonucleotides were made using light-directed, in situ microarray synthesis. The results indicate that the fluorescence intensity of both dyes is sensitive to all five bases or base pairs, that the sequence dependence is stronger for double- (vs single-) stranded DNA, and that the dyes are sensitive to both the adjacent dsDNA sequence and the 3′-ssDNA overhang. Purine-rich sequences result in higher fluorescence. The results can be used to estimate measurement error in experiments with fluorescent-labeled DNA, as well as to optimize the fluorescent signal by considering the nucleobase environment of the labeling cyanine dye. PMID:26895222

  1. Isothermal DNA amplification in vitro: the helicase-dependent amplification system.

    PubMed

    Jeong, Yong-Joo; Park, Kkothanahreum; Kim, Dong-Eun

    2009-10-01

    Since the development of polymerase chain reaction, amplification of nucleic acids has emerged as an elemental tool for molecular biology, genomics, and biotechnology. Amplification methods often use temperature cycling to exponentially amplify nucleic acids; however, isothermal amplification methods have also been developed, which do not require heating the double-stranded nucleic acid to dissociate the synthesized products from templates. Among the several methods used for isothermal DNA amplification, the helicase-dependent amplification (HDA) is discussed in this review with an emphasis on the reconstituted DNA replication system. Since DNA helicase can unwind the double-stranded DNA without the need for heating, the HDA system provides a very useful tool to amplify DNA in vitro under isothermal conditions with a simplified reaction scheme. This review describes components and detailed aspects of current HDA systems using Escherichia coli UvrD helicase and T7 bacteriophage gp4 helicase with consideration of the processivity and efficiency of DNA amplification. PMID:19629390

  2. Supercoiling-dependent flexibility of adenosine-tract-containing DNA detected by a topological method

    PubMed Central

    Tsen, Hua; Levene, Stephen D.

    1997-01-01

    Intrinsically bent DNA sequences have been implicated in the activation of transcription by promoting juxtaposition of DNA sequences near the terminal loop of a superhelical domain. We have developed a novel topological assay for DNA looping based on λ integrative recombination to study the effects of intrinsically bent DNA sequences on the tertiary structure of negatively supercoiled DNA. Remarkably, the localization of adenosine-tract (A-tract) sequences in the terminal loop of a supercoiled plasmid is independent of the extent of intrinsic bending. The results suggest that A-tract-containing sequences have other properties that organize the structure of superhelical domains apart from intrinsic bending and may explain the lack of conservation in the degree of A-tract-dependent bending among DNA sequences located upstream of bacterial promoters. PMID:9096303

  3. Reversibility, Dopant Desorption, and Tunneling in the Temperature-Dependent Conductivity of Type-Separated, Conductive Carbon Nanotube Networks

    SciTech Connect

    Barnes, T. M.; Blackburn, J. L.; van de Lagemaat, J.; Coutts, T. J.; Heben, M. J.

    2008-09-01

    We present a comprehensive study of the effects of doping and temperature on the conductivity of single-walled carbon nanotube (SWNT) networks. We investigated nearly type-pure networks as well as networks comprising precisely tuned mixtures of metallic and semiconducting tubes. Networks were studied in their as-produced state and after treatments with nitric acid, thionyl chloride, and hydrazine to explore the effects of both intentional and adventitious doping. For intentionally and adventitiously doped networks, the sheet resistance (R{sub s}) exhibits an irreversible increase with temperature above {approx}350 K. Dopant desorption is shown to be the main cause of this increase and the observed hysteresis in the temperature-dependent resistivity. Both thermal and chemical dedoping produced networks free of hysteresis. Temperature-programmed desorption data showed that dopants are most strongly bound to the metallic tubes and that networks consisting of metallic tubes exhibit the best thermal stability. At temperatures below the dopant desorption threshold, conductivity in the networks is primarily controlled by thermally assisted tunneling through barriers at the intertube or interbundle junctions.

  4. DNA electrophoresis in agarose gels: A new mobility vs. DNA length dependence

    NASA Astrophysics Data System (ADS)

    Beheshti, Afshin

    2002-04-01

    Separations were performed on double stranded DNA (dsDNA) using electrophoresis. Electrophoresis is the steady transport of particles under the influence of an external electric field. Double stranded DNA fragments ranging in length from 200 base pairs (bp) to 194,000 bp (0.34 nm = 1 bp) were electrophoresed at agarose gel concentrations T = 0.4%--1.5%. The electric field was varied from 0.62 V/cm to 6.21 V/cm. A wide range of electric fields and gel concentrations were used to study the usefulness of a new interpolation equation, 1mL =1mL-( 1mL-1 ms)e-L/g , where mL,ms , and g are independent free fitting parameters. The long length mobility limit is interpreted as mL , the short length mobility limit is ms , and g is the crossover between the long length limit and the short length limit. This exponential relation fit very well (chi2 ≥ 0.999) when there are two smooth transitions observed in the "reptation plots" (plotting 3mL/m∘ vs. L) (J. Rousseau, G. Drouin, and G. W. Slater, Phys Rev Lett. 1997, 79, 1945--1948). Fits deviate from the data when three different slopes were observed in the reptation plots. Reptation plots were used to determine a phase diagram for dsDNA migration regimes. The phase diagrams define different regions where mechanisms for molecular transport affect the migration of dsDNA in agarose gels during electrophoresis. The parameters from the equation have also been interpreted to provide a physical description of the structure of the agarose gel by calculating the pore sizes. The relations between the values for the pore sizes and the phase diagrams are interpreted to better understand the migration of the DNA through agarose gels.

  5. Transcription-dependent DNA transactions in the mitochondrial genome of a yeast hypersuppressive petite mutant.

    PubMed

    Van Dyck, E; Clayton, D A

    1998-05-01

    Mitochondrial DNA (mtDNA) of Saccharomyces cerevisiae contains highly conserved sequences, called rep/ori, that are associated with several aspects of its metabolism. These rep/ori sequences confer the transmission advantage exhibited by a class of deletion mutants called hypersuppressive petite mutants. In addition, because they share features with the mitochondrial leading-strand DNA replication origin of mammals, rep/ori sequences have also been proposed to participate in mtDNA replication initiation. Like the mammalian origins, where transcription is used as a priming mechanism for DNA synthesis, yeast rep/ori sequences contain an active promoter. Although transcription is required for maintenance of wild-type mtDNA in yeast, the role of the rep/ori promoter as a cis-acting element involved in the replication of wild-type mtDNA is unclear, since mitochondrial deletion mutants need neither transcription nor a rep/ori sequence to maintain their genome. Similarly, transcription from the rep/ori promoter does not seem to be necessary for biased inheritance of mtDNA. As a step to elucidate the function of the rep/ori promoter, we have attempted to detect transcription-dependent DNA transactions in the mtDNA of a hypersuppressive petite mutant. We have examined the mtDNA of the well-characterized petite mutant a-1/1R/Z1, whose repeat unit shelters the rep/ori sequence ori1, in strains carrying either wild-type or null alleles of the nuclear genes encoding the mitochondrial transcription apparatus. Complex DNA transactions were detected that take place around GC-cluster C, an evolutionarily conserved GC-rich sequence block immediately downstream from the rep/ori promoter. These transactions are strictly dependent upon mitochondrial transcription. PMID:9566917

  6. Lead-position dependent regular oscillations and random fluctuations of conductance in graphene quantum dots.

    PubMed

    Huang, Liang; Yang, Rui; Lai, Ying-Cheng; Ferry, David K

    2013-02-27

    Quantum interference causes a wavefunction to have sensitive spatial dependence, and this has a significant effect on quantum transport. For example, in a quantum-dot system, the conductance can depend on the lead positions. We investigate, for graphene quantum dots, the conductance variations with the lead positions. Since for graphene the types of boundaries, e.g., zigzag and armchair, can fundamentally affect the quantum transport characteristics, we focus on rectangular graphene quantum dots, for which the effects of boundaries can be systematically studied. For both zigzag and armchair horizontal boundaries, we find that changing the positions of the leads can induce significant conductance variations. Depending on the Fermi energy, the variations can be either regular oscillations or random conductance fluctuations. We develop a physical theory to elucidate the origin of the conductance oscillation/fluctuation patterns. In particular, quantum interference leads to standing-wave-like-patterns in the quantum dot which, in the absence of leads, are regulated by the energy-band structure of the corresponding vertical graphene ribbon. The observed 'coexistence' of regular oscillations and random fluctuations in the conductance can be exploited for the development of graphene-based nanodevices. PMID:23343960

  7. Functional significance of voltage-dependent conductances in Limulus ventral photoreceptors

    PubMed Central

    1982-01-01

    The influence of voltage-dependent conductances on the receptor potential of Limulus ventral photoreceptors was investigated. During prolonged, bright illumination, the receptor potential consists of an initial transient phase followed by a smaller plateau phase. Generally, a spike appears on the rising edge of the transient phase, and often a dip occurs between the transient and plateau. Block of the rapidly inactivating outward current, iA, by 4-aminopyridine eliminates the dip under some conditions. Block of maintained outward current by internal tetraethylammonium increases the height of the plateau phase, but does not eliminate the dip. Block of the voltage-dependent Na+ and Ca2+ current by external Ni2+ eliminates the spike. The voltage-dependent Ca2+ conductance also influences the sensitivity of the photoreceptor to light as indicated by the following evidence: depolarizing voltage- clamp pulses reduce sensitivity to light. This reduction is blocked by removal of external Ca2+ or by block of inward Ca2+ current with Ni2+. The reduction of sensitivity depends on the amplitude of the pulse, reaching a maximum at or approximately +15 mV. The voltage dependence is consistent with the hypothesis that the desensitization results from passive Ca2+ entry through a voltage-dependent conductance. PMID:7057162

  8. Diameter dependence of the thermal conductivity of InAs nanowires.

    PubMed

    Swinkels, M Y; van Delft, M R; Oliveira, D S; Cavalli, A; Zardo, I; van der Heijden, R W; Bakkers, E P A M

    2015-09-25

    The diameter dependence of the thermal conductivity of InAs nanowires in the range of 40-1500 nm has been measured. We demonstrate a reduction in thermal conductivity of 80% for 40 nm nanowires, opening the way for further design strategies for nanoscaled thermoelectric materials. Furthermore, we investigate the effect of thermal contact in the most common measurement method for nanoscale thermal conductivity. Our study allows for the determination of the thermal contact using existing measurement setups. The thermal contact resistance is found to be comparable to the wire thermal resistance for wires with a diameter of 90 nm and higher. PMID:26329133

  9. WEE1 inhibition in pancreatic cancer cells is dependent on DNA repair status in a context dependent manner.

    PubMed

    Lal, Shruti; Zarei, Mahsa; Chand, Saswati N; Dylgjeri, Emanuela; Mambelli-Lisboa, Nicole C; Pishvaian, Michael J; Yeo, Charles J; Winter, Jordan M; Brody, Jonathan R

    2016-01-01

    Pancreatic ductal adenocarcinoma (PDA) is a lethal disease, in part, because of the lack of effective targeted therapeutic options. MK-1775 (also known as AZD1775), a mitotic inhibitor, has been demonstrated to enhance the anti-tumor effects of DNA damaging agents such as gemcitabine. We evaluated the efficacy of MK-1775 alone or in combination with DNA damaging agents (MMC or oxaliplatin) in PDA cell lines that are either DNA repair proficient (DDR-P) or deficient (DDR-D). PDA cell lines PL11, Hs 766T and Capan-1 harboring naturally selected mutations in DNA repair genes FANCC, FANCG and BRCA2 respectively, were less sensitive to MK-1775 as compared to two out of four representative DDR-P (MIA PaCa2 and PANC-1) cell lines. Accordingly, DDR-P cells exhibit reduced sensitivity to MK-1775 upon siRNA silencing of DNA repair genes, BRCA2 or FANCD2, compared to control cells. Only DDR-P cells showed increased apoptosis as a result of early mitotic entry and catastrophe compared to DDR-D cells. Taken together with other recently published reports, our results add another level of evidence that the efficacy of WEE1 inhibition is influenced by the DNA repair status of a cell and may also be dependent on the tumor type and model evaluated. PMID:27616351

  10. Glycemic control and nerve conduction abnormalities in non-insulin-dependent diabetic subjects.

    PubMed

    Graf, R J; Halter, J B; Pfeifer, M A; Halar, E; Brozovich, F; Porte, D

    1981-03-01

    The influence of therapy of hyperglycemia on the progression of diabetic neuropathy is unclear. We studied variables of glycemia and motor and sensory nerve conduction velocity in a group of 18 non-insulin-dependent diabetic subjects before and after institution of diabetes therapy. Diabetes therapy significantly reduced variables of glycemia after 1, 3, 6, and 12 months. Conduction velocity of the median motor nerve was improved from baseline at each time tested during treatment. In addition, peroneal and tibial motor nerve conduction velocities improved in patients whose levels of hyperglycemia were lowered. Moreover, extent of improvement of conduction velocity of some motor nerves was related to the degree of reduction of hyperglycemia. Sensory nerve conduction velocity was not altered by diabetes therapy. These findings support the hypothesis of a metabolic component to diabetic neuropathy and suggest that optimal glycemic control may be beneficial to patients with this disorder. PMID:7013592

  11. Sequence dependence of isothermal DNA amplification via EXPAR

    PubMed Central

    Qian, Jifeng; Ferguson, Tanya M.; Shinde, Deepali N.; Ramírez-Borrero, Alissa J.; Hintze, Arend; Adami, Christoph; Niemz, Angelika

    2012-01-01

    Isothermal nucleic acid amplification is becoming increasingly important for molecular diagnostics. Therefore, new computational tools are needed to facilitate assay design. In the isothermal EXPonential Amplification Reaction (EXPAR), template sequences with similar thermodynamic characteristics perform very differently. To understand what causes this variability, we characterized the performance of 384 template sequences, and used this data to develop two computational methods to predict EXPAR template performance based on sequence: a position weight matrix approach with support vector machine classifier, and RELIEF attribute evaluation with Naïve Bayes classification. The methods identified well and poorly performing EXPAR templates with 67–70% sensitivity and 77–80% specificity. We combined these methods into a computational tool that can accelerate new assay design by ruling out likely poor performers. Furthermore, our data suggest that variability in template performance is linked to specific sequence motifs. Cytidine, a pyrimidine base, is over-represented in certain positions of well-performing templates. Guanosine and adenosine, both purine bases, are over-represented in similar regions of poorly performing templates, frequently as GA or AG dimers. Since polymerases have a higher affinity for purine oligonucleotides, polymerase binding to GA-rich regions of a single-stranded DNA template may promote non-specific amplification in EXPAR and other nucleic acid amplification reactions. PMID:22416064

  12. DNA methylation results depend on DNA integrity—role of post mortem interval

    PubMed Central

    Rhein, Mathias; Hagemeier, Lars; Klintschar, Michael; Muschler, Marc; Bleich, Stefan; Frieling, Helge

    2015-01-01

    Major questions of neurological and psychiatric mechanisms involve the brain functions on a molecular level and cannot be easily addressed due to limitations in access to tissue samples. Post mortem studies are able to partly bridge the gap between brain tissue research retrieved from animal trials and the information derived from peripheral analysis (e.g., measurements in blood cells) in patients. Here, we wanted to know how fast DNA degradation is progressing under controlled conditions in order to define thresholds for tissue quality to be used in respective trials. Our focus was on the applicability of partly degraded samples for bisulfite sequencing and the determination of simple means to define cut-off values. After opening the brain cavity, we kept two consecutive pig skulls at ambient temperature (19–21°C) and removed cortex tissue up to a post mortem interval (PMI) of 120 h. We calculated the percentage of degradation on DNA gel electrophoresis of brain DNA to estimate quality and relate this estimation spectrum to the quality of human post mortem control samples. Functional DNA quality was investigated by bisulfite sequencing of two functionally relevant genes for either the serotonin receptor 5 (SLC6A4) or aldehyde dehydrogenase 2 (ALDH2). Testing our approach in a heterogeneous collective of human blood and brain samples, we demonstrate integrity of measurement quality below the threshold of 72 h PMI. While sequencing technically worked for all timepoints irrespective of conceivable DNA degradation, there is a good correlation between variance of methylation to degradation levels documented in the gel (R2 = 0.4311, p = 0.0392) for advancing post mortem intervals (PMI). This otherwise elusive phenomenon is an important prerequisite for the interpretation and evaluation of samples prior to in-depth processing via an affordable and easy assay to estimate identical sample quality and thereby comparable methylation measurements. PMID:26042147

  13. Repression of DNA-binding dependent glucocorticoid receptor-mediated gene expression

    PubMed Central

    Muzikar, Katy A.; Nickols, Nicholas G.; Dervan, Peter B.

    2009-01-01

    The glucocorticoid receptor (GR) affects the transcription of genes involved in diverse processes, including energy metabolism and the immune response, through DNA-binding dependent and independent mechanisms. The DNA-binding dependent mechanism occurs by direct binding of GR to glucocorticoid response elements (GREs) at regulatory regions of target genes. The DNA-binding independent mechanism involves binding of GR to transcription factors and coactivators that, in turn, contact DNA. A small molecule that competes with GR for binding to GREs could be expected to affect the DNA-dependent pathway selectively by interfering with the protein-DNA interface. We show that a DNA-binding polyamide that targets the consensus GRE sequence binds the glucocorticoid-induced zipper (GILZ) GRE, inhibits expression of GILZ and several other known GR target genes, and reduces GR occupancy at the GILZ promoter. Genome-wide expression analysis of the effects of this polyamide on a set of glucocorticoid-induced and -repressed genes could help to elucidate the mechanism of GR regulation for these genes. PMID:19805343

  14. A versatile proximity-dependent probe based on light-up DNA-scaffolded silver nanoclusters.

    PubMed

    Ma, Jin-Liang; Yin, Bin-Cheng; Ye, Bang-Ce

    2016-02-01

    It is well-known that proximity-dependent probes containing an analyte recognization site and a signal formation domain could be assembled specifically into a sandwich-like structure (probe-analyte-probe) via introducing an analyte. In this work, using the design for zirconium ion (Zr(4+)) detection as the model, we develop a novel and reliable proximity-dependent DNA-scaffolded silver nanocluster (DNA/AgNC) probe for Zr(4+) detection via target-induced emitter proximity. The proposed strategy undergoes the two following processes: target-mediated emitter pair proximity as target recognition implement and the synthesis of DNA/AgNCs with fluorescence as a signal reporter. Upon combination of the rationally designed probe with Zr(4+), the intact templates were obtained according to the -PO3(2-)-Zr(4+)-PO3(2-)- pattern. The resultant structure with an emitter pair serves as a potent template to achieve highly fluorescent DNA/AgNCs. To verify the universality of the proposed proximity-dependent DNA/AgNC probe, we extend the application of the proximity-dependent probe to DNA and adenosine triphosphate (ATP) detection by virtue of a specific DNA complementary sequence and ATP aptamer as a recognition unit, respectively. The produced fluorescence enhancement of the DNA/AgNCs in response to the analyte concentration allows a quantitative evaluation of the target, including Zr(4+), DNA, and ATP with detection limits of ∼3.00 μM, ∼9.83 nM, and ∼0.81 mM, respectively. The proposed probe possesses good performance with simple operation, cost-effectiveness, good selectivity, and without separation procedures. PMID:26814697

  15. Long conducting polymer nanonecklaces with a `beads-on-a-string' morphology: DNA nanotube-template synthesis and electrical properties

    NASA Astrophysics Data System (ADS)

    Chen, Guofang; Mao, Chengde

    2016-05-01

    Complex and functional nanostructures are always desired. Herein, we present the synthesis of novel long conducting polymer nanonecklaces with a `beads-on-a-string' morphology by the DNA nanotube-template approach and in situ oxidative polymerization of the 3-methylthiophene monomer with FeCl3 as the oxidant/catalyst. The length of the nanonecklaces is up to 60 μm, and the polymer beads of around 20-25 nm in diameter are closely packed along the axis of the DNA nanotube template with a density of ca. 45 particles per μm. The formation of porous DNA nanotubes impregnated with FeCl3 was also demonstrated as intermediate nanostructures. The mechanisms for the formation of both the porous DNA nanotubes and the conducting polymer nanonecklaces are discussed in detail. The as-synthesized polymer/DNA nanonecklaces exhibit good electrical properties.Complex and functional nanostructures are always desired. Herein, we present the synthesis of novel long conducting polymer nanonecklaces with a `beads-on-a-string' morphology by the DNA nanotube-template approach and in situ oxidative polymerization of the 3-methylthiophene monomer with FeCl3 as the oxidant/catalyst. The length of the nanonecklaces is up to 60 μm, and the polymer beads of around 20-25 nm in diameter are closely packed along the axis of the DNA nanotube template with a density of ca. 45 particles per μm. The formation of porous DNA nanotubes impregnated with FeCl3 was also demonstrated as intermediate nanostructures. The mechanisms for the formation of both the porous DNA nanotubes and the conducting polymer nanonecklaces are discussed in detail. The as-synthesized polymer/DNA nanonecklaces exhibit good electrical properties. Electronic supplementary information (ESI) available. See DOI: 10.1039/c6nr01603k

  16. Diameter Dependence of Lattice Thermal Conductivity of Single-Walled Carbon Nanotubes: Study from Ab Initio.

    PubMed

    Yue, Sheng-Ying; Ouyang, Tao; Hu, Ming

    2015-01-01

    The effects of temperature, tube length, defects, and surface functionalization on the thermal conductivity (κ) of single-walled carbon nanotubes (SWCNTs) were well documented in literature. However, diameter dependence of thermal conductivity of SWCNTs received less attentions. So far, diverse trends of the diameter dependence have been discussed by different methods and all the previous results were based on empirical interatomic potentials. In this paper, we emphasize to clarify accurate κ values of SWCNTs with different diameters and in-plane κ of graphene. All the studies were under the framework of anharmonic lattice dynamics and Boltzmann transport equation (BTE) based on first principle calculations. We try to infer the right trend of diameter dependent thermal conductivity of SWCNTs. We infer that graphene is the limitation as SWCNT with an infinite diameter. We analyzed the thermal conductivity contributions from each phonon mode in SWCNTs to explain the trend. Meanwhile, we also identify the extremely low thermal conductivity of ultra-thin SWCNTs. PMID:26490342

  17. Diameter Dependence of Lattice Thermal Conductivity of Single-Walled Carbon Nanotubes: Study from Ab Initio

    PubMed Central

    Yue, Sheng-Ying; Ouyang, Tao; Hu, Ming

    2015-01-01

    The effects of temperature, tube length, defects, and surface functionalization on the thermal conductivity (κ) of single-walled carbon nanotubes (SWCNTs) were well documented in literature. However, diameter dependence of thermal conductivity of SWCNTs received less attentions. So far, diverse trends of the diameter dependence have been discussed by different methods and all the previous results were based on empirical interatomic potentials. In this paper, we emphasize to clarify accurate κ values of SWCNTs with different diameters and in-plane κ of graphene. All the studies were under the framework of anharmonic lattice dynamics and Boltzmann transport equation (BTE) based on first principle calculations. We try to infer the right trend of diameter dependent thermal conductivity of SWCNTs. We infer that graphene is the limitation as SWCNT with an infinite diameter. We analyzed the thermal conductivity contributions from each phonon mode in SWCNTs to explain the trend. Meanwhile, we also identify the extremely low thermal conductivity of ultra-thin SWCNTs. PMID:26490342

  18. Time dependent variation of human blood conductivity as a method for an estimation of RBC aggregation.

    PubMed

    Antonova, Nadia; Riha, Pavel; Ivanov, Ivan

    2008-01-01

    Time variation of whole human blood conductivity and shear stresses were investigated at rectangular and trapezium-shaped Couette viscometric flow under electric field of 2 kHz. The kinetics of conductivity signals were recorded both under transient flow and after the complete stoppage of shearing at shear rates from 0.94 to 94.5 s(-1) and temperatures T=25 degrees C and 37 degrees C. Contraves Low Shear 30 rotational viscometer as a base unit and a concurrent measuring system, including a device, developed by the conductometric method with a software for measurement of conductivity of biological fluids (data acquisition system), previously described (IFMBE Proceedings Series, Vol. 11, 2005, pp. 4247-4252; Clin. Hemorheol. Microcirc. 35(1/2) (2006), 19-29), were used for the experiments. The obtained experimental relationships show that the human blood conductivity is time, shear rate, hematocrit and temperature dependent under transient flow. It is also dependent on the regime of the applied shear rates. Non-linear curve approximation of the growth and relaxation curves is done. The results show that valuable information could be received about the kinetics of "rouleaux formation" and the time dependences of the blood conductivity follow the structural transformations of RBC aggregates during the aggregation-disaggregation processes. The results suggest that this technique may be used to clarify the mechanism of dynamics of RBC aggregates. PMID:18503112

  19. Mutation dependance of the mitochondrial DNA copy number in the first stages of human embryogenesis.

    PubMed

    Monnot, Sophie; Samuels, David C; Hesters, Laetitia; Frydman, Nelly; Gigarel, Nadine; Burlet, Philippe; Kerbrat, Violaine; Lamazou, Frédéric; Frydman, René; Benachi, Alexandra; Feingold, Josué; Rotig, Agnes; Munnich, Arnold; Bonnefont, Jean-Paul; Steffann, Julie

    2013-05-01

    Mitochondrial DNA (mtDNA) content is thought to remain stable over the preimplantation period of human embryogenesis that is, therefore, suggested to be entirely dependent on ooplasm mtDNA capital. We have explored the impact of two disease-causing mutations [m.3243A>G myopathy, encephalopathy, lactic acidosis and stroke-like syndrome (MELAS) and m.8344A>G myoclonic epilepsy associated with ragged-red fibers (MERRF)] on mtDNA amounts in human oocytes and day 4-5 preimplantation embryos. The mtDNA amount was stable in MERRF and control materials, whereas gradually increasing from the germinal vesicle of oogenesis to the blastocyst stage of embryogenesis in MELAS cells, MELAS embryos carrying ∼3-fold higher mtDNA amount than control embryos (P = 0.0003). A correlation between mtDNA copy numbers and mutant loads was observed in MELAS embryos (R(2) = 0.42, P < 0.0013), suggestive of a compensation for the respiratory chain defect resulting from high mutation levels. These results suggest that mtDNA can replicate in early embryos and emphasize the need for sufficient amount of wild-type mtDNA to sustain embryonic development in humans. PMID:23390135

  20. Concentration-dependent organization of DNA by the dinoflagellate histone-like protein HCc3

    PubMed Central

    Chan, Yuk-Hang; Wong, Joseph T. Y.

    2007-01-01

    The liquid crystalline chromosomes of dinoflagellates are the alternative to the nucleosome-based organization of chromosomes in the eukaryotes. These nucleosome-less chromosomes have to devise novel ways to maintain active parts of the genome. The dinoflagellate histone-like protein HCc3 has significant sequence identity with the bacterial DNA-binding protein HU. HCc3 also has a secondary structure resembling HU in silico. We have examined HCc3 in its recombinant form. Experiments on DNA-cellulose revealed its DNA-binding activity is on the C-terminal domain. The N-terminal domain is responsible for intermolecular oligomerization as demonstrated by cross-linking studies. However, HCc3 could not complement Escherichia coli HU-deficient mutants, suggesting functional differences. In ligation assays, HCc3-induced DNA concatenation but not ring closure as the DNA-bending HU does. The basic HCc3 was an efficient DNA condensing agent, but it did not behave like an ordinary polycationic compound. HCc3 also induced specific structures with DNA in a concentration-dependent manner, as demonstrated by atomic force microscopy (AFM). At moderate concentration of HCc3, DNA bridging and bundling were observed; at high concentrations, the complexes were even more condensed. These results are consistent with a biophysical role for HCc3 in maintaining extended DNA loops at the periphery of liquid crystalline chromosomes. PMID:17412706

  1. Preparation, characterization and scanned conductance microscopy studies of DNA-templated one-dimensional copper nanostructures.

    PubMed

    Watson, Scott M D; Wright, Nicholas G; Horrocks, Benjamin R; Houlton, Andrew

    2010-02-01

    The synthesis of one-dimensional metal nanostructures can be achieved through the use of DNA molecules as templates to control and direct metal deposition. Copper nanostructures have been fabricated using this strategy, through association of Cu(2+) ions to DNA templates and reduced with ascorbic acid. Due to the possibility that the reduction of the Cu(2+) can result in the preferential formation of Cu(2)O over metallic Cu(0), X-ray photoelectron spectroscopy and X-ray diffraction have been carried out to establish the chemical identity of the nanostructures. Conclusive evidence is found that reduction of the Cu(2+) ions does result in the formation of the desired metallic Cu(0) structures. The morphology of the nanostructured Cu(0) material has also been observed by atomic force microscopy, showing the structures to have a "beads-on-a-string" appearance and being 3.0-5.5 nm in height. The electrical properties of the structures have been investigated by scanned conductance microscopy, showing the Cu(0) structures exhibit much larger electrical resistance than expected for a metallic nanowire. This is thought to be a consequence of their "beads-on-a-string" morphology and small lateral dimensions (sub-10 nm); both these factors would be expected to increase the electron scattering rate, and, further, there are likely to be significant tunneling barriers at the Cu(0) particle-particle junctions. PMID:19754197

  2. Mutational analysis of human DNase I at the DNA binding interface: implications for DNA recognition, catalysis, and metal ion dependence.

    PubMed

    Pan, C Q; Ulmer, J S; Herzka, A; Lazarus, R A

    1998-03-01

    Human deoxyribonuclease I (DNase I), an enzyme used to treat cystic fibrosis patients, has been systematically analyzed by site-directed mutagenesis of residues at the DNA binding interface. Crystal structures of bovine DNase I complexed with two different oligonucleotides have implicated the participation of over 20 amino acids in catalysis or DNA recognition. These residues have been classified into four groups based on the characterization of over 80 human DNase I variants. Mutations at any of the four catalytic amino acids His 134, His 252, Glu 78, and Asp 212 drastically reduced the hydrolytic activity of DNase I. Replacing the three putative divalent metal ion-coordinating residues Glu 39, Asp 168, or Asp 251 led to inactive variants. Amino acids Gln 9, Arg 41, Tyr 76, Arg 111, Asn 170, Tyr 175, and Tyr 211 were also critical for activity, presumably because of their close proximity to the active site, while more peripheral DNA interactions stemming from 13 other positions were of minimal significance. The relative importance of these 27 positions is consistent with evolutionary relationships among DNase I across different species, DNase I-like proteins, and bacterial sphingomyelinases, suggesting a fingerprint for a family of DNase I-like proteins. Furthermore, we found no evidence for a second active site that had been previously implicated in Mn2+-dependent DNA degradation. Finally, we correlated our mutational analysis of human DNase I to that of bovine DNase I with respect to their specific activity and dependence on divalent metal ions. PMID:9541395

  3. Effect of temperature-dependent electrical conductivity on transport processes in magnetosolidmechanics

    NASA Technical Reports Server (NTRS)

    Craig, G. T.; Arnas, O. A.

    1975-01-01

    The effect of temperature-dependent electrical conductivity on transport processes for a solid block is analyzed on the basis of a one-dimensional steady-state model under specified thermal boundary conditions. Assumptions are that the solid has an infinitely segmented electrode configuration, the magnetic field (By) may be resolved into a constant applied field and an induced field, the gradient of the electrochemical potential is equal to the electrostatic potential, a constant potential difference is applied externally across each pair of opposite electrodes, and all material properties except electrical conductivity are constant. Conductivity is expressed in normalized form in terms of a baseline conductivity and a constant for the material. The application of the assumptions of the model to the general phenomenological relations yields the governing equations. Solution of these equations gives the distribution of temperature, electric current density, and magnetic field strength along the length of the solid. It is shown that significant differences exist between the case for constant electrical conductivity and the case where electrical conductivity is temperature dependent.

  4. Phonon focusing and temperature dependences of thermal conductivity of silicon nanofilms

    SciTech Connect

    Kuleyev, I. I. Bakharev, S. M.; Kuleyev, I. G.; Ustinov, V. V.

    2015-04-15

    The effect of phonon focusing on the anisotropy and temperature dependences of the thermal conductivities of silicon nanofilms is analyzed using the three-mode Callaway model. The orientations of the film planes and the directions of the heat flux for maximal or minimal heat removal from silicon chip elements at low temperatures, as well as at room temperature, are determined. It is shown that in the case of diffuse reflection of phonons from the boundaries, the plane with the (100) orientation exhibits the lowest scattering ability (and the highest thermal conductivity), while the plane with the (111) orientation is characterized by the highest scattering ability (and the lowest thermal conductivity). The thermal conductivity of wide films is determined to a considerable extent by the orientation of the film plane, while for nanowires with a square cross section, the thermal conductivity is mainly determined by the direction of the heat flux. The effect of elastic energy anisotropy on the dependences of the thermal conductivity on the geometrical parameters of films is analyzed. The temperatures of transition from boundary scattering to bulk relaxation mechanisms are determined.

  5. Thermal conductivity of simple liquids: temperature and packing-fraction dependence.

    PubMed

    Ohtori, Norikazu; Ishii, Yoshiki; Togawa, Yoshinori; Oono, Takuya; Takase, Keiichi

    2014-02-01

    The thermal conductivity of rare gases in liquid and dense fluid states has been evaluated using molecular dynamics simulation with the Lennard-Jones (LJ) potentials and the Green-Kubo (GK) formula. All the calculated thermal conductivities are in very good agreement with experimental results for a wide range of temperature and density. Special attention was paid to temperature and packing-fraction dependence which is nontrivial from dimensional analysis on the LJ potentials and the GK formula. First, the temperature dependence of T(1/4) was determined from the calculations at constant densities. Secondly, in order to obtain the dependence on packing fraction from that on number density separately, a scaling method of particle and/or cell size was introduced. The number density dependence of (N/V)(2/3) which is expected from the dimensional analysis of the GK formulas was confirmed and the packing-fraction dependence of η(3/2) was determined by using the scaling method. It turned out that the summarized functional form of m(-1/2)(N/V)(2/3)η(3/2)T(1/4) can well express both the calculated and experimental thermal conductivities for Ar, Kr, and Xe, where m is the atomic mass. The scaling method has also been applied to molten NaCl and KCl so that it has been found that the thermal conductivity has the packing-fraction dependence of η(2/3) which is much weaker than that of the simple LJ liquids. PMID:25353444

  6. Thermal conductivity of simple liquids: Temperature and packing-fraction dependence

    NASA Astrophysics Data System (ADS)

    Ohtori, Norikazu; Ishii, Yoshiki; Togawa, Yoshinori; Oono, Takuya; Takase, Keiichi

    2014-02-01

    The thermal conductivity of rare gases in liquid and dense fluid states has been evaluated using molecular dynamics simulation with the Lennard-Jones (LJ) potentials and the Green-Kubo (GK) formula. All the calculated thermal conductivities are in very good agreement with experimental results for a wide range of temperature and density. Special attention was paid to temperature and packing-fraction dependence which is nontrivial from dimensional analysis on the LJ potentials and the GK formula. First, the temperature dependence of T1/4 was determined from the calculations at constant densities. Secondly, in order to obtain the dependence on packing fraction from that on number density separately, a scaling method of particle and/or cell size was introduced. The number density dependence of (N/V)2/3 which is expected from the dimensional analysis of the GK formulas was confirmed and the packing-fraction dependence of η3/2 was determined by using the scaling method. It turned out that the summarized functional form of m-1/2(N/V)2/3η3/2T1/4 can well express both the calculated and experimental thermal conductivities for Ar, Kr, and Xe, where m is the atomic mass. The scaling method has also been applied to molten NaCl and KCl so that it has been found that the thermal conductivity has the packing-fraction dependence of η2/3 which is much weaker than that of the simple LJ liquids.

  7. An Organometallic Compound which Exhibits a DNA Topology-Dependent One-Stranded Intercalation Mode.

    PubMed

    Ma, Zhujun; Palermo, Giulia; Adhireksan, Zenita; Murray, Benjamin S; von Erlach, Thibaud; Dyson, Paul J; Rothlisberger, Ursula; Davey, Curt A

    2016-06-20

    Understanding how small molecules interact with DNA is essential since it underlies a multitude of pathological conditions and therapeutic interventions. Many different intercalator compounds have been studied because of their activity as mutagens or drugs, but little is known regarding their interaction with nucleosomes, the protein-packaged form of DNA in cells. Here, using crystallographic methods and molecular dynamics simulations, we discovered that adducts formed by [(η(6) -THA)Ru(ethylenediamine)Cl][PF6 ] (THA=5,8,9,10-tetrahydroanthracene; RAED-THA-Cl[PF6 ]) in the nucleosome comprise a novel one-stranded intercalation and DNA distortion mode. Conversely, the THA group in fact remains solvent exposed and does not disrupt base stacking in RAED-THA adducts on B-form DNA. This newly observed DNA binding mode and topology dependence may actually be prevalent and should be considered when studying covalently binding intercalating compounds. PMID:27184539

  8. DNA methyltransferase-3-dependent nonrandom template segregation in differentiating embryonic stem cells.

    PubMed

    Elabd, Christian; Cousin, Wendy; Chen, Robert Y; Chooljian, Marc S; Pham, Joey T; Conboy, Irina M; Conboy, Michael J

    2013-10-14

    Asymmetry of cell fate is one fundamental property of stem cells, in which one daughter cell self-renews, whereas the other differentiates. Evidence of nonrandom template segregation (NRTS) of chromosomes during asymmetric cell divisions in phylogenetically divergent organisms, such as plants, fungi, and mammals, has already been shown. However, before this current work, asymmetric inheritance of chromatids has never been demonstrated in differentiating embryonic stem cells (ESCs), and its molecular mechanism has remained unknown. Our results unambiguously demonstrate NRTS in asymmetrically dividing, differentiating human and mouse ESCs. Moreover, we show that NRTS is dependent on DNA methylation and on Dnmt3 (DNA methyltransferase-3), indicating a molecular mechanism that regulates this phenomenon. Furthermore, our data support the hypothesis that retention of chromatids with the "old" template DNA preserves the epigenetic memory of cell fate, whereas localization of "new" DNA strands and de novo DNA methyltransferase to the lineage-destined daughter cell facilitates epigenetic adaptation to a new cell fate. PMID:24127215

  9. A DNA break- and phosphorylation-dependent positive feedback loop promotes immunoglobulin class-switch recombination.

    PubMed

    Vuong, Bao Q; Herrick-Reynolds, Kayleigh; Vaidyanathan, Bharat; Pucella, Joseph N; Ucher, Anna J; Donghia, Nina M; Gu, Xiwen; Nicolas, Laura; Nowak, Urszula; Rahman, Numa; Strout, Matthew P; Mills, Kevin D; Stavnezer, Janet; Chaudhuri, Jayanta

    2013-11-01

    The ability of activation-induced cytidine deaminase (AID) to efficiently mediate class-switch recombination (CSR) is dependent on its phosphorylation at Ser38; however, the trigger that induces AID phosphorylation and the mechanism by which phosphorylated AID drives CSR have not been elucidated. Here we found that phosphorylation of AID at Ser38 was induced by DNA breaks. Conversely, in the absence of AID phosphorylation, DNA breaks were not efficiently generated at switch (S) regions in the immunoglobulin heavy-chain locus (Igh), consistent with a failure of AID to interact with the endonuclease APE1. Additionally, deficiency in the DNA-damage sensor ATM impaired the phosphorylation of AID at Ser38 and the interaction of AID with APE1. Our results identify a positive feedback loop for the amplification of DNA breaks at S regions through the phosphorylation- and ATM-dependent interaction of AID with APE1. PMID:24097111

  10. Temperature dependent electrical conductivity measurement of Qn-(TCNQ)2 grown by different methods

    NASA Astrophysics Data System (ADS)

    Singh, Yadunath

    2013-06-01

    We measured the temperature dependent electrical conductivity on single crystal of charge transfer complex (CTC), Qn-(TCNQ)2 grown by different methods. Where, Qn and TCNQ are representing qunolinium and tetracyanoquinodimethane. The room temperature conductivity is found 100 ohm-1 cm-1 with activation energy 0.021 eV in the sample grown by electrochemical method. Whereas it is found 22 ohm-1 cm-1 with activation energy 0.026 eV for the sample grown by solution growth method. In all conductivity measurements, the observations are carried out along high conducting chain direction, which happens to be needle direction of the single crystal and known as a-direction.

  11. Size and edge roughness dependence of thermal conductivity for vacancy-defective graphene ribbons.

    PubMed

    Xie, Guofeng; Shen, Yulu

    2015-04-14

    By incorporating the phonon-phonon scattering, phonon-boundary scattering and phonon-vacancy scattering into the linearized Boltzmann transport equation, we theoretically investigate the effects of size and edge roughness on thermal conductivity of single vacancy-defective graphene ribbons. Due to the severe suppression of high-frequency phonons by phonon-vacancy scattering which includes the impacts of missing mass and linkages, as well as the variation of the force constant of bonds associated with vacancies, the low-frequency ballistic phonons have a higher contribution to the thermal conductivity, which results in the stronger length, weaker width and weaker edge roughness dependence on thermal conductivity of vacancy-defective graphene ribbons than that of pristine ones. Our findings are helpful to understand and manipulate thermal conductivity of graphene by phononic engineering. PMID:25743638

  12. Length Dependent Thermal Conductivity Measurements Yield Phonon Mean Free Path Spectra in Nanostructures

    PubMed Central

    Zhang, Hang; Hua, Chengyun; Ding, Ding; Minnich, Austin J.

    2015-01-01

    Thermal conductivity measurements over variable lengths on nanostructures such as nanowires provide important information about the mean free paths (MFPs) of the phonons responsible for heat conduction. However, nearly all of these measurements have been interpreted using an average MFP even though phonons in many crystals possess a broad MFP spectrum. Here, we present a reconstruction method to obtain MFP spectra of nanostructures from variable-length thermal conductivity measurements. Using this method, we investigate recently reported length-dependent thermal conductivity measurements on SiGe alloy nanowires and suspended graphene ribbons. We find that the recent measurements on graphene imply that 70% of the heat in graphene is carried by phonons with MFPs longer than 1 micron. PMID:25764977

  13. Temperature dependent thermal conductivity of pure silica MEL and MFI zeolite thin films

    NASA Astrophysics Data System (ADS)

    Fang, Jin; Huang, Yi; Lew, Christopher M.; Yan, Yushan; Pilon, Laurent

    2012-03-01

    This paper reports the temperature dependent cross-plane thermal conductivity of pure silica zeolite (PSZ) MFI and MEL thin films measured using the 3ω method between 30 and 315 K. PSZ MFI thin films were b-oriented, fully crystalline, and had a 33% microporosity. PSZ MEL thin films consisted of MEL nanoparticles embedded in a nonuniform and porous silica matrix. They featured porosity, relative crystallinity, and particle size ranging from 40% to 59%, 23% to 47%, and 55 to 80 nm, respectively. Despite their crystallinity, MFI films had smaller thermal conductivity than that of amorphous silica due to strong phonon scattering by micropores. In addition, the effects of increased relative crystallinity and particle size on thermal conductivity of MEL thin films were compensated by the simultaneous increase in porosity. Finally, thermal conductivity of MFI zeolite was predicted and discussed using the Callaway model based on the Debye approximation.

  14. Length dependent thermal conductivity measurements yield phonon mean free path spectra in nanostructures.

    PubMed

    Zhang, Hang; Hua, Chengyun; Ding, Ding; Minnich, Austin J

    2015-01-01

    Thermal conductivity measurements over variable lengths on nanostructures such as nanowires provide important information about the mean free paths (MFPs) of the phonons responsible for heat conduction. However, nearly all of these measurements have been interpreted using an average MFP even though phonons in many crystals possess a broad MFP spectrum. Here, we present a reconstruction method to obtain MFP spectra of nanostructures from variable-length thermal conductivity measurements. Using this method, we investigate recently reported length-dependent thermal conductivity measurements on SiGe alloy nanowires and suspended graphene ribbons. We find that the recent measurements on graphene imply that 70% of the heat in graphene is carried by phonons with MFPs longer than 1 micron. PMID:25764977

  15. Increased mitochondrial DNA deletions and copy number in transfusion-dependent thalassemia

    PubMed Central

    Lal, Ashutosh; Gomez, Esteban; Calloway, Cassandra

    2016-01-01

    BACKGROUND Iron overload is the primary cause of morbidity in transfusion-dependent thalassemia. Increase in iron causes mitochondrial dysfunction under experimental conditions, but the occurrence and significance of mitochondrial damage is not understood in patients with thalassemia. METHODS Mitochondrial DNA (mtDNA) to nuclear DNA copy number (Mt/N) and frequency of the common 4977-bp mitochondrial deletion (ΔmtDNA4977) were quantified using a quantitative PCR assay on whole blood samples from 38 subjects with thalassemia who were receiving regular transfusions. RESULTS Compared with healthy controls, Mt/N and ΔmtDNA4977 frequency were elevated in thalassemia (P = 0.038 and P < 0.001, respectively). ΔmtDNA4977 was increased in the presence of either liver iron concentration > 15 mg/g dry-weight or splenectomy, with the highest levels observed in subjects who had both risk factors (P = 0.003). Myocardial iron (MRI T2* < 20 ms) was present in 0%, 22%, and 46% of subjects with ΔmtDNA4977 frequency < 20, 20–40, and > 40/1 × 107 mtDNA, respectively (P = 0.025). Subjects with Mt/N values below the group median had significantly lower Matsuda insulin sensitivity index (5.76 ± 0.53) compared with the high Mt/N group (9.11 ± 0.95, P = 0.008). CONCLUSION Individuals with transfusion-dependent thalassemia demonstrate age-related increase in mtDNA damage in leukocytes. These changes are markedly amplified by splenectomy and are associated with extrahepatic iron deposition. Elevated mtDNA damage in blood cells may predict the risk of iron-associated organ damage in thalassemia. PMID:27583305

  16. An Oligonucleotide Affinity Column for RNA-Dependent DNA Polymerase from RNA Tumor Viruses

    PubMed Central

    Gerwin, Brenda I.; Milstien, Julie B.

    1972-01-01

    Columns of (dT)12-18-cellulose provide a one-step enrichment procedure for RNA-dependent DNA polymerase. The enzyme of the virus from RD-114 cells, as well as that from Rauscher murine leukemia virus, have been purified in this way. The preference of viral as compared to cellular DNA polymerases for (dT)12-18 as a primer is reflected in the fact that the DNA polymerases of uninfected cells do not bind to this column. Viral enzymes have been purified and identified from crude cellular extracts. PMID:4506781

  17. Site-Dependent Evolution of Electrical Conductance from Tunneling to Atomic Point Contact

    NASA Astrophysics Data System (ADS)

    Kim, Howon; Hasegawa, Yukio

    2015-05-01

    Using scanning tunneling microscopy (STM), we investigated the evolution of electrical conductance between a Pb tip and Pb(111) surface from tunneling to atomic point contact at a site that was defined with atomic precision. We found that the conductance evolution depended on the contact site, for instance, on-top, bridge, or hollow (hcp and fcc) sites in the Pb lattice. In the transition from tunneling to contact regimes, the conductance measured at the on-top site was enhanced. In the point contact regime, the hollow sites had conductances larger than those of the other sites, and between the hollow sites, the hcp site had a conductance larger than that of the fcc site. We also observed the enhancement and reversal of the apparent height in atomically resolved high-current STM images, consistent with the results of the conductance traces. Our results indicate the importance of atomic configuration in the conductance of atomic junctions and suggest that attractive chemical interactions have a significant role in electron transport between contacting atoms.

  18. Self-consistent modeling of terahertz waveguide and cavity with frequency-dependent conductivity

    SciTech Connect

    Huang, Y. J.; Chu, K. R.; Thumm, M.

    2015-01-15

    The surface resistance of metals, and hence the Ohmic dissipation per unit area, scales with the square root of the frequency of an incident electromagnetic wave. As is well recognized, this can lead to excessive wall losses at terahertz (THz) frequencies. On the other hand, high-frequency oscillatory motion of conduction electrons tends to mitigate the collisional damping. As a result, the classical theory predicts that metals behave more like a transparent medium at frequencies above the ultraviolet. Such a behavior difference is inherent in the AC conductivity, a frequency-dependent complex quantity commonly used to treat electromagnetics of metals at optical frequencies. The THz region falls in the gap between microwave and optical frequencies. However, metals are still commonly modeled by the DC conductivity in currently active vacuum electronics research aimed at the development of high-power THz sources (notably the gyrotron), although a small reduction of the DC conductivity due to surface roughness is sometimes included. In this study, we present a self-consistent modeling of the gyrotron interaction structures (a metallic waveguide or cavity) with the AC conductivity. The resulting waveguide attenuation constants and cavity quality factors are compared with those of the DC-conductivity model. The reduction in Ohmic losses under the AC-conductivity model is shown to be increasingly significant as the frequency reaches deeper into the THz region. Such effects are of considerable importance to THz gyrotrons for which the minimization of Ohmic losses constitutes a major design consideration.

  19. Anion Conductance of Frog Muscle Membranes: One Channel, Two Kinds of pH Dependence

    PubMed Central

    Woodbury, J. W.; Miles, P. R.

    1973-01-01

    Anion conductance and permeability sequences were obtained for frog skeletal muscle membranes from the changes in characteristic resistance and transmembrane potential after the replacement of one anion by another in the bathing solution. Permeability and conductance sequences are the same. The conductance sequence at pH = 7.4 is Cl- Br- > NO3- > I- > trichloroacetate ≥ benzoate > valerate > butyrate > proprionate > formate > acetate ≥ lactate > benzenesulfonate ≥ isethionate > methylsulfonate > glutamate ≥ cysteate. The anions are divided into two classes: (a) Chloride-like anions (Cl- through trichloroacetate) have membrane conductances that decrease as pH decreases. The last six members of the complete sequence are also chloride like. (b) Benzoate-like anions (benzoate through acetate) have conductances that increase as pH decreases. At pH = 6.7 zinc ions block Cl- and benzoate conductances with inhibitory dissociation constants of 0.12 and 0.16 mM, respectively. Chloride-like and benzoate-like anions probably use the same channels. The minimum size of the channel aperture is estimated as 5.5 x 6.5 Å from the dimensions of the largest permeating anions. A simple model of the channel qualitatively explains chloride-like and benzoate-like conductance sequences and their dependence on pH. PMID:4542368

  20. Orientation dependent thermal conductance in single-layer MoS2.

    PubMed

    Jiang, Jin-Wu; Zhuang, Xiaoying; Rabczuk, Timon

    2013-01-01

    We investigate the thermal conductivity in the armchair and zigzag MoS2 nanoribbons, by combining the non-equilibrium Green's function approach and the first-principles method. A strong orientation dependence is observed in the thermal conductivity. Particularly, the thermal conductivity for the armchair MoS2 nanoribbon is about 673.6 Wm(-1) K(-1) in the armchair nanoribbon, and 841.1 Wm(-1) K(-1) in the zigzag nanoribbon at room temperature. By calculating the Caroli transmission, we disclose the underlying mechanism for this strong orientation dependence to be the fewer phonon transport channels in the armchair MoS2 nanoribbon in the frequency range of [150, 200] cm(-1). Through the scaling of the phonon dispersion, we further illustrate that the thermal conductivity calculated for the MoS2 nanoribbon is esentially in consistent with the superior thermal conductivity found for graphene. PMID:23860436

  1. Temperature dependence of thermal conductivity of VO2 thin films across metal-insulator transition

    NASA Astrophysics Data System (ADS)

    Kizuka, Hinako; Yagi, Takashi; Jia, Junjun; Yamashita, Yuichiro; Nakamura, Shinichi; Taketoshi, Naoyuki; Shigesato, Yuzo

    2015-05-01

    Thermal conductivity of a 300-nm-thick VO2 thin film and its temperature dependence across the metal-insulator phase transition (TMIT) were studied using a pulsed light heating thermoreflectance technique. The VO2 and Mo/VO2/Mo films with a VO2 thickness of 300 nm were prepared on quartz glass substrates: the former was used for the characterization of electrical properties, and the latter was used for the thermal conductivity measurement. The VO2 films were deposited by reactive rf magnetron sputtering using a V2O3 target and an Ar-O2 mixture gas at 645 K. The VO2 films consisted of single phase VO2 as confirmed by X-ray diffraction and electron beam diffraction. With increased temperature, the electrical resistivity of the VO2 film decreased abruptly from 6.3 × 10-1 to 5.3 × 10-4 Ω cm across the TMIT of around 325-340 K. The thermal conductivity of the VO2 film increased from 3.6 to 5.4 W m-1 K-1 across the TMIT. This discontinuity and temperature dependence of thermal conductivity can be explained by the phonon heat conduction and the Wiedemann-Franz law.

  2. Orientation Dependent Thermal Conductance in Single-Layer MoS2

    PubMed Central

    Jiang, Jin-Wu; Zhuang, Xiaoying; Rabczuk, Timon

    2013-01-01

    We investigate the thermal conductivity in the armchair and zigzag MoS2 nanoribbons, by combining the non-equilibrium Green's function approach and the first-principles method. A strong orientation dependence is observed in the thermal conductivity. Particularly, the thermal conductivity for the armchair MoS2 nanoribbon is about 673.6 Wm−1 K−1 in the armchair nanoribbon, and 841.1 Wm−1 K−1 in the zigzag nanoribbon at room temperature. By calculating the Caroli transmission, we disclose the underlying mechanism for this strong orientation dependence to be the fewer phonon transport channels in the armchair MoS2 nanoribbon in the frequency range of [150, 200] cm−1. Through the scaling of the phonon dispersion, we further illustrate that the thermal conductivity calculated for the MoS2 nanoribbon is esentially in consistent with the superior thermal conductivity found for graphene. PMID:23860436

  3. Length dependence of thermal conductivity by approach-to-equilibrium molecular dynamics

    NASA Astrophysics Data System (ADS)

    Zaoui, Hayat; Palla, Pier Luca; Cleri, Fabrizio; Lampin, Evelyne

    2016-08-01

    The length dependence of thermal conductivity over more than two orders of magnitude has been systematically studied for a range of materials, interatomic potentials, and temperatures using the atomistic approach-to-equilibrium molecular dynamics (AEMD) method. By comparing the values of conductivity obtained for a given supercell length and maximum phonon mean free path (MFP), we find that such values are strongly correlated, demonstrating that the AEMD calculation with a supercell of finite length actually probes the thermal conductivity corresponding to a maximum phonon MFP. As a consequence, the less pronounced length dependence usually observed for poorer thermal conductors, such as amorphous silica, is physically justified by their shorter average phonon MFP. Finally, we compare different analytical extrapolations of the conductivity to infinite length and demonstrate that the frequently used Matthiessen rule is not applicable in AEMD. An alternative extrapolation more suitable for transient-time, finite-supercell simulations is derived. This approximation scheme can also be used to classify the quality of different interatomic potential models with respect to their capability of predicting the experimental thermal conductivity.

  4. Temperature Dependence of the Thermal Conductivity of Single Wall Carbon Nanotubes

    NASA Technical Reports Server (NTRS)

    Osman, Mohamed A.; Srivastava, Deepak

    2000-01-01

    The thermal conductivity of several single wall carbon nanotubes (CNT) has been calculated over a temperature range of 100-500 K using molecular dynamics simulations with Tersoff-Brenner potential for C-C interactions. In all cases, starting from similar values at 100K, thermal conductivities show a peaking behavior before falling off at higher temperatures. The peak position shifts to higher temperatures for nanotubes of larger diameter, and no significant dependence on the tube chirality is observed. It is shown that this phenomenon is due to onset of Umklapp scattering, which shifts to higher temperatures for nanotubes of larger diameter.

  5. Temperature and donor concentration dependence of the conduction electron Lande g-factor in silicon

    NASA Astrophysics Data System (ADS)

    Konakov, Anton A.; Ezhevskii, Alexander A.; Soukhorukov, Andrey V.; Guseinov, Davud V.; Popkov, Sergey A.; Burdov, Vladimir A.

    2013-12-01

    Temperature and donor concentration dependence of the conduction electron g-factor in silicon has been investigated both experimentally and theoretically. We performed electron spin resonance experiments on Si samples doped with different densities of phosphorus and lithium. Theoretical consideration is based on the renormalization of the electron energy in a weak magnetic field by the interaction with possible perturbing agents, such as phonons and impurity centers. In the second-order perturbation theory interaction of the electron subsystem with the lattice vibrations as well as ionized donors results in decreasing the conduction electron g-factor, which becomes almost linear function both of temperature and impurity concentration.

  6. The temperature dependence of the heat conductivity of a liquid crystal studied by molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Sarman, Sten; Laaksonen, Aatto

    2010-01-01

    The temperature dependence of the heat conductivity has been obtained for a liquid crystal model based on the Gay-Berne fluid, from the isotropic phase at high temperatures through the nematic phase to the smectic A phase at low temperatures. The ratio of the parallel and the perpendicular components of the heat conductivity is about 2.5:1 in the nematic phase, which is similar to that of real systems. Both Green-Kubo methods and nonequilibrium molecular dynamics methods have been applied and the results agree within in a relative error of a couple of percent, but the latter method is much more efficient.

  7. Introducing improved structural properties and salt dependence into a coarse-grained model of DNA

    SciTech Connect

    Snodin, Benedict E. K. Mosayebi, Majid; Schreck, John S.; Romano, Flavio; Doye, Jonathan P. K.; Randisi, Ferdinando; Šulc, Petr; Ouldridge, Thomas E.; Tsukanov, Roman; Nir, Eyal; Louis, Ard A.

    2015-06-21

    We introduce an extended version of oxDNA, a coarse-grained model of deoxyribonucleic acid (DNA) designed to capture the thermodynamic, structural, and mechanical properties of single- and double-stranded DNA. By including explicit major and minor grooves and by slightly modifying the coaxial stacking and backbone-backbone interactions, we improve the ability of the model to treat large (kilobase-pair) structures, such as DNA origami, which are sensitive to these geometric features. Further, we extend the model, which was previously parameterised to just one salt concentration ([Na{sup +}] = 0.5M), so that it can be used for a range of salt concentrations including those corresponding to physiological conditions. Finally, we use new experimental data to parameterise the oxDNA potential so that consecutive adenine bases stack with a different strength to consecutive thymine bases, a feature which allows a more accurate treatment of systems where the flexibility of single-stranded regions is important. We illustrate the new possibilities opened up by the updated model, oxDNA2, by presenting results from simulations of the structure of large DNA objects and by using the model to investigate some salt-dependent properties of DNA.

  8. Single DNA molecule jamming and history-dependent dynamics during motor-driven viral packaging

    NASA Astrophysics Data System (ADS)

    Keller, Nicholas; Grimes, Shelley; Jardine, Paul J.; Smith, Douglas E.

    2016-08-01

    In many viruses, molecular motors forcibly pack single DNA molecules to near-crystalline density into ~50-100 nm prohead shells. Unexpectedly, we found that packaging frequently stalls in conditions that induce net attractive DNA-DNA interactions. Here, we present findings suggesting that this stalling occurs because the DNA undergoes a nonequilibrium jamming transition analogous to that observed in many soft-matter systems, such as colloidal and granular systems. Experiments in which conditions are changed during packaging to switch DNA-DNA interactions between purely repulsive and net attractive reveal strongly history-dependent dynamics. An abrupt deceleration is usually observed before stalling, indicating that a transition in DNA conformation causes an abrupt increase in resistance. Our findings suggest that the concept of jamming can be extended to a single polymer molecule. However, compared with macroscopic samples of colloidal particles we find that single DNA molecules jam over a much larger range of densities. We attribute this difference to the nanoscale system size, consistent with theoretical predictions for jamming of attractive athermal particles.

  9. Human ClCa1 modulates anionic conduction of calcium-dependent chloride currents

    PubMed Central

    Hamann, Martine; Gibson, Adele; Davies, Noel; Jowett, Amanda; Walhin, Jean Philippe; Partington, Leanne; Affleck, Karen; Trezise, Derek; Main, Martin

    2009-01-01

    Proteins of the CLCA gene family including the human ClCa1 (hClCa1) have been suggested to constitute a new family of chloride channels mediating Ca2+-dependent Cl− currents. The present study examines the relationship between the hClCa1 protein and Ca2+-dependent Cl− currents using heterologous expression of hClCa1 in HEK293 and NCIH522 cell lines and whole cell recordings. By contrast to previous reports claiming the absence of Cl− currents in HEK293 cells, we find that HEK293 and NCIH522 cell lines express constitutive Ca2+-dependent Cl− currents and show that hClCa1 increases the amplitude of Ca2+-dependent Cl− currents in those cells. We further show that hClCa1 does not modify the permeability sequence but increases the Cl− conductance while decreasing the GSCN−/GCl− conductance ratio from ∼2–3 to ∼1. We use an Eyring rate theory (two barriers, one site channel) model and show that the effect of hClCa1 on the anionic channel can be simulated by its action on lowering the first and the second energy barriers. We conclude that hClCa1 does not form Ca2+-dependent Cl− channels per se or enhance the trafficking/insertion of constitutive channels in the HEK293 and NCIH522 expression systems. Rather, hClCa1 elevates the single channel conductance of endogenous Ca2+-dependent Cl− channels by lowering the energy barriers for ion translocation through the pore. PMID:19307298

  10. Dynamic DNA methylation in the brain: a new epigenetic mark for experience-dependent plasticity

    PubMed Central

    Tognini, Paola; Napoli, Debora; Pizzorusso, Tommaso

    2015-01-01

    Experience-dependent plasticity is the ability of brain circuits to undergo molecular, structural and functional changes as a function of neural activity. Neural activity continuously shapes our brain during all the stages of our life, from infancy through adulthood and beyond. Epigenetic modifications of histone proteins and DNA seem to be a leading molecular mechanism to modulate the transcriptional changes underlying the fine-tuning of synaptic connections and circuitry rewiring during activity-dependent plasticity. The recent discovery that cytosine methylation is an epigenetic mark particularly dynamic in brain cells has strongly increased the interest of neuroscientists in understanding the role of covalent modifications of DNA in activity-induced remodeling of neuronal circuits. Here, we provide an overview of the role of DNA methylation and hydroxylmethylation in brain plasticity both during adulthood, with emphasis on learning and memory related processes, and during postnatal development, focusing specifically on experience-dependent plasticity in the visual cortex. PMID:26379502

  11. Prooxidant action of knipholone anthrone: copper dependent reactive oxygen species generation and DNA damage.

    PubMed

    Habtemariam, S; Dagne, E

    2009-07-01

    Knipholone (KP) and knipholone anthrone (KA) are natural 4-phenylanthraquinone structural analogues with established differential biological activities including in vitro antioxidant and cytotoxic properties. By using DNA damage as an experimental model, the comparative Cu(II)-dependent prooxidant action of these two compounds were studied. In the presence of Cu(II) ions, the antioxidant KA (3.1-200 microM) but not KP (6-384 microM) caused a concentration-dependent pBR322 plasmid DNA strand scission. The DNA damage induced by KA could be abolished by reactive oxygen species scavengers, glutathione and catalase as well as EDTA and a specific Cu(I) chelator bathocuproine disulfonic acid. In addition to Cu(II) chelating activity, KA readily reduces Cu(II) to Cu(I). Copper-dependent generation of reactive oxygen species and the subsequent macromolecular damage may be involved in the antimicrobial and cytotoxic activity of KA. PMID:19345716

  12. Assays for Hepatitis B Virus DNA-and RNA-Dependent DNA Polymerase Activities.

    PubMed

    Shaw, T; Locarnini, S A

    2000-01-01

    Genomes of the hepatitis B viruses (HBVs) consist of approx 3.2 kb of partly double-stranded DNA containing three or four overlapping open reading frames, the largest of which encodes the viral polymerase (Pol) protein. After entry into the cell and uncoating, the viral genome is transported to the nucleus where it is converted into a covalently closed circular (CCC) or supercoiled molecule by cellular repair mechanisms. The viral CCC DNA is transcribed, presumably by host cell RNA polymerase II, into unspliced, capped polyadenylated mRNA species from which viral proteins are transcribed. In addition, terminally redundant 3.5-kb RNA transcripts, which function as pregenomes, are produced and exported to the cytoplasm where they are packaged into viral core particles in which reverse transcription, pregenome degradation, and duplication occurs, reproducing the partly double-stranded HBV genome (for recent review, see ref. 1). Besides its essential role in HBV genome replication, HBV Pol is also involved in virus assembly, and because hepadnaviruses do not encode enzymes functionally equivalent to deoxynucleoside kinases (2), functions associated with HBV Pol are probably the only virus-specific targets for antiviral activity of nucleoside analogs. In vitro assays for inhibition of HBV Pol functions by deoxynucleoside triphosphate (dNTP) analogs are useful indicators but, because of restrictions imposed by hepatocyte enzymology, provide no guarantee of potential anti-HBV activity of the parent (deoxy)nucleoside analogs in intact cells (2). PMID:21331902

  13. Nanoscale size dependence parameters on lattice thermal conductivity of Wurtzite GaN nanowires

    SciTech Connect

    Mamand, S.M.; Omar, M.S.; Muhammad, A.J.

    2012-05-15

    Graphical abstract: Temperature dependence of calculated lattice thermal conductivity of Wurtzite GaN nanowires. Highlights: Black-Right-Pointing-Pointer A modified Callaway model is used to calculate lattice thermal conductivity of Wurtzite GaN nanowires. Black-Right-Pointing-Pointer A direct method is used to calculate phonon group velocity for these nanowires. Black-Right-Pointing-Pointer 3-Gruneisen parameter, surface roughness, and dislocations are successfully investigated. Black-Right-Pointing-Pointer Dislocation densities are decreases with the decrease of wires diameter. -- Abstract: A detailed calculation of lattice thermal conductivity of freestanding Wurtzite GaN nanowires with diameter ranging from 97 to 160 nm in the temperature range 2-300 K, was performed using a modified Callaway model. Both longitudinal and transverse modes are taken into account explicitly in the model. A method is used to calculate the Debye and phonon group velocities for different nanowire diameters from their related melting points. Effect of Gruneisen parameter, surface roughness, and dislocations as structure dependent parameters are successfully used to correlate the calculated values of lattice thermal conductivity to that of the experimentally measured curves. It was observed that Gruneisen parameter will decrease with decreasing nanowire diameters. Scattering of phonons is assumed to be by nanowire boundaries, imperfections, dislocations, electrons, and other phonons via both normal and Umklapp processes. Phonon confinement and size effects as well as the role of dislocation in limiting thermal conductivity are investigated. At high temperatures and for dislocation densities greater than 10{sup 14} m{sup -2} the lattice thermal conductivity would be limited by dislocation density, but for dislocation densities less than 10{sup 14} m{sup -2}, lattice thermal conductivity would be independent of that.

  14. Reduced temperature-dependent thermal conductivity of magnetite thin films by controlling film thickness

    PubMed Central

    2014-01-01

    We report on the out-of-plane thermal conductivities of epitaxial Fe3O4 thin films with thicknesses of 100, 300, and 400 nm, prepared using pulsed laser deposition (PLD) on SiO2/Si substrates. The four-point probe three-omega (3-ω) method was used for thermal conductivity measurements of the Fe3O4 thin films in the temperature range of 20 to 300 K. By measuring the temperature-dependent thermal characteristics of the Fe3O4 thin films, we realized that their thermal conductivities significantly decreased with decreasing grain size and thickness of the films. The out-of-plane thermal conductivities of the Fe3O4 films were found to be in the range of 0.52 to 3.51 W/m · K at 300 K. For 100-nm film, we found that the thermal conductivity was as low as approximately 0.52 W/m · K, which was 1.7 to 11.5 order of magnitude lower than the thermal conductivity of bulk material at 300 K. Furthermore, we calculated the temperature dependence of the thermal conductivity of these Fe3O4 films using a simple theoretical Callaway model for comparison with the experimental data. We found that the Callaway model predictions agree reasonably with the experimental data. We then noticed that the thin film-based oxide materials could be efficient thermoelectric materials to achieve high performance in thermoelectric devices. PMID:24571956

  15. Molecular Pathways: Targeting the Dependence of Mutant RAS Cancers on the DNA Damage Response

    PubMed Central

    Grabocka, Elda; Commisso, Cosimo; Bar-Sagi, Dafna

    2014-01-01

    Of the genes mutated in cancer, RAS remains the most elusive to target. Recent technological advances and discoveries have greatly expanded our knowledge of the biology of oncogenic Ras and its role in cancer. As such, it has become apparent that a property that intimately accompanies RAS-driven tumorigenesis is the dependence of RAS mutant cells on a number of non-oncogenic signaling pathways. These dependencies arise as a means of adaptation to Ras-driven intracellular stresses and represent unique vulnerabilities of mutant RAS cancers. A number of studies have highlighted the dependence of mutant RAS cancers on the DNA damage response and identified the molecular pathways that mediate this process including signaling from wild-type Ras isoforms, ATR/Chk1, and DNA damage repair pathways. Here we review these findings, and discuss the combinatorial use of DNA damaging chemotherapy with blockade of wild-type H- and N-Ras signaling by farnesyltransferase inhibitors, Chk1 inhibitors, or small molecule targeting DNA damage repair as potential strategies through which the dependence of RAS cancers on the DNA damage response can be harnessed for therapeutic intervention. PMID:25424849

  16. Temperature and frequency dependent conductivity of bismuth zinc vanadate semiconducting glassy system

    NASA Astrophysics Data System (ADS)

    Punia, R.; Kundu, R. S.; Dult, Meenakshi; Murugavel, S.; Kishore, N.

    2012-10-01

    The ac conductivity of bismuth zinc vanadate glasses with compositions 50V2O5. xBi2O3. (50-x) ZnO has been studied in the frequency range 10-1 Hz to 2 MHz and in temperature range 333.16 K to 533.16 K. The temperature and frequency dependent conductivity is found to obey Jonscher's universal power law for all the compositions of bismuth zinc vanadate glass system. The dc conductivity (σdc), crossover frequency (ωH), and frequency exponent (s) have been estimated from the fitting of experimental data of ac conductivity with Jonscher's universal power law. Enthalpy to dissociate the cation from its original site next to a charge compensating center (Hf) and enthalpy of migration (Hm) have also been estimated. It has been observed that mobility of charge carriers and ac conductivity in case of zinc vanadate glass system increases with increase in Bi2O3 content. In order to determine the conduction mechanism, the ac conductivity and its frequency exponent have been analyzed in the frame work of various theoretical models based on classical hopping over barriers and quantum mechanical tunneling. The ac conduction takes place via tunneling of overlapping large polarons in all the compositions of presently studied vanadate glasses. The fitting of experimental data of ac conductivity with overlapping large polarons tunneling model has also been done. The parameters; density of states at Fermi level (N(EF)), activation energy associated with charge transfer between the overlapping sites (WHO), inverse localization length (α) and polaron radius (rp) obtained from fitting of this model with experimental data are reasonable.

  17. In Situ Study of Strain-Dependent Ion Conductivity of Stretchable Polyethylene Oxide Electrolyte

    PubMed Central

    Kelly, Taylor; Ghadi, Bahar Moradi; Berg, Sean; Ardebili, Haleh

    2016-01-01

    There is a strong need in developing stretchable batteries that can accommodate stretchable or irregularly shaped applications including medical implants, wearable devices and stretchable electronics. Stretchable solid polymer electrolytes are ideal candidates for creating fully stretchable lithium ion batteries mainly due to their mechanical and electrochemical stability, thin-film manufacturability and enhanced safety. However, the characteristics of ion conductivity of polymer electrolytes during tensile deformation are not well understood. Here, we investigate the effects of tensile strain on the ion conductivity of thin-film polyethylene oxide (PEO) through an in situ study. The results of this investigation demonstrate that both in-plane and through-plane ion conductivities of PEO undergo steady and linear growths with respect to the tensile strain. The coefficients of strain-dependent ion conductivity enhancement (CSDICE) for in-plane and through-plane conduction were found to be 28.5 and 27.2, respectively. Tensile stress-strain curves and polarization light microscopy (PLM) of the polymer electrolyte film reveal critical insights on the microstructural transformation of stretched PEO and the potential consequences on ionic conductivity. PMID:26831948

  18. In Situ Study of Strain-Dependent Ion Conductivity of Stretchable Polyethylene Oxide Electrolyte

    NASA Astrophysics Data System (ADS)

    Kelly, Taylor; Ghadi, Bahar Moradi; Berg, Sean; Ardebili, Haleh

    2016-02-01

    There is a strong need in developing stretchable batteries that can accommodate stretchable or irregularly shaped applications including medical implants, wearable devices and stretchable electronics. Stretchable solid polymer electrolytes are ideal candidates for creating fully stretchable lithium ion batteries mainly due to their mechanical and electrochemical stability, thin-film manufacturability and enhanced safety. However, the characteristics of ion conductivity of polymer electrolytes during tensile deformation are not well understood. Here, we investigate the effects of tensile strain on the ion conductivity of thin-film polyethylene oxide (PEO) through an in situ study. The results of this investigation demonstrate that both in-plane and through-plane ion conductivities of PEO undergo steady and linear growths with respect to the tensile strain. The coefficients of strain-dependent ion conductivity enhancement (CSDICE) for in-plane and through-plane conduction were found to be 28.5 and 27.2, respectively. Tensile stress-strain curves and polarization light microscopy (PLM) of the polymer electrolyte film reveal critical insights on the microstructural transformation of stretched PEO and the potential consequences on ionic conductivity.

  19. Modeling activity-dependent changes of axonal spike conduction in primary afferent C-nociceptors

    PubMed Central

    Tigerholm, Jenny; Petersson, Marcus E.; Obreja, Otilia; Lampert, Angelika; Carr, Richard; Schmelz, Martin

    2013-01-01

    Action potential initiation and conduction along peripheral axons is a dynamic process that displays pronounced activity dependence. In patients with neuropathic pain, differences in the modulation of axonal conduction velocity by activity suggest that this property may provide insight into some of the pathomechanisms. To date, direct recordings of axonal membrane potential have been hampered by the small diameter of the fibers. We have therefore adopted an alternative approach to examine the basis of activity-dependent changes in axonal conduction by constructing a comprehensive mathematical model of human cutaneous C-fibers. Our model reproduced axonal spike propagation at a velocity of 0.69 m/s commensurate with recordings from human C-nociceptors. Activity-dependent slowing (ADS) of axonal propagation velocity was adequately simulated by the model. Interestingly, the property most readily associated with ADS was an increase in the concentration of intra-axonal sodium. This affected the driving potential of sodium currents, thereby producing latency changes comparable to those observed for experimental ADS. The model also adequately reproduced post-action potential excitability changes (i.e., recovery cycles) observed in vivo. We performed a series of control experiments replicating blockade of particular ion channels as well as changing temperature and extracellular ion concentrations. In the absence of direct experimental approaches, the model allows specific hypotheses to be formulated regarding the mechanisms underlying activity-dependent changes in C-fiber conduction. Because ADS might functionally act as a negative feedback to limit trains of nociceptor activity, we envisage that identifying its mechanisms may also direct efforts aimed at alleviating neuronal hyperexcitability in pain patients. PMID:24371290

  20. Activation of an Mg2+-dependent DNA endonuclease of avian myeloblastosis virus alpha beta DNA polymerase by in vitro proteolytic cleavage.

    PubMed Central

    Grandgenett, D P; Golomb, M; Vora, A C

    1980-01-01

    Partial chymotryptic digestion of purified avian myeloblastosis virus alpha beta DNA polymerase resulted in the activation of a Mg2+-dependent DNA endonuclease activity. Incubation of the polymerase-protease mixture in the presence of super-coiled DNA and Mg2+ permitted detection of the cleaved polymerase fragment possessing DNA nicking activity. Protease digestion conditions were established permitting selective cleavage of beta to alpha, which contained DNA polymerase and RNase H activity and to a family of polypeptides ranging in size from 30,000 to 34,000 daltons. These latter beta-unique fragments were purified by polyuridylate-Sepharose 4B chromatography and were shown to contain both DNA binding and DNA endonuclease activities. We have demonstrated that this group of polymerase fragments derived by chymotryptic digestion of alpha beta DNA polymerase is similar to the in vivo-isolated avian myeloblastosis virus p32pol in size, sequence, and DNA endonuclease activity. Images PMID:6154149

  1. A DNA-dependent stress response involving DNA-PK occurs in hypoxic cells and contributes to cellular adaptation to hypoxia.

    PubMed

    Bouquet, Fanny; Ousset, Marielle; Biard, Denis; Fallone, Frédérique; Dauvillier, Stéphanie; Frit, Philippe; Salles, Bernard; Muller, Catherine

    2011-06-01

    DNA-dependent protein kinase (DNA-PK) is involved in DNA double-strand break (DSB) signalling and repair. We report that DNA-PK is activated by mild hypoxia conditions (0.1-1% O₂) as shown by (1) its autophosphorylation on Ser2056, and (2) its mobilisation from a soluble nucleoplasmic compartment to a less extractable nuclear fraction. The recruitment of DNA-PK was not followed by activation and recruitment of the XRCC4-DNA-ligase-IV complex, suggesting that DSBs are not responsible for activation of DNA-PK. To unravel the mechanism of DNA-PK activation, we show that exposure of cells to trichostatin A, a histone deacetylase inhibitor, leads to DNA-PK autophosphorylation and relocalisation to DNA. Histone acetylation (mainly H3K14) is increased in hypoxic cells and treatment with anacardic acid, an inhibitor of histone acetyl transferase, prevented both histone modifications and DNA-PK activation in hypoxic conditions. Importantly, in using either silenced DNA-PK cells or cells exposed to a specific DNA-PK inhibitor (NU7026), we demonstrated that hypoxic DNA-PK activation positively regulates the key transcription factor HIF-1 and one subsequent target gene, GLUT1. Our results show that hypoxia initiates chromatin modification and consequently DNA-PK activation, which positively regulate cellular oxygen-sensing and oxygen-signalling pathways. PMID:21576354

  2. Size-dependent conductivity-type inversion in Cu2O nanoparticles

    NASA Astrophysics Data System (ADS)

    Balamurugan, B.; Aruna, I.; Mehta, B. R.; Shivaprasad, S. M.

    2004-04-01

    X-ray photoemission spectroscopy and optical absorption studies have been carried out on Cu2O nanoparticles prepared using the activated reactive evaporation technique. A strong shift of the valence band edge (from 0.7 to 1.8 eV) has been observed on reduction of the nanoparticle size from 20 nm to 4 nm. The size-dependent modifications in the energy level diagram and metal-Cu2O nanoparticle Schottky junction characteristics confirm the observation of the inversion of conductivity type from p-type bulk conductivity to n-type conductivity in Cu2O nanoparticles at lower dimensions. This study can initiate a further methodology for tailoring the semiconductor properties of a material by controlling the nanoparticle size.

  3. Defect association mediated ionic conductivity of rare earth doped nanoceria: Dependency on ionic radius

    NASA Astrophysics Data System (ADS)

    Anirban, Sk.; Sinha, A.; Bandyopadhyay, S.; Dutta, A.

    2016-05-01

    Rare earth doped nanoceria Ce0.9RE0.1O1.95 (RE = Pr, Nd, Eu and Gd) were prepared through citrate auto-ignition method. The single phase cubic fluorite structure with space group Fm3 ¯m of the compositions were confirmed from Rietveld analysis of XRD data. The particle size of the compositions were in the range 49.77 nm to 66.20 nm. An ionic radius dependent lattice parameter variation was found. The DC conductivity of each composition was evaluated using Random Barrier Model. The conductivity decreased and activation energy increased with increasing ionic radius from Gd to Pr doping due to the size mismatch with host ions and formation of stable defect associate. The formation of different defect associates and their correlation with ionic conductivity has been discussed.

  4. Effect of gases on the temperature dependence of the electric conductivity of CVD multiwalled carbon nanotubes

    SciTech Connect

    Buryakov, T. I. Romanenko, A. I.; Anikeeva, O. B.; Kuznetsov, V. L.; Usol'tseva, A. N.; Tkachev, E. N.

    2007-07-15

    The influence of various gaseous media on the temperature dependence of the electric conductivity {sigma} of multiwalled carbon nanotubes (MWNTs) synthesized using the method of catalytical chemical vapor deposition (CVD) has been studied. The {sigma}(T) curves were measured in a temperature range from 4.2 to 300 K in helium and its mixtures with air, methane, oxygen, and hydrogen. The introduction of various gaseous components into a helium atmosphere leads to a significant decrease in the conductivity of MWNTs in the interval between the temperatures of condensation and melting of the corresponding gas. Upon a heating-cooling cycle, the conductivity restores on the initial level. It is concluded that a decrease in {sigma} is caused by the adsorption of gases on the surface of nanotubes.

  5. Conductivity of natural and modified DNA measured by scanning tunneling microscopy. The effect of sequence, charge and stacking.

    PubMed

    Kratochvílová, Irena; Král, Karel; Buncek, Martin; Vísková, Alena; Nespůrek, Stanislav; Kochalska, Anna; Todorciuc, Tatiana; Weiter, Martin; Schneider, Bohdan

    2008-11-01

    The conductivity of DNA covalently bonded to a gold surface was studied by means of the STM technique. Various single- and double-stranded 32-nucleotide-long DNA sequences were measured under ambient conditions so as to provide a better understanding of the complex process of charge-carrier transport in natural as well as chemically modified DNA molecules. The investigations focused on the role of several features of DNA structure, namely the role of the negative charge at the backbone phosphate group and the related complex effects of counterions, and of the stacking interactions between the bases in Watson-Crick and other types of base pairs. The measurements have indicated that the best conductor is DNA in its biologically most relevant double-stranded form with Watson-Crick base pairs and charged phosphates equilibrated with counterions and water. All the studied modifications, including DNA with non-Watson-Crick base pairs, the abasic form, and especially the form with phosphate charges eliminated by chemical modifications, lower the conductivity of natural DNA. PMID:18801607

  6. Caveolae in Ventricular Myocytes are Required for Stretch-Dependent Conduction Slowing

    PubMed Central

    Pfeiffer, E.R.; Wright, A.T.; Edwards, A.G.; Stowe, J.C.; McNall, K.; Tan, J.; Niesman, I.; Patel, H.H.; Roth, D.M.; Omens, J.H.; McCulloch, A.D.

    2014-01-01

    Mechanical stretch of cardiac muscle modulates action potential propagation velocity, causing potentially arrhythmogenic conduction slowing. The mechanisms by which stretch alters cardiac conduction remain unknown, but previous studies suggest that stretch can affect the conformation of caveolae in myocytes and other cell types. We tested the hypothesis that slowing of action potential conduction due to cardiac myocyte stretch is dependent on caveolae. Cardiac action potential propagation velocities, measured by optical mapping in isolated mouse hearts and in micropatterned mouse cardiomyocyte cultures, decreased reversibly with volume loading or stretch, respectively (by 19±5% and 26±4%). Stretch-dependent conduction slowing was not altered by stretch-activated channel blockade with gadolinium or by GsMTx-4 peptide, but was inhibited when caveolae were disrupted via genetic deletion of caveolin-3 (Cav3 KO) or membrane cholesterol depletion by methyl-β-cyclodextrin. In wild-type mouse hearts, stretch coincided with recruitment of caveolae to the sarcolemma, as observed by electron microscopy. In myocytes from wild-type but not Cav3 KO mice, stretch significantly increased cell membrane capacitance (by 98±64%), electrical time constant (by 285±149%), and lipid recruitment to the bilayer (by 84±39%). Recruitment of caveolae to the sarcolemma during physiologic cardiomyocyte stretch slows ventricular action potential propagation by increasing cell membrane capacitance. PMID:25257915

  7. Large Conductance Switching in a Single-Molecule Device through Room Temperature Spin-Dependent Transport.

    PubMed

    Aragonès, Albert C; Aravena, Daniel; Cerdá, Jorge I; Acís-Castillo, Zulema; Li, Haipeng; Real, José Antonio; Sanz, Fausto; Hihath, Josh; Ruiz, Eliseo; Díez-Pérez, Ismael

    2016-01-13

    Controlling the spin of electrons in nanoscale electronic devices is one of the most promising topics aiming at developing devices with rapid and high density information storage capabilities. The interface magnetism or spinterface resulting from the interaction between a magnetic molecule and a metal surface, or vice versa, has become a key ingredient in creating nanoscale molecular devices with novel functionalities. Here, we present a single-molecule wire that displays large (>10000%) conductance switching by controlling the spin-dependent transport under ambient conditions (room temperature in a liquid cell). The molecular wire is built by trapping individual spin crossover Fe(II) complexes between one Au electrode and one ferromagnetic Ni electrode in an organic liquid medium. Large changes in the single-molecule conductance (>100-fold) are measured when the electrons flow from the Au electrode to either an α-up or a β-down spin-polarized Ni electrode. Our calculations show that the current flowing through such an interface appears to be strongly spin-polarized, thus resulting in the observed switching of the single-molecule wire conductance. The observation of such a high spin-dependent conductance switching in a single-molecule wire opens up a new door for the design and control of spin-polarized transport in nanoscale molecular devices at room temperature. PMID:26675052

  8. Temperature-dependent thermal conductivity in silicon nanostructured materials studied by the Boltzmann transport equation

    NASA Astrophysics Data System (ADS)

    Romano, Giuseppe; Esfarjani, Keivan; Strubbe, David A.; Broido, David; Kolpak, Alexie M.

    2016-01-01

    Nanostructured materials exhibit low thermal conductivity because of the additional scattering due to phonon-boundary interactions. As these interactions are highly sensitive to the mean free path (MFP) of phonons, MFP distributions in nanostructures can be dramatically distorted relative to bulk. Here we calculate the MFP distribution in periodic nanoporous Si for different temperatures, using the recently developed MFP-dependent Boltzmann transport equation. After analyzing the relative contribution of each phonon branch to thermal transport in nanoporous Si, we find that at room temperature optical phonons contribute 17 % to heat transport, compared to 5 % in bulk Si. Interestingly, we observe a constant thermal conductivity over the range 200 K dependence of the heat capacity. Our findings, which are in qualitative agreement with the temperature trend of thermal conductivities measured in nanoporous Si-based systems, shed light on the origin of the reduction of thermal conductivity in nanostructured materials and demonstrate the necessity of multiscale heat transport engineering, in which the bulk material and geometry are optimized concurrently.

  9. DNA-Dependent Protein Kinase As Molecular Target for Radiosensitization of Neuroblastoma Cells

    PubMed Central

    Dolman, M. Emmy M.; van der Ploeg, Ida; Koster, Jan; Bate-Eya, Laurel Tabe; Versteeg, Rogier; Caron, Huib N.; Molenaar, Jan J.

    2015-01-01

    Tumor cells might resist therapy with ionizing radiation (IR) by non-homologous end-joining (NHEJ) of IR-induced double-strand breaks. One of the key players in NHEJ is DNA-dependent protein kinase (DNA-PK). The catalytic subunit of DNA-PK, i.e. DNA-PKcs, can be inhibited with the small-molecule inhibitor NU7026. In the current study, the in vitro potential of NU7026 to radiosensitize neuroblastoma cells was investigated. DNA-PKcs is encoded by the PRKDC (protein kinase, DNA-activated, catalytic polypeptide) gene. We showed that PRKDC levels were enhanced in neuroblastoma patients and correlated with a more advanced tumor stage and poor prognosis, making DNA-PKcs an interesting target for radiosensitization of neuroblastoma tumors. Optimal dose finding for combination treatment with NU7026 and IR was performed using NGP cells. One hour pre-treatment with 10 μM NU7026 synergistically sensitized NGP cells to 0.63 Gy IR. Radiosensitizing effects of NU7026 increased in time, with maximum effects observed from 96 h after IR-exposure on. Combined treatment of NGP cells with 10 μM NU7026 and 0.63 Gy IR resulted in apoptosis, while no apoptotic response was observed for either of the therapies alone. Inhibition of IR-induced DNA-PK activation by NU7026 confirmed the capability of NGP cells to, at least partially, resist IR by NHEJ. NU7026 also synergistically radiosensitized other neuroblastoma cell lines, while no synergistic effect was observed for low DNA-PKcs-expressing non-cancerous fibroblasts. Results obtained for NU7026 were confirmed by PRKDC knockdown in NGP cells. Taken together, the current study shows that DNA-PKcs is a promising target for neuroblastoma radiosensitization. PMID:26716839

  10. Metal electrode dependent field effect transistors made of lanthanide ion-doped DNA crystals

    NASA Astrophysics Data System (ADS)

    Reddy Dugasani, Sreekantha; Hwang, Taehyun; Kim, Jang Ah; Gnapareddy, Bramaramba; Kim, Taesung; Park, Sung Ha

    2016-03-01

    We fabricated lanthanide ion (Ln3+, e.g. Dy3+, Er3+, Eu3+, and Gd3+)-doped self-assembled double-crossover (DX) DNA crystals grown on the surface of field effect transistors (FETs) containing either a Cr, Au, or Ni electrode. Here we demonstrate the metal electrode dependent FET characteristics as a function of various Ln3+. The drain-source current (I ds), controlled by the drain-source voltage (V ds) of Ln3+-doped DX DNA crystals with a Cr electrode on an FET, changed significantly under various gate voltages (V g) due to the relative closeness of the work function of Cr to the energy band gap of Ln3+-DNA crystals compared to those of Au and Ni. For Ln3+-DNA crystals on an FET with either a Cr or Ni electrode at a fixed V ds, I ds decreased with increasing V g ranging from  -2 to 0 V and from 0 to  +3 V in the positive and negative regions, respectively. By contrast, I ds for Ln3+-DNA crystals on an FET with Au decreased with increasing V g in only the positive region due to the greater electronegativity of Au. Furthermore, Ln3+-DNA crystals on an FET exhibited behaviour sensitive to V g due to the appreciable charge carriers generated from Ln3+. Finally, we address the resistivity and the mobility of Ln3+-DNA crystals on an FET with different metal electrodes obtained from I ds-V ds and I ds-V g curves. The resistivities of Ln3+-DNA crystals on FETs with Cr and Au electrodes were smaller than those of pristine DNA crystals on an FET, and the mobility of Ln3+-DNA crystals on an FET with Cr was relatively higher than that associated with other electrodes.

  11. Thermal conduction by dark matter with velocity and momentum-dependent cross-sections

    SciTech Connect

    Vincent, Aaron C.; Scott, Pat E-mail: patscott@physics.mcgill.ca

    2014-04-01

    We use the formalism of Gould and Raffelt [1] to compute the dimensionless thermal conduction coefficients for scattering of dark matter particles with standard model nucleons via cross-sections that depend on the relative velocity or momentum exchanged between particles. Motivated by models invoked to reconcile various recent results in direct detection, we explicitly compute the conduction coefficients α and κ for cross-sections that go as v{sub rel}{sup 2}, v{sub rel}{sup 4}, v{sub rel}{sup −2}, q{sup 2}, q{sup 4} and q{sup −2}, where v{sub rel} is the relative DM-nucleus velocity and q is the momentum transferred in the collision. We find that a v{sub rel}{sup −2} dependence can significantly enhance energy transport from the inner solar core to the outer core. The same can true for any q-dependent coupling, if the dark matter mass lies within some specific range for each coupling. This effect can complement direct searches for dark matter; combining these results with state-of-the-art solar simulations should greatly increase sensitivity to certain DM models. It also seems possible that the so-called Solar Abundance Problem could be resolved by enhanced energy transport in the solar core due to such velocity- or momentum-dependent scatterings.

  12. Viral Single-Strand DNA Induces p53-Dependent Apoptosis in Human Embryonic Stem Cells

    PubMed Central

    Hirsch, Matthew L.; Fagan, B. Matthew; Dumitru, Raluca; Bower, Jacquelyn J.; Yadav, Swati; Porteus, Matthew H.; Pevny, Larysa H.; Samulski, R. Jude

    2011-01-01

    Human embryonic stem cells (hESCs) are primed for rapid apoptosis following mild forms of genotoxic stress. A natural form of such cellular stress occurs in response to recombinant adeno-associated virus (rAAV) single-strand DNA genomes, which exploit the host DNA damage response for replication and genome persistence. Herein, we discovered a unique DNA damage response induced by rAAV transduction specific to pluripotent hESCs. Within hours following rAAV transduction, host DNA damage signaling was elicited as measured by increased gamma-H2AX, ser15-p53 phosphorylation, and subsequent p53-dependent transcriptional activation. Nucleotide incorporation assays demonstrated that rAAV transduced cells accumulated in early S-phase followed by the induction of apoptosis. This lethal signaling sequalae required p53 in a manner independent of transcriptional induction of Puma, Bax and Bcl-2 and was not evident in cells differentiated towards a neural lineage. Consistent with a lethal DNA damage response induced upon rAAV transduction of hESCs, empty AAV protein capsids demonstrated no toxicity. In contrast, DNA microinjections demonstrated that the minimal AAV origin of replication and, in particular, a 40 nucleotide G-rich tetrad repeat sequence, was sufficient for hESC apoptosis. Our data support a model in which rAAV transduction of hESCs induces a p53-dependent lethal response that is elicited by a telomeric sequence within the AAV origin of replication. PMID:22114676

  13. Response-coefficient method for heat-conduction transients with time-dependent inputs

    NASA Technical Reports Server (NTRS)

    Ceylan, Tamer

    1993-01-01

    A theoretical overview of the response coefficient method for heat conduction transients with time-dependent input forcing functions is presented with a number of illustrative applications. The method may be the most convenient and economical if the same problem is to be solved many times with different input-time histories or if the solution time is relatively long. The method is applicable to a wide variety of problems, including irregular geometries, position-dependent boundary conditions, position-dependent physical properties, and nonperiodic irregular input histories. Nonuniform internal energy generation rates within the structure can also be handled by the method. The area of interest is long-time solutions, in which initial condition is unimportant, and not the early transient period. The method can be applied to one dimensional problems in cartesian, cylindrical, and spherical coordinates as well as to two dimensional problems in cartesian and cylindrical coordinates.

  14. DNA-dependent DNA polymerase from yeast mitochondria. Dependence of enzyme activity on conditions of cell growth, and properties of the highly purified polymerase.

    PubMed

    Wintersberger, U; Blutsch, H

    1976-09-01

    The activity of DNA polymerase was determined in gradient-purified mitochondria from yeast cells grown under a variety of conditions. The specific enzyme activity was found to be dependent on the degree of aeration of the cells, and on the carbon source used for the medium. It was sensitive to glucose repression, and was enhanced about two-fold by the growth of yeast cells in the presence of ethidium bromide. Mitochondria DNA polymerase was highly purified and several properties were determined. Sucrose density gradient centrifugation, and dodecylsulfate-polyacylamide gel electrophoresis revealed the following structure: a monomer of molecular weight around 60 000 aggregated under relatively high salt concentration (0.2 M phosphate buffer) to a dimer of about 120 000 which under low salt concentration (0.2 M Tris-HCl buffer) formed higher aggregates. For optimal activity an Mg2+ ion concentration of 50 mM was found necessary, Mn ions did not promote activity at any concentration tested (0.5--50 mM). Indeed, if added to Mg2+-containing assays, Mn2+ strongly inhibited enzyme activity at low concentrations. This might be an explanation for the inducation of mitochondrial mutants in yeast cells grown in the presence of Mn2+ ions. Mitochondrial DNA polymerase activity was strongly inhibited by low concentrations of the -SH reagent p-chloromercuribenzoate, the nucleotide analogue cytosine arabinoside triphosphate also exerted an inhibitory effect. An about 50% decrease of activity was observed in the presence of 1 mM o-phenanthroline in assay mixture containing DNA at about the Km concentration. The enzyme preferred a gapped template primer, poly(dA) - (dT)10, over nicked DNA and was unable to use a polyribonucleotide template, poly(rA) - (dT)10. In the purest preparations no exonuclease activity could be detected. PMID:786635

  15. Mitochondrial DNA deletions detected by Multiplex Ligation-dependent Probe Amplification.

    PubMed

    Mayorga, Lía; Laurito, Sergio R; Loos, Mariana A; Eiroa, Hernán D; de Pinho, Silvina; Lubieniecki, Fabiana; Arroyo, Hugo A; Pereyra, Marcela F; Kauffman, Marcelo A; Roqué, María

    2016-07-01

    The genetic diagnosis algorithm for mitochondrial (mt) diseases starts looking for deletions and common mutations in mtDNA. MtDNA's special features, such as large and variable genome copies, heteroplasmy, polymorphisms, and its duplication in the nuclear genome as pseudogenes (NUMTs), make it vulnerable to diagnostic misleading interpretations. Multiplex Ligation-dependent Probe Amplification (MLPA) is used to detect copy number variations in nuclear genes and its application on mtDNA has not been widely spread. We report three Kearns Sayre Syndrome patients and one Chronic Progressive External Ophthalmoplegia adult, whose diagnostic mtDNA deletions were detected by MLPA using a very low amount of DNA. This managed to "dilute" the NUMT interference as well as enhance MLPA's efficiency. By this report, we conclude that when MLPA is performed upon a reduced amount of DNA, it can detect effectively mtDNA deletions. We propose MLPA as a possible first step method in the diagnosis of mt diseases. PMID:26114318

  16. Force-dependent persistence length of DNA-intercalator complexes measured in single molecule stretching experiments.

    PubMed

    Bazoni, R F; Lima, C H M; Ramos, E B; Rocha, M S

    2015-06-01

    By using optical tweezers with an adjustable trap stiffness, we have performed systematic single molecule stretching experiments with two types of DNA-intercalator complexes, in order to investigate the effects of the maximum applied forces on the mechanical response of such complexes. We have explicitly shown that even in the low-force entropic regime the persistence length of the DNA-intercalator complexes is strongly force-dependent, although such behavior is not exhibited by bare DNA molecules. We discuss the possible physicochemical effects that can lead to such results. In particular, we propose that the stretching force can promote partial denaturation on the highly distorted double-helix of the DNA-intercalator complexes, which interfere strongly in the measured values of the persistence length. PMID:25913936

  17. Direct observation of DNA motions into solid state nanopore under applied electrical potentials on conductive surface

    NASA Astrophysics Data System (ADS)

    Hayashi, Yoshitaka; Ando, Genki; Idutsu, Ichiro; Mitsui, Toshiyuki

    2011-03-01

    Solid state nanopore is one of emerging methods for rapid single DNA molecule detection because the translocation of the DNA though nanopore produces ionic current changes. One of issues in this method is clogging long DNA molecules. Once DNA molecules clogged, the molecules are rarely removed by varying or switching the polarity of applied bias voltages across the nanopore. We develop a modified nanopore by 50nm Au coating on top of the nanopore surface to be able to remove the clogged DNA molecules during the DNA translocation experiment. Fluorescence microscopy was implemented for observation of stained DNA molecules. The nanopores with diameters near 100 nm can be used initially. DNA translocation rates changes dramatically by tuning the applied electrical potentials on surface higher or lower than the potentials across the nanopore. Furthermore, the Au potentials modifies IV characteristic of the ionic current across the nanopore which is similar to the gate voltages controlling the SD current in FET. We will discuss the influence of surface potential on DNA motion and translocation and clogged DNA molecules. Finally, we will present the recent results of DNA translocation into the SiN-Au-SiO2 nanopore and discuss the effect of applied voltages on Au.

  18. Layer thickness-dependent phonon properties and thermal conductivity of MoS2

    NASA Astrophysics Data System (ADS)

    Gu, Xiaokun; Li, Baowen; Yang, Ronggui

    2016-02-01

    For conventional materials, the thermal conductivity of thin films is usually suppressed when the thickness decreases due to phonon-boundary scattering. However, this is not necessarily true for the van der Waals solids if the thickness is reduced to only a few layers. In this letter, the layer thickness-dependent phonon properties and thermal conductivity in the few-layer MoS2 are studied using the first-principles-based Peierls-Boltzmann transport equation approach. The basal-plane thermal conductivity of 10-μm-long samples is found to monotonically reduce from 138 W/mK to 98 W/mK for naturally occurring MoS2, and from 155 W/mK to 115 W/mK for isotopically pure MoS2, when its thickness increases from one layer to three layers. The thermal conductivity of tri-layer MoS2 approaches to that of bulk MoS2. Both the change of phonon dispersion and the thickness-induced anharmonicity are important for explaining such a thermal conductivity reduction. The increased anharmonicity in bi-layer MoS2 results in stronger phonon scattering for ZAi modes, which is linked to the breakdown of the symmetry in single-layer MoS2.

  19. Trisomy 21 Alters DNA Methylation in Parent-of-Origin-Dependent and -Independent Manners

    PubMed Central

    Alves da Silva, Antônio Francisco; Machado, Filipe Brum; Pavarino, Érika Cristina; Biselli-Périco, Joice Matos; Zampieri, Bruna Lancia; da Silva Francisco Junior, Ronaldo; Mozer Rodrigues, Pedro Thyago; Terra Machado, Douglas; Santos-Rebouças, Cíntia Barros; Gomes Fernandes, Maria; Chuva de Sousa Lopes, Susana Marina; Lopes Rios, Álvaro Fabricio

    2016-01-01

    The supernumerary chromosome 21 in Down syndrome differentially affects the methylation statuses at CpG dinucleotide sites and creates genome-wide transcriptional dysregulation of parental alleles, ultimately causing diverse pathologies. At present, it is unknown whether those effects are dependent or independent of the parental origin of the nondisjoined chromosome 21. Linkage analysis is a standard method for the determination of the parental origin of this aneuploidy, although it is inadequate in cases with deficiency of samples from the progenitors. Here, we assessed the reliability of the epigenetic 5mCpG imprints resulting in the maternally (oocyte)-derived allele methylation at a differentially methylated region (DMR) of the candidate imprinted WRB gene for asserting the parental origin of chromosome 21. We developed a methylation-sensitive restriction enzyme-specific PCR assay, based on the WRB DMR, across single nucleotide polymorphisms (SNPs) to examine the methylation statuses in the parental alleles. In genomic DNA from blood cells of either disomic or trisomic subjects, the maternal alleles were consistently methylated, while the paternal alleles were unmethylated. However, the supernumerary chromosome 21 did alter the methylation patterns at the RUNX1 (chromosome 21) and TMEM131 (chromosome 2) CpG sites in a parent-of-origin-independent manner. To evaluate the 5mCpG imprints, we conducted a computational comparative epigenomic analysis of transcriptome RNA sequencing (RNA-Seq) and histone modification expression patterns. We found allele fractions consistent with the transcriptional biallelic expression of WRB and ten neighboring genes, despite the similarities in the confluence of both a 17-histone modification activation backbone module and a 5-histone modification repressive module between the WRB DMR and the DMRs of six imprinted genes. We concluded that the maternally inherited 5mCpG imprints at the WRB DMR are uncoupled from the parental allele

  20. Broadband conductivity spectra of fast-ion-conducting silver selenite glasses: Dependence on power law and scaling

    NASA Astrophysics Data System (ADS)

    Deb, B.; Bhattacharya, S.; Ghosh, A.

    2011-11-01

    In this letter we have studied broadband conductivity spectra (10 Hz-3 GHz) of fast-ion-conducting silver selenite glasses of compositions xAgI-(1-x)(yAg2O-(1-y)SeO2). We have observed that the conductivity spectra below 10 MHz are characterized by a power law with exponent less than unity, while the conductivity spectra in the high-frequency range (above 10 MHz) have been adequately explained in the framework of the unified site relaxation model with exponent greater than unity. The scaling of the conductivity spectra indicates that the time-temperature superposition principle is valid in the low-frequency regime, but not in the high-frequency regime.

  1. Twisting motion dependent charge transport properties of poly(dG)-poly(dC) DNA molecular wire

    NASA Astrophysics Data System (ADS)

    Yudiarsah, E.; Suhendro, D. K.; Saleh, R.

    2014-09-01

    The effect of twisting motion of bases on charge transport properties of Poly(dG)-Poly(dC) DNA molecule have been studied. The effect is studied by taking into account twisting angle dependent on-site energy and hopping constant in the tight binding Hamiltonian of double-strand DNA model. The average kinetic energy of twisting motions is assumed to be proportional to system temperature. Transfer matrix method has been used in calculating the localization length of the molecule. The results show that increase in temperature shortens the localization length. The transmission probability of charge on the molecule was calculated using transfer and scattering matrix methods simultaneously on the DNA model sandwiched in between two metallic electrodes. The contacts between molecule and both electrodes were chosen such that the presence of metallic electrodes does not change the main features of transport properties of the molecule much. The temperature tends to widen the area with zero transmission around the Fermi energy. The I-V characteristic of the molecule connected to electrodes has been calculated from transmission probability within Landauer-Buttiker Formalism by assuming the voltage drops symmetrically at the contacts. The results show that temperature lowers the magnitude of the I-V characteristic and the differential conductance. In addition to that, the I-V characteristic and the differential conductance also decrease in magnitude with lowering the twisting frequency.

  2. Sequence Dependent Interactions Between DNA and Single-Walled Carbon Nanotubes

    NASA Astrophysics Data System (ADS)

    Roxbury, Daniel

    solution, which suggested an energy-dependent pathway. Additionally, by means of pharmacological inhibition and vector-induced gene knockout studies, the DNA-SWCNTs were shown to enter the cells via Rac1-mediated macropinocytosis.

  3. Electrical conductivity of metals from real-time time-dependent density functional theory

    NASA Astrophysics Data System (ADS)

    Andrade, Xavier; Correa, Alfredo

    In this presentation, I will discuss how to apply real-time electron dynamics to study electronic currents in crystalline systems and, in particular, how to use this method to predict electrical conductivities in different regimes. This approach presents many interesting theoretical challenges associated to the representation of bulk systems as infinitely periodic. For example, in order to induce electronic currents in the system, we use a gauge transformation that allows us to include finite electric fields in the simulation. We have implemented this approach using time-dependent density functional theory (TDDFT). This implementation allows us to induce, measure and visualize the current density as a function of time, in simulations with thousands of electrons (hundreds and even thousands of atoms). We have found that real-time TDDFT can describe how currents naturally decay in metals. From this dissipation process we can directly calculate the frequency-dependent conductivity, including the direct current (DC) conductivity that is not accessible from linear-response approaches like Kubo-Greenwood.

  4. Spatial dependence of polycrystalline FTO’s conductance analyzed by conductive atomic force microscope (C-AFM)

    SciTech Connect

    Peixoto, Alexandre Pessoa; Costa, J. C. da

    2014-05-15

    Fluorine-doped Tin oxide (FTO) is a highly transparent, electrically conductive polycrystalline material frequently used as an electrode in organic solar cells and optical-electronic devices [1–2]. In this work a spatial analysis of the conductive behavior of FTO was carried out by Conductive-mode Atomic Force Microscopy (C-AFM). Rare highly oriented grains sample give us an opportunity to analyze the top portion of polycrystalline FTO and compare with the border one. It is shown that the current flow essentially takes place through the polycrystalline edge at grain boundaries.

  5. Landau-Zener and Rabi oscillations in the spin-dependent conductance

    NASA Astrophysics Data System (ADS)

    Fernández-Alcázar, L. J.; Pastawski, H. M.

    2014-01-01

    We describe the spin-dependent quantum conductance in a wire where a magnetic field is spatially modulated. The change in direction and intensity of the magnetic field acts as a perturbation that mixes spin projections. This is exemplified by a ferromagnetic nanowire. There the local field varies smoothly its direction generating a domain wall (DW) as described by the well-known Cabrera-Falicov model. Here, we generalize this model to include also a strength modulation. We identify two striking diabatic regimes that appear when such magnetic inhogeneity occurs. 1) If the field strength at the DW is weak enough, the local Zeeman energies result in an avoided crossing. Thus, the spin-flip probability follows the Landau-Zener formula. 2) For strong fields, the spin-dependent conductance shows oscillations as a function of the DW width. We interpret them in terms of Rabi oscillations. Time and length scales obtained from this simplified view show an excellent agreement with the exact dynamical solution of the spin-dependent transport. These results remain valid for other situations involving modulated magnetic structures and thus they open new prospects for the use of quantum interferences in spin-based devices. This paper is dedicated to the memory of the lifelong collaborator Patricia Rebeca Levstein.

  6. Conducting antireflection coatings with low polarization dependent loss for telecommunication applications.

    PubMed

    Dobrowolski, J; Ford, Joseph; Sullivan, Brian; Lu, Liping; Osborne, Norman

    2004-12-13

    Conducting optical coatings for the visible light range are commonly made of Indium Tin Oxide (ITO), but ITO is unsuitable for near-infrared telecommunications wavelengths because it can become absorptive after extended illumination. In this paper we show an alternative approach which uses conventional coating materials to create either non-conducting or conducting antireflection (AR) coatings that are effective over a fairly broad spectral region ( lambdalong/lambdashort approximately 1.40) and also usable for a wide range of angles of incidence (0-38 masculine, or 0-55 masculine) in the telecom wavelength range. Not only is the transmittance of windows treated with such coatings quite high, but they can be made to have extreme polarization independence (low polarization dependent loss values). A number of such coating designs are presented in the paper. A prototype of one of the conducting AR coating designs was fabricated and the measurements were found to be in reasonable agreement with the calculated performance. Such AR coatings should be of interest for telecommunication applications and especially for anti-static hermetic packaging of MEMS devices such as optical switches. PMID:19488272

  7. Saturation-Dependent Hydraulic Conductivity Anisotropy for Multifluid Systems in Porous Media

    SciTech Connect

    Zhang, Z. F.; Oostrom, Mart; Ward, Andy L.

    2007-11-01

    The hydraulic conductivity of unsaturated anisotropic soils has recently been described with a tensorial connectivity-tortuosity (TCT) concept. We extend this concept to unsaturated porous media with two or three immiscible fluids. Mathematical expressions to describe the conductivity of each fluid in anisotropic porous media under unsaturated condition are derived in the form of symmetric second order tensors. The theory is applicable to the combination of any type of saturation-pressure formulation and a generalized hydraulic conductivity model. The extended model shows that the anisotropic coefficient of a fluid is independent of the saturation of other fluids. Synthetic Miller-similar soils having hypothetical anisotropy were defined by allowing the saturated hydraulic conductivity to have different correlation ranges for different directions of flow. The extended TCT concept was tested using synthetic soils with four levels of heterogeneity and four levels of anisotropy. Numerical experiments of infiltration of two liquid phases, i.e., water and the nonaqueous phase liquid (NAPL) carbon tetrachloride, were carried out to test the extended model. The results show that, similar to water in a two-fluid (air-water) system, NAPL retention curves in a three-fluid (air-NAPL-water) system were independent of flow direction but dependent on soil heterogeneity, while the connectivity-tortuosity coefficients are functions of both soil heterogeneity and anisotropy. The extended TCT model accurately describes unsaturated hydraulic functions of anisotropic soils and can be combined into commonly used relative permeability functions for use in multifluid flow and transport numerical simulations.

  8. Temperature-Dependent Thermal Conductivity of High Strength Lightweight Raw Perlite Aggregate Concrete

    NASA Astrophysics Data System (ADS)

    Tandiroglu, Ahmet

    2010-06-01

    Twenty-four types of high strength lightweight concrete have been designed with raw perlite aggregate (PA) from the Erzincan Mollaköy region as new low-temperature insulation material. The effects of the water/cement ratio, the amount of raw PA, and the temperature on high strength lightweight raw perlite aggregate concrete (HSLWPAC) have been investigated. Three empirical equations were derived to correlate the thermal conductivity of HSLWPAC as a function of PA percentage and temperature depending on the water/cement ratio. Experimentally observed thermal conductivities of concrete samples were predicted 92 % of the time for each set of concrete matrices within 97 % accuracy and over the range from 1.457 W · m-1 · K-1 to 1.777 W · m-1 · K-1. The experimental investigation revealed that the usage of raw PA from the Erzincan Mollaköy region in concrete production reduces the concrete unit mass, increases the concrete strength, and furthermore, the thermal conductivity of the concrete has been improved. The proposed empirical correlations of thermal conductivity were considered to be applicable within the range of temperatures 203.15 K ≤ T ≤ 303.15 K in the form of λ = a( PAP b ) + c( T d ).

  9. DNA polymerase β-dependent cell survival independent of XRCC1 expression.

    PubMed

    Horton, Julie K; Gassman, Natalie R; Dunigan, Brittany D; Stefanick, Donna F; Wilson, Samuel H

    2015-02-01

    Base excision repair (BER) is a primary mechanism for repair of base lesions in DNA such as those formed by exposure to the DNA methylating agent methyl methanesulfonate (MMS). Both DNA polymerase β (pol β)- and XRCC1-deficient mouse fibroblasts are hypersensitive to MMS. This is linked to a repair deficiency as measured by accumulation of strand breaks and poly(ADP-ribose) (PAR). The interaction between pol β and XRCC1 is important for recruitment of pol β to sites of DNA damage. Endogenous DNA damage can substitute for MMS-induced damage such that BER deficiency as a result of either pol β- or XRCC1-deletion is associated with sensitivity to PARP inhibitors. Pol β shRNA was used to knock down pol β in Xrcc1(+/+) and Xrcc1(-/-) mouse fibroblasts. We determined whether pol β-mediated cellular resistance to MMS and PARP inhibitors resulted entirely from coordination with XRCC1 within the same BER sub-pathway. We find evidence for pol β-dependent cell survival independent of XRCC1 expression for both types of agents. The results suggest a role for pol β-dependent, XRCC1-independent repair. PAR immunofluorescence data are consistent with the hypothesis of a decrease in repair in both pol β knock down cell variants. PMID:25541391

  10. Highly thymine-dependent formation of fluorescent copper nanoparticles templated by ss-DNA

    NASA Astrophysics Data System (ADS)

    Liu, Guiying; Shao, Yong; Peng, Jian; Dai, Wei; Liu, Lingling; Xu, Shujuan; Wu, Fei; Wu, Xiaohua

    2013-08-01

    Double-stranded DNAs (ds-DNAs) have been identified as efficient templates favoring the formation of fluorescent copper nanoparticles (Cu NPs). Herein, we have tried to synthesize fluorescent Cu NPs using single-stranded DNAs (ss-DNAs) as templates and to identify the critical DNA sequences. By comparing the results using homopolymer DNAs, hairpin DNAs, and pristine ss-DNAs as templates, we found that DNA thymine base plays a dominant role in producing red-emissive fluorescent Cu NPs on ss-DNA templates. The thymine-dependent growth of the fluorescent Cu NPs is confirmed by Hg2+ mediated T-T base pair in comparison with the other non-specific metal ions, which could be developed into a practical sensor for turn-on fluorescence detection of Hg2+ with a high selectivity. The mechanism is briefly discussed according the DNA sequence-dependent formation of fluorescent Cu NPs. This work demonstrates the sequence role in producing fluorescent Cu NPs that could serve as promising fluorescent nanoprobes in biosensing and DNA-hosted Cu nanomaterials.

  11. DNA polymerase β-dependent cell survival independent of XRCC1 expression

    PubMed Central

    Horton, Julie K.; Gassman, Natalie R.; Dunigan, Brittany B.; Stefanick, Donna F.; Wilson, Samuel H.

    2014-01-01

    Base excision repair (BER) is a primary mechanism for repair of base lesions in DNA such as those formed by exposure to the DNA methylating agent methyl methanesulfonate (MMS). Both DNA polymerase β (pol β)- and XRCC1-deficient mouse fibroblasts are hypersensitive to MMS. This is linked to a repair deficiency as measured by accumulation of strand breaks and poly(ADP-ribose) (PAR). The interaction between pol β and XRCC1 is important for recruitment of pol β to sites of DNA damage. Endogenous DNA damage can substitute for MMS-induced damage such that BER deficiency as a result of either pol β- or XRCC1-deletion is associated with sensitivity to PARP inhibitors. Pol β shRNA was used to knock down pol β in Xrcc1+/+ and Xrcc1−/− mouse fibroblasts. We determined whether pol β-mediated cellular resistance to MMS and PARP inhibitors resulted entirely from coordination with XRCC1 within the same BER sub-pathway. We find evidence for pol β- dependent cell survival independent of XRCC1 expression for both types of agents. The results suggest a role for pol β-dependent, XRCC1-independent repair. PAR immunofluorescence data are consistent with the hypothesis of a decrease in repair in both pol β knock down cell variants. PMID:25541391

  12. Disparate Strain Dependent Thermal Conductivity of Two-dimensional Penta-Structures.

    PubMed

    Liu, Huake; Qin, Guangzhao; Lin, Yuan; Hu, Ming

    2016-06-01

    Two-dimensional (2D) carbon allotrope called penta-graphene was recently proposed from first-principles calculations and various similar penta-structures emerged. Despite significant effort having been dedicated to electronic structures and mechanical properties, little research has been focused on thermal transport in penta-structures. Motivated by this, we performed a comparative study of thermal transport properties of three representative pentagonal structures, namely penta-graphene, penta-SiC2, and penta-SiN2, by solving the phonon Boltzmann transport equation with interatomic force constants extracted from first-principles calculations. Unexpectedly, the thermal conductivity of the three penta-structures exhibits diverse strain dependence, despite their very similar geometry structures. While the thermal conductivity of penta-graphene exhibits standard monotonic reduction by stretching, penta-SiC2 possesses an unusual nonmonotonic up-and-down behavior. More interestingly, the thermal conductivity of penta-SiN2 has 1 order of magnitude enhancement due to the strain induced buckled to planar structure transition. The mechanism governing the diverse strain dependence is identified as the competition between the change of phonon group velocity and phonon lifetime of acoustic phonon modes with combined effect from the unique structure transition for penta-SiN2. The disparate thermal transport behavior is further correlated to the fundamentally different bonding nature in the atomic structures with solid evidence from the distribution of deformation charge density and more in-depth molecular orbital analysis. The reported giant and robust tunability of thermal conductivity may inspire intensive research on other derivatives of penta-structures as potential materials for emerging nanoelectronic devices. The fundamental physics understood from this study also solidifies the strategy to engineer thermal transport properties of broad 2D materials by simple mechanical

  13. pH-dependence of conduction type in cuprous oxide synthesized from solution

    NASA Astrophysics Data System (ADS)

    Wang, Weichao; Wu, Dangxin; Zhang, Qiming; Wang, Longcheng; Tao, Meng

    2010-06-01

    The formation of native point defects in cuprous oxide, Cu2O, synthesized from solution has been studied by first-principles calculations. Although p-type conduction is obtained in Cu2O synthesized from vacuum regardless of copper-rich or oxygen-rich conditions, intrinsically n-type Cu2O without doping can be grown in a strong acidic environment from solution. Our calculations show that both n-type and p-type Cu2O can be obtained depending on the solution pH value, which are in good agreement with our experimental results.

  14. Delineating Species with DNA Barcodes: A Case of Taxon Dependent Method Performance in Moths

    PubMed Central

    Kekkonen, Mari; Mutanen, Marko; Kaila, Lauri; Nieminen, Marko; Hebert, Paul D. N.

    2015-01-01

    The accelerating loss of biodiversity has created a need for more effective ways to discover species. Novel algorithmic approaches for analyzing sequence data combined with rapidly expanding DNA barcode libraries provide a potential solution. While several analytical methods are available for the delineation of operational taxonomic units (OTUs), few studies have compared their performance. This study compares the performance of one morphology-based and four DNA-based (BIN, parsimony networks, ABGD, GMYC) methods on two groups of gelechioid moths. It examines 92 species of Finnish Gelechiinae and 103 species of Australian Elachistinae which were delineated by traditional taxonomy. The results reveal a striking difference in performance between the two taxa with all four DNA-based methods. OTU counts in the Elachistinae showed a wider range and a relatively low (ca. 65%) OTU match with reference species while OTU counts were more congruent and performance was higher (ca. 90%) in the Gelechiinae. Performance rose when only monophyletic species were compared, but the taxon-dependence remained. None of the DNA-based methods produced a correct match with non-monophyletic species, but singletons were handled well. A simulated test of morphospecies-grouping performed very poorly in revealing taxon diversity in these small, dull-colored moths. Despite the strong performance of analyses based on DNA barcodes, species delineated using single-locus mtDNA data are best viewed as OTUs that require validation by subsequent integrative taxonomic work. PMID:25849083

  15. Sequence-dependent dynamics of duplex DNA: the applicability of a dinucleotide model.

    PubMed Central

    Okonogi, T M; Alley, S C; Reese, A W; Hopkins, P B; Robinson, B H

    2002-01-01

    The short-time (submicrosecond) bending dynamics of duplex DNA were measured to determine the effect of sequence on dynamics. All measurements were obtained from a single site on duplex DNA, using a single, site-specific modified base containing a rigidly tethered, electron paramagnetic resonance active spin probe. The observed dynamics are interpreted in terms of single-step sequence-dependent bending force constants, determined from the mean squared amplitude of bending relative to the end-to-end vector using the modified weakly bending rod model. The bending dynamics at a single site are a function of the sequence of the nucleotides constituting the duplex DNA. We developed and examined several dinucleotide-based models for flexibility. The models indicate that the dominant feature of the dynamics is best explained in terms of purine- and pyrimidine-type steps, although distinction is made among all 10 unique steps: It was found that purine-purine steps (which are the same as pyrimidine-pyrimidine steps) were near average in flexibility, but the pyrimidine-purine steps (5' to 3') were nearly twice as flexible, whereas purine-pyrimidine steps were more than half as flexible as average DNA. Therefore, the range of stepwise flexibility is approximately fourfold and is characterized by both the type of base pair step (pyrimidine/purine combination) and the identity of the bases within the pair (G, A, T, or C). All of the four models considered here underscore the complexity of the dependence of dynamics on DNA sequence with certain sequences not satisfactorily explainable in terms of any dinucleotide model. These findings provide a quantitative basis for interpreting the dynamics and kinetics of DNA-sequence-dependent biological processes, including protein recognition and chromatin packaging. PMID:12496111

  16. Unusual sequence length-dependent gold nanoparticles aggregation of the ssDNA sticky end and its application for enzyme-free and signal amplified colorimetric DNA detection

    PubMed Central

    He, Hongfei; Dai, Jianyuan; Duan, Zhijuan; Zheng, Baozhan; Meng, Yan; Guo, Yong; Dan Xiao

    2016-01-01

    It is known that the adsorption of short single-stranded DNA (ssDNA) on unmodified gold nanoparticles (AuNPs) is much faster than that for long ssDNA, and thus leads to length-dependent AuNPs aggregation after addition of salt, the color of the solutions sequentially changed from red to blue in accordance with the increase of ssDNA length. However, we found herein that the ssDNA sticky end of hairpin DNA exhibited a completely different adsorption behavior compared to ssDNA, an inverse blue-to-red color variation was observed in the colloid solution with the increase of sticky end length when the length is within a certain range. This unusual sequence length-dependent AuNPs aggregation might be ascribed to the effect of the stem of hairpin DNA. On the basis of this unique phenomenon and catalytic hairpin assembly (CHA) based signal amplification, a novel AuNPs-based colorimetric DNA assay with picomolar sensitivity and specificity was developed. This unusual sequence length-dependent AuNPs aggregation of the ssDNA sticky end introduces a new direction for the AuNPs-based colorimetric assays. PMID:27477392

  17. Unusual sequence length-dependent gold nanoparticles aggregation of the ssDNA sticky end and its application for enzyme-free and signal amplified colorimetric DNA detection

    NASA Astrophysics Data System (ADS)

    He, Hongfei; Dai, Jianyuan; Duan, Zhijuan; Zheng, Baozhan; Meng, Yan; Guo, Yong; Dan Xiao

    2016-08-01

    It is known that the adsorption of short single-stranded DNA (ssDNA) on unmodified gold nanoparticles (AuNPs) is much faster than that for long ssDNA, and thus leads to length-dependent AuNPs aggregation after addition of salt, the color of the solutions sequentially changed from red to blue in accordance with the increase of ssDNA length. However, we found herein that the ssDNA sticky end of hairpin DNA exhibited a completely different adsorption behavior compared to ssDNA, an inverse blue-to-red color variation was observed in the colloid solution with the increase of sticky end length when the length is within a certain range. This unusual sequence length-dependent AuNPs aggregation might be ascribed to the effect of the stem of hairpin DNA. On the basis of this unique phenomenon and catalytic hairpin assembly (CHA) based signal amplification, a novel AuNPs-based colorimetric DNA assay with picomolar sensitivity and specificity was developed. This unusual sequence length-dependent AuNPs aggregation of the ssDNA sticky end introduces a new direction for the AuNPs-based colorimetric assays.

  18. ATP-dependent partitioning of the DNA template into supercoiled domains by Escherichia coli UvrAB

    SciTech Connect

    Koo, Hyeon-Sook; Liu, L.F.; Claassen, L.; Grossman, L. )

    1991-02-15

    The helicase action of the Escherichia coli UvrAB complex on a covalently closed circular DNA template was monitored using bacterial DNA topoisomerase I, which specifically removes negative supercoils. In the presence of E. coli DNA topoisomerase I and ATP, the UvrAB complex gradually introduced positive supercoils into the input relaxed plasmid DNA template. Positive supercoils were not produced when E. coli DNA topoisomerase I was replaced by eukaryotic DNA topoisomerase I or when both E. coli and eukaryotic DNA topoisomerases I were added simultaneously. These results suggest that like other DNA helix-tracking processes, the ATP-dependent action of the UvrAM complex on duplex DNA simultaneously generates both positive and negative supercoils, which are not constrained by protein binding but are torsionally strained. The supercoiling activity of UvrAB on UV-damaged DNA was also studied using UV-damaged plasmid DNA and a mutant UvrA protein that lacks the 40 C-terminal amino acids and is defective in preferential binding to UV-damaged DNA. UvrAB was found to preferentially supercoil the UV-damaged DNA template, whereas the mutant protein supercoiled UV-damaged and undamaged DNA with equal efficiency. The authors results therefore suggest that the DNA helix-tracking activity of UvrAB may be involved in searching and/or prepriming the damaged DNA for UvrC incision. A possible role of supercoiled domains in the incision process is discussed.

  19. Synthesis of DNA templated trifunctional electrically conducting, optical, and magnetic nanochain of Nicore-Aushell for biodevice

    NASA Astrophysics Data System (ADS)

    Mandal, Madhuri; Mandal, Kalyan

    2009-07-01

    Synthesis of trifunctional, e.g., electrically conducting, optical, and magnetic nanochains of Nicore-Aushell, has been discussed here. Properties of the materials were investigated from the view of its application in bionanodevice. Our investigation indicates that such material attached to biomolecule "DNA chain" and having three main properties in one material will have great potentiality in medical instrumentation and biocomputer device.

  20. Hydroxyl-radical-dependent DNA damage by ambient particulate matter from contrasting sampling locations

    SciTech Connect

    Shi Tingming; Duffin, Rodger; Borm, Paul J.A.; Li Hui; Weishaupt, Christel; Schins, Roel P.F. . E-mail: roel.schins@uni-duesseldorf.de

    2006-05-15

    Exposure to ambient particulate matter (PM) has been reported to be associated with increased respiratory, cardiovascular, and malignant lung disease. Previously we have shown that PM can induce oxidative DNA damage in A549 human lung epithelial cells. The aims of the present study were to investigate the variability of the DNA-damaging properties of PM sampled at different locations and times and to relate the observed effects to the hydroxyl-radical ({center_dot}OH)-generating activities of these samples. Weekly samples of coarse (10-2.5 {mu}m) and fine (<2.5 {mu}m) PM from four sites (Nordrheim Westfalen, Germany) were analyzed for hydrogen-peroxide-dependent {center_dot}OH formation using electron paramagnetic resonance and formation of 8-hydroxydeoxyguanosine (8-OHdG) in calf thymus DNA using an immuno-dot-blot assay. DNA strand breakage by fine PM in A549 human lung epithelial cells was quantified using the alkaline comet assay. Both PM size distribution fractions elicited {center_dot}OH generation and 8-OHdG formations in calf thymus DNA. Significantly higher {center_dot}OH generation was observed for PM sampled at urban/industrial locations and for coarse PM. Samples of fine PM also caused DNA strand breakage in A549 cells and this damage could be prevented using the hydroxyl-radical scavengers 5,5-dimethyl-1-pyrroline-N-oxide and dimethyl sulfoxide. The observed DNA strand breakage appeared to correlate with the hydroxyl-radical-generating capacities of the PM samples but with different profiles for rural versus urban/industrial samples. In conclusion, when considered at equal mass, {center_dot}OH formation of PM shows considerable variability with regard to the sampling location and time and is correlated with its ability to cause DNA damage.

  1. The Wavelength Dependence of Some Effects of Ultraviolet Radiation on In Vitro DNA of Phage α

    PubMed Central

    Cremonese, M.

    1968-01-01

    The wavelength dependence of some of the effects of ultraviolet radiation on the physicochemical properties of DNA of phage α irradiated in vitro are discussed. An analytical ultracentrifuge and a spectrophotometer were used to study (a) the breaking of individual polynucleotide strands; (b) the local denaturation; (c) the presence of a fraction of molecules resistant to denaturation; and (d) the increase in the buoyant density of irradiated DNA. All the curves show a slight variation of the radiation efficiency in the range 2600-2800 A, and a well defined peak at λ = 2880 A. PMID:5639933

  2. Cellular transcription factors enhance herpes simplex virus type 1 oriS-dependent DNA replication.

    PubMed

    Nguyen-Huynh, A T; Schaffer, P A

    1998-05-01

    The herpes simplex virus type 1 (HSV-1) origin of DNA replication, oriS, contains three binding sites for the viral origin binding protein (OBP) flanked by transcriptional regulatory elements of the immediate-early genes encoding ICP4 and ICP22/47. To assess the role of flanking sequences in oriS function, plasmids containing oriS and either wild-type or mutant flanking sequences were tested in transient DNA replication assays. Although the ICP4 and ICP22/47 regulatory regions were shown to enhance oriS function, most individual elements in these regions, including the VP16-responsive TAATGARAT elements, were found to be dispensable for oriS function. In contrast, two oriS core-adjacent regulatory (Oscar) elements, OscarL and OscarR, at the base of the oriS palindrome were shown to enhance oriS function significantly and additively. Specifically, mutational disruption of either element reduced oriS-dependent DNA replication by 60 to 70%, and disruption of both elements reduced replication by 90%. The properties of protein-DNA complexes formed in gel mobility shift assays using uninfected and HSV-1-infected Vero cell nuclear extracts demonstrated that both OscarL and OscarR are binding sites for cellular proteins. Whereas OscarR does not correspond to the consensus binding site of any known transcription factor, OscarL contains a consensus binding site for the transcription factor Sp1. Gel mobility shift and supershift experiments using antibodies directed against members of the Sp1 family of transcription factors demonstrated the presence of Sp1 and Sp3, but not Sp2 or Sp4, in the protein-DNA complexes formed at OscarL. The abilities of OscarL and OscarR to bind their respective cellular proteins correlated directly with the efficiency of oriS-dependent DNA replication. Cooperative interactions between the Oscar-binding factors and proteins binding to adjacent OBP binding sites were not observed. Notably, Oscar element mutations that impaired oriS-dependent DNA

  3. Thermal conductivity of monolayer molybdenum disulfide obtained from temperature-dependent Raman spectroscopy.

    PubMed

    Yan, Rusen; Simpson, Jeffrey R; Bertolazzi, Simone; Brivio, Jacopo; Watson, Michael; Wu, Xufei; Kis, Andras; Luo, Tengfei; Hight Walker, Angela R; Xing, Huili Grace

    2014-01-28

    Atomically thin molybdenum disulfide (MoS2) offers potential for advanced devices and an alternative to graphene due to its unique electronic and optical properties. The temperature-dependent Raman spectra of exfoliated, monolayer MoS2 in the range of 100-320 K are reported and analyzed. The linear temperature coefficients of the in-plane E2g 1 and the out-of-plane A1g modes for both suspended and substrate-supported monolayer MoS2 are measured. These data, when combined with the first-order coefficients from laser power-dependent studies, enable the thermal conductivity to be extracted. The resulting thermal conductivity κ = (34.5(4) W/mK at room temperature agrees well with the first principles lattice dynamics simulations. However, this value is significantly lower than that of graphene. The results from this work provide important input for the design of MoS2-based devices where thermal management is critical. PMID:24377295

  4. Dependence of Hydraulic Conductivity on Test Scale: Artifact or Something More?

    NASA Astrophysics Data System (ADS)

    Butler, J. J., Jr.

    2014-12-01

    Over the years, there have been frequent reports of a dependence of hydraulic conductivity (K) estimates on test volume (scale). This dependence is commonly demonstrated using results from laboratory permeameter tests and from slug and pumping tests. Typically, K estimates from pumping tests are reported to be considerably larger than those from slug tests, which, in turn, are considerably larger than those from permeameter tests. Despite the large body of evidence, a key question remains unresolved - is this relationship produced by methodological differences or a natural underlying scale dependence in K? The most effective means to resolve this question is to use a single technique that can be configured to span orders of magnitude in test scale. The constant-rate pumping test is just such a technique. In the first few minutes to tens of minutes of pumping, the affected volume is relatively small. In contrast, after days of pumping, this volume can be orders of magnitude larger. If there is an underlying scale dependence, it should be revealed by K estimates determined from different durations of pumping. We have been investigating this issue using pumping tests in unconsolidated aquifers in central and western Kansas. In western Kansas, irrigation wells are pumped nearly continuously for the entire growing season. If nearby observation wells are available, we can use this near-continuous pumping as a long-duration, albeit imperfectly controlled, pumping test to increase the scale of the investigation. An initial assessment of these formal and ad-hoc pumping tests has found no evidence of a scale dependence in K; these tests are typically characterized by homogeneous aquifer behavior at small to moderate times of pumping after which boundary effects become dominant. Thus, if there is an underlying scale dependence, it is below the scale of these observations, which would have to be considered rather serendipitous. We can assess the relationship at smaller scales

  5. Voltage-dependent flickery block of an open cystic fibrosis transmembrane conductance regulator (CFTR) channel pore.

    PubMed

    Zhou, Z; Hu, S; Hwang, T C

    2001-04-15

    1. Fast flickery block of the cystic fibrosis transmembrane conductance regulator (CFTR) was studied with cell-attached and whole-cell patch-clamp recordings from mouse NIH3T3 cells stably expressing a mutant CFTR channel, K1250A-CFTR. This mutant CFTR channel, once open, can stay open for minutes. Within a prolonged opening, the kinetics of fast flickery closures can be readily quantified. 2. Flickering block of K1250A-CFTR channels was voltage dependent since the open probability within an opening burst decreased as the membrane was hyperpolarized. 3. Mean open time (tau(o)) and mean closed time (tau(c)), obtained from single-channel kinetic analysis, were corrected for missed events. Our data show that corrected tau(c) was voltage dependent while corrected tau(o) exhibited little voltage dependence. Results from whole-cell current relaxation upon voltage jump further indicate that tau(c) at a membrane potential of -100 mV was at least 10-fold longer than that at +100 mV. 4. tau(c), but not tau(o), was sensitive to external permeant anions. After complete replacement of external Cl(-) with impermeant anions, tau(c) showed little voltage dependence and approximated a value observed under strong hyperpolarization in the presence of high external permeant anions. These results suggest that the resident time of the blocker is prolonged by conditions (i.e. hyperpolarization or the absence of external permeant anions) that deplete Cl(-) in the CFTR pore. 5. Results from macroscopic current noise analysis of both wild-type CFTR and K1250A-CFTR channels further confirm the voltage dependence and Cl(-) sensitivity of the fast flickery block observed with single-channel analysis. 6. We conclude that the voltage dependence of the flickery block in CFTR is mainly due to the voltage-dependent occupancy of an anion-binding site in the channel pore by trans-anions. The blocker acquires a voltage-dependent off rate through an electrostatic interaction with Cl(-) in the pore

  6. Voltage-dependent flickery block of an open cystic fibrosis transmembrane conductance regulator (CFTR) channel pore

    PubMed Central

    Zhou, Zhen; Hu, Shenghui; Hwang, Tzyh-Chang

    2001-01-01

    Fast flickery block of the cystic fibrosis transmembrane conductance regulator (CFTR) was studied with cell-attached and whole-cell patch-clamp recordings from mouse NIH3T3 cells stably expressing a mutant CFTR channel, K1250A-CFTR. This mutant CFTR channel, once open, can stay open for minutes. Within a prolonged opening, the kinetics of fast flickery closures can be readily quantified. Flickering block of K1250A-CFTR channels was voltage dependent since the open probability within an opening burst decreased as the membrane was hyperpolarized. Mean open time (τo) and mean closed time (τc), obtained from single-channel kinetic analysis, were corrected for missed events. Our data show that corrected τc was voltage dependent while corrected τo exhibited little voltage dependence. Results from whole-cell current relaxation upon voltage jump further indicate that τc at a membrane potential of -100 mV was at least 10-fold longer than that at +100 mV. τc, but not τo, was sensitive to external permeant anions. After complete replacement of external Cl− with impermeant anions, τc showed little voltage dependence and approximated a value observed under strong hyperpolarization in the presence of high external permeant anions. These results suggest that the resident time of the blocker is prolonged by conditions (i.e. hyperpolarization or the absence of external permeant anions) that deplete Cl− in the CFTR pore. Results from macroscopic current noise analysis of both wild-type CFTR and K1250A-CFTR channels further confirm the voltage dependence and Cl− sensitivity of the fast flickery block observed with single-channel analysis. We conclude that the voltage dependence of the flickery block in CFTR is mainly due to the voltage-dependent occupancy of an anion-binding site in the channel pore by trans-anions. The blocker acquires a voltage-dependent off rate through an electrostatic interaction with Cl− in the pore. PMID:11306662

  7. Manipulating graphene's lattice to create pseudovector potentials, discover anomalous friction, and measure strain dependent thermal conductivity

    NASA Astrophysics Data System (ADS)

    Kitt, Alexander Luke

    Graphene is a single atomic sheet of graphite that exhibits a diverse range of unique properties. The electrons in intrinsic graphene behave like relativistic Dirac fermions; graphene has a record high Young's modulus but extremely low bending rigidity; and suspended graphene exhibits very high thermal conductivity. These properties are made more intriguing because with a thickness of only a single atomic layer, graphene is both especially affected by its environment and readily manipulated. In this dissertation the interaction between graphene and its environment as well as the exciting new physics realized by manipulating graphene's lattice are investigated. Lattice manipulations in the form of strain cause alterations in graphene's electrical dispersion mathematically analogous to the vector potential associated with a magnetic field. We complete the standard description of the strain-induced vector potential by explicitly including the lattice deformations and find new, leading order terms. Additionally, a strain engineered device with large, localized, plasmonically enhanced pseudomagnetic fields is proposed to couple light to pseudomagnetic fields. Accurate strain engineering requires a complete understanding of the interactions between a two dimensional material and its environment, particularly the adhesion and friction between graphene and its supporting substrate. We measure the load dependent sliding friction between mono-, bi-, and trilayer graphene and the commonly used silicon dioxide substrate by analyzing Raman spectra of circular, graphene sealed microchambers under variable external pressure. We find that the sliding friction for trilayer graphene behaves normally, scaling with the applied load, whereas the friction for monolayer and bilayer graphene is anomalous, scaling with the inverse of the strain in the graphene. Both strain and graphene's environment are expected to affect the quadratically dispersed out of plane acoustic phonon. Although

  8. Carrier interactions and porosity initiated reversal of temperature dependence of thermal conduction in nanoscale tin films

    SciTech Connect

    Kaul, Pankaj B.; Prakash, Vikas

    2014-01-14

    Recently, tin has been identified as an attractive electrode material for energy storage/conversion technologies. Tin thin films have also been utilized as an important constituent of thermal interface materials in thermal management applications. In this regards, in the present paper, we investigate thermal conductivity of two nanoscale tin films, (i) with thickness 500 ± 50 nm and 0.45% porosity and (ii) with thickness 100 ± 20 nm and 12.21% porosity. Thermal transport in these films is characterized over the temperature range from 40 K–310 K, using a three-omega method for multilayer configurations. The experimental results are compared with analytical predictions obtained by considering both phonon and electron contributions to heat conduction as described by existing frequency-dependent phenomenological models and BvK dispersion for phonons. The thermal conductivity of the thicker tin film (500 nm) is measured to be 46.2 W/m-K at 300 K and is observed to increase with reduced temperatures; the mechanisms for thermal transport are understood to be governed by strong phonon-electron interactions in addition to the normal phonon-phonon interactions within the temperature range 160 K–300 K. In the case of the tin thin film with 100 nm thickness, porosity and electron-boundary scattering supersede carrier interactions, and a reversal in the thermal conductivity trend with reduced temperatures is observed; the thermal conductivity falls to 1.83 W/m-K at 40 K from its room temperature value of 36.1 W/m-K. In order to interpret the experimental results, we utilize the existing analytical models that account for contributions of electron-boundary scattering using the Mayadas-Shatzkes and Fuchs-Sondheimer models for the thin and thick films, respectively. Moreover, the effects of porosity on carrier transport are included using a previous treatment based on phonon radiative transport involving frequency-dependent mean free paths

  9. Drude-type conductivity of charged sphere colloidal crystals: density and temperature dependence.

    PubMed

    Medebach, Martin; Jordán, Raquel Chuliá; Reiber, Holger; Schöpe, Hans-Joachim; Biehl, Ralf; Evers, Martin; Hessinger, Dirk; Olah, Julianna; Palberg, Thomas; Schönberger, Ernest; Wette, Patrick

    2005-09-01

    We report on extensive measurements in the low-frequency limit of the ac conductivity of colloidal fluids and crystals formed from charged colloidal spheres suspended in de-ionized water. Temperature was varied in a range of 5 degrees C < Theta < 35 degrees C and the particle number density n between 0.2 and 25 microm(-3) for the larger, respectively, 2.75 and 210 microm(-3) for the smaller of two investigated species. At fixed Theta the conductivity increased linearly with increasing n without any significant change at the fluid-solid phase boundary. At fixed n it increased with increasing Theta and the increase was more pronounced for larger n. Lacking a rigorous electrohydrodynamic treatment for counterion-dominated systems we describe our data with a simple model relating to Drude's theory of metal conductivity. The key parameter is an effectively transported particle charge or valence Z(*). All temperature dependencies other than that of Z(*) were taken from literature. Within experimental resolution Z(*) was found to be independent of n irrespective of the suspension structure. Interestingly, Z(*) decreases with temperature in near quantitative agreement with numerical calculations. PMID:16178620

  10. Substrate-dependent thermal conductivity of aluminum nitride thin-films processed at low temperature

    SciTech Connect

    Belkerk, B. E.; Bensalem, S.; Soussou, A.; Carette, M.; Djouadi, M. A.; Scudeller, Y.; Al Brithen, H.

    2014-12-01

    In this paper, we report on investigation concerning the substrate-dependent thermal conductivity (k) of Aluminum Nitride (AlN) thin-films processed at low temperature by reactive magnetron sputtering. The thermal conductivity of AlN films grown at low temperature (<200 °C) on single-crystal silicon (Si) and amorphous silicon nitride (SiN) with thicknesses ranging from 100 nm to 4000 nm was measured with the transient hot-strip technique. The k values for AlN films on SiN were found significantly lower than those on Silicon consistently with their microstructures revealed by X-ray diffraction, high resolution scanning electron microscopy, and transmission electron microscopy. The change in k was due to the thermal boundary resistance found to be equal to 10 × 10{sup −9} Km{sup 2}W{sup −1} on SiN against 3.5 × 10{sup −9} Km{sup 2}W{sup −1} on Si. However, the intrinsic thermal conductivity was determined with a value as high as 200 Wm{sup −1}K{sup −1} whatever the substrate.

  11. Simultaneous detection of DNA from 10 food allergens by ligation-dependent probe amplification.

    PubMed

    Ehlert, Alexandra; Demmel, Anja; Hupfer, Christine; Busch, Ulrich; Engel, Karl-Heinz

    2009-04-01

    The simultaneous detection of DNA from different allergenic food ingredients by a ligation-dependent probe amplification (LPA) system is described. The approach allows detection of several targets in a one-tube assay. Synthetic oligonucleotides were designed to detect DNA from peanuts, cashews, pecans, pistachios, hazelnuts, sesame seeds, macadamia nuts, almonds, walnuts and brazil nuts. The specificity of the system was tested with DNA from more than 50 plant and animal species. The sensitivity of the method was suitable to detect allergenic ingredients in the low mg kg(-1) range. The limit of detection (LOD) for single allergens in different food matrices was 5 mg kg(-1). The novel analytical strategy represents a useful tool for the surveillance of established legislation on food allergens within the European Union. PMID:19680915

  12. Cy3-DNA Stacking Interactions Strongly Depend on the Identity of the Terminal Basepair

    PubMed Central

    Spiriti, Justin; Binder, Jennifer K.; Levitus, Marcia; van der Vaart, Arjan

    2011-01-01

    We characterized the effect of the first basepair on the conformational dynamics of the fluorescent dye Cy3 attached to the 5′ end of double-stranded DNA using Gaussian-mixture adaptive umbrella sampling simulations. In the simulations, the sampling of all five dihedral angles along the linker was enhanced, so that both stacked and unstacked states were sampled. The affinity of Cy3 for a T·A basepair (with the dye attached to T) was found to be significantly less than for the other basepairs. This was verified experimentally by measuring the activation energies for cis-trans isomerization of the dye. The simulation and experimental results indicate the existence of partially unstacked conformations amenable to photoisomerization. The simulations also showed that stacking of Cy3 straightens the DNA while stabilizing the first basepair. Our findings indicate that fluorescence is modulated by Cy3-DNA interactions in a sequence-dependent manner. PMID:21320450

  13. Identification of the vaccinia virus gene encoding nucleoside triphosphate phosphohydrolase I, a DNA-dependent ATPase.

    PubMed Central

    Broyles, S S; Moss, B

    1987-01-01

    Vaccinia virus encapsidates a DNA-dependent ATPase known as nucleoside triphosphate phosphohydrolase I (NPH I). A bacteriophage lambda gt11 expression library of poxvirus DNA was screened with antibodies specific for NPH I. Positive clones were used to probe restriction fragments of vaccinia virus genomic DNA to locate the NPH I gene. The identity of the open reading frame (ORF) was confirmed by placing it downstream of a bacteriophage T7 promoter, transcribing the ORF in vitro, and translating the RNA in a reticulocyte lysate. A polypeptide of the correct molecular weight, which was recognized by anti-NPH I antibody, was synthesized. Inspection of the deduced amino acid sequence of the NPH I ORF revealed consensus ATP-binding sites. Images PMID:2437324

  14. Opposing roles of RNF8/RNF168 and deubiquitinating enzymes in ubiquitination-dependent DNA double-strand break response signaling and DNA-repair pathway choice

    PubMed Central

    Nakada, Shinichiro

    2016-01-01

    The E3 ubiquitin ligases ring finger protein (RNF) 8 and RNF168 transduce the DNA double-strand break (DSB) response (DDR) signal by ubiquitinating DSB sites. The depletion of RNF8 or RNF168 suppresses the accumulation of DNA-repair regulating factors such as 53BP1 and RAP80 at DSB sites, suggesting roles for RNF8- and RNF168-mediated ubiquitination in DSB repair. This mini-review provides a brief overview of the RNF8- and RNF168-dependent DDR-signaling and DNA-repair pathways. The choice of DNA-repair pathway when RNF8- and RNF168-mediated ubiquitination-dependent DDR signaling is negatively regulated by deubiquitinating enzymes (DUBs) is reviewed to clarify how the opposing roles of RNF8/RNF168 and DUBs regulate ubiquitination-dependent DDR signaling and the choice of DNA-repair pathway. PMID:26983989

  15. STING-Dependent Cytosolic DNA Sensing Promotes Radiation-Induced Type I Interferon-Dependent Antitumor Immunity in Immunogenic Tumors.

    PubMed

    Deng, Liufu; Liang, Hua; Xu, Meng; Yang, Xuanming; Burnette, Byron; Arina, Ainhoa; Li, Xiao-Dong; Mauceri, Helena; Beckett, Michael; Darga, Thomas; Huang, Xiaona; Gajewski, Thomas F; Chen, Zhijian J; Fu, Yang-Xin; Weichselbaum, Ralph R

    2014-11-20

    Ionizing radiation-mediated tumor regression depends on type I interferon (IFN) and the adaptive immune response, but several pathways control I IFN induction. Here, we demonstrate that adaptor protein STING, but not MyD88, is required for type I IFN-dependent antitumor effects of radiation. In dendritic cells (DCs), STING was required for IFN-? induction in response to irradiated-tumor cells. The cytosolic DNA sensor cyclic GMP-AMP (cGAMP) synthase (cGAS) mediated sensing of irradiated-tumor cells in DCs. Moreover, STING was essential for radiation-induced adaptive immune responses, which relied on type I IFN signaling on DCs. Exogenous IFN-? treatment rescued the cross-priming by cGAS or STING-deficient DCs. Accordingly, activation of STING by a second messenger cGAMP administration enhanced antitumor immunity induced by radiation. Thus radiation-mediated antitumor immunity in immunogenic tumors requires a functional cytosolic DNA-sensing pathway and suggests that cGAMP treatment might provide a new strategy to improve radiotherapy. PMID:25517616

  16. DNA-programmed modular assembly of cyclic and linear nanoarrays for the synthesis of two-dimensional conducting polymers.

    PubMed

    Chen, Wen; Schuster, Gary B

    2012-01-18

    Nanometer-scale arrays of conducting polymers were prepared on scaffolds of self-assembling DNA modules. A series of DNA oligomers was prepared, each containing six 2,5-bis(2-thienyl)pyrrole (SNS) monomer units linked covalently to N4 atoms of alternating cytosines placed between leading and trailing 12-nucleobase recognition sequences. These DNA modules were encoded so the recognition sequences would uniquely associate through Watson-Crick assembly to form closed-cycle or linear arrays of aligned SNS monomers. The melting behavior and electrophoretic migration of these assemblies showed cooperative formation of multicomponent arrays containing two to five DNA modules (i.e., 12-30 SNS monomers). The treatment of these arrays with horseradish peroxidase and H(2)O(2) resulted in oxidative polymerization of the SNS monomers with concomitant ligation of the DNA modules. The resulting cyclic and linear arrays exhibited chemical and optical properties typical of conducting thiophene-like polymers, with a red-end absorption beyond 1250 nm. AFM images of the cyclic array containing 18 SNS units revealed highly regular 10 nm diameter objects. PMID:22242713

  17. Suppression of TET1-Dependent DNA Demethylation is Essential for KRAS-Mediated Transformation

    PubMed Central

    Wu, Bo-Kuan

    2014-01-01

    Summary Hypermethylation-mediated tumor suppressor gene (TSG) silencing is a central epigenetic alteration in RAS-dependent tumorigenesis. Ten-eleven translocation (TET) enzymes can depress DNA methylation by hydroxylation of 5-methylcytosine (5mC) bases to 5-hydroxymethylcytosine (5hmC). Here we report that suppression of TET1 is required for KRAS-induced DNA hypermethylation and cellular transformation. In distinct non-malignant cell lines, oncogenic KRAS promotes transformation by inhibiting TET1 expression via the ERK signaling pathway. This reduces chromatin occupancy of TET1 at TSG promoters, lowers levels of 5hmC, and increases levels of 5mC and 5mC-dependent transcriptional silencing. Restoration of TET1 expression by ERK pathway inhibition or ectopic TET1 reintroduction in KRAS-transformed cells reactivates TSGs and inhibits colony formation. KRAS knockdown increases TET1 expression and diminishes colony-forming ability, while KRAS/TET1 double knockdown bypasses the KRAS dependence of KRAS-addicted cancer cells. Thus, suppression of TET1-dependent DNA demethylation is critical for KRAS-mediated transformation. PMID:25466250

  18. Modeling the Time-dependent Changes in Electrical Conductivity of Basaltic Melts With Redox State

    NASA Astrophysics Data System (ADS)

    Pommier, A.; Gaillard, F.; Pichavant, M.

    2008-12-01

    The electrical conductivity σ is an efficient probe of mass transfer processes within silicate melts and magmas. Little attention has been given to the influence of redox state (fO2) on the melts conductivity. We present an experimental setup allowing electrical conductivity measurements for basaltic melts under variable fO2. We demonstrate a significant dependence of σ with fO2, allowing to characterize in situ the mechanisms and kinetics of redox changes in the melt. Experiments were conducted on basalts from Pu'u 'O'o, Hawaii, and Mt.Vesuvius, Italy. Measurements were performed cylindrical glass samples (OD: 6mm, ID: 1mm, L: 8mm) using an impedance spectrometer. Experiments were conducted in a 1atm vertical furnace, from 1200°C to 1400°C. Variable gas atmosphere (air, CO2 or CO-CO2 gas mixtures) were used, imposing ΔNNO from -1 to +7. Electrical conductivities were determined for the two melts at constant fO2, different T (constant fO2) and constant T, different fO2 (variable fO2) obtained by changing the gas composition. Isothermal reduction and oxidation cycles were performed. Glasses quenched from different T and fO2 conditions were analyzed by electron microprobe, the FeO concentration was determined by wet chemistry. In constant fO2 experiments, a small but detectable effect of fO2 on σ is evidenced. At 1300°C, the difference in the Kilauea sample conductivity between reduced (ΔNNO=-1) and oxidized (ΔNNO=+7) fO2 is <1(ohm.m)-1, the sample being more conductive when reduced. The temperature dependence of σ was fitted using Arrhenian equations, the activation energy Ea being 100kJ/mol. Sodium was identified as the main charge carrier in the melts. The fO2-effect on σ can thus be attributed to the influence of the Fe2+/Fe3+ ratio on sodium mobility. The fO2-dependence of σ was included in the model of Pommier et al.(2008), allowing the conductivity of natural melts to be calculated as a function of T, P, H2O, and fO2. Variable fO2 experiments

  19. Hippocampal glucocorticoid receptor activation enhances voltage-dependent Ca2+ conductances: relevance to brain aging.

    PubMed Central

    Kerr, D S; Campbell, L W; Thibault, O; Landfield, P W

    1992-01-01

    Glucocorticoids (GCs) activate several biochemical/molecular processes in the hippocampus through two receptor types. In addition, GCs influence cognitive behaviors and hippocampal neural activity and can also increase the rate of aging-dependent cell loss in the hippocampus. However, the ionic mechanisms through which GCs modulate hippocampal neuronal function are not well understood. We report here direct evidence that activation of cytosolic steroid receptors, specifically of the type II GC receptor, can enhance voltage-dependent Ca2+ conductances in brain neurons. Ca2+ current was assessed by current-clamp measures of Ca2+ action potentials and by sharp electrode voltage-clamp analyses of voltage-sensitive currents in cesium-, tetrodotoxin-, and tetraethylammonium-treated CA1 neurons in hippocampal slices. Both Ca2+ action potentials and voltage-activated Ca2+ currents (N- and L-like) were increased by 2-hr exposure to the synthetic GC receptor agonist, RU 28362. This effect of RU 28362 was blocked by coincubation with cycloheximide, indicating that the GC receptor-Ca2+ channel interaction depends on de novo protein synthesis. Dysregulated calcium homeostasis is also viewed as a candidate mechanism in brain aging. Thus, present results are consistent with the hypothesis that excessive GC-receptor activation and resultant increased Ca2+ influx may be two sequential phases of a brain-aging process that results initially in impairment of function and eventually in neuronal loss. PMID:1528857

  20. Dependence of 5-fluorouracil-mediated radiosensitization on DNA-directed effects

    SciTech Connect

    Lawrence, T.S.; Davis, M.A.; Maybaum, J. )

    1994-06-15

    Although 5-fluorouracil (FUra) has been demonstrated to be a radiation sensitizer both in the laboratory and the clinic, it is not known whether radiosensitization results primary from FUra's DNA or RNA-directed effects. The authors studied the radiosensitizing effects of FUra [+-] thymidine (dThd) on HT29 human colon cancer cells, which are relatively sensitive to the DNA-directed action of FUra, in comparison to SW620 and HuTu80 human colon cancer cells, which are relatively resistant to FUra's DNA-directed effects. They hypothesized that if FUra were acting chiefly through DNA dependent mechanisms, HT29 cells would (a) show greater radiosensitization than SW620 and HuTu80 cells under the same conditions of exposure; and (b) demonstrate selective reversal of radiation sensitivity (compared to cytotoxicity) in the presence of FUra + dThd, compared to FUra alone. They found that the enhancement ratio produced by a 24 h exposure to 10 [mu]M FUra was significantly greater in HT29 cells compared to SW620 and HuTu80 cells (enhancement ratios of 2.1 [+-] 0.1; 1.1 [+-] 0.1, and 1.3 [+-] 0.1, respectively). Furthermore, in HT29 cells, dThd blocked FUra-mediated radiosensitization to a greater extent than FUra-mediated cytotoxicity. Thus, the hypotheses were confirmed. These findings support the concept that the manipulation of FUra's DNA-dependent actions, for example, through modulators of thymidylate synthase (TS) activity, may increase radiosensitization in clinical trials in the treatment of gastrointestinal cancers. However, since resistance to the DNA-directed effects of fluoropyrimidines can result from mechanisms unrelated to TS inhibition, additional strategies will be required to potentiate fluoropyrimidine-mediated radiosensitization. 15 refs., 2 figs., 1 tab.

  1. CFTR: Temperature-dependent cysteine reactivity suggests different stable conformers of the conduction pathway

    PubMed Central

    Liu, Xuehong; Dawson, David C.

    2011-01-01

    Cysteine scanning has been widely used to identify pore-lining residues in mammalian ion channels, including the cystic fibrosis transmembrane conductance regulator (CFTR). These studies, however, have been typically conducted at room temperature rather than human body temperature. Reports of substantial effects of temperature on gating and anion conduction in CFTR channels as well as an unexpected pattern of cysteine reactivity in the sixth transmembrane segment (TM6), prompted us to investigate the effect of temperature on the reactivity of cysteines engineered into TM6 of CFTR. We compared reaction rates at temperatures ranging from 22°C to 37°C for cysteines placed on either side of an apparent size-selective, accessibility barrier previously defined by comparing reactivity toward channel-permeant and channel-impermeant, thiol-directed reagents. The results indicate that reactivity of cysteines at three positions extracellular to the position of the accessibility barrier, 334, 336 and 337, is highly temperature dependent, such that at 37°C cysteines at these positions were highly reactive toward MTSES−, whereas at 22°C the reaction rates ranged from two to six-fold slower to undetectable. An activation energy of 157 kJ/mole for the reaction at 337 is consistent with the hypothesis that, at physiological temperature, the extracellular portion of the CFTR pore can adopt conformations that differ significantly from those accessible at room temperature. However, the position of the accessibility barrier defined empirically by applying channel-permeant and channel-impermeant reagents to the extracellular aspect of the pore is not altered. The results illuminate previous scanning results and indicate that assay temperature is a critical variable in studies designed to use chemical modification to test structural models for the CFTR anion conduction pathway. PMID:22014307

  2. Geological dates and molecular rates: fish DNA sheds light on time dependency.

    PubMed

    Burridge, Christopher P; Craw, Dave; Fletcher, David; Waters, Jonathan M

    2008-04-01

    Knowledge of DNA evolution is central to our understanding of biological history, but how fast does DNA change? Previously, pedigree and ancient DNA studies--focusing on evolution in the short term--have yielded molecular rate estimates substantially faster than those based on deeper phylogenies. It has recently been suggested that short-term, elevated molecular rates decay exponentially over 1-2 Myr to long-term, phylogenetic rates, termed "time dependency of molecular rates." This transition has potential to confound molecular inferences of demographic parameters and dating of many important evolutionary events. Here, we employ a novel approach--geologically dated changes in river drainages and isolation of fish populations--to document rates of mitochondrial DNA change over a range of temporal scales. This method utilizes precise spatiotemporal disruptions of linear freshwater systems and hence avoids many of the limitations associated with typical DNA calibration methods involving fossil data or island formation. Studies of freshwater-limited fishes across the South Island of New Zealand have revealed that genetic relationships reflect past, rather than present, drainage connections. Here, we use this link between drainage geology and genetics to calibrate rates of molecular evolution across nine events ranging in age from 0.007 Myr (Holocene) to 5.0 Myr (Pliocene). Molecular rates of change in galaxiid fishes from calibration points younger than 200 kyr were faster than those based on older calibration points. This study provides conclusive evidence of time dependency in molecular rates as it is based on a robust calibration system that was applied to closely related taxa, and analyzed using a consistent and rigorous methodology. The time dependency observed here appears short-lived relative to previous suggestions (1-2 Myr), which has bearing on the accuracy of molecular inferences drawn from processes operating within the Quaternary and mechanisms invoked to

  3. PEGylated Cationic Liposome – DNA Complexation in Brine is Pathway-Dependent

    PubMed Central

    Silva, Bruno F.B.; Majzoub, Ramsey N.; Chan, Chia-Ling; Li, Youli; Olsson, Ulf; Safinya, Cyrus R.

    2013-01-01

    Cationic liposome-DNA (CL-DNA) complexes, are regarded as promising materials for safe and efficient delivery of genes for therapeutical applications. In order to be used in vivo, these complexes may be coated with a hydrophilic polymer (e.g. polyethylene-glycol, PEG) that provides steric stabilization towards adhesion of proteins and removal by the immune system. In this work we study the influence of the initial salt concentration (Cs) – which modulates the electrostatic interaction between oppositely charged vesicles and DNA – on the structure and stability of PEGylated CL-DNA particles. Previous small-angle X-ray scattering has shown that if non-PEGylated or PEGylated CL-DNA lamellar complexes are prepared in water, their structure is well defined with a high number of lipid membrane-DNA layers (larger than 20). Here we show that if these complexes are transferred to saline media (150 mM NaCl or DMEM, both near physiological conditions), this structure remains nearly unchanged. Conversely, if PEGylated complexes are prepared in saline media, their lamellar structure is much looser, with fewer number of layers. This pathway dependent behavior of PEGylated complex formation in brine is modulated by the liposome membrane charge density and the mole fraction of PEG 2000 in the membranes, with the average number of layers decreasing with increasing Cs and in going from 5 mol% to 10 mol% PEG-lipid. Each of these structures (high and low number of layers) is stable with time, suggesting that despite complex formation being thermodynamically favored, the complexation process in PEGylated membranes, which determines the number of layers per particle, is kinetically controlled. In the extreme case (when polymer repulsions from 10 mol% PEG-lipid are maximized and electrostatic attraction between PEGylated CLs and DNA are minimized at low membrane charge density) complex formation is suppressed at high Cs=150 mM. PMID:24060564

  4. A nonlinear dynamic model of DNA with a sequence-dependent stacking term

    PubMed Central

    Alexandrov, Boian S.; Gelev, Vladimir; Monisova, Yevgeniya; Alexandrov, Ludmil B.; Bishop, Alan R.; Rasmussen, Kim Ø.; Usheva, Anny

    2009-01-01

    No simple model exists that accurately describes the melting behavior and breathing dynamics of double-stranded DNA as a function of nucleotide sequence. This is especially true for homogenous and periodic DNA sequences, which exhibit large deviations in melting temperature from predictions made by additive thermodynamic contributions. Currently, no method exists for analysis of the DNA breathing dynamics of repeats and of highly G/C- or A/T-rich regions, even though such sequences are widespread in vertebrate genomes. Here, we extend the nonlinear Peyrard–Bishop–Dauxois (PBD) model of DNA to include a sequence-dependent stacking term, resulting in a model that can accurately describe the melting behavior of homogenous and periodic sequences. We collect melting data for several DNA oligos, and apply Monte Carlo simulations to establish force constants for the 10 dinucleotide steps (CG, CA, GC, AT, AG, AA, AC, TA, GG, TC). The experiments and numerical simulations confirm that the GG/CC dinucleotide stacking is remarkably unstable, compared with the stacking in GC/CG and CG/GC dinucleotide steps. The extended PBD model will facilitate thermodynamic and dynamic simulations of important genomic regions such as CpG islands and disease-related repeats. PMID:19264801

  5. Protein kinase A-dependent phosphorylation modulates DNA-binding activity of hepatocyte nuclear factor 4.

    PubMed

    Viollet, B; Kahn, A; Raymondjean, M

    1997-08-01

    Hepatocyte nuclear factor 4 (HNF4), a liver-enriched transcription factor of the nuclear receptor superfamily, is critical for development and liver-specific gene expression. Here, we demonstrate that its DNA-binding activity is modulated posttranslationally by phosphorylation in vivo, ex vivo, and in vitro. In vivo, HNF4 DNA-binding activity is reduced by fasting and by inducers of intracellular cyclic AMP (cAMP) accumulation. A consensus protein kinase A (PKA) phosphorylation site located within the A box of its DNA-binding domain has been identified, and its role in phosphorylation-dependent inhibition of HNF4 DNA-binding activity has been investigated. Mutants of HNF4 in which two potentially phosphorylatable serines have been replaced by either neutral or charged amino acids were able to bind DNA in vitro with affinity similar to that of the wild-type protein. However, phosphorylation by PKA strongly repressed the binding affinity of the wild-type factor but not that of HNF4 mutants. Accordingly, in transfection assays, expression vectors for the mutated HNF4 proteins activated transcription more efficiently than that for the wild-type protein-when cotransfected with the PKA catalytic subunit expression vector. Therefore, HNF4 is a direct target of PKA which might be involved in the transcriptional inhibition of liver genes by cAMP inducers. PMID:9234678

  6. p53-dependent SIRT6 expression protects Aβ42-induced DNA damage

    PubMed Central

    Jung, Eun Sun; Choi, Hyunjung; Song, Hyundong; Hwang, Yu Jin; Kim, Ahbin; Ryu, Hoon; Mook-Jung, Inhee

    2016-01-01

    Alzheimer’s disease (AD) is the most common type of dementia and age-related neurodegenerative disease. Elucidating the cellular changes that occur during ageing is an important step towards understanding the pathogenesis and progression of neurodegenerative disorders. SIRT6 is a member of the mammalian sirtuin family of anti-aging genes. However, the relationship between SIRT6 and AD has not yet been elucidated. Here, we report that SIRT6 protein expression levels are reduced in the brains of both the 5XFAD AD mouse model and AD patients. Aβ42, a major component of senile plaques, decreases SIRT6 expression, and Aβ42-induced DNA damage is prevented by the overexpression of SIRT6 in HT22 mouse hippocampal neurons. Also, there is a strong negative correlation between Aβ42-induced DNA damage and p53 levels, a protein involved in DNA repair and apoptosis. In addition, upregulation of p53 protein by Nutlin-3 prevents SIRT6 reduction and DNA damage induced by Aβ42. Taken together, this study reveals that p53-dependent SIRT6 expression protects cells from Aβ42-induced DNA damage, making SIRT6 a promising new therapeutic target for the treatment of AD. PMID:27156849

  7. Protein kinase A-dependent phosphorylation modulates DNA-binding activity of hepatocyte nuclear factor 4.

    PubMed Central

    Viollet, B; Kahn, A; Raymondjean, M

    1997-01-01

    Hepatocyte nuclear factor 4 (HNF4), a liver-enriched transcription factor of the nuclear receptor superfamily, is critical for development and liver-specific gene expression. Here, we demonstrate that its DNA-binding activity is modulated posttranslationally by phosphorylation in vivo, ex vivo, and in vitro. In vivo, HNF4 DNA-binding activity is reduced by fasting and by inducers of intracellular cyclic AMP (cAMP) accumulation. A consensus protein kinase A (PKA) phosphorylation site located within the A box of its DNA-binding domain has been identified, and its role in phosphorylation-dependent inhibition of HNF4 DNA-binding activity has been investigated. Mutants of HNF4 in which two potentially phosphorylatable serines have been replaced by either neutral or charged amino acids were able to bind DNA in vitro with affinity similar to that of the wild-type protein. However, phosphorylation by PKA strongly repressed the binding affinity of the wild-type factor but not that of HNF4 mutants. Accordingly, in transfection assays, expression vectors for the mutated HNF4 proteins activated transcription more efficiently than that for the wild-type protein-when cotransfected with the PKA catalytic subunit expression vector. Therefore, HNF4 is a direct target of PKA which might be involved in the transcriptional inhibition of liver genes by cAMP inducers. PMID:9234678

  8. DNA sequence-dependent morphological evolution of silver nanoparticles and their optical and hybridization properties.

    PubMed

    Wu, Jiangjiexing; Tan, Li Huey; Hwang, Kevin; Xing, Hang; Wu, Peiwen; Li, Wei; Lu, Yi

    2014-10-29

    A systematic investigation of the effects of different DNA sequences on the morphologies of silver nanoparticles (AgNPs) grown from Ag nanocube seeds is reported. The presence of 10-mer oligo-A, -T, and -C directed AgNPs growth from cubic seeds into edge-truncated octahedra of different truncation extents and truncated tetrahedral AgNPs, while AgNPs in the presence of oligo-G remained cubic. The shape and morphological evolution of the nanoparticle growth for each system is investigated using SEM and TEM and correlated with UV-vis absorption kinetic studies. In addition, the roles of oligo-C and oligo-G secondary structures in modulating the morphologies of AgNPs are elucidated, and the morphological evolution for each condition of AgNPs growth is proposed. The shapes were found to be highly dependent on the binding affinity of each of the bases and the DNA secondary structures, favoring the stabilization of the Ag{111} facet. The AgNPs synthesized through this method have morphologies and optical properties that can be varied by using different DNA sequences, while the DNA molecules on these AgNPs are also stable against glutathione. The AgNP functionalization can be realized in a one-step synthesis while retaining the biorecognition ability of the DNA, which allows for programmable assembly. PMID:25243485

  9. Comparative Dynamics and Sequence Dependence of DNA and RNA Binding to Single Walled Carbon Nanotubes

    PubMed Central

    Landry, Markita P.; Vuković, Lela; Kruss, Sebastian; Bisker, Gili; Landry, Alexandra M.; Islam, Shahrin; Jain, Rishabh; Schulten, Klaus; Strano, Michael S.

    2015-01-01

    Noncovalent polymer-single walled carbon nanotube (SWCNT) conjugates have gained recent interest due to their prevalent use as electrochemical and optical sensors, SWCNT-based therapeutics, and for SWCNT separation. However, little is known about the effects of polymer-SWCNT molecular interactions on functional properties of these conjugates. In this work, we show that SWCNT complexed with related polynucleotide polymers (DNA, RNA) have dramatically different fluorescence stability. Surprisingly, we find a difference of nearly 2500-fold in fluorescence emission between the most fluorescently stable DNA-SWCNT complex, C30 DNA-SWCNT, compared to the least fluorescently stable complex, (AT)7A-(GU)7G DNA-RNA hybrid-SWCNT. We further reveal the existence of three regimes in which SWCNT fluorescence varies nonmonotonically with SWCNT concentration. We utilize molecular dynamics simulations to elucidate the conformation and atomic details of SWCNT-corona phase interactions. Our results show that variations in polynucleotide sequence or sugar backbone can lead to large changes in the conformational stability of the polymer SWCNT corona and the SWCNT optical response. Finally, we demonstrate the effect of the coronae on the response of a recently developed dopamine nanosensor, based on (GT)15 DNA- and (GU)15 RNA-SWCNT complexes. Our results clarify several features of the sequence dependence of corona phases produced by polynucleotides adsorbed to single walled carbon nanotubes, and the implications for molecular recognition in such phases. PMID:26005509

  10. Translesion synthesis mechanisms depend on the nature of DNA damage in UV-irradiated human cells

    PubMed Central

    Quinet, Annabel; Martins, Davi Jardim; Vessoni, Alexandre Teixeira; Biard, Denis; Sarasin, Alain; Stary, Anne; Menck, Carlos Frederico Martins

    2016-01-01

    Ultraviolet-induced 6-4 photoproducts (6-4PP) and cyclobutane pyrimidine dimers (CPD) can be tolerated by translesion DNA polymerases (TLS Pols) at stalled replication forks or by gap-filling. Here, we investigated the involvement of Polη, Rev1 and Rev3L (Polζ catalytic subunit) in the specific bypass of 6-4PP and CPD in repair-deficient XP-C human cells. We combined DNA fiber assay and novel methodologies for detection and quantification of single-stranded DNA (ssDNA) gaps on ongoing replication forks and postreplication repair (PRR) tracts in the human genome. We demonstrated that Rev3L, but not Rev1, is required for postreplicative gap-filling, while Polη and Rev1 are responsible for TLS at stalled replication forks. Moreover, specific photolyases were employed to show that in XP-C cells, CPD arrest replication forks, while 6-4PP are responsible for the generation of ssDNA gaps and PRR tracts. On the other hand, in the absence of Polη or Rev1, both types of lesion block replication forks progression. Altogether, the data directly show that, in the human genome, Polη and Rev1 bypass CPD and 6-4PP at replication forks, while only 6-4PP are also tolerated by a Polζ-dependent gap-filling mechanism, independent of S phase. PMID:27095204

  11. Structure and mutagenesis of the DNA modification-dependent restriction endonuclease AspBHI

    PubMed Central

    Horton, John R.; Nugent, Rebecca L.; Li, Andrew; Mabuchi, Megumu Yamada; Fomenkov, Alexey; Cohen-Karni, Devora; Griggs, Rose M.; Zhang, Xing; Wilson, Geoffrey G.; Zheng, Yu; Xu, Shuang-yong; Cheng, Xiaodong

    2014-01-01

    The modification-dependent restriction endonuclease AspBHI recognizes 5-methylcytosine (5mC) in the double-strand DNA sequence context of (C/T)(C/G)(5mC)N(C/G) (N = any nucleotide) and cleaves the two strands a fixed distance (N12/N16) 3′ to the modified cytosine. We determined the crystal structure of the homo-tetrameric AspBHI. Each subunit of the protein comprises two domains: an N-terminal DNA-recognition domain and a C-terminal DNA cleavage domain. The N-terminal domain is structurally similar to the eukaryotic SET and RING-associated (SRA) domain, which is known to bind to a hemi-methylated CpG dinucleotide. The C-terminal domain is structurally similar to classic Type II restriction enzymes and contains the endonuclease catalytic-site motif of DX20EAK. To understand how specific amino acids affect AspBHI recognition preference, we generated a homology model of the AspBHI-DNA complex, and probed the importance of individual amino acids by mutagenesis. Ser41 and Arg42 are predicted to be located in the DNA minor groove 5′ to the modified cytosine. Substitution of Ser41 with alanine (S41A) and cysteine (S41C) resulted in mutants with altered cleavage activity. All 19 Arg42 variants resulted in loss of endonuclease activity. PMID:24604015

  12. Translesion synthesis mechanisms depend on the nature of DNA damage in UV-irradiated human cells.

    PubMed

    Quinet, Annabel; Martins, Davi Jardim; Vessoni, Alexandre Teixeira; Biard, Denis; Sarasin, Alain; Stary, Anne; Menck, Carlos Frederico Martins

    2016-07-01

    Ultraviolet-induced 6-4 photoproducts (6-4PP) and cyclobutane pyrimidine dimers (CPD) can be tolerated by translesion DNA polymerases (TLS Pols) at stalled replication forks or by gap-filling. Here, we investigated the involvement of Polη, Rev1 and Rev3L (Polζ catalytic subunit) in the specific bypass of 6-4PP and CPD in repair-deficient XP-C human cells. We combined DNA fiber assay and novel methodologies for detection and quantification of single-stranded DNA (ssDNA) gaps on ongoing replication forks and postreplication repair (PRR) tracts in the human genome. We demonstrated that Rev3L, but not Rev1, is required for postreplicative gap-filling, while Polη and Rev1 are responsible for TLS at stalled replication forks. Moreover, specific photolyases were employed to show that in XP-C cells, CPD arrest replication forks, while 6-4PP are responsible for the generation of ssDNA gaps and PRR tracts. On the other hand, in the absence of Polη or Rev1, both types of lesion block replication forks progression. Altogether, the data directly show that, in the human genome, Polη and Rev1 bypass CPD and 6-4PP at replication forks, while only 6-4PP are also tolerated by a Polζ-dependent gap-filling mechanism, independent of S phase. PMID:27095204

  13. Statistics of time-dependent rupture of single ds-DNA.

    PubMed

    Liang, Hua; Severin, Nikolai; Fugmann, Simon; Sokolov, Igor M; Rabe, Jürgen P

    2013-07-25

    Double-stranded (ds-) DNA molecules were stretched and ruptured on molecularly modified graphite surfaces with a scanning force microscope (SFM) exerting a force parallel to the surface. The stretching force was either large enough to break the molecule immediately or compensated by the elastic restoring force of the DNA backbone, which stabilized the molecular length. However, the size-stabilized molecules broke gradually from longer molecules to shorter ones with time. The breakage of different lengths of stabilized molecules was recorded in order to study time-dependent mechanical properties of the molecules under constant forces. From these data, a relatively high rate constant, k0 = (2.2 ± 0.1) × 10(-7) s(-1), was calculated. Moreover, we found a nonlinear stress-strain dependence of DNA on the surface which we attributed to DNA conformational transition. Assuming that the structural transition on the surface is similar to that in solution we estimated the forces needed to stretch the molecules and thereby verify the estimation of the activation energy barrier. PMID:23829161

  14. Viscoelastic Properties of Entangled DNA Solutions: Dependence on Molecular Length and Concentration

    NASA Astrophysics Data System (ADS)

    Smith, Patrick; Dobrev, Veselin S.; Urbach, Jeff; Anderson, Rae

    2014-03-01

    We use macroscopic rheology to investigate the viscoelastic properties of solutions of monodisperse linear DNA, as a function of DNA length and concentration. We span from the unentangled to the entangled regime by using DNA lengths that vary from 11 to 115 kilobasepairs (3.7 to 39 μm) and solution concentrations that range between 0.5 and 4.0 mg/ml. We investigate the effects of oscillatory frequency on the linear elastic (G') and viscous (G'') moduli, with frequency values of 0.01 - 100 Hz. In addition, the dependence of viscosity on strain rate is studied with strain rates ranging from 0.01 to 100 Hz. Importantly, these studies are the first to examine the molecular length dependence of linear viscoelastic properties for concentrated DNA solutions. Results are compared to theoretical predictions based on the Rouse model and reptation model for unentangled and entangled polymer solutions, respectively. This research was funded by AFOSR YIP (Grant No. FA9550-12-1-0315) and NSF (Grant No. REU DMR-1004268).

  15. Discovery of bacterial NAD⁺-dependent DNA ligase inhibitors: improvements in clearance of adenosine series.

    PubMed

    Stokes, Suzanne S; Gowravaram, Madhusudhan; Huynh, Hoan; Lu, Min; Mullen, George B; Chen, Brendan; Albert, Robert; O'Shea, Thomas J; Rooney, Michael T; Hu, Haiqing; Newman, Joseph V; Mills, Scott D

    2012-01-01

    Optimization of clearance of adenosine inhibitors of bacterial NAD(+)-dependent DNA ligase is discussed. To reduce Cytochrome P-450-mediated metabolic clearance, many strategies were explored; however, most modifications resulted in compounds with reduced antibacterial activity and/or unchanged total clearance. The alkyl side chains of the 2-cycloalkoxyadenosines were fluorinated, and compounds with moderate antibacterial activity and favorable pharmacokinetic properties in rat and dog were identified. PMID:22154350

  16. Hippocampal adult neurogenesis is maintained by Neil3-dependent repair of oxidative DNA lesions in neural progenitor cells.

    PubMed

    Regnell, Christine Elisabeth; Hildrestrand, Gunn Annette; Sejersted, Yngve; Medin, Tirill; Moldestad, Olve; Rolseth, Veslemøy; Krokeide, Silje Zandstra; Suganthan, Rajikala; Luna, Luisa; Bjørås, Magnar; Bergersen, Linda H

    2012-09-27

    Accumulation of oxidative DNA damage has been proposed as a potential cause of age-related cognitive decline. The major pathway for removal of oxidative DNA base lesions is base excision repair, which is initiated by DNA glycosylases. In mice, Neil3 is the main DNA glycosylase for repair of hydantoin lesions in single-stranded DNA of neural stem/progenitor cells, promoting neurogenesis. Adult neurogenesis is crucial for maintenance of hippocampus-dependent functions involved in behavior. Herein, behavioral studies reveal learning and memory deficits and reduced anxiety-like behavior in Neil3(-/-) mice. Neural stem/progenitor cells from aged Neil3(-/-) mice show impaired proliferative capacity and reduced DNA repair activity. Furthermore, hippocampal neurons in Neil3(-/-) mice display synaptic irregularities. It appears that Neil3-dependent repair of oxidative DNA damage in neural stem/progenitor cells is required for maintenance of adult neurogenesis to counteract the age-associated deterioration of cognitive performance. PMID:22959434

  17. Anomalous pressure dependence of thermal conductivities of large mass ratio compounds

    DOE PAGESBeta

    Lindsay, Lucas R; Broido, David A.; Carrete, Jesus; Mingo, Natalio; Reinecke, Tom L.

    2015-03-27

    The lattice thermal conductivities (k) of binary compound materials are examined as a function of hydrostatic pressure P using a first-principles approach. Compound materials with relatively small mass ratios, such as MgO, show an increase in k with P, consistent with measurements. Conversely, compounds with large mass ratios (e.g., BSb, BAs, BeTe, BeSe) exhibit decreasing with increasing P, a behavior that cannot be understood using simple theories of k. This anomalous P dependence of k arises from the fundamentally different nature of the intrinsic scattering processes for heat-carrying acoustic phonons in large mass ratio compounds compared to those with smallmore » mass ratios. We find this work demonstrates the power of first principles methods for thermal properties and advances the understanding of thermal transport in non-metals.« less

  18. Anomalous temperature dependent magneto-conductance in organic light-emitting diodes with multiple emissive states

    SciTech Connect

    Zhao, Chen-xiao; Jia, Wei-yao; Huang, Ke-Xun; Zhang, Qiao-ming; Yang, Xiao-hui; Xiong, Zu-hong

    2015-07-13

    The temperature dependence of the magneto-conductance (MC) in organic electron donor-acceptor hybrid and layer heterojunction diodes was studied. The MC value increased with temperature in layer heterojunction and in 10 wt. % hybrid devices. An anomalous decrease of the MC with temperature was observed in 25 wt. %–50 wt. % hybrid devices. Further increasing donor concentration to 75 wt. %, the MC again increased with temperature. The endothermic exciplex-exciton energy transfer and the change in electroplex/exciton ratio caused by change in charge transport with temperature may account for these phenomena. Comparative studies of the temperature evolutions of the IV curves and the electroluminescence and photoluminescence spectra back our hypothesis.

  19. Anomalous pressure dependence of thermal conductivities of large mass ratio compounds

    SciTech Connect

    Lindsay, Lucas R; Broido, David A.; Carrete, Jesus; Mingo, Natalio; Reinecke, Tom L.

    2015-03-27

    The lattice thermal conductivities (k) of binary compound materials are examined as a function of hydrostatic pressure P using a first-principles approach. Compound materials with relatively small mass ratios, such as MgO, show an increase in k with P, consistent with measurements. Conversely, compounds with large mass ratios (e.g., BSb, BAs, BeTe, BeSe) exhibit decreasing with increasing P, a behavior that cannot be understood using simple theories of k. This anomalous P dependence of k arises from the fundamentally different nature of the intrinsic scattering processes for heat-carrying acoustic phonons in large mass ratio compounds compared to those with small mass ratios. We find this work demonstrates the power of first principles methods for thermal properties and advances the understanding of thermal transport in non-metals.

  20. Temperature dependence of the InGaPN conduction band structure

    NASA Astrophysics Data System (ADS)

    Lin, K. I.; Wang, T. S.; Hwang, J. S.

    2008-03-01

    Material properties of III-N-V alloys, such as GaAsN, InGaAsN, and InGaPN, have been intensively studied, because a small amount of nitrogen (N) incorporation results in very large bandgap bowing and dramatic change in the band structure.^1,2 Recently, temperature dependence of the parameters, i.e. the localized states energy EN introduced by an isolated N and the interaction potential V, of the band anticrossing (BAC) model in GaAsN epilayers has been reported.^3 These properties have never been studied for InGaPN. In this work, temperature-dependent photoreflectance (PR) measurements are employed to characterize the conduction band structure of In0.54Ga0.46P1-yNy (y = 0 and 0.02) grown on GaAs substrates. The band gap and the upper subband E+ are observed in InGaPN as predicted by the BAC model. To investigate the energetic positions of the features in the PR spectra, a Kramers-Kronig analysis is proposed. Based on these PR data and the BAC model, we find EN=2.054 eV and V=1.513 eV at 293 K. With decreasing temperature, the energy of EN shifts significantly to higher energies. Simultaneously, the interaction potential V between the N states and the host conduction band also rises to higher values. The thermal shifts of EN and V are dEN/dT -0.43 meV/K and dV/dT -0.67 meV/K, respectively. 1.APL 88, 031907 (2006). 2.APL 89, 192116 (2006). 3.APL 89, 202105 (2006).

  1. Use of Data Comm by Flight Crew to Conduct Interval Management Operations to Parallel Dependent Runways

    NASA Technical Reports Server (NTRS)

    Baxley, Brian T.; Hubbs, Clay; Shay, Rick; Karanian, James

    2011-01-01

    The Interval Management (IM) concept is being developed as a method to maintain or increase high traffic density airport arrival throughput while allowing aircraft to conduct near idle thrust descents. The Interval Management with Spacing to Parallel Dependent Runways (IMSPiDR1) experiment at NASA Langley Research Center used 24 commercial pilots to examine IM procedures to conduct parallel dependent runway arrival operations while maintaining safe but efficient intervals behind the preceding aircraft. The use of IM procedures during these operations requires a lengthy and complex clearance from Air Traffic Control (ATC) to the participating aircraft, thereby making the use of Controller Pilot Data Link Communications (CPDLC) highly desirable as the communication method. The use of CPDLC reduces the need for voice transmissions between controllers and flight crew, and enables automated transfer of IM clearance elements into flight management systems or other aircraft avionics. The result is reduced crew workload and an increase in the efficiency of crew procedures. This paper focuses on the subset of data collected related to the use of CPDLC for IM operations into a busy airport. Overall, the experiment and results were very successful, with the mean time under 43 seconds for the flight crew to load the clearance into the IM spacing tool, review the calculated speed, and respond to ATC. An overall mean rating of Moderately Agree was given when the crews were asked if the use of CPDLC was operationally acceptable as simulated in this experiment. Approximately half of the flight crew reported the use of CPDLC below 10,000 for IM operations was unacceptable, with 83% reporting below 5000 was unacceptable. Also described are proposed modifications to the IM operations that may reduce CPDLC Respond time to less than 30 seconds and should significantly reduce the complexity of crew procedures, as well as follow-on research issues for operational use of CPDLC during IM

  2. Sequence-dependent DNA curvature and flexibility from scanning force microscopy images.

    PubMed Central

    Scipioni, Anita; Anselmi, Claudio; Zuccheri, Giampaolo; Samori, Bruno; De Santis, Pasquale

    2002-01-01

    This paper reports a study of the sequence-dependent DNA curvature and flexibility based on scanning force microscopy (SFM) images. We used a palindromic dimer of a 1878-bp pBR322 fragment and collected a large pool of SFM images. The curvature of each imaged chain was measured in modulus and direction. It was found that the ensemble curvature modulus does not allow the separation of static and dynamic contributions to the curvature, whereas the curvature, when its direction in the two dimensions is taken into account, permits the direct separation of the intrinsic curvature contributions static and dynamic contributions. The palindromic symmetry also acted as an internal gauge of the validity of the SFM images statistical analysis. DNA static curvature resulted in good agreement with the predicted sequence-dependent intrinsic curvature. Furthermore, DNA sequence-dependent flexibility was found to correlate with the occurrence of A.T-rich dinucleotide steps along the chain and, in general, with the normalized basepair stacking energy distribution. PMID:12414677

  3. DNA Concentration-Dependent Dissociation of EcoRI: Direct Transfer or Reaction during Hopping

    PubMed Central

    Sidorova, Nina Y.; Scott, Thomas; Rau, Donald C.

    2013-01-01

    Direct transfer of proteins between DNA helices is a recognized important feature of the recognition site search process. Direct transfer is characterized by a dissociation rate that depends on total DNA concentration. This is taken as evidence for the formation of an intermediate DNA-protein-DNA ternary complex. We find that the dissociation rate of EcoRI-DNA-specific complexes at 80 mM NaCl depends on the concentration of competitor oligonucleotide suggesting that direct transfer contributes to EcoRI dissociation. This dependence on competitor DNA concentration is not seen at 180 mM salt. A careful examination of the salt concentration dependence of the dissociation rate, however, shows that the predictions for the formation of a ternary complex are not observed experimentally. The findings can be rationalized by considering that just after dissociating from a DNA fragment the protein remains in close proximity to that fragment, can reassociate with it, and diffuse back to the recognition site rather than bind to an oligonucleotide in solution, a hopping excursion. The probability that a protein will bind to an oligonucleotide during a hop can be approximately calculated and shown to explain the data. A dependence of the dissociation rate of a DNA-protein complex on competitor DNA concentration does not necessarily mean direct transfer. PMID:23528089

  4. Lead titanate/cyclic carbonate dependence on ionic conductivity of ferro/acrylate blend polymer composites

    NASA Astrophysics Data System (ADS)

    Jayaraman, R.; Vickraman, P.; Subramanian, N. M. V.; Justin, A. Simon

    2016-05-01

    Impedance, XRD, DSC and FTIR studies had been carried out for PVdF-co-HFP/LIBETI based system for three plasticizer (EC/DMC) - filler (PbTiO3) weight ratios. The enhanced conductivity 4.18 × 10-5 Scm-1 was noted for 57.5 wt% -7.5 wt% plasticizer - filler. while blending PEMA to PVdF-co-HFP respectively 7.5: 22.5 wt % (3/7), 15 wt%: 15 wt % (5/5) and 22.5wt %: 7.5 wt % (7/3), the improved conductivity was noted for 3/7 ratio 1.22 × 10-5 S cm-1 and its temperature dependence abide Arrhenius behavior. The intensity of peaks in XRD diffractogram registered dominance of lead titanate, from 2θ = 10° to 80° and absence of VdF crystallites (α+β phase) was noted. In DSC studies, the presence of the exotherm events, filler effect was distinctively seen exhibiting recrystallization of VdF crystallites. In blending PEMA, however, no trace of exotherms was found suggestive of PEMA better inhibiting recrystallization. FTIR study confirmed molecular interactions of various constituents in the vibrational band 500 - 1000 cm-1 both in pristine PVdF-co-HFP and PEMA blended composites with reference to C-F stretching, C-H stretching and C=O carbonyl bands.

  5. Photoluminescence of InNAs alloys: S-shaped temperature dependence and conduction-band nonparabolicity

    NASA Astrophysics Data System (ADS)

    Merrick, M.; Cripps, S. A.; Murdin, B. N.; Hosea, T. J. C.; Veal, T. D.; McConville, C. F.; Hopkinson, M.

    2007-08-01

    Photoluminescence (PL) has been used as a means of unambiguously observing band gap reduction in InNAs epilayers grown by molecular beam epitaxy. The observed redshift in room temperature emission as a function of nitrogen concentration is in agreement with the predictions of the band anticrossing (BAC) model, as implemented with model parameters derived from tight-binding calculations. The temperature dependence of the emission from certain samples exhibits a signature non-Varshni-like behavior indicative of electron trapping in nitrogen-related localized states below the conduction-band edge, as predicted by the linear combination of isolated nitrogen states (LCINS) model. This non-Varshni-like behavior tends to grow more pronounced with increasing nitrogen content, but for the highest nitrogen concentration studied, the more familiar Varshni-like behavior is recovered. Although unexpected, this observation is found to be consistent with the BAC and LCINS models. With consideration given to the effects of conduction-band nonparabolicity on the emission line shapes, the BAC model parameters extracted from the measured PL transition energies are found to be in excellent agreement with the predictions of the aforementioned tight-binding calculations.

  6. Thickness, humidity, and polarization dependent ferroelectric switching and conductivity in Mg doped lithium niobate

    SciTech Connect

    Neumayer, Sabine M.; Strelcov, Evgheni; Manzo, Michele; Gallo, Katia; Kravchenko, Ivan I.; Kholkin, Andrei L.; Kalinin, Sergei V.; Rodriguez, Brian J.

    2015-12-28

    Mg doped lithium niobate (Mg:LN) exhibits several advantages over undoped LN such as resistance to photorefraction, lower coercive fields, and p-type conductivity that is particularly pronounced at domain walls and opens up a range of applications, e.g., in domain wall electronics. Engineering of precise domain patterns necessitates well founded knowledge of switching kinetics, which can differ significantly from that of undoped LN. In this work, the role of humidity and sample composition in polarization reversal has been investigated under application of the same voltage waveform. Control over domain sizes has been achieved by varying the sample thickness and initial polarization as well as atmospheric conditions. Additionally, local introduction of proton exchanged phases allows for inhibition of domain nucleation or destabilization, which can be utilized to modify domain patterns. In polarization dependent current flow, attributed to charged domain walls and band bending, it the rectifying ability of Mg: LN in combination with suitable metal electrodes that allow for further tailoring of conductivity is demonstrated.

  7. Thickness, humidity, and polarization dependent ferroelectric switching and conductivity in Mg doped lithium niobate

    DOE PAGESBeta

    Neumayer, Sabine M.; Strelcov, Evgheni; Manzo, Michele; Gallo, Katia; Kravchenko, Ivan I.; Kholkin, Andrei L.; Kalinin, Sergei V.; Rodriguez, Brian J.

    2015-12-28

    Mg doped lithium niobate (Mg:LN) exhibits several advantages over undoped LN such as resistance to photorefraction, lower coercive fields, and p-type conductivity that is particularly pronounced at domain walls and opens up a range of applications, e.g., in domain wall electronics. Engineering of precise domain patterns necessitates well founded knowledge of switching kinetics, which can differ significantly from that of undoped LN. In this work, the role of humidity and sample composition in polarization reversal has been investigated under application of the same voltage waveform. Control over domain sizes has been achieved by varying the sample thickness and initial polarizationmore » as well as atmospheric conditions. Additionally, local introduction of proton exchanged phases allows for inhibition of domain nucleation or destabilization, which can be utilized to modify domain patterns. In polarization dependent current flow, attributed to charged domain walls and band bending, it the rectifying ability of Mg: LN in combination with suitable metal electrodes that allow for further tailoring of conductivity is demonstrated.« less

  8. Temperature Dependent Thermal Conductivity and Thermal Interface Resistance of Pentacene Thin Films with Varying Morphology.

    PubMed

    Epstein, Jillian; Ong, Wee-Liat; Bettinger, Christopher J; Malen, Jonathan A

    2016-07-27

    Temperature dependent thermal conductivities and thermal interface resistances of pentacene (Pn) thin films deposited on silicon substrates and self-assembled monolayer-modified [octadecyltrichlorosilane (OTS) and (3-aminopropyl)triethoxysilane (APTES)] silicon substrates were measured using frequency domain thermoreflectance. Atomic force microscopy images were used to derive an effective film thickness for thermal transport that accounts for surface roughness. Data taken over a temperature range of 77-300 K for various morphologies and film thicknesses show that the thermal conductivity increases with increasing Pn grain size. The sum of the substrate-Pn and Pn-gold thermal interface resistances was isolated from the intrinsic thermal resistance of the Pn films and found to be independent of surface chemistry. Corresponding Kapitza lengths of approximately 150 nm are larger than the physical thicknesses of typical Pn thin films and indicate that the interfaces play a dominant role in the total thermal resistance. This study has implications for increasing the performance and effective thermal management of small molecule electronic and energy conversion devices. PMID:27391107

  9. Thickness, humidity, and polarization dependent ferroelectric switching and conductivity in Mg doped lithium niobate

    NASA Astrophysics Data System (ADS)

    Neumayer, Sabine M.; Strelcov, Evgheni; Manzo, Michele; Gallo, Katia; Kravchenko, Ivan I.; Kholkin, Andrei L.; Kalinin, Sergei V.; Rodriguez, Brian J.

    2015-12-01

    Mg doped lithium niobate (Mg:LN) exhibits several advantages over undoped LN such as resistance to photorefraction, lower coercive fields, and p-type conductivity that is particularly pronounced at domain walls and opens up a range of applications, e.g., in domain wall electronics. Engineering of precise domain patterns necessitates well founded knowledge of switching kinetics, which can differ significantly from that of undoped LN. In this work, the role of humidity and sample composition in polarization reversal has been investigated under application of the same voltage waveform. Control over domain sizes has been achieved by varying the sample thickness and initial polarization as well as atmospheric conditions. In addition, local introduction of proton exchanged phases allows for inhibition of domain nucleation or destabilization, which can be utilized to modify domain patterns. Polarization dependent current flow, attributed to charged domain walls and band bending, demonstrates the rectifying ability of Mg:LN in combination with suitable metal electrodes that allow for further tailoring of conductivity.

  10. Thickness, humidity, and polarization dependent ferroelectric switching and conductivity in Mg doped lithium niobate

    SciTech Connect

    Neumayer, Sabine M.; Rodriguez, Brian J.; Strelcov, Evgheni; Kravchenko, Ivan I.; Kalinin, Sergei V.; Manzo, Michele; Gallo, Katia; Kholkin, Andrei L.

    2015-12-28

    Mg doped lithium niobate (Mg:LN) exhibits several advantages over undoped LN such as resistance to photorefraction, lower coercive fields, and p-type conductivity that is particularly pronounced at domain walls and opens up a range of applications, e.g., in domain wall electronics. Engineering of precise domain patterns necessitates well founded knowledge of switching kinetics, which can differ significantly from that of undoped LN. In this work, the role of humidity and sample composition in polarization reversal has been investigated under application of the same voltage waveform. Control over domain sizes has been achieved by varying the sample thickness and initial polarization as well as atmospheric conditions. In addition, local introduction of proton exchanged phases allows for inhibition of domain nucleation or destabilization, which can be utilized to modify domain patterns. Polarization dependent current flow, attributed to charged domain walls and band bending, demonstrates the rectifying ability of Mg:LN in combination with suitable metal electrodes that allow for further tailoring of conductivity.

  11. DNA sequence-dependent ionic currents in ultra-small solid-state nanopores

    NASA Astrophysics Data System (ADS)

    Comer, Jeffrey; Aksimentiev, Aleksei

    2016-05-01

    Measurements of ionic currents through nanopores partially blocked by DNA have emerged as a powerful method for characterization of the DNA nucleotide sequence. Although the effect of the nucleotide sequence on the nanopore blockade current has been experimentally demonstrated, prediction and interpretation of such measurements remain a formidable challenge. Using atomic resolution computational approaches, here we show how the sequence, molecular conformation, and pore geometry affect the blockade ionic current in model solid-state nanopores. We demonstrate that the blockade current from a DNA molecule is determined by the chemical identities and conformations of at least three consecutive nucleotides. We find the blockade currents produced by the nucleotide triplets to vary considerably with their nucleotide sequences despite having nearly identical molecular conformations. Encouragingly, we find blockade current differences as large as 25% for single-base substitutions in ultra small (1.6 nm × 1.1 nm cross section; 2 nm length) solid-state nanopores. Despite the complex dependence of the blockade current on the sequence and conformation of the DNA triplets, we find that, under many conditions, the number of thymine bases is positively correlated with the current, whereas the number of purine bases and the presence of both purines and pyrimidines in the triplet are negatively correlated with the current. Based on these observations, we construct a simple theoretical model that relates the ion current to the base content of a solid-state nanopore. Furthermore, we show that compact conformations of DNA in narrow pores provide the greatest signal-to-noise ratio for single base detection, whereas reduction of the nanopore length increases the ionic current noise. Thus, the sequence dependence of the nanopore blockade current can be theoretically rationalized, although the predictions will likely need to be customized for each nanopore type.Measurements of ionic

  12. Doping and Field Dependent Electrical Conductivity of Angle-Resolved Twisted Bilayer Graphene

    NASA Astrophysics Data System (ADS)

    Huang, Lujie; Kim, Cheol-Joo; Tsen, Adam Wei; Brown, Lola; Park, Jiwoong

    2015-03-01

    In twisted bilayer graphene (tBLG), the interlayer interaction induces additional van Hove singularities (VHS) and mini-gaps near the intersections between the Dirac cones of the two layers; this results in several electrical and optical phenomena at an energy level that monotonically increases with the twist angle θ. While there exist previous studies on the electrical and optical properties of tBLG, the electrical conductivity of tBLG and its dependence on the overall doping and interlayer potential (field) have not been measured using tBLG samples with known θ. Here, we report the electrical conductivity of θ-resolved tBLG in a dual-gate field effect transistor geometry which allows an independent control of the doping and interlayer potential. In large θ tBLG, the total conductivity is approximately proportional to the total carrier density (the sum of the carrier number densities from the top and the bottom layers), indicating that large θ tBLG acts as two independent single layers carrying the electrical current in parallel. Among tBLG samples with a small θ, however, we observe an extra resistance peak besides the Dirac point, which may correspond to the minigap near the VHS. In order to perform further experiments for this small- θ tBLG samples, we use a doubletransfer of CVD grown graphene films with a uniform lattice orientation over a large scale. This allows a direct optical characterization in the relevant IR wavelengths, a critical capability for determining and the twist angle θ.

  13. Dependence of Thermal Conductivity of Carbon Nanopeapods on Filling Ratios of Fullerene Molecules.

    PubMed

    Cui, Liu; Feng, Yanhui; Zhang, Xinxin

    2015-11-12

    Focusing on carbon nanopeapods (CNPs), i.e., carbon nanotubes (CNTs) filled with fullerene C60 molecules, the thermal conductivity and its dependence on the filling ratio of C60 molecules have been investigated by equilibrium molecular dynamics simulations. It turns out that the CNP thermal conductivity increases first, reaches its maximum value at filling ratio of 50%, and then decreases with increasing filling ratio. The heat transfer mechanisms were analyzed by the motion of C60 molecules, the mass transfer contribution, the phonon vibrational density of states, and the relative contributions of tube and C60 molecules to the total heat flux. The mass transfer in CNPs is mainly attributed to the rotational and translational motion of C60 molecules in tubes. As the filling ratio is larger than 50%, the axially translational motion of C60 molecules gets more and more restricted with increasing filling ratio. For either the mass transfer contribution to heat transfer or the phonon coupling between the tube wall and C60, the peaking behavior occurs at a filling ratio of 50%, which confirms the corresponding maximum thermal conductivity of CNP. With the filling ratio increasing, the dominating contribution to heat transfer changes from tube-wall atoms to fullerene atoms. Their relative contributions almost keep stable when the filling ratio is larger than 50% until it reaches 100%, where the contribution from fullerene atoms suddenly drops because of strong confinement of translational motion of C60 molecules. This work may offer valuable routes for probing heat transport in CNT hybrid structures, and possible device applications. PMID:26485312

  14. The calcium-dependent protein kinase CPK7 acts on root hydraulic conductivity.

    PubMed

    Li, Guowei; Boudsocq, Marie; Hem, Sonia; Vialaret, Jérôme; Rossignol, Michel; Maurel, Christophe; Santoni, Véronique

    2015-07-01

    The hydraulic conductivity of plant roots (Lp(r)) is determined in large part by the activity of aquaporins. Mechanisms occurring at the post-translational level, in particular phosphorylation of aquaporins of the plasma membrane intrinsic protein 2 (PIP2) subfamily, are thought to be of critical importance for regulating root water transport. However, knowledge of protein kinases and phosphatases acting on aquaporin function is still scarce. In the present work, we investigated the Lp(r) of knockout Arabidopsis plants for four Ca(2+)-dependent protein kinases. cpk7 plants showed a 30% increase in Lp(r) because of a higher aquaporin activity. A quantitative proteomic analysis of wild-type and cpk7 plants revealed that PIP gene expression and PIP protein quantity were not correlated and that CPK7 has no effect on PIP2 phosphorylation. In contrast, CPK7 exerts a negative control on the cellular abundance of PIP1s, which likely accounts for the higher Lp(r) of cpk7. In addition, this study revealed that the cellular amount of a few additional proteins including membrane transporters is controlled by CPK7. The overall work provides evidence for CPK7-dependent stability of specific membrane proteins. PMID:25366820

  15. History dependence of human muscle-fiber conduction velocity during voluntary isometric contractions

    PubMed Central

    Lateva, Zoia C.

    2011-01-01

    The conduction velocity (CV) of a muscle fiber is affected by the fiber's discharge history going back ∼1 s. We investigated this dependence by measuring CV fluctuations during voluntary isometric contractions of the human brachioradialis muscle. We recorded electromyogram (EMG) signals simultaneously from multiple intramuscular electrodes, identified potentials belonging to the same motor unit using EMG decomposition, and estimated the CV of each discharge from the interpotential interval. In 12 of 14 subjects, CV increased by ∼10% during the first second after recruitment and then fluctuated by about ±2% in a way that mirrored the fluctuations in the instantaneous firing rate. The CV profile could be precisely described in terms of the discharge history by a simple mathematical model. In the other two subjects, and one subject retested after cooling the arm, the CV fluctuations were inversely correlated with instantaneous firing rate. In all subjects, CV was additionally affected by very short interdischarge intervals (<25 ms): it was increased in doublets at recruitment, but decreased in doublets during continuous firing and after short interdischarge intervals in doubly innervated fibers. CV also exhibited a slow trend of about −0.05%/s that did not depend on the immediate discharge history. We suggest that measurements of CV fluctuations during voluntary contractions, or during stimulation protocols that involve longer and more complex stimulation patterns than are currently being used, may provide a sensitive approach for estimating the dynamic characteristics of ion channels in the human muscle-fiber membrane. PMID:21565985

  16. Calcium activates the light-dependent conductance in melanopsin-expressing photoreceptors of amphioxus

    PubMed Central

    Peinado, Gabriel; Osorno, Tomás; Gomez, María del Pilar; Nasi, Enrico

    2015-01-01

    Melanopsin, the photopigment of the “circadian” receptors that regulate the biological clock and the pupillary reflex in mammals, is homologous to invertebrate rhodopsins. Evidence supporting the involvement of phosphoinositides in light-signaling has been garnered, but the downstream effectors that control the light-dependent conductance remain unknown. Microvillar photoreceptors of the primitive chordate amphioxus also express melanopsin and transduce light via phospholipase-C, apparently not acting through diacylglycerol. We therefore examined the role of calcium in activating the photoconductance, using simultaneous, high time-resolution measurements of membrane current and Ca2+ fluorescence. The light-induced calcium rise precedes the onset of the photocurrent, making it a candidate in the activation chain. Moreover, photolysis of caged Ca elicits an inward current of similar size, time course and pharmacology as the physiological photoresponse, but with a much shorter latency. Internally released calcium thus emerges as a key messenger to trigger the opening of light-dependent channels in melanopsin-expressing microvillar photoreceptors of early chordates. PMID:26056310

  17. Calcium activates the light-dependent conductance in melanopsin-expressing photoreceptors of amphioxus.

    PubMed

    Peinado, Gabriel; Osorno, Tomás; Gomez, María del Pilar; Nasi, Enrico

    2015-06-23

    Melanopsin, the photopigment of the "circadian" receptors that regulate the biological clock and the pupillary reflex in mammals, is homologous to invertebrate rhodopsins. Evidence supporting the involvement of phosphoinositides in light-signaling has been garnered, but the downstream effectors that control the light-dependent conductance remain unknown. Microvillar photoreceptors of the primitive chordate amphioxus also express melanopsin and transduce light via phospholipase-C, apparently not acting through diacylglycerol. We therefore examined the role of calcium in activating the photoconductance, using simultaneous, high time-resolution measurements of membrane current and Ca(2+) fluorescence. The light-induced calcium rise precedes the onset of the photocurrent, making it a candidate in the activation chain. Moreover, photolysis of caged Ca elicits an inward current of similar size, time course and pharmacology as the physiological photoresponse, but with a much shorter latency. Internally released calcium thus emerges as a key messenger to trigger the opening of light-dependent channels in melanopsin-expressing microvillar photoreceptors of early chordates. PMID:26056310

  18. History dependence of human muscle-fiber conduction velocity during voluntary isometric contractions.

    PubMed

    McGill, Kevin C; Lateva, Zoia C

    2011-09-01

    The conduction velocity (CV) of a muscle fiber is affected by the fiber's discharge history going back ∼1 s. We investigated this dependence by measuring CV fluctuations during voluntary isometric contractions of the human brachioradialis muscle. We recorded electromyogram (EMG) signals simultaneously from multiple intramuscular electrodes, identified potentials belonging to the same motor unit using EMG decomposition, and estimated the CV of each discharge from the interpotential interval. In 12 of 14 subjects, CV increased by ∼10% during the first second after recruitment and then fluctuated by about ±2% in a way that mirrored the fluctuations in the instantaneous firing rate. The CV profile could be precisely described in terms of the discharge history by a simple mathematical model. In the other two subjects, and one subject retested after cooling the arm, the CV fluctuations were inversely correlated with instantaneous firing rate. In all subjects, CV was additionally affected by very short interdischarge intervals (<25 ms): it was increased in doublets at recruitment, but decreased in doublets during continuous firing and after short interdischarge intervals in doubly innervated fibers. CV also exhibited a slow trend of about -0.05%/s that did not depend on the immediate discharge history. We suggest that measurements of CV fluctuations during voluntary contractions, or during stimulation protocols that involve longer and more complex stimulation patterns than are currently being used, may provide a sensitive approach for estimating the dynamic characteristics of ion channels in the human muscle-fiber membrane. PMID:21565985

  19. DNA sequence-dependent ionic currents in ultra-small solid-state nanopores.

    PubMed

    Comer, Jeffrey; Aksimentiev, Aleksei

    2016-05-01

    Measurements of ionic currents through nanopores partially blocked by DNA have emerged as a powerful method for characterization of the DNA nucleotide sequence. Although the effect of the nucleotide sequence on the nanopore blockade current has been experimentally demonstrated, prediction and interpretation of such measurements remain a formidable challenge. Using atomic resolution computational approaches, here we show how the sequence, molecular conformation, and pore geometry affect the blockade ionic current in model solid-state nanopores. We demonstrate that the blockade current from a DNA molecule is determined by the chemical identities and conformations of at least three consecutive nucleotides. We find the blockade currents produced by the nucleotide triplets to vary considerably with their nucleotide sequences despite having nearly identical molecular conformations. Encouragingly, we find blockade current differences as large as 25% for single-base substitutions in ultra small (1.6 nm × 1.1 nm cross section; 2 nm length) solid-state nanopores. Despite the complex dependence of the blockade current on the sequence and conformation of the DNA triplets, we find that, under many conditions, the number of thymine bases is positively correlated with the current, whereas the number of purine bases and the presence of both purines and pyrimidines in the triplet are negatively correlated with the current. Based on these observations, we construct a simple theoretical model that relates the ion current to the base content of a solid-state nanopore. Furthermore, we show that compact conformations of DNA in narrow pores provide the greatest signal-to-noise ratio for single base detection, whereas reduction of the nanopore length increases the ionic current noise. Thus, the sequence dependence of the nanopore blockade current can be theoretically rationalized, although the predictions will likely need to be customized for each nanopore type. PMID:27103233

  20. Multiple Levels of Affinity-Dependent DNA Discrimination in Cre-LoxP Recombination†

    PubMed Central

    Gelato, Kathy A.; Martin, Shelley S.; Wong, Scott; Baldwin, Enoch P.

    2010-01-01

    Cre recombinase residue Arg259 mediates a canonical bidentate hydrogen-bonded contact with Gua27 of its LoxP DNA substrate. Substituting Cyt8-Gua27 with the three other basepairs, to give LoxAT, LoxTA, and LoxGC, reduced Cre-mediated recombination in vitro, with the preference order of Gua27 >Ade27 ~ Thy27 ≫ Cyt27. While LoxAT and LoxTA exhibited 2.5-fold reduced affinity and 2.5-5-fold slower reaction rates, LoxGC was a barely functional substrate. Its maximum level of turnover was 6-fold reduced over other substrates, and it exhibited 8.5-fold reduced Cre binding and 6.3-fold slower turnover rate. With LoxP, the rate-limiting step for recombination occurs after protein-DNA complex assembly but before completion of the first strand exchange to form the Holliday junction (HJ) intermediate. With the mutant substrates, it occurs after HJ formation. Using an increased DNA-binding E262Q/E266Q “CreQQ” variant, all four substrates react more readily, but with much less difference between them, and maintained the earlier rate-limiting step. The data indicate that Cre discriminates substrates through differences in (i) concentration dependence of active complex assembly, (ii) turnover rate, and (iii) maximum yield of product at saturation, all of which are functions of the Cre-DNA binding interaction. CreQQ suppression of Lox mutant defects implies that coupling between binding and turnover involves a change in Cre subunit DNA affinities during the “conformational switch” that occurs prior to the second strand exchange. These results provide an example of how a DNA-binding enzyme can exert specificity via affinity modulation of conformational transitions that occur along its reaction pathway. PMID:17014075

  1. Multiple levels of affinity-dependent DNA discrimination in Cre-LoxP recombination.

    PubMed

    Gelato, Kathy A; Martin, Shelley S; Wong, Scott; Baldwin, Enoch P

    2006-10-10

    Cre recombinase residue Arg259 mediates a canonical bidentate hydrogen-bonded contact with Gua27 of its LoxP DNA substrate. Substituting Cyt8-Gua27 with the three other basepairs, to give LoxAT, LoxTA, and LoxGC, reduced Cre-mediated recombination in vitro, with the preference order of Gua27 > Ade27 approximately Thy27 > Cyt27. While LoxAT and LoxTA exhibited 2.5-fold reduced affinity and 2.5-5-fold slower reaction rates, LoxGC was a barely functional substrate. Its maximum level of turnover was 6-fold reduced over other substrates, and it exhibited 8.5-fold reduced Cre binding and 6.3-fold slower turnover rate. With LoxP, the rate-limiting step for recombination occurs after protein-DNA complex assembly but before completion of the first strand exchange to form the Holliday junction (HJ) intermediate. With the mutant substrates, it occurs after HJ formation. Using an increased DNA-binding E262Q/E266Q "CreQQ" variant, all four substrates react more readily, but with much less difference between them, and maintained the earlier rate-limiting step. The data indicate that Cre discriminates substrates through differences in (i) concentration dependence of active complex assembly, (ii) turnover rate, and (iii) maximum yield of product at saturation, all of which are functions of the Cre-DNA binding interaction. CreQQ suppression of Lox mutant defects implies that coupling between binding and turnover involves a change in Cre subunit DNA affinities during the "conformational switch" that occurs prior to the second strand exchange. These results provide an example of how a DNA-binding enzyme can exert specificity via affinity modulation of conformational transitions that occur along its reaction pathway. PMID:17014075

  2. Coordinateendonucleolytic 5' and 3' trimming of terminally blocked blunt DNA double-strand break ends by Artemis nuclease and DNA-dependent protein kinase

    SciTech Connect

    Povirk, Lawrence; Yannone, Steven M.; Khan, Imran S.; Zhou, Rui-Zhe; Zhou, Tong; Valerie, Kristoffer; F., Lawrence

    2008-02-18

    Previous work showed that, in the presence of DNA-PK, Artemis slowly trims 3'-phosphoglycolate-terminated blunt ends. To examine the trimming reaction in more detail, long internally labeled DNA substrates were treated with Artemis. In the absence of DNA-PK, Artemis catalyzed extensive 5' {yields} 3' exonucleolytic resection of double-stranded DNA. This resection required a 5'-phosphate but did not require ATP, and was accompanied by endonucleolytic cleavage of the resulting 3' overhang. In the presence of DNA-PK, Artemis-mediated trimming was more limited, was ATP-dependent, and did not require a 5'-phosphate. For a blunt end with either a 3'-phosphoglycolate or 3'-hydroxyl terminus, endonucleolytic trimming of 2-4 nucleotides from the 3'-terminal strand was accompanied by trimming of 6 nucleotides from the 5'-terminal strand. The results suggest that autophosphorylated DNA-PK suppresses the exonuclease activity of Artemis toward blunt-ended DNA, and promotes slow and limited endonucleolytic trimming of the 5'-terminal strand, resulting in short 3' overhangs that are trimmed endonucleolytically. Thus, Artemis and DNA-PK can convert terminally blocked DNA ends of diverse geometry and chemical structure to a form suitable for polymerase mediated patching and ligation, with minimal loss of terminal sequence. Such processing could account for the very small deletions often found at DNA double-strand break repair sites.

  3. Single-molecule derivation of salt dependent base-pair free energies in DNA.

    PubMed

    Huguet, Josep M; Bizarro, Cristiano V; Forns, Núria; Smith, Steven B; Bustamante, Carlos; Ritort, Felix

    2010-08-31

    Accurate knowledge of the thermodynamic properties of nucleic acids is crucial to predicting their structure and stability. To date most measurements of base-pair free energies in DNA are obtained in thermal denaturation experiments, which depend on several assumptions. Here we report measurements of the DNA base-pair free energies based on a simplified system, the mechanical unzipping of single DNA molecules. By combining experimental data with a physical model and an optimization algorithm for analysis, we measure the 10 unique nearest-neighbor base-pair free energies with 0.1 kcal mol(-1) precision over two orders of magnitude of monovalent salt concentration. We find an improved set of standard energy values compared with Unified Oligonucleotide energies and a unique set of 10 base-pair-specific salt-correction values. The latter are found to be strongest for AA/TT and weakest for CC/GG. Our unique energy values and salt corrections improve predictions of DNA unzipping forces and are fully compatible with melting temperatures for oligos. The method should make it possible to obtain free energies, enthalpies, and entropies in conditions not accessible by bulk methodologies. PMID:20716688

  4. ATM-dependent Phosphorylation of the Fanconi Anemia Protein PALB2 Promotes the DNA Damage Response.

    PubMed

    Guo, Yingying; Feng, Wanjuan; Sy, Shirley M H; Huen, Michael S Y

    2015-11-13

    The Fanconi anemia protein PALB2, also known as FANCN, protects genome integrity by regulating DNA repair and cell cycle checkpoints. Exactly how PALB2 functions may be temporally coupled with detection and signaling of DNA damage is not known. Intriguingly, we found that PALB2 is transformed into a hyperphosphorylated state in response to ionizing radiation (IR). IR treatment specifically triggered PALB2 phosphorylation at Ser-157 and Ser-376 in manners that required the master DNA damage response kinase Ataxia telangiectasia mutated, revealing potential mechanistic links between PALB2 and the Ataxia telangiectasia mutated-dependent DNA damage responses. Consistently, dysregulated PALB2 phosphorylation resulted in sustained activation of DDRs. Full-blown PALB2 phosphorylation also required the breast and ovarian susceptible gene product BRCA1, highlighting important roles of the BRCA1-PALB2 interaction in orchestrating cellular responses to genotoxic stress. In summary, our phosphorylation analysis of tumor suppressor protein PALB2 uncovers new layers of regulatory mechanisms in the maintenance of genome stability and tumor suppression. PMID:26420486

  5. Quantitative analysis of the ion-dependent folding stability of DNA triplexes

    NASA Astrophysics Data System (ADS)

    Chen, Gengsheng; Chen, Shi-Jie

    2011-12-01

    A DNA triplex is formed through binding of a third strand to the major groove of a duplex. Due to the high charge density of a DNA triplex, metal ions are critical for its stability. We recently developed the tightly bound ion (TBI) model for ion-nucleic acids interactions. The model accounts for the potential correlation and fluctuations of the ion distribution. We now apply the TBI model to analyze the ion dependence of the thermodynamic stability for DNA triplexes. We focus on two experimentally studied systems: a 24-base DNA triplex and a pair of interacting 14-base triplexes. Our theoretical calculations for the number of bound ions indicate that the TBI model provides improved predictions for the number of bound ions than the classical Poisson-Boltzmann (PB) equation. The improvement is more significant for a triplex, which has a higher charge density than a duplex. This is possibly due to the higher ion concentration around the triplex and hence a stronger ion correlation effect for a triplex. In addition, our analysis for the free energy landscape for a pair of 14-mer triplexes immersed in an ionic solution shows that divalent ions could induce an attractive force between the triplexes. Furthermore, we investigate how the protonated cytosines in the triplexes affect the stability of the triplex helices.

  6. Single-molecule derivation of salt dependent base-pair free energies in DNA

    PubMed Central

    Huguet, Josep M.; Bizarro, Cristiano V.; Forns, Núria; Smith, Steven B.; Bustamante, Carlos; Ritort, Felix

    2010-01-01

    Accurate knowledge of the thermodynamic properties of nucleic acids is crucial to predicting their structure and stability. To date most measurements of base-pair free energies in DNA are obtained in thermal denaturation experiments, which depend on several assumptions. Here we report measurements of the DNA base-pair free energies based on a simplified system, the mechanical unzipping of single DNA molecules. By combining experimental data with a physical model and an optimization algorithm for analysis, we measure the 10 unique nearest-neighbor base-pair free energies with 0.1 kcal mol-1 precision over two orders of magnitude of monovalent salt concentration. We find an improved set of standard energy values compared with Unified Oligonucleotide energies and a unique set of 10 base-pair-specific salt-correction values. The latter are found to be strongest for AA/TT and weakest for CC/GG. Our unique energy values and salt corrections improve predictions of DNA unzipping forces and are fully compatible with melting temperatures for oligos. The method should make it possible to obtain free energies, enthalpies, and entropies in conditions not accessible by bulk methodologies. PMID:20716688

  7. Identification of a DNA methylation-dependent activator sequence in the pseudoxanthoma elasticum gene, ABCC6.

    PubMed

    Arányi, Tamás; Ratajewski, Marcin; Bardóczy, Viola; Pulaski, Lukasz; Bors, András; Tordai, Attila; Váradi, András

    2005-05-13

    ABCC6 encodes MRP6, a member of the ABC protein family with an unknown physiological role. The human ABCC6 and its two pseudogenes share 99% identical DNA sequence. Loss-of-function mutations of ABCC6 are associated with the development of pseudoxanthoma elasticum (PXE), a recessive hereditary disorder affecting the elastic tissues. Various disease-causing mutations were found in the coding region; however, the mutation detection rate in the ABCC6 coding region of bona fide PXE patients is only approximately 80%. This suggests that polymorphisms or mutations in the regulatory regions may contribute to the development of the disease. Here, we report the first characterization of the ABCC6 gene promoter. Phylogenetic in silico analysis of the 5' regulatory regions revealed the presence of two evolutionarily conserved sequence elements embedded in CpG islands. The study of DNA methylation of ABCC6 and the pseudogenes identified a correlation between the methylation of the CpG island in the proximal promoter and the ABCC6 expression level in cell lines. Both activator and repressor sequences were uncovered in the proximal promoter by reporter gene assays. The most potent activator sequence was one of the conserved elements protected by DNA methylation on the endogenous gene in non-expressing cells. Finally, in vitro methylation of this sequence inhibits the transcriptional activity of the luciferase promoter constructs. Altogether these results identify a DNA methylation-dependent activator sequence in the ABCC6 promoter. PMID:15760889

  8. Liquid-layering induced, temperature-dependent thermal conductivity enhancement in ZnO-propylene glycol nanofluids

    NASA Astrophysics Data System (ADS)

    Suganthi, Kuppusamy Swaminathan; Parthasarathy, Meera; Rajan, Kalpoondi Sekar

    2013-03-01

    Experiments were carried out on preparation of colloidal dispersions of ZnO nanoparticles in propylene glycol leading to ZnO-propylene glycol nanofluids. Thermal conductivity of these nanofluids was measured as a function of nanoparticle concentration (⩽2 vol.%), temperature (10-60 °C) and aggregate size. A strong dependence of thermal conductivity enhancement on temperature with higher enhancements at lower temperatures has been observed. Our results on temperature and aggregation dependence of thermal conductivity enhancement show that the thermal conductivity enhancement in ZnO-propylene glycol nanofluids is attributed to formation of solvation layers (liquid layers) of base fluid on the ZnO nanoparticle surfaces.

  9. Srs2 mediates PCNA-SUMO-dependent inhibition of DNA repair synthesis

    PubMed Central

    Burkovics, Peter; Sebesta, Marek; Sisakova, Alexandra; Plault, Nicolas; Szukacsov, Valeria; Robert, Thomas; Pinter, Lajos; Marini, Victoria; Kolesar, Peter; Haracska, Lajos; Gangloff, Serge; Krejci, Lumir

    2013-01-01

    Completion of DNA replication needs to be ensured even when challenged with fork progression problems or DNA damage. PCNA and its modifications constitute a molecular switch to control distinct repair pathways. In yeast, SUMOylated PCNA (S-PCNA) recruits Srs2 to sites of replication where Srs2 can disrupt Rad51 filaments and prevent homologous recombination (HR). We report here an unexpected additional mechanism by which S-PCNA and Srs2 block the synthesis-dependent extension of a recombination intermediate, thus limiting its potentially hazardous resolution in association with a cross-over. This new Srs2 activity requires the SUMO interaction motif at its C-terminus, but neither its translocase activity nor its interaction with Rad51. Srs2 binding to S-PCNA dissociates Polδ and Polη from the repair synthesis machinery, thus revealing a novel regulatory mechanism controlling spontaneous genome rearrangements. Our results suggest that cycling cells use the Siz1-dependent SUMOylation of PCNA to limit the extension of repair synthesis during template switch or HR and attenuate reciprocal DNA strand exchanges to maintain genome stability. PMID:23395907

  10. Srs2 mediates PCNA-SUMO-dependent inhibition of DNA repair synthesis.

    PubMed

    Burkovics, Peter; Sebesta, Marek; Sisakova, Alexandra; Plault, Nicolas; Szukacsov, Valeria; Robert, Thomas; Pinter, Lajos; Marini, Victoria; Kolesar, Peter; Haracska, Lajos; Gangloff, Serge; Krejci, Lumir

    2013-03-01

    Completion of DNA replication needs to be ensured even when challenged with fork progression problems or DNA damage. PCNA and its modifications constitute a molecular switch to control distinct repair pathways. In yeast, SUMOylated PCNA (S-PCNA) recruits Srs2 to sites of replication where Srs2 can disrupt Rad51 filaments and prevent homologous recombination (HR). We report here an unexpected additional mechanism by which S-PCNA and Srs2 block the synthesis-dependent extension of a recombination intermediate, thus limiting its potentially hazardous resolution in association with a cross-over. This new Srs2 activity requires the SUMO interaction motif at its C-terminus, but neither its translocase activity nor its interaction with Rad51. Srs2 binding to S-PCNA dissociates Polδ and Polη from the repair synthesis machinery, thus revealing a novel regulatory mechanism controlling spontaneous genome rearrangements. Our results suggest that cycling cells use the Siz1-dependent SUMOylation of PCNA to limit the extension of repair synthesis during template switch or HR and attenuate reciprocal DNA strand exchanges to maintain genome stability. PMID:23395907

  11. Dielectrophoresis of DNA: time- and frequency-dependent collections on microelectrodes.

    PubMed

    Bakewell, David J; Morgan, Hywel

    2006-06-01

    This paper reports measurements that characterize the collection of DNA onto interdigitated microelectrodes by high-frequency dielectrophoresis. Measurements of time-dependent collection of 12 kilobase pair plasmid DNA onto microelectrodes by dielectrophoresis show significant reduction in the response as the frequency increases from 100 kHz to 20 MHz. Collection time profiles are quantitatively measured using fluorescence microscopy over the range 100 kHz to 5 MHz and are represented in terms of two parameters: the initial dielectrophoretic collection rate, and the initial to steady-state collection transition. Measured values for both parameters are consistent with trends in the frequency-dependent real part of the effective polarizability measured for the same plasmid DNA using dielectric spectroscopy. The experimentally measured parameters are qualitatively compared with trends predicted by theory that takes into account dielectrophoretic particle movement and diffusion. The differences between experiment and theory are discussed with suggested improvements to theoretical models, for example, including the effects of electrohydrodynamically driven fluid motion. PMID:16805110

  12. Dielectrophoresis of DNA: time- and frequency-dependent collections on microelectrodes.

    PubMed

    Bakewell, David J; Morgan, Hywel

    2006-03-01

    This paper reports measurements that characterize the collection of DNA onto interdigitated microelectrodes by high-frequency dielectrophoresis. Measurements of time-dependent collection of 12 kilobase pair plasmid DNA onto microelectrodes by dielectrophoresis show significant reduction in the response as the frequency increases from 100 kHz to 20 MHz. Collection time profiles are quantitatively measured using fluorescence microscopy over the range 100 kHz to 5 MHz and are represented in terms of two parameters: the initial dielectrophoretic collection rate, and the initial to steady-state collection transition. Measured values for both parameters are consistent with trends in the frequency-dependent real part of the effective polarizability measured for the same plasmid DNA using dielectric spectroscopy. The experimentally measured parameters are qualitatively compared with trends predicted by theory that takes into account dielectrophoretic particle movement and diffusion. The differences between experiment and theory are discussed with suggested improvements to theoretical models, for example, including the effects of electrohydrodynamically driven fluid motion. PMID:16570867

  13. Gel mobilities of linking-number topoisomers and their dependence on DNA helical repeat and elasticity

    PubMed Central

    Vetcher, Alexandre A.; McEwen, Abbye E.; Abujarour, Ramzey; Hanke, Andreas; Levene, Stephen D.

    2010-01-01

    Agarose-gel electrophoresis has been used for more than thirty years to characterize the linking-number (Lk) distribution of closed-circular DNA molecules. Although the physical basis of this technique remains poorly understood, the gel-electrophoretic behavior of covalently closed DNAs has been used to determine the local unwinding of DNA by proteins and small-molecule ligands, characterize supercoiling-dependent conformational transitions in duplex DNA, and to measure helical-repeat changes due to shifts in temperature and ionic strength. Those results have been analyzed by assuming that the absolute mobility of a particular topoisomer is mainly a function of the integral number of superhelical turns, and thus a slowly varying function of plasmid molecular weight. In examining the mobilities of Lk topoisomers for a series of plasmids that differ incrementally in size over more than one helical turn, we found that the size-dependent agarose-gel mobility of individual topoisomers with identical values of Lk (but different values of the excess linking number, ΔLk) vary dramatically over a duplex turn. Our results suggest that a simple semi-empirical relationship holds between the electrophoretic mobility of linking-number topoisomers and their average writhe in solution. PMID:20346570

  14. Gli1/DNA interaction is a druggable target for Hedgehog-dependent tumors

    PubMed Central

    Infante, Paola; Mori, Mattia; Alfonsi, Romina; Ghirga, Francesca; Aiello, Federica; Toscano, Sara; Ingallina, Cinzia; Siler, Mariangela; Cucchi, Danilo; Po, Agnese; Miele, Evelina; D'Amico, Davide; Canettieri, Gianluca; De Smaele, Enrico; Ferretti, Elisabetta; Screpanti, Isabella; Uccello Barretta, Gloria; Botta, Maurizio; Botta, Bruno; Gulino, Alberto; Di Marcotullio, Lucia

    2015-01-01

    Hedgehog signaling is essential for tissue development and stemness, and its deregulation has been observed in many tumors. Aberrant activation of Hedgehog signaling is the result of genetic mutations of pathway components or other Smo-dependent or independent mechanisms, all triggering the downstream effector Gli1. For this reason, understanding the poorly elucidated mechanism of Gli1-mediated transcription allows to identify novel molecules blocking the pathway at a downstream level, representing a critical goal in tumor biology. Here, we clarify the structural requirements of the pathway effector Gli1 for binding to DNA and identify Glabrescione B as the first small molecule binding to Gli1 zinc finger and impairing Gli1 activity by interfering with its interaction with DNA. Remarkably, as a consequence of its robust inhibitory effect on Gli1 activity, Glabrescione B inhibited the growth of Hedgehog-dependent tumor cells in vitro and in vivo as well as the self-renewal ability and clonogenicity of tumor-derived stem cells. The identification of the structural requirements of Gli1/DNA interaction highlights their relevance for pharmacologic interference of Gli signaling. PMID:25476449

  15. HERC2 coordinates ubiquitin-dependent assembly of DNA repair factors on damaged chromosomes.

    PubMed

    Bekker-Jensen, Simon; Rendtlew Danielsen, Jannie; Fugger, Kasper; Gromova, Irina; Nerstedt, Annika; Lukas, Claudia; Bartek, Jiri; Lukas, Jiri; Mailand, Niels

    2010-01-01

    Regulatory ubiquitylation is emerging as an important mechanism to protect genome integrity in cells exposed to DNA damage. However, the spectrum of known ubiquitin regulators of the DNA damage response (DDR) is limited and their functional interplay is poorly understood. Here, we identify HERC2 as a factor that regulates ubiquitin-dependent retention of repair proteins on damaged chromosomes. In response to ionising radiation (IR), HERC2 forms a complex with RNF8, a ubiquitin ligase involved in the DDR. The HERC2-RNF8 interaction requires IR-inducible phosphorylation of HERC2 at Thr 4827, which in turn binds to the forkhead-associated (FHA) domain of RNF8. Mechanistically, we provide evidence that HERC2 facilitates assembly of the ubiquitin-conjugating enzyme Ubc13 with RNF8, thereby promoting DNA damage-induced formation of Lys 63-linked ubiquitin chains. We also show that HERC2 interacts with, and maintains the levels of, RNF168, another ubiquitin ligase operating downstream of RNF8 (Refs 7, 8). Consequently, knockdown of HERC2 abrogates ubiquitin-dependent retention of repair factors such as 53BP1, RAP80 and BRCA1. Together with the increased radiosensitivity of HERC2-depleted cells, these results uncover a regulatory layer in the orchestration of protein interactions on damaged chromosomes and they underscore the role of ubiquitin-mediated signalling in genome maintenance. PMID:20023648

  16. 53BP1 deficiency combined with telomere dysfunction activates ATR-dependent DNA damage response.

    PubMed

    Martínez, Paula; Flores, Juana M; Blasco, Maria A

    2012-04-16

    TRF1 protects mammalian telomeres from fusion and fragility. Depletion of TRF1 leads to telomere fusions as well as accumulation of γ-H2AX foci and activation of both the ataxia telangiectasia mutated (ATM)- and the ataxia telangiectasia and Rad3 related (ATR)-mediated deoxyribonucleic acid (DNA) damage response (DDR) pathways. 53BP1, which is also present at dysfunctional telomeres, is a target of ATM that accumulates at DNA double-strand breaks and favors nonhomologous end-joining (NHEJ) repair over ATM-dependent resection and homology-directed repair (homologous recombination [HR]). To address the role of 53BP1 at dysfunctional telomeres, we generated mice lacking TRF1 and 53BP1. 53BP1 deficiency significantly rescued telomere fusions in mouse embryonic fibroblasts (MEFs) lacking TRF1, but they showed evidence of a switch from the NHEJ- to HR-mediated repair of uncapped telomeres. Concomitantly, double-mutant MEFs showed evidence of hyperactivation of the ATR-dependent DDR. In intact mice, combined 53BP1/TRF1 deficiency in stratified epithelia resulted in earlier onset of DNA damage and increased CHK1 phosphorylation during embryonic development, leading to aggravation of skin phenotypes. PMID:22508511

  17. Lyn tyrosine kinase promotes silencing of ATM-dependent checkpoint signaling during recovery from DNA double-strand breaks

    SciTech Connect

    Fukumoto, Yasunori Kuki, Kazumasa; Morii, Mariko; Miura, Takahito; Honda, Takuya; Ishibashi, Kenichi; Hasegawa, Hitomi; Kubota, Sho; Ide, Yudai; Yamaguchi, Noritaka; Nakayama, Yuji; Yamaguchi, Naoto

    2014-09-26

    Highlights: • Inhibition of Src family kinases decreased γ-H2AX signal. • Inhibition of Src family increased ATM-dependent phosphorylation of Chk2 and Kap1. • shRNA-mediated knockdown of Lyn increased phosphorylation of Kap1 by ATM. • Ectopic expression of Src family kinase suppressed ATM-mediated Kap1 phosphorylation. • Src is involved in upstream signaling for inactivation of ATM signaling. - Abstract: DNA damage activates the DNA damage checkpoint and the DNA repair machinery. After initial activation of DNA damage responses, cells recover to their original states through completion of DNA repair and termination of checkpoint signaling. Currently, little is known about the process by which cells recover from the DNA damage checkpoint, a process called checkpoint recovery. Here, we show that Src family kinases promote inactivation of ataxia telangiectasia mutated (ATM)-dependent checkpoint signaling during recovery from DNA double-strand breaks. Inhibition of Src activity increased ATM-dependent phosphorylation of Chk2 and Kap1. Src inhibition increased ATM signaling both in G2 phase and during asynchronous growth. shRNA knockdown of Lyn increased ATM signaling. Src-dependent nuclear tyrosine phosphorylation suppressed ATM-mediated Kap1 phosphorylation. These results suggest that Src family kinases are involved in upstream signaling that leads to inactivation of the ATM-dependent DNA damage checkpoint.

  18. The catalytic subunit of DNA-dependent protein kinase is required for cellular resistance to oxidative stress independent of DNA double strand break repair

    PubMed Central

    Li, Mengxia; Lin, Yu-Fen; Palchik, Guillermo; Matsunaga, Shinji; Wang, Dong; Chen, Benjamin P.C.

    2014-01-01

    DNA-dependent protein kinase catalytic subunit (DNA-PKcs) and Ataxia telangiectasia mutated (ATM) are the two major kinases involved in DNA double-strand break (DSB) repair, and are required for cellular resistance to ionizing radiation. While ATM is the key upstream kinase for DSB signaling, DNA-PKcs is primarily involved in DSB repair through the non-homologous end-joining (NHEJ) mechanism. In addition to DSB repair, ATM has been shown to be involved in oxidative stress response and could be activated directly in vitro upon hydrogen peroxide (H2O2) treatment. However, the role of DNA-PKcs in cellular response to oxidative stress is not clear. We hypothesize that DNA-PKcs may participate in the regulation of ATM activation in response to oxidative stress, and that this regulatory role is independent of its role in DNA double strand break repair. Our findings reveal that H2O2 induces hyperactivation of ATM signaling in DNA-PKcs deficient, but not Ligase 4 deficient cells, suggesting an NHEJ-independent role for DNA-PKcs. Furthermore, DNA-PKcs deficiency leads to the elevation of reactive oxygen species (ROS) production, and to a decrease in cellular survival against H2O2. For the first time, our results reveal that DNA-PKcs plays a non-canonical role in the cellular response to oxidative stress, which is independent from its role in NHEJ. In addition, DNA-PKcs is a critical regulator of the oxidative stress response and contributes to the maintenance of redox homeostasis. Our findings reveal that DNA-PKcs is required for cellular resistance to oxidative stress and suppression of ROS build-up independently to its function in DSB repair. PMID:25224041

  19. Signalling of DNA damage and cytokines across cell barriers exposed to nanoparticles depends on barrier thickness

    NASA Astrophysics Data System (ADS)

    Sood, A.; Salih, S.; Roh, D.; Lacharme-Lora, L.; Parry, M.; Hardiman, B.; Keehan, R.; Grummer, R.; Winterhager, E.; Gokhale, P. J.; Andrews, P. W.; Abbott, C.; Forbes, K.; Westwood, M.; Aplin, J. D.; Ingham, E.; Papageorgiou, I.; Berry, M.; Liu, J.; Dick, A. D.; Garland, R. J.; Williams, N.; Singh, R.; Simon, A. K.; Lewis, M.; Ham, J.; Roger, L.; Baird, D. M.; Crompton, L. A.; Caldwell, M. A.; Swalwell, H.; Birch-Machin, M.; Lopez-Castejon, G.; Randall, A.; Lin, H.; Suleiman, M.-S.; Evans, W. H.; Newson, R.; Case, C. P.

    2011-12-01

    The use of nanoparticles in medicine is ever increasing, and it is important to understand their targeted and non-targeted effects. We have previously shown that nanoparticles can cause DNA damage to cells cultured below a cellular barrier without crossing this barrier. Here, we show that this indirect DNA damage depends on the thickness of the cellular barrier, and it is mediated by signalling through gap junction proteins following the generation of mitochondrial free radicals. Indirect damage was seen across both trophoblast and corneal barriers. Signalling, including cytokine release, occurred only across bilayer and multilayer barriers, but not across monolayer barriers. Indirect toxicity was also observed in mice and using ex vivo explants of the human placenta. If the importance of barrier thickness in signalling is a general feature for all types of barriers, our results may offer a principle with which to limit the adverse effects of nanoparticle exposure and offer new therapeutic approaches.

  20. Coarse-grained model of conformation-dependent electrophoretic mobility and its influence on DNA dynamics.

    PubMed

    Pandey, Harsh; Underhill, Patrick T

    2015-11-01

    The electrophoretic mobility of molecules such as λ-DNA depends on the conformation of the molecule. It has been shown that electrohydrodynamic interactions between parts of the molecule lead to a mobility that depends on conformation and can explain some experimental observations. We have developed a new coarse-grained model that incorporates these changes of mobility into a bead-spring chain model. Brownian dynamics simulations have been performed using this model. The model reproduces the cross-stream migration that occurs in capillary electrophoresis when pressure-driven flow is applied parallel or antiparallel to the electric field. The model also reproduces the change of mobility when the molecule is stretched significantly in an extensional field. We find that the conformation-dependent mobility can lead to a new type of unraveling of the molecule in strong fields. This occurs when different parts of the molecule have different mobilities and the electric field is large. PMID:26651689

  1. Coarse-grained model of conformation-dependent electrophoretic mobility and its influence on DNA dynamics

    NASA Astrophysics Data System (ADS)

    Pandey, Harsh; Underhill, Patrick T.

    2015-11-01

    The electrophoretic mobility of molecules such as λ -DNA depends on the conformation of the molecule. It has been shown that electrohydrodynamic interactions between parts of the molecule lead to a mobility that depends on conformation and can explain some experimental observations. We have developed a new coarse-grained model that incorporates these changes of mobility into a bead-spring chain model. Brownian dynamics simulations have been performed using this model. The model reproduces the cross-stream migration that occurs in capillary electrophoresis when pressure-driven flow is applied parallel or antiparallel to the electric field. The model also reproduces the change of mobility when the molecule is stretched significantly in an extensional field. We find that the conformation-dependent mobility can lead to a new type of unraveling of the molecule in strong fields. This occurs when different parts of the molecule have different mobilities and the electric field is large.

  2. TNKS1BP1 functions in DNA double-strand break repair though facilitating DNA-PKcs autophosphorylation dependent on PARP-1

    PubMed Central

    Zou, Lian-Hong; Shang, Zeng-Fu; Tan, Wei; Liu, Xiao-Dan; Xu, Qin-Zhi; Song, Man; Wang, Yu; Guan, Hua; Zhang, Shi-Meng; Yu, Lan; Zhong, Cai-Gao; Zhou, Ping-Kun

    2015-01-01

    TNKS1BP1 was originally identified as an interaction protein of tankyrase 1, which belongs to the poly(ADP-ribose) polymerase (PARP) superfamily. PARP members play important roles for example in DNA repair, telomere stability and mitosis regulation. Although the TNKS1BP1 protein was considered to be a poly(ADP-ribosyl)ation acceptor of tankyrase 1, its function is still unknown. Here we firstly identified that TNKS1BP1 was up-regulated by ionizing radiation (IR) and the depletion of TNKS1BP1 significantly sensitized cancer cells to IR. Neutral comet assay, pulsed-field gel electrophoresis, and γH2AX foci analysis indicated that TNKS1BP1 is required for the efficient repair of DNA double-strand breaks (DSB). The TNKS1BP1 protein was demonstrated to interact with DNA-dependent protein kinase (DNA-PKcs) and poly(ADP-ribose) polymerase 1 (PARP-1), by co-immunoprecipitation analysis. Moreover, TNKS1BP1 was shown to promote the association of PARP-1 and DNA-PKcs. Overexpression of TNKS1BP1 induced the autophosphorylation of DNA-PKcs/Ser2056 in a PARP-1 dependent manner, which contributed to an increased capability of DNA DSB repair. Inhibition of PARP-1 blocked the TNKS1BP1-mediated DNA-PKcs autophosphorylation and attenuated the PARylation of DNA-PKcs. TNKS1BP1 is a newly described component of the DNA DSB repair machinery, which provides much more mechanistic evidence for the rationale of developing effective anticancer measures by targeting PARP-1 and DNA-PKcs. PMID:25749521

  3. Coordinate 5′ and 3′ endonucleolytic trimming of terminally blocked blunt DNA double-strand break ends by Artemis nuclease and DNA-dependent protein kinase

    PubMed Central

    Yannone, Steven M.; Khan, Imran S.; Zhou, Rui-Zhe; Zhou, Tong; Valerie, Kristoffer; Povirk, Lawrence F.

    2008-01-01

    Previous work showed that, in the presence of DNA-dependent protein kinase (DNA-PK), Artemis slowly trims 3′-phosphoglycolate-terminated blunt ends. To examine the trimming reaction in more detail, long internally labeled DNA substrates were treated with Artemis. In the absence of DNA-PK, Artemis catalyzed extensive 5′→3′ exonucleolytic resection of double-stranded DNA. This resection required a 5′-phosphate, but did not require ATP, and was accompanied by endonucleolytic cleavage of the resulting 3′ overhang. In the presence of DNA-PK, Artemis-mediated trimming was more limited, was ATP-dependent and did not require a 5′-phosphate. For a blunt end with either a 3′-phosphoglycolate or 3′-hydroxyl terminus, endonucleolytic trimming of 2–4 nucleotides from the 3′-terminal strand was accompanied by trimming of 6 nt from the 5′-terminal strand. The results suggest that autophosphorylated DNA-PK suppresses the exonuclease activity of Artemis toward blunt-ended DNA, and promotes slow and limited endonucleolytic trimming of the 5′-terminal strand, resulting in short 3′ overhangs that are trimmed endonucleolytically. Thus, Artemis and DNA-PK can convert terminally blocked DNA ends of diverse geometry and chemical structure to a form suitable for polymerase-mediated patching and ligation, with minimal loss of terminal sequence. Such processing could account for the very small deletions often found at DNA double-strand break repair sites. PMID:18440975

  4. Carbon monoxide stimulates Ca2+ -dependent big-conductance K channels in the cortical collecting duct.

    PubMed

    Wang, Zhijian; Yue, Peng; Lin, Dao-Hong; Wang, Wen-Hui

    2013-03-01

    We used the patch-clamp technique to examine the role of carbon monoxide (CO) in regulating Ca(2+)-activated big-conductance K (BK) channels in the principal cell of the cortical collecting duct (CCD). Application of CORM3 or CORM2, a CO donor, activated BK channels in the CCD, whereas adding inactivated CORM2/3 had no effect. Superfusion of the CCD with CO-bubbled bath solution also activated the BK channels in the cell-attached patches. The effect of CO on BK channels was not dependent on nitric oxide synthase (NOS) because the effect of CORM3 was also observed in the CCD treated with l-NAME, an agent that inhibits the NOS. Adding a membrane-permeable cGMP analog, 8-bromo-cGMP, significantly increased the BK channel in the CCD. However, inhibition of soluble guanylate cyclase failed to abolish the stimulatory effect of CORM3 on BK channels. Moreover, inhibition of cGMP-dependent protein kinase G did not block the stimulatory effect of CORM3 on the BK channels, suggesting that the stimulatory effect of CO on the BK channels was, at least partially, induced by a cGMP-independent mechanism. Western blot demonstrated that heme oxygenase type 1 (HO-1) and HO-2 were expressed in the kidney. Moreover, a high-K (HK) intake increased the expression of HO-1 but not HO-2 in the kidney. A HK intake also increased renal HO activity defined by NADPH-dependent CO generation following addition of heme in the cell lysate from renal cortex and outer medulla. The role of HO in regulating BK channel activity in the CCD was also suggested by experiments in which application of hemin increased the BK channels. The stimulatory effect of hemin on the BK channels was blocked by SnMP, a HO inhibitor. But, adding CORM3 was still able to activate the BK channels in the presence of SnMP. We conclude that CO activates the BK channels, at least partially, through a NO-cGMP-independent pathway and that HO plays a role in mediating the effect of HK intake on the BK channels in the CCD. PMID

  5. Simple Elastic Network Models for Exhaustive Analysis of Long Double-Stranded DNA Dynamics with Sequence Geometry Dependence

    PubMed Central

    Isami, Shuhei; Sakamoto, Naoaki; Nishimori, Hiraku; Awazu, Akinori

    2015-01-01

    Simple elastic network models of DNA were developed to reveal the structure-dynamics relationships for several nucleotide sequences. First, we propose a simple all-atom elastic network model of DNA that can explain the profiles of temperature factors for several crystal structures of DNA. Second, we propose a coarse-grained elastic network model of DNA, where each nucleotide is described only by one node. This model could effectively reproduce the detailed dynamics obtained with the all-atom elastic network model according to the sequence-dependent geometry. Through normal-mode analysis for the coarse-grained elastic network model, we exhaustively analyzed the dynamic features of a large number of long DNA sequences, approximately ∼150 bp in length. These analyses revealed positive correlations between the nucleosome-forming abilities and the inter-strand fluctuation strength of double-stranded DNA for several DNA sequences. PMID:26624614

  6. iTRAQ-based chromatin proteomic screen reveals CHD4-dependent recruitment of MBD2 to sites of DNA damage.

    PubMed

    Sun, Yazhou; Yang, Yeran; Shen, Hongyan; Huang, Min; Wang, Zhifeng; Liu, Yang; Zhang, Hui; Tang, Tie-Shan; Guo, Caixia

    2016-02-26

    Many DNA repair proteins can be recruited to DNA damage sites upon genotoxic stress. In order to search potential DNA repair proteins involved in cellular response to mitomycin C treatment, we utilized a quantitative proteome to uncover proteins that manifest differentially enrichment in the chromatin fraction after DNA damage. 397 proteins were identified, among which many factors were shown to be involved in chromatin modification and DNA repair by GO analysis. Specifically, methyl-CpG-binding domain protein 2 (MBD2) is revealed to be recruited to DNA damage sites after laser microirradiation, which was mediated through MBD domain and MBD2 C-terminus. Additionally, the recruitment of MBD2 is dependent on poly (ADP-ribose) and chromodomain helicase DNA-binding protein 4 (CHD4). Moreover, knockdown of MBD2 by CRISPR-Cas9 technique results in MMC sensitivity in mammalian cells. PMID:26827827

  7. State-dependent access of anions to the cystic fibrosis transmembrane conductance regulator chloride channel pore.

    PubMed

    Fatehi, Mohammad; Linsdell, Paul

    2008-03-01

    The cystic fibrosis transmembrane conductance regulator (CFTR) Cl(-) channel is gated by intracellular factors; however, conformational changes in the channel pore associated with channel activation have not been identified. We have used patch clamp recording to investigate the state-dependent accessibility of substituted cysteine residues in the CFTR channel pore to a range of cysteine-reactive reagents applied to the extracellular side of the membrane. Using functional modification of the channel current-voltage relationship as a marker of modification, we find that several positively charged reagents are able to penetrate deeply into the pore from the outside irrespective of whether or not the channels have been activated. In contrast, access of three anionic cysteine-reactive reagents, the methanesulfonate sodium (2-sulfonatoethyl)methanesulfonate, the organic mercurial p-chloromercuriphenylsulfonic acid, and the permeant anion Au(CN)(2)(-), to several different sites in the pore is strictly limited prior to channel activation. This suggests that in nonactivated channels some ion selectivity mechanism exists to exclude anions yet permit cations into the channel pore from the extracellular solution. We suggest that activation of CFTR channels involves a conformational change in the pore that removes a strong selectivity against anion entry from the extracellular solution. We propose further that this conformational change occurs in advance of channel opening, suggesting that multiple distinct closed pore conformations exist. PMID:18167343

  8. Purification of two DNA-dependent adenosinetriphosphatases having DNA helicase activity from HeLa cells and comparison of the properties of the two enzymes.

    PubMed

    Seki, M; Yanagisawa, J; Kohda, T; Sonoyama, T; Ui, M; Enomoto, T

    1994-03-01

    DNA-dependent ATPase activities in crude extracts prepared from HeLa cells were separated into five peaks designated Q1 to Q5 by FPLC Mono Q column chromatography. In our previous study, we observed that crude extracts prepared from xeroderma pigmentosum complementation group C (XP-C) cells contained no DNA-dependent ATPase activity at the peak position of Q1 and exhibited a broader peak with higher activity than normal Q2 at the peak position of Q2 [Yanagisawa, J., Seki, M., Ui, M., & Enomoto, T. (1992) J. Biol. Chem. 267, 3585-3588]. We have purified two DNA-dependent ATPases Q1 and Q2 from HeLa cells and characterized their properties in order to obtain a means to discriminate ATPase Q1 from Q2 in XP-C cells. The apparent molecular masses of Q1 and Q2 on SDS-polyacrylamide gel electrophoresis were 73 and 100 kDa, respectively. The two enzymes required a divalent cation for activity. DNA-dependent ATPase Q1 hydrolyzed ATP and dATP and Q2 hydrolyzed ATP preferentially among the nucleotides tested. Both enzymes preferred single-stranded DNA as a cofactor. The DNA-dependent ATPase activity of Q2 was inhibited by 90% in the presence of 200 mM NaCl, whereas that of Q1 was not affected by NaCl at concentrations up to 200 mM. Both enzymes had DNA helicase activity, that of Q1 being more resistant to NaCl than that of Q2. The DNA helicase activity of Q2 was about 150-fold higher than that of Q1, when compared with units of ATPase activity.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:8056767

  9. Universal scaling of crowding-induced DNA mobility is coupled with topology-dependent molecular compaction and elongation.

    PubMed

    Gorczyca, Stephanie M; Chapman, Cole D; Robertson-Anderson, Rae M

    2015-10-21

    Using single-molecule fluorescence microscopy and particle-tracking techniques, we elucidate the role DNA topology plays in the diffusion and conformational dynamics of crowded DNA molecules. We focus on large (115 kbp), double-stranded ring and linear DNA crowded by varying concentrations (0-40%) of dextran (10, 500 kDa) that mimic cellular conditions. By tracking the center-of-mass and measuring the lengths of the major and minor axes of single DNA molecules, we characterize both DNA mobility reduction as well as crowding-induced conformational changes (from random spherical coils). We reveal novel topology-dependent conformations, with single ring molecules undergoing compaction to ordered spherical configurations ∼20% smaller than dilute random coils, while linear DNA elongates by ∼2-fold. Surprisingly, these highly different conformations result in nearly identical exponential mobility reduction dependent solely on crowder volume fraction Φ, revealing a universal critical crowding concentration of Φc≅ 2.3. Beyond Φc DNA exhibits topology-independent conformational relaxation dynamics despite highly distinct topology-driven conformations. Our collective results reveal that topology-dependent conformational changes, unique to crowded environments, enable DNA to overcome the classically expected mobility reduction that high-viscosity crowded environments impose. Such coupled universal dynamics suggest a mechanism for DNA to maintain sufficient mobility required for wide-ranging biological processes despite severe cellular crowding. PMID:26303877

  10. Comparison of Large Subunits of Type II DNA-dependent RNA Polymerases from Higher Plants.

    PubMed

    Kidd, G H; Link, G; Bogorad, L

    1979-10-01

    Two-dimensional tryptic mapping of (125)I-labeled polypeptides has been employed to compare the large subunits of type II DNA-dependent RNA polymerases from maize, parsley (Petroselinum sativum), and wheat. Maps of the 220 kilodalton (kd) and 140 kd subunits from wheat RNA polymerase II differ from those of the corresponding subunits from parsley enzyme II. The 180 kd subunits from maize and parsley type II enzymes also yield dissimilar tryptic maps. Thus, despite similarities in molecular mass, the large subunits of wheat, parsley, and maize type II RNA polymerases are unique to each individual plant species. PMID:16661032

  11. Temperature dependence of electronic heat capacity in Holstein model of DNA

    NASA Astrophysics Data System (ADS)

    Fialko, N.; Sobolev, E.; Lakhno, V.

    2016-04-01

    The dynamics of charge migration was modeled to calculate temperature dependencies of its thermodynamic equilibrium values such as energy and electronic heat capacity in homogeneous adenine fragments. The energy varies from nearly polaron one at T ∼ 0 to midpoint of the conductivity band at high temperatures. The peak on the graph of electronic heat capacity is observed at the polaron decay temperature.

  12. Correlating Humidity-Dependent Ionically Conductive Surface Area with Transport Phenomena in Proton-Exchange Membranes

    SciTech Connect

    He, Qinggang; Kusoglu, Ahmet; Lucas, Ivan T.; Clark, Kyle; Weber, Adam Z.; Kostecki, Robert

    2011-08-01

    The objective of this effort was to correlate the local surface ionic conductance of a Nafion? 212 proton-exchange membrane with its bulk and interfacial transport properties as a function of water content. Both macroscopic and microscopic proton conductivities were investigated at different relative humidity levels, using electrochemical impedance spectroscopy and current-sensing atomic force microscopy (CSAFM). We were able to identify small ion-conducting domains that grew with humidity at the surface of the membrane. Numerical analysis of the surface ionic conductance images recorded at various relative humidity levels helped determine the fractional area of ion-conducting active sites. A simple square-root relationship between the fractional conducting area and observed interfacial mass-transport resistance was established. Furthermore, the relationship between the bulk ionic conductivity and surface ionic conductance pattern of the Nafion? membrane was examined.

  13. XPD-dependent activation of apoptosis in response to triplex-induced DNA damage

    PubMed Central

    Kaushik Tiwari, Meetu; Rogers, Faye A.

    2013-01-01

    DNA sequences capable of forming triplexes are prevalent in the human genome and have been found to be intrinsically mutagenic. Consequently, a balance between DNA repair and apoptosis is critical to counteract their effect on genomic integrity. Using triplex-forming oligonucleotides to synthetically create altered helical distortions, we have determined that pro-apoptotic pathways are activated by the formation of triplex structures. Moreover, the TFIIH factor, XPD, occupies a central role in triggering apoptosis in response to triplex-induced DNA strand breaks. Here, we show that triplexes are capable of inducing XPD-independent double strand breaks, which result in the formation of γH2AX foci. XPD was subsequently recruited to the triplex-induced double strand breaks and co-localized with γH2AX at the damage site. Furthermore, phosphorylation of H2AX tyrosine 142 was found to stimulate the signaling pathway of XPD-dependent apoptosis. We suggest that this mechanism may play an active role in minimizing genomic instability induced by naturally occurring noncanonical structures, perhaps protecting against cancer initiation. PMID:23913414

  14. DNA forms indicate rolling circle and recombination-dependent replication of Abutilon mosaic virus

    PubMed Central

    Jeske, Holger; Lütgemeier, Martin; Preiß, Werner

    2001-01-01

    Geminiviruses have spread worldwide and have become increasingly important in crop plants during recent decades. Recombination among geminiviruses was one major source of new variants. Geminiviruses replicate via rolling circles, confirmed here by electron microscopic visualization and two-dimensional gel analysis of Abutilon mosaic virus (AbMV) DNA. However, only a minority of DNA intermediates are consistent with this model. The majority are compatible with recombination-dependent replication (RDR). During development of naturally infected leaves, viral intermediates compatible with both models appeared simultaneously, whereas agro-infection of leaf discs with AbMV led to an early appearance of RDR forms but no RCR intermediates. Inactivation of viral genes ac2 and ac3 delayed replication, but produced the same DNA types as after wild-type infection, indicating that these genes were not essential for RDR in leaf discs. In conclusion, host factors alone or in combination with the viral AC1 protein are necessary and sufficient for the production of RDR intermediates. The consequences of an inherent geminiviral recombination activity for the use of pathogen-derived resistance traits are discussed. PMID:11689455

  15. Repressor activity of the RpoS/σS-dependent RNA polymerase requires DNA binding.

    PubMed

    Lévi-Meyrueis, Corinne; Monteil, Véronique; Sismeiro, Odile; Dillies, Marie-Agnès; Kolb, Annie; Monot, Marc; Dupuy, Bruno; Duarte, Sara Serradas; Jagla, Bernd; Coppée, Jean-Yves; Beraud, Mélanie; Norel, Françoise

    2015-02-18

    The RpoS/σ(S) sigma subunit of RNA polymerase (RNAP) activates transcription of stationary phase genes in many Gram-negative bacteria and controls adaptive functions, including stress resistance, biofilm formation and virulence. In this study, we address an important but poorly understood aspect of σ(S)-dependent control, that of a repressor. Negative regulation by σ(S) has been proposed to result largely from competition between σ(S) and other σ factors for binding to a limited amount of core RNAP (E). To assess whether σ(S) binding to E alone results in significant downregulation of gene expression by other σ factors, we characterized an rpoS mutant of Salmonella enterica serovar Typhimurium producing a σ(S) protein proficient for Eσ(S) complex formation but deficient in promoter DNA binding. Genome expression profiling and physiological assays revealed that this mutant was defective for negative regulation, indicating that gene repression by σ(S) requires its binding to DNA. Although the mechanisms of repression by σ(S) are likely specific to individual genes and environmental conditions, the study of transcription downregulation of the succinate dehydrogenase operon suggests that σ competition at the promoter DNA level plays an important role in gene repression by Eσ(S). PMID:25578965

  16. Repressor activity of the RpoS/σS-dependent RNA polymerase requires DNA binding

    PubMed Central

    Lévi-Meyrueis, Corinne; Monteil, Véronique; Sismeiro, Odile; Dillies, Marie-Agnès; Kolb, Annie; Monot, Marc; Dupuy, Bruno; Duarte, Sara Serradas; Jagla, Bernd; Coppée, Jean-Yves; Beraud, Mélanie; Norel, Françoise

    2015-01-01

    The RpoS/σS sigma subunit of RNA polymerase (RNAP) activates transcription of stationary phase genes in many Gram-negative bacteria and controls adaptive functions, including stress resistance, biofilm formation and virulence. In this study, we address an important but poorly understood aspect of σS-dependent control, that of a repressor. Negative regulation by σS has been proposed to result largely from competition between σS and other σ factors for binding to a limited amount of core RNAP (E). To assess whether σS binding to E alone results in significant downregulation of gene expression by other σ factors, we characterized an rpoS mutant of Salmonella enterica serovar Typhimurium producing a σS protein proficient for EσS complex formation but deficient in promoter DNA binding. Genome expression profiling and physiological assays revealed that this mutant was defective for negative regulation, indicating that gene repression by σS requires its binding to DNA. Although the mechanisms of repression by σS are likely specific to individual genes and environmental conditions, the study of transcription downregulation of the succinate dehydrogenase operon suggests that σ competition at the promoter DNA level plays an important role in gene repression by EσS. PMID:25578965

  17. RNF4 regulates DNA double-strand break repair in a cell cycle-dependent manner

    PubMed Central

    Kuo, Ching-Ying; Li, Xu; Stark, Jeremy M.; Shih, Hsiu-Ming; Ann, David K.

    2016-01-01

    Abstract Both RNF4 and KAP1 play critical roles in the response to DNA double-strand breaks (DSBs), but the functional interplay of RNF4 and KAP1 in regulating DNA damage response remains unclear. We have previously demonstrated the recruitment and degradation of KAP1 by RNF4 require the phosphorylation of Ser824 (pS824) and SUMOylation of KAP1. In this report, we show the retention of DSB-induced pS824-KAP1 foci and RNF4 abundance are inversely correlated as cell cycle progresses. Following irradiation, pS824-KAP1 foci predominantly appear in the cyclin A (-) cells, whereas RNF4 level is suppressed in the G0-/G1-phases and then accumulates during S-/G2-phases. Notably, 53BP1 foci, but not BRCA1 foci, co-exist with pS824-KAP1 foci. Depletion of KAP1 yields opposite effect on the dynamics of 53BP1 and BRCA1 loading, favoring homologous recombination repair. In addition, we identify p97 is present in the RNF4-KAP1 interacting complex and the inhibition of p97 renders MCF7 breast cancer cells relatively more sensitive to DNA damage. Collectively, these findings suggest that combined effect of dynamic recruitment of RNF4 to KAP1 regulates the relative occupancy of 53BP1 and BRCA1 at DSB sites to direct DSB repair in a cell cycle-dependent manner. PMID:26766492

  18. Activated platelets rescue apoptotic cells via paracrine activation of EGFR and DNA-dependent protein kinase

    PubMed Central

    Au, A E-L; Sashindranath, M; Borg, R J; Kleifeld, O; Andrews, R K; Gardiner, E E; Medcalf, R L; Samson, A L

    2014-01-01

    Platelet activation is a frontline response to injury, not only essential for clot formation but also important for tissue repair. Indeed, the reparative influence of platelets has long been exploited therapeutically where application of platelet concentrates expedites wound recovery. Despite this, the mechanisms of platelet-triggered cytoprotection are poorly understood. Here, we show that activated platelets accumulate in the brain to exceptionally high levels following injury and release factors that potently protect neurons from apoptosis. Kinomic microarray and subsequent kinase inhibitor studies showed that platelet-based neuroprotection relies upon paracrine activation of the epidermal growth factor receptor (EGFR) and downstream DNA-dependent protein kinase (DNA-PK). This same anti-apoptotic cascade stimulated by activated platelets also provided chemo-resistance to several cancer cell types. Surprisingly, deep proteomic profiling of the platelet releasate failed to identify any known EGFR ligand, indicating that activated platelets release an atypical activator of the EGFR. This study is the first to formally associate platelet activation to EGFR/DNA-PK – an endogenous cytoprotective cascade. PMID:25210793

  19. RNF4 regulates DNA double-strand break repair in a cell cycle-dependent manner.

    PubMed

    Kuo, Ching-Ying; Li, Xu; Stark, Jeremy M; Shih, Hsiu-Ming; Ann, David K

    2016-03-18

    Both RNF4 and KAP1 play critical roles in the response to DNA double-strand breaks (DSBs), but the functional interplay of RNF4 and KAP1 in regulating DNA damage response remains unclear. We have previously demonstrated the recruitment and degradation of KAP1 by RNF4 require the phosphorylation of Ser824 (pS824) and SUMOylation of KAP1. In this report, we show the retention of DSB-induced pS824-KAP1 foci and RNF4 abundance are inversely correlated as cell cycle progresses. Following irradiation, pS824-KAP1 foci predominantly appear in the cyclin A (-) cells, whereas RNF4 level is suppressed in the G0-/G1-phases and then accumulates during S-/G2-phases. Notably, 53BP1 foci, but not BRCA1 foci, co-exist with pS824-KAP1 foci. Depletion of KAP1 yields opposite effect on the dynamics of 53BP1 and BRCA1 loading, favoring homologous recombination repair. In addition, we identify p97 is present in the RNF4-KAP1 interacting complex and the inhibition of p97 renders MCF7 breast cancer cells relatively more sensitive to DNA damage. Collectively, these findings suggest that combined effect of dynamic recruitment of RNF4 to KAP1 regulates the relative occupancy of 53BP1 and BRCA1 at DSB sites to direct DSB repair in a cell cycle-dependent manner. PMID:26766492

  20. Temperature and frequency dependence of AC conductivity of new quaternary Se-Te-Bi-Pb chalcogenide glasses

    NASA Astrophysics Data System (ADS)

    Yadav, Preeti; Sharma, Ambika

    2016-05-01

    The aim of the present work is to study the temperature and frequency dependence of ac conductivity of new quaternary Se84-xTe15Bi1.0Pbx chalcogenide glasses. The Se84-xTe15Bi1.0Pbx (x = 2, 6) glassy alloys are prepared by using melt quenching technique. The temperature and frequency dependent behavior of ac conductivity σac(ω) has been carried out in the frequency range 42 Hz to 5 MHz and in the temperature range of 298-323 K below glass transition temperature. The behavior of ac conductivity is described in terms of the power law ωs. The obtained temperature dependence behavior of ac conductivity and frequency component (s) are explained by means of correlated barrier hopping model recommended by Elliot.

  1. Dependence of the conductance change on the molecular orbitals in Ag and Au electrodes

    NASA Astrophysics Data System (ADS)

    Kim, Hyun Sung; Kim, Taekyeong

    2016-01-01

    The conductance change in single-molecule junctions due to the molecular orbitals and the metal's Fermi energy was investigated by using a scanning tunneling microscopy break-junction technique with Ag and Au electrodes. 4,4'-diaminobiphenyl and 4,4'-dicyanobiphenyl as the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) junctions were used. The amine-linked HOMO-conducting junction had a lower conductance, and cyano-linked LUMO-conducting junction had a higher conductance for Ag electrode compared to Au electrode. These results are attributed to the difference between the metal electrode Fermi energy and the molecular orbital level in the metal-molecule junction. Furthermore, 2,7-diaminofluorene exhibited a higher conductance but the identical molecular plateau length for the Ag electrodes compared to that of 4,4'-diaminobiphenyl indicating that the twist angle of the molecular backbone affects the conductance.

  2. Inverse Temperature Dependence of Nuclear Quantum Effects in DNA Base Pairs.

    PubMed

    Fang, Wei; Chen, Ji; Rossi, Mariana; Feng, Yexin; Li, Xin-Zheng; Michaelides, Angelos

    2016-06-01

    Despite the inherently quantum mechanical nature of hydrogen bonding, it is unclear how nuclear quantum effects (NQEs) alter the strengths of hydrogen bonds. With this in mind, we use ab initio path integral molecular dynamics to determine the absolute contribution of NQEs to the binding in DNA base pair complexes, arguably the most important hydrogen-bonded systems of all. We find that depending on the temperature, NQEs can either strengthen or weaken the binding within the hydrogen-bonded complexes. As a somewhat counterintuitive consequence, NQEs can have a smaller impact on hydrogen bond strengths at cryogenic temperatures than at room temperature. We rationalize this in terms of a competition of NQEs between low-frequency and high-frequency vibrational modes. Extending this idea, we also propose a simple model to predict the temperature dependence of NQEs on hydrogen bond strengths in general. PMID:27195654

  3. Inverse Temperature Dependence of Nuclear Quantum Effects in DNA Base Pairs

    PubMed Central

    2016-01-01

    Despite the inherently quantum mechanical nature of hydrogen bonding, it is unclear how nuclear quantum effects (NQEs) alter the strengths of hydrogen bonds. With this in mind, we use ab initio path integral molecular dynamics to determine the absolute contribution of NQEs to the binding in DNA base pair complexes, arguably the most important hydrogen-bonded systems of all. We find that depending on the temperature, NQEs can either strengthen or weaken the binding within the hydrogen-bonded complexes. As a somewhat counterintuitive consequence, NQEs can have a smaller impact on hydrogen bond strengths at cryogenic temperatures than at room temperature. We rationalize this in terms of a competition of NQEs between low-frequency and high-frequency vibrational modes. Extending this idea, we also propose a simple model to predict the temperature dependence of NQEs on hydrogen bond strengths in general. PMID:27195654

  4. High-Capacity Conductive Nanocellulose Paper Sheets for Electrochemically Controlled Extraction of DNA Oligomers

    PubMed Central

    Razaq, Aamir; Nyström, Gustav; Strømme, Maria; Mihranyan, Albert; Nyholm, Leif

    2011-01-01

    Highly porous polypyrrole (PPy)-nanocellulose paper sheets have been evaluated as inexpensive and disposable electrochemically controlled three-dimensional solid phase extraction materials. The composites, which had a total anion exchange capacity of about 1.1 mol kg−1, were used for extraction and subsequent release of negatively charged fluorophore tagged DNA oligomers via galvanostatic oxidation and reduction of a 30–50 nm conformal PPy layer on the cellulose substrate. The ion exchange capacity, which was, at least, two orders of magnitude higher than those previously reached in electrochemically controlled extraction, originated from the high surface area (i.e. 80 m2 g−1) of the porous composites and the thin PPy layer which ensured excellent access to the ion exchange material. This enabled the extractions to be carried out faster and with better control of the PPy charge than with previously employed approaches. Experiments in equimolar mixtures of (dT)6, (dT)20, and (dT)40 DNA oligomers showed that all oligomers could be extracted, and that the smallest oligomer was preferentially released with an efficiency of up to 40% during the reduction of the PPy layer. These results indicate that the present material is very promising for the development of inexpensive and efficient electrochemically controlled ion-exchange membranes for batch-wise extraction of biomolecules. PMID:22195031

  5. The Catalytic Subunit of DNA-Dependent Protein Kinase Coordinates with Polo-Like Kinase 1 to Facilitate Mitotic Entry.

    PubMed

    Lee, Kyung-Jong; Shang, Zeng-Fu; Lin, Yu-Fen; Sun, Jingxin; Morotomi-Yano, Keiko; Saha, Debabrata; Chen, Benjamin P C

    2015-04-01

    DNA-dependent protein kinase catalytic subunit (DNA-PKcs) is the key regulator of the non-homologous end joining pathway of DNA double-strand break repair. We have previously reported that DNA-PKcs is required for maintaining chromosomal stability and mitosis progression. Our further investigations reveal that deficiency in DNA-PKcs activity caused a delay in mitotic entry due to dysregulation of cyclin-dependent kinase 1 (Cdk1), the key driving force for cell cycle progression through G2/M transition. Timely activation of Cdk1 requires polo-like kinase 1 (Plk1), which affects modulators of Cdk1. We found that DNA-PKcs physically interacts with Plk1 and could facilitate Plk1 activation both in vitro and in vivo. Further, DNA-PKcs-deficient cells are highly sensitive to Plk1 inhibitor BI2536, suggesting that the coordination between DNA-PKcs and Plk1 is not only crucial to ensure normal cell cycle progression through G2/M phases but also required for cellular resistance to mitotic stress. On the basis of the current study, it is predictable that combined inhibition of DNA-PKcs and Plk1 can be employed in cancer therapy strategy for synthetic lethality. PMID:25925375

  6. A cDNA-dependent scintillation proximity assay for quantifying apolipoprotein A-I.

    PubMed

    Hanselman, J C; Schwab, D A; Rea, T J; Bisgaier, C L; Pape, M E

    1997-11-01

    We have developed a cDNA-dependent scintillation proximity assay (SPA) for rabbit apolipoprotein A-I that follows a classic radioimmunoassay scheme, in that antiserum and radiolabeled ligand are used in a process to quantify a source containing unlabeled ligand. To synthesize radiolabeled ligand we isolated a full-length rabbit apolipoprotein A-I (apoA-I) cDNA, transcribed the corresponding RNA in vitro, and synthesized radiolabeled apoA-I by including tritiated leucine in an in vitro translation reaction. Assay conditions were established which allowed quantification of unlabeled apoA-I over a range of 0.2 to 4 nanograms with intra- and interassay coefficients of variation of 5% and 10%, respectively. Purified rabbit apoA-I, apoA-I in rabbit liver parenchymal cell conditioned media, and apoA-I contained in rabbit plasma all generated parallel titration curves. Quantification of rabbit plasma apoA-I was not affected when sheep anti-rabbit apoA-I serum was mixed with sheep anti-rabbit apoB or apoE serum; thus, the antibody need not be specific to quantify the ligand of interest. To show utility of the assay, apoA-I mass was quantified in in vitro and in vivo models displaying altered apoA-I levels. In each model apoA-I values from the cDNA-dependent SPA and the established methodologies of Western blotting and electroimmunodiffusion were highly correlated. The approach outlined in this report should permit rapid development of scintillation proximity assays for other proteins given the widespread availability of full-length cDNAs. PMID:9392434

  7. Quantitative site-specific ADP-ribosylation profiling of DNA-dependent PARPs.

    PubMed

    Gagné, Jean-Philippe; Ethier, Chantal; Defoy, Daniel; Bourassa, Sylvie; Langelier, Marie-France; Riccio, Amanda A; Pascal, John M; Moon, Kyung-Mee; Foster, Leonard J; Ning, Zhibin; Figeys, Daniel; Droit, Arnaud; Poirier, Guy G

    2015-06-01

    An important feature of poly(ADP-ribose) polymerases (PARPs) is their ability to readily undergo automodification upon activation. Although a growing number of substrates were found to be poly(ADP-ribosyl)ated, including histones and several DNA damage response factors, PARPs themselves are still considered as the main acceptors of poly(ADP-ribose). By monitoring spectral counts of specific hydroxamic acid signatures generated after the conversion of the ADP-ribose modification onto peptides by hydroxylamine hydrolysis, we undertook a thorough mass spectrometry mapping of the glutamate and aspartate ADP-ribosylation sites onto automodified PARP-1, PARP-2 and PARP-3. Thousands of hydroxamic acid-conjugated peptides were identified with high confidence and ranked based on their spectral count. This semi-quantitative approach allowed us to locate the preferentially targeted residues in DNA-dependent PARPs. In contrast to what has been reported in the literature, automodification of PARP-1 is not predominantly targeted towards its BRCT domain. Our results show that interdomain linker regions that connect the BRCT to the WGR module and the WGR to the PRD domain undergo prominent ADP-ribosylation during PARP-1 automodification. We also found that PARP-1 efficiently automodifies the D-loop structure within its own catalytic fold. Interestingly, additional major ADP-ribosylation sites were identified in functional domains of PARP-1, including all three zinc fingers. Similar to PARP-1, specific residues located within the catalytic sites of PARP-2 and PARP-3 are major targets of automodification following their DNA-dependent activation. Together our results suggest that poly(ADP-ribosyl)ation hot spots make a dominant contribution to the overall automodification process. PMID:25800440

  8. Genomewide analysis of Drosophila GAGA factor target genes reveals context-dependent DNA binding

    PubMed Central

    van Steensel, Bas; Delrow, Jeffrey; Bussemaker, Harmen J.

    2003-01-01

    The association of sequence-specific DNA-binding factors with their cognate target sequences in vivo depends on the local molecular context, yet this context is poorly understood. To address this issue, we have performed genomewide mapping of in vivo target genes of Drosophila GAGA factor (GAF). The resulting list of ≈250 target genes indicates that GAF regulates many cellular pathways. We applied unbiased motif-based regression analysis to identify the sequence context that determines GAF binding. Our results confirm that GAF selectively associates with (GA)n repeat elements in vivo. GAF binding occurs in upstream regulatory regions, but less in downstream regions. Surprisingly, GAF binds abundantly to introns but is virtually absent from exons, even though the density of (GA)n is roughly the same. Intron binding occurs equally frequently in last introns compared with first introns, suggesting that GAF may not only regulate transcription initiation, but possibly also elongation. We provide evidence for cooperative binding of GAF to closely spaced (GA)n elements and explain the lack of GAF binding to exons by the absence of such closely spaced GA repeats. Our approach for revealing determinants of context-dependent DNA binding will be applicable to many other transcription factors. PMID:12601174

  9. Two recombination-dependent DNA replication pathways of bacteriophage T4, and their roles in mutagenesis and horizontal gene transfer

    PubMed Central

    Mosig, Gisela; Gewin, John; Luder, Andreas; Colowick, Nancy; Vo, Daniel

    2001-01-01

    Two major pathways of recombination-dependent DNA replication, “join-copy” and “join-cut-copy,” can be distinguished in phage T4: join-copy requires only early and middle genes, but two late proteins, endonuclease VII and terminase, are uniquely important in the join-cut-copy pathway. In wild-type T4, timing of these pathways is integrated with the developmental program and related to transcription and packaging of DNA. In primase mutants, which are defective in origin-dependent lagging-strand DNA synthesis, the late pathway can bypass the lack of primers for lagging-strand DNA synthesis. The exquisitely regulated synthesis of endo VII, and of two proteins from its gene, explains the delay of recombination-dependent DNA replication in primase (as well as topoisomerase) mutants, and the temperature-dependence of the delay. Other proteins (e.g., the single-stranded DNA binding protein and the products of genes 46 and 47) are important in all recombination pathways, but they interact differently with other proteins in different pathways. These homologous recombination pathways contribute to evolution because they facilitate acquisition of any foreign DNA with limited sequence homology during horizontal gene transfer, without requiring transposition or site-specific recombination functions. Partial heteroduplex repair can generate what appears to be multiple mutations from a single recombinational intermediate. The resulting sequence divergence generates barriers to formation of viable recombinants. The multiple sequence changes can also lead to erroneous estimates in phylogenetic analyses. PMID:11459968

  10. The cation selectivity and voltage dependence of the light-activated potassium conductance in scallop distal photoreceptor.

    PubMed Central

    Cornwall, M C; Gorman, A L

    1983-01-01

    Light-dependent voltage and current responses were measured from the distal hyperpolarizing photoreceptors of the scallop (Pecten irradians) retina. In normal external solution, the hyperpolarizing receptor potential was caused by a light-dependent K+ outward current. The magnitude of the hyperpolarizing receptor potential and the light-dependent outward current, measured at the resting potential, was graded with light intensity. In normal external solution, during prolonged illumination the light-dependent K+ outward current was characterized by an early peak and a subsequent plateau. Current responses to brief light flashes were reduced progressively during background illumination. In the absence of external Na+ ions, the reversal potential for the receptor potential changed 58 mV per 10-fold change in the extracellular K+ concentration. The estimated internal K+ concentration was 385 mM. The hyperpolarizing receptor potential produced by prolonged bright illumination consists of an early peak which decays to a plateau. This decay was determined by a decrease in the light-dependent K+ conductance during maintained illumination. The light-dependent conductance pathway passed outward currents better than inward K+ currents. The light-dependent K+ conductance was estimated to increase e-fold per 23-34 mV depolarization at the peak and during the plateau of the light response. The light-dependent conductance pathway was highly selective for K+ ions. The selectivity sequence for monovalent cations was T1+, K+ greater than Rb+ greater than NH4 greater than Cs+, Li+, Na+. External caesium and tetraethylammonium blocked inward but not outward K+ currents through the light-dependent K+ conductance pathway. The data suggest that K+ ions move through an aqueous pore which is controlled by light. PMID:6887051

  11. Doping dependence of electrical and thermal conductivity of nanoscale polyaniline thin films

    NASA Astrophysics Data System (ADS)

    Jin, Jiezhu; Wang, Qing; Haque, M. A.

    2010-05-01

    We performed simultaneous characterization of electrical and thermal conductivity of 55 nm thick polyaniline (PANI) thin films doped with different levels of camphor sulfonic acids (CSAs). The effect of the doping level is more pronounced on electrical conductivity than on thermal conductivity of PANIs, thereby greatly affecting their ratio that determines the thermoelectric efficiency. At the 60% (the molar ratio of CSA to phenyl-N repeat unit of PANI) doping level, PANI exhibited the maximum electrical and thermal conductivity due to the formation of mostly delocalized structures. Whereas polarons are the charge carriers responsible for the electrical conduction, phonons are believed to play a dominant role in the heat conduction in nanoscale doped PANI thin films.

  12. Homology-dependent repair is involved in 45S rDNA loss in plant CAF-1 mutants

    PubMed Central

    Muchová, Veronika; Amiard, Simon; Mozgová, Iva; Dvořáčková, Martina; Gallego, Maria E; White, Charles; Fajkus, Jiří

    2015-01-01

    Arabidopsis thaliana mutants in FAS1 and FAS2 subunits of chromatin assembly factor 1 (CAF1) show progressive loss of 45S rDNA copies and telomeres. We hypothesized that homology-dependent DNA damage repair (HDR) may contribute to the loss of these repeats in fas mutants. To test this, we generated double mutants by crossing fas mutants with knock-out mutants in RAD51B, one of the Rad51 paralogs of A. thaliana. Our results show that the absence of RAD51B decreases the rate of rDNA loss, confirming the implication of RAD51B-dependent recombination in rDNA loss in the CAF1 mutants. Interestingly, this effect is not observed for telomeric repeat loss, which thus differs from that acting in rDNA loss. Involvement of DNA damage repair in rDNA dynamics in fas mutants is further supported by accumulation of double-stranded breaks (measured as γ-H2AX foci) in 45S rDNA. Occurrence of the foci is not specific for S-phase, and is ATM-independent. While the foci in fas mutants occur both in the transcribed (intranucleolar) and non-transcribed (nucleoplasmic) fraction of rDNA, double fas rad51b mutants show a specific increase in the number of the intranucleolar foci. These results suggest that the repair of double-stranded breaks present in the transcribed rDNA region is RAD51B dependent and that this contributes to rDNA repeat loss in fas mutants, presumably via the single-stranded annealing recombination pathway. Our results also highlight the importance of proper chromatin assembly in the maintenance of genome stability. PMID:25359579

  13. Specific antigenic relationships between the RNA-dependent DNA polymerases of avian reticuloendotheliosis viruses and mammalian type C retroviruses.

    PubMed Central

    Bauer, G; Temin, H M

    1980-01-01

    Immunoglobulin G directed against the DNA polymerase of Rauscher murine leukemia virus (R-MuLV) could bind to 125I-labeled DNA polymerase of spleen necrosis virus (SNV), a member of the reticuloendotheliosis virus (REV) species. Competition radioimmunoassays showed the specificity of this cross-reaction. The antigenic determinants common to SNV and R-MuLV DNA polymerases were shared completely by the DNA polymerases of Gross MuLV, Moloney MuLV, RD 114 virus, REV-T, and duck infectious anemia virus. Baboon endogenous virus and chicken syncytial virus competed partially for antibodies directed against the common antigenic determinants of SNV and R-MuLV DNA polymerases. DNA polymerases of avian leukosis viruses, pheasant viruses, and mammalian type B and D retroviruses and particles with RNA-dependent DNA polymerase activity from the allantoic fluid of normal chicken eggs and from the medium of a goose cell culture did not compete for the antibodies directed against the common antigenic determinants of SNV and R-MuLV DNA polymerases. We also present data about a factor in normal mammalian immunoglobulin G that specifically inhibits the DNA polymerases of REV and mammalian type C retrovirus DNA polymerases. PMID:6154804

  14. Dendritic cells induce Th2-mediated airway inflammatory responses to house dust mite via DNA-dependent protein kinase

    PubMed Central

    Mishra, Amarjit; Brown, Alexandra L.; Yao, Xianglan; Yang, Shutong; Park, Sung-Jun; Liu, Chengyu; Dagur, Pradeep K.; McCoy, J. Philip; Keeran, Karen J.; Nugent, Gayle Z.; Jeffries, Kenneth R.; Qu, Xuan; Yu, Zu-Xi; Levine, Stewart J.; Chung, Jay H.

    2015-01-01

    DNA-dependent protein kinase (DNA-PK) mediates double stranded DNA break repair, V(D)J recombination, and immunoglobulin class switch recombination, as well as innate immune and pro-inflammatory responses. However, there is limited information regarding the role of DNA-PK in adaptive immunity mediated by dendritic cells (DCs), which are the primary antigen-presenting cells in allergic asthma. Here we show that house dust mite induces DNA-PK phosphorylation, which is a marker of DNA-PK activation, in DCs via the generation of intracellular reactive oxygen species. We also demonstrate that pharmacological inhibition of DNA-PK, as well as the specific deletion of DNA-PK in DCs, attenuates the induction of allergic sensitization and Th2 immunity via a mechanism that involves the impaired presentation of mite antigens. Furthermore, pharmacological inhibition of DNA-PK following antigen priming similarly reduces the manifestations of mite-induced airway disease. Collectively, these findings suggest that DNA-PK may be a potential target for treatment of allergic asthma. PMID:25692509

  15. Negative superhelicity promotes ATP-dependent binding of yeast RAD3 protein to ultraviolet-damaged DNA.

    PubMed

    Sung, P; Watkins, J F; Prakash, L; Prakash, S

    1994-03-18

    The RAD3 gene of Saccharomyces cerevisiae is required for excision repair of UV-damaged DNA and is essential for cell viability. Remarkable homology exists between RAD3 and the human excision repair gene XPD, whose mutational inactivation underlies the cancer-prone disorder in xeroderma pigmentosum group D patients. Our previous work demonstrated that RAD3-encoded protein contains a DNA helicase activity. Here, we show that RAD3 binds preferentially to UV-damaged DNA over nondamaged DNA. Removal of pyrimidine dimers from damaged DNA by enzymatic photoreactivation does not affect binding, suggesting an affinity of RAD3 for pyrimidine (6-4) pyrimidone photoproducts. Damage-specific binding by RAD3 is strongly dependent on ATP and on the degree of negative superhelicity in DNA. The requirement of superhelicity in damage binding may target RAD3 to regions of DNA undergoing transcription, resulting in the preferential repair of these regions. The rad3 Arg-48 mutant protein, which lacks the DNA helicase activity, also binds UV-damaged DNA preferentially, indicating that DNA helicase and damage binding are two distinct and separable functional entities in RAD3. PMID:8132553

  16. A new family of polymerases related to superfamily A DNA polymerases and T7-like DNA-dependent RNA polymerases.

    PubMed

    Iyer, Lakshminarayan M; Abhiman, Saraswathi; Aravind, L

    2008-01-01

    Using sequence profile methods and structural comparisons we characterize a previously unknown family of nucleic acid polymerases in a group of mobile elements from genomes of diverse bacteria, an algal plastid and certain DNA viruses, including the recently reported Sputnik virus. Using contextual information from domain architectures and gene-neighborhoods we present evidence that they are likely to possess both primase and DNA polymerase activity, comparable to the previously reported prim-pol proteins. These newly identified polymerases help in defining the minimal functional core of superfamily A DNA polymerases and related RNA polymerases. Thus, they provide a framework to understand the emergence of both DNA and RNA polymerization activity in this class of enzymes. They also provide evidence that enigmatic DNA viruses, such as Sputnik, might have emerged from mobile elements coding these polymerases. PMID:18834537

  17. A new family of polymerases related to superfamily A DNA polymerases and T7-like DNA-dependent RNA polymerases

    PubMed Central

    Iyer, Lakshminarayan M; Abhiman, Saraswathi; Aravind, L

    2008-01-01

    Using sequence profile methods and structural comparisons we characterize a previously unknown family of nucleic acid polymerases in a group of mobile elements from genomes of diverse bacteria, an algal plastid and certain DNA viruses, including the recently reported Sputnik virus. Using contextual information from domain architectures and gene-neighborhoods we present evidence that they are likely to possess both primase and DNA polymerase activity, comparable to the previously reported prim-pol proteins. These newly identified polymerases help in defining the minimal functional core of superfamily A DNA polymerases and related RNA polymerases. Thus, they provide a framework to understand the emergence of both DNA and RNA polymerization activity in this class of enzymes. They also provide evidence that enigmatic DNA viruses, such as Sputnik, might have emerged from mobile elements coding these polymerases. This article was reviewed by Eugene Koonin and Mark Ragan. PMID:18834537

  18. Salt-Dependent DNA-DNA Spacings in Intact Bacteriophage lambda Reflect Relative Importance of DNA Self-Repulsion and Bending Energies

    SciTech Connect

    X Qiu; D Rau; V Parsegian; L Fang; C Knobler; W Gelbart

    2011-12-31

    Using solution synchrotron x-ray scattering, we measure the variation of DNA-DNA d spacings in bacteriophage {lambda} with mono-, di-, and polyvalent salt concentrations, for wild-type [48.5 x 10{sup 3} base pairs (bp)] and short-genome-mutant (37.8 kbp) strains. From the decrease in d spacings with increasing salt, we deduce the relative contributions of DNA self-repulsion and bending to the energetics of packaged phage genomes. We quantify the DNA-DNA interaction energies within the intact phage by combining the measured d spacings in the capsid with measurements of osmotic pressure in DNA assemblies under the same salt conditions in bulk solution. In the commonly used Tris-Mg buffer, the DNA-DNA interaction energies inside the phage capsids are shown to be about 1 kT/bp, an order of magnitude larger than the bending energies.

  19. Salt-Dependent DNA-DNA Spacings in Intact Bacteriophage λ Reflect Relative Importance of DNA Self-Repulsion and Bending Energies

    NASA Astrophysics Data System (ADS)

    Qiu, Xiangyun; Rau, Donald C.; Parsegian, V. Adrian; Fang, Li Tai; Knobler, Charles M.; Gelbart, William M.

    2011-01-01

    Using solution synchrotron x-ray scattering, we measure the variation of DNA-DNA d spacings in bacteriophage λ with mono-, di-, and polyvalent salt concentrations, for wild-type [48.5×103 base pairs (bp)] and short-genome-mutant (37.8 kbp) strains. From the decrease in d spacings with increasing salt, we deduce the relative contributions of DNA self-repulsion and bending to the energetics of packaged phage genomes. We quantify the DNA-DNA interaction energies within the intact phage by combining the measured d spacings in the capsid with measurements of osmotic pressure in DNA assemblies under the same salt conditions in bulk solution. In the commonly used Tris-Mg buffer, the DNA-DNA interaction energies inside the phage capsids are shown to be about 1kT/bp, an order of magnitude larger than the bending energies.

  20. Sensing the water content of honey from temperature-dependent electrical conductivity

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In order to predict water content in honey, electrical conductivity was measured on blossom honey types of milk-vetch, jujube and yellow-locust with water content of 18%-37% between 5-40ºC. Regression models of electrical conductivity were developed as functions of water content and temperature. The...

  1. DNA damage drives accelerated bone aging via an NF-κB-dependent mechanism

    PubMed Central

    Chen, Qian; Liu, Kai; Robinson, Andria R.; Clauson, Cheryl L.; Blair, Harry C.; Robbins, Paul D.; Niedernhofer, Laura J.; Ouyang, Hongjiao

    2013-01-01

    Advanced age is one of the most important risk factors for osteoporosis. Accumulation of oxidative DNA damage has been proposed to contribute to age-related deregulation of osteoblastic and osteoclastic cells. ERCC1 (Excision Repair Cross Complementary group 1)-XPF (Xeroderma Pigmentosum Group F) is an evolutionarily conserved structure-specific endonuclease that is required for multiple DNA repair pathways. Inherited mutations affecting expression of ERCC1-XPF cause a severe progeroid syndrome in humans, including early onset of osteopenia and osteoporosis, or anomalies in skeletal development. Herein, we used progeroid ERCC1-XPF deficient mice, including Ercc1-null (Ercc1−/−) and hypomorphic (Ercc1−/Δ) mice, to investigate the mechanism by which DNA damage leads to accelerated bone aging. Compared to their wild-type littermates, both Ercc1−/− and Ercc1−/Δ mice display severe, progressive osteoporosis caused by reduced bone formation and enhanced osteoclastogenesis. ERCC1 deficiency leads to atrophy of osteoblastic progenitors in the bone marrow stromal cell (BMSC) population. There is increased cellular senescence of BMSCs and osteoblastic cells, as characterized by reduced proliferation, accumulation of DNA damage and a senescence-associated secretory phenotype (SASP). This leads to enhanced secretion of inflammatory cytokines known to drive osteoclastogenesis, such as IL-6, TNFα, and RANKL and thereby induces an inflammatory bone microenvironment favoring osteoclastogenesis. Furthermore, we found that the transcription factor NF-κB is activated in osteoblastic and osteoclastic cells of the Ercc1 mutant mice. Importantly, we demonstrated that haploinsufficiency of the p65 NF-κB subunit partially rescued the osteoporosis phenotype of Ercc1−/Δ mice. Finally, pharmacological inhibition of the NF-κB signaling via an IKK inhibitor reversed cellular senescence and SASP in Ercc1−/Δ BMSCs. These results demonstrate that DNA damage drives

  2. Efficient Capture and Isolation of Tumor-Related Circulating Cell-Free DNA from Cancer Patients Using Electroactive Conducting Polymer Nanowire Platforms

    PubMed Central

    Jeon, SeungHyun; Lee, HyungJae; Bae, Kieun; Yoon, Kyong-Ah; Lee, Eun Sook; Cho, Youngnam

    2016-01-01

    Circulating cell-free DNA (cfDNA) is currently recognized as a key non-invasive biomarker for cancer diagnosis and progression and therapeutic efficacy monitoring. Because cfDNA has been detected in patients with diverse types of cancers, the use of efficient strategies to isolate cfDNA not only provides valuable insights into tumour biology, but also offers the potential for developing new cancer-specific targets. However, the challenges associated with conventional cfDNA extraction methods prevent their further clinical applications. Here, we developed a nanostructured conductive polymer platform for the efficient capture and release of circulating cfDNA and demonstrated its potential clinical utility using unprocessed plasma samples from patients with breast and lung cancers. Our results confirmed that the platform's enhanced efficiency allows tumor-specific circulating cfDNA to be recovered at high yield and purity. PMID:27162553

  3. Ion Concentration- and Voltage-Dependent Push and Pull Mechanisms of Potassium Channel Ion Conduction

    PubMed Central

    Kasahara, Kota; Shirota, Matsuyuki; Kinoshita, Kengo

    2016-01-01

    The mechanism of ion conduction by potassium channels is one of the central issues in physiology. In particular, it is still unclear how the ion concentration and the membrane voltage drive ion conduction. We have investigated the dynamics of the ion conduction processes in the Kv1.2 pore domain, by molecular dynamics (MD) simulations with several different voltages and ion concentrations. By focusing on the detailed ion movements through the pore including selectivity filter (SF) and cavity, we found two major conduction mechanisms, called the III-IV-III and III-II-III mechanisms, and the balance between the ion concentration and the voltage determines the mechanism preference. In the III-IV-III mechanism, the outermost ion in the pore is pushed out by a new ion coming from the intracellular fluid, and four-ion states were transiently observed. In the III-II-III mechanism, the outermost ion is pulled out first, without pushing by incoming ions. Increases in the ion concentration and voltage accelerated ion conductions, but their mechanisms were different. The increase in the ion concentrations facilitated the III-IV-III conductions, while the higher voltages increased the III-II-III conductions, indicating that the pore domain of potassium channels permeates ions by using two different driving forces: a push by intracellular ions and a pull by voltage. PMID:26950215

  4. Ion Concentration- and Voltage-Dependent Push and Pull Mechanisms of Potassium Channel Ion Conduction.

    PubMed

    Kasahara, Kota; Shirota, Matsuyuki; Kinoshita, Kengo

    2016-01-01

    The mechanism of ion conduction by potassium channels is one of the central issues in physiology. In particular, it is still unclear how the ion concentration and the membrane voltage drive ion conduction. We have investigated the dynamics of the ion conduction processes in the Kv1.2 pore domain, by molecular dynamics (MD) simulations with several different voltages and ion concentrations. By focusing on the detailed ion movements through the pore including selectivity filter (SF) and cavity, we found two major conduction mechanisms, called the III-IV-III and III-II-III mechanisms, and the balance between the ion concentration and the voltage determines the mechanism preference. In the III-IV-III mechanism, the outermost ion in the pore is pushed out by a new ion coming from the intracellular fluid, and four-ion states were transiently observed. In the III-II-III mechanism, the outermost ion is pulled out first, without pushing by incoming ions. Increases in the ion concentration and voltage accelerated ion conductions, but their mechanisms were different. The increase in the ion concentrations facilitated the III-IV-III conductions, while the higher voltages increased the III-II-III conductions, indicating that the pore domain of potassium channels permeates ions by using two different driving forces: a push by intracellular ions and a pull by voltage. PMID:26950215

  5. Length dependence of carbon nanotube thermal conductivity and the "problem of long waves"

    NASA Technical Reports Server (NTRS)

    Mingo, N.; Broido, D. A.

    2005-01-01

    We present the first calculations of finite length carbon nanotube thermal conductivity that extend from the ballistic to the diffusive regime, throughout a very wide range of lengths and temperatures. The long standing problem of vanishing scattering of the "long wavelength phonf dramatically here, making the thermal conductivity diverge as the nanotube length increases. We show that the divergence disappears if 3-phonon scattering processes are considered to second or higher order. Nevertheless, for defect free nanotubes, the thermal conductivity keeps increasing up to very large lengths (10 gm at 300 K). Defects in the nanotube are also able to remove the long wavelength divergence.

  6. Cordycepin Decreases Compound Action Potential Conduction of Frog Sciatic Nerve In Vitro Involving Ca (2+) -Dependent Mechanisms.

    PubMed

    Yao, Li-Hua; Yu, Hui-Min; Xiong, Qiu-Ping; Sun, Wei; Xu, Yan-Liang; Meng, Wei; Li, Yu-Ping; Liu, Xin-Ping; Yuan, Chun-Hua

    2015-01-01

    Cordycepin has been widely used in oriental countries to maintain health and improve physical performance. Compound nerve action potential (CNAP), which is critical in signal conduction in the peripheral nervous system, is necessary to regulate physical performance, including motor system physiological and pathological processes. Therefore, regulatory effects of cordycepin on CNAP conduction should be elucidated. In this study, the conduction ability of CNAP in isolated frog sciatic nerves was investigated. Results revealed that cordycepin significantly decreased CNAP amplitude and conductive velocity in a reversible and concentration-dependent manner. At 50 mg/L cordycepin, CNAP amplitude and conductive velocity decreased by 62.18 ± 8.06% and 57.34% ± 6.14% compared with the control amplitude and conductive velocity, respectively. However, the depressive action of cordycepin on amplitude and conductive velocity was not observed in Ca(2+)-free medium or in the presence of Ca(2+) channel blockers (CdCl2/LaCl3). Pretreatment with L-type Ca(2+) channel antagonist (nifedipine/deltiazem) also blocked cordycepin-induced responses; by contrast, T-type and P-type Ca(2+) channel antagonists (Ni(2+)) failed to block such responses. Therefore, cordycepin decreased the conduction ability of CNAP in isolated frog sciatic nerves via L-type Ca(2+) channel-dependent mechanism. PMID:26078886

  7. Competing mechanism driving diverse pressure dependence of thermal conductivity of X Te (X =Hg ,Cd , and Zn)

    NASA Astrophysics Data System (ADS)

    Ouyang, Tao; Hu, Ming

    2015-12-01

    Effectively engineering the lattice thermal conductivity of materials is a key interest of the current thermal science community. Pressure or compressive strain is one of the most worthwhile processes to modify the thermal transport property of materials, due to its robust tunability and flexibility of realization. While it is well documented in the literature that the application of hydrostatic pressure normally increases the thermal conductivity of bulk materials, little work has been performed on abnormal pressure-dependent thermal conductivity and the governing mechanism has not been fully understood yet. In this paper, taking bulk telluride systems X Te (X =Hg ,Cd ,Zn ) as examples, we show, by combining first-principle calculation and the phonon Boltzmann transport equation, that the thermal conductivity presents diverse pressure dependence although they belong to the same group. The thermal conductivity of ZnTe is independent of pressure, while abnormal negative pressure dependence of thermal conductivity is observed in HgTe. As for CdTe, the trend falls in between HgTe and ZnTe and relies largely on the temperature. By comparing the key contributors of the lattice thermal conductivity, we find that the diverse pressure dependence of the lattice thermal conductivity is governed by the competition between the enhancement of group velocity of longitudinal acoustic and optic modes and the reduction of phonon relaxation time of transverse acoustic modes, with both effects being fully quantified by our calculation. Comparison with traditional bulk systems such as silicon further underpins the governing mechanism. The correlation between the diverse thermal transport phenomena and the nature of the atomic bonding is also qualitatively established. These findings are expected to deepen our understanding of manipulating phonon transport of bulk materials via simple compressive strain and are also helpful for related applications, such as optimizing thermoelectric

  8. Length-dependent thermal conductivity in suspended single-layer graphene

    NASA Astrophysics Data System (ADS)

    Xu, Xiangfan; Pereira, Luiz F. C.; Wang, Yu; Wu, Jing; Zhang, Kaiwen; Zhao, Xiangming; Bae, Sukang; Tinh Bui, Cong; Xie, Rongguo; Thong, John T. L.; Hong, Byung Hee; Loh, Kian Ping; Donadio, Davide; Li, Baowen; Özyilmaz, Barbaros

    2014-04-01

    Graphene exhibits extraordinary electronic and mechanical properties, and extremely high thermal conductivity. Being a very stable atomically thick membrane that can be suspended between two leads, graphene provides a perfect test platform for studying thermal conductivity in two-dimensional systems, which is of primary importance for phonon transport in low-dimensional materials. Here we report experimental measurements and non-equilibrium molecular dynamics simulations of thermal conduction in suspended single-layer graphene as a function of both temperature and sample length. Interestingly and in contrast to bulk materials, at 300 K, thermal conductivity keeps increasing and remains logarithmically divergent with sample length even for sample lengths much larger than the average phonon mean free path. This result is a consequence of the two-dimensional nature of phonons in graphene, and provides fundamental understanding of thermal transport in two-dimensional materials.

  9. Chiral Differentiation of DNA Adducts Formed by Enantiomeric Analogues of Antitumor Cisplatin Is Sequence-Dependent

    PubMed Central

    Delalande, Olivier; Malina, Jaroslav; Brabec, Viktor; Kozelka, Jiří

    2005-01-01

    1,2-GG intrastrand cross-links formed in DNA by the enantiomeric complexes [PtCl2(R,R-2,3-diaminobutane (DAB))] and [PtCl2(S,S-DAB)] were studied by biophysical methods. Molecular modeling revealed that structure of the cross-links formed at the TGGT sequence was affected by repulsion between the 5′-directed methyl group of the DAB ligand and the methyl group of the 5′-thymine of the TGGT fragment. Molecular dynamics simulations of the solvated platinated duplexes and our recent structural data indicated that the adduct of [PtCl2(R,R-DAB)] alleviated this repulsion by unwinding the TpG step, whereas the adduct of [PtCl2(S,S-DAB)] avoided the unfavorable methyl-methyl interaction by decreasing the kink angle. Electrophoretic retardation measurements on DNA duplexes containing 1,2-GG intrastrand cross-links of Pt(R,R-DAB)2+ or Pt(S,S-DAB)2+ at a CGGA site showed that in this sequence both enantiomers distorted the double helix to the identical extent similar to that found previously for the same sequence containing the cross-links of the parent antitumor \\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\setlength{\\oddsidemargin}{-69pt} \\begin{document} \\begin{equation*}cis-{\\mathrm{Pt}}({\\mathrm{NH}}_{3})_{2}^{2+}\\end{equation*}\\end{document} (cisplatin). In addition, the adducts showed similar affinities toward the high-mobility-group box 1 proteins. Hence, whereas the structural perturbation induced in DNA by 1,2-GG intrastrand cross-links of cisplatin does not depend largely on the bases flanking the cross-links, the perturbation related to GG cross-linking by bulkier platinum diamine derivatives does. PMID:15805172

  10. Sensing the water content of honey from temperature-dependent electrical conductivity

    NASA Astrophysics Data System (ADS)

    Guo, Wenchuan; Liu, Yi; Zhu, Xinhua; Zhuang, Hong

    2011-08-01

    In order to predict the water content in honey, electrical conductivity was measured on blossom honey types milk-vetch, jujube and yellow-locust with the water content of 18-37% between 5 and 40 °C. The regression models of electrical conductivity were developed as functions of water content and temperature. The results showed that increases in either water content or temperature resulted in an increase in the electrical conductivity of honey with greater changes at higher water content and/or higher temperature. The linear terms of water content and temperature, a quadratic term of water content, and the interaction effect of water content and temperature had significant influence on the electrical conductivity of honey (p < 0.0001). Regardless of blossom honey type, the linear coefficient of the determination of measured and calculated electrical conductivities was 0.998 and the range error ratio was larger than 100. These results suggest that the electrical conductivity of honey might be used to develop a detector for rapidly predicting the water content in blossom honey.

  11. Saturation dependence of the quadrature conductivity of oil-bearing sands

    NASA Astrophysics Data System (ADS)

    Schmutz, M.; Blondel, A.; Revil, A.

    2012-02-01

    We have investigated the complex conductivity of oil-bearing sands with six distinct oil types including sunflower oil, silicone oil, gum rosin, paraffin, engine oil, and an industrial oil of complex composition. In all these experiments, the oil was the non-wetting phase. The in-phase (real) conductivity follows a power law relationship with the saturation (also known as the second Archie's law) but with a saturation exponent n raging from 1.1 to 3.1. In most experiments, the quadrature conductivity follows also a power law relationship with the water saturation but with a power law exponent p can be either positive or negative. For some samples, the quadrature conductivity first increases with saturation and then decreases indicating that two processes compete in controlling the quadrature conductivity. One is related to the insulating nature of the oil phase and a second could be associated with the surface area of the oil / water interface. The quadrature conductivity seems to be influenced not only by the value of the saturation exponent n (according to the Vinegar and Waxman model, p = n - 1), but also by the surface area between the oil phase and the water phase especially for very water-repellent oil having a fractal oil-water interface.

  12. The unexpected non-monotonic inter-layer bonding dependence of the thermal conductivity of bilayered boron nitride

    NASA Astrophysics Data System (ADS)

    Gao, Yufei; Zhang, Xiaoliang; Jing, Yuhang; Hu, Ming

    2015-04-01

    Hexagonal boron nitride (BN) and its bilayer form are very fascinating two-dimensional materials that have attracted tremendous interest recently. Their realistic applications in emerging nanoelectronics usually quest for manipulating the thermal transport properties in a precise manner. Using nonequilibrium molecular dynamics simulations, we herein studied the effect of inter-layer covalent bonding on the thermal conductivity of bilayered BN. We found that the in-plane thermal conductivity of bilayered BN, which can be largely tuned by introducing covalent bonding between the two BN layers, depends not only on the inter-layer bonding density, but also on the detailed topological configuration of the inter-layer bonds. For randomly distributed inter-layer bonding the thermal conductivity of bilayered BN decreases monotonically with inter-layer bonding density, the same behavior already found for bilayered graphene. However, for regularly arranged inter-layer bonding the thermal conductivity of bilayered BN surprisingly possesses a non-monotonic dependence on the inter-layer bonding density. This non-intuitive non-monotonic dependence is further explained by performing spectral energy density analysis, where the peak and valley values of the thermal conductivity are governed by different mechanisms. These results suggest the application of inter-layer covalent bonding in designing nanoscale devices with precisely tunable thermal conductivities.

  13. Excision of DNA loop domains as a common step in caspase-dependent and -independent types of neuronal cell death.

    PubMed

    Bezvenyuk, Z; Salminen, A; Solovyan, V

    2000-09-30

    Treatment of rat cerebellar granule neurons with the phosphatase inhibitor, okadaic acid (OKA) or the excitatory neurotransmitter, L-glutamate, resulted in progressive cell death associated with apoptotic-like changes in nuclear morphology. The OKA-induced neurotoxicity was accompanied by the activation of caspase-3 (ICE-related cysteine protease) and the development of an oligonucleosomal DNA ladder, whereas neither activation of caspase-1, -2, -3, -5, or -9, nor internucleosomal DNA fragmentation accompanied L-glutamate-induced neurotoxicity. At the same time, both OKA and L-glutamate induced a similar pattern of nuclear DNA disintegration into high molecular weight (HMW)-DNA fragments of about 50-100 kb, which are widely believed to originate from the excision of DNA loop domains. Z-DEVD-fmk, a specific caspase-3 inhibitor, as well as a general caspase inhibitor, z-VAD-fmk, inhibited both the internucleosomal- and HMW-DNA fragmentation in OKA-treated neurons. However neither z-DEVD-fmk nor z-VAD-fmk had any obvious inhibitory effect on the formation of HMW-DNA fragments induced by L-glutamate. The results indicate that the formation of the HMW-DNA fragments in cerebellar granule neurons accompanies both caspase-dependent and -independent types of cell death, indicative of multiple mechanisms in the regulation of excision of DNA loop domains during neuronal cell death. PMID:11000492

  14. DNA-binding dependent and independent functions of WT1 protein during human hematopoiesis

    SciTech Connect

    Svensson, Emelie; Eriksson, Helena; Gekas, Christos; Olofsson, Tor; Richter, Johan; Gullberg, Urban . E-mail: urban.gullberg@hematologi.lu.se

    2005-08-01

    The Wilms tumor gene 1 (WT1) encodes a zinc-finger-containing transcription factor highly expressed in immature hematopoietic progenitor cells. Overexpression and presence of somatic mutations in acute leukemia indicate a role for WT1 in the pathogenesis of leukemia. CD34{sup +} progenitor cells were transduced with one splice variant of human WT1 without the KTS insert in the zinc-finger domain, WT1(+/-), and with a deleted mutant of WT1 lacking the entire zinc-finger region, WT1(delZ), thus incapable of binding DNA. We show that inhibition of erythroid colony formation and differentiation is absolutely dependent on the DNA-binding zinc-finger domain of WT1. Unexpectedly, however, WT1(delZ) was equally effective as wild type protein in the reduction of myeloid clonogenic growth as well as in stimulation of myeloid differentiation, as judged by the expression of cell surface CD11b. Expression of neither WT1(+/-) nor WT1(delZ) upregulated mRNA for the cdk inhibitor p21{sup Waf1/Cip1} or p27{sup Kip1}. Our results demonstrate that WT1 affects proliferation and differentiation in erythroid and myeloid cells by different molecular mechanisms, and suggest that mutations affecting the zinc-finger domain of WT1 could interfere with normal differentiation in the pathogenesis of leukemia.

  15. Chromosome Synapsis Alleviates Mek1-Dependent Suppression of Meiotic DNA Repair

    PubMed Central

    Subramanian, Vijayalakshmi V.; MacQueen, Amy J.; Vader, Gerben; Shinohara, Miki; Sanchez, Aurore; Borde, Valérie; Shinohara, Akira; Hochwagen, Andreas

    2016-01-01

    Faithful meiotic chromosome segregation and fertility require meiotic recombination between homologous chromosomes rather than the equally available sister chromatid, a bias that in Saccharomyces cerevisiae depends on the meiotic kinase, Mek1. Mek1 is thought to mediate repair template bias by specifically suppressing sister-directed repair. Instead, we found that when Mek1 persists on closely paired (synapsed) homologues, DNA repair is severely delayed, suggesting that Mek1 suppresses any proximal repair template. Accordingly, Mek1 is excluded from synapsed homologues in wild-type cells. Exclusion requires the AAA+-ATPase Pch2 and is directly coupled to synaptonemal complex assembly. Stage-specific depletion experiments further demonstrate that DNA repair in the context of synapsed homologues requires Rad54, a repair factor inhibited by Mek1. These data indicate that the sister template is distinguished from the homologue primarily by its closer proximity to inhibitory Mek1 activity. We propose that once pairing or synapsis juxtaposes homologues, exclusion of Mek1 is necessary to avoid suppression of all templates and accelerate repair progression. PMID:26870961

  16. Reprint of "Functional overlaps between XLF and the ATM-dependent DNA double strand break response".

    PubMed

    Kumar, Vipul; Alt, Frederick W; Oksenych, Valentyn

    2014-05-01

    Developing B and T lymphocytes generate programmed DNA double strand breaks (DSBs) during the V(D)J recombination process that assembles exons that encode the antigen-binding variable regions of antibodies. In addition, mature B lymphocytes generate programmed DSBs during the immunoglobulin heavy chain (IgH) class switch recombination (CSR) process that allows expression of different antibody heavy chain constant regions that provide different effector functions. During both V(D)J recombination and CSR, DSB intermediates are sensed by the ATM-dependent DSB response (DSBR) pathway, which also contributes to their joining via classical non-homologous end-joining (C-NHEJ). The precise nature of the interplay between the DSBR and C-NHEJ pathways in the context of DSB repair via C-NHEJ remains under investigation. Recent studies have shown that the XLF C-NHEJ factor has functional redundancy with several members of the ATM-dependent DSBR pathway in C-NHEJ, highlighting unappreciated major roles for both XLF as well as the DSBR in V(D)J recombination, CSR and C-NHEJ in general. In this review, we discuss current knowledge of the mechanisms that contribute to the repair of DSBs generated during B lymphocyte development and activation with a focus on potential functionally redundant roles of XLF and ATM-dependent DSBR factors. PMID:24767946

  17. Functional Overlaps Between XLF and The ATM-dependent DNA Double Strand Break Response

    PubMed Central

    Kumar, Vipul; Alt, Frederick W.; Oksenych, Valentyn

    2014-01-01

    Developing B and T lymphocytes generate programmed DNA Double Strand Breaks (DSBs) during the V(D)J recombination process that assembles exons that encode the antigen-binding variable regions of antibodies. In addition, mature B lymphocytes generate programmed DSBs during the Immunoglobulin Heavy chain (IgH) Class Switch Recombination (CSR) process that allows expression of different antibody heavy chain constant regions that provide different effector functions. During both V(D)J recombination and CSR, DSB intermediates are sensed by the ATM-dependent DSB response (DSBR) pathway, which also contributes to their joining via Classical Non-Homologous End-Joining (C-NHEJ). The precise nature of the interplay between the DSBR and C-NHEJ pathways in the context of DSB repair via C-NHEJ remains under investigation. Recent studies have shown that the XLF C-NHEJ factor has functional redundancy with several members of the ATM-dependent DSBR pathway in C-NHEJ, highlighting unappreciated major roles for both XLF as well as the DSBR in V(D)J recombination, CSR and C-NHEJ in general. In this review, we discuss current knowledge of the mechanisms that contribute to the repair of DSBs generated during B lymphocyte development and activation with a focus on potential functionally redundant roles of XLF and ATM-dependent DSBR factors. PMID:24674624

  18. Functional overlaps between XLF and the ATM-dependent DNA double strand break response.

    PubMed

    Kumar, Vipul; Alt, Frederick W; Oksenych, Valentyn

    2014-04-01

    Developing B and T lymphocytes generate programmed DNA double strand breaks (DSBs) during the V(D)J recombination process that assembles exons that encode the antigen-binding variable regions of antibodies. In addition, mature B lymphocytes generate programmed DSBs during the immunoglobulin heavy chain (IgH) class switch recombination (CSR) process that allows expression of different antibody heavy chain constant regions that provide different effector functions. During both V(D)J recombination and CSR, DSB intermediates are sensed by the ATM-dependent DSB response (DSBR) pathway, which also contributes to their joining via classical non-homologous end-joining (C-NHEJ). The precise nature of the interplay between the DSBR and C-NHEJ pathways in the context of DSB repair via C-NHEJ remains under investigation. Recent studies have shown that the XLF C-NHEJ factor has functional redundancy with several members of the ATM-dependent DSBR pathway in C-NHEJ, highlighting unappreciated major roles for both XLF as well as the DSBR in V(D)J recombination, CSR and C-NHEJ in general. In this review, we discuss current knowledge of the mechanisms that contribute to the repair of DSBs generated during B lymphocyte development and activation with a focus on potential functionally redundant roles of XLF and ATM-dependent DSBR factors. PMID:24674624

  19. Recombination-Dependent Oligomerization of Human Papillomavirus Genomes upon Transient DNA Replication

    PubMed Central

    Orav, Marit; Henno, Liisi; Isok-Paas, Helen; Geimanen, Jelizaveta; Ustav, Mart

    2013-01-01

    We describe the extensive and progressive oligomerization of human papillomavirus (HPV) genomes after transfection into the U2OS cell line. The HPV genomic oligomers are extrachromosomal concatemeric molecules containing the viral genome in a head-to-tail orientation. The process of oligomerization does not depend on the topology of the input DNA, and it does not require any other viral factors besides replication proteins E1 and E2. We provide evidence that oligomerization of the HPV18 and HPV11 genomes involves homologous recombination. We also demonstrate oligomerization of the HPV18 and HPV11 genomes in SiHa, HeLa, and C-33 A cell lines and provide examples of oligomeric HPV genomes in clinical samples obtained from HPV-infected patients. PMID:23986589

  20. Rate dependence of electrical and mechanical properties of conductive polymer nanocomposites

    NASA Astrophysics Data System (ADS)

    Foley, J. R.; Stilson, C. L.; Smith, K. K. G.; McKinion, C. M.; Chen, C.; Ganguli, S.; Roy, A. K.

    2015-09-01

    Conductive polymer nanocomposites with enhanced electrical and thermal properties show promise as an alternative solution for electronic materials. For example, electronic interconnect materials will have comparable electrical and thermal conductivity to solder with an increased operating range of strain and temperature. This paper documents the fabrication and experimental evaluation of a prototype conductive polymer nanocomposite. Material selection, fabrication processes, and initial characterization of a low Tg polymer with a high fill ratio of carbon nanotubes is presented. The electrical and thermal properties of the composite are measured and compared with predictions. The mechanical properties are measured using dynamic mechanical analysis (DMA) over a wide temperature range. The mechanical and electrical responses of the conductive polymer composite are simultaneously measured at higher strain rates using a modified split Hopkinson pressure bar (SHPB) apparatus. The dynamic stress-strain response is obtained using traditional analytic methods (e.g., two- and three-wave analysis). The electrical response is observed using constant current excitation with high bandwidth (>500 kHz) instrumentation. The dynamic compression data implies the change in electrical resistance is solely a function of the material deformation, i.e., the material exhibits constant electrical conductivity and is insensitive to the applied loads. DMA and SHPB dynamic data are used to estimate the parameters in a Mulliken-Boyce constitutive model, and the resulting behavior is critically evaluated. Finally, progress towards improving the polymer composite's mechanical, electrical, and thermal properties are discussed.

  1. Effects of conductivity perturbations in time-dependent global electric circuit model

    NASA Astrophysics Data System (ADS)

    Jánský, Jaroslav; Pasko, Victor P.

    2015-12-01

    This paper contributes to the understanding of the influence of conductivity perturbations on the ionospheric potential in the Earth's global electric circuit (GEC). The conductivity perturbations appearing in the middle atmosphere produced by γ ray bursts from magnetars are studied first. The transient response of the ionospheric potential is modeled in this case, and timescales of interest are identified (0.01-10s). In this case modification of ionospheric potential is small. Additionally, the principal effects of topography and reduction of conductivity inside the thundercloud are studied. Both of these factors effectively increase the ionospheric potential for a classic source in the GEC represented by a current dipole leading to formation of two main charge centers of the thunderstorm. On the other hand, for GEC including topography and conductivity reduction in thunderclouds the contribution of sequence of negative cloud-to-ground lightning discharges to the ionospheric potential is decreased. Simulation results show a very good agreement with equivalent circuit models for conductivity perturbations with horizontal dimensions exceeding 20 km.

  2. Global analysis of ion dependence unveils hidden steps in DNA binding and bending by integration host factor

    NASA Astrophysics Data System (ADS)

    Vivas, Paula; Velmurugu, Yogambigai; Kuznetsov, Serguei V.; Rice, Phoebe A.; Ansari, Anjum

    2013-09-01

    Proteins that recognize and bind to specific sites on DNA often distort the DNA at these sites. The rates at which these DNA distortions occur are considered to be important in the ability of these proteins to discriminate between specific and nonspecific sites. These rates have proven difficult to measure for most protein-DNA complexes in part because of the difficulty in separating the kinetics of unimolecular conformational rearrangements (DNA bending and kinking) from the kinetics of bimolecular complex association and dissociation. A notable exception is the Integration Host Factor (IHF), a eubacterial architectural protein involved in chromosomal compaction and DNA recombination, which binds with subnanomolar affinity to specific DNA sites and bends them into sharp U-turns. The unimolecular DNA bending kinetics has been resolved using both stopped-flow and laser temperature-jump perturbation. Here we expand our investigation by presenting a global analysis of the ionic strength dependence of specific binding affinity and relaxation kinetics of an IHF-DNA complex. This analysis enables us to obtain each of the underlying elementary rates (DNA bending/unbending and protein-DNA association/dissociation), and their ionic strength dependence, even under conditions where the two processes are coupled. Our analysis indicates interesting differences in the ionic strength dependence of the bi- versus unimolecular steps. At moderate [KCl] (100-500 mM), nearly all the ionic strength dependence to the overall equilibrium binding affinity appears in the bimolecular association/dissociation of an initial, presumably weakly bent, encounter complex, with a slope SKbi ≈ 8 describing the loglog-dependence of the equilibrium constant to form this complex on [KCl]. In contrast, the unimolecular equilibrium constant to form the fully wrapped specific complex from the initial complex is nearly independent of [KCl], with SKuni < 0.5. This result is counterintuitive because there

  3. Epigenetic control of viral life-cycle by a DNA-methylation dependent transcription factor.

    PubMed

    Flower, Kirsty; Thomas, David; Heather, James; Ramasubramanyan, Sharada; Jones, Susan; Sinclair, Alison J

    2011-01-01

    Epstein-Barr virus (EBV) encoded transcription factor Zta (BZLF1, ZEBRA, EB1) is the prototype of a class of transcription factor (including C/EBPalpha) that interact with CpG-containing DNA response elements in a methylation-dependent manner. The EBV genome undergoes a biphasic methylation cycle; it is extensively methylated during viral latency but is reset to an unmethylated state following viral lytic replication. Zta is expressed transiently following infection and again during the switch between latency and lytic replication. The requirement for CpG-methylation at critical Zta response elements (ZREs) has been proposed to regulate EBV replication, specifically it could aid the activation of viral lytic gene expression from silenced promoters on the methylated genome during latency in addition to preventing full lytic reactivation from the non-methylated EBV genome immediately following infection. We developed a computational approach to predict the location of ZREs which we experimentally assessed using in vitro and in vivo DNA association assays. A remarkably different binding motif is apparent for the CpG and non-CpG ZREs. Computational prediction of the location of these binding motifs in EBV revealed that the majority of lytic cycle genes have at least one and many have multiple copies of methylation-dependent CpG ZREs within their promoters. This suggests that the abundance of Zta protein coupled with the methylation status of the EBV genome act together to co-ordinate the expression of lytic cycle genes at the majority of EBV promoters. PMID:22022468

  4. Wavelength dependence for the photoreactions of DNA-Psoralen monoadducts. 1. Photoreversal of monoadducts

    SciTech Connect

    Shi, Y.; Hearst, J.E.

    1987-06-30

    The authors have studied the wavelength dependence for the photoreversal of a monoadducted psoralen derivative, HMT (4'(hydroxymethyl)-4,5',8-trimethylpsoralen), in a single-stranded deoxyoligonucleotide (5'-GAAGCTACGAGC-3'). The psoralen was covalently attached to the thymidine residue in the oligonucleotide as either a furan-side monoadduct, which is formed through the cycloaddition between the 4',5' double bond of the psoralen and the 5,6 double bond of the thymidine, or a pyrone-side monoadduct, which is formed through the cycloaddition between the 3,4 double bond of the psoralen and the 5,6 double bond of the thymidine. As a comparison, they have also investigated the wavelength-dependent photoreversal of the isolated thymidine-HMT monoadducts. All photoreversal action spectra correlate with the extinction spectra of the isolate monoadducts. In the case of the pyrone-side monoadduct, two absorption bands contribute to the photoreversal with a quantum yield of 2 x 10/sup -2/ at wavelengths below 250 nm and 7 x 10/sup -3/ at wavelengths from 287 to 314 nm. The incorporation of the monoadduct into the DNA oligomer had little effect upon the photoreversal rate. For the furan-side monoadduct at least three absorption bands contribute to the photoreversal. The quantum yield varied from 5 x 10/sup -2/ at wavelengths below 250 nm to 7 x 10/sup -4/ at wavelengths between 295 and 365 nm. In contrast to the case of the pyrone-side monoadduct, the incorporation of the furan-side monoadduct into the DNA oligomer reduced the photoreversal rate constant at wavelengths above 285 nm.

  5. Temperature-dependent thermal conductivity of silicone-Al2O3 nanocomposites

    NASA Astrophysics Data System (ADS)

    Moreira, D. C.; Braga Junior, N. R.; Benevides, R. O.; Sphaier, L. A.; Nunes, L. C. S.

    2015-11-01

    This paper presents an experimental investigation of thermophysical properties of elastomeric nano-composites. Spherical alumina nanoparticles with a diameter of 150 nm were added to polydimethylsiloxane (PDMS), and batches of nanocomposites with different volume concentrations (up to 5 %) were produced. The thermal conductivity of the samples was acquired through the guarded heat flow meter method at nine temperature setpoints, ranging from 0 to 80 °C, and density measurements were carried out, in order to evaluate the composition of the samples. The results showed a significant increase in the thermal conductivity of PDMS with small additions of alumina nanoparticles. In addition, a notable linear decrease in conductivity was observed with increasing temperature. Finally, classical models were fitted to the experimental data and a discussion about the physical meaning of the adjusted parameters was carried out.

  6. Protein kinase A dependent membrane protein phosphorylation and chloride conductance in endosomal vesicles from kidney cortex

    SciTech Connect

    Reenstra, W.W.; Bae, H.R.; Verkman, A.S. Univ. of California, San Francisco ); Sabolic, I. Harvard Medical School, Charlestown, MA )

    1992-01-14

    Regulation of Cl conductance by protein kinase A action, cell-free measurements of Cl transport and membrane protein phosphorylation were carried out in apical endocytic vesicles from rabbit kidney proximal tubule. Cl transport was measured by a stopped-flow quenching assay in endosomes labeled in vivo with the fluorescent Cl indicator 6-methoxy-N-(3-sulfopropyl)quinolinium. Phosphorylation was studied in a purified endosomal preparation by SDS-PAGE and autoradiography of membrane proteins labeled by ({gamma}-{sup 32}P)ATP. These results suggest that, in a cell-free system, protein kinase A increases Cl conductance in endosomes from kidney proximal tubule by a phosphorylation mechanism. The labeled protein has a size similar to that of the 64-kDa putative kidney Cl channel reported by Landry et al. but is much smaller than the {approximately}170-kDa cystic fibrosis transmembrane conductance regulatory protein.

  7. Giant humidity dependence of conductivity in a single exfoliated titania nanosheet

    SciTech Connect

    Tanaka, Ayaka; Hatakeyama, Kazuto; Oku, Azusa; Matsuzaki, Koji; Saitou, Natsumi; Yokoi, Hiroyuki; Taniguchi, Takaaki; Matsumoto, Yasumichi; Hara, Masahiro

    2014-04-21

    We have investigated an in-plane electrical transport in an individual titania nanosheet, which forms a lepidocrocite structure with a few atomic layer thickness. The conductivity in the titania nanosheet varied five orders for the change of the relative humidity from 45% to 95%. The drastic change in the conductivity is due to a sensitive response with respect to water molecules adsorbed on the surface of the two-dimensional nanosheet. The results may open an avenue for nanodevices built from various oxide nanosheets.

  8. CCAR2/DBC1 is required for Chk2-dependent KAP1 phosphorylation and repair of DNA damage

    PubMed Central

    Magni, Martina; Ruscica, Vincenzo; Restelli, Michela; Fontanella, Enrico; Buscemi, Giacomo; Zannini, Laura

    2015-01-01

    Cell cycle and apoptosis regulator 2 (CCAR2, formerly known as DBC1) is a nuclear protein largely involved in DNA damage response, apoptosis, metabolism, chromatin structure and transcription regulation. Upon DNA lesions, CCAR2 is phosphorylated by the apical kinases ATM/ATR and this phosphorylation enhances CCAR2 binding to SIRT1, leading to SIRT1 inhibition, p53 acetylation and p53-dependent apoptosis. Recently, we found that also the checkpoint kinase Chk2 and the proteasome activator REGγ are required for efficient CCAR2-mediated inhibition of SIRT1 and induction of p53-dependent apoptosis. Here, we report that CCAR2 is required for the repair of heterochromatic DNA lesions, as cells knock-out for CCAR2 retain, at late time-points after genotoxic treatment, abnormal levels of DNA damage-associated nuclear foci, whose timely resolution is reinstated by HP1β depletion. Conversely, repair of DNA damages in euchromatin are not affected by CCAR2 absence. We also report that the impairment in heterochromatic DNA repair is caused by defective Chk2 activation, detectable in CCAR2 ablated cells, which finally impacts on the phosphorylation of the Chk2 substrate KAP1 that is required for the induction of heterochromatin relaxation and DNA repair. These studies further extend and confirm the role of CCAR2 in the DNA damage response and DNA repair and illustrate a new mechanism of Chk2 activity regulation. Moreover, the involvement of CCAR2 in the repair of heterochromatic DNA breaks suggests a new role for this protein in the maintenance of chromosomal stability, which is necessary to prevent cancer formation. PMID:26158765

  9. DNA Damage Response Checkpoint Activation Drives KP1019 Dependent Pre-Anaphase Cell Cycle Delay in S. cerevisiae

    PubMed Central

    Bierle, Lindsey A.; Reich, Kira L.; Taylor, Braden E.; Blatt, Eliot B.; Middleton, Sydney M.; Burke, Shawnecca D.; Stultz, Laura K.; Hanson, Pamela K.; Partridge, Janet F.; Miller, Mary E.

    2015-01-01

    Careful regulation of the cell cycle is required for proper replication, cell division, and DNA repair. DNA damage–including that induced by many anticancer drugs–results in cell cycle delay or arrest, which can allow time for repair of DNA lesions. Although its molecular mechanism of action remains a matter of debate, the anticancer ruthenium complex KP1019 has been shown to bind DNA in biophysical assays and to damage DNA of colorectal and ovarian cancer cells in vitro. KP1019 has also been shown to induce mutations and induce cell cycle arrest in Saccharomyces cerevisiae, suggesting that budding yeast can serve as an appropriate model for characterizing the cellular response to the drug. Here we use a transcriptomic approach to verify that KP1019 induces the DNA damage response (DDR) and find that KP1019 dependent expression of HUG1 requires the Dun1 checkpoint; both consistent with KP1019 DDR in budding yeast. We observe a robust KP1019 dependent delay in cell cycle progression as measured by increase in large budded cells, 2C DNA content, and accumulation of Pds1 which functions to inhibit anaphase. Importantly, we also find that deletion of RAD9, a gene required for the DDR, blocks drug-dependent changes in cell cycle progression, thereby establishing a causal link between the DDR and phenotypes induced by KP1019. Interestingly, yeast treated with KP1019 not only delay in G2/M, but also exhibit abnormal nuclear position, wherein the nucleus spans the bud neck. This morphology correlates with short, misaligned spindles and is dependent on the dynein heavy chain gene DYN1. We find that KP1019 creates an environment where cells respond to DNA damage through nuclear (transcriptional changes) and cytoplasmic (motor protein activity) events. PMID:26375390

  10. Staggered AID-dependent DNA double strand breaks are the predominant DNA lesions targeted to S mu in Ig class switch recombination.

    PubMed

    Rush, James S; Fugmann, Sebastian D; Schatz, David G

    2004-04-01

    Class switch recombination (CSR) is the process whereby B cells alter the effector properties of their Ig molecules. Whilst much is known about the cellular regulation of this process, many of the molecular details remain elusive. Recent evidence suggests that CSR involves blunt DNA double strand breaks (dsbs), and that formation of these dsbs requires the function of the activation-induced cytidine deaminase (AID). We sought to characterize the structural properties and kinetics of induction of the DNA lesions associated with CSR. Using ligation-mediated PCR, we found that AID-dependent DNA dsbs were specifically induced in the S mu region of murine B cells stimulated to undergo CSR. While blunt dsbs were detected, they were only a minor species, with staggered breaks being more than an order of magnitude more abundant. In addition, these breaks could be detected at equal frequency at upstream and downstream portions of S mu, and were induced prior to expression of newly switched isotypes. Collectively, these results provide direct evidence that staggered, S mu-targeted AID-dependent dsbs are the predominant DNA lesion associated with CSR, with important implications for the mechanisms by which CSR DNA lesions are made and processed. PMID:15039385

  11. Selenite activates the ATM kinase-dependent DNA repair pathway in human osteosarcoma cells with mitochondrial dysfunction.

    PubMed

    Wojewoda, Marta; Walczak, Jarosław; Duszyński, Jerzy; Szczepanowska, Joanna

    2015-06-01

    Mitochondrial dysfunction and reactive oxygen species (ROS) induced oxidative damage are implicated in the pathogenesis of several human diseases. Based on our previous findings that ROS level was higher in human osteosarcoma cybrids--Neuropathy, Ataxia and Retinitis Pigmentosa (NARP) and was reduced by selenite treatment, this study was designed to elucidate the effects of selenite administration on oxidative and nitrosative damage to lipids, proteins and DNA. Oxidative and nitrosative damage to lipids and proteins was not increased in NARP cybrids or mitochondrial DNA-lacking Rho0 cells (displaying mitochondrial dysfunction) when compared with control WT cells. However, we found the enhanced formation of DNA double-strand breaks based on the level of histone γH2AX (phosphorylated at Ser 139), which is known to be phosphorylated by ATM (Ataxia Telangiectasia Mutated) kinase in response to DNA damage. Selenite increased the activity of ATM kinase in NARP cybrids and Rho0 cells without concomitant increase in levels of histone γH2AX. Activation of the ATM kinase-dependent DNA repair pathway triggered by selenite could not be associated with enhanced DNA damage but might rather result from selenite-induced activation of ATM-dependent DNA repair mechanisms which could account for protective effects of this agent. PMID:25862479

  12. The Dependence of Peat Soil Hydraulic Conductivity on Dominant Vegetation Type in Mountain Fens

    NASA Astrophysics Data System (ADS)

    Crockett, A. C.; Ronayne, M. J.; Cooper, D. J.

    2014-12-01

    The peat soil within fen wetlands provides water storage that can substantially influence the hydrology of mountain watersheds. In this study, we investigated the relationship between hydraulic conductivity and vegetation type for fens occurring in Rocky Mountain National Park (RMNP), Colorado, USA. Vegetation in RMNP fens can be dominated by woody plants and shrubs, such as willows; by mosses; or by herbaceous plants such as sedges. Fens dominated by each vegetation type were selected for study. Six fens were investigated, all of which are in the Colorado River watershed on the west side of RMNP. For each site, soil hydraulic conductivity was measured at multiple locations using a single-ring infiltrometer. As a result of the shallow water table in these fens (the water table was always within 10 cm of the surface), horizontal hydraulic gradients were produced during the field tests. The measured infiltration rates were analyzed using the numerical model HYDRUS. In order to determine the hydraulic conductivity, a parameter estimation problem was solved using HYDRUS as the forward simulator. Horizontal flow was explicitly accounted for in the model. This approach produced more accurate estimates of hydraulic conductivity than would be obtained using an analytical solution that assumes strictly vertical flow. Significant differences in hydraulic properties between fens appear to result at least in part from the effects of different dominant vegetation types on peat soil formation.

  13. Xenopus Cds1 Is Regulated by DNA-Dependent Protein Kinase and ATR during the Cell Cycle Checkpoint Response to Double-Stranded DNA Ends

    PubMed Central

    McSherry, Troy D.; Mueller, Paul R.

    2004-01-01

    The checkpoint kinase Cds1 (Chk2) plays a key role in cell cycle checkpoint responses with functions in cell cycle arrest, DNA repair, and induction of apoptosis. Proper regulation of Cds1 is essential for appropriate cellular responses to checkpoint-inducing insults. While the kinase ATM has been shown to be important in the regulation of human Cds1 (hCds1), here we report that the kinases ATR and DNA-dependent protein kinase (DNA-PK) play more significant roles in the regulation of Xenopus Cds1 (XCds1). Under normal cell cycle conditions, nonactivated XCds1 constitutively associates with a Xenopus ATR complex. The association of XCds1 with this complex does not require a functional forkhead activation domain but does require a putative SH3 binding region that is found in XCds1. In response to double-stranded DNA ends, the amino terminus of XCds1 is rapidly phosphorylated in a sequential pattern. First DNA-PK phosphorylates serine 39, a site not previously recognized as important in Cds1 regulation. Xenopus ATM, ATR, and/or DNA-PK then phosphorylate three consensus serine/glutamine sites. Together, these phosphorylations have the dual function of inducing dissociation from the ATR complex and independently promoting the full activation of XCds1. Thus, the checkpoint-mediated activation of XCds1 requires phosphorylation by multiple phosphoinositide 3-kinase-related kinases, protein-protein dissociation, and autophosphorylation. PMID:15509799

  14. Mutation of a Conserved Active Site Residue Converts Tyrosyl-DNA Phosphodiesterase l Into a DNA Topoisomerase l-Dependent Poison

    SciTech Connect

    He,X.; van Waardenburg, R.; Babaoglu, K.; Price, A.; Nitiss, K.; Nitiss, J.; Bjornsti, M.; White, S.

    2007-01-01

    Tyrosyl-DNA phosphodiesterase 1 (Tdp1) catalyzes the resolution of 3' and 5' phospho-DNA adducts. A defective mutant, associated with the recessive neurodegenerative disease SCAN1, accumulates Tdp1-DNA complexes in vitro. To assess the conservation of enzyme architecture, a 2.0 {angstrom} crystal structure of yeast Tdp1 was determined that is very similar to human Tdp1. Poorly conserved regions of primary structure are peripheral to an essentially identical catalytic core. Enzyme mechanism was also conserved, because the yeast SCAN1 mutant (H{sub 432}R) enhanced cell sensitivity to the DNA topoisomerase I (Top1) poison camptothecin. A more severe Top1-dependent lethality of Tdp1H{sub 432}N was drug-independent, coinciding with increased covalent Top1-DNA and Tdp1-DNA complex formation in vivo. However, both H432 mutants were recessive to wild-type Tdp1. Thus, yeast H{sub 432} acts in the general acid/base catalytic mechanism of Tdp1 to resolve 3' phosphotyrosyl and 3' phosphoamide linkages. However, the distinct pattern of mutant Tdp1 activity evident in yeast cells, suggests a more severe defect in Tdp1H{sub 432}N-catalyzed resolution of 3' phospho-adducts.

  15. Trifluridine Induces p53-Dependent Sustained G2 Phase Arrest with Its Massive Misincorporation into DNA and Few DNA Strand Breaks.

    PubMed

    Matsuoka, Kazuaki; Iimori, Makoto; Niimi, Shinichiro; Tsukihara, Hiroshi; Watanabe, Sugiko; Kiyonari, Shinichi; Kiniwa, Mamoru; Ando, Koji; Tokunaga, Eriko; Saeki, Hiroshi; Oki, Eiji; Maehara, Yoshihiko; Kitao, Hiroyuki

    2015-04-01

    Trifluridine (FTD) is a key component of the novel oral antitumor drug TAS-102, which consists of FTD and a thymidine phosphorylase inhibitor. Like 5-fluoro-2'-deoxyuridine (FdUrd), a deoxynucleoside form of 5-fluorouracil metabolite, FTD is sequentially phosphorylated and not only inhibits thymidylate synthase activity, but is also incorporated into DNA. Although TAS-102 was effective for the treatment of refractory metastatic colorectal cancer in clinical trials, the mechanism of FTD-induced cytotoxicity is not completely understood. Here, we show that FTD as well as FdUrd induce transient phosphorylation of Chk1 at Ser345, and that this is followed by accumulation of p53 and p21 proteins in p53-proficient human cancer cell lines. In particular, FTD induced p53-dependent sustained arrest at G2 phase, which was associated with a proteasome-dependent decrease in the Cyclin B1 protein level and the suppression of CCNB1 and CDK1 gene expression. In addition, a p53-dependent increase in p21 protein was associated with an FTD-induced decrease in Cyclin B1 protein. Although numerous ssDNA and dsDNA breaks were induced by FdUrd, few DNA strand breaks were detected in FTD-treated HCT-116 cells despite massive FTD misincorporation into genomic DNA, suggesting that the antiproliferative effect of FTD is not due to the induction of DNA strand breaks. These distinctive effects of FTD provide insights into the cellular mechanism underlying its antitumor effect and may explain the clinical efficacy of TAS-102. PMID:25700705

  16. Sequence-dependent Structural Variation in DNA Undergoing Intrahelical Inspection by the DNA glycosylase MutM

    SciTech Connect

    Sung, Rou-Jia; Zhang, Michael; Qi, Yan; Verdine, Gregory L.

    2012-08-31

    MutM, a bacterial DNA-glycosylase, plays a critical role in maintaining genome integrity by catalyzing glycosidic bond cleavage of 8-oxoguanine (oxoG) lesions to initiate base excision DNA repair. The task faced by MutM of locating rare oxoG residues embedded in an overwhelming excess of undamaged bases is especially challenging given the close structural similarity between oxoG and its normal progenitor, guanine (G). MutM actively interrogates the DNA to detect the presence of an intrahelical, fully base-paired oxoG, whereupon the enzyme promotes extrusion of the target nucleobase from the DNA duplex and insertion into the extrahelical active site. Recent structural studies have begun to provide the first glimpse into the protein-DNA interactions that enable MutM to distinguish an intrahelical oxoG from G; however, these initial studies left open the important question of how MutM can recognize oxoG residues embedded in 16 different neighboring sequence contexts (considering only the 5'- and 3'-neighboring base pairs). In this study we set out to understand the manner and extent to which intrahelical lesion recognition varies as a function of the 5'-neighbor. Here we report a comprehensive, systematic structural analysis of the effect of the 5'-neighboring base pair on recognition of an intrahelical oxoG lesion. These structures reveal that MutM imposes the same extrusion-prone ('extrudogenic') backbone conformation on the oxoG lesion irrespective of its 5'-neighbor while leaving the rest of the DNA relatively free to adjust to the particular demands of individual sequences.

  17. DNA and its cationic lipid complexes induce CpG motif-dependent activation of murine dendritic cells

    PubMed Central

    Yoshinaga, Takaharu; Yasuda, Kei; Ogawa, Yoshiyuki; Nishikawa, Makiya; Takakura, Yoshinobu

    2007-01-01

    Unmethylated CpG motifs in bacterial DNA, but not in vertebrate DNA, are known to trigger an inflammatory response of antigen-presenting cells (APC). In this study, we investigated the cytokine release from murine dendritic cells (DC) by the addition of various types of DNA in the free or complexed form with cationic lipids. Naked plasmid DNA and Escherichia coli DNA with immunostimulatory unmethylated CpG motifs induced pro-inflammatory cytokine secretion from granulocyte–macrophage colony-stimulating factor (GM-CSF)-cultured bone marrow-derived DC and the DC cell-line, DC2.4 cells, though vertebrate calf thymus DNA (CT DNA) with less CpG motifs did not. These characteristics differed from mouse peritoneal resident macrophages that do not respond to any naked DNA. The amount of cytokines released from the DC was significantly increased by complex formation with cationic lipids when CpG-motif positive DNAs were used. Unlike murine macrophages or Flt-3 L cultured DC, GM-CSF DC did not release inflammatory cytokines in response to the addition of CT DNA/cationic lipid complex, suggesting that the activation is completely dependent on CpG motifs. Taken together, the results of the present study demonstrate that murine DC produce pro-inflammatory cytokines upon stimulation with CpG-containing DNAs and the responses are enhanced by cationic lipids. These results also suggest that DC are the major cells that respond to naked CpG DNA in vivo, although both DC and macrophages will release inflammatory cytokines after the administration of a DNA/cationic lipid complex. PMID:17199803

  18. Shape-dependent bactericidal activity of copper oxide nanoparticle mediated by DNA and membrane damage

    SciTech Connect

    Laha, Dipranjan; Pramanik, Arindam; Laskar, Aparna; Jana, Madhurya; Pramanik, Panchanan; Karmakar, Parimal

    2014-11-15

    Highlights: • Spherical and sheet shaped copper oxide nanoparticles were synthesized. • Physical characterizations of these nanoparticles were done by TEM, DLS, XRD, FTIR. • They showed shape dependent antibacterial activity on different bacterial strain. • They induced both membrane damage and ROS mediated DNA damage in bacteria. - Abstract: In this work, we synthesized spherical and sheet shaped copper oxide nanoparticles and their physical characterizations were done by the X-ray diffraction, fourier transform infrared spectroscopy, transmission electron microscopy and dynamic light scattering. The antibacterial activity of these nanoparticles was determined on both gram positive and gram negative bacterial. Spherical shaped copper oxide nanoparticles showed more antibacterial property on gram positive bacteria where as sheet shaped copper oxide nanoparticles are more active on gram negative bacteria. We also demonstrated that copper oxide nanoparticles produced reactive oxygen species in both gram negative and gram positive bacteria. Furthermore, they induced membrane damage as determined by atomic force microscopy and scanning electron microscopy. Thus production of and membrane damage are major mechanisms of the bactericidal activity of these copper oxide nanoparticles. Finally it was concluded that antibacterial activity of nanoparticles depend on physicochemical properties of copper oxide nanoparticles and bacterial strain.

  19. Ligand-dependent recruitment of the Arnt coregulator determines DNA recognition by the dioxin receptor

    SciTech Connect

    Whitelaw, M.; Pongratz, I.; Wilhelmsson, A.; Gustafsson, J.; Poellinger, L. )

    1993-04-01

    Signal transduction by dioxins is mediated by the intracellular dioxin or aryl hydrocarbon receptor. This receptor binds dioxin and its planar aromatic congeners in a saturable manner with high affinity. The extreme toxicity of dioxin has been demonstrated in animals but not in humans. In animals, dioxin causes thymic wasting, immune suppression, severe epithelial disorders and tumor promotion. On a molecular level, dioxins are inducers of transcription of a battery of target genes encoding xenobiotic metabolizing enzymes. Dioxin also appears to transcriptionally regulate the expression of the growth modulatory genes for interleukin-1 Beta and plasminogen activator inhibitor-2. The dioxin induction response is mediated by single or multiple copies of dioxin-inducible transcriptional control elements in target promoters. The research data detailed in this paper examines the ligand-dependent recruitment of the Arnt coregulator which determines DNA recognition by the dioxin receptor. This data suggests that dioxin receptor activity is governed by a complex pattern of combinatorial regulation involving repression by hsp90 and then by ligand-dependent recruitment of the positive coregulator Arnt and that the dioxin receptor system provides the first example of signal-controlled dimerization of bHLH factors.

  20. Shear Strength of Conductive Adhesive Joints on Rigid and Flexible Substrates Depending on Adhesive Quantity

    NASA Astrophysics Data System (ADS)

    Hirman, Martin; Steiner, Frantisek

    2016-05-01

    This article deals with the impact of electrically conductive adhesive quantity on the shear strength of joints glued by adhesives "EPO-TEKⓇ H20S" and "MG8331S" on three types of substrates (FR-4, MELINEXⓇST504, DuPont™ PyraluxⓇAC). These joints were made by gluing chip resistors 1206, 0805 and 0603, with two curing profiles for each adhesive. Different thicknesses of stencil and reductions in the size of the hole in stencils were used for this experiment. These differences have an effect on the quantity of conductive adhesives which must be used on the samples. Samples were measured after the curing process by using a shear strength test applied by the device LabTest 3.030. This article presents the effects of different curing profiles, various types of substrates, and different quantities of adhesives on the mechanical strength of the joint.

  1. Controlled synthesis and size-dependent thermal conductivity of Fe3O4 magnetic nanofluids.

    PubMed

    Wang, Baodui; Wang, Baogang; Wei, Pengfei; Wang, Xiaobo; Lou, Wenjing

    2012-01-21

    The effect of nanoparticle size (4~44 nm) on the thermal conductivities of heat transfer oils has been systematically examined using iron oxide nanoparticles. Such Fe(3)O(4) nanoparticles were synthesized by a simple one-pot pyrolysis method. The size (16~44 nm), shape and assembly patterns of monodisperse Fe(3)O(4) nanoparticles were modulated by only controlling the amount of Fe(acac)(3). After the as-prepared Fe(3)O(4) NPs were dispersed in heat transfer oils, the prepared magnetic nanofluids exhibit higher thermal conductivity than heat transfer oils, and the enhanced values increase with a decrease in particle size. In addition, the viscosities of all nanofliuids are remarkably lower than that of the base fluid, which has been found for the first time in the nanofluid field. The promising features offer potential application in thermal energy engineering. PMID:22086086

  2. Measurement of temperature-dependent viscosity and thermal conductivity of alumina and titania thermal oil nanofluids

    NASA Astrophysics Data System (ADS)

    Cieśliński, Janusz T.; Ronewicz, Katarzyna; Smoleń, Sławomir

    2015-12-01

    In this study the results of simultaneous measurements of dynamic viscosity, thermal conductivity, electrical conductivity and pH of two nanofluids, i.e., thermal oil/Al2O3 and thermal oil/TiO2 are presented. Thermal oil is selected as a base liquid because of possible application in ORC systems as an intermediate heating agent. Nanoparticles were tested at the concentration of 0.1%, 1%, and 5% by weight within temperature range from 20 °C to 60 °C. Measurement devices were carefully calibrated by comparison obtained results for pure base liquid (thermal oil) with manufacturer's data. The results obtained for tested nanofluids were compared with predictions made by use of existing models for liquid/solid particles mixtures.

  3. Architecture-dependent signal conduction in model networks of endothelial cells

    NASA Astrophysics Data System (ADS)

    Deymier, Pierre A.; Eray, Mete; Deymier, Martin J.; Runge, Keith; Hoying, James B.; Vasseur, Jérome O.

    2010-04-01

    Signal conduction between endothelial cells along the walls of vessels appears to play an important role in circulatory function. A recently developed approach to calculate analytically the spectrum of propagating compositional waves in models of multicellular architectures is extended to study putative signal conduction dynamics across networks of endothelial cells. Here, compositional waves originate from negative feedback loops, such as between Ca2+ and inositol triphosphate (IP3) in endothelial cells, and are shaped by their connection topologies. We consider models of networks constituted of a main chain of endothelial cells and multiple side chains. The resulting transmission spectra encode information concerning the position and size of the side branches in the form of gaps. This observation suggests that endothelial cell networks may be able to “communicate” information regarding long-range order in their architecture.

  4. Current-dependent anisotropic conductivity of locally assembled silver nanoparticles in hybrid polymer films.

    PubMed

    Goel, Pooja; Vinokur, Rostislav; Weichold, Oliver

    2010-12-15

    The electrical behaviour of hybrid poly(ethylene terephthalate) films containing localised, percolating networks of silver nanoparticles separated by pure polymer is studied. The films resemble an array of parallel wires in the submicron range and, thus, exhibit anisotropic conductivity. In the high-conductivity direction at low amplitudes, the films show Ohmic behaviour, while at moderate voltage, non-linearity and a decreasing resistance is observed. The samples were found to heat up during the measurements and the deviation from Ohm's law coincides with the Tg of the polymer. Microstructural analysis of the samples revealed an irreversible agglomeration of the particles at moderate voltages leading to the formation of filaments with higher metallic character than the random particle network. PMID:20843521

  5. A TRP conductance modulates repolarization after sensory-dependent depolarization in Chlamydomonas reinhardtii

    PubMed Central

    Arias-Darraz, Luis; Colenso, Charlotte K; Veliz, Luis A; Vivar, Juan P; Cardenas, Sylvana; Brauchi, Sebastian

    2015-01-01

    Sensory integration is vital for motile organisms constantly exposed to changing surroundings. Chlamydomonas reinhardtii is a single-celled green alga found swimming in freshwater. In this type of alga, sensory input is first detected by membrane receptors located in the cell body, and then transduced to the beating cilia by membrane depolarization. Many components of the machinery associated with sensory integration in C. reinhardtii, such as chemoreceptors and repolarization-associated channels, are yet uncharacterized. TRP channels are known mediators for cellular sensing in animal cells and it has been suggested that the C. reinhardtii genome encodes for a set of TRP proteins. Here, by combining behavioral studies with electrophysiological experiments conducted on both population and single alga, we test whether TRP channel blockers affect algal swimming behavior. Our results suggest that a TRP conductance is associated to the repolarization that follows a depolarizing receptor potential, highlighting a primitive function of TRP proteins. PMID:26186626

  6. Anomalous length dependence of conductance of aromatic nanoribbons with amine anchoring groups

    NASA Astrophysics Data System (ADS)

    Bilić, Ante; Sanvito, Stefano

    2012-09-01

    Two sets of aromatic nanoribbons, based around a common hexagonal scaffolding, with single and dual terminal amine groups have been considered as potential molecular wires in a junction formed by gold leads. Charge transport through the two-terminal device has been modeled using density functional theory (with and without self-interaction correction) and the nonequilibrium Green's function method. The effects of wire length, multiple terminal contacts, and pathways across the junction have been investigated. For nanoribbons with the oligopyrene motif and conventional single amine terminal groups, an increase in the wire length causes an exponential drop in the conductance. In contrast, for the nanoribbons with the oligoperylene motif and dual amine anchoring groups the predicted conductance rises with the wire length over the whole range of investigated lengths. Only when the effects of self-interaction correction are taken into account, the conductance of the oligoperylene ribbons exhibits saturation for longer members of the series. The oligoperylene nanoribbons, with dual amine groups at both terminals, show the potential to fully harness the highly conjugated system of π molecular orbitals across the junction.

  7. Electrical conduction of ion tracks in tetrahedral amorphous carbon: temperature, field and doping dependence and comparison with matrix data

    NASA Astrophysics Data System (ADS)

    Krauser, J.; Gehrke, H.-G.; Hofsäss, H.; Amani, J.; Trautmann, C.; Weidinger, A.

    2015-12-01

    This paper gives an extended overview of the electrical properties of ion tracks in hydrogen-free tetrahedral amorphous carbon (ta-C) with a sp3 bond fraction of about 80%. The films were grown by mass selected ion beam deposition of 100 eV 12C+ ions. The ion tracks are generated by irradiation of ta-C films with uranium ions of 1 GeV kinetic energy. Along the ion path a conversion from diamond-like (sp3) carbon to graphite-like (sp2) carbon takes place. Topography and current measurements of individual ion tracks were performed by atomic force microscopy at ambient temperature. The temperature dependence of the electric conductivity was studied between 15 and 390 K by means of 0.28 mm2 large contact pads averaging over about 107 tracks. For each sample and at each temperature the conductivity as a function of the applied electrical field (non-ohmic behaviour) was measured separately and the data were extrapolated to field zero. In this way, the zero-field conductivity was determined independent from the field dependence. In spite of large differences in the absolute values, the temperature dependence of the zero-field conductivities is found to be very similar in shape for all samples. The conductivities follow a {T}-{1/4} law up to temperatures slightly below room temperature. At higher temperatures a transport mechanism based on over-barrier hopping dominates with an activation energy of about 220 meV for tracks and 260 meV for the ta-C matrix. The field dependence measurements show that the deviation of the I-V characteristics from ohmic behaviour decreases with increasing zero-field conductivity. We also tested Cu-doped ta-C samples and found that they conduct significantly better than pure ta-C. However, the doping also increases the zero-field conductivity resulting in a weaker contrast between the track and matrix. The data are interpreted within the so-called ‘barrier model’ where the electrons are assumed to move fairly freely in well-conducting sp2

  8. Prenatal Exposure to DEHP Affects Spermatogenesis and Sperm DNA Methylation in a Strain-Dependent Manner.

    PubMed

    Prados, Julien; Stenz, Ludwig; Somm, Emmanuel; Stouder, Christelle; Dayer, Alexandre; Paoloni-Giacobino, Ariane

    2015-01-01

    Di-(2-ethylhexyl)phtalate (DEHP) is a plasticizer with endocrine disrupting properties found ubiquitously in the environment and altering reproduction in rodents. Here we investigated the impact of prenatal exposure to DEHP on spermatogenesis and DNA sperm methylation in two distinct, selected, and sequenced mice strains. FVB/N and C57BL/6J mice were orally exposed to 300 mg/kg/day of DEHP from gestation day 9 to 19. Prenatal DEHP exposure significantly decreased spermatogenesis in C57BL/6J (fold-change = 0.6, p-value = 8.7*10-4), but not in FVB/N (fold-change = 1, p-value = 0.9). The number of differentially methylated regions (DMRs) by DEHP-exposure across the entire genome showed increased hyper- and decreased hypo-methylation in C57BL/6J compared to FVB/N. At the promoter level, three important subsets of genes were massively affected. Promoters of vomeronasal and olfactory receptors coding genes globally followed the same trend, more pronounced in the C57BL/6J strain, of being hyper-methylated in DEHP related conditions. In contrast, a large set of micro-RNAs were hypo-methylated, with a trend more pronounced in the FVB/N strain. We additionally analyze both the presence of functional genetic variations within genes that were associated with the detected DMRs and that could be involved in spermatogenesis, and DMRs related with the DEHP exposure that affected both strains in an opposite manner. The major finding in this study indicates that prenatal exposure to DEHP can decrease spermatogenesis in a strain-dependent manner and affects sperm DNA methylation in promoters of large sets of genes putatively involved in both sperm chemotaxis and post-transcriptional regulatory mechanisms. PMID:26244509

  9. Prenatal Exposure to DEHP Affects Spermatogenesis and Sperm DNA Methylation in a Strain-Dependent Manner

    PubMed Central

    Somm, Emmanuel; Stouder, Christelle; Dayer, Alexandre; Paoloni-Giacobino, Ariane

    2015-01-01

    Di-(2-ethylhexyl)phtalate (DEHP) is a plasticizer with endocrine disrupting properties found ubiquitously in the environment and altering reproduction in rodents. Here we investigated the impact of prenatal exposure to DEHP on spermatogenesis and DNA sperm methylation in two distinct, selected, and sequenced mice strains. FVB/N and C57BL/6J mice were orally exposed to 300 mg/kg/day of DEHP from gestation day 9 to 19. Prenatal DEHP exposure significantly decreased spermatogenesis in C57BL/6J (fold-change = 0.6, p-value = 8.7*10-4), but not in FVB/N (fold-change = 1, p-value = 0.9). The number of differentially methylated regions (DMRs) by DEHP-exposure across the entire genome showed increased hyper- and decreased hypo-methylation in C57BL/6J compared to FVB/N. At the promoter level, three important subsets of genes were massively affected. Promoters of vomeronasal and olfactory receptors coding genes globally followed the same trend, more pronounced in the C57BL/6J strain, of being hyper-methylated in DEHP related conditions. In contrast, a large set of micro-RNAs were hypo-methylated, with a trend more pronounced in the FVB/N strain. We additionally analyze both the presence of functional genetic variations within genes that were associated with the detected DMRs and that could be involved in spermatogenesis, and DMRs related with the DEHP exposure that affected both strains in an opposite manner. The major finding in this study indicates that prenatal exposure to DEHP can decrease spermatogenesis in a strain-dependent manner and affects sperm DNA methylation in promoters of large sets of genes putatively involved in both sperm chemotaxis and post-transcriptional regulatory mechanisms. PMID:26244509

  10. Impact of Temperature-dependent Resistivity and Thermal Conduction on Plasmoid Instabilities in Current Sheets in the Solar Corona

    NASA Astrophysics Data System (ADS)

    Ni, Lei; Roussev, Ilia I.; Lin, Jun; Ziegler, Udo

    2012-10-01

    In this paper, we investigate, by means of two-dimensional magnetohydrodynamic simulations, the impact of temperature-dependent resistivity and thermal conduction on the development of plasmoid instabilities in reconnecting current sheets in the solar corona. We find that the plasma temperature in the current-sheet region increases with time and it becomes greater than that in the inflow region. As secondary magnetic islands appear, the highest temperature is not always found at the reconnection X-points, but also inside the secondary islands. One of the effects of anisotropic thermal conduction is to decrease the temperature of the reconnecting X-points and transfer the heat into the O-points, the plasmoids, where it gets trapped. In the cases with temperature-dependent magnetic diffusivity, η ~ T -3/2, the decrease in plasma temperature at the X-points leads to (1) an increase in the magnetic diffusivity until the characteristic time for magnetic diffusion becomes comparable to that of thermal conduction, (2) an increase in the reconnection rate, and (3) more efficient conversion of magnetic energy into thermal energy and kinetic energy of bulk motions. These results provide further explanation of the rapid release of magnetic energy into heat and kinetic energy seen during flares and coronal mass ejections. In this work, we demonstrate that the consideration of anisotropic thermal conduction and Spitzer-type, temperature-dependent magnetic diffusivity, as in the real solar corona, are crucially important for explaining the occurrence of fast reconnection during solar eruptions.

  11. Stereochemistry-Dependent Proton Conduction in Proton Exchange Membrane Fuel Cells.

    PubMed

    Thimmappa, Ravikumar; Devendrachari, Mruthyunjayachari Chattanahalli; Kottaichamy, Alagar Raja; Tiwari, Omshanker; Gaikwad, Pramod; Paswan, Bhuneshwar; Thotiyl, Musthafa Ottakam

    2016-01-12

    Graphene oxide (GO) is impermeable to H2 and O2 fuels while permitting H(+) shuttling, making it a potential candidate for proton exchange membrane fuel cells (PEMFC), albeit with a large anisotropy in their proton transport having a dominant in plane (σIP) contribution over the through plane (σTP). If GO-based membranes are ever to succeed in PEMFC, it inevitably should have a dominant through-plane proton shuttling capability (σTP), as it is the direction in which proton gets transported in a real fuel-cell configuration. Here we show that anisotropy in proton conduction in GO-based fuel cell membranes can be brought down by selectively tuning the geometric arrangement of functional groups around the dopant molecules. The results show that cis isomer causes a selective amplification of through-plane proton transport, σTP, pointing to a very strong geometry angle in ionic conduction. Intercalation of cis isomer causes significant expansion of GO (001) planes involved in σTP transport due to their mutual H-bonding interaction and efficient bridging of individual GO planes, bringing down the activation energy required for σTP, suggesting the dominance of a Grotthuss-type mechanism. This isomer-governed amplification of through-plane proton shuttling resulted in the overall boosting of fuel-cell performance, and it underlines that geometrical factors should be given prime consideration while selecting dopant molecules for bringing down the anisotropy in proton conduction and enhancing the fuel-cell performance in GO-based PEMFC. PMID:26652316

  12. General method to predict voltage-dependent ionic conduction in a solid electrolyte coating on electrodes

    NASA Astrophysics Data System (ADS)

    Pan, Jie; Cheng, Yang-Tse; Qi, Yue

    2015-04-01

    Understanding the ionic conduction in solid electrolytes in contact with electrodes is vitally important to many applications, such as lithium ion batteries. The problem is complex because both the internal properties of the materials (e.g., electronic structure) and the characteristics of the externally contacting phases (e.g., voltage of the electrode) affect defect formation and transport. In this paper, we developed a method based on density functional theory to study the physics of defects in a solid electrolyte in equilibrium with an external environment. This method was then applied to predict the ionic conduction in lithium fluoride (LiF), in contact with different electrodes which serve as reservoirs with adjustable Li chemical potential (μLi) for defect formation. LiF was chosen because it is a major component in the solid electrolyte interphase (SEI) formed on lithium ion battery electrodes. Seventeen possible native defects with their relevant charge states in LiF were investigated to determine the dominant defect types on various electrodes. The diffusion barrier of dominant defects was calculated by the climbed nudged elastic band method. The ionic conductivity was then obtained from the concentration and mobility of defects using the Nernst-Einstein relationship. Three regions for defect formation were identified as a function of μLi: (1) intrinsic, (2) transitional, and (3) p -type region. In the intrinsic region (high μLi, typical for LiF on the negative electrode), the main defects are Schottky pairs and in the p -type region (low μLi, typical for LiF on the positive electrode) are Li ion vacancies. The ionic conductivity is calculated to be approximately 10-31Scm-1 when LiF is in contact with a negative electrode but it can increase to 10-12Scm-1 on a positive electrode. This insight suggests that divalent cation (e.g., Mg2+) doping is necessary to improve Li ion transport through the engineered LiF coating, especially for LiF on negative

  13. Establishment of an inducible HBV stable cell line that expresses cccDNA-dependent epitope-tagged HBeAg for screening of cccDNA modulators.

    PubMed

    Cai, Dawei; Wang, Xiaohe; Yan, Ran; Mao, Richeng; Liu, Yuanjie; Ji, Changhua; Cuconati, Andrea; Guo, Haitao

    2016-08-01

    Hepatitis B virus (HBV) covalently closed circular (ccc) DNA is essential to the virus life cycle, its elimination during chronic infection is considered critical to a durable therapy but has not been achieved by current antivirals. Despite being essential, cccDNA has not been the major target of high throughput screening (HTS), largely because of the limitations of current HBV tissue culture systems, including the impracticality of detecting cccDNA itself. In response to this need, we have previously developed a proof-of-concept HepDE19 cell line in which the production of wildtype e antigen (HBeAg) is dependent upon cccDNA. However, the existing assay system is not ideal for HTS because the HBeAg ELISA cross reacts with a viral HBeAg homologue, which is the core antigen (HBcAg) expressed largely in a cccDNA-independent fashion in HepDE19 cells. To further improve the assay specificity, we report herein a "second-generation" cccDNA reporter cell line, termed HepBHAe82. In the similar principle of HepDE19 line, an in-frame HA epitope tag was introduced into the precore domain of HBeAg open reading frame in the transgene of HepBHAe82 cells without disrupting any cis-element critical for HBV replication and HBeAg secretion. A chemiluminescence ELISA assay (CLIA) for the detection of HA-tagged HBeAg with HA antibody serving as capture antibody and HBeAb serving as detection antibody has been developed to eliminate the confounding signal from HBcAg. The miniaturized HepBHAe82 cell based assay system exhibits high level of cccDNA-dependent HA-HBeAg production and high specific readout signals with low background. We have also established a HepHA-HBe4 cell line expressing transgene-dependent HA-HBeAg as a counter screen to identify HBeAg inhibitors. The HepBHAe82 system is amenable to antiviral HTS development, and can be used to identify host factors that regulate cccDNA metabolism and transcription. PMID:27185623

  14. Mitochondrial genome of the moon jelly Aurelia aurita (Cnidaria, Scyphozoa): A linear DNA molecule encoding a putative DNA-dependent DNA polymerase.

    PubMed

    Shao, Zhiyong; Graf, Shannon; Chaga, Oleg Y; Lavrov, Dennis V

    2006-10-15

    The 16,937-nuceotide sequence of the linear mitochondrial DNA (mt-DNA) molecule of the moon jelly Aurelia aurita (Cnidaria, Scyphozoa) - the first mtDNA sequence from the class Scypozoa and the first sequence of a linear mtDNA from Metazoa - has been determined. This sequence contains genes for 13 energy pathway proteins, small and large subunit rRNAs, and methionine and tryptophan tRNAs. In addition, two open reading frames of 324 and 969 base pairs in length have been found. The deduced amino-acid sequence of one of them, ORF969, displays extensive sequence similarity with the polymerase [but not the exonuclease] domain of family B DNA polymerases, and this ORF has been tentatively identified as dnab. This is the first report of dnab in animal mtDNA. The genes in A. aurita mtDNA are arranged in two clusters with opposite transcriptional polarities; transcription proceeding toward the ends of the molecule. The determined sequences at the ends of the molecule are nearly identical but inverted and lack any obvious potential secondary structures or telomere-like repeat elements. The acquisition of mitochondrial genomic data for the second class of Cnidaria allows us to reconstruct characteristic features of mitochondrial evolution in this animal phylum. PMID:16945488

  15. Examination of genetic variation in GABRA2 with conduct disorder and alcohol abuse and dependence in a longitudinal study

    PubMed Central

    Melroy, Whitney E.; Stephens, Sarah H.; Sakai, Joseph T.; Kamens, Helen M.; McQueen, Matthew B.; Corley, Robin P.; Stallings, Michael C.; Hopfer, Christian J.; Krauter, Kenneth S.; Brown, Sandra A.; Hewitt, John K.; Ehringer, Marissa A.

    2014-01-01

    Previous studies have shown associations between SNPs in GABRA2 and adolescent conduct disorder (CD) and alcohol dependence in adulthood, but not adolescent alcohol dependence. The present study was intended as a replication and extension of this work, focusing on adolescent CD, adolescent alcohol abuse and dependence (AAD), and adult AAD. Family based association tests were run using Hispanics and non-Hispanic European American subjects from two independent longitudinal samples. Although the analysis provided nominal support for an association with rs9291283 and AAD in adulthood and CD in adolescence, the current study failed to replicate previous associations between two well replicated GABRA2 NPs and CD and alcohol dependence. Overall, these results emphasize the utility of including an independent replication sample in the study design, so that the results from an individual sample can be weighted in the context of its reproducibility. PMID:24687270

  16. DNA.

    ERIC Educational Resources Information Center

    Felsenfeld, Gary

    1985-01-01

    Structural form, bonding scheme, and chromatin structure of and gene-modification experiments with deoxyribonucleic acid (DNA) are described. Indicates that DNA's double helix is variable and also flexible as it interacts with regulatory and other molecules to transfer hereditary messages. (DH)

  17. Temperature Dependence of Electrical and Thermal Conduction in Single Silver Nanowire

    PubMed Central

    Cheng, Zhe; Liu, Longju; Xu, Shen; Lu, Meng; Wang, Xinwei

    2015-01-01

    In this work, the thermal and electrical transport in an individual silver nanowire is characterized down to 35 K for in-depth understanding of the strong structural defect induced electron scattering. The results indicate that, at room temperature, the electrical resistivity increases by around 4 folds from that of bulk silver. The Debye temperature (151 K) of the silver nanowire is found 36% lower than that (235 K) of bulk silver, confirming strong phonon softening. At room temperature, the thermal conductivity is reduced by 55% from that of bulk silver. This reduction becomes larger as the temperature goes down. To explain the opposite trends of thermal conductivity (κ) ~ temperature (T) of silver nanowire and bulk silver, a unified thermal resistivity () is used to elucidate the electron scattering mechanism. A large residual Θ is observed for silver nanowire while that of the bulk silver is almost zero. The same ~T trend proposes that the silver nanowire and bulk silver share the similar phonon-electron scattering mechanism for thermal transport. Due to phonon-assisted electron energy transfer across grain boundaries, the Lorenz number of the silver nanowire is found much larger than that of bulk silver and decreases with decreasing temperature. PMID:26035288

  18. Temperature dependence of electrical and thermal conduction in single silver nanowire.

    PubMed

    Cheng, Zhe; Liu, Longju; Xu, Shen; Lu, Meng; Wang, Xinwei

    2015-01-01

    In this work, the thermal and electrical transport in an individual silver nanowire is characterized down to 35 K for in-depth understanding of the strong structural defect induced electron scattering. The results indicate that, at room temperature, the electrical resistivity increases by around 4 folds from that of bulk silver. The Debye temperature (151 K) of the silver nanowire is found 36% lower than that (235 K) of bulk silver, confirming strong phonon softening. At room temperature, the thermal conductivity is reduced by 55% from that of bulk silver. This reduction becomes larger as the temperature goes down. To explain the opposite trends of thermal conductivity (κ) ~ temperature (T) of silver nanowire and bulk silver, a unified thermal resistivity (Θ ~ T/k ) is used to elucidate the electron scattering mechanism. A large residual Θ is observed for silver nanowire while that of the bulk silver is almost zero. The same Θ ~ T trend proposes that the silver nanowire and bulk silver share the similar phonon-electron scattering mechanism for thermal transport. Due to phonon-assisted electron energy transfer across grain boundaries, the Lorenz number of the silver nanowire is found much larger than that of bulk silver and decreases with decreasing temperature. PMID:26035288

  19. A yeast gene, MGS1, encoding a DNA-dependent AAA(+) ATPase is required to maintain genome stability.

    PubMed

    Hishida, T; Iwasaki, H; Ohno, T; Morishita, T; Shinagawa, H

    2001-07-17

    Changes in DNA superhelicity during DNA replication are mediated primarily by the activities of DNA helicases and topoisomerases. If these activities are defective, the progression of the replication fork can be hindered or blocked, which can lead to double-strand breaks, elevated recombination in regions of repeated DNA, and genome instability. Hereditary diseases like Werner's and Bloom's Syndromes are caused by defects in DNA helicases, and these diseases are associated with genome instability and carcinogenesis in humans. Here we report a Saccharomyces cerevisiae gene, MGS1 (Maintenance of Genome Stability 1), which encodes a protein belonging to the AAA(+) class of ATPases, and whose central region is similar to Escherichia coli RuvB, a Holliday junction branch migration motor protein. The Mgs1 orthologues are highly conserved in prokaryotes and eukaryotes. The Mgs1 protein possesses DNA-dependent ATPase and single-strand DNA annealing activities. An mgs1 deletion mutant has an elevated rate of mitotic recombination, which causes genome instability. The mgs1 mutation is synergistic with a mutation in top3 (encoding topoisomerase III), and the double mutant exhibits severe growth defects and markedly increased genome instability. In contrast to the mgs1 mutation, a mutation in the sgs1 gene encoding a DNA helicase homologous to the Werner and Bloom helicases suppresses both the growth defect and the increased genome instability of the top3 mutant. Therefore, evolutionarily conserved Mgs1 may play a role together with RecQ family helicases and DNA topoisomerases in maintaining proper DNA topology, which is essential for genome stability. PMID:11459965

  20. Temperature-dependent capillary forces at nano-contacts for estimating the heat conduction through a water meniscus.

    PubMed

    Assy, Ali; Gomès, Séverine

    2015-09-01

    The temperature dependence of the capillary forces at nano-sized contacts is investigated. Two different resistive scanning thermal microscopy (SThM) nanoprobes are used in this study. Measurements of the capillary forces are reported as a function of the probe temperature on hydrophilic samples of different thermal properties. These forces appear to be largely reduced for probe temperatures larger than a threshold temperature, where the value depends on the sample thermal conductance. This could pave the way to an alternative solution to reduce the stiction in nano/ micro-electromechanical (NEMS/MEMS) devices. The dimensions of the water meniscus at the probe-sample contact were then estimated. Moreover, these results help the evaluation of thermal conductance through the water meniscus. It is found, through this work, that the values of the thermal conductance through the water meniscus can represent 6% of those of the contact thermal conductance in the case of the KNT probe (from Kelvin nanotechnology). These values can be equal to 4% of those of thermal conduction in the cantilever-sample air gap in the case of a doped-silicon probe. PMID:26245265

  1. Temperature-dependent capillary forces at nano-contacts for estimating the heat conduction through a water meniscus

    NASA Astrophysics Data System (ADS)

    Assy, Ali; Gomès, Séverine

    2015-09-01

    The temperature dependence of the capillary forces at nano-sized contacts is investigated. Two different resistive scanning thermal microscopy (SThM) nanoprobes are used in this study. Measurements of the capillary forces are reported as a function of the probe temperature on hydrophilic samples of different thermal properties. These forces appear to be largely reduced for probe temperatures larger than a threshold temperature, where the value depends on the sample thermal conductance. This could pave the way to an alternative solution to reduce the stiction in nano/ micro-electromechanical (NEMS/MEMS) devices. The dimensions of the water meniscus at the probe-sample contact were then estimated. Moreover, these results help the evaluation of thermal conductance through the water meniscus. It is found, through this work, that the values of the thermal conductance through the water meniscus can represent 6% of those of the contact thermal conductance in the case of the KNT probe (from Kelvin nanotechnology). These values can be equal to 4% of those of thermal conduction in the cantilever-sample air gap in the case of a doped-silicon probe.

  2. Ligand-activated PPARα-dependent DNA demethylation regulates the fatty acid β-oxidation genes in the postnatal liver.

    PubMed

    Ehara, Tatsuya; Kamei, Yasutomi; Yuan, Xunmei; Takahashi, Mayumi; Kanai, Sayaka; Tamura, Erina; Tsujimoto, Kazutaka; Tamiya, Takashi; Nakagawa, Yoshimi; Shimano, Hitoshi; Takai-Igarashi, Takako; Hatada, Izuho; Suganami, Takayoshi; Hashimoto, Koshi; Ogawa, Yoshihiro

    2015-03-01

    The metabolic function of the liver changes sequentially during early life in mammals to adapt to the marked changes in nutritional environment. Accordingly, hepatic fatty acid β-oxidation is activated after birth to produce energy from breast milk lipids. However, how it is induced during the neonatal period is poorly understood. Here we show DNA demethylation and increased mRNA expression of the fatty acid β-oxidation genes in the postnatal mouse liver. The DNA demethylation does not occur in the fetal mouse liver under the physiologic condition, suggesting that it is specific to the neonatal period. Analysis of mice deficient in the nuclear receptor peroxisome proliferator-activated receptor α (PPARα) and maternal administration of a PPARα ligand during the gestation and lactation periods reveal that the DNA demethylation is PPARα dependent. We also find that DNA methylation of the fatty acid β-oxidation genes are reduced in the adult human liver relative to the fetal liver. This study represents the first demonstration that the ligand-activated PPARα-dependent DNA demethylation regulates the hepatic fatty acid β-oxidation genes during the neonatal period, thereby highlighting the role of a lipid-sensing nuclear receptor in the gene- and life-stage-specific DNA demethylation of a particular metabolic pathway. PMID:25311726

  3. Self-catalytic growth of unmodified gold nanoparticles as conductive bridges mediated gap-electrical signal transduction for DNA hybridization detection.

    PubMed

    Zhang, Jing; Nie, Huagui; Wu, Zhan; Yang, Zhi; Zhang, Lijie; Xu, Xiangju; Huang, Shaoming

    2014-01-21

    A simple and sensitive gap-electrical biosensor based on self-catalytic growth of unmodified gold nanoparticles (AuNPs) as conductive bridges has been developed for amplifying DNA hybridization events. In this strategy, the signal amplification degree of such conductive bridges is closely related to the variation of the glucose oxidase (GOx)-like catalytic activity of AuNPs upon interaction with single- and double-stranded DNA (ssDNA and dsDNA), respectively. In the presence of target DNA, the obtained dsDNA product cannot adsorb onto the surface of AuNPs due to electrostatic interaction, which makes the unmodified AuNPs exhibit excellent GOx-like catalytic activity. Such catalytic activity can enlarge the diameters of AuNPs in the glucose and HAuCl4 solution and result in a connection between most of the AuNPs and a conductive gold film formation with a dramatically increased conductance. For the control sample, the catalytic activity sites of AuNPs are fully blocked by ssDNA due to the noncovalent interaction between nucleotide bases and AuNPs. Thus, the growth of the assembled AuNPs will not happen and the conductance between microelectrodes will be not changed. Under the optimal experimental conditions, the developed strategy exhibited a sensitive response to target DNA with a high signal-to-noise ratio. Moreover, this strategy was also demonstrated to provide excellent differentiation ability for single-nucleotide polymorphism. Such performances indicated the great potential of this label-free electrical strategy for clinical diagnostics and genetic analysis under real biological sample separation. PMID:24313362

  4. Direct evidence for sequence-dependent attraction between double-stranded DNA controlled by methylation

    NASA Astrophysics Data System (ADS)

    Yoo, Jejoong; Kim, Hajin; Aksimentiev, Aleksei; Ha, Taekjip

    2016-03-01

    Although proteins mediate highly ordered DNA organization in vivo, theoretical studies suggest that homologous DNA duplexes can preferentially associate with one another even in the absence of proteins. Here we combine molecular dynamics simulations with single-molecule fluorescence resonance energy transfer experiments to examine the interactions between duplex DNA in the presence of spermine, a biological polycation. We find that AT-rich DNA duplexes associate more strongly than GC-rich duplexes, regardless of the sequence homology. Methyl groups of thymine acts as a steric block, relocating spermine from major grooves to interhelical regions, thereby increasing DNA-DNA attraction. Indeed, methylation of cytosines makes attraction between GC-rich DNA as strong as that between AT-rich DNA. Recent genome-wide chromosome organization studies showed that remote contact frequencies are higher for AT-rich and methylated DNA, suggesting that direct DNA-DNA interactions that we report here may play a role in the chromosome organization and gene regulation.

  5. Direct evidence for sequence-dependent attraction between double-stranded DNA controlled by methylation.

    PubMed

    Yoo, Jejoong; Kim, Hajin; Aksimentiev, Aleksei; Ha, Taekjip

    2016-01-01

    Although proteins mediate highly ordered DNA organization in vivo, theoretical studies suggest that homologous DNA duplexes can preferentially associate with one another even in the absence of proteins. Here we combine molecular dynamics simulations with single-molecule fluorescence resonance energy transfer experiments to examine the interactions between duplex DNA in the presence of spermine, a biological polycation. We find that AT-rich DNA duplexes associate more strongly than GC-rich duplexes, regardless of the sequence homology. Methyl groups of thymine acts as a steric block, relocating spermine from major grooves to interhelical regions, thereby increasing DNA-DNA attraction. Indeed, methylation of cytosines makes attraction between GC-rich DNA as strong as that between AT-rich DNA. Recent genome-wide chromosome organization studies showed that remote contact frequencies are higher for AT-rich and methylated DNA, suggesting that direct DNA-DNA interactions that we report here may play a role in the chromosome organization and gene regulation. PMID:27001929

  6. DNA-binding protein searches for its target: Non-monotonic dependence of the search time on the density of roadblocks bound on the DNA chain.

    PubMed

    Liu, Lin; Luo, Kaifu

    2015-03-28

    The search of DNA-binding proteins for their target sites positioned on DNA plays a very important role in many cellular processes, and this search process combines 3D excursions in the bulk solution with one-dimensional sliding along the DNA chain. In living cells, there exist roadblocks along DNA chain formed by other proteins; however, the role of the roadblock in search rate is poorly understood. Based on 3D Langevin dynamics simulations, we have investigated the effect of the blocker on the search dynamics. For a pair of symmetrically placed blockers with respect to the target, we find that, with increasing the distance between the blocker and the target, the search time, τ, rapidly decreases and then saturates. For randomly placed blockers with density ϕ, τ may initially increase to its maximum and then unexpectedly decreases with increasing ϕ, or always increase with ϕ, depending on the nonspecific interaction strength and the volume fraction of DNA in the system. The previous contradicted results on the role of the blocker in search time are reconciled by these findings. Particularly, the nonmonotonic behavior of τ with ϕ indicates that blockers may facilitate the search after a critical ϕ. PMID:25833608

  7. DNA-binding protein searches for its target: Non-monotonic dependence of the search time on the density of roadblocks bound on the DNA chain

    NASA Astrophysics Data System (ADS)

    Liu, Lin; Luo, Kaifu

    2015-03-01

    The search of DNA-binding proteins for their target sites positioned on DNA plays a very important role in many cellular processes, and this search process combines 3D excursions in the bulk solution with one-dimensional sliding along the DNA chain. In living cells, there exist roadblocks along DNA chain formed by other proteins; however, the role of the roadblock in search rate is poorly understood. Based on 3D Langevin dynamics simulations, we have investigated the effect of the blocker on the search dynamics. For a pair of symmetrically placed blockers with respect to the target, we find that, with increasing the distance between the blocker and the target, the search time, τ, rapidly decreases and then saturates. For randomly placed blockers with density ϕ, τ may initially increase to its maximum and then unexpectedly decreases with increasing ϕ, or always increase with ϕ, depending on the nonspecific interaction strength and the volume fraction of DNA in the system. The previous contradicted results on the role of the blocker in search time are reconciled by these findings. Particularly, the nonmonotonic behavior of τ with ϕ indicates that blockers may facilitate the search after a critical ϕ.

  8. Prolonged mitotic arrest induces a caspase-dependent DNA damage response at telomeres that determines cell survival.

    PubMed

    Hain, Karolina O; Colin, Didier J; Rastogi, Shubhra; Allan, Lindsey A; Clarke, Paul R

    2016-01-01

    A delay in the completion of metaphase induces a stress response that inhibits further cell proliferation or induces apoptosis. This response is thought to protect against genomic instability and is important for the effects of anti-mitotic cancer drugs. Here, we show that mitotic arrest induces a caspase-dependent DNA damage response (DDR) at telomeres in non-apoptotic cells. This pathway is under the control of Mcl-1 and other Bcl-2 family proteins and requires caspase-9, caspase-3/7 and the endonuclease CAD/DFF40. The gradual caspase-dependent loss of the shelterin complex protein TRF2 from telomeres promotes a DDR that involves DNA-dependent protein kinase (DNA-PK). Suppression of mitotic telomere damage by enhanced expression of TRF2, or the inhibition of either caspase-3/7 or DNA-PK during mitotic arrest, promotes subsequent cell survival. Thus, we demonstrate that mitotic stress is characterised by the sub-apoptotic activation of a classical caspase pathway, which promotes telomere deprotection, activates DNA damage signalling, and determines cell fate in response to a prolonged delay in mitosis. PMID:27230693

  9. Prolonged mitotic arrest induces a caspase-dependent DNA damage response at telomeres that determines cell survival

    PubMed Central

    Hain, Karolina O.; Colin, Didier J.; Rastogi, Shubhra; Allan, Lindsey A.; Clarke, Paul R.

    2016-01-01

    A delay in the completion of metaphase induces a stress response that inhibits further cell proliferation or induces apoptosis. This response is thought to protect against genomic instability and is important for the effects of anti-mitotic cancer drugs. Here, we show that mitotic arrest induces a caspase-dependent DNA damage response (DDR) at telomeres in non-apoptotic cells. This pathway is under the control of Mcl-1 and other Bcl-2 family proteins and requires caspase-9, caspase-3/7 and the endonuclease CAD/DFF40. The gradual caspase-dependent loss of the shelterin complex protein TRF2 from telomeres promotes a DDR that involves DNA-dependent protein kinase (DNA-PK). Suppression of mitotic telomere damage by enhanced expression of TRF2, or the inhibition of either caspase-3/7 or DNA-PK during mitotic arrest, promotes subsequent cell survival. Thus, we demonstrate that mitotic stress is characterised by the sub-apoptotic activation of a classical caspase pathway, which promotes telomere deprotection, activates DNA damage signalling, and determines cell fate in response to a prolonged delay in mitosis. PMID:27230693

  10. Context dependence between subdomains in the DNA binding interface of the I-CreI homing endonuclease

    PubMed Central

    Grizot, Sylvestre; Duclert, Aymeric; Thomas, Séverine; Duchateau, Philippe; Pâques, Frédéric

    2011-01-01

    Homing endonucleases (HE) have emerged as precise tools for achieving gene targeting events. Redesigned HEs with tailored specificities can be used to cleave new sequences, thereby considerably expanding the number of targetable genes and loci. With HEs, as well as with other protein scaffolds, context dependence of DNA/protein interaction patterns remains one of the major limitations for rational engineering of new DNA binders. Previous studies have shown strong crosstalk between different residues and regions of the DNA binding interface. To investigate this phenomenon, we systematically combined mutations from three groups of amino acids in the DNA binding regions of the I-CreI HE. Our results confirm that important crosstalk occurs throughout this interface in I-CreI. Detailed analysis of success rates identified a nearest-neighbour effect, with a more pronounced level of dependence between adjacent regions. Taken together, these data suggest that combinatorial engineering does not necessarily require the identification of separable functional or structural regions, and that groups of amino acids provide acceptable building blocks that can be assembled, overcoming the context dependency of the DNA binding interface. Furthermore, the present work describes a sequential method to engineer tailored HEs, wherein three contiguous regions are individually mutated and assembled to create HEs with engineered specificity. PMID:21482539

  11. Composition Dependence of the Optical Conductivity of NiPt Alloys Determined by Spectroscopic Ellipsometry

    NASA Astrophysics Data System (ADS)

    Abdallah, Lina; Tawalbeh, Tarek; Vasiliev, Igor; Zollner, Stefan; Lavoie, Christian; Ozcan, Ahmet; Raymond, Mark

    2012-10-01

    The complex dielectric function of different Ni-Pt alloys (0% to 25% Pt concentration, 10nm thickness) was determined using spectroscopic ellipsometry over a broad photon energy range from 0.6 to 6.6eV. Data were fitted using basis spline functions as well as Drude-Lorentz oscillators to describe free carrier absorption and interband transitions. We found absorption peaks at 1.5 and 4.7 eV due to interband transitions. Results showed a broadening in the absorption peak of Nickel with increasing the Platinum concentration in the alloy. The experimental results were compared with ab initio density functional theory band structure calculations which showed that adding Platinum enhances the density of states of Nickel especially at low energies. Annealing the metals at 500^o C for 30 s increases the optical conductivity.

  12. Deoxyribonucleic acid of Cancer pagurus. II. Tempiate activity for a DNA-dependent DNA polymerase of eukaryotic cells

    PubMed Central

    De Recondo, Anne-Marie; Londos-Gagliardi, Danielle; Aubel-Sadron, Geneviève

    1974-01-01

    The template activity of Cancer pagurus DNA and its two components (poly d(A-T) and main component) in response to a DNA polymerase purified from regenerating rat liver has been studied and compared to the results previously obtained with synthetic templates. In the double-stranded native state, whole crab DNA and the main component were poor templates. Their replication was increased by thermal denaturation and inhibited by actinomycin. Like the synthetic copolymer poly[d(A-T)·d(T-A)], native crab poly d(A-T) could be copied and its duplication was not inhibited by actinomycin. The structural difference between native poly d(A-T) Form I, isolated on a density gradient, and partially renatured poly d(A-T) Form II, isolated on hydroxylapatite, resulted in a modification of their template activity. The kinetic studies of [3H] dGMP and [3H] dAMP incorporation confirmed the importance of single-stranded regions (particulary dC regions) in the initiation of the in vitro duplication. PMID:10793685

  13. Temperature Dependence of Density, Viscosity and Electrical Conductivity for Hg-Based II-VI Semiconductor Melts

    NASA Technical Reports Server (NTRS)

    Li, C.; Ban, H.; Lin, B.; Scripa, R. N.; Su, C.-H.; Lehoczky, S. L.

    2004-01-01

    The relaxation phenomenon of semiconductor melts, or the change of melt structure with time, impacts the crystal growth process and the eventual quality of the crystal. The thermophysical properties of the melt are good indicators of such changes in melt structure. Also, thermophysical properties are essential to the accurate predication of the crystal growth process by computational modeling. Currently, the temperature dependent thermophysical property data for the Hg-based II-VI semiconductor melts are scarce. This paper reports the results on the temperature dependence of melt density, viscosity and electrical conductivity of Hg-based II-VI compounds. The melt density was measured using a pycnometric method, and the viscosity and electrical conductivity were measured by a transient torque method. Results were compared with available published data and showed good agreement. The implication of the structural changes at different temperature ranges was also studied and discussed.

  14. Oversized AAV Transductifon Is Mediated via a DNA-PKcs-independent, Rad51C-dependent Repair Pathway

    PubMed Central

    Hirsch, Matthew L; Li, Chengwen; Bellon, Isabella; Yin, Chaoying; Chavala, Sai; Pryadkina, Marina; Richard, Isabelle; Samulski, Richard Jude

    2013-01-01

    A drawback of gene therapy using adeno-associated virus (AAV) is the DNA packaging restriction of the viral capsid (<4.7 kb). Recent observations demonstrate oversized AAV genome transduction through an unknown mechanism. Herein, AAV production using an oversized reporter (6.2 kb) resulted in chloroform and DNase-resistant particles harboring distinct “fragment” AAV (fAAV) genomes (5.0, 2.4, and 1.6 kb). Fractionation experiments determined that only the larger “fragments” mediated transduction in vitro, and relatively efficient transduction was also demonstrated in the muscle, the eye, and the liver. In contrast with concatemerization-dependent large-gene delivery by split AAV, fAAV transduction is independent of the catalytic subunit of DNA-dependent protein kinase (DNA-PKcs) in vitro and in vivo while disproportionately reliant on the DNA strand–annealing protein Rad51C. Importantly, fAAV's unique dependence on DNA repair proteins, compared with intact AAV, strongly suggests that the majority of oversized AAV transduction is mediated by fragmented genomes. Although fAAV transduction is less efficient than intact AAV, it is enhanced fourfold in muscle and sevenfold in the retina compared with split AAV transduction. Furthermore, fAAV carrying codon-optimized therapeutic dysferlin cDNA in a 7.5 kb expression cassette restored dysferlin levels in a dystrophic model. Collectively, oversized AAV genome transduction requires unique DNA repair pathways and offers an alternative, more efficient strategy for large-gene therapy. PMID:23939025

  15. Dependence of particle size on the effective thermal diffusivity and conductivity of nanofluids: role of base fluid properties

    NASA Astrophysics Data System (ADS)

    Nisha, M. R.; Philip, J.

    2012-10-01

    Effect of nanoparticle size on effective thermal diffusivity and conductivity of polymeric and water based nanofluids are investigated following thermal wave interference technique. Two sets of nanofluids, prepared by dispersing TiO2 nanoparticles, with average sizes in the range 5-100 nm, in polyvinyl alcohol and water show opposing particle size dependences. Variations are explained invoking effective medium theory, including size of nanoparticles, molecular weight of base fluid and effects associated with it.

  16. Aromatic-dependent salmonella as anti-bacterial vaccines and as presenters of heterologous antigens or of DNA encoding them.

    PubMed

    Stocker, B A

    2000-09-29

    The development of live bacterial vaccines is reviewed, in particular aromatic-dependent Salmonella, either for protection against the corresponding infections (including typhoid fever) or as carrier-presenter of antigens of unrelated pathogens or of DNA specifying them. Aromatic-dependent Salmonella live vaccines are also compared with BCG and Ty21a and the recent records of exceptional situations are discussed in which aroA (deletion) strains of Salmonella typhimurium cause progressive disease in mice. PMID:11000459

  17. Layer-by-layer coated gold nanoparticles: size-dependent delivery of DNA into cells.

    PubMed

    Elbakry, Asmaa; Wurster, Eva-Christina; Zaky, Alaa; Liebl, Renate; Schindler, Edith; Bauer-Kreisel, Petra; Blunk, Torsten; Rachel, Reinhard; Goepferich, Achim; Breunig, Miriam

    2012-12-21

    Because nanoparticles are finding uses in myriad biomedical applications, including the delivery of nucleic acids, a detailed knowledge of their interaction with the biological system is of utmost importance. Here the size-dependent uptake of gold nanoparticles (AuNPs) (20, 30, 50 and 80 nm), coated with a layer-by-layer approach with nucleic acid and poly(ethylene imine) (PEI), into a variety of mammalian cell lines is studied. In contrast to other studies, the optimal particle diameter for cellular uptake is determined but also the number of therapeutic cargo molecules per cell. It is found that 20 nm AuNPs, with diameters of about 32 nm after the coating process and about 88 nm including the protein corona after incubation in cell culture medium, yield the highest number of nanoparticles and therapeutic DNA molecules per cell. Interestingly, PEI, which is known for its toxicity, can be applied at significantly higher concentrations than its IC(50) value, most likely because it is tightly bound to the AuNP surface and/or covered by a protein corona. These results are important for the future design of nanomaterials for the delivery of nucleic acids in two ways. They demonstrate that changes in the nanoparticle size can lead to significant differences in the number of therapeutic molecules delivered per cell, and they reveal that the toxicity of polyelectrolytes can be modulated by an appropriate binding to the nanoparticle surface. PMID:22911477

  18. Enhancing helicase-dependent amplification by fusing the helicase with the DNA polymerase.

    PubMed

    Motré, Aurélie; Li, Ying; Kong, Huimin

    2008-08-15

    In this study, we have engineered a new bifunctional protein named "helimerase", by physically linking Thermoanaerobacter tengcongensis UvrD helicase (TteUvrD) and Bacillus stearothermophilus DNA polymerase I Large Fragment (Bstpol) using a coiled-coil. TteUvrD is fused with one part of the coiled-coil, WinZip-A2 (WZA2), through a linker L1 and possesses a Maltose Binding Protein (MBP) tag at the N terminal end. Bstpol is fused with the other part of the coiled-coil, WinZip-B1 (WZB1), through the same linker and possesses a His tag at the N terminal end. Therefore, the two fusion proteins MBP-WZA2-L1-TteUvrD and His-WZB1-L1-Bstpol composed the helimerase. We showed that this complex could be formed in vivo as well as in vitro and possessed specific activities of both TteUvrD and Bstpol. Moreover, we demonstrated that significantly longer fragments could be amplified by the helimerase in Helicase-Dependent Amplification (HDA) reactions instead of using TteUvrD and Bstpol proteins that do not form a complex. PMID:18556147

  19. Disruption of DNA methylation-dependent long gene repression in Rett syndrome

    PubMed Central

    Gabel, Harrison W.; Kinde, Benyam Z.; Stroud, Hume; Gilbert, Caitlin S.; Harmin, David A.; Kastan, Nathaniel R.; Hemberg, Martin; Ebert, Daniel H.; Greenberg, Michael E.

    2015-01-01

    Disruption of the MECP2 gene leads to Rett syndrome (RTT), a severe neurological disorder with features of autism1. MECP2 encodes a methyl-DNA-binding protein2 that has been proposed to function as a transcriptional repressor, but despite numerous studies examining neuronal gene expression in Mecp2 mutants, no clear model has emerged for how MeCP2 regulates transcription3–9. Here we identify a genome-wide length-dependent increase in gene expression in MeCP2 mutant mouse models and human RTT brains. We present evidence that MeCP2 represses gene expression by binding to methylated CA sites within long genes, and that in neurons lacking MeCP2, decreasing the expression of long genes attenuates RTT-associated cellular deficits. In addition, we find that long genes as a population are enriched for neuronal functions and selectively expressed in the brain. These findings suggest that mutations in MeCP2 may cause neurological dysfunction by specifically disrupting long gene expression in the brain. PMID:25762136

  20. RecA-dependent programmable endonuclease Ref cleaves DNA in two distinct steps

    PubMed Central

    Ronayne, Erin A.; Cox, Michael M.

    2014-01-01

    The bacteriophage P1 recombination enhancement function (Ref) protein is a RecA-dependent programmable endonuclease. Ref targets displacement loops formed when an oligonucleotide is bound by a RecA filament and invades homologous double-stranded DNA sequences. Mechanistic details of this reaction have been explored, revealing that (i) Ref is nickase, cleaving the two target strands of a displacement loop sequentially, (ii) the two strands are cleaved in a prescribed order, with the paired strand cut first and (iii) the two cleavage events have different requirements. Cutting the paired strand is rapid, does not require RecA-mediated ATP hydrolysis and is promoted even by Ref active site variant H153A. The displaced strand is cleaved much more slowly, requires RecA-mediated ATP hydrolysis and does not occur with Ref H153A. The two cleavage events are also affected differently by solution conditions. We postulate that the second cleavage (displaced strand) is limited by some activity of RecA protein. PMID:24371286

  1. Simultaneous determination of temperature-dependent thermal conductivity and volumetric heat capacity by an inverse technique

    SciTech Connect

    Woodbury, K.A.; Boohaker, C.G.

    1996-12-31

    Determination of thermal properties by inverse methods often involves limited thermal excitation of a relatively small sample. If these thermal properties are to be found as functions of temperature, then this procedure must be replicated at several artificially elevated temperatures. For some types of materials (for example, those bearing moisture) this approach is impractical. In this paper, a procedure is developed for determining thermal properties (conductivity k and volumetric heat capacity C {equivalent_to} {rho}c{sub p}) as functions of temperature from a single experiment. This procedure is targeted for determination of k(T) and C(T) for sand molds used in castings. An inverse method based on a Gauss linearization is used to estimate these functions. The experiment used to determine these properties consists of heating a one-dimensional specimen of the material from one end. The variation of thermal properties with temperature is assumed to be a piecewise linear function, with values of properties to be determined at prescribed temperatures. A numerical experiment is used to demonstrate the technique.

  2. Roughness-dependent dynamics of a point charge near a conducting plane

    SciTech Connect

    Gintautas, Vadas; Hubler, Alfred

    2008-01-01

    Nearly any surface in the real world is rough at some scale. Fmthermore, in most experiments there is some limit at which a surface is too rough to approximate by a smooth one. In this work the dynamics of a point charge near a rough surface are studied as the roughness of the surface is allowed to vary. The equation of motion of a charged pendulum near a rough, grounded, conducting plane is derived analytically and then analyzed both analytically and numerically . As the roughness is varied, a phase transition is observed in the fixed points of the pendulum. The consequences of a roughness phase transition on waveguide and electromagnetic scattering applications are considered. Also, the grounded plane may be considered to be a rough mirror and the point charge to be interacting with its image in this mirror. The quality of the image degrades with increasing roughness; the implications of this to interactions between systems in the real world and synthetic models are explored.

  3. Investigation on Temperature-Dependent Electrical Conductivity of Carbon Nanotube/Epoxy Composites for Sustainable Energy Applications.

    PubMed

    Njuguna, Michael K; Galpaya, Dilini; Yan, Cheng; Colwell, John M; Will, Geoffrey; Hu, Ning; Yarlagadda, Prasad; Bell, John M

    2015-09-01

    Composites with carbon nanotubes are becoming increasingly used in energy storage and electronic devices, due to incorporated excellent properties from carbon nanotubes and polymers. Although their properties make them more attractive than conventional smart materials, their electrical properties have been found to be temperature-dependent which is important to consider for the design of devices. To study the effects of temperature in electrically conductive multi-wall carbon nanotube/epoxy composites, thin films were prepared and the effect of temperature on the resistivity, thermal properties and Raman spectral characteristics of the composite films was evaluated. Resistivity-temperature profiles showed three distinct regions in as-cured samples and only two regions in samples whose thermal histories had been erased. In the vicinity of the glass transition temperature, the as-cured composites exhibited pronounced resistivity and enthalpic relaxation peaks, which both disappeared after erasing the composites' thermal histories by temperature cycling. Combined DSC, Raman spectroscopy, and resistivity-temperature analyses indicated that this phenomenon can be attributed to the physical aging of the epoxy matrix and that, in the region of the observed thermal history-dependent resistivity peaks, structural rearrangement of the conductive carbon nanotube network occurs through a volume expansion/relaxation process. These results have led to an overall greater understanding of the temperature-dependent behaviour of conductive carbon nanotube/epoxy composites, including the positive temperature coefficient effect. PMID:26716268

  4. Temperature dependent hopping conduction in lithium-doped zinc oxide in the range 10-300 K

    NASA Astrophysics Data System (ADS)

    Majumdar, S.; Banerji, P.

    2010-08-01

    A temperature-dependent hopping conduction was studied in lithium (Li)-doped zinc oxide (ZnO) in the temperature range 10-300 K. Monodoping of Li in ZnO was made as suggested by the theory based on the first principle calculations. Li-doped ZnO films were deposited both on glass and quartz substrates by pulsed laser deposition (PLD) in presence and absence of oxygen ambience. The films were found to be p-type. It was found that whereas in the temperature range 10-40 K, variable range hopping resulted in Mott's conductivity, above 40 K, the conductivity was governed by the thermal assisted hopping.

  5. FORTRAN 77 programs for conductive cooling of dikes with temperature-dependent thermal properties and heat of crystallization

    USGS Publications Warehouse

    Delaney, P.T.

    1988-01-01

    Temperature histories obtained from transient heat-conduction theory are applicable to most dikes despite potential complicating effects related to magma flow during emplacement, groundwater circulation, and metamorphic reaction during cooling. Here. machine-independent FORTRAN 77 programs are presented to calculate temperatures in and around dikes as they cool conductively. Analytical solutions can treat thermal-property contrasts between the dike and host rocks, but cannot address the release of magmatic heat of crystallization after the early stages of cooling or the appreciable temperature dependence of thermal conductivity and diffusivity displayed by most rock types. Numerical solutions can incorporate these additional factors. The heat of crystallization can raise the initial temperature at the dike contact, ??c1, about 100??C above that which would be estimated if it were neglected, and can decrease the rate at which the front of solidified magma moves to the dike center by a factor of as much as three. Thermal conductivity and diffusivity of rocks increase with decreasing temperature and, at low temperatures, these properties increase more if the rocks are saturated with water. Models that treat these temperature dependencies yield estimates of ??c1 that are as much as 75??C beneath those which would be predicted if they were neglected. ?? 1988.

  6. Magnetic field dependent thermal conductance in La0.67Ca0.33MnO3

    NASA Astrophysics Data System (ADS)

    Euler, C.; Hołuj, P.; Talkenberger, A.; Jakob, G.

    2015-05-01

    Using the differential 3 ω technique we measured the low-temperature out-of-plane thermal conductance of heteroepitaxial thin film La0.67Ca0.33MnO3 (LCMO). The magnetic field dependence of the thermal conductance reached values of up to 23%. The effect was observed to be largest in the vicinity of the metal-insulator transition, since the enhancement in thermal conductance is triggered by the colossal magnetoresistance effect increasing the electronic contribution to the thermal conductance. The point of the maximal change was adjusted by post-annealing the samples in an oxygen atmosphere. Samples with a higher transition temperature and lower epitaxial strain displayed a lower magnetic field dependence of up to 8% of the zero-field value. While the samples with a low strain state seemingly obeyed the Wiedemann-Franz law, those under high strain did not. Raman spectroscopy was applied to explain this discrepancy by an enhanced phononic density of states caused by rotational distortions of the unit cell. Our results show that in systems with strong electron-lattice interaction manipulation of the phonon spectrum is possible by magnetic fields.

  7. Composition-dependent structural and transport properties of amorphous transparent conducting oxides

    NASA Astrophysics Data System (ADS)

    Khanal, Rabi; Buchholz, D. Bruce; Chang, Robert P. H.; Medvedeva, Julia E.

    2015-05-01

    Structural properties of amorphous In-based oxides, In -X -O with X =Zn , Ga, Sn, or Ge, are investigated using ab initio molecular dynamics liquid-quench simulations. The results reveal that indium retains its average coordination of 5.0 upon 20% X fractional substitution for In, whereas X cations satisfy their natural coordination with oxygen atoms. This finding suggests that the carrier generation is primarily governed by In atoms, in accord with the observed carrier concentration in amorphous In-O and In -X -O . At the same time, the presence of X affects the number of six-coordinated In atoms as well as the oxygen sharing between the InO6 polyhedra. Based on the obtained interconnectivity and spatial distribution of the InO6 and XO x polyhedra in amorphous In -X -O , composition-dependent structural models of the amorphous oxides are derived. The results help explain our Hall mobility measurements in In -X -O thin films grown by pulsed-laser deposition and highlight the importance of long-range structural correlations in the formation of amorphous oxides and their transport properties.

  8. Temperature dependent dielectric and conductivity studies of polyvinyl alcohol-ZnO nanocomposite films by impedance spectroscopy

    SciTech Connect

    Hemalatha, K. S.; Damle, R.; Rukmani, K.; Sriprakash, G.; Ambika Prasad, M. V. N.

    2015-10-21

    Dielectric and conductivity behaviors of nano ZnO doped polyvinyl alcohol (PVA) composites for various concentrations of dopant were investigated using impedance spectroscopy for a wide range of temperatures (303 K–423 K) and frequencies (5 Hz–30 MHZ). The dielectric properties of host polymer matrix have been improved by the addition of nano ZnO and are found to be highly temperature dependent. Anomalous dielectric behavior was observed in the frequency range of 2.5 MHz–5 MHz. Increase in dielectric permittivity and dielectric loss was observed with respect to temperature. The Cole-Cole plot could be modeled by low resistance regions in a high resistance matrix and the lowest resistance was observed for the 10 mol. % films. The imaginary part of the electric modulus showed asymmetric peaks with the relaxation following Debye nature below and non-Debye nature above the peaks. The ac conductivity is found to obey Jonscher's power law, whereas the variation of dc conductivity with temperature was found to follow Arrhenius behavior. Two different activation energy values were obtained from Arrhenius plot indicating that two conduction mechanisms are involved in the composite films. Fitting the ac conductivity data to Jonscher's law indicates that large polaron assisted tunneling is the most likely conduction mechanism in the composites. Maximum conductivity is observed at 423 K for all the samples and it is optimum for 10 mol. % ZnO doped PVA composite film. Significant increase in dc and ac conductivities in these composite films makes them a potential candidate for application in electronic devices.

  9. Restriction and sequence alterations affect DNA uptake sequence-dependent transformation in Neisseria meningitidis.

    PubMed

    Ambur, Ole Herman; Frye, Stephan A; Nilsen, Mariann; Hovland, Eirik; Tønjum, Tone

    2012-01-01

    Transformation is a complex process that involves several interactions from the binding and uptake of naked DNA to homologous recombination. Some actions affect transformation favourably whereas others act to limit it. Here, meticulous manipulation of a single type of transforming DNA allowed for quantifying the impact of three different mediators of meningococcal transformation: NlaIV restriction, homologous recombination and the DNA Uptake Sequence (DUS). In the wildtype, an inverse relationship between the transformation frequency and the number of NlaIV restriction sites in DNA was observed when the transforming DNA harboured a heterologous region for selection (ermC) but not when the transforming DNA was homologous with only a single nucleotide heterology. The influence of homologous sequence in transforming DNA was further studied using plasmids with a small interruption or larger deletions in the recombinogenic region and these alterations were found to impair transformation frequency. In contrast, a particularly potent positive driver of DNA uptake in Neisseria sp. are short DUS in the transforming DNA. However, the molecular mechanism(s) responsible for DUS specificity remains unknown. Increasing the number of DUS in the transforming DNA was here shown to exert a positive effect on transformation. Furthermore, an influence of variable placement of DUS relative to the homologous region in the donor DNA was documented for the first time. No effect of altering the orientation of DUS was observed. These observations suggest that DUS is important at an early stage in the recognition of DNA, but does not exclude the existence of more than one level of DUS specificity in the sequence of events that constitute transformation. New knowledge on the positive and negative drivers of transformation may in a larger perspective illuminate both the mechanisms and the evolutionary role(s) of one of the most conserved mechanisms in nature: homologous recombination. PMID

  10. Restriction and Sequence Alterations Affect DNA Uptake Sequence-Dependent Transformation in Neisseria meningitidis

    PubMed Central

    Ambur, Ole Herman; Frye, Stephan A.; Nilsen, Mariann; Hovland, Eirik; Tønjum, Tone

    2012-01-01

    Transformation is a complex process that involves several interactions from the binding and uptake of naked DNA to homologous recombination. Some actions affect transformation favourably whereas others act to limit it. Here, meticulous manipulation of a single type of transforming DNA allowed for quantifying the impact of three different mediators of meningococcal transformation: NlaIV restriction, homologous recombination and the DNA Uptake Sequence (DUS). In the wildtype, an inverse relationship between the transformation frequency and the number of NlaIV restriction sites in DNA was observed when the transforming DNA harboured a heterologous region for selection (ermC) but not when the transforming DNA was homologous with only a single nucleotide heterology. The influence of homologous sequence in transforming DNA was further studied using plasmids with a small interruption or larger deletions in the recombinogenic region and these alterations were found to impair transformation frequency. In contrast, a particularly potent positive driver of DNA uptake in Neisseria sp. are short DUS in the transforming DNA. However, the molecular mechanism(s) responsible for DUS specificity remains unknown. Increasing the number of DUS in the transforming DNA was here shown to exert a positive effect on transformation. Furthermore, an influence of variable placement of DUS relative to the homologous region in the donor DNA was documented for the first time. No effect of altering the orientation of DUS was observed. These observations suggest that DUS is important at an early stage in the recognition of DNA, but does not exclude the existence of more than one level of DUS specificity in the sequence of events that constitute transformation. New knowledge on the positive and negative drivers of transformation may in a larger perspective illuminate both the mechanisms and the evolutionary role(s) of one of the most conserved mechanisms in nature: homologous recombination. PMID

  11. In the absence of writhe, DNA relieves torsional stress with localized, sequence-dependent structural failure to preserve B-form

    PubMed Central

    Randall, Graham L.; Zechiedrich, Lynn; Pettitt, B. Montgomery

    2009-01-01

    To understand how underwinding and overwinding the DNA helix affects its structure, we simulated 19 independent DNA systems with fixed degrees of twist using molecular dynamics in a system that does not allow writhe. Underwinding DNA induced spontaneous, sequence-dependent base flipping and local denaturation, while overwinding DNA induced the formation of Pauling-like DNA (P-DNA). The winding resulted in a bimodal state simultaneously including local structural failure and B-form DNA for both underwinding and extreme overwinding. Our simulations suggest that base flipping and local denaturation may provide a landscape influencing protein recognition of DNA sequence to affect, for examples, replication, transcription and recombination. Additionally, our findings help explain results from single-molecule experiments and demonstrate that elastic rod models are strictly valid on average only for unstressed or overwound DNA up to P-DNA formation. Finally, our data support a model in which base flipping can result from torsional stress. PMID:19586933

  12. In the Absence of Writhe, DNA Relieves Torsional Stress with Localized, Sequence-Dependent Structural Failure to Preserve B-form

    SciTech Connect

    Randall, Graham L.; Zechiedrich, E. L.; Pettitt, Bernard M.

    2009-09-01

    To understand how underwinding and overwinding the DNA helix affects its structure, we simulated 19 independent DNA systems with fixed degrees of twist using molecular dynamics in a system that does not allow writhe. Underwinding DNA induced spontaneous, sequence-dependent base flipping and local denaturation, while overwinding DNA induced the formation of Pauling-like DNA (P-DNA). The winding resulted in a bimodal state simultaneously including local structural failure and B-form DNA for both underwinding and extreme overwinding. Our simulations suggest that base flipping and local denaturation may provide a landscape influencing protein recognition of DNA sequence to affect, for examples, replication, transcription and recombination. Additionally, our findings help explain results from singlemolecule experiments and demonstrate that elastic rod models are strictly valid on average only for unstressed or overwound DNA up to P-DNA formation. Finally, our data support a model in which base flipping can result from torsional stress.

  13. Sequence-dependent Kink-and-Slide Deformations of Nucleosomal DNA Facilitated by Histone Arginines Bound in the Minor Groove

    PubMed Central

    Wang, Difei; Ulyanov, Nikolai B.; Zhurkin, Victor B.

    2010-01-01

    In addition to bending and twisting deformabilities, the lateral displacements of the DNA axis (Kink-and-Slide) play an important role in DNA wrapping around the histone core (M. Y. Tolstorukov, A. V. Colasanti, D. M. McCandlish, W. K. Olson, V. B. Zhurkin, J. Mol. Biol. 371, 725-738 (2007)). Here, we show that these Kink-and-Slide deformations are likely to be stabilized by the arginine residues of histones interacting with the minor groove of DNA. The arginines are positioned asymmetrically in the minor groove, being closer to one strand. The asymmetric arginine-DNA interactions facilitate lateral displacement of base pairs across the DNA grooves, thus leading to a stepwise accumulation of the superhelical pitch of nucleosomal DNA. To understand the sequence dependence of such Kink-and-Slide deformations, we performed all-atom calculations of DNA hexamers with the YR and RY steps in the center. We found that when the unrestrained DNA deformations are allowed, the YR steps tend to bend into the major groove, and RY steps bend into the minor groove. However, when the nucleosomal Kink-and-Slide deformation is considered, the YR steps prove to be more favorable for bending into the minor groove. Overall, the Kink-and-Slide deformation energy of DNA increases in the order TA < CA < CG < GC < AC < AT. We propose a simple stereochemical model accounting for this sequence dependence. Our results agree with experimental data indicating that the TA step most frequently occurs in the minor-groove kink positions in the most stable nucleosomes. Our computations demonstrate that the Kink-and-Slide distortion is accompanied by the BI to BII transition. This fact, together with irregularities in the two-dimensional (Roll, Slide) energy contour maps, suggest that the Kink-and-Slide deformations represent a nonharmonic behavior of the duplex. This explains the difference between the two estimates of the DNA deformation energy in nucleosome – the earlier one made using knowledge

  14. Repair of Alkylation Damage in Eukaryotic Chromatin Depends on Searching Ability of Alkyladenine DNA Glycosylase.

    PubMed

    Zhang, Yaru; O'Brien, Patrick J

    2015-11-20

    Human alkyladenine DNA glycosylase (AAG) initiates the base excision repair pathway by excising alkylated and deaminated purine lesions. In vitro biochemical experiments demonstrate that AAG uses facilitated diffusion to efficiently search DNA to find rare sites of damage and suggest that electrostatic interactions are critical to the searching process. However, it remains an open question whether DNA searching limits the rate of DNA repair in vivo. We constructed AAG mutants with altered searching ability and measured their ability to protect yeast from alkylation damage in order to address this question. Each of the conserved arginine and lysine residues that are near the DNA binding interface were mutated, and the functional impacts were evaluated using kinetic and thermodynamic analysis. These mutations do not perturb catalysis of N-glycosidic bond cleavage, but they decrease the ability to capture rare lesion sites. Nonspecific and specific DNA binding properties are closely correlated, suggesting that the electrostatic interactions observed in the specific recognition complex are similarly important for DNA searching complexes. The ability of the mutant proteins to complement repair-deficient yeast cells is positively correlated with the ability of the proteins to search DNA in vitro, suggesting that cellular resistance to DNA alkylation is governed by the ability to find and efficiently capture cytotoxic lesions. It appears that chromosomal access is not restricted and toxic sites of alkylation damage are readily accessible to a searching protein. PMID:26317160

  15. Direct evidence for sequence-dependent attraction between double-stranded DNA controlled by methylation

    PubMed Central

    Yoo, Jejoong; Kim, Hajin; Aksimentiev, Aleksei; Ha, Taekjip

    2016-01-01

    Although proteins mediate highly ordered DNA organization in vivo, theoretical studies suggest that homologous DNA duplexes can preferentially associate with one another even in the absence of proteins. Here we combine molecular dynamics simulations with single-molecule fluorescence resonance energy transfer experiments to examine the interactions between duplex DNA in the presence of spermine, a biological polycation. We find that AT-rich DNA duplexes associate more strongly than GC-rich duplexes, regardless of the sequence homology. Methyl groups of thymine acts as a steric block, relocating spermine from major grooves to interhelical regions, thereby increasing DNA–DNA attraction. Indeed, methylation of cytosines makes attraction between GC-rich DNA as strong as that between AT-rich DNA. Recent genome-wide chromosome organization studies showed that remote contact frequencies are higher for AT-rich and methylated DNA, suggesting that direct DNA–DNA interactions that we report here may play a role in the chromosome organization and gene regulation. PMID:27001929

  16. Chicken Fetal Liver DNA Damage and Adduct Formation by Activation-Dependent DNA-Reactive Carcinogens and Related Compounds of Several Structural Classes

    PubMed Central

    Williams, Gary M.; Duan, Jian-Dong; Brunnemann, Klaus D.; Iatropoulos, Michael J.; Vock, Esther; Deschl, Ulrich

    2014-01-01

    The chicken egg genotoxicity assay (CEGA), which utilizes the liver of an intact and aseptic embryo-fetal test organism, was evaluated using four activation-dependent DNA-reactive carcinogens and four structurally related less potent carcinogens or non-carcinogens. In the assay, three daily doses of test substances were administered to eggs containing 9–11-day-old fetuses and the fetal livers were assessed for two endpoints, DNA breaks using the alkaline single cell gel electrophoresis (comet) assay and DNA adducts using the 32P-nucleotide postlabeling (NPL) assay. The effects of four carcinogens of different structures requiring distinct pathways of bioactivation, i.e., 2-acetylaminofluorene (AAF), aflatoxin B1 (AFB1), benzo[a]pyrene (B[a]P), and diethylnitrosamine (DEN), were compared with structurally related non-carcinogens fluorene (FLU) and benzo[e]pyrene (B[e]P) or weak carcinogens, aflatoxin B2 (AFB2) and N-nitrosodiethanolamine (NDELA). The four carcinogens all produced DNA breaks at microgram or low milligram total doses, whereas less potent carcinogens and non-carcinogens yielded borderline or negative results, respectively, at higher doses. AAF and B[a]P produced DNA adducts, whereas none was found with the related comparators FLU or B[e]P, consistent with comet results. DEN and NDELA were also negative for adducts, as expected in the case of DEN for an alkylating agent in the standard NPL assay. Also, AFB1 and AFB2 were negative in NPL, as expected, due to the nature of ring opened aflatoxin adducts, which are resistant to enzymatic digestion. Thus, the CEGA, using comet and NPL, is capable of detection of the genotoxicity of diverse DNA-reactive carcinogens, while not yielding false positives for non-carcinogens. PMID:24973097

  17. ORC-dependent and origin-specific initiation of DNA replication at defined foci in isolated yeast nuclei.

    PubMed

    Pasero, P; Braguglia, D; Gasser, S M

    1997-06-15

    We describe an in vitro replication assay from yeast in which the addition of intact nuclei to an S-phase nuclear extract results in the incorporation of deoxynucleotides into genomic DNA at spatially discrete foci. When BrdUTP is substituted for dTTP, part of the newly synthesized DNA shifts to a density on CsCl gradients, indicative of semiconservative replication. Initiation occurs in an origin-specific manner and can be detected in G1- or S-phase nuclei, but not in G2-phase or mitotic nuclei. The S-phase extract contains a heat- and 6-DMAP-sensitive component necessary to promote replication in G1-phase nuclei. Replication of nuclear DNA is blocked at the restrictive temperature in an orc2-1 mutant, and the inactive Orc2p cannot be complemented in trans by an extract containing wild-type ORC. The initiation of DNA replication in cln-deficient nuclei blocked in G1 indicates that the ORC-dependent prereplication complex is formed before Start. This represents the first nonviral and nonembryonic replication system in which DNA replication initiates in an ORC-dependent and origin-specific manner in vitro. PMID:9203578

  18. RAE1 ligands for the NKG2D receptor are regulated by STING-dependent DNA sensor pathways in lymphoma.

    PubMed

    Lam, Adeline R; Le Bert, Nina; Ho, Samantha S W; Shen, Yu J; Tang, Melissa L F; Xiong, Gordon M; Croxford, J Ludovic; Koo, Christine X; Ishii, Ken J; Akira, Shizuo; Raulet, David H; Gasser, Stephan

    2014-04-15

    The immunoreceptor NKG2D originally identified in natural killer (NK) cells recognizes ligands that are upregulated on tumor cells. Expression of NKG2D ligands (NKG2DL) is induced by the DNA damage response (DDR), which is often activated constitutively in cancer cells, revealing them to NK cells as a mechanism of immunosurveillance. Here, we report that the induction of retinoic acid early transcript 1 (RAE1) ligands for NKG2D by the DDR relies on a STING-dependent DNA sensor pathway involving the effector molecules TBK1 and IRF3. Cytosolic DNA was detected in lymphoma cell lines that express RAE1 and its occurrence required activation of the DDR. Transfection of DNA into ligand-negative cells was sufficient to induce RAE1 expression. Irf3(+/-);Eμ-Myc mice expressed lower levels of RAE1 on tumor cells and showed a reduced survival rate compared with Irf3(+/+);Eμ-Myc mice. Taken together, our results suggest that genomic damage in tumor cells leads to activation of STING-dependent DNA sensor pathways, thereby activating RAE1 and enabling tumor immunosurveillance. PMID:24590060

  19. The large conductance, voltage-dependent, and calcium-sensitive K+ channel, Hslo, is a target of cGMP-dependent protein kinase phosphorylation in vivo.

    PubMed

    Alioua, A; Tanaka, Y; Wallner, M; Hofmann, F; Ruth, P; Meera, P; Toro, L

    1998-12-01

    Native large conductance, voltage-dependent, and Ca2+-sensitive K+ channels are activated by cGMP-dependent protein kinase. Two possible mechanisms of kinase action have been proposed: 1) direct phosphorylation of the channel and 2) indirect via PKG-dependent activation of a phosphatase. To scrutinize the first possibility, at the molecular level, we used the human pore-forming alpha-subunit of the Ca2+-sensitive K+ channel, Hslo, and the alpha-isoform of cGMP-dependent protein kinase I. In cell-attached patches of oocytes co-expressing the Hslo channel and the kinase, 8-Br-cGMP significantly increased the macroscopic currents. This increase in current was due to an increase in the channel voltage sensitivity by approximately 20 mV and was reversed by alkaline phosphatase treatment after patch excision. In inside-out patches, however, the effect of purified kinase was negative in 12 of 13 patches. In contrast, and consistent with the intact cell experiments, purified kinase applied to the cytoplasmic side of reconstituted channels increased their open probability. This stimulatory effect was absent when heat-denatured kinase was used. Biochemical experiments show that the purified kinase incorporates gamma-33P into the immunopurified Hslo band of approximately 125 kDa. Furthermore, in vivo phosphorylation largely attenuates this labeling in back-phosphorylation experiments. These results demonstrate that the alpha-subunit of large conductance Ca2+-sensitive K+ channels is substrate for G-Ialpha kinase in vivo and support direct phosphorylation as a mechanism for PKG-Ialpha-induced activation of maxi-K channels. PMID:9830046

  20. IMPACT OF TEMPERATURE-DEPENDENT RESISTIVITY AND THERMAL CONDUCTION ON PLASMOID INSTABILITIES IN CURRENT SHEETS IN THE SOLAR CORONA

    SciTech Connect

    Ni Lei; Roussev, Ilia I.; Lin Jun; Ziegler, Udo E-mail: iroussev@ifa.hawaii.edu

    2012-10-10

    In this paper, we investigate, by means of two-dimensional magnetohydrodynamic simulations, the impact of temperature-dependent resistivity and thermal conduction on the development of plasmoid instabilities in reconnecting current sheets in the solar corona. We find that the plasma temperature in the current-sheet region increases with time and it becomes greater than that in the inflow region. As secondary magnetic islands appear, the highest temperature is not always found at the reconnection X-points, but also inside the secondary islands. One of the effects of anisotropic thermal conduction is to decrease the temperature of the reconnecting X-points and transfer the heat into the O-points, the plasmoids, where it gets trapped. In the cases with temperature-dependent magnetic diffusivity, {eta} {approx} T {sup -3/2}, the decrease in plasma temperature at the X-points leads to (1) an increase in the magnetic diffusivity until the characteristic time for magnetic diffusion becomes comparable to that of thermal conduction, (2) an increase in the reconnection rate, and (3) more efficient conversion of magnetic energy into thermal energy and kinetic energy of bulk motions. These results provide further explanation of the rapid release of magnetic energy into heat and kinetic energy seen during flares and coronal mass ejections. In this work, we demonstrate that the consideration of anisotropic thermal conduction and Spitzer-type, temperature-dependent magnetic diffusivity, as in the real solar corona, are crucially important for explaining the occurrence of fast reconnection during solar eruptions.

  1. Mechanism of ATP-dependent translocation of E.coli UvrD monomers along single-stranded DNA.

    PubMed

    Fischer, Christopher J; Maluf, Nasib K; Lohman, Timothy M

    2004-12-10

    Escherichia coli UvrD protein is a 3' to 5' SF1 DNA helicase involved in methyl-directed mismatch repair and nucleotide excision repair of DNA. Using stopped-flow methods we have examined the kinetic mechanism of translocation of UvrD monomers along single-stranded DNA (ssDNA) in vitro by monitoring the transient kinetics of arrival of protein at the 5'-end of the ssDNA. Arrival at the 5'-end was monitored by the effect of protein on the fluorescence intensity of fluorophores (Cy3 or fluorescein) attached to the 5'-end of a series of oligodeoxythymidylates varying in length from 16 to 124 nt. We find that UvrD monomers are capable of ATP-dependent translocation along ssDNA with a biased 3' to 5' directionality. Global non-linear least-squares analysis of the full kinetic time-courses in the presence of a protein trap to prevent rebinding of free protein to the DNA using the methods described in the accompanying paper enabled us to obtain quantitative estimates of the kinetic parameters for translocation. We find that UvrD monomers translocate in discrete steps with an average kinetic step-size, m=3.68(+/-0.03) nt step(-1), a translocation rate constant, kt=51.3(+/-0.6) steps s(-1), (macroscopic translocation rate, mkt=189.0(+/-0.7) nt s(-1)), with a processivity corresponding to an average translocation distance of 2400(+/-600) nt before dissociation (10 mM Tris-HCl (pH 8.3), 20 mM NaCl, 20% (v/v) glycerol, 25 degrees C). However, in spite of its ability to translocate rapidly and efficiently along ssDNA, a UvrD monomer is unable to unwind even an 18 bp duplex in vitro. DNA helicase activity in vitro requires a UvrD dimer that unwinds DNA with a similar kinetic step-size of 4-5 bp step(-1), but an approximately threefold slower unwinding rate of 68(+/-9) bp s(-1) under the same solution conditions, indicating that DNA unwinding activity requires more than the ability to simply translocate directionally along ss-DNA. PMID:15561144

  2. The effect of methylene dimethanesulphonate (MDMS) on the conformation of DNA and its dependence on base composition.

    PubMed

    Poppitt, D G; Fox, B W

    1975-09-01

    The interaction of the alkanesulphonate, methylene dimethanesulphonate (MDMS) with DNA has been studied. Thermal denaturation studies on mixtures of MDMS and DNA showed a dose-dependent decrease of the melting temperature midpoint (Tm) of the DNA. In addition, an irreversible decrease in ultraviolet absorption (hypochromism) preceded the hyperchromic shift, the magnitude of the former being linearly related to both the relative concentration of MDMS and the G-C content of the DNA used. Neither the reduction in melting temperature nor the initial UV absorption decrease occurred after dialysis of the reaction mixture. Equimolar proportions of the hydrolysis products of MDMS did not give the same effects as observed with the unhydrolysed agent. A similar hypochromism followed by strand separation occurs when DNA is allowed to stand with MDMS at room temperature, the time of subsequent strand separation being related to the treatment level of the drug. A weak association of MDMS with DNA is considered to be involved resulting in a local compression of the helical structure in the vicinity of the G-C pairs. It is suggested that this conformational change may act as a substrate for repair enzymes in vivo. PMID:168977

  3. Biochemical reconstitution of TET1–TDG–BER-dependent active DNA demethylation reveals a highly coordinated mechanism

    PubMed Central

    Weber, Alain R.; Krawczyk, Claudia; Robertson, Adam B.; Kuśnierczyk, Anna; Vågbø, Cathrine B.; Schuermann, David; Klungland, Arne; Schär, Primo

    2016-01-01

    Cytosine methylation in CpG dinucleotides is an epigenetic DNA modification dynamically established and maintained by DNA methyltransferases and demethylases. Molecular mechanisms of active DNA demethylation began to surface only recently with the discovery of the 5-methylcytosine (5mC)-directed hydroxylase and base excision activities of ten–eleven translocation (TET) proteins and thymine DNA glycosylase (TDG). This implicated a pathway operating through oxidation of 5mC by TET proteins, which generates substrates for TDG-dependent base excision repair (BER) that then replaces 5mC with C. Yet, direct evidence for a productive coupling of TET with BER has never been presented. Here we show that TET1 and TDG physically interact to oxidize and excise 5mC, and proof by biochemical reconstitution that the TET–TDG–BER system is capable of productive DNA demethylation. We show that the mechanism assures a sequential demethylation of symmetrically methylated CpGs, thereby avoiding DNA double-strand break formation but contributing to the mutability of methylated CpGs. PMID:26932196

  4. Cell cycle-dependent DNA damage signaling induced by ICRF-193 involves ATM, ATR, CHK2, and BRCA1

    SciTech Connect

    Park, Iha; Avraham, Hava Karsenty . E-mail: havraham@bidmc.harvard.edu

    2006-07-01

    Topoisomerase II is essential for cell proliferation and survival and has been a target of various anticancer drugs. ICRF-193 has long been used as a catalytic inhibitor to study the function of topoisomerase II. Here, we show that ICRF-193 treatment induces DNA damage signaling. Treatment with ICRF-193 induced G2 arrest and DNA damage signaling involving {gamma}-H2AX foci formation and CHK2 phosphorylation. DNA damage by ICRF-193 was further demonstrated by formation of the nuclear foci of 53BP1, NBS1, BRCA1, MDC1, and FANCD2 and increased comet tail moment. The DNA damage signaling induced by ICRF-193 was mediated by ATM and ATR and was restricted to cells in specific cell cycle stages such as S, G2, and mitosis including late and early G1 phases. Downstream signaling of ATM and ATR involved the phosphorylation of CHK2 and BRCA1. Altogether, our results demonstrate that ICRF-193 induces