WorldWideScience

Sample records for dna ladder pattern

  1. cGAS senses long and HMGB/TFAM-bound U-turn DNA by forming protein-DNA ladders.

    Science.gov (United States)

    Andreeva, Liudmila; Hiller, Björn; Kostrewa, Dirk; Lässig, Charlotte; de Oliveira Mann, Carina C; Jan Drexler, David; Maiser, Andreas; Gaidt, Moritz; Leonhardt, Heinrich; Hornung, Veit; Hopfner, Karl-Peter

    2017-09-21

    Cytosolic DNA arising from intracellular pathogens triggers a powerful innate immune response. It is sensed by cyclic GMP-AMP synthase (cGAS), which elicits the production of type I interferons by generating the second messenger 2'3'-cyclic-GMP-AMP (cGAMP). Endogenous nuclear or mitochondrial DNA can also be sensed by cGAS under certain conditions, resulting in sterile inflammation. The cGAS dimer binds two DNA ligands shorter than 20 base pairs side-by-side, but 20-base-pair DNA fails to activate cGAS in vivo and is a poor activator in vitro. Here we show that cGAS is activated in a strongly DNA length-dependent manner both in vitro and in human cells. We also show that cGAS dimers form ladder-like networks with DNA, leading to cooperative sensing of DNA length: assembly of the pioneering cGAS dimer between two DNA molecules is ineffective; but, once formed, it prearranges the flanking DNA to promote binding of subsequent cGAS dimers. Remarkably, bacterial and mitochondrial nucleoid proteins HU and mitochondrial transcription factor A (TFAM), as well as high-mobility group box 1 protein (HMGB1), can strongly stimulate long DNA sensing by cGAS. U-turns and bends in DNA induced by these proteins pre-structure DNA to nucleate cGAS dimers. Our results suggest a nucleation-cooperativity-based mechanism for sensitive detection of mitochondrial DNA and pathogen genomes, and identify HMGB/TFAM proteins as DNA-structuring host factors. They provide an explanation for the peculiar cGAS dimer structure and suggest that cGAS preferentially binds incomplete nucleoid-like structures or bent DNA.

  2. Double-helical - ladder structural transition in the B-DNA is induced by a loss of dispersion energy

    Czech Academy of Sciences Publication Activity Database

    Černý, Jiří; Kabeláč, Martin; Hobza, Pavel

    2008-01-01

    Roč. 130, č. 47 (2008), s. 16055-16059 ISSN 0002-7863 R&D Projects: GA MŠk LC512; GA AV ČR IAA400550808 Institutional research plan: CEZ:AV0Z40550506 Keywords : B-DNA * double-helical structure * ladder-like structure Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 8.091, year: 2008

  3. Detection of apoptotic DNA ladder in pig leukocytes and its precision using LM - PCR (ligation mediated polymerase chain reaction)

    Czech Academy of Sciences Publication Activity Database

    Matalová, Eva; Španová, A.

    2002-01-01

    Roč. 71, č. 3 (2002), s. 163-168 ISSN 0001-7213 R&D Projects: GA ČR GA304/01/0850; GA AV ČR KSK6005114 Keywords : apoptosis * phagocytosis * DNA ladder Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 0.370, year: 2002

  4. Ladder Safety Live #12985

    Energy Technology Data Exchange (ETDEWEB)

    Chochoms, Michael [Los Alamos National Laboratory

    2017-02-23

    This course presents information for working safely with portable ladders: specifically, stepladders, extensions ladders, and their derivations. Additionally, this course provides limited information on the safe use of stepstools and fixed ladders. The skills, techniques, and good practices needed for selecting, inspecting, setting up and securing, and using ladders are presented in this course.

  5. Effective career ladders.

    Science.gov (United States)

    Bryant, B; Rabbitts, D; Shover, J; Torres, M; VanDerHeyden, B; Violand-Jones, S

    1992-01-01

    Motivation, quality improvement, productivity enhancement. These are just some of the benefits of an effective career ladder program. The key term here is effective. It is easy for laboratory personnel to stagnate professionally if they do not have a career ladder program, but it is even easier for them to become frustrated--even cynical--over a program that fails to live up to its expectations to encourage, support, and reward professional advancement. If you have been looking form some ideas to get your own career ladder program off the ground, the following responses from your colleagues may help as CLMR asks: What makes your career ladder program effective?

  6. Available friction of ladder shoes and slip potential for climbing on a straight ladder.

    Science.gov (United States)

    Chang, Wen-Ruey; Chang, Chien-Chi; Matz, Simon

    2005-07-15

    Straight ladder accidents are a major safety problem. As a leading cause of injuries involving straight ladders, slips at the ladder base occur when the required friction exceeds the available friction at the ladder shoe and floor interface. The objectives of this experiment were to measure the available friction at the base of a portable straight ladder in contact with a floor and to estimate the slip potential of the ladder. The results of friction measurements indicated that the measured friction coefficient on the oily surfaces differed among the six commercially available ladder shoes evaluated. A statistical model was used to compare the available friction results from the current study with the friction requirements under different climbing conditions from a previous study based on their stochastic distributions to estimate the slip potential at the base of the ladder. The results showed that different climbing conditions used in the previous study could be supported by available friction on dry surfaces. However, when the ladder was put onto oily surfaces, resulting in a significant reduction in the available friction due to contamination, slip potential was significantly increased.

  7. 29 CFR 1926.1053 - Ladders.

    Science.gov (United States)

    2010-07-01

    ... plastic ladder shall sustain at least 3.3 times the maximum intended load. The ability of a ladder to... that each extra-heavy-duty type 1A metal or plastic ladders shall sustain at least 3.3 times the... from anticipated usage of the ladder, shall also be included), plus anticipated loads caused by ice...

  8. 29 CFR 1917.119 - Portable ladders.

    Science.gov (United States)

    2010-07-01

    ... Requirements for Portable Reinforced Plastic Ladders (d) Standards for job-made portable ladders. Job-made... usage. (1) Ladders made by fastening rungs or devices across a single rail are prohibited. (2) Ladders...

  9. 29 CFR 1915.72 - Ladders.

    Science.gov (United States)

    2010-07-01

    ...). (b) Construction of portable wood cleated ladders up to 30 feet in length. (1) Wood side rails shall... shall be at least 25/32×33/4 inches in cross section. (c) Construction of portable wood cleated ladders... split side rails, or other faulty or defective construction is prohibited. When ladders with such...

  10. Ladder variational autoencoders

    DEFF Research Database (Denmark)

    Sønderby, Casper Kaae; Raiko, Tapani; Maaløe, Lars

    2016-01-01

    Variational autoencoders are powerful models for unsupervised learning. However deep models with several layers of dependent stochastic variables are difficult to train which limits the improvements obtained using these highly expressive models. We propose a new inference model, the Ladder...... Variational Autoencoder, that recursively corrects the generative distribution by a data dependent approximate likelihood in a process resembling the recently proposed Ladder Network. We show that this model provides state of the art predictive log-likelihood and tighter log-likelihood lower bound compared...

  11. Ladder Variational Autoencoder

    DEFF Research Database (Denmark)

    Sønderby, Casper Kaae; Raiko, Tapani; Maaløe, Lars

    2016-01-01

    Variational autoencoders are powerful models for unsupervised learning. However deep models with several layers of dependent stochastic variables are difficult to train which limits the improvements obtained using these highly expressive models. We propose a new inference model, the Ladder...... Variational Autoencoder, that recursively corrects the generative distribution by a data dependent approximate likelihood in a process resembling the recently proposed Ladder Network. We show that this model provides state of the art predictive log-likelihood and tighter log-likelihood lower bound compared...

  12. De optimale sportafstand voor de ladder van de glazenwasser

    NARCIS (Netherlands)

    Reijneveld, C.N.; Looze, M.P. de; Hoozemans, M.J.M.; Grinten, M.P. van der; Korte, E.M. de; Kingma, I.

    2002-01-01

    Voor de glazenwasser die werkt met staande ladder, is een goede ladder zeer belangrijk. Hij loopt en werkt op en verplaatst de ladder veelvuldig. Er is veel discussie over ladders en de optimale sportafstand bij staande ladders. De meeste glazenwassers geven de voorkeur aan een sportafstand van 35

  13. DNA typing by capillary electrophoresis

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, N.

    1997-10-08

    Capillary electrophoresis is becoming more and more important in nucleic acid analysis including DNA sequencing, typing and disease gene measurements. This work summarized the background of DNA typing. The recent development of capillary electrophoresis was also discussed. The second part of the thesis showed the principle of DNA typing based on using the allelic ladder as the absolute standard ladder in capillary electrophoresis system. Future work will be focused on demonstrating DNA typing on multiplex loci and examples of disease diagnosis in the on-line format of PCR-CE. Also capillary array electrophoresis system should allow high throughput, fast speed DNA typing. Only the introduction and conclusions for this report are available here. A reprint was removed for separate processing.

  14. Electric field induced localization phenomena in a ladder network with superlattice configuration: Effect of backbone environment

    Energy Technology Data Exchange (ETDEWEB)

    Dutta, Paramita; Karmakar, S. N. [Condensed Matter Physics Division, Saha Institute of Nuclear Physics, Sector-I, Block-AF, Bidhannagar, Kolkata-700 064 (India); Maiti, Santanu K., E-mail: santanu.maiti@isical.ac.in [Physics and Applied Mathematics Unit, Indian Statistical Institute, 203 Barrackpore Trunk Road, Kolkata-700 108 (India)

    2014-09-15

    Electric field induced localization properties of a tight-binding ladder network in presence of backbone sites are investigated. Based on Green's function formalism we numerically calculate two-terminal transport together with density of states for different arrangements of atomic sites in the ladder and its backbone. Our results lead to a possibility of getting multiple mobility edges which essentially plays a switching action between a completely opaque to fully or partly conducting region upon the variation of system Fermi energy, and thus, support in fabricating mesoscopic or DNA-based switching devices.

  15. 29 CFR 1917.118 - Fixed ladders.

    Science.gov (United States)

    2010-07-01

    ... tubular scaffold framing; and (4) Ladders used only for fire-fighting or emergency purposes. (b... of equipment. (3) Ladder safety device means a support system limiting an employee's drop or fall...

  16. Origin of DNA in human serum and usefulness of serum as a material for DNA typing.

    Science.gov (United States)

    Takayama, T; Yamada, S; Watanabe, Y; Hirata, K; Nagai, A; Nakamura, I; Bunai, Y; Ohya, I

    2001-06-01

    The aims of this study were to clarify the origin of DNA in human serum and to investigate whether serum is a material available for DNA typing in routine forensic practice. Blood was donated from 10 healthy adult volunteers and stored for up to 8 days, at 4 degrees C and at room temperature. The serum DNA concentration at zero time was in the range of 5.6 to 21.8 ng/ml with a mean of 12.2+/-1.6 ng/ml. The concentrations increased with storage time. On agarose gel electrophoresis, all serum samples showed ladder patterns and the size of each band was an integer multiple of approximately 180 bp considered to be characteristic of apoptosis. DNA typing from DNA released by apoptosis was possible. Exact DNA typing of D1S80, HLA DQA1, PM, CSF1PO, TPOX, TH01 and vWA was possible for each sample. These results indicate that serum contains fragmented DNA derived from apoptosis of leukocytes, especially neutrophils, and that fragmented DNA is an appropriate material for DNA typing.

  17. Perspective on rainbow-ladder truncation

    International Nuclear Information System (INIS)

    Eichmann, G.; Alkofer, R.; Krassnigg, A.; Cloeet, I. C.; Roberts, C. D.

    2008-01-01

    Prima facie the systematic implementation of corrections to the rainbow-ladder truncation of QCD's Dyson-Schwinger equations will uniformly reduce in magnitude those calculated mass-dimensioned results for pseudoscalar and vector meson properties that are not tightly constrained by symmetries. The aim and interpretation of studies employing rainbow-ladder truncation are reconsidered in this light

  18. Evolution of the low-energy excitation spectrum from the pure Hubbard ladder to the SO(5) ladder: A numerical study

    International Nuclear Information System (INIS)

    Duffy, D.; Haas, S.; Kim, E.

    1998-01-01

    The Hubbard Hamiltonian on a two-leg ladder is studied numerically using quantum Monte Carlo and exact diagonalization techniques. A rung interaction, V, is turned on such that the resulting model has an exact SO(5) symmetry when V=-U. The evolution of the low-energy excitation spectrum is presented from the pure Hubbard ladder to the SO(5) ladder. It is shown that the low-energy excitations in the pure Hubbard ladder have an approximate SO(5) symmetry. copyright 1998 The American Physical Society

  19. Passage and behaviour of cultured Lake Sturgeon in a prototype side-baffle fish ladder: I. Ladder hydraulics and fish ascent

    Science.gov (United States)

    Kynard, B.; Pugh, D.; Parker, T.

    2011-01-01

    Research and development of a fish ladder for sturgeons requires understanding ladder hydraulics and sturgeon behaviour in the ladder to insure the ladder is safe and provides effective passage. After years of research and development, we designed and constructed a full-scale prototype side-baffle ladder inside a spiral flume (38.3m long??1m wide??1m high) on a 6% (1:16.5) slope with a 1.92-m rise in elevation (bottom to top) to test use by sturgeons. Twenty-eight triangular side baffles, each extending part way across the flume, alternated from inside wall to outside wall down the ladder creating two major flow habitats: a continuous, sinusoidal flow down the ladder through the vertical openings of side-baffles and an eddy below each side baffle. Ascent and behaviour was observed on 22 cultured Lake Sturgeon=LS (Acipenser fulvescens) repeatedly tested in groups as juveniles (as small as 105.1cm TL, mean) or as adults (mean TL, 118cm) during four periods (fall 2002 and 2003; spring 2003 and 2007). Percent of juveniles entering the ladder that ascended to the top was greater in spring (72.7%) than in fall (40.9-45.5%) and 90.9% of 11 adults, which ascended as juveniles, ascended to the top. Six LS (27.3%) never swam to the top and seven (31.8%) swam to the top in all tests, indicating great variability among individuals for ascent drive. Some LS swam directly to the top in <1min, but most rested in an eddy during ascent. Juveniles swimming through outside wall baffle slots (mean velocity, 1.2ms-1) swam at 1.8-2.2body lengthss-1 and 3.2-3.3tail beatss-1, either at or approaching prolonged swimming speed. The side-baffle ladder was stream-like and provided key factors for a sturgeon ladder: a continuous flow and no full cross-channel walls, abundant eddies for resting, an acceptable water depth, and a water velocity fish could ascend swimming 2bls-1. A side-baffle ladder passes LS and other moderate-swimming fishes. ?? 2011 Blackwell Verlag, Berlin.

  20. Career ladder program for registered nurses in ambulatory care.

    Science.gov (United States)

    Nelson, Joan; Sassaman, Becky; Phillips, Alison

    2008-01-01

    RN ladder programs are designed to inspire and reward clinical excellence. Kaiser Permanente Colorado's (KPCO) career ladder program emerged as a result of a labor-management partnership. Career ladder point assignments are reflective of the organization's priorities and values. KPCO's career ladder point tool awards RNs for formal and continuing education, professional presentations, organizational experience and experience as an RN, certifications and active professional memberships, leadership activities, research and publications, and nursing-related volunteer work. Participation in the RN career ladder requires that the nurse achieve a self-determined, manager-approved, measurable goal that will improve patient care. Career ladder nurses at KPCO were significantly more involved in leadership and interdisciplinary activities, quality improvement projects, and preceptorship.

  1. Edge currents in frustrated Josephson junction ladders

    Science.gov (United States)

    Marques, A. M.; Santos, F. D. R.; Dias, R. G.

    2016-09-01

    We present a numerical study of quasi-1D frustrated Josephson junction ladders with diagonal couplings and open boundary conditions, in the large capacitance limit. We derive a correspondence between the energy of this Josephson junction ladder and the expectation value of the Hamiltonian of an analogous tight-binding model, and show how the overall superconducting state of the chain is equivalent to the minimum energy state of the tight-binding model in the subspace of one-particle states with uniform density. To satisfy the constraint of uniform density, the superconducting state of the ladder is written as a linear combination of the allowed k-states of the tight-binding model with open boundaries. Above a critical value of the parameter t (ratio between the intra-rung and inter-rung Josephson couplings) the ladder spontaneously develops currents at the edges, which spread to the bulk as t is increased until complete coverage is reached. Above a certain value of t, which varies with ladder size (t = 1 for an infinite-sized ladder), the edge currents are destroyed. The value t = 1 corresponds, in the tight-binding model, to the opening of a gap between two bands. We argue that the disappearance of the edge currents with this gap opening is not coincidental, and that this points to a topological origin for these edge current states.

  2. Transport properties of a ladder with two random dimer chains

    International Nuclear Information System (INIS)

    Hu Dong-Sheng; Zhu Chen-Ping; Zhang Yong-Mei

    2011-01-01

    We investigate the transport properties of a ladder with two random dimer (RD) chains. It is found that there are two extended states in the ladder with identical RD chains and a critical state regarded as an extended state in the ladder with pairing RD chains. Such a critical state is caused by the chiral symmetry. The ladder with identical RD chains can be decoupled into two isolated RD chains and the ladder with pairing RD chains can not. The analytic expressions of the extended states are presented for the ladder with identical RD chains. (condensed matter: electronic structure, electrical, magnetic, and optical properties)

  3. Modeling the Sliding/Falling Ladder Paradox

    Science.gov (United States)

    Fox, William P.; Fox, James B.

    2003-01-01

    Recently we were presented with an interesting twist to the sliding ladder problem viewed in the related rates section of most calculus textbooks. Our problem concerning a sliding ladder that eventually hits the ground. At first, those attempting this problem fell into the calculus trap using only related rates. Previous work for this problem…

  4. 5 CFR 335.104 - Eligibility for career ladder promotion.

    Science.gov (United States)

    2010-01-01

    ... 5 Administrative Personnel 1 2010-01-01 2010-01-01 false Eligibility for career ladder promotion... REGULATIONS PROMOTION AND INTERNAL PLACEMENT General Provisions § 335.104 Eligibility for career ladder promotion. No employee shall receive a career ladder promotion unless his or her current rating of record...

  5. DNA-imprinted polymer nanoparticles with monodispersity and prescribed DNA-strand patterns

    Science.gov (United States)

    Trinh, Tuan; Liao, Chenyi; Toader, Violeta; Barłóg, Maciej; Bazzi, Hassan S.; Li, Jianing; Sleiman, Hanadi F.

    2018-02-01

    As colloidal self-assembly increasingly approaches the complexity of natural systems, an ongoing challenge is to generate non-centrosymmetric structures. For example, patchy, Janus or living crystallization particles have significantly advanced the area of polymer assembly. It has remained difficult, however, to devise polymer particles that associate in a directional manner, with controlled valency and recognition motifs. Here, we present a method to transfer DNA patterns from a DNA cage to a polymeric nanoparticle encapsulated inside the cage in three dimensions. The resulting DNA-imprinted particles (DIPs), which are 'moulded' on the inside of the DNA cage, consist of a monodisperse crosslinked polymer core with a predetermined pattern of different DNA strands covalently 'printed' on their exterior, and further assemble with programmability and directionality. The number, orientation and sequence of DNA strands grafted onto the polymeric core can be controlled during the process, and the strands are addressable independently of each other.

  6. Doped spin ladders under magnetic field

    International Nuclear Information System (INIS)

    Roux, G.

    2007-07-01

    This thesis deals with the physics of doped two-leg ladders which are a quasi one-dimensional and unconventional superconductor. We particularly focus on the properties under magnetic field. Models for strongly correlated electrons on ladders are studied using exact diagonalization and density-matrix renormalization group (DMRG). Results are also enlightened by using the bosonization technique. Taking into account a ring exchange it highlights the relation between the pairing of holes and the spin gap. Its influence on the dynamics of the magnetic fluctuations is also tackled. Afterwards, these excitations are probed by the magnetic field by coupling it to the spin degree of freedom of the electrons through Zeeman effect. We show the existence of doping-dependent magnetization plateaus and also the presence of an inhomogeneous superconducting phase (FFLO phase) associated with an exceeding of the Pauli limit. When a flux passes through the ladder, the magnetic field couples to the charge degree of freedom of the electrons via orbital effect. The diamagnetic response of the doped ladder probes the commensurate phases of the t-J model at low J/t. Algebraic transverse current fluctuations are also found once the field is turned on. Lastly, we report numerical evidences of a molecular superfluid phase in the 3/2-spin attractive Hubbard model: at a density low enough, bound states of four fermions, called quartets, acquire dominant superfluid fluctuations. The observed competition between the superfluid and density fluctuations is connected to the physics of doped ladders. (author)

  7. The Static Ladder Problem with Two Sources of Friction

    Science.gov (United States)

    Bennett, Jonathan; Mauney, Alex

    2011-01-01

    The problem of a ladder leaning against a wall in static equilibrium is a classic example encountered in introductory mechanics texts. Most discussions of this problem assume that the static frictional force between the ladder and wall can be ignored. A few authors consider the case where the static friction coefficients between ladder/wall…

  8. Superconductivity in doped two-leg ladder cuprates

    International Nuclear Information System (INIS)

    Qin Jihong; Yuan Feng; Feng Shiping

    2006-01-01

    Within the t-J ladder model, superconductivity with a modified d-wave symmetry in doped two-leg ladder cuprates is investigated based on the kinetic energy driven superconducting mechanism. It is shown that the spin-liquid ground-state at the half-filling evolves into the superconducting ground-state upon doping. In analogy to the doping dependence of the superconducting transition temperature in the planar cuprate superconductors, the superconducting transition temperature in doped two-leg ladder cuprates increases with increasing doping in the underdoped regime, and reaches a maximum in the optimal doping, then decreases in the overdoped regime

  9. Quantifying Ladder Fuels: A New Approach Using LiDAR

    Science.gov (United States)

    Heather Kramer; Brandon Collins; Maggi Kelly; Scott Stephens

    2014-01-01

    We investigated the relationship between LiDAR and ladder fuels in the northern Sierra Nevada, California USA. Ladder fuels are often targeted in hazardous fuel reduction treatments due to their role in propagating fire from the forest floor to tree crowns. Despite their importance, ladder fuels are difficult to quantify. One common approach is to calculate canopy base...

  10. Selectivity of fish ladders: a bottleneck in Neotropical fish movement

    Directory of Open Access Journals (Sweden)

    Carlos Sérgio Agostinho

    Full Text Available Although dozens of fish ladders have been constructed at dams of Brazilian reservoirs, there are few studies evaluating their efficiency as a tool for the conservation of Neotropical ichthyofauna, especially for migratory species. Therefore, the present study evaluated the selectivity of the species that entered and ascended the fish ladder located next to Lajeado Dam (Luis Eduardo Magalhães Hydroelectric Power Plant on the Tocantins River. Samples were taken monthly from November, 2002 through October, 2003, in the resting pools of the ladder, using cast nets, and in the downstream stretch, using gillnets. The selectivity of the ladder in attracting fish was evaluated by comparing the occurrence, relative abundance, dominance and the congruence of abundance ranks of migratory and non-migratory species in the ladder and in the stretch of river immediately downstream. Species richness and fish abundance in the resting pools were used to evaluate selectivity along the ladder. The effects on selectivity by temporal variations in water level downriver and maximum flow velocity in the fish ladder were also analyzed. Out of the 130 species recorded downriver, 62.3% were caught in the ladder, and migratory species were clearly favored. However, more than 2/3 of the catch belonged to only three species (Rhaphiodon vulpinus, Psectrogaster amazonica and Oxydoras niger. Although the majority of the species that entered the ladder were able to reach its top, there was a sharp reduction in abundance of individuals towards the top. Temporal variations in the water level below the dam influenced richness and abundance of fish concentrated downstream and in the ladder, with lower values during periods of low water. In the ladder, a maximum flow velocity of 2.3 m/s, although also selective, proved to be more appropriate for fish ascension than a velocity of 2.8 m/s. It was concluded that the entry and ascension of the fish in the ladder were not congruent with

  11. The snakes and ladders of FM service excellence

    OpenAIRE

    Price, Ilfryn; Mccarroll, Patricia

    2015-01-01

    A report to accompany a workshop and gamification event at EFMC 2015 in Glasgow.\\ud \\ud Snakes and Ladders is an ancient Indian board game regarded today as a worldwide classic. The historic version had its root in morality lessons, where a player's progression up the board represented a life journey complicated by virtues (ladders) and vices (snakes). Our version brings back the morality element by associating each ladder and snake with enablers or barriers to service excellence in FM all id...

  12. Baryons and ladders

    International Nuclear Information System (INIS)

    Ball, R.D.

    1990-01-01

    By formal manipulation of the QCD functional integral we arrive at a relativistic low energy effective theory of non-local color singlet mesons and baryons, which at tree level sums up ladders of effective glue exchange between constituent quarks. (orig.)

  13. 29 CFR 1910.25 - Portable wood ladders.

    Science.gov (United States)

    2010-07-01

    ... for the construction, care, and use of the common types of portable wood ladders, in order to insure... density wood shall not be used. (ii) [Reserved] (2) [Reserved] (c) Construction requirements. (1... 29 Labor 5 2010-07-01 2010-07-01 false Portable wood ladders. 1910.25 Section 1910.25 Labor...

  14. Understanding the Behaviour of Infinite Ladder Circuits

    Science.gov (United States)

    Ucak, C.; Yegin, K.

    2008-01-01

    Infinite ladder circuits are often encountered in undergraduate electrical engineering and physics curricula when dealing with series and parallel combination of impedances, as a part of filter design or wave propagation on transmission lines. The input impedance of such infinite ladder circuits is derived by assuming that the input impedance does…

  15. Gluing Ladder Feynman Diagrams into Fishnets

    International Nuclear Information System (INIS)

    Basso, Benjamin; Dixon, Lance J.; Stanford University, CA; University of California, Santa Barbara, CA

    2017-01-01

    We use integrability at weak coupling to compute fishnet diagrams for four-point correlation functions in planar Φ "4 theory. Our results are always multilinear combinations of ladder integrals, which are in turn built out of classical polylogarithms. The Steinmann relations provide a powerful constraint on such linear combinations, which leads to a natural conjecture for any fishnet diagram as the determinant of a matrix of ladder integrals.

  16. Laser mass spectrometry for DNA sequencing, disease diagnosis, and fingerprinting

    Energy Technology Data Exchange (ETDEWEB)

    Winston Chen, C.H.; Taranenko, N.I.; Zhu, Y.F.; Chung, C.N.; Allman, S.L.

    1997-03-01

    Since laser mass spectrometry has the potential for achieving very fast DNA analysis, the authors recently applied it to DNA sequencing, DNA typing for fingerprinting, and DNA screening for disease diagnosis. Two different approaches for sequencing DNA have been successfully demonstrated. One is to sequence DNA with DNA ladders produced from Snager`s enzymatic method. The other is to do direct sequencing without DNA ladders. The need for quick DNA typing for identification purposes is critical for forensic application. The preliminary results indicate laser mass spectrometry can possibly be used for rapid DNA fingerprinting applications at a much lower cost than gel electrophoresis. Population screening for certain genetic disease can be a very efficient step to reducing medical costs through prevention. Since laser mass spectrometry can provide very fast DNA analysis, the authors applied laser mass spectrometry to disease diagnosis. Clinical samples with both base deletion and point mutation have been tested with complete success.

  17. Fish ladders: safe fish passage or hotspot for predation?

    Directory of Open Access Journals (Sweden)

    Angelo Antonio Agostinho

    Full Text Available Fish ladders are a strategy for conserving biodiversity, as they can provide connectivity between fragmented habitats and reduce predation on shoals that accumulate immediately below dams. Although the impact of predation downstream of reservoirs has been investigated, especially in juvenile salmonids during their downstream movements, nothing is known about predation on Neotropical fish in the attraction and containment areas commonly found in translocation facilities. This study analysed predation in a fish passage system at the Lajeado Dam on the Tocantins River in Brazil. The abundance, distribution, and the permanence (time spent of large predatory fish along the ladder, the injuries imposed by piranhas during passage and the presence of other vertebrate predators were investigated. From December 2002 to October 2003, sampling was conducted in four regions (downstream, along the ladder, in the forebay, and upstream of the reservoir using gillnets, cast nets and counts or visual observations. The captured fish were tagged with thread and beads, and any mutilations were registered. Fish, birds and dolphins were the main predator groups observed, with a predominance of the first two groups. The entrance to the ladder, in the downstream region, was the area with the highest number of large predators and was the only region with relevant non-fish vertebrates. The main predatory fish species were Rhaphiodon vulpinus, Hydrolycus armatus, and Serrasalmus rhombeus. Tagged individuals were detected predating along the ladder for up to 90 days. Mutilations caused by Serrasalmus attacks were noted in 36% of species and 4% of individuals at the top of the ladder. Our results suggested that the high density of fish in the restricted ladder environment, which is associated with injuries suffered along the ladder course and the presence of multiple predator groups with different predation strategies, transformed the fish corridor into a hotspot for

  18. A balanced intervention ladder: promoting autonomy through public health action.

    Science.gov (United States)

    Griffiths, P E; West, C

    2015-08-01

    The widely cited Nuffield Council on Bioethics 'Intervention Ladder' structurally embodies the assumption that personal autonomy is maximized by non-intervention. Consequently, the Intervention Ladder encourages an extreme 'negative liberty' view of autonomy. Yet there are several alternative accounts of autonomy that are both arguably superior as accounts of autonomy and better suited to the issues facing public health ethics. We propose to replace the one-sided ladder, which has any intervention coming at a cost to autonomy, with a two-sided 'Balanced Intervention Ladder,' where intervention can either enhance or diminish autonomy. We show that not only the alternative, richer accounts of autonomy but even Mill's classic version of negative liberty puts some interventions on the positive side of the ladder. Crown Copyright © 2015. Published by Elsevier Ltd. All rights reserved.

  19. Boat boarding ladder placement

    Science.gov (United States)

    1998-04-01

    Presented in three volumes; 'Boat Boarding Ladder Placement,' which explores safety considerations including potential for human contact with a rotating propeller; 'Boat Handhold Placement,' which explores essential principles and methods of fall con...

  20. Designing and Implementing Performance-Based Career Ladder Plans.

    Science.gov (United States)

    Hawley, Willis D.

    1985-01-01

    Reviews the factors that any teacher motivation plan must incorporate to be effective and outlines 11 principles that should be followed in designing career ladder plans to meet teacher needs, increase teacher competence, and facilitate effective instruction. Warns against potential pitfalls in career ladder plans. (PGD)

  1. Directed nucleation assembly of DNA tile complexes for barcode-patterned lattices

    Science.gov (United States)

    Yan, Hao; Labean, Thomas H.; Feng, Liping; Reif, John H.

    2003-07-01

    The programmed self-assembly of patterned aperiodic molecular structures is a major challenge in nanotechnology and has numerous potential applications for nanofabrication of complex structures and useful devices. Here we report the construction of an aperiodic patterned DNA lattice (barcode lattice) by a self-assembly process of directed nucleation of DNA tiles around a scaffold DNA strand. The input DNA scaffold strand, constructed by ligation of shorter synthetic oligonucleotides, provides layers of the DNA lattice with barcode patterning information represented by the presence or absence of DNA hairpin loops protruding out of the lattice plane. Self-assembly of multiple DNA tiles around the scaffold strand was shown to result in a patterned lattice containing barcode information of 01101. We have also demonstrated the reprogramming of the system to another patterning. An inverted barcode pattern of 10010 was achieved by modifying the scaffold strands and one of the strands composing each tile. A ribbon lattice, consisting of repetitions of the barcode pattern with expected periodicity, was also constructed by the addition of sticky ends. The patterning of both classes of lattices was clearly observable via atomic force microscopy. These results represent a step toward implementation of a visual readout system capable of converting information encoded on a 1D DNA strand into a 2D form readable by advanced microscopic techniques. A functioning visual output method would not only increase the readout speed of DNA-based computers, but may also find use in other sequence identification techniques such as mutation or allele mapping.

  2. Measuring a Country's Product Ladder and Technology Level based on Trade Flow

    Directory of Open Access Journals (Sweden)

    Jong-il Kim

    2006-06-01

    Full Text Available This study tries to quantify the technology level of products based on the concept of product ladder. While many studies on country technology competitiveness use the aggregate indices such as total factor productivity and revealed comparative advantage, this study estimates the ranking of about 2000 products in product ladder by using SITC 5 digit level export data. Based on the product ladder, this study measures the country and industry ranking and explores the characteristics of the ranking. It provides the international comparison of inter-industry and intra-industry ranking differences in product ladder. The statistical relationships between the ranking in product ladder and the determinants of technology level such as R&D and physical capital investment and wage, confirms that the measured ranking in product ladder could be regarded as an indirect indicator of technology level. The product ladder is applied to the estimation of production function to see the effect of the product differentiation on labor productivity.

  3. Dipoles on a Two-leg Ladder

    DEFF Research Database (Denmark)

    Gammelmark, Søren; Zinner, Nikolaj Thomas

    2013-01-01

    We study polar molecules with long-range dipole-dipole interactions confined to move on a two-leg ladder for different orientations of the molecular dipole moments with respect to the ladder. Matrix product states are employed to calculate the many-body ground state of the system as function...... that there is a critical angle at which ordering disappears. This angle is slightly larger than the angle at which the dipoles are non-interacting along a single leg. This behavior should be observable using current experimental techniques....

  4. PT-symmetric ladders with a scattering core

    Energy Technology Data Exchange (ETDEWEB)

    D' Ambroise, J. [Department of Mathematics, Amherst College, Amherst, MA 01002-5000 (United States); Lepri, S. [CNR – Consiglio Nazionale delle Ricerche, Istituto dei Sistemi Complessi, via Madonna del piano 10, I-50019 Sesto Fiorentino (Italy); Istituto Nazionale di Fisica Nucleare, Sezione di Firenze, via G. Sansone 1, I-50019 Sesto Fiorentino (Italy); Malomed, B.A. [Department of Physical Electronics, School of Electrical Engineering, Faculty of Engineering, Tel Aviv University, Tel Aviv 69978 (Israel); Kevrekidis, P.G. [Department of Mathematics and Statistics, University of Massachusetts, Amherst, MA 01003-9305 (United States)

    2014-08-01

    We consider a PT-symmetric chain (ladder-shaped) system governed by the discrete nonlinear Schrödinger equation where the cubic nonlinearity is carried solely by two central “rungs” of the ladder. Two branches of scattering solutions for incident plane waves are found. We systematically construct these solutions, analyze their stability, and discuss non-reciprocity of the transmission associated with them. To relate the results to finite-size wavepacket dynamics, we also perform direct simulations of the evolution of the wavepackets, which confirm that the transmission is indeed asymmetric in this nonlinear system with the mutually balanced gain and loss. - Highlights: • We model a PT-symmetric ladder system with cubic nonlinearity on two central rungs. • We examine non-reciprocity and stability of incident plane waves. • Simulations of wavepackets confirm our results.

  5. Analysis of an "off-ladder" allele at the Penta D short tandem repeat locus.

    Science.gov (United States)

    Yang, Y L; Wang, J G; Wang, D X; Zhang, W Y; Liu, X J; Cao, J; Yang, S L

    2015-11-25

    Kinship testing of a father and his son from Guangxi, China, the location of the Zhuang minority people, was performed using the PowerPlex® 18D System with a short tandem repeat typing kit. The results indicated that both the father and his son had an off-ladder allele at the Penta D locus, with a genetic size larger than that of the maximal standard allelic ladder. To further identify this locus, monogenic amplification, gene cloning, and genetic sequencing were performed. Sequencing analysis demonstrated that the fragment size of the Penta D-OL locus was 469 bp and the core sequence was [AAAGA]21, also called Penta D-21. The rare Penta D-21 allele was found to be distributed among the Zhuang population from the Guangxi Zhuang Autonomous Region of China; therefore, this study improved the range of DNA data available for this locus and enhanced our ability for individual identification of gene loci.

  6. Development of ultra-light pixelated ladders for an ILC vertex detector

    CERN Document Server

    Chon-Sen, N.; Claus, G.; De Masi, R.; Deveaux, M.; Dulinski, W.; Goffe, M.; Goldstein, J.; Gregor, I.-M.; Hu-Guo, Ch.; Imhoff, M.; Muntz, C.; Nomerotski, A.; Santos, C.; Schrader, C.; Specht, M.; Stroth, J.; Winter, M.

    2010-01-01

    The development of ultra-light pixelated ladders is motivated by the requirements of the ILD vertex detector at ILC. This paper summarizes three projects related to system integration. The PLUME project tackles the issue of assembling double-sided ladders. The SERWIETE project deals with a more innovative concept and consists in making single-sided unsupported ladders embedded in an extra thin plastic enveloppe. AIDA, the last project, aims at building a framework reproducing the experimental running conditions where sets of ladders could be tested.

  7. DNA pattern recognition using canonical correlation algorithm.

    Science.gov (United States)

    Sarkar, B K; Chakraborty, Chiranjib

    2015-10-01

    We performed canonical correlation analysis as an unsupervised statistical tool to describe related views of the same semantic object for identifying patterns. A pattern recognition technique based on canonical correlation analysis (CCA) was proposed for finding required genetic code in the DNA sequence. Two related but different objects were considered: one was a particular pattern, and other was test DNA sequence. CCA found correlations between two observations of the same semantic pattern and test sequence. It is concluded that the relationship possesses maximum value in the position where the pattern exists. As a case study, the potential of CCA was demonstrated on the sequence found from HIV-1 preferred integration sites. The subsequences on the left and right flanking from the integration site were considered as the two views, and statistically significant relationships were established between these two views to elucidate the viral preference as an important factor for the correlation.

  8. The latrine ownership ladder

    DEFF Research Database (Denmark)

    Obeng, Peter Appiah; Keraita, Bernard; Oduro-Kwarteng, Sampson

    2015-01-01

    the challenges that undermine sanitation uptake in low-income peri-urban areas and the prospects of various levels of facility sharing as conceived in the latrine ownership ladder approach. Findings – The authors argue that the infrastructural and other socio-economic challenges of low-income peri-urban areas...... to the promotion of household latrines. The paper identifies provision of special concessions for peri-urban areas in policy formulation, education and technical support to households, regulation and enforcement of sanitation by-laws among complimentary policy interventions to make the latrine ownership ladder...... approach more effective. Originality/value – The paper provides an insight into the debate on redefining improved sanitation in the post-2015 era of the Millennium Development Goals and offers policy alternatives to policy makers in low-income countries seeking to accelerate the uptake of improved latrines...

  9. Role of Structural Asymmetry in Controlling Drop Spacing in Microfluidic Ladder Networks

    Science.gov (United States)

    Wang, William; Maddala, Jeevan; Vanapalli, Siva; Rengasamy, Raghunathan

    2012-02-01

    Manipulation of drop spacing is crucial to many processes in microfluidic devices including drop coalescence, detection and storage. Microfluidic ladder networks ---where two droplet-carrying parallel channels are connected by narrow bypass channels through which the motion of drops is forbidden---have been proposed as a means to control relative separation between pairs of drops. Prior studies in microfluidic ladder networks with vertical bypasses, which possess fore-aft structural symmetry, have revealed that pairs of drops can only undergo reduction in drop spacing at the ladder exit. We investigate the dynamics of drops in microfluidic ladder networks with both vertical and slanted bypasses. Our analytical results indicate that unlike symmetric ladder networks, structural asymmetry introduced by a single slanted bypass can be used to modulate the relative spacing between drops, enabling them to contract, synchronize, expand or even flip at the ladder exit. Our experiments confirm all the behaviors predicted by theory. Numerical analysis further shows that ladders containing several identical bypasses can only linearly transform the input drop spacing. Finally, we find that ladders with specific combinations of vertical and slanted bypasses can generate non-linear transformation of input drop spacing, despite the absence of drop decision-making events at the bypass junctions.

  10. Modification of the Ladder Rung Walking Task—New Options for Analysis of Skilled Movements

    Directory of Open Access Journals (Sweden)

    Iwa Antonow-Schlorke

    2013-01-01

    Full Text Available Method sensitivity is critical for evaluation of poststroke motor function. Skilled walking was assessed in horizontal, upward, and downward rung ladder walking to compare the demands of the tasks and test sensitivity. The complete step sequence of a walk was subjected to analysis aimed at demonstrating the walking pattern, step sequence, step cycle, limb coordination, and limb interaction to complement the foot fault scoring system. Rats (males, n=10 underwent unilateral photothrombotic lesion of the motor cortex of the forelimb and hind limb areas. Locomotion was video recorded before the insult and at postischemic days 7 and 28. Analysis of walking was performed frame-by-frame. Walking along the rung ladder revealed different results that were dependent on ladder inclination. Horizontal walking was found to discriminate lesion-related motor deficits in forelimb, whereas downward walking demonstrates hind limb use most sensitively. A more frequent use of the impaired forelimb that possibly supported poststroke motor learning in rats was shown. The present study provides a novel system for a detailed analysis of the complete walking sequence and will help to provide a better understanding of how rats deal with motor impairments.

  11. Towards automatic verification of ladder logic programs

    OpenAIRE

    Zoubek , Bohumir; Roussel , Jean-Marc; Kwiatkowska , Martha

    2003-01-01

    International audience; Control system programs are usually validated by testing prior to their deployment. Unfortunately, testing is not exhaustive and therefore it is possible that a program which passed all the required tests still contains errors. In this paper we apply techniques of automatic verification to a control program written in ladder logic. A model is constructed mechanically from the ladder logic program and subjected to automatic verification against requirements that include...

  12. The massless supersymmetric ladder with L rungs

    International Nuclear Information System (INIS)

    Rossi, G.C.; Stanev, Ya.S.

    2009-01-01

    We show that in the massless N=1 supersymmetric Wess-Zumino theory it is possible to devise a computational strategy by which the x-space calculation of the ladder 4-point correlators can be carried out without introducing any regularization. As an application we derive a representation valid at all loop orders in terms of conformal invariant integrals. We obtain an explicit expression of the 3-loop ladder diagram for collinear external points

  13. Real-time Tracking of DNA Fragment Separation by Smartphone.

    Science.gov (United States)

    Tao, Chunxian; Yang, Bo; Li, Zhenqing; Zhang, Dawei; Yamaguchi, Yoshinori

    2017-06-01

    Slab gel electrophoresis (SGE) is the most common method for the separation of DNA fragments; thus, it is broadly applied to the field of biology and others. However, the traditional SGE protocol is quite tedious, and the experiment takes a long time. Moreover, the chemical consumption in SGE experiments is very high. This work proposes a simple method for the separation of DNA fragments based on an SGE chip. The chip is made by an engraving machine. Two plastic sheets are used for the excitation and emission wavelengths of the optical signal. The fluorescence signal of the DNA bands is collected by smartphone. To validate this method, 50, 100, and 1,000 bp DNA ladders were separated. The results demonstrate that a DNA ladder smaller than 5,000 bp can be resolved within 12 min and with high resolution when using this method, indicating that it is an ideal substitute for the traditional SGE method.

  14. Magnetic susceptibilities of integrable quantum ladders

    International Nuclear Information System (INIS)

    Park, Soo A; Lee, K.

    2001-01-01

    As an extension of previous studies, we consider the magnetic susceptibilities of a coupled spin chain model at low temperature and of a more realistic model at low temperature and of a more realistic model having a t-J ladder structure at zero temperature. The magnetic susceptibilities for both models are obtained numerically when the coupling constant is greater than its critical value. In this region, the ladders behave as a single chain for H c and as two independent chains for H>H c , showing a divergence at H c . This divergence is expected to smear out at a finite temperature

  15. Patterning nanocrystals using DNA

    Energy Technology Data Exchange (ETDEWEB)

    Williams, Shara Carol [Univ. of California, Berkeley, CA (United States)

    2003-01-01

    One of the goals of nanotechnology is to enable programmed self-assembly of patterns made of various materials with nanometer-sized control. This dissertation describes the results of experiments templating arrangements of gold and semiconductor nanocrystals using 2'-deoxyribonucleic acid (DNA). Previously, simple DNA-templated linear arrangements of two and three nanocrystals structures have been made.[1] Here, we have sought to assemble larger and more complex nanostructures. Gold-DNA conjugates with 50 to 100 bases self-assembled into planned arrangements using strands of DNA containing complementary base sequences. We used two methods to increase the complexity of the arrangements: using branched synthetic doublers within the DNA covalent backbone to create discrete nanocrystal groupings, and incorporating the nanocrystals into a previously developed DNA lattice structure [2][3] that self-assembles from tiles made of DNA double-crossover molecules to create ordered nanoparticle arrays. In the first project, the introduction of a covalently-branched synthetic doubler reagent into the backbone of DNA strands created a branched DNA ''trimer.'' This DNA trimer templated various structures that contained groupings of three and four gold nanoparticles, giving promising, but inconclusive transmission electron microscopy (TEM) results. Due to the presence of a variety of possible structures in the reaction mixtures, and due to the difficulty of isolating the desired structures, the TEM and gel electrophoresis results for larger structures having four particles, and for structures containing both 5 and 10 nm gold nanoparticles were inconclusive. Better results may come from using optical detection methods, or from improved sample preparation. In the second project, we worked toward making two-dimensional ordered arrays of nanocrystals. We replicated and improved upon previous results for making DNA lattices, increasing the size of the lattices

  16. Ladder Ising spin configurations. Pt. 1. Heat capacity

    International Nuclear Information System (INIS)

    Mejdani, R.; Lambros, A.

    1996-01-01

    We consider a ladder Ising spin model (with two coupled Ising spin chains), characterized by two couplings (interchain and intrachain couplings), to study in detail, in an analytical way, its thermal behaviour and particularly the variation of the specific heat versus temperature, the ratio of interaction constants, and the magnetic field. It is interesting that when the competition between interchain and intrachain interactions is strong the specific heat exhibits a double peak and when the competition is not so strong the specific heat has a single peak. Further, without entering into details, we give, in a numerical way, some similar results for more complicated ladder configurations (with more than two linear Ising chains). The spin-1/2 ladders or systems of spin chains may be realized in nature by vanadyl pyrophosphate ((VO) 2 P 2 O 7 ) or similar materials. All these intermediate systems are today important to gain further insight into the physics of one-dimensional spin chains and two-dimensional high-T c spin systems, both of which have shown interesting and unusual magnetic and superconducting properties. It is plausible that experimental and theoretical studies of ladders may lead to other interesting physical phenomena. (orig.)

  17. Discussing Laddering Application by the Means-End Chain Theory

    Science.gov (United States)

    Veludo-de-Oliveira, Tania Modesto; Ikeda, Ana Akemi; Campomar, Marcos Cortez

    2006-01-01

    This article aims at analyzing laddering as a technique of qualitative research, emphasizing the procedures for data collection, analysis and interpretation, and its main limitations as well. "Laddering refers to an in-depth, one-on-one interviewing technique used to develop an understanding of how consumers translate the attributes of products…

  18. Biomechanical analysis of loading/unloading a ladder on a truck.

    Science.gov (United States)

    Moriguchi, Cristiane Shinohara; Carnaz, Leticia; de Miranda, Luiz Carlos; Marklin, Richard William; Coury, Helenice Jane Cote Gil

    2012-01-01

    Loading/unloading a ladder on vehicles are frequent tasks and involve overhead handling that may expose workers to risk factors of shoulder musculoskeletal disorders. The objective of the present study was to evaluate posture, forces required and perceived exertion when loading and unloading the ladder on a utility truck. Thirteen male overhead line workers from an electric utility in Brazil participated in this study. Shoulder elevation angle was measured using inclinometers. The required force to load/unload the ladder was measured by dynamometer. Subjective assessment of the perceived exertion was recorded to compare the exertion reported during the test conditions to the field conditions. The task of loading/unloading the ladder presented risks of shoulder musculoskeletal disorders (MSDs) to workers because it requires high levels of force (approximately 60% of the maximal force) combined with overhead posture of the shoulders (more than 100° from the neutral posture). Age and height presented to interfere in biomechanical risks presented in load/unload task. There was no significant difference between the subjective exertion during the test conditions and handling the ladder in the field. Ergonomic intervention is recommended to reduce these risks for shoulder MSDs.

  19. Cells immobilized on patterns printed in DNA by an inkjet printer.

    Science.gov (United States)

    Sakurai, Kengo; Teramura, Yuji; Iwata, Hiroo

    2011-05-01

    The ability to two-dimensionally align various kinds of cells freely onto substrate would be a useful tool for analysis of cell-cell interactions. In this study, we aimed to establish a method for attaching cells to the substrate, in which the pattern is drawn by an inkjet printer. Poly-deoxyribonucleic acid (DNA) was immobilized onto the cell surface by use of DNA-conjugated poly(ethylene) glycol-phospholipid (DNA-PEG-lipid), which is the amphiphilic conjugate of PEG-lipid and single-stranded DNA. The surface of the substrate was then modified with the complementary DNA using an inkjet printer. Finally, DNA-immobilized cells were attached onto the substrate through DNA hybridization. The use of the inkjet printer enabled us to draw the DNA pattern accurately on the substrate with a resolution of a few hundred micrometers. DNA-immobilized cells could be attached precisely along the DNA pattern on the substrate. In addition, various kinds of cells could be attached simultaneously by using various sequences of DNA. Our technique is promising for analysis of cell-cell interactions and differentiation induction in stem cell research. Copyright © 2011 Elsevier Ltd. All rights reserved.

  20. Influence of seasonal, diel, lunar, and other environmental factors on upstream fish passage in the igarapava fish ladder, Brazil

    Science.gov (United States)

    Bizzotto, P.M.; Godinho, Alexandre L.; Vono, V.; Kynard, B.; Godinho, Hugo P.

    2009-01-01

    Upstream fish passage was evaluated during 12 months in the vertical-slot Igarapava Fish Ladder constructed around Igarapava Dam, in the heavily dammed Grande River, Southeast Brazil. A video monitoring system was used to observe 61,621 fish that passed the ladder, of which 93.5% were identified to 15 taxa. Among the migratory species, the most abundant were Pimelodus maculatus (33.6% of all fish), Leporinus octofasciatus (31.4%), Leporinus friderici (4.5%), and Prochilodus lineatus (3.1%). Seven taxa were classified as nonmigratory, and of these taxa, the small Bryconamericus stramineus was the most abundant (12.7%) of all fishes. Passage of the 'nonmigratory' taxa upstream in the ladder shows they are migratory in this system and have a strong behavioural drive to move to upstream habitat. Passage of most taxa had a strong seasonal pattern. While some species passed primarily during the day, others showed a distinct nocturnal pattern. Lunar phase and water temperature also strongly affected passage of some taxa. Rainfall and dam discharge had a small or null influence on most taxa; perhaps due to the fairly small catchment area of the reservoir and the highly regulated discharge at Igarapava Dam. ?? 2009 John Wiley & Sons A/S.

  1. 46 CFR 72.05-20 - Stairways, ladders, and elevators.

    Science.gov (United States)

    2010-10-01

    ... 46 Shipping 3 2010-10-01 2010-10-01 false Stairways, ladders, and elevators. 72.05-20 Section 72.05-20 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) PASSENGER VESSELS CONSTRUCTION AND ARRANGEMENT Structural Fire Protection § 72.05-20 Stairways, ladders, and elevators. (a)(1) Except as further noted the provisions of this...

  2. Topological phases in frustrated synthetic ladders with an odd number of legs

    Science.gov (United States)

    Barbarino, Simone; Dalmonte, Marcello; Fazio, Rosario; Santoro, Giuseppe E.

    2018-01-01

    The realization of the Hofstadter model in a strongly anisotropic ladder geometry has now become possible in one-dimensional optical lattices with a synthetic dimension. In this work, we show how the Hofstadter Hamiltonian in such ladder configurations hosts a topological phase of matter which is radically different from its two-dimensional counterpart. This topological phase stems directly from the hybrid nature of the ladder geometry and is protected by a properly defined inversion symmetry. We start our analysis by considering the paradigmatic case of a three-leg ladder which supports a topological phase exhibiting the typical features of topological states in one dimension: robust fermionic edge modes, a degenerate entanglement spectrum, and a nonzero Zak phase; then, we generalize our findings—addressable in the state-of-the-art cold-atom experiments—to ladders with a higher number of legs.

  3. Triptycene-based ladder monomers and polymers, methods of making each, and methods of use

    KAUST Repository

    Pinnau, Ingo

    2015-02-05

    Embodiments of the present disclosure provide for a triptycene-based A-B monomer, a method of making a triptycene-based A-B monomer, a triptycene-based ladder polymer, a method of making a triptycene-based ladder polymers, a method of using triptycene-based ladder polymers, a structure incorporating triptycene-based ladder polymers, a method of gas separation, and the like.

  4. Progress in the Supramolecular Architecture-directed Synthesis of Perfect Ladder Polysiloxanes

    Institute of Scientific and Technical Information of China (English)

    C; C; Han

    2007-01-01

    1 Introduction Ladder polysiloxanes (LPSs) including organo-bridged ladder polyorganosiloxanes (R-OLPSs, R is side group) and ladder polyorganosilsesquioxanes (R-LPSQs) have intrigued polymer chemists for about 50 years due to their excellent resistance to all kinds of degradations. However, their synthesis has been a great challenge to polymer chemists. Here, we describe a new approach based on supramolecular concerted interactions as follows.2 Results2.1 Synthesis of Perfect R-OLPSsA series of real ...

  5. Sequence Dependent Electrophoretic Separations of DNA in Pluronic F127 Gels

    Science.gov (United States)

    You, Seungyong; van Winkle, David H.

    2010-03-01

    Two-dimensional (2-D) electrophoresis has successfully been used to visualize the separation of DNA fragments of the same length. We electrophorese a double-stranded DNA ladder in an Agarose gel for the first dimension and in gels of Pluronic F127 for the second dimension at room temperature. The 1000 bp band that travels together as a single band in an Agarose gel is split into two bands in Pluronic gels. The slower band follows the exponential decay trend that the other ladder constituents do. After sequencing the DNA fragments, the faster band has an apparently random sequence, while the slower band and the others have two A-tracts in each 250 bp segment. The A-tracts consist of a series of at least five adenine bases pairing with thymine bases. This result leads to the conclusion that the migration of the DNA molecules bent with A-tracts is more retarded in Pluronic gels than the wild-type of DNA molecules.

  6. LAMP assay for rapid diagnosis of cow DNA in goat milk and meat samples.

    Science.gov (United States)

    Deb, R; Sengar, G S; Singh, U; Kumar, S; Raja, T V; Alex, R; Alyethodi, R R; Prakash, B

    2017-01-01

    Animal species detection is one of the crucial steps for consumer's food analysis. In the present study we developed an in-house built loop-mediated isothermal amplification (LAMP) assay for rapid detection of adulterated cow DNA in goat milk/meat samples. The cow milk/tissue DNA in goat milk/meat samples were identified in the developed LAMP assay by either naked eye visualizing with SYBR Green I dyes or by detecting the typical ladder pattern on gel electrophoresis. This test can detect up to minimum 5% level of cow components admixed in goat milk/meat samples and can be completed within 1 h 40 min starting from DNA extraction from milk/meat samples and can be performed in a water bath. Developed LAMP methodology is simple; rapid and sensitive techniques that can detect adulterant like cow components in goat milk/meat are more accurate than other existing DNA based technologies.

  7. Developmental heterogeneity in DNA packaging patterns influences T-cell activation and transmigration.

    Directory of Open Access Journals (Sweden)

    Soumya Gupta

    Full Text Available Cellular differentiation programs are accompanied by large-scale changes in nuclear organization and gene expression. In this context, accompanying transitions in chromatin assembly that facilitates changes in gene expression and cell behavior in a developmental system are poorly understood. Here, we address this gap and map structural changes in chromatin organization during murine T-cell development, to describe an unusual heterogeneity in chromatin organization and associated functional correlates in T-cell lineage. Confocal imaging of DNA assembly in cells isolated from bone marrow, thymus and spleen reveal the emergence of heterogeneous patterns in DNA organization in mature T-cells following their exit from the thymus. The central DNA pattern dominated in immature precursor cells in the thymus whereas both central and peripheral DNA patterns were observed in naïve and memory cells in circulation. Naïve T-cells with central DNA patterns exhibited higher mechanical pliability in response to compressive loads in vitro and transmigration assays in vivo, and demonstrated accelerated expression of activation-induced marker CD69. T-cell activation was characterized by marked redistribution of DNA assembly to a central DNA pattern and increased nuclear size. Notably, heterogeneity in DNA patterns recovered in cells induced into quiescence in culture, suggesting an internal regulatory mechanism for chromatin reorganization. Taken together, our results uncover an important component of plasticity in nuclear organization, reflected in chromatin assembly, during T-cell development, differentiation and transmigration.

  8. Pericentric satellite DNA sequences in Pipistrellus pipistrellus (Vespertilionidae; Chiroptera).

    Science.gov (United States)

    Barragán, M J L; Martínez, S; Marchal, J A; Fernández, R; Bullejos, M; Díaz de la Guardia, R; Sánchez, A

    2003-09-01

    This paper reports the molecular and cytogenetic characterization of a HindIII family of satellite DNA in the bat species Pipistrellus pipistrellus. This satellite is organized in tandem repeats of 418 bp monomer units, and represents approximately 3% of the whole genome. The consensus sequence from five cloned monomer units has an A-T content of 62.20%. We have found differences in the ladder pattern of bands between two populations of the same species. These differences are probably because of the absence of the target sites for the HindIII enzyme in most monomer units of one population, but not in the other. Fluorescent in situ hybridization (FISH) localized the satellite DNA in the pericentromeric regions of all autosomes and the X chromosome, but it was absent from the Y chromosome. Digestion of genomic DNAs with HpaII and its isoschizomer MspI demonstrated that these repetitive DNA sequences are not methylated. Other bat species were tested for the presence of this repetitive DNA. It was absent in five Vespertilionidae and one Rhinolophidae species, indicating that it could be a species/genus specific, repetitive DNA family.

  9. Fractal assembly of micrometre-scale DNA origami arrays with arbitrary patterns

    Science.gov (United States)

    Tikhomirov, Grigory; Petersen, Philip; Qian, Lulu

    2017-12-01

    Self-assembled DNA nanostructures enable nanometre-precise patterning that can be used to create programmable molecular machines and arrays of functional materials. DNA origami is particularly versatile in this context because each DNA strand in the origami nanostructure occupies a unique position and can serve as a uniquely addressable pixel. However, the scale of such structures has been limited to about 0.05 square micrometres, hindering applications that demand a larger layout and integration with more conventional patterning methods. Hierarchical multistage assembly of simple sets of tiles can in principle overcome this limitation, but so far has not been sufficiently robust to enable successful implementation of larger structures using DNA origami tiles. Here we show that by using simple local assembly rules that are modified and applied recursively throughout a hierarchical, multistage assembly process, a small and constant set of unique DNA strands can be used to create DNA origami arrays of increasing size and with arbitrary patterns. We illustrate this method, which we term ‘fractal assembly’, by producing DNA origami arrays with sizes of up to 0.5 square micrometres and with up to 8,704 pixels, allowing us to render images such as the Mona Lisa and a rooster. We find that self-assembly of the tiles into arrays is unaffected by changes in surface patterns on the tiles, and that the yield of the fractal assembly process corresponds to about 0.95m - 1 for arrays containing m tiles. When used in conjunction with a software tool that we developed that converts an arbitrary pattern into DNA sequences and experimental protocols, our assembly method is readily accessible and will facilitate the construction of sophisticated materials and devices with sizes similar to that of a bacterium using DNA nanostructures.

  10. Assembly procedure for the silicon pixel ladder for PHENIX silicon vertex tracker

    International Nuclear Information System (INIS)

    Onuki, Y.; Akiba, Y.; En'yo, H.; Fujiwara, K.; Haki, Y.; Hashimoto, K.; Ichimiya, R.; Kasai, M.; Kawashima, M.; Kurita, K.; Kurosawa, M.; Mannel, E.J.; Nakano, K.; Pak, R.; Sekimoto, M.; Sondheim, W.E.; Taketani, A.; Togawa, M.; Yamamoto, Y.

    2009-01-01

    The silicon vertex tracker (VTX) will be installed in the summer of 2010 to enhance the physics capabilities of the Pioneering High Energy Nuclear Interaction eXperiment (PHENIX) experiment at Brookhaven National Laboratory. The VTX consists of two types of silicon detectors: a pixel detector and a strip detector. The pixel detector consists of 30 pixel ladders placed on the two inner cylindrical layers of the VTX. The ladders are required to be assembled with high precision, however, they should be assembled in both cost and time efficient manner. We have developed an assembly bench for the ladder with several assembly fixtures and a quality assurance (Q/A) system using a 3D measurement machine. We have also developed an assembly procedure for the ladder, including a method for dispensing adhesive uniformly and encapsulation of bonding wires. The developed procedures were adopted in the assembly of the first pixel ladder and satisfy the requirements.

  11. Movements of adult Atlantic salmon in relation to a hydroelectric dam and fish ladder

    International Nuclear Information System (INIS)

    Gowans, A.R.D.; Priede, I.G.

    1999-01-01

    The movements of adult Atlantic salmon were recorded as they approached, entered and ascended the pool-and-orifice fish ladder at Pitlochry Dam, Scotland. Thirty-nine returning salmon were captured in the River Tummel by rod-and-line angling, radio-tagged and released near where they were caught. The subsequent movements of each fish were then monitored. An electronic fish counter collected additional data on movements of untagged fish past a fixed point in the ladder. Of the 39 fish that were radio-tagged, 29 individuals were recorded approaching and ascending the ladder. The remaining fish either did not approach the dam (three fish), approached the dam after detailed tracking had ended (two fish), were recaptured by anglers (three fish), or the radio tags failed (two fish). Salmon released earlier in the year delayed longer before first approaching the dam. Delays between first approaching the dam and ascent of the ladder were greater for fish that approached the dam earlier. The majority of salmon visited the ladder entrance more than once (maximum 10 visits) before ascending. Having entered, all but four salmon ascended the fish ladder successfully on their first attempt. The four individuals that failed to do so succeeded on their second attempt. The rate at which salmon ascended the ladder was related directly to temperature. The shortest ascent time of a radio-tagged salmon was 5.25 h. Movements of eight of 11 tagged fish through the ladder ceased with the onset of darkness but continued on the following morning. No radio-tagged fish entered the ladder at temperatures below 9 o C. Similarly, few untagged fish were recorded ascending the ladder by the electronic fish counter at water temperatures below 8.5 o C. Records from the fish counter indicated that 92% of upstream movements were made during daylight. (author)

  12. Work-related falls from ladders--a follow-back study of US emergency department cases.

    Science.gov (United States)

    Lombardi, David A; Smith, Gordon S; Courtney, Theodore K; Brennan, Melanye J; Kim, Jae Young; Perry, Melissa J

    2011-11-01

    Ladder falls comprise 16% of all US workplace fall-related fatalities, and ladder use may be particularly hazardous among older workers. This follow-back study of injured workers from a nationally representative sample of US emergency departments (ED) focused on factors related to ladder falls in three domains of the work environment: work equipment, work practices, and worker-related factors. Risk factors for fractures, the most frequent and severe outcome, were also evaluated. Workers injured from a ladder fall, treated in one of the 65 participating ED in the occupational National Electronic Injury Surveillance System (NEISS) were asked to participate. The questionnaire included worker demographics, injury, ladder and work equipment and environment characteristics, work tasks, and activities. Multivariate logistic regression models estimated odds ratios and 95% confidence intervals of a work-related fracture. Three-hundred and six workers experiencing an injury from an--on average--7.5-foot-fall from a step, extension, or straight ladder were interviewed primarily from construction, installation, maintenance, and repair professions. Injuries were most frequently to the arm, elbow or shoulder; head, neck, or face with diagnoses were primarily fracture, strain, sprain, contusion or abrasion. Workers were most frequently standing or sitting on the ladder while installing, hanging an item, or performing a repair when they fell. Ladder movement was the mechanism in 40% of falls. Environmental conditions played a role in cases. There was a significant association between fracture risk and fall height while working on the ladder that was also influenced by older work age. This study advances knowledge of falls from ladders to support those who specify means and methods, select equipment, and plan, supervise, or manage the performance of employees working at heights.

  13. Single-particle potential from resummed ladder diagrams

    International Nuclear Information System (INIS)

    Kaiser, N.

    2013-01-01

    A recent work on the resummation of fermionic in-medium ladder diagrams to all orders is extended by calculating the complex single-particle potential U(p, k f ) + i W(p, k f ) p > k f . The on-shell single-particle potential is constructed by means of a complex-valued in-medium loop that includes corrections from a test particle of momentum vector p added to the filled Fermi sea. The single-particle potential U(k f , k f ) at the Fermi surface as obtained from the resummation of the combined particle and hole ladder diagrams is shown to satisfy the Hugenholtz-Van-Hove theorem. The perturbative contributions at various orders a n in the scattering length are deduced and checked against the known analytical results at order a 1 and a 2 . The limit a → ∞ is studied as a special case and a strong momentum dependence of the real (and imaginary) single-particle potential is found. This feature indicates an instability against a phase transition to a state with an empty shell inside the Fermi sphere such that the density gets reduced by about 5%. The imaginary single-particle potential vanishes linearly at the Fermi surface. For comparison, the same analysis is performed for the resummed particle-particle ladder diagrams alone. In this truncation an instability for hole excitations near the Fermi surface is found at strong coupling. For the set of particle-hole ring diagrams the single-particle potential is calculated as well. Furthermore, the resummation of in-medium ladder diagrams to all orders is studied for a two-dimensional Fermi gas with a short-range two-body contact interaction. (orig.)

  14. Implantable bladder volume sensor based on resistor ladder network composed of conductive hydrogel composite.

    Science.gov (United States)

    Mi Kyung Kim; Hyojung Kim; Jung, Yeon Su; Adem, Kenana M A; Bawazir, Sarah S; Stefanini, Cesare; Lee, Hyunjoo J

    2017-07-01

    An accurate bladder volume monitoring system is a critical component in diagnosis and treatment of urological disorders. Here, we report an implantable bladder volume sensor with a multi-level resistor ladder which estimates the bladder volume through discrete resistance values. Discretization allows the sensor output to be resilient to the long-term drift, hysteresis, and degradation of the sensor materials. Our sensor is composed of biocompatible polypyrrole/agarose hydrogel composite. Because Young's modulus of this composite is comparable to that of the bladder wall, the effect of mechanical loading of the sensor on the bladder movement is minimized which allows more accurate volume monitoring. We also demonstrate the patterning and molding capability of this material by fabrication various structures. Lastly, we successfully demonstrate the functionality of the multi-level resistor ladder sensor as a bladder volume sensor by attaching the sensor on the pig's bladder and observing the impedance change of the sensor.

  15. Excitation spectrum of Heisenberg spin ladders

    International Nuclear Information System (INIS)

    Barnes, T.; Dagotto, E.; Riera, J.; Swanson, E.S.

    1993-01-01

    Heisenberg antiferromagnetic spin ''ladders'' (two coupled spin chains) are low-dimensional magnetic systems which for S=1/2 interpolate between half-integer-spin chains, when the chains are decoupled, and effective integer-spin one-dimensional chains in the strong-coupling limit. The spin-1/2 ladder may be realized in nature by vanadyl pyrophosphate, (VO) 2 P 2 O 7 . In this paper we apply strong-coupling perturbation theory, spin-wave theory, Lanczos techniques, and a Monte Carlo method to determine the ground-state energy and the low-lying excitation spectrum of the ladder. We find evidence of a nonzero spin gap for all interchain couplings J perpendicular >0. A band of spin-triplet excitations above the gap is also analyzed. These excitations are unusual for an antiferromagnet, since their long-wavelength dispersion relation behaves as (k-k 0 ) 2 (in the strong-coupling limit J perpendicular much-gt J, where J is the in-chain antiferromagnetic coupling). Their band is folded, with a minimum energy at k 0 =π, and a maximum between k 1 =π/2 (for J perpendicular =0) and 0 (for J perpendicular =∞). We also give numerical results for the dynamical structure factor S(q,ω), which can be determined in neutron scattering experiments. Finally, possible experimental techniques for studying the excitation spectrum are discussed

  16. Non-ladder extended renormalization group analysis of the dynamical chiral symmetry breaking

    Energy Technology Data Exchange (ETDEWEB)

    Aoki, Ken-Ichi; Takagi, Kaoru; Terao, Haruhiko; Tomoyose, Masashi [Kanazawa Univ., Inst. for Theoretical Physics, Kanazawa, Ishikawa (Japan)

    2000-04-01

    The order parameters of dynamical chiral symmetry breaking in QCD, the dynamical mass of quarks and the chiral condensates, are evaluated by numerically solving the non-perturbative renormalization group (NPRG) equations. We employ an approximation scheme beyond 'the ladder', that is, beyond the (improved) ladder Schwinger-Dyson equations. The chiral condensates are enhanced in comparison with the ladder approximation, which is phenomenologically favorable. The gauge dependence of the order parameters is reduced significantly in this scheme. (author)

  17. Non-ladder extended renormalization group analysis of the dynamical chiral symmetry breaking

    International Nuclear Information System (INIS)

    Aoki, Ken-Ichi; Takagi, Kaoru; Terao, Haruhiko; Tomoyose, Masashi

    2000-01-01

    The order parameters of dynamical chiral symmetry breaking in QCD, the dynamical mass of quarks and the chiral condensates, are evaluated by numerically solving the non-perturbative renormalization group (NPRG) equations. We employ an approximation scheme beyond 'the ladder', that is, beyond the (improved) ladder Schwinger-Dyson equations. The chiral condensates are enhanced in comparison with the ladder approximation, which is phenomenologically favorable. The gauge dependence of the order parameters is reduced significantly in this scheme. (author)

  18. Patterning protein complexes on DNA nanostructures using a GFP nanobody.

    Science.gov (United States)

    Sommese, R F; Hariadi, R F; Kim, K; Liu, M; Tyska, M J; Sivaramakrishnan, S

    2016-11-01

    DNA nanostructures have become an important and powerful tool for studying protein function over the last 5 years. One of the challenges, though, has been the development of universal methods for patterning protein complexes on DNA nanostructures. Herein, we present a new approach for labeling DNA nanostructures by functionalizing them with a GFP nanobody. We demonstrate the ability to precisely control protein attachment via our nanobody linker using two enzymatic model systems, namely adenylyl cyclase activity and myosin motility. Finally, we test the power of this attachment method by patterning unpurified, endogenously expressed Arp2/3 protein complex from cell lysate. By bridging DNA nanostructures with a fluorescent protein ubiquitous throughout cell and developmental biology and protein biochemistry, this approach significantly streamlines the application of DNA nanostructures as a programmable scaffold in biological studies. © 2016 The Protein Society.

  19. Laddering em pesquisa de marketing

    Directory of Open Access Journals (Sweden)

    Tânia Modesto Veludo-de-Oliveira

    Full Text Available O artigo discute a técnica de pesquisa laddering em marketing, considerando a proposta de renovação de conhecimentos sobre metodologia na área. Para isso investiga diversos estudos, artigos e pesquisas que tratam do assunto em nível nacional e internacional. O conceito de cadeias meios-fins é abordado pela estrutura teórica que fundamenta a técnica, ligando atributos, conseqüências percebidas do consumo e valores pessoais relativos a um produto. O artigo segue com a explicação dos procedimentos de campo, como a entrevista e a análise dos dados. A laddering é um instrumento de pesquisa qualitativa bastante útil e poderoso, mas ainda pouco utilizado tanto por acadêmicos como por profissionais de mercado, no Brasil, provavelmente por desconhecimento e pouca divulgação. Cabe, portanto, uma maior disseminação de seu uso.

  20. Nested Bethe Ansatz for Spin Ladder Model with Open Boundary Conditions

    International Nuclear Information System (INIS)

    Wu Junfang; Zhang Chunmin; Yue Ruihong; Li Runling

    2005-01-01

    The nested Bethe ansatz (BA) method is applied to find the eigenvalues and the eigenvectors of the transfer matrix for spin-ladder model with open boundary conditions. Based on the reflection equation, we find the general diagonal solution, which determines the general boundary interaction in the Hamiltonian. We introduce the spin-ladder model with open boundary conditions. By finding the solution K ± of the reflection equation which determines the nontrivial boundary terms in the Hamiltonian, we diagonalize the transfer matrix of the spin-ladder model with open boundary conditions in the framework of nested BA.

  1. An in-vitro assessment of the genotoxic impacts of Acid Mine Drainage in the human MCF7 cell line

    CSIR Research Space (South Africa)

    Botha, S

    2012-10-01

    Full Text Available the degree of DNA damage or DNA repair level. The progression of cell death can be further elucidated with the detection of small fragmented DNA particles viewed as an apoptotic laddering pattern. Laddering of highly damaged cell types gives insight... into the type of programmed cell death initiated and clearly establishes when degradation occurs. This study proposes the use of the above described tools as reliable detection mechanisms of genomic impairment and damage in human cell types exposed to AMD...

  2. Environmental influences on DNA curvature

    DEFF Research Database (Denmark)

    Ussery, David; Higgins, C.F.; Bolshoy, A.

    1999-01-01

    DNA curvature plays an important role in many biological processes. To study environmentalinfluences on DNA curvature we compared the anomalous migration on polyacrylamide gels ofligation ladders of 11 specifically-designed oligonucleotides. At low temperatures (25 degreesC and below) most......, whilst spermine enhanced theanomalous migration of a different set of sequences. Sequences with a GGC motif exhibitedgreater curvature than predicted by the presently-used angles for the nearest-neighbour wedgemodel and are especially sensitive to Mg2+. The data have implications for models...... for DNAcurvature and for environmentally-sensitive DNA conformations in the regulation of geneexpression....

  3. Corrosion Control Specialist Career Ladder AFSC 53530, 53550, 53570, and 53690. Occupational Survey Report.

    Science.gov (United States)

    Air Force Occupational Measurement Center, Lackland AFB, TX.

    The report describes the results of a detailed occupational survey of the corrosion control career ladder. Responses to a 457-task, time rating inventory from 1,015 personnel (representing 64 percent of the career field) were analyzed to produce seven specific findings and the career ladder structure. The career ladder includes a variety of jobs…

  4. The chiral Ward-Takahashi identity in the ladder approximation

    International Nuclear Information System (INIS)

    Kugo, Taichiro; Mitchard, M.G.

    1992-01-01

    We show that the ladder approximation to the Schwinger-Dyson and Bethe-Salpeter equations preserves the Ward-Takahashi identity for the axial vector vertex if and only if we use the gluon momentum as the argument of the running coupling constant. However, in the usual Landau gauge this is inconsistent with the vector Ward identity. We propose a new method for making the ladder approximation scheme consistent with both vector and axial vector Ward identities. (orig.)

  5. Ladder physics in the spin fermion model

    Science.gov (United States)

    Tsvelik, A. M.

    2017-05-01

    A link is established between the spin fermion (SF) model of the cuprates and the approach based on the analogy between the physics of doped Mott insulators in two dimensions and the physics of fermionic ladders. This enables one to use nonperturbative results derived for fermionic ladders to move beyond the large-N approximation in the SF model. It is shown that the paramagnon exchange postulated in the SF model has exactly the right form to facilitate the emergence of the fully gapped d -Mott state in the region of the Brillouin zone at the hot spots of the Fermi surface. Hence, the SF model provides an adequate description of the pseudogap.

  6. Ladder physics in the spin fermion model

    International Nuclear Information System (INIS)

    Tsvelik, A. M.

    2017-01-01

    A link is established between the spin fermion (SF) model of the cuprates and the approach based on the analogy between the physics of doped Mott insulators in two dimensions and the physics of fermionic ladders. This enables one to use nonperturbative results derived for fermionic ladders to move beyond the large-N approximation in the SF model. Here, it is shown that the paramagnon exchange postulated in the SF model has exactly the right form to facilitate the emergence of the fully gapped d-Mott state in the region of the Brillouin zone at the hot spots of the Fermi surface. Hence, the SF model provides an adequate description of the pseudogap.

  7. cDNA structure, genomic organization and expression patterns of ...

    African Journals Online (AJOL)

    Visfatin was a newly identified adipocytokine, which was involved in various physiologic and pathologic processes of organisms. The cDNA structure, genomic organization and expression patterns of silver Prussian carp visfatin were described in this report. The silver Prussian carp visfatin cDNA cloned from the liver was ...

  8. Dynamic parameterization and ladder operators for the Kratzer molecular potential

    International Nuclear Information System (INIS)

    Devi, O Babynanda; Singh, C Amuba

    2014-01-01

    Introducing independent parameters k and δ to represent the strength of the attractive and repulsive components, respectively, we write the Kratzer molecular potential as V(k,δ)=(ℏ 2 /2 m)(−k/r+δ(δ−1)/r 2 ). This parameterisation is not only natural, but also convenient for the construction of ladder operators for the system. Adopting the straightforward method of deriving recurrence relations among confluent hypergeometric functions, we construct seven pairs of ladder operators for the Kratzer potential system. Detailed analysis of the laddering actions of these operators is given to show that they connect eigenstates of equal energy but belong to a hierarchy of Kratzer potential systems corresponding to different values of the parameters k and δ. Significantly, it is pointed out that it may not be possible to construct, in the position representation, a ladder operator which would connect different eigenstates belonging to the same potential V(k,δ). Transition to the hydrogen atom case is discussed. A number (14 altogether) of functional relations among the confluent hypergeometric functions have been derived and reported separately in an appendix. (paper)

  9. Estimating Ladder Fuels: A New Approach Combining Field Photography with LiDAR

    Directory of Open Access Journals (Sweden)

    Heather A. Kramer

    2016-09-01

    Full Text Available Forests historically associated with frequent fire have changed dramatically due to fire suppression and past harvesting over the last century. The buildup of ladder fuels, which carry fire from the surface of the forest floor to tree crowns, is one of the critical changes, and it has contributed to uncharacteristically large and severe fires. The abundance of ladder fuels makes it difficult to return these forests to their natural fire regime or to meet management objectives. Despite the importance of ladder fuels, methods for quantifying them are limited and imprecise. LiDAR (Light Detection and Ranging, a form of active remote sensing, is able to estimate many aspects of forest structure across a landscape. This study investigates a new method for quantifying ladder fuel in the field (using photographs with a calibration banner and remotely (using LiDAR data. We apply these new techniques in the Klamath Mountains of Northern California to predict ladder fuel levels across the study area. Our results demonstrate a new utility of LiDAR data to identify fire hazard and areas in need of fuels reduction.

  10. Evaluation through research of a three-track career ladder program for registered nurses.

    Science.gov (United States)

    Korman, Carol; Eliades, Aris Beoglos

    2010-01-01

    A descriptive study design was employed to survey registered nurse participants in a career ladder program comprising of three tracks: clinical, education, and management. Findings indicate that participation allows nurses of varying education preparation and roles to demonstrate professional development. Implications for staff development include efficacy of the online survey technique, provision of a reliable tool to evaluate a career ladder, and evaluation of a career ladder that includes the staff development educator.

  11. Dissipation, Voltage Profile and Levy Dragon in a Special Ladder Network

    Science.gov (United States)

    Ucak, C.

    2009-01-01

    A ladder network constructed by an elementary two-terminal network consisting of a parallel resistor-inductor block in series with a parallel resistor-capacitor block sometimes is said to have a non-dispersive dissipative response. This special ladder network is created iteratively by replacing the elementary two-terminal network in place of the…

  12. Application of DNA Machineries for the Barcode Patterned Detection of Genes or Proteins.

    Science.gov (United States)

    Zhou, Zhixin; Luo, Guofeng; Wulf, Verena; Willner, Itamar

    2018-06-05

    The study introduces an analytical platform for the detection of genes or aptamer-ligand complexes by nucleic acid barcode patterns generated by DNA machineries. The DNA machineries consist of nucleic acid scaffolds that include specific recognition sites for the different genes or aptamer-ligand analytes. The binding of the analytes to the scaffolds initiate, in the presence of the nucleotide mixture, a cyclic polymerization/nicking machinery that yields displaced strands of variable lengths. The electrophoretic separation of the resulting strands provides barcode patterns for the specific detection of the different analytes. Mixtures of DNA machineries that yield, upon sensing of different genes (or aptamer ligands), one-, two-, or three-band barcode patterns are described. The combination of nucleic acid scaffolds acting, in the presence of polymerase/nicking enzyme and nucleotide mixture, as DNA machineries, that generate multiband barcode patterns provide an analytical platform for the detection of an individual gene out of many possible genes. The diversity of genes (or other analytes) that can be analyzed by the DNA machineries and the barcode patterned imaging is given by the Pascal's triangle. As a proof-of-concept, the detection of one of six genes, that is, TP53, Werner syndrome, Tay-Sachs normal gene, BRCA1, Tay-Sachs mutant gene, and cystic fibrosis disorder gene by six two-band barcode patterns is demonstrated. The advantages and limitations of the detection of analytes by polymerase/nicking DNA machineries that yield barcode patterns as imaging readout signals are discussed.

  13. Convergence and periodic solutions for the input impedance of a standard ladder network

    International Nuclear Information System (INIS)

    Ucak, C; Acar, C

    2007-01-01

    The input impedance of an infinite ladder network is computed by using the recursive relation and by assuming that the input impedance does not change when a new block is added to the network. However, this assumption is not true in general and standard textbooks do not always treat these networks correctly. This paper develops a general solution to obtain the input impedance of a standard ladder network of impedances and admittances for any number of blocks. Then, this result is used to provide the convergence condition for the infinite ladder network. The conditions which lead to periodic input impedance are exploited. It is shown that there are infinite numbers of periodic points and no paradoxical behaviour exists in the standard ladder network

  14. A Review and Modern Approach to LC Ladder Synthesis

    Directory of Open Access Journals (Sweden)

    Alexander J. Casson

    2011-01-01

    Full Text Available Ultra low power circuits require robust and reliable operation despite the unavoidable use of low currents and the weak inversion transistor operation region. For analogue domain filtering doubly terminated LC ladder based filter topologies are thus highly desirable as they have very low sensitivities to component values: non-exact component values have a minimal effect on the realised transfer function. However, not all transfer functions are suitable for implementation via a LC ladder prototype, and even when the transfer function is suitable the synthesis procedure is not trivial. The modern circuit designer can thus benefit from an updated treatment of this synthesis procedure. This paper presents a methodology for the design of doubly terminated LC ladder structures making use of the symbolic maths engines in programs such as MATLAB and MAPLE. The methodology is explained through the detailed synthesis of an example 7th order bandpass filter transfer function for use in electroencephalogram (EEG analysis.

  15. Controlled parity switch of persistent currents in quantum ladders

    Science.gov (United States)

    Filippone, Michele; Bardyn, Charles-Edouard; Giamarchi, Thierry

    2018-05-01

    We investigate the behavior of persistent currents for a fixed number of noninteracting fermions in a periodic quantum ladder threaded by Aharonov-Bohm and transverse magnetic fluxes Φ and χ . We show that the coupling between ladder legs provides a way to effectively change the ground-state fermion-number parity, by varying χ . Specifically, we demonstrate that varying χ by 2 π (one flux quantum) leads to an apparent fermion-number parity switch. We find that persistent currents exhibit a robust 4 π periodicity as a function of χ , despite the fact that χ →χ +2 π leads to modifications of order 1 /N of the energy spectrum, where N is the number of sites in each ladder leg. We show that these parity-switch and 4 π periodicity effects are robust with respect to temperature and disorder, and outline potential physical realizations using cold atomic gases and photonic lattices, for bosonic analogs of the effects.

  16. Molecular mechanisms of DNA photodamage

    International Nuclear Information System (INIS)

    Starrs, S.M.

    2000-05-01

    Photodamage in DNA, caused by ultraviolet (UV) light, can occur by direct excitation of the nucleobases or indirectly via the action of photosensitisers. Such, DNA photodamage can be potentially mutagenic or lethal. Among the methods available for detecting UV-induced DNA damage, gel sequencing protocols, utilising synthetic oligodeoxyribonucleotides as targets for UV radiation, allow photolesions to be mapped at nucleotide resolution. This approach has been applied to investigate both DNA damage mechanisms. Following a general overview of DNA photoreactivity, and a description of the main experimental procedures, Chapter 3 identifies the origin of an anomalous mobility shift observed in purine chemical sequence ladders that can confuse the interpretation of DNA cleavage results; measures to abolish this shift are also described. Chapters 4 and 5 examine the alkali-labile DNA damage photosensitised by representative nonsteroidal antiinflammatory drugs (NSAIDs) and the fluoroquinolone antibiotics. Suprofen was the most photoactive NSAID studied, producing different patterns of guanine-specific damage in single-stranded and duplex DNA. Uniform modification of guanine bases, typifying attack by singlet oxygen, was observed in single-stranded oligodeoxyribonucleotides. In duplex molecules, modification was limited to the 5'-G of GG doublets, which is indicative of an electron transfer. The effect of quenchers and photoproduct analysis substantiated these findings. The quinolone, nalidixic acid, behaves similarly. The random base cleavage photosensitised by the fluoroquinolones, has been attributed to free radicals produced during their photodecomposition. Chapter 6 addresses the photoreactivity of purines within unusual DNA structures formed by the repeat sequences (GGA) n and (GA) n , and a minihairpin. There was no definitive evidence for enhanced purine reactivity caused by direct excitation. Finally, Chapter 7 investigates the mutagenic potential of a dimeric

  17. ABC of ladder operators for rationally extended quantum harmonic oscillator systems

    Science.gov (United States)

    Cariñena, José F.; Plyushchay, Mikhail S.

    2017-07-01

    The problem of construction of ladder operators for rationally extended quantum harmonic oscillator (REQHO) systems of a general form is investigated in the light of existence of different schemes of the Darboux-Crum-Krein-Adler transformations by which such systems can be generated from the quantum harmonic oscillator. Any REQHO system is characterized by the number of separated states in its spectrum, the number of ‘valence bands’ in which the separated states are organized, and by the total number of the missing energy levels and their position. All these peculiarities of a REQHO system are shown to be detected and reflected by a trinity (A^+/- , B^+/- , C^+/-) of the basic (primary) lowering and raising ladder operators related between themselves by certain algebraic identities with coefficients polynomially-dependent on the Hamiltonian. We show that all the secondary, higher-order ladder operators are obtainable by a composition of the basic ladder operators of the trinity which form the set of the spectrum-generating operators. Each trinity, in turn, can be constructed from the intertwining operators of the two complementary minimal schemes of the Darboux-Crum-Krein-Adler transformations.

  18. Influence of LET on repair of DNA damages in Deinococcus radiodurans

    Energy Technology Data Exchange (ETDEWEB)

    Kobayashi, Y; Tanaka, A; Kikuchi, M; Shimizu, T; Watanabe, H [Japan Atomic Energy Research Inst., Takasaki, Gunma (Japan). Takasaki Radiation Chemistry Research Establishment; Cao, J P; Taucher-Scholz, G

    1997-03-01

    Inactivation caused by heavy ions was studied in dry cells of radioresistant bacterium Deinococcus radiodurans. All survival curves were characterized by a large shoulder of the curves. No final slopes of the exponential part of survival curves for heavy ion irradiation were steeper than that for 2.0 MeV electron irradiation. The plots of RBE versus LET showed no obvious peaks, suggesting that this bacterium can repair not only DNA double strand breaks (DSBs) but also clustered damage in DNA which may be induced by heavy ions. The genomic DNA of D. radiodurans was cleaved into large fragments with restriction enzyme Not I after post-irradiation incubation and the fragments were separated using pulsed-field gel electrophoresis (PFGE). DSBs induction and rejoining process were analyzed by detection of the reappearance of ladder pattern of DNA fragments. The required repair time after heavy ions irradiation was longer than the repair time for electrons at the same dose of irradiation, however, the rate of repair enzyme induction was almost similar to each other between electrons and heavy ions, suggesting that the same repair system is likely to be used after both low and high LET irradiations. (author)

  19. Studies of Single Biomolecules, DNA Conformational Dynamics, and Protein Binding

    Science.gov (United States)

    2008-07-11

    Nucleotide Base pairs Hydrogen bonds FIG. 1: Ladder structure of DNA showing the Watson - Crick bonding of the bases A, T, G, and C which are suspended by a...protected against unwanted action of chemicals and proteins. The three-dimensional structure of DNA is the famed Watson - Crick double-helix, the equilibrium...quantitative analysis [88]. [1] A. Kornberg and T. A. Baker, DNA Replication (W. H. Freeman, New York, 1992). [2] J. D. Watson and F. H. C. Crick

  20. 29 CFR 1910.27 - Fixed ladders.

    Science.gov (United States)

    2010-07-01

    ...) All rungs shall have a minimum diameter of three-fourths inch for metal ladders, except as covered in... appurtenances shall be painted or otherwise treated to resist corrosion and rusting when location demands... areas under floors, are frequently located in an atmosphere that causes corrosion and rusting. To...

  1. Hadron structure in the ladder model

    International Nuclear Information System (INIS)

    Soper, D.E.

    1979-01-01

    The (flavor non-singlet) Green's function to find a far-off-shell quark in a hadron is obtained in the renormalization group improved ladder model for QCD in the space-like axial gauge. Particular attention is paid to the role of the singularity in the gluon propagator. 4 figures

  2. Laughlin-like States in Bosonic and Fermionic Atomic Synthetic Ladders

    Directory of Open Access Journals (Sweden)

    Marcello Calvanese Strinati

    2017-06-01

    Full Text Available The combination of interactions and static gauge fields plays a pivotal role in our understanding of strongly correlated quantum matter. Cold atomic gases endowed with a synthetic dimension are emerging as an ideal platform to experimentally address this interplay in quasi-one-dimensional systems. A fundamental question is whether these setups can give access to pristine two-dimensional phenomena, such as the fractional quantum Hall effect, and how. We show that unambiguous signatures of bosonic and fermionic Laughlin-like states can be observed and characterized in synthetic ladders. We theoretically diagnose these Laughlin-like states focusing on the chiral current flowing in the ladder, on the central charge of the low-energy theory, and on the properties of the entanglement entropy. Remarkably, Laughlin-like states are separated from conventional liquids by Lifschitz-type transitions, characterized by sharp discontinuities in the current profiles, which we address using extensive simulations based on matrix-product states. Our work provides a qualitative and quantitative guideline towards the observability and understanding of strongly correlated states of matter in synthetic ladders. In particular, we unveil how state-of-the-art experimental settings constitute an ideal starting point to progressively tackle two-dimensional strongly interacting systems from a ladder viewpoint, opening a new perspective for the observation of non-Abelian states of matter.

  3. DUNDRUM Restriction-Intrusion of Liberty Ladders (DRILL) Audit Toolkit

    LENUS (Irish Health Repository)

    Kennedy, Harry G

    2011-09-01

    This series of rating \\'ladders\\' is intended to allow a quantitative and qualitative analysis of the use of restrictive and intrusive interventions as part of the therapeutic management of violence and aggression in psychiatric hospital settings. This is an evolving handbook. The ladders are currently organised to facilitate a behavioural analysis. Context, antecedents, behaviour, interventions, consequences are conceptualised as a series of events organised in temporal sequence so that causes, interactions and effects can be considered. The complexity of analysis possible is limited by the statistical power of the numbers of cases and events available. \\r\

  4. A Continuous Game of Sankes and Ladders

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 14; Issue 8. The Control of Tuberculosis: A Continuous Game of Sankes and Ladders. T Ramakrishnan P Chandrasekhar. Classics Volume 14 Issue 8 August 2009 pp 820-834 ...

  5. Cavity-induced artificial gauge field in a Bose-Hubbard ladder

    Science.gov (United States)

    Halati, Catalin-Mihai; Sheikhan, Ameneh; Kollath, Corinna

    2017-12-01

    We consider theoretically ultracold interacting bosonic atoms confined to quasi-one-dimensional ladder structures formed by optical lattices and coupled to the field of an optical cavity. The atoms can collect a spatial phase imprint during a cavity-assisted tunneling along a rung via Raman transitions employing a cavity mode and a transverse running wave pump beam. By adiabatic elimination of the cavity field we obtain an effective Hamiltonian for the bosonic atoms, with a self-consistency condition. Using the numerical density-matrix renormalization-group method, we obtain a rich steady-state diagram of self-organized steady states. Transitions between superfluid to Mott-insulating states occur, on top of which we can have Meissner, vortex liquid, and vortex lattice phases. Also a state that explicitly breaks the symmetry between the two legs of the ladder, namely, the biased-ladder phase, is dynamically stabilized. We investigate the influence that a trapping potential has on the stability of the self-organized phases.

  6. Estimating ladder fuels: a new approach combining field photography with LiDAR

    Science.gov (United States)

    Heather Kramer; Brandon Collins; Frank Lake; Marek Jakubowski; Scott Stephens; Maggi Kelly

    2016-01-01

    Forests historically associated with frequent fire have changed dramatically due to fire suppression and past harvesting over the last century. The buildup of ladder fuels, which carry fire from the surface of the forest floor to tree crowns, is one of the critical changes, and it has contributed to uncharacteristically large and severe fires. The abundance of ladder...

  7. T-DNA integration patterns in transgenic maize lines mediated by ...

    African Journals Online (AJOL)

    These results demonstrate that cleavage occurs not only during the T-DNA borders but also inside or outside the borders. The border sequences and some inside sequences can be deleted, and filler sequences can be inserted. Illegitimate recombination is a major pattern of T-DNA integration, while some hot spots and ...

  8. Quantum entanglement and thermal reduced density matrices in fermion and spin systems on ladders

    International Nuclear Information System (INIS)

    Chen, Xiao; Fradkin, Eduardo

    2013-01-01

    Numerical studies of the reduced density matrix of a gapped spin-1/2 Heisenberg antiferromagnet on a two-leg ladder find that it has the same form as the Gibbs density matrix of a gapless spin-1/2 Heisenberg antiferromagnetic chain at a finite temperature determined by the spin gap of the ladder. We investigate this interesting result by considering a model of free fermions on a two-leg ladder (gapped by the inter-chain tunneling operator) and in spin systems on a ladder with a gapped ground state using exact solutions and several controlled approximations. We calculate the reduced density matrix and the entanglement entropy for a leg of the ladder (i.e. a cut made between the chains). In the fermionic system we find the exact form of the reduced density matrix for one of the chains and determine the entanglement spectrum explicitly. Here we find that in the weak tunneling limit of the ladder the entanglement entropy of one chain of the gapped ladder has a simple and universal form dictated by conformal invariance. In the case of the spin system, we consider the strong coupling limit by using perturbation theory and get the reduced density matrix by the Schmidt decomposition. The entanglement entropies of a general gapped system of two coupled conformal field theories (in 1 + 1 dimensions) are discussed using the replica trick and scaling arguments. We show that (1) for a system with a bulk gap the reduced density matrix has the form of a thermal density matrix, (2) the long-wavelength modes of one subsystem (a chain) of a gapped coupled system are always thermal, (3) the von Neumann entropy equals the thermodynamic entropy of one chain, and (4) the bulk gap plays the role of effective temperature. (paper)

  9. Strength Analysis on Ship Ladder Using Finite Element Method

    Science.gov (United States)

    Budianto; Wahyudi, M. T.; Dinata, U.; Ruddianto; Eko P., M. M.

    2018-01-01

    In designing the ship’s structure, it should refer to the rules in accordance with applicable classification standards. In this case, designing Ladder (Staircase) on a Ferry Ship which is set up, it must be reviewed based on the loads during ship operations, either during sailing or at port operations. The classification rules in ship design refer to the calculation of the structure components described in Classification calculation method and can be analysed using the Finite Element Method. Classification Regulations used in the design of Ferry Ships used BKI (Bureau of Classification Indonesia). So the rules for the provision of material composition in the mechanical properties of the material should refer to the classification of the used vessel. The analysis in this structure used program structure packages based on Finite Element Method. By using structural analysis on Ladder (Ladder), it obtained strength and simulation structure that can withstand load 140 kg both in static condition, dynamic, and impact. Therefore, the result of the analysis included values of safety factors in the ship is to keep the structure safe but the strength of the structure is not excessive.

  10. Triptycene-based ladder monomers and polymers, methods of making each, and methods of use

    KAUST Repository

    Pinnau, Ingo; Ghanem, Bader; Swaidan, Raja

    2015-01-01

    Embodiments of the present disclosure provide for a triptycene-based A-B monomer, a method of making a triptycene-based A-B monomer, a triptycene-based ladder polymer, a method of making a triptycene-based ladder polymers, a method of using

  11. Using career ladders to motivate and retain employees: an implementation success story.

    Science.gov (United States)

    Garletts, Joseph A

    2002-01-01

    In October 2000, Phoenix-based Sonora Quest Laboratories, LLC (SQL), commissioned The Gelfond Group to survey SQL employees. Responding to negative survey scores, SQL developed and implemented an entry-level career ladder for line staff of the specimen management/referral testing department. The program was piloted in February 2001, and was implemented fully shortly thereafter. The ladder was designed to provide job enrichment opportunities through company-conducted training and advancement provisions. It contained requirements for productivity and quality of work performed in addition to increasingly rigorous training and competency documentation. Employees were accountable for their own advancement and for ensuring that all documentation was complete. Advancement was automatic once requirements were completed. Pay increases accompanied each advancement on a predetermined scale. At the end of 12 months, employee turnover dropped from 39% to less than 20% annually. Both productivity and morale improved, and results on a second employee survey indicated dramatic improvement in five key areas. The career ladder concept has been replicated successfully in several other departments, including phlebotomy, and a six-tiered ladder is under development for the clinical laboratory. It will encompass CLA, MLT, and MT positions from entry level to technical coordinator.

  12. Design Pattern Mining Using Distributed Learning Automata and DNA Sequence Alignment

    Science.gov (United States)

    Esmaeilpour, Mansour; Naderifar, Vahideh; Shukur, Zarina

    2014-01-01

    Context Over the last decade, design patterns have been used extensively to generate reusable solutions to frequently encountered problems in software engineering and object oriented programming. A design pattern is a repeatable software design solution that provides a template for solving various instances of a general problem. Objective This paper describes a new method for pattern mining, isolating design patterns and relationship between them; and a related tool, DLA-DNA for all implemented pattern and all projects used for evaluation. DLA-DNA achieves acceptable precision and recall instead of other evaluated tools based on distributed learning automata (DLA) and deoxyribonucleic acid (DNA) sequences alignment. Method The proposed method mines structural design patterns in the object oriented source code and extracts the strong and weak relationships between them, enabling analyzers and programmers to determine the dependency rate of each object, component, and other section of the code for parameter passing and modular programming. The proposed model can detect design patterns better that available other tools those are Pinot, PTIDEJ and DPJF; and the strengths of their relationships. Results The result demonstrate that whenever the source code is build standard and non-standard, based on the design patterns, then the result of the proposed method is near to DPJF and better that Pinot and PTIDEJ. The proposed model is tested on the several source codes and is compared with other related models and available tools those the results show the precision and recall of the proposed method, averagely 20% and 9.6% are more than Pinot, 27% and 31% are more than PTIDEJ and 3.3% and 2% are more than DPJF respectively. Conclusion The primary idea of the proposed method is organized in two following steps: the first step, elemental design patterns are identified, while at the second step, is composed to recognize actual design patterns. PMID:25243670

  13. Design pattern mining using distributed learning automata and DNA sequence alignment.

    Directory of Open Access Journals (Sweden)

    Mansour Esmaeilpour

    Full Text Available CONTEXT: Over the last decade, design patterns have been used extensively to generate reusable solutions to frequently encountered problems in software engineering and object oriented programming. A design pattern is a repeatable software design solution that provides a template for solving various instances of a general problem. OBJECTIVE: This paper describes a new method for pattern mining, isolating design patterns and relationship between them; and a related tool, DLA-DNA for all implemented pattern and all projects used for evaluation. DLA-DNA achieves acceptable precision and recall instead of other evaluated tools based on distributed learning automata (DLA and deoxyribonucleic acid (DNA sequences alignment. METHOD: The proposed method mines structural design patterns in the object oriented source code and extracts the strong and weak relationships between them, enabling analyzers and programmers to determine the dependency rate of each object, component, and other section of the code for parameter passing and modular programming. The proposed model can detect design patterns better that available other tools those are Pinot, PTIDEJ and DPJF; and the strengths of their relationships. RESULTS: The result demonstrate that whenever the source code is build standard and non-standard, based on the design patterns, then the result of the proposed method is near to DPJF and better that Pinot and PTIDEJ. The proposed model is tested on the several source codes and is compared with other related models and available tools those the results show the precision and recall of the proposed method, averagely 20% and 9.6% are more than Pinot, 27% and 31% are more than PTIDEJ and 3.3% and 2% are more than DPJF respectively. CONCLUSION: The primary idea of the proposed method is organized in two following steps: the first step, elemental design patterns are identified, while at the second step, is composed to recognize actual design patterns.

  14. Design pattern mining using distributed learning automata and DNA sequence alignment.

    Science.gov (United States)

    Esmaeilpour, Mansour; Naderifar, Vahideh; Shukur, Zarina

    2014-01-01

    Over the last decade, design patterns have been used extensively to generate reusable solutions to frequently encountered problems in software engineering and object oriented programming. A design pattern is a repeatable software design solution that provides a template for solving various instances of a general problem. This paper describes a new method for pattern mining, isolating design patterns and relationship between them; and a related tool, DLA-DNA for all implemented pattern and all projects used for evaluation. DLA-DNA achieves acceptable precision and recall instead of other evaluated tools based on distributed learning automata (DLA) and deoxyribonucleic acid (DNA) sequences alignment. The proposed method mines structural design patterns in the object oriented source code and extracts the strong and weak relationships between them, enabling analyzers and programmers to determine the dependency rate of each object, component, and other section of the code for parameter passing and modular programming. The proposed model can detect design patterns better that available other tools those are Pinot, PTIDEJ and DPJF; and the strengths of their relationships. The result demonstrate that whenever the source code is build standard and non-standard, based on the design patterns, then the result of the proposed method is near to DPJF and better that Pinot and PTIDEJ. The proposed model is tested on the several source codes and is compared with other related models and available tools those the results show the precision and recall of the proposed method, averagely 20% and 9.6% are more than Pinot, 27% and 31% are more than PTIDEJ and 3.3% and 2% are more than DPJF respectively. The primary idea of the proposed method is organized in two following steps: the first step, elemental design patterns are identified, while at the second step, is composed to recognize actual design patterns.

  15. An Efficient Approach to Mining Maximal Contiguous Frequent Patterns from Large DNA Sequence Databases

    Directory of Open Access Journals (Sweden)

    Md. Rezaul Karim

    2012-03-01

    Full Text Available Mining interesting patterns from DNA sequences is one of the most challenging tasks in bioinformatics and computational biology. Maximal contiguous frequent patterns are preferable for expressing the function and structure of DNA sequences and hence can capture the common data characteristics among related sequences. Biologists are interested in finding frequent orderly arrangements of motifs that are responsible for similar expression of a group of genes. In order to reduce mining time and complexity, however, most existing sequence mining algorithms either focus on finding short DNA sequences or require explicit specification of sequence lengths in advance. The challenge is to find longer sequences without specifying sequence lengths in advance. In this paper, we propose an efficient approach to mining maximal contiguous frequent patterns from large DNA sequence datasets. The experimental results show that our proposed approach is memory-efficient and mines maximal contiguous frequent patterns within a reasonable time.

  16. Molecular mechanisms of DNA photodamage

    Energy Technology Data Exchange (ETDEWEB)

    Starrs, S.M

    2000-05-01

    Photodamage in DNA, caused by ultraviolet (UV) light, can occur by direct excitation of the nucleobases or indirectly via the action of photosensitisers. Such, DNA photodamage can be potentially mutagenic or lethal. Among the methods available for detecting UV-induced DNA damage, gel sequencing protocols, utilising synthetic oligodeoxyribonucleotides as targets for UV radiation, allow photolesions to be mapped at nucleotide resolution. This approach has been applied to investigate both DNA damage mechanisms. Following a general overview of DNA photoreactivity, and a description of the main experimental procedures, Chapter 3 identifies the origin of an anomalous mobility shift observed in purine chemical sequence ladders that can confuse the interpretation of DNA cleavage results; measures to abolish this shift are also described. Chapters 4 and 5 examine the alkali-labile DNA damage photosensitised by representative nonsteroidal antiinflammatory drugs (NSAIDs) and the fluoroquinolone antibiotics. Suprofen was the most photoactive NSAID studied, producing different patterns of guanine-specific damage in single-stranded and duplex DNA. Uniform modification of guanine bases, typifying attack by singlet oxygen, was observed in single-stranded oligodeoxyribonucleotides. In duplex molecules, modification was limited to the 5'-G of GG doublets, which is indicative of an electron transfer. The effect of quenchers and photoproduct analysis substantiated these findings. The quinolone, nalidixic acid, behaves similarly. The random base cleavage photosensitised by the fluoroquinolones, has been attributed to free radicals produced during their photodecomposition. Chapter 6 addresses the photoreactivity of purines within unusual DNA structures formed by the repeat sequences (GGA){sub n} and (GA){sub n}, and a minihairpin. There was no definitive evidence for enhanced purine reactivity caused by direct excitation. Finally, Chapter 7 investigates the mutagenic potential of a

  17. One-particle versus two-particle crossover in weakly coupled Hubbard chains and ladders: perturbative renormalization group approach

    International Nuclear Information System (INIS)

    Kishine, Jun-Ichiro; Yonemitsu, Kenji

    1998-01-01

    Physical nature of dimensional crossovers in weakly coupled Hubbard chains and ladders has been discussed within the framework of the perturbative renormalization-group (PRG) approach. The difference between these two cases originates from different universality classes which the corresponding isolated systems belong to. In the present work, we discuss the nature of the dimensional crossovers in the weakly coupled chains and ladders, with emphasis on the difference between the two cases within the framework of the PRG approach. The difference of the universality class of the isolated chain and ladder profoundly affects the relevance or irrelevance of the inter-chain/ladder one-particle hopping. The strong coupling phase of the isolated ladder makes the one-particle process irrelevant so that the d-wave superconducting transition can be induced via the two-particle crossover in the weakly coupled ladders. The weak coupling phase of the isolated chain makes the one-particle process relevant so that the two-particle crossover can hardly be realized in the coupled chains. (Copyright (1998) World Scientific Publishing Co. Pte. Ltd)

  18. Construction and test of the first Belle II SVD ladder implementing the origami chip-on-sensor design

    International Nuclear Information System (INIS)

    Irmler, C.; Bauer, A.; Bergauer, T.; Adamczyk, K.; Bacher, S.; Aihara, H.; Angelini, C.; Batignani, G.; Bettarini, S.; Bosi, F.; Aziz, T.; Babu, V.; Bahinipati, S.; Barberio, E.; Baroncelli, Ti.; Baroncelli, To.; Basith, A.K.; Behera, P.K.; Bhuyan, B.; Bilka, T.

    2016-01-01

    The Belle II Silicon Vertex Detector comprises four layers of double-sided silicon strip detectors (DSSDs), consisting of ladders with two to five sensors each. All sensors are individually read out by APV25 chips with the Origami chip-on-sensor concept for the central DSSDs of the ladders. The chips sit on flexible circuits that are glued on the top of the sensors. This concept allows a low material budget and an efficient cooling of the chips by a single pipe per ladder. We present the construction of the first SVD ladders and results from precision measurements and electrical tests

  19. Fermion-boson scattering in ladder approximation

    International Nuclear Information System (INIS)

    Jafarov, R.G.; Hadjiev, S.A.

    1992-10-01

    A method of calculation of forward scattering amplitude for fermions and scalar bosons with exchanging of scalar particle is suggested. The Bethe-Salpeter ladder equation for the imaginary part of the amplitude is constructed and a solution in Regge asymptotical form is found and the corrections to the amplitude due to the exit from mass shell are calculated. (author). 8 refs

  20. The laddering method in service innovation research

    DEFF Research Database (Denmark)

    Grünbaum, Niels Nolsøe

    2017-01-01

    The laddering method is a qualitative interview technique applied in a situation with one interviewer and one informant with the aim of creating an understanding of the value that business-to-consumer (B2C) customers extract from product attributes. Thus, this methodology aims to depict a mental ...

  1. A robustification of the chain-ladder method

    NARCIS (Netherlands)

    Verdonck, T.; van Wouwe, M.; Dhaene, J.

    2009-01-01

    In a non-life insurance business an insurer often needs to build up a reserve to able to meet his or her future obligations arising from incurred but not reported completely claims. To forecast these claims reserves, a simple but generally accepted algorithm is the classical chain-ladder method.

  2. Doped spin ladders under magnetic field; Echelles de spins dopees sous champ magnetique

    Energy Technology Data Exchange (ETDEWEB)

    Roux, G

    2007-07-15

    This thesis deals with the physics of doped two-leg ladders which are a quasi one-dimensional and unconventional superconductor. We particularly focus on the properties under magnetic field. Models for strongly correlated electrons on ladders are studied using exact diagonalization and density-matrix renormalization group (DMRG). Results are also enlightened by using the bosonization technique. Taking into account a ring exchange it highlights the relation between the pairing of holes and the spin gap. Its influence on the dynamics of the magnetic fluctuations is also tackled. Afterwards, these excitations are probed by the magnetic field by coupling it to the spin degree of freedom of the electrons through Zeeman effect. We show the existence of doping-dependent magnetization plateaus and also the presence of an inhomogeneous superconducting phase (FFLO phase) associated with an exceeding of the Pauli limit. When a flux passes through the ladder, the magnetic field couples to the charge degree of freedom of the electrons via orbital effect. The diamagnetic response of the doped ladder probes the commensurate phases of the t-J model at low J/t. Algebraic transverse current fluctuations are also found once the field is turned on. Lastly, we report numerical evidences of a molecular superfluid phase in the 3/2-spin attractive Hubbard model: at a density low enough, bound states of four fermions, called quartets, acquire dominant superfluid fluctuations. The observed competition between the superfluid and density fluctuations is connected to the physics of doped ladders. (author)

  3. Utilization of the fish ladder at the Engenheiro Sergio Motta Dam, Brazil, by long distance migrating potamodromous species

    Directory of Open Access Journals (Sweden)

    Sérgio Makrakis

    Full Text Available Utilization of the fish ladder installed at the Engenheiro Sergio Motta Dam (also known as Porto Primavera on the Paraná River, Southern Brazil, by long-distance migrating potamodromous species (sampling Protocol I, and ascending and descending movements (Protocol II were evaluated. Three pools along the fish ladder (designated as lower, middle, and upper were sampled monthly between December, 2004 and March, 2005 to determine the abundance of species in the ladder. The ascending and descending movements of the species in the ladder were also analyzed in the same period. In the samples for both protocols, 37 species representing 17 families and 5 orders (Characiformes, Siluriformes, Perciformes, Gymnotiformes, and Myliobatiformes were recorded. Characiformes were represented by 21 species. Long- distance migratory species (11 species predominated in the ladder (60% of the total number of individuals, with high abundance of Rhinelepis aspera (5645 individuals. For protocol I, mean abundance varied greatly among the months and pools, with lowest values in December and March for all pools, and highest in January for the lower pool due to high capture of R. aspera. Fish abundance declined from the lower to the upper pool, especially for R. aspera and Rhaphiodon vulpinus. For Protocol II, 17 species were recorded ascending the ladder, where Astyanax altiparanae and Leporinus friderici were the most abundant species (684 and 111 individuals, respectively. However, 18 species showed descending movements, with high captures of Metynnis maculatus and A. altiparanae (339 and 319 individuals, respectively. Twelve species (52% moved in both directions, and among the seven migratory species sampled, four were recorded ascending and descending, and three species only ascending the ladder. The fish ladder appears to selectively favor species with high swimming capabilities. A discussion is presented on the requirements for future research on attraction to the

  4. Adaptation of a ladder beam walking task to assess locomotor recovery in mice following spinal cord injury

    Science.gov (United States)

    Cummings, Brian J.; Engesser-Cesar, Christie; Anderson, Aileen J.

    2007-01-01

    Locomotor impairments after spinal cord injury (SCI) are often assessed using open-field rating scales. These tasks have the advantage of spanning the range from complete paralysis to normal walking; however, they lack sensitivity at specific levels of recovery. Additionally, most supplemental assessments were developed in rats, not mice. For example, the horizontal ladder beam has been used to measure recovery in the rat after SCI. This parametric task results in a videotaped archival record of the event, is easily administered, and is unambiguously scored. Although a ladder beam apparatus for mice is available, its use in the assessment of recovery in SCI mice is rare, possibly because normative data for uninjured mice and the type of step misplacements injured mice exhibit is lacking. We report the development of a modified ladder beam instrument and scoring system to measure hindlimb recovery in vertebral T9 contusion spinal cord injured mice. The mouse ladder beam allows for the use of standard parametric statistical tests to assess locomotor recovery. Ladder beam performance is consistent across four strains of mice, there are no sex differences, and inter-rater reliability between observers is high. The ladder beam score is proportional to injury severity and can be used to easily separate mice capable of weight-supported stance up to mice with consistent forelimb to hindlimb coordination. Critically, horizontal ladder beam testing discriminates between mice that score identically in terms of stepping frequency in open-field testing. PMID:17197044

  5. Adaptation of a ladder beam walking task to assess locomotor recovery in mice following spinal cord injury.

    Science.gov (United States)

    Cummings, Brian J; Engesser-Cesar, Christie; Cadena, Gilbert; Anderson, Aileen J

    2007-02-27

    Locomotor impairments after spinal cord injury (SCI) are often assessed using open-field rating scales. These tasks have the advantage of spanning the range from complete paralysis to normal walking; however, they lack sensitivity at specific levels of recovery. Additionally, most supplemental assessments were developed in rats, not mice. For example, the horizontal ladder beam has been used to measure recovery in the rat after SCI. This parametric task results in a videotaped archival record of the event, is easily administered, and is unambiguously scored. Although a ladder beam apparatus for mice is available, its use in the assessment of recovery in SCI mice is rare, possibly because normative data for uninjured mice and the type of step misplacements injured mice exhibit is lacking. We report the development of a modified ladder beam instrument and scoring system to measure hindlimb recovery in vertebral T9 contusion spinal cord injured mice. The mouse ladder beam allows for the use of standard parametric statistical tests to assess locomotor recovery. Ladder beam performance is consistent across four strains of mice, there are no sex differences, and inter-rater reliability between observers is high. The ladder beam score is proportional to injury severity and can be used to easily separate mice capable of weight-supported stance up to mice with consistent forelimb to hindlimb coordination. Critically, horizontal ladder beam testing discriminates between mice that score identically in terms of stepping frequency in open-field testing.

  6. DNA methylation patterns in cord blood DNA and body size in childhood.

    Directory of Open Access Journals (Sweden)

    Caroline L Relton

    Full Text Available Epigenetic markings acquired in early life may have phenotypic consequences later in development through their role in transcriptional regulation with relevance to the developmental origins of diseases including obesity. The goal of this study was to investigate whether DNA methylation levels at birth are associated with body size later in childhood.A study design involving two birth cohorts was used to conduct transcription profiling followed by DNA methylation analysis in peripheral blood. Gene expression analysis was undertaken in 24 individuals whose biological samples and clinical data were collected at a mean ± standard deviation (SD age of 12.35 (0.95 years, the upper and lower tertiles of body mass index (BMI were compared with a mean (SD BMI difference of 9.86 (2.37 kg/m(2. This generated a panel of differentially expressed genes for DNA methylation analysis which was then undertaken in cord blood DNA in 178 individuals with body composition data prospectively collected at a mean (SD age of 9.83 (0.23 years. Twenty-nine differentially expressed genes (>1.2-fold and p<10(-4 were analysed to determine DNA methylation levels at 1-3 sites per gene. Five genes were unmethylated and DNA methylation in the remaining 24 genes was analysed using linear regression with bootstrapping. Methylation in 9 of the 24 (37.5% genes studied was associated with at least one index of body composition (BMI, fat mass, lean mass, height at age 9 years, although only one of these associations remained after correction for multiple testing (ALPL with height, p(Corrected = 0.017.DNA methylation patterns in cord blood show some association with altered gene expression, body size and composition in childhood. The observed relationship is correlative and despite suggestion of a mechanistic epigenetic link between in utero life and later phenotype, further investigation is required to establish causality.

  7. Role of minor groove width and hydration pattern on amsacrine interaction with DNA.

    Directory of Open Access Journals (Sweden)

    Deepak K Jangir

    Full Text Available Amsacrine is an anilinoacridine derivative anticancer drug, used to treat a wide variety of malignancies. In cells, amsacrine poisons topoisomerase 2 by stabilizing DNA-drug-enzyme ternary complex. Presence of amsacrine increases the steady-state concentration of these ternary complexes which in turn hampers DNA replication and results in subsequent cell death. Due to reversible binding and rapid slip-out of amsacrine from DNA duplex, structural data is not available on amsacrine-DNA complexes. In the present work, we designed five oligonucleotide duplexes, differing in their minor groove widths and hydration pattern, and examined their binding with amsacrine using attenuated total reflection Fourier transform infrared (ATR-FTIR spectroscopy. Complexes of amsacrine with calf thymus DNA were also evaluated for a comparison. Our results demonstrate for the first time that amsacrine is not a simple intercalator; rather mixed type of DNA binding (intercalation and minor groove takes place between amsacrine and DNA. Further, this binding is highly sensitive towards the geometries and hydration patterns of different minor grooves present in the DNA. This study shows that ligand binding to DNA could be very sensitive to DNA base composition and DNA groove structures. Results demonstrated here could have implication for understanding cytotoxic mechanism of aminoacridine based anticancer drugs and provide directions to modify these drugs for better efficacy and few side-effects.

  8. Fish ladder of Lajeado Dam: migrations on one-way routes?

    Directory of Open Access Journals (Sweden)

    Angelo Antônio Agostinho

    Full Text Available Fish ladders are generally conceived to reestablish connectivity among critical habitats for migratory species, thus mitigating the impacts of the blockage of migration routes by dams. If this management tool is to be meaningful for conserving fish species, it must provide a fully permeable connection and assure both upward and downward movements. However, because reservoirs have very different hydrodynamics than the original river, it is expected that, at least in the inner area, they may constitute an additional barrier to this movement, especially for descending fish. Thus, the present study sought to determine if migratory fish and their offspring disperse downstream from the dam after ascending a ladder and spawning in the upper reaches of a basin. To achieve this purpose, we evaluated the limitation imposed by lentic areas to the descent of eggs, larvae and adults of migratory species; we also determined the abundance and composition of larvae present in the plankton near the dam, and compared the intensity of the upward and downward movements of adult fish. Samples of ichthyoplankton were taken upriver, inside the reservoir, in the river downstream from the dam, and in the forebay of the Lajeado Dam on the Tocantins River (Luis Eduardo Magalhães Hydroelectric Plant, from October, 1999 through September, 2004. The densities of fish ascending and descending the ladder were determined experimentally on eight occasions, from June, 2004 to March, 2005. Due to difficulties in identifying the true fish origin (up or down in the environments connected by the fish passage system, the evaluation of the distribution of migratory fish in reservoirs was based on the landings of the commercial fishery conducted along the Itaipu Reservoir during the four years preceding (2001 through 2003 the construction of the lateral channel (fish-passage mechanism. Fish eggs and larvae drifting down the Tocantins River did not appear in samples taken in the lower

  9. 49 CFR 214.519 - Floors, decks, stairs, and ladders of on-track roadway maintenance machines.

    Science.gov (United States)

    2010-10-01

    ... roadway maintenance machines. 214.519 Section 214.519 Transportation Other Regulations Relating to... SAFETY On-Track Roadway Maintenance Machines and Hi-Rail Vehicles § 214.519 Floors, decks, stairs, and ladders of on-track roadway maintenance machines. Floors, decks, stairs, and ladders of on-track roadway...

  10. Explaining choice option attractiveness by beliefs elicited by the laddering method

    DEFF Research Database (Denmark)

    Grunert, Klaus G.; Bech-Larsen, Tino

    2005-01-01

    option. The laddering method is used to elicit beliefs of all three types for a choice between conventional and organic pork. As a benchmark, beliefs were also elicited in the traditional way advocated by Ajzen and Fishbein. Using both sets of beliefs in a subsequent survey, it was shown that the beliefs...... elicited by the laddering method increase explanatory power with regard to choice option attractiveness beyond the beliefs elicited by the Ajzen and Fishbein method, and that this additional explanatory power was due to those beliefs which relate the choice option to concepts with a higher level...

  11. Phase diagram of a bosonic ladder with two coupled chains

    International Nuclear Information System (INIS)

    Luthra, Meetu Sethi; Mishra, Tapan; Pai, Ramesh V.; Das, B. P.

    2008-01-01

    We study a bosonic ladder with two coupled chains using the finite-size density-matrix renormalization group method. We show that in a commensurate bosonic ladder the critical on-site interaction (U C ) for the superfluid to Mott insulator transition gets larger as the interchain hopping (t perpendicular ) increases. We analyze this quantum phase transition and obtain the phase diagram in the t perpendicular -U plane. We also consider the asymmetric case where the on-site interactions are different in the two chains and have shown that the system as a whole will not be in the Mott insulator phase unless both the chains have on-site interactions greater than the critical value

  12. The search for competing charge orders in frustrated ladder systems

    International Nuclear Information System (INIS)

    Lal, Siddhartha; Laad, Mukul S.

    2007-08-01

    A recent study revealed the dynamics of the charge sector of a one-dimensional quarter- filled electronic system with extended Hubbard interactions to be that of an effective pseudospin transverse-field Ising model (TFIM) in the strong coupling limit. With the twin motivations of studying the co-existing charge and spin order found in strongly correlated chain systems and the effects of inter-chain couplings, we investigate the phase diagram of coupled effective (TFIM) systems. A bosonisation and RG analysis for a two-leg TFIM ladder yields a rich phase diagram showing Wigner/Peierls charge order and Neel/dimer spin order. In a broad parameter regime, the orbital antiferromagnetic phase is found to be stable. An intermediate gapless phase of finite width is found to lie in between two charge-ordered gapped phases. Kosterlitz-Thouless transitions are found to lead from the gapless phase to either of the charge-ordered phases. Low energy effective Hamiltonian analyses of a strongly coupled 2-chain ladder system confirm a phase diagram with in-chain CO, rung-dimer, and orbital antiferromagnetic ordered phases with varying interchain couplings as well as superconductivity upon hole-doping. Our work is potentially relevant for a unified description of a class of strongly correlated, quarter-filled chain and ladder systems. (autor)

  13. Action–angle variables, ladder operators and coherent states

    International Nuclear Information System (INIS)

    Campoamor-Stursberg, R.; Gadella, M.; Kuru, Ş.; Negro, J.

    2012-01-01

    This Letter is devoted to the building of coherent states from arguments based on classical action–angle variables. First, we show how these classical variables are associated to an algebraic structure in terms of Poisson brackets. In the quantum context these considerations are implemented by ladder type operators and a structure known as spectrum generating algebra. All this allows to generate coherent states and thereby the correspondence of classical–quantum properties by means of the aforementioned underlying structure. This approach is illustrated with the example of the one-dimensional Pöschl–Teller potential system. -- Highlights: ► We study the building of coherent states from classical action–angle variables arguments. ► The classical variables are associated to an algebraic structure in terms of Poisson brackets. ► In the quantum context these considerations are implemented by ladder type operators. ► All this allows to formulate coherent states and the correspondence of classical–quantum properties.

  14. Resonance self-shielding calculation with regularized random ladders

    Energy Technology Data Exchange (ETDEWEB)

    Ribon, P.

    1986-01-01

    The straightforward method for calculation of resonance self-shielding is to generate one or several resonance ladders, and to process them as resolved resonances. The main drawback of Monte Carlo methods used to generate the ladders, is the difficulty of reducing the dispersion of data and results. Several methods are examined, and it is shown how one (a regularized sampling method) improves the accuracy. Analytical methods to compute the effective cross-section have recently appeared: they are basically exempt from dispersion, but are inevitably approximate. The accuracy of the most sophisticated one is checked. There is a neutron energy range which is improperly considered as statistical. An examination is presented of what happens when it is treated as statistical, and how it is possible to improve the accuracy of calculations in this range. To illustrate the results calculations have been performed in a simple case: nucleus /sup 238/U, at 300 K, between 4250 and 4750 eV.

  15. Dynamics of blood flow and thrombus formation in a multi-bypass microfluidic ladder network.

    Science.gov (United States)

    Zilberman-Rudenko, Jevgenia; Sylman, Joanna L; Lakshmanan, Hari H S; McCarty, Owen J T; Maddala, Jeevan

    2017-02-01

    The reaction dynamics of a complex mixture of cells and proteins, such as blood, in branched circulatory networks within the human microvasculature or extravascular therapeutic devices such as extracorporeal oxygenation machine (ECMO) remains ill-defined. In this report we utilize a multi-bypass microfluidics ladder network design with dimensions mimicking venules to study patterns of blood platelet aggregation and fibrin formation under complex shear. Complex blood fluid dynamics within multi-bypass networks under flow were modeled using COMSOL. Red blood cells and platelets were assumed to be non-interacting spherical particles transported by the bulk fluid flow, and convection of the activated coagulation factor II, thrombin, was assumed to be governed by mass transfer. This model served as the basis for predicting formation of local shear rate gradients, stagnation points and recirculation zones as dictated by the bypass geometry. Based on the insights from these models, we were able to predict the patterns of blood clot formation at specific locations in the device. Our experimental data was then used to adjust the model to account for the dynamical presence of thrombus formation in the biorheology of blood flow. The model predictions were then compared to results from experiments using recalcified whole human blood. Microfluidic devices were coated with the extracellular matrix protein, fibrillar collagen, and the initiator of the extrinsic pathway of coagulation, tissue factor. Blood was perfused through the devices at a flow rate of 2 µL/min, translating to physiologically relevant initial shear rates of 300 and 700 s -1 for main channels and bypasses, respectively. Using fluorescent and light microscopy, we observed distinct flow and thrombus formation patterns near channel intersections at bypass points, within recirculation zones and at stagnation points. Findings from this proof-of-principle ladder network model suggest a specific correlation between

  16. Helicobacter pylori Infection Causes Characteristic DNA Damage Patterns in Human Cells

    Directory of Open Access Journals (Sweden)

    Max Koeppel

    2015-06-01

    Full Text Available Infection with the human pathogen Helicobacter pylori (H. pylori is a major risk factor for gastric cancer. Since the bacterium exerts multiple genotoxic effects, we examined the circumstances of DNA damage accumulation and identified regions within the host genome with high susceptibility to H. pylori-induced damage. Infection impaired several DNA repair factors, the extent of which depends on a functional cagPAI. This leads to accumulation of a unique DNA damage pattern, preferentially in transcribed regions and proximal to telomeres, in both gastric cell lines and primary gastric epithelial cells. The observed pattern correlates with focal amplifications in adenocarcinomas of the stomach and partly overlaps with known cancer genes. We thus demonstrate an impact of a bacterial infection directed toward specific host genomic regions and describe underlying characteristics that make such regions more likely to acquire heritable changes during infection, which could contribute to cellular transformation.

  17. Crystal structure and thin film morphology of BBL ladder polymer

    Energy Technology Data Exchange (ETDEWEB)

    Song, H H [Department of Macromolecular Science, Han Nam University, Taejon (Korea, Republic of); Fratini, A V [Department of Chemistry, University of Dayton, Dayton, OH (United States); Chabinyc, M [Department of Chemistry, University of Dayton, Dayton, OH (United States); Price, G E [University of Dayton Research, Dayton, OH (United States); Agrawal, A K [Systran Corporation, Dayton, OH (United States); Wang, C S [University of Dayton Research, Dayton, OH (United States); Burkette, J [University of Dayton Research, Dayton, OH (United States); Dudis, D S [Materials Directorate, Wright Laboratory, Wright-Patterson Air Force Base, OH (United States); Arnold, F E [Materials Directorate, Wright Laboratory, Wright-Patterson Air Force Base, OH (United States)

    1995-03-01

    Crystal structure and morphology of poly[7-oxo-7H-benz(d,e)imidazo(4`,5`:5,6)-benzimidazo(2,1-a)isoquinoline-3,4:10,11-tetrayl-10-carbonyl] (BBL) ladder-like polymer were studied. The polymer forms a two-dimensional lattice of nematic liquid crystalline structure. An orthorhombic unit cell with cell parameters of a=7.87 b=3.37 c=11.97A was determined from the fiber diffraction pattern. In thin films, the rigid chains spontaneously form a layered structure across the film thickness, but in a very unusual manner, i.e. the very large molecular plane is standing perpendicularly to the film surface plane. The results are identical to our recent results of poly(p-phenylene benzobisthiazole) (PBT) film [7]. The polymer, however, lost its anisotropic order upon extrusion into a film and resulted in a fiber-like structure. (orig.)

  18. Regulation of DNA Methylation Patterns by CK2-Mediated Phosphorylation of Dnmt3a

    Directory of Open Access Journals (Sweden)

    Rachel Deplus

    2014-08-01

    Full Text Available DNA methylation is a central epigenetic modification that is established by de novo DNA methyltransferases. The mechanisms underlying the generation of genomic methylation patterns are still poorly understood. Using mass spectrometry and a phosphospecific Dnmt3a antibody, we demonstrate that CK2 phosphorylates endogenous Dnmt3a at two key residues located near its PWWP domain, thereby downregulating the ability of Dnmt3a to methylate DNA. Genome-wide DNA methylation analysis shows that CK2 primarily modulates CpG methylation of several repeats, most notably of Alu SINEs. This modulation can be directly attributed to CK2-mediated phosphorylation of Dnmt3a. We also find that CK2-mediated phosphorylation is required for localization of Dnmt3a to heterochromatin. By revealing phosphorylation as a mode of regulation of de novo DNA methyltransferase function and by uncovering a mechanism for the regulation of methylation at repetitive elements, our results shed light on the origin of DNA methylation patterns.

  19. Epigenetic Patterns of PTSD: DNA Methylation In Serum of OIF/OEF Servicemembers

    Science.gov (United States)

    2011-01-01

    also have no data on other relevant exposures which are known to affect DNA methylation , such as dietary factors ( folate , vitamin B12 intake), (54, 55...ANSI Std. Z39.18 W81XWH-08-2-0053 31 MAR 2008 - 31 DEC 2010Final01-01-2011 Epigenetic Patterns of PTSD: DNA Methylation in Serum of OIF/OEF...distribution unlimited PTSD, epigenetics, DNA methylation , cytokines, serum, pre-deployment, post-deployment Abstract on next page. 38 jrusiecki@usuhs.mil

  20. "Ladder" structure in tonal noise generated by laminar flow around an airfoil.

    Science.gov (United States)

    Chong, Tze Pei; Joseph, Phillip

    2012-06-01

    The presence of a "ladder" structure in the airfoil tonal noise was discovered in the 1970s, but its mechanism hitherto remains a subject of continual investigation in the research community. Based on the measured noise results and some numerical analysis presented in this letter, the variations of four types of airfoil tonal noise frequencies with the flow velocity were analyzed individually. The ladder structure is proposed to be caused by the acoustic/hydrodynamic frequency lag between the scattering of the boundary layer instability noise and the discrete noise produced by an aeroacoustic feedback loop.

  1. High-energy, large-momentum-transfer processes: Ladder diagrams in var-phi 3 theory

    International Nuclear Information System (INIS)

    Newton, C.L.J.

    1990-01-01

    Relativistic quantum field theories may help one to understand high-energy, large-momentum-transfer processes, where the center-of-mass energy is much larger than the transverse momentum transfers, which are in turn much larger than the masses of the participating particles. With this possibility in mind, the author studies ladder diagrams in var-phi 3 theory. He shows that in the limit s much-gt |t| much-gt m 2 , the scattering amplitude for the N-rung ladder diagram takes the form s -1 |t| -N+1 times a homogeneous polynomial of degree 2N - 2 and ln s and ln |t|. This polynomial takes different forms depending on the relation of ln |t| to ln s. More precisely, the asymptotic formula for the N-rung ladder diagram has points of non-analytically when ln |t| = γ ln s for γ = 1/2, 1/3, hor-ellipsis, 1/N-2

  2. Hopping ladder and power relaxation due to donor-acceptor pairs

    International Nuclear Information System (INIS)

    Kostadinov, I.Z.

    1985-11-01

    Hopping between donor-acceptor pairs leads to peculiar temperature dependence of the conductivity and the photoconductivity under subband gap illumination in the form of non-linear activation energies ladder. The correlated and uncorrelated distributions of pairs are considered and the conditions for the ladder existence are determined. The relaxation of the carrier concentration fluctuations is studied and power type decay is found. The temperature dependence of the exponent is calculated in agreement with the non-exponential decay of the pulse excited luminescence observed by Dean et al. The temperature dependence of the luminescence intensity also shows variable activation energy as found here. The exponent value α=1.316 is also in agreement with the data for crystalline and amorphous materials. (author)

  3. Model Comparison Exercise Circuit Training Game and Circuit Ladder Drills to Improve Agility and Speed

    Directory of Open Access Journals (Sweden)

    Susilaturochman Hendrawan Koestanto

    2017-11-01

    Full Text Available The purpose of this study was to compare: (1 the effect of circuit training game and circuit ladder drill for the agility; (2 the effect of circuit training game and circuit ladder drill on speed; (3 the difference effect of circuit training game and circuit ladder drill for the speed (4 the difference effect of circuit training game and circuit ladder drill on agility. The type of this research was quantitative with quasi-experimental methods. The design of this research was Factorial Design, with analysing data using ANOVA. The process of data collection was done by using 30 meters sprint speed test and shuttle run test during the pretest and posttest. Furthermore, the data was analyzed by using SPSS 22.0 series. Result: The circuit training game exercise program and circuit ladder drill were significant to increase agility and speed (sig 0.000 < α = 0.005 Group I, II, III had significant differences (sig 0.000 < α = 0.005. The mean of increase in speed of group I = 0.20 seconds, group II = 0.31 seconds, and group III = 0.11 seconds. The average increase agility to group I = 0.34 seconds group II = 0.60 seconds, group III = 0.13 seconds. Based on the analysis above, it could be concluded that there was an increase in the speed and agility of each group after being given a training.

  4. Development of a recombinant DNA assay system for the detection of genetic change in astronauts' cells

    International Nuclear Information System (INIS)

    Atchley, S.V.; Chen, D.J.C.; Strniste, G.F.; Walters, R.A.; Moyzis, R.K.

    1984-01-01

    We are developing a new recombinant DNA system for the detection and measurement of genetic change in humans caused by exposure to low level ionizing radiation. A unique feature of the method is the use of cloned repetitive DNA probes to assay human DNA for structural changes during or after irradiation. Repetitive sequences exist in different families. Collectively they constitute over 25% of the DNA in a human cell. Repeat families have between 10 and 500,000 members. We have constructed repetitive DNA sequence libraries using recombinant DNA techniques. From these libraries we have isolated and characterized individual repeats comprising 75 to 90% of the mass of human repetitive DNA. Repeats used in our assay system exist in tandem arrays in the genome. Perturbation of these sequences in a cell, followed by detection with a repeat probe, produces a new, multimeric ''ladder'' pattern on an autoradiogram. The repeat probe used in our initial study is complementary to 1% of human DNA. Therefore, the sensitivity of this method is several orders of magnitude better than existing assays. Preliminary evidence from human skin cells exposed to acute, low-dose x-ray treatments indicates that DNA is affected at a dose as low as 5R. The radiation doses used in this system are well within the range of doses received by astronauts during spaceflight missions. Due to its small material requirements, this technique could easily be adapted for use in space. 16 refs., 1 fig

  5. Healthcare organization-education partnerships and career ladder programs for health care workers.

    Science.gov (United States)

    Dill, Janette S; Chuang, Emmeline; Morgan, Jennifer C

    2014-12-01

    Increasing concerns about quality of care and workforce shortages have motivated health care organizations and educational institutions to partner to create career ladders for frontline health care workers. Career ladders reward workers for gains in skills and knowledge and may reduce the costs associated with turnover, improve patient care, and/or address projected shortages of certain nursing and allied health professions. This study examines partnerships between health care and educational organizations in the United States during the design and implementation of career ladder training programs for low-skill workers in health care settings, referred to as frontline health care workers. Mixed methods data from 291 frontline health care workers and 347 key informants (e.g., administrators, instructors, managers) collected between 2007 and 2010 were analyzed using both regression and fuzzy-set qualitative comparative analysis (QCA). Results suggest that different combinations of partner characteristics, including having an education leader, employer leader, frontline management support, partnership history, community need, and educational policies, were necessary for high worker career self-efficacy and program satisfaction. Whether a worker received a wage increase, however, was primarily dependent on leadership within the health care organization, including having an employer leader and employer implementation policies. Findings suggest that strong partnerships between health care and educational organizations can contribute to the successful implementation of career ladder programs, but workers' ability to earn monetary rewards for program participation depends on the strength of leadership support within the health care organization. Copyright © 2014 Elsevier Ltd. All rights reserved.

  6. Phase diagram and re-entrant fermionic entanglement in a hybrid Ising-Hubbard ladder

    Science.gov (United States)

    Sousa, H. S.; Pereira, M. S. S.; de Oliveira, I. N.; Strečka, J.; Lyra, M. L.

    2018-05-01

    The degree of fermionic entanglement is examined in an exactly solvable Ising-Hubbard ladder, which involves interacting electrons on the ladder's rungs described by Hubbard dimers at half-filling on each rung, accounting for intrarung hopping and Coulomb terms. The coupling between neighboring Hubbard dimers is assumed to have an Ising-like nature. The ground-state phase diagram consists of four distinct regions corresponding to the saturated paramagnetic, the classical antiferromagnetic, the quantum antiferromagnetic, and the mixed classical-quantum phase. We have exactly computed the fermionic concurrence, which measures the degree of quantum entanglement between the pair of electrons on the ladder rungs. The effects of the hopping amplitude, the Coulomb term, temperature, and magnetic fields on the fermionic entanglement are explored in detail. It is shown that the fermionic concurrence displays a re-entrant behavior when quantum entanglement is being generated at moderate temperatures above the classical saturated paramagnetic ground state.

  7. Nestling diets and provisioning rates of sympatric Golden-fronted and Ladder-backed Woodpeckers

    Science.gov (United States)

    Schroeder, Evonne L.; Boal, Clint W.; Glasscock, Selma N.

    2013-01-01

    We examined comparative food use and provisioning of Golden-fronted (Melanerpes aurifrons) and Ladder-backed (Picoides scalaris) woodpeckers at the Rob and Bessie Welder Wildlife Foundation Refuge, in San Patricio County, Texas. We combined video surveillance and direct observations to monitor provisioning rates and identify items delivered by adult woodpeckers to nestlings. We collected 328 hours of data at Ladder-backed Woodpecker nest cavities and 230 hours of data at Golden-fronted Woodpecker nest cavities. Ladder-backed Woodpecker nestling diets consisted of 100% animal matter, comprised of invertebrate larvae (99%) and invertebrate adults (nestlings were also high in animal matter (77%) with more invertebrate adults (55%) and fewer invertebrate larvae (27%), but also included vegetable matter (16%). Morisita's measure of overlap suggested a relatively low dietary overlap of 31% between nestlings of these two sympatric woodpecker species. Foraging methods used by these species may explain their low dietary overlap and facilitate their coexistence.

  8. Regular Nanoscale Protein Patterns via Directed Adsorption through Self-Assembled DNA Origami Masks.

    Science.gov (United States)

    Ramakrishnan, Saminathan; Subramaniam, Sivaraman; Stewart, A Francis; Grundmeier, Guido; Keller, Adrian

    2016-11-16

    DNA origami has become a widely used method for synthesizing well-defined nanostructures with promising applications in various areas of nanotechnology, biophysics, and medicine. Recently, the possibility to transfer the shape of single DNA origami nanostructures into different materials via molecular lithography approaches has received growing interest due to the great structural control provided by the DNA origami technique. Here, we use ordered monolayers of DNA origami nanostructures with internal cavities on mica surfaces as molecular lithography masks for the fabrication of regular protein patterns over large surface areas. Exposure of the masked sample surface to negatively charged proteins results in the directed adsorption of the proteins onto the exposed surface areas in the holes of the mask. By controlling the buffer and adsorption conditions, the protein coverage of the exposed areas can be varied from single proteins to densely packed monolayers. To demonstrate the versatility of this approach, regular nanopatterns of four different proteins are fabricated: the single-strand annealing proteins Redβ and Sak, the iron-storage protein ferritin, and the blood protein bovine serum albumin (BSA). We furthermore demonstrate the desorption of the DNA origami mask after directed protein adsorption, which may enable the fabrication of hierarchical patterns composed of different protein species. Because selectivity in adsorption is achieved by electrostatic interactions between the proteins and the exposed surface areas, this approach may enable also the large-scale patterning of other charged molecular species or even nanoparticles.

  9. THE COMPARISON OF USING SNAKE LADDERS AND SCRABBLE MEDIA TOWARDS VOCABULARY MASTERY OF STUDENTS

    Directory of Open Access Journals (Sweden)

    Eka Pra Setiawati

    2017-02-01

    Full Text Available Vocabulary is an essential component in learning English. It influences four English skills; they are listening, speaking, reading, and writing, for getting a good result in English. In teaching learning process, the teacher often implements the less interesting method, technique, or even media of vocabulary mastery in teaching and learning process which make the students to be bored, inactive, an uniterested in memorizing English vocabulary. Some media can be interested as the solutions in vocabulary mastery, they are Snake Ladders media and Scrabble media. The investigation was undergone by quantitative research. The researcher applied experimental research. This research underwent pre-test post-test control group design. To analyze data, t-test formula is used to measure the result of collected data. From the t-test measurement, it showed that t-test is 3.15 and t-table is 2.66. It means that t-hit > t-table. Based on the collected data, there is different result of using Snake Ladders from Scrabble media toward students’ vocabulary mastery. It was found that the students who are taught by using Snake Ladders resulted significant outcome than those are instructed by Scrabble media. It means that Snake Ladders is effective to improve the students’ vocabulary mastery.

  10. Means-end chains and laddering: An inventory of problems and an agenda for research

    DEFF Research Database (Denmark)

    Grunert, Klaus G.; Grunert, Suzanne C.; Sørensen, Elin

    Executive summary 1. Means-end chains are a device used to understand how consumers mentally link products to self-relevant consequences. Means-end chains are usually measured by a method called laddering. 2. Means-end chains may fall short of tapping all relevant aspects of how consumers think...... about products. Specifically, nonverbal imagery, episodic information, and procedural knowledge are not included in means-end chains. 3. A number of methodological problems can be identified in the collection of means-end chain data. Major problems, which should be addressed in research, are methods...... to elicit the product attributes the laddering is to start with, the integration of a usage situation in the interview, and the basic decision on how much direct the respondent. 4. Concerning the coding of laddering data, a higher degree of transparency of the coding process would be desirable. 5...

  11. Means-end chains and laddering: An inventory of problems and an agenda for research

    DEFF Research Database (Denmark)

    Grunert, Klaus G.; Beckmann, Suzanne C.; Sørensen, Elin

    2001-01-01

    and unconscious (or, at least, semiconscious) factors. It is intuitively appealing to the practitioner but has, likewise, attracted academic research. Increased acceptance and use of a new approach inevitably leads to the detection of unresolved issues and problems. Many of these unresolved issues are related...... to the collection and analysis of laddering data. However, many of these also point at problems of a more theoretical nature. In this chapter presented are some of the issues regarded as unresolved and suggested research that could help in solving these problems. The mayor part of this chapter deals...... with methodological problems of the interview technique called laddering, og coding laddering data, and of analysing the coded data. However, also shown, methodological and theoretical issues are partly interlinked: resolutions of methodological problems may require theoretical progress or at least a clarification...

  12. Temporal patterns of damage and decay kinetics of DNA retrieved from plant herbarium specimens.

    Science.gov (United States)

    Weiß, Clemens L; Schuenemann, Verena J; Devos, Jane; Shirsekar, Gautam; Reiter, Ella; Gould, Billie A; Stinchcombe, John R; Krause, Johannes; Burbano, Hernán A

    2016-06-01

    Herbaria archive a record of changes of worldwide plant biodiversity harbouring millions of specimens that contain DNA suitable for genome sequencing. To profit from this resource, it is fundamental to understand in detail the process of DNA degradation in herbarium specimens. We investigated patterns of DNA fragmentation and nucleotide misincorporation by analysing 86 herbarium samples spanning the last 300 years using Illumina shotgun sequencing. We found an exponential decay relationship between DNA fragmentation and time, and estimated a per nucleotide fragmentation rate of 1.66 × 10(-4) per year, which is six times faster than the rate estimated for ancient bones. Additionally, we found that strand breaks occur specially before purines, and that depurination-driven DNA breakage occurs constantly through time and can to a great extent explain decreasing fragment length over time. Similar to what has been found analysing ancient DNA from bones, we found a strong correlation between the deamination-driven accumulation of cytosine to thymine substitutions and time, which reinforces the importance of substitution patterns to authenticate the ancient/historical nature of DNA fragments. Accurate estimations of DNA degradation through time will allow informed decisions about laboratory and computational procedures to take advantage of the vast collection of worldwide herbarium specimens.

  13. Variation in DNA Methylation Patterns is More Common among Maize Inbreds than among Tissues

    Directory of Open Access Journals (Sweden)

    Steven R. Eichten

    2013-07-01

    Full Text Available Chromatin modifications, such as DNA methylation, can provide heritable, epigenetic regulation of gene expression in the absence of genetic changes. A role for DNA methylation in meiotically stable marking of repetitive elements and other sequences has been demonstrated in plants. Methylation of DNA is also proposed to play a role in development through providing a mitotic memory of gene expression states established during cellular differentiation. We sought to clarify the relative levels of DNA methylation variation among different genotypes and tissues in maize ( L.. We have assessed genomewide DNA methylation patterns in leaf, immature tassel, embryo, and endosperm tissues of two inbred maize lines: B73 and Mo17. There are hundreds of regions of differential methylation present between the two genotypes. In general, the same regions exhibit differential methylation between B73 and Mo17 in each of the tissues that were surveyed. In contrast, there are few examples of tissue-specific DNA methylation variation. Only a subset of regions with tissue-specific variation in DNA methylation show similar patterns in both genotypes of maize and even fewer are associated with altered gene expression levels among the tissues. Our data indicates a limited impact of DNA methylation on developmental gene regulation within maize.

  14. Analytical recursive method to ascertain multisite entanglement in doped quantum spin ladders

    Science.gov (United States)

    Roy, Sudipto Singha; Dhar, Himadri Shekhar; Rakshit, Debraj; SenDe, Aditi; Sen, Ujjwal

    2017-08-01

    We formulate an analytical recursive method to generate the wave function of doped short-range resonating valence bond (RVB) states as a tool to efficiently estimate multisite entanglement as well as other physical quantities in doped quantum spin ladders. We prove that doped RVB ladder states are always genuine multipartite entangled. Importantly, our results show that within specific doping concentration and model parameter regimes, the doped RVB state essentially characterizes the trends of genuine multiparty entanglement in the exact ground states of the Hubbard model with large on-site interactions, in the limit that yields the t -J Hamiltonian.

  15. In-line digital holography with phase-shifting Greek-ladder sieves

    Science.gov (United States)

    Xie, Jing; Zhang, Junyong; Zhang, Yanli; Zhou, Shenlei; Zhu, Jianqiang

    2018-04-01

    Phase shifting is the key technique in in-line digital holography, but traditional phase shifters have their own limitations in short wavelength regions. Here, phase-shifting Greek-ladder sieves with amplitude-only modulation are introduced into in-line digital holography, which are essentially a kind of diffraction lens with three-dimensional array diffraction-limited foci. In the in-line digital holographic experiment, we design two kinds of sieves by lithography and verify the validity of their phase-shifting function by measuring a 1951 U.S. Air Force resolution test target and three-dimensional array foci. With advantages of high resolving power, low cost, and no limitations at shorter wavelengths, phase-shifting Greek-ladder sieves have great potential in X-ray holography or biochemical microscopy for the next generation of synchrotron light sources.

  16. The snakes and ladders of National Health Service management in England.

    Science.gov (United States)

    Powell, Martin

    2014-01-01

    This article explores managerial careers in the National Health Service (NHS) through the lens of talent management, particularly focusing on how managers view barriers (snakes) and facilitators (ladders) to career progression. There is a significant literature on enablers and barriers to career progression, but much of this focuses on specific groups such as black and minority ethnic and female workers, and there is relatively little material on the general workforce of the NHS. The research design is a mixed method quantitative (questionnaire) and qualitative (interview and focus group) approach consisting of a quasi-probability element that focuses on a maximum variety sample and a purposive element that seeks policy views at central and strategic health authority level, and examines talent management in high-performing NHS organisations. Ladders are identified as follows: volunteering, secondment, networking, mentoring, academic qualifications, development, good role models/managers and appraisal/personal development plan. Snakes are identified as managing expectations; identity and cognitive diversity; location; sector; NHS toxic and favouritism culture; poor talent spotting; credentialism; exclusive approach to talent; and sustainability. It concludes that while previous conceptual and empirical work is fairly clear on any ladders, it is less clear on snakes. Copyright © 2013 John Wiley & Sons, Ltd.

  17. High-Performance and Simply-Synthesized Ladder-Like Structured Methacrylate Siloxane Hybrid Material for Flexible Hard Coating

    Directory of Open Access Journals (Sweden)

    Yun Hyeok Kim

    2018-04-01

    Full Text Available A high performance ladder-like structured methacrylate siloxane hybrid material (LMSH was fabricated via simple hydrolytic sol–gel reaction, followed by free-radical polymerization. A structurally ordered siloxane backbone, the ladder-like structure, which is an essential factor for high performance, could be achieved by a short period of sol–gel reaction in only 4 h. This results in superior optical (Transmittance > 90% at 550 nm, thermal (T5 wt % decomposition > 400 ℃ , mechanical properties(elastic recovery = 0.86, hardness = 0.6 GPa compared to the random- and even commercialized cage-structured silsesquioxane, which also has ordered structure. It was investigated that the fabricated ladder-like structured MSH showed the highest overall density of organic/inorganic co-networks that are originated from highly ordered siloxane network, along with high conversion rate of polymerizable methacrylate groups. Our findings suggest a potential of the ladder-like structured MSH as a powerful alternative for the methacrylate polysilsesquioxane, which can be applied to thermally stable and flexible optical coatings, even with an easier and simpler preparation process.

  18. Chemodiversity of Ladder-Frame Prymnesin Polyethers in Prymnesium parvum

    DEFF Research Database (Denmark)

    Rasmussen, Silas Anselm; Meier, Sebastian; Andersen, Nikolaj Gedsted

    2016-01-01

    Blooms of the microalga Prymnesium parvum cause devastating fish kills worldwide, which are suspected to be caused by the supersized ladder-frame polyether toxins prymnesin-1 and -2. These toxins have, however, only been detected from P. parvum in rare cases since they were originally described two...

  19. The resonance self-shielding calculation with regularized random ladders

    International Nuclear Information System (INIS)

    Ribon, P.

    1986-01-01

    The straightforward method for calculation of resonance self-shielding is to generate one or several resonance ladders, and to process them as resolved resonances. The main drawback of Monte Carlo methods used to generate the ladders, is the difficulty of reducing the dispersion of data and results. Several methods are examined, and it is shown how one (a regularized sampling method) improves the accuracy. Analytical methods to compute the effective cross-section have recently appeared: they are basically exempt from dispersion, but are inevitably approximate. The accuracy of the most sophisticated one is checked. There is a neutron energy range which is improperly considered as statistical. An examination is presented of what happens when it is treated as statistical, and how it is possible to improve the accuracy of calculations in this range. To illustrate the results calculations have been performed in a simple case: nucleus 238 U, at 300 K, between 4250 and 4750 eV. (author)

  20. Groundstate fidelity phase diagram of the fully anisotropic two-leg spin-½ XXZ ladder

    Science.gov (United States)

    Li, Sheng-Hao; Shi, Qian-Qian; Batchelor, Murray T.; Zhou, Huan-Qiang

    2017-11-01

    The fully anisotropic two-leg spin-\\tfrac{1}{2} XXZ ladder model is studied in terms of an algorithm based on the tensor network (TN) representation of quantum many-body states as an adaptation of projected entangled pair states to the geometry of translationally invariant infinite-size quantum spin ladders. The TN algorithm provides an effective method to generate the groundstate wave function, which allows computation of the groundstate fidelity per lattice site, a universal marker to detect phase transitions in quantum many-body systems. The groundstate fidelity is used in conjunction with local order and string order parameters to systematically map out the groundstate phase diagram of the ladder model. The phase diagram exhibits a rich diversity of quantum phases. These are the ferromagnetic, stripe ferromagnetic, rung singlet, rung triplet, Néel, stripe Néel and Haldane phases, along with the two XY phases XY1 and XY2.

  1. Creating a Professional Ladder for Interpreters for Improvement of Care.

    Science.gov (United States)

    Marshall, Lori; Fischer, Anna; Noyes Soeller, Allison; Cordova, Richard; Gutierrez, Yvonne R; Alford, Luis

    2016-01-01

    Children's Hospital Los Angeles (CHLA), a metropolitan academic medical center, recognized limitations in how the professional interpreters from the Diversity Services Department were used to support effective patient-provider communication across the organization. Given the importance of mitigating language and communication barriers, CHLA sought to minimize clinical and structural barriers to health care for limited English proficiency populations through a comprehensive restructuring of the Diversity Services Department. This approach entailed a new delivery model for hospital language assistance and cultural consultancy resources. The intervention focused on restructuring the Diversity Services Department, redefining priorities, reallocating resources, and redefining the roles of the language staff positions in the department. The language staff role was redesigned to fit a four-level professional career ladder modeled after the professional career ladders commonly used in hospitals for the RN role and other professional disciplines. The approach involved creating new levels of language specialist, each with progressive requirements for performance, leadership, and accountability for patient care outcomes. Language staff in the inpatient, clinic, and emergency department settings worked alongside nurses, physicians, and other disciplines to care for a specific set of patients. The result of this work was a positive culture change resulting in service efficiencies, care improvements, and improved access to language services. A professional career ladder for language staff contributed to improving the quality and access of language services and advancing the interpreting profession by incorporating care coordination support, vital document translation, and cultural consultancy.

  2. Ground Radio Operator Career Ladder AFSC 293X3.

    Science.gov (United States)

    1981-07-01

    formal resident training, OJT, and ,her Air Force management decisions . The structure of jobs within the Ground ! odio Operatoi career ladder was...33 ADJUST ANTENNA TUNING UNITS 33 TYPE RECORDS, REPORTS, OR FORMS :33 OPERATE AUXILLARY GENERATORS 33 A8 ’iT’ TASKS PERFORMED BY SUPERVISORS AND

  3. High-energy, large-momentum-transfer processes: Ladder diagrams in φ3 theory. Pt. 1

    International Nuclear Information System (INIS)

    Osland, P.; Wu, T.T.; Harvard Univ., Cambridge, MA

    1987-01-01

    Relativistic quantum field theories may give us useful guidance to understanding high-energy, large-momentum-transfer processes, where the center-of-mass energy is much larger than the transverse momentum transfers, which are in turn much larger than the masses of the participating particles. With this possibility in mind, we study the ladder diagrams in φ 3 theory. In this paper, some of the necessary techniques are developed and applied to the simplest cases of the fourth- and sixth-order ladder diagrams. (orig.)

  4. Wolbachia and DNA barcoding insects: patterns, potential, and problems.

    Science.gov (United States)

    Smith, M Alex; Bertrand, Claudia; Crosby, Kate; Eveleigh, Eldon S; Fernandez-Triana, Jose; Fisher, Brian L; Gibbs, Jason; Hajibabaei, Mehrdad; Hallwachs, Winnie; Hind, Katharine; Hrcek, Jan; Huang, Da-Wei; Janda, Milan; Janzen, Daniel H; Li, Yanwei; Miller, Scott E; Packer, Laurence; Quicke, Donald; Ratnasingham, Sujeevan; Rodriguez, Josephine; Rougerie, Rodolphe; Shaw, Mark R; Sheffield, Cory; Stahlhut, Julie K; Steinke, Dirk; Whitfield, James; Wood, Monty; Zhou, Xin

    2012-01-01

    Wolbachia is a genus of bacterial endosymbionts that impacts the breeding systems of their hosts. Wolbachia can confuse the patterns of mitochondrial variation, including DNA barcodes, because it influences the pathways through which mitochondria are inherited. We examined the extent to which these endosymbionts are detected in routine DNA barcoding, assessed their impact upon the insect sequence divergence and identification accuracy, and considered the variation present in Wolbachia COI. Using both standard PCR assays (Wolbachia surface coding protein--wsp), and bacterial COI fragments we found evidence of Wolbachia in insect total genomic extracts created for DNA barcoding library construction. When >2 million insect COI trace files were examined on the Barcode of Life Datasystem (BOLD) Wolbachia COI was present in 0.16% of the cases. It is possible to generate Wolbachia COI using standard insect primers; however, that amplicon was never confused with the COI of the host. Wolbachia alleles recovered were predominantly Supergroup A and were broadly distributed geographically and phylogenetically. We conclude that the presence of the Wolbachia DNA in total genomic extracts made from insects is unlikely to compromise the accuracy of the DNA barcode library; in fact, the ability to query this DNA library (the database and the extracts) for endosymbionts is one of the ancillary benefits of such a large scale endeavor--which we provide several examples. It is our conclusion that regular assays for Wolbachia presence and type can, and should, be adopted by large scale insect barcoding initiatives. While COI is one of the five multi-locus sequence typing (MLST) genes used for categorizing Wolbachia, there is limited overlap with the eukaryotic DNA barcode region.

  5. Breathers in Josephson junction ladders: Resonances and electromagnetic wave spectroscopy

    DEFF Research Database (Denmark)

    Miroshnichenko, A. E.; Flach, S.; Fistul, M.

    2001-01-01

    We present a theoretical study of the resonant interaction between dynamical localized states (discrete breathers) and linear electromagnetic excitations (EE's) in Josephson junction ladders. By making use of direct numerical simulations we find that such an interaction manifests itself by resonant...

  6. 29 CFR Appendix A to Subpart X of... - Ladders

    Science.gov (United States)

    2010-07-01

    ... 29 Labor 8 2010-07-01 2010-07-01 false Ladders A Appendix A to Subpart X of Part 1926 Labor Regulations Relating to Labor (Continued) OCCUPATIONAL SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF LABOR... designed and built in accordance with the applicable national consensus standards, as set forth below, will...

  7. 46 CFR 116.438 - Stairtowers, stairways, ladders, and elevators.

    Science.gov (United States)

    2010-10-01

    ... 46 Shipping 4 2010-10-01 2010-10-01 false Stairtowers, stairways, ladders, and elevators. 116.438 Section 116.438 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) SMALL PASSENGER VESSELS CARRYING MORE THAN 150 PASSENGERS OR WITH OVERNIGHT ACCOMMODATIONS FOR MORE THAN 49 PASSENGERS CONSTRUCTION AND ARRANGEMENT Fire Protection §...

  8. Cutting and dismantling of the South West ladder of the Atucha I nuclear power plant

    International Nuclear Information System (INIS)

    Anasco, Roberto

    2006-01-01

    The metallic ladder built in stainless steel was used originally to check the welding of the reactor pressure vessel. It was located between the thermal insulation and reactor pressure vessel. Because of a failure in the mechanism, which let the ladder runs around the vessel, it had to be removed. A special tool remotely operated was designed to make different cuts in the bottom of the structure in a very high radioactive location [es

  9. Forensic DNA Banding Patterns: How to Simulate & Explain DNA Fingerprinting in a Classroom with No Budget

    Science.gov (United States)

    Christensen, Doug

    2013-01-01

    Understanding how DNA banding patterns in a gel can aid in the conviction or exoneration of suspects and be utilized for positive identification of biological fathers in paternity cases can be intimidating. In reality, the logistics and technology used in such cases are rather straightforward. This exercise is designed for use in high school…

  10. New insights into the origin of ladder dikes: Implications for punctuated growth and crystal accumulation in the Cathedral Peak granodiorite

    Science.gov (United States)

    Wiebe, R. A.; Jellinek, A. M.; Hodge, K. F.

    2017-04-01

    Ladder dikes are steep tabular bodies, typically a meter or less thick, composed of moderately dipping, concave upward, alternating dark (i.e. schlieren) and light bands oriented roughly perpendicular to the ladder dike margins. These structures occur widely but sparsely in granitic rocks and are found prominently in the Cathedral Peak granodiorite (CPG) of the Tuolumne Intrusive suite. Previous studies have interpreted that ladder dikes form as a result of processes including the downward flow of crystal mush in cracks within strong crystal mush or by upward flow in steep tubes that migrate within a strong crystal mush. Our new observations indicate that ladder dikes formed by downward flow of crystal mush in troughs or valleys, in a manner potentially comparable to trough bands in mafic layered intrusions. Extensions of the schlieren outward and upward away from the ladder dike margins into the host granite demonstrate that the host granite was deposited as mounds on both sides at the same time as the ladder dikes. Ladder dikes, therefore, record lateral flows of crystal mush on a magma chamber floor. Vertical exposures suggest these flows are on the order of ten meters thick. Some steep exposures on granite domes indicate multiple ladder dikes (and flows) over a stratigraphic height of 80-100 m. Later (stratigraphically higher) flows commonly deform and erode the top of an earlier flow, and granitic material rich in K-feldspar megacrysts has locally engulfed large blocks of ladder dikes, demonstrating that the megacrysts were also transported in flows. Flows in the CPG are directed away from the center of the pluton toward the western and eastern margins and apparently spread along a strong crystal mush floor and into a rheologically complex CPG magma. Whereas established dynamical models for spreading (single phase) gravity currents with simple and complex rheologies explain the elongate geometry, spacing and orientation of the tabular bodies, the origin and

  11. “Why Caipirinha?”- The Online via Chat Laddering Technique CAN Answer

    Directory of Open Access Journals (Sweden)

    Bruno Bordeaux-Rego

    2011-04-01

    Full Text Available As customers are becoming increasingly connected to the internet, this means that they are available for online interviews, thus opening up a space for investigating research methods, especially qualitative research, in an attempt to identify how to adapt data collecting instruments to the so-called “connected customer era”. In this context, the focus of this article is on the application viability analysis of the laddering technique used online and in real-time chat by asking the following question: “Why caipirinha?”. Conducting online in-depth interviews through the MSN Messenger and Skype (the most commonly used chat tools in Brazil, 23 attributes, 22 consequences and 13 values were identified, resulting in 133 ladders, 71 of which reached the value level. Along with friends/mates, Integration, Entertainment and Fun, in addition to Alcohol, Insouciance/ relaxation and Pleasure constitute the most frequent ladders. Concerning the application itself, the participants gave positive feedback, even though some of them did not feel satisfied because they became tired. Convenience, objectivity, disinhibition, easy scheduling and flexibility were identified. The viability of online in-depth interviewing via real-time chats was confirmed, raising the question of the possibility of it achieving other qualitative research techniques.

  12. DNA methylation patterns of candidate genes regulated by thymine DNA glycosylase in patients with TP53 germline mutations

    Energy Technology Data Exchange (ETDEWEB)

    Fortes, F.P. [CIPE, Laboratrio de Oncogentica Molecular, A.C. Camargo Cancer Center, São Paulo, SP (Brazil); Kuasne, H. [CIPE, Laboratrio NeoGene, A.C. Camargo Cancer Center, São Paulo, SP (Brazil); Departamento de Urologia, Faculdade de Medicina, Universidade Estadual Paulista, Botucatu, SP (Brazil); Marchi, F.A. [CIPE, Laboratrio NeoGene, A.C. Camargo Cancer Center, São Paulo, SP (Brazil); Programa Inter-Institucional em Bioinformtica, Instituto de Matemtica e Estatstica, Universidade So Paulo, So Paulo, SP (Brazil); Miranda, P.M. [CIPE, Laboratrio NeoGene, A.C. Camargo Cancer Center, São Paulo, SP (Brazil); Rogatto, S.R. [CIPE, Laboratrio NeoGene, A.C. Camargo Cancer Center, São Paulo, SP (Brazil); Departamento de Urologia, Faculdade de Medicina, Universidade Estadual Paulista, Botucatu, SP (Brazil); Achatz, M.I. [CIPE, Laboratrio de Oncogentica Molecular, A.C. Camargo Cancer Center, São Paulo, SP (Brazil); Departamento de Oncogentica, A.C. Camargo Cancer Center, So Paulo, SP (Brazil)

    2015-04-28

    Li-Fraumeni syndrome (LFS) is a rare, autosomal dominant, hereditary cancer predisposition disorder. In Brazil, the p.R337H TP53 founder mutation causes the variant form of LFS, Li-Fraumeni-like syndrome. The occurrence of cancer and age of disease onset are known to vary, even in patients carrying the same mutation, and several mechanisms such as genetic and epigenetic alterations may be involved in this variability. However, the extent of involvement of such events has not been clarified. It is well established that p53 regulates several pathways, including the thymine DNA glycosylase (TDG) pathway, which regulates the DNA methylation of several genes. This study aimed to identify the DNA methylation pattern of genes potentially related to the TDG pathway (CDKN2A, FOXA1, HOXD8, OCT4, SOX2, and SOX17) in 30 patients with germline TP53mutations, 10 patients with wild-type TP53, and 10 healthy individuals. We also evaluated TDG expression in patients with adrenocortical tumors (ADR) with and without the p.R337H TP53 mutation. Gene methylation patterns of peripheral blood DNA samples assessed by pyrosequencing revealed no significant differences between the three groups. However, increased TDG expression was observed by quantitative reverse transcription PCR in p.R337H carriers with ADR. Considering the rarity of this phenotype and the relevance of these findings, further studies using a larger sample set are necessary to confirm our results.

  13. Generalized ladder operators for the Dirac-Coulomb problem via SUSY QM

    International Nuclear Information System (INIS)

    Rodrigues, R. de Lima; Universidade Federal de Campina Grande, PB

    2003-12-01

    The supersymmetry in quantum mechanics and shape invariance condition are applied as an algebraic method to solving the Dirac-Coulomb problem. The ground state and the excited states are investigated via new generalized ladder operators. (author)

  14. Orbital currents and charge density waves in a generalized Hubbard ladder

    International Nuclear Information System (INIS)

    Fjaerestad, J.O.; Marston, J.B.; Schollwoeck, U.

    2006-01-01

    We study a generalized Hubbard model on the two-leg ladder at zero temperature, focusing on a parameter region with staggered flux (SF)/d-density wave (DDW) order. To guide our numerical calculations, we first investigate the location of a SF/DDW phase in the phase diagram of the half-filled weakly interacting ladder using a perturbative renormalization group (RG) and bosonization approach. For hole doping δ away from half-filling, finite-system density-matrix renormalization-group (DMRG) calculations are used to study ladders with up to 200 rungs for intermediate-strength interactions. In the doped SF/DDW phase, the staggered rung current and the rung electron density both show periodic spatial oscillations, with characteristic wavelengths 2/δ and 1/δ, respectively, corresponding to ordering wavevectors 2k F and 4k F for the currents and densities, where 2k F = π (1 - δ). The density minima are located at the anti-phase domain walls of the staggered current. For sufficiently large dopings, SF/DDW order is suppressed. The rung density modulation also exists in neighboring phases where currents decay exponentially. We show that most of the DMRG results can be qualitatively understood from weak-coupling RG/bosonization arguments. However, while these arguments seem to suggest a crossover from non-decaying correlations to power-law decay at a length scale of order 1/δ, the DMRG results are consistent with a true long-range order scenario for the currents and densities

  15. Molecular recognition of AT-DNA sequences by the induced CD pattern of dibenzotetraaza[14]annulene (DBTAA)-adenine derivatives.

    Science.gov (United States)

    Stojković, Marijana Radić; Skugor, Marko; Dudek, Lukasz; Grolik, Jarosław; Eilmes, Julita; Piantanida, Ivo

    2014-01-01

    An investigation of the interactions of two novel and several known DBTAA-adenine conjugates with double-stranded DNA and RNA has revealed the DNA/RNA groove as the dominant binding site, which is in contrast to the majority of previously studied DBTAA analogues (DNA/RNA intercalators). Only DBTAA-propyladenine conjugates revealed the molecular recognition of AT-DNA by an ICD band pattern > 300 nm, whereas significant ICD bands did not appear for other ds-DNA/RNA. A structure-activity relation for the studied series of compounds showed that the essential structural features for the ICD recognition are a) the presence of DNA-binding appendages (adenine side chain and positively charged side chain) on both DBTAA side chains, and b) the presence of a short propyl linker, which does not support intramolecular aromatic stacking between DBTAA and adenine. The observed AT-DNA-ICD pattern differs from previously reported ss-DNA (poly dT) ICD recognition by a strong negative ICD band at 350 nm, which allows for the dynamic differentiation between ss-DNA (poly dT) and coupled ds-AT-DNA.

  16. SUSY’s Ladder: reframing sequestering at Large Volume

    Energy Technology Data Exchange (ETDEWEB)

    Reece, Matthew [Department of Physics, Harvard University,Cambridge, MA 02138 (United States); Xue, Wei [Center for Theoretical Physics, Massachusetts Institute of Technology,Cambridge, MA 02139 (United States)

    2016-04-07

    Theories with approximate no-scale structure, such as the Large Volume Scenario, have a distinctive hierarchy of multiple mass scales in between TeV gaugino masses and the Planck scale, which we call SUSY’s Ladder. This is a particular realization of Split Supersymmetry in which the same small parameter suppresses gaugino masses relative to scalar soft masses, scalar soft masses relative to the gravitino mass, and the UV cutoff or string scale relative to the Planck scale. This scenario has many phenomenologically interesting properties, and can avoid dangers including the gravitino problem, flavor problems, and the moduli-induced LSP problem that plague other supersymmetric theories. We study SUSY’s Ladder using a superspace formalism that makes the mysterious cancelations in previous computations manifest. This opens the possibility of a consistent effective field theory understanding of the phenomenology of these scenarios, based on power-counting in the small ratio of string to Planck scales. We also show that four-dimensional theories with approximate no-scale structure enforced by a single volume modulus arise only from two special higher-dimensional theories: five-dimensional supergravity and ten-dimensional type IIB supergravity. This gives a phenomenological argument in favor of ten dimensional ultraviolet physics which is different from standard arguments based on the consistency of superstring theory.

  17. End States, Ladder Compounds, and Domain-Wall Fermions

    International Nuclear Information System (INIS)

    Creutz, M.

    1999-01-01

    A magnetic field applied to a cross-linked ladder compound can generate isolated electronic states bound to the ends of the chain. After exploring the interference phenomena responsible, I discuss a connection to the domain-wall approach to chiral fermions in lattice gauge theory. The robust nature of the states under small variations of the bond strengths is tied to chiral symmetry and the multiplicative renormalization of fermion masses. copyright 1999 The American Physical Society

  18. Gluon ladders in pp (pp-bar) collisions

    International Nuclear Information System (INIS)

    Machado, Magno Valerio Trindade; Ducati, Maria Beatriz Gay

    2000-01-01

    Full text follows: We study the contribution of a finite sum of gluon ladders to the hadronic processes showing that a reliable description is obtained using two order on perturbation theory. The pp(pp-bar) total cross sections are described with good agreement, consistent with unitarity bound. We also calculate the elastic scattering amplitude at non zero momentum transfer t, introducing two distinct Ansatz for the proton impact factor. As a by product the elastic differential cross section is obtained at small t approximation and compared with the data. (author)

  19. Interband optical absorption in the Wannier-Stark ladder under the electron-LO-phonon resonance condition

    International Nuclear Information System (INIS)

    Govorov, A.O.

    1993-08-01

    Interband optical absorption in the Wannier-Stark ladder in the presence of the electron-LO-phonon resonance is investigated theoretically. The electron-LO-phonon resonance occurs when the energy spacing between adjacent Stark-ladder levels coincides with the LO-phonon energy. We propose a model describing the polaron effect in a superlattice. Calculations show that the absorption line shape is strongly modified due to the polaron effect under the electron-LO-phonon resonance condition. We consider optical phenomena in a normal magnetic field that leads to enhancement of polaron effects. (author). 17 refs, 5 figs

  20. Low-Field Bi-Skyrmion Formation in a Noncentrosymmetric Chimney Ladder Ferromagnet

    Science.gov (United States)

    Takagi, R.; Yu, X. Z.; White, J. S.; Shibata, K.; Kaneko, Y.; Tatara, G.; Rønnow, H. M.; Tokura, Y.; Seki, S.

    2018-01-01

    The real-space spin texture and the relevant magnetic parameters were investigated for an easy-axis noncentrosymmetric ferromagnet Cr11 Ge19 with Nowotny chimney ladder structure. Using Lorentz transmission electron microscopy, we report the formation of bi-Skyrmions, i.e., pairs of spin vortices with opposite magnetic helicities. The quantitative evaluation of the magnetocrystalline anisotropy and Dzyaloshinskii-Moriya interaction (DMI) proves that the magnetic dipolar interaction plays a more important role than the DMI on the observed bi-Skyrmion formation. Notably, the critical magnetic field value required for the formation of bi-Skyrmions turned out to be extremely small in this system, which is ascribed to strong easy-axis anisotropy associated with the characteristic helix crystal structure. The family of Nowotny chimney ladder compounds may offer a unique material platform where two distinctive Skyrmion formation mechanisms favoring different topological spin textures can become simultaneously active.

  1. Two-leg ladder systems with dipole–dipole Fermion interactions

    Science.gov (United States)

    Mosadeq, Hamid; Asgari, Reza

    2018-05-01

    The ground-state phase diagram of a two-leg fermionic dipolar ladder with inter-site interactions is studied using density matrix renormalization group (DMRG) techniques. We use a state-of-the-art implementation of the DMRG algorithm and finite size scaling to simulate large system sizes with high accuracy. We also consider two different model systems and explore stable phases in half and quarter filling factors. We find that in the half filling, the charge and spin gaps emerge in a finite value of the dipole–dipole and on-site interactions. In the quarter filling case, s-wave superconducting state, charge density wave, homogenous insulating and phase separation phases occur depend on the interaction values. Moreover, in the dipole–dipole interaction, the D-Mott phase emerges when the hopping terms along the chain and rung are the same, whereas, this phase has been only proposed for the anisotropic Hubbard model. In the half filling case, on the other hand, there is either charge-density wave or charged Mott order phase depends on the orientation of the dipole moments of the particles with respect to the ladder geometry.

  2. Genome-wide DNA methylation patterns and transcription analysis in sheep muscle.

    Directory of Open Access Journals (Sweden)

    Christine Couldrey

    Full Text Available DNA methylation plays a central role in regulating many aspects of growth and development in mammals through regulating gene expression. The development of next generation sequencing technologies have paved the way for genome-wide, high resolution analysis of DNA methylation landscapes using methodology known as reduced representation bisulfite sequencing (RRBS. While RRBS has proven to be effective in understanding DNA methylation landscapes in humans, mice, and rats, to date, few studies have utilised this powerful method for investigating DNA methylation in agricultural animals. Here we describe the utilisation of RRBS to investigate DNA methylation in sheep Longissimus dorsi muscles. RRBS analysis of ∼1% of the genome from Longissimus dorsi muscles provided data of suitably high precision and accuracy for DNA methylation analysis, at all levels of resolution from genome-wide to individual nucleotides. Combining RRBS data with mRNAseq data allowed the sheep Longissimus dorsi muscle methylome to be compared with methylomes from other species. While some species differences were identified, many similarities were observed between DNA methylation patterns in sheep and other more commonly studied species. The RRBS data presented here highlights the complexity of epigenetic regulation of genes. However, the similarities observed across species are promising, in that knowledge gained from epigenetic studies in human and mice may be applied, with caution, to agricultural species. The ability to accurately measure DNA methylation in agricultural animals will contribute an additional layer of information to the genetic analyses currently being used to maximise production gains in these species.

  3. Recurrent variational approach to the two-leg Hubbard ladder

    International Nuclear Information System (INIS)

    Kim, E.H.; Sierra, G.; Duffy, D.

    1999-01-01

    We applied the recurrent variational approach to the two-leg Hubbard ladder. At half filling, our variational ansatz was a generalization of the resonating valence-bond state. At finite doping, hole pairs were allowed to move in the resonating valence-bond background. The results obtained by the recurrent variational approach were compared with results from density matrix renormalization group. copyright 1999 The American Physical Society

  4. Resonant states and wavepacket super-diffusion in intra-chain correlated ladders with diluted disorder

    International Nuclear Information System (INIS)

    De Moura, F A B F; Leao, F F S; Lyra, M L

    2011-01-01

    In this work, we study a tight-binding Hamiltonian model system of a binary correlated ladder with diluted disorder. We introduce intra-chain correlations between the on-site potentials by imposing that ε i, s = - ε i,-s where s = ± 1 indexes the two ladder chains. Further, we consider each ladder chain as composed of inter-penetrating ordered and random sub-chains. We show that the presence of a random on-site distribution in one of the inter-penetrating chains leads to Anderson localization except at a specific symmetric pair of energy eigenmodes. Further, by integrating the time-dependent Schroedinger equation, we follow the time-evolution of an initially localized one-electron wavepacket. We report that the remaining delocalized resonant modes are responsible for a super-diffusive spread of the wavepacket dispersion while the wavepacket participation function remains finite. A scaling analysis of the wavepacket distribution shows that it obeys a universal scaling form with the development of a power-law tail followed by a super-diffusively evolving cutoff. We obtain three exponents characterizing this super-diffusive dynamics and show that they satisfy a simple scaling relation.

  5. Comparative analysis of protocols for DNA extraction from soybean caterpillars.

    Science.gov (United States)

    Palma, J; Valmorbida, I; da Costa, I F D; Guedes, J V C

    2016-04-07

    Genomic DNA extraction is crucial for molecular research, including diagnostic and genome characterization of different organisms. The aim of this study was to comparatively analyze protocols of DNA extraction based on cell lysis by sarcosyl, cetyltrimethylammonium bromide, and sodium dodecyl sulfate, and to determine the most efficient method applicable to soybean caterpillars. DNA was extracted from specimens of Chrysodeixis includens and Spodoptera eridania using the aforementioned three methods. DNA quantification was performed using spectrophotometry and high molecular weight DNA ladders. The purity of the extracted DNA was determined by calculating the A260/A280 ratio. Cost and time for each DNA extraction method were estimated and analyzed statistically. The amount of DNA extracted by these three methods was sufficient for PCR amplification. The sarcosyl method yielded DNA of higher purity, because it generated a clearer pellet without viscosity, and yielded high quality amplification products of the COI gene I. The sarcosyl method showed lower cost per extraction and did not differ from the other methods with respect to preparation times. Cell lysis by sarcosyl represents the best method for DNA extraction in terms of yield, quality, and cost effectiveness.

  6. Multi-material size optimization of a ladder frame chassis

    Science.gov (United States)

    Baker, Michael

    The Corporate Average Fuel Economy (CAFE) is an American fuel standard that sets regulations on fuel economy in vehicles. This law ultimately shapes the development and design research for automakers. Reducing the weight of conventional cars offers a way to improve fuel efficiency. This research investigated the optimality of an automobile's ladder frame chassis (LFC) by conducting multi-objective optimization on the LFC in order to reduce the weight of the chassis. The focus of the design and optimization was a ladder frame chassis commonly used for mass production light motor vehicles with an open-top rear cargo area. This thesis is comprised of two major sections. The first looked to perform thickness optimization in the outer walls of the ladder frame. In the second section, many multi-material distributions, including steel and aluminium varieties, were investigated. A simplified model was used to do an initial hand calculation analysis of the problem. This was used to create a baseline validation to compare the theory with the modeling. A CAD model of the LFC was designed. From the CAD model, a finite element model was extracted and joined using weld and bolt connectors. Following this, a linear static analysis was performed to look at displacement and stresses when subjected to loading conditions that simulate harsh driving conditions. The analysis showed significant values of stress and displacement on the ends of the rails, suggesting improvements could be made elsewhere. An optimization scheme was used to find the values of an all steel frame an optimal thickness distribution was found. This provided a 13% weight reduction over the initial model. To advance the analysis a multi-material approach was used to push the weight savings even further. Several material distributions were analyzed and the lightest utilized aluminium in all but the most strenuous subjected components. This enabled a reduction in weight of 15% over the initial model, equivalent to

  7. THE PAN-STARRS 1 PHOTOMETRIC REFERENCE LADDER, RELEASE 12.01

    International Nuclear Information System (INIS)

    Magnier, E. A.; Tonry, J. L.; Burgett, W. S.; Chambers, K. C.; Flewelling, H. A.; Kaiser, N.; Kudritzki, R.-P.; Morgan, J. S.; Sweeney, W. E.; Schlafly, E.; Finkbeiner, D.; Juric, M.; Stubbs, C. W.; Price, P. A.

    2013-01-01

    As of 2012 January 21, the Pan-STARRS 1 3π Survey has observed the 3/4 of the sky visible from Hawaii with a minimum of 2 and mean of 7.6 observations in five filters, g P1 , r P1 , i P1 , z P1 , y P1 . Now at the end of the second year of the mission, we are in a position to make an initial public release of a portion of this unprecedented data set. This article describes the PS1 Photometric Ladder, Release 12.01. This is the first of a series of data releases to be generated as the survey coverage increases and the data analysis improves. The Photometric Ladder has rungs every hour in right ascension and at four intervals in declination. We will release updates with increased area coverage (more rungs) from the latest data set until the PS1 survey and the final re-reduction are completed. The currently released catalog presents photometry of ∼1000 objects per square degree in the rungs of the ladder. Saturation occurs at g P1 , r P1 , i P1 ∼ 13.5; z P1 ∼ 13.0; and y P1 ∼ 12.0. Photometry is provided for stars down to g P1 , r P1 , i P1 ∼ 19.1 in the AB system. This data release depends on the rigid 'Ubercal' photometric calibration using only the photometric nights, with systematic uncertainties of (8.0, 7.0, 9.0, 10.7, 12.4) mmag in (g P1 , r P1 , i P1 , z P1 , y P1 ). Areas covered only with lower quality nights are also included, and have been tied to the Ubercal solution via relative photometry; photometric accuracy of the non-photometric regions is lower and should be used with caution.

  8. Direct observation of magnon fractionalization in the quantum spin ladder

    NARCIS (Netherlands)

    Thielemann, B.; Rüegg, C.; Rønnow, H.M.; Läuchli, A.M.; Caux, J.S.; Normand, B.; Biner, D.; Krämer, K.W.; Güdel, H.U.; Stahn, J.; Habicht, K.; Kiefer, K.; Boehm, M.; McMorrow, D.F.; Mesot, J.

    2009-01-01

    We measure by inelastic neutron scattering the spin excitation spectra as a function of applied magnetic field in the quantum spin-ladder material (C5H12N)2CuBr4. Discrete magnon modes at low fields in the quantum disordered phase and at high fields in the saturated phase contrast sharply with a

  9. Improving energy and carbon management in construction and civil engineering companies—evaluating the impacts of the CO2 Performance Ladder

    NARCIS (Netherlands)

    Rietbergen, Martijn G.; Opstelten, Ivo J.; Blok, Kornelis

    In the Netherlands, the CO2 Performance Ladder has been introduced as an energy management programme to facilitate continuous energy efficiency and carbon performance improvement in non-industrial sectors. This paper addresses the question: ‘What is the impact of the CO2 Performance Ladder on

  10. Patterns of exchange of forensic DNA data in the European Union through the Pr?m system

    OpenAIRE

    Santos, Filipe; Machado, Helena

    2017-01-01

    Article in press This paper presents a study of the 5-year operation (2011–2015) of the transnational exchange of forensic DNA data between Member States of the European Union (EU) for the purpose of combating cross-border crime and terrorism within the so-called Prüm system. This first systematisation of the full official statistical dataset provides an overall assessment of the match figures and patterns of operation of the Prüm system for DNA exchange. These figures and patterns are ana...

  11. Molecular recognition of AT-DNA sequences by the induced CD pattern of dibenzotetraaza[14]annulene (DBTAA)–adenine derivatives

    Science.gov (United States)

    Stojković, Marijana Radić; Škugor, Marko; Dudek, Łukasz; Grolik, Jarosław; Eilmes, Julita

    2014-01-01

    Summary An investigation of the interactions of two novel and several known DBTAA–adenine conjugates with double-stranded DNA and RNA has revealed the DNA/RNA groove as the dominant binding site, which is in contrast to the majority of previously studied DBTAA analogues (DNA/RNA intercalators). Only DBTAA–propyladenine conjugates revealed the molecular recognition of AT-DNA by an ICD band pattern > 300 nm, whereas significant ICD bands did not appear for other ds-DNA/RNA. A structure–activity relation for the studied series of compounds showed that the essential structural features for the ICD recognition are a) the presence of DNA-binding appendages (adenine side chain and positively charged side chain) on both DBTAA side chains, and b) the presence of a short propyl linker, which does not support intramolecular aromatic stacking between DBTAA and adenine. The observed AT-DNA-ICD pattern differs from previously reported ss-DNA (poly dT) ICD recognition by a strong negative ICD band at 350 nm, which allows for the dynamic differentiation between ss-DNA (poly dT) and coupled ds-AT-DNA. PMID:25246976

  12. Menadione-induced DNA fragmentation without 8-oxo-2'-deoxyguanosine formation in isolated rat hepatocytes

    DEFF Research Database (Denmark)

    Fischer-Nielsen, A; Corcoran, G B; Poulsen, H E

    1995-01-01

    Menadione (2-methyl-1,4-naphthoquinone) induces oxidative stress in cells causing perturbations in the cytoplasm as well as nicking of DNA. The mechanisms by which DNA damage occurs are still unclear, but a widely discussed issue is whether menadione-generated reactive oxygen species (ROS) directly...... damage DNA. In the present study, we measured the effect of menadione on formation of 7,8-dihydro-8-oxo-2'-deoxyguanosine (8-oxodG), an index of oxidative DNA base modifications, and on DNA fragmentation. Isolated hepatocytes from phenobarbital-pretreated rats were exposed to menadione, 25-400 micro......M, for 15, 90 or 180 min with or without prior depletion of reduced glutathione (GSH) by diethyl maleate. Menadione caused profound GSH depletion and internucleosomal DNA fragmentation, which was demonstrated by a prominent fragmentation ladder on agarose gel electrophoresis. We found no oxidative...

  13. Parents' Participation on School Councils Analysed through Arnstein's Ladder of Participation

    Science.gov (United States)

    Stelmach, Bonnie

    2016-01-01

    Although parent school councils are the archetypal arrangement for engaging parents in school improvement planning, their effectiveness is negligible when it comes to building parents' capacity for and confidence in educational decision-making. Using Arnstein's ladder of citizen participation, this qualitative case study investigated the nature…

  14. Biomolecular and structural analyses of cauliflower-like DNAs by ultraviolet, circular dichroism, and fluorescence spectroscopies in comparison with natural DNA.

    Science.gov (United States)

    Gill, Pooria; Ranjbar, Bijan; Saber, Reza; Khajeh, Khosro; Mohammadian, Mehdi

    2011-07-01

    Cauliflower-like DNAs are stem-loop DNAs that are fabricated periodically in inverted repetitions from deoxyribonucleic acid phosphates (dNTPs) by loop-mediated isothermal amplification (LAMP). Cauliflower-like DNAs have ladder-shape behaviors on gel electrophoresis, and increasing the time of LAMP leads to multiplying the repetitions, stem-loops, and electrophoretic bands. Cauliflower-like DNAs were fabricated via LAMP using two loop primers, two bumper primers, dNTPs, a λ-phage DNA template, and a Bst DNA polymerase in 75- and 90-min periods. These times led to manufacturing two types of cauliflower-like DNAs with different contents of inverted repetitions and stem-loops, which were clearly indicated by two comparable electrophoresis patterns in agarose gel. LAMP-fabricated DNAs and natural dsB-DNA (salmon genomic DNA) were dialyzed in Gomori phosphate buffer (10 mM, pH 7.4) to be isolated from salts, nucleotides, and primers. Dialyzed DNAs were studied using UV spectroscopy, circular dichroism spectropolarimetry, and fluorescence spectrophotometry. Structural analyses indicated reduction of the molecular ellipticity and extinction coefficients in comparison with B-DNA. Also, cauliflower-like DNAs demonstrated less intrinsic and more extrinsic fluorescence in comparison with natural DNA. The overwinding and lengthening of the cauliflower-like configurations of LAMP DNAs led to changes in physical parameters of this type of DNA in comparison with natural DNA. The results obtained introduced new biomolecular characteristics of DNA macromolecules fabricated within a LAMP process and show the effects of more inverted repeats and stem-loops, which are manufactured by lengthening the process.

  15. Bethe-Salpeter equation for fermion-antifermion system in the ladder approximation

    International Nuclear Information System (INIS)

    Fukui, Ichio; Seto, Noriaki; Yoshida, Toshihiro.

    1977-01-01

    The Bethe-Salpeter (B-S) equation is important for studying hadron physics. Especially intensive investigation on the fermion-antifermion B-S equation is indispensable for the phenomenological studies of hardrons. However, many components of the B-S amplitude and the Wick-rotated integral kernel of non-Fredholm type have prevented from knowing details the solutions even in the ladder approximation. Some particular solutions are known in case of the vanishing four-momenta of bound states. The B-S equation for the bound state of fermion-anti-fermion system interacting through vector (axial-vector) particle exchange was studied in the ladder approximation with Feynman gauge. The reduced equations were obtained for suitably decomposed amplitude, and it is shown that, in the S-wave case, the coupled equations separate into two parts. In the nonrelativistic limit, large components of the amplitude satisfy the Wick-Cutkosky equation, and small components are expressed in terms of the large ones. Equations are derived for the equal-time amplitudes. (Kobatake, H.)

  16. Efficient representation of DNA data for pattern recognition using failure factor oracles

    NARCIS (Netherlands)

    Cleophas, Loek; Kourie, Derrick G.; Watson, Bruce W.

    2013-01-01

    In indexing of and pattern matching on DNA sequences, representing all factors of a sequence is important. One efficient, compact representation is the factor oracle (FO). At the same time, any classical deterministic finite automata (DFA) can be transformed to a so-called failure one (FDFA), which

  17. A new sieving matrix for DNA sequencing, genotyping and mutation detection and high-throughput genotyping with a 96-capillary array system

    Energy Technology Data Exchange (ETDEWEB)

    Gao, David [Iowa State Univ., Ames, IA (United States)

    1999-11-08

    Capillary electrophoresis has been widely accepted as a fast separation technique in DNA analysis. In this dissertation, a new sieving matrix is described for DNA analysis, especially DNA sequencing, genetic typing and mutation detection. A high-throughput 96 capillary array electrophoresis system was also demonstrated for simultaneous multiple genotyping. The authors first evaluated the influence of different capillary coatings on the performance of DNA sequencing. A bare capillary was compared with a DB-wax, an FC-coated and a polyvinylpyrrolidone dynamically coated capillary with PEO as sieving matrix. It was found that covalently-coated capillaries had no better performance than bare capillaries while PVP coating provided excellent and reproducible results. The authors also developed a new sieving Matrix for DNA separation based on commercially available poly(vinylpyrrolidone) (PVP). This sieving matrix has a very low viscosity and an excellent self-coating effect. Successful separations were achieved in uncoated capillaries. Sequencing of M13mp18 showed good resolution up to 500 bases in treated PVP solution. Temperature gradient capillary electrophoresis and PVP solution was applied to mutation detection. A heteroduplex sample and a homoduplex reference were injected during a pair of continuous runs. A temperature gradient of 10 C with a ramp of 0.7 C/min was swept throughout the capillary. Detection was accomplished by laser induced fluorescence detection. Mutation detection was performed by comparing the pattern changes between the homoduplex and the heteroduplex samples. High throughput, high detection rate and easy operation were achieved in this system. They further demonstrated fast and reliable genotyping based on CTTv STR system by multiple-capillary array electrophoresis. The PCR products from individuals were mixed with pooled allelic ladder as an absolute standard and coinjected with a 96-vial tray. Simultaneous one-color laser-induced fluorescence

  18. Spin ordering in three-leg ladders in Ludwigite systems

    International Nuclear Information System (INIS)

    Vallejo, E.; Avignon, M.

    2007-01-01

    We study the spin ordering in a three-leg ladder present in Ludwigite systems formed of localized spins interacting with an extra electron per rung. We also consider the competition with super exchange interactions resulting in a very rich phase diagram. Among the phases we find the possibility of ferromagnetic rungs ordered antiferromagnetically and a zigzag spin ordering linked to the formation of a charge ordering as observed

  19. Patterns of DNA barcode variation in Canadian marine molluscs.

    Science.gov (United States)

    Layton, Kara K S; Martel, André L; Hebert, Paul D N

    2014-01-01

    Molluscs are the most diverse marine phylum and this high diversity has resulted in considerable taxonomic problems. Because the number of species in Canadian oceans remains uncertain, there is a need to incorporate molecular methods into species identifications. A 648 base pair segment of the cytochrome c oxidase subunit I gene has proven useful for the identification and discovery of species in many animal lineages. While the utility of DNA barcoding in molluscs has been demonstrated in other studies, this is the first effort to construct a DNA barcode registry for marine molluscs across such a large geographic area. This study examines patterns of DNA barcode variation in 227 species of Canadian marine molluscs. Intraspecific sequence divergences ranged from 0-26.4% and a barcode gap existed for most taxa. Eleven cases of relatively deep (>2%) intraspecific divergence were detected, suggesting the possible presence of overlooked species. Structural variation was detected in COI with indels found in 37 species, mostly bivalves. Some indels were present in divergent lineages, primarily in the region of the first external loop, suggesting certain areas are hotspots for change. Lastly, mean GC content varied substantially among orders (24.5%-46.5%), and showed a significant positive correlation with nearest neighbour distances. DNA barcoding is an effective tool for the identification of Canadian marine molluscs and for revealing possible cases of overlooked species. Some species with deep intraspecific divergence showed a biogeographic partition between lineages on the Atlantic, Arctic and Pacific coasts, suggesting the role of Pleistocene glaciations in the subdivision of their populations. Indels were prevalent in the barcode region of the COI gene in bivalves and gastropods. This study highlights the efficacy of DNA barcoding for providing insights into sequence variation across a broad taxonomic group on a large geographic scale.

  20. Measurement of the Rise-Time in a Single Sided Ladder Detector

    International Nuclear Information System (INIS)

    Gerber, C.E.

    1997-01-01

    In this note we report on the measurement of the preamplifier output rise time for a SVXII chip mounted on a D0 single sided ladder. The measurements were performed on the ladder 001-883-L, using the laser test stand of Lab D. The rise time was measured for different values of the response (or bandwidth) of the preamplifier. As a bigger bandwidth results in longer rise times and therefore in less noise, the largest possible bandwidth consistent with the time between bunch crossings should be chosen to operate the detectors. The rise time is defined as the time elapsed between 10% and 90% of the charge is collected. It is also interesting to measure the time for full charge collection and the percentage of charge collected in 132 ns and 396 ns. The results are shown in table 1, for bandwidths between 2 and 63 (binary numbers). The uncertainty on the time measurement is considered to be ∼ 10 ns. Figure 1 schematically defines the four quantities measured: rise time, time of full charge collection, and percentage of charge collected in 132 ns and 396 ns. Figures 2 to 8 are the actual measurements for bandwidths of 2, 4, 8, 12, 24, 32 and 63. Figure 9 is a second measurement for BW=24, used as a consistency check of the system and the time measurement performed on the plots. The data indicate that the single sided ladders can be operated at BW=63 for 396 ns and BW=12 for 132 ns, achieving full charge collection. This will result in smaller noise than originally anticipated.

  1. Surface Acoustic Analog of Bloch Oscillations, Wannier-Stark Ladders and Landau-Zener Tunneling

    Science.gov (United States)

    de Lima, M. M.; Kosevich, Yu. A.; Santos, P. V.; Cantarero, A.

    2011-12-01

    In this contribution, we discuss the recent experimental demonstration of Wannier-Stark ladders, Bloch Oscillations and Landau Zener tunneling in a solid by means of surface acoustic waves propagating through perturbed grating structures.

  2. Vibronic dephasing model for coherent-to-incoherent crossover in DNA

    Science.gov (United States)

    Karasch, Patrick; Ryndyk, Dmitry A.; Frauenheim, Thomas

    2018-05-01

    In this paper, we investigate the interplay between coherent and incoherent charge transport in cytosine-guanine (GC-) rich DNA molecules. Our objective is to introduce a physically grounded approach to dephasing in large molecules and to understand the length-dependent charge transport characteristics, and especially the crossover from the coherent tunneling to incoherent hopping regime at different temperatures. Therefore, we apply the vibronic dephasing model and compare the results to the Büttiker probe model which is commonly used to describe decoherence effects in charge transport. Using the full ladder model and simplified one-dimensional model of DNA, we consider molecular junctions with alternating and stacked GC sequences and compare our results to recent experimental measurements.

  3. Using a familiar risk comparison within a risk ladder to improve risk understanding by low numerates: a study of visual attention.

    Science.gov (United States)

    Keller, Carmen

    2011-07-01

    Previous experimental research provides evidence that a familiar risk comparison within a risk ladder is understood by low- and high-numerate individuals. It especially helps low numerates to better evaluate risk. In the present study, an eye tracker was used to capture individuals' visual attention to a familiar risk comparison, such as the risk associated with smoking. Two parameters of information processing-efficiency and level-were derived from visual attention. A random sample of participants from the general population (N= 68) interpreted a given risk level with the help of the risk ladder. Numeracy was negatively correlated with overall visual attention on the risk ladder (r(s) =-0.28, p= 0.01), indicating that the lower the numeracy, the more the time spent looking at the whole risk ladder. Numeracy was positively correlated with the efficiency of processing relevant frequency (r(s) = 0.34, p improving risk communication formats. © 2011 Society for Risk Analysis.

  4. Adolescent binge-pattern alcohol exposure alters genome-wide DNA methylation patterns in the hypothalamus of alcohol-naïve male offspring.

    Science.gov (United States)

    Asimes, AnnaDorothea; Torcaso, Audrey; Pinceti, Elena; Kim, Chun K; Zeleznik-Le, Nancy J; Pak, Toni R

    2017-05-01

    Teenage binge drinking is a major health concern in the United States, with 21% of teenagers reporting binge-pattern drinking behavior in the previous 30 days. Recently, our lab showed that alcohol-naïve offspring of rats exposed to alcohol during adolescence exhibited altered gene expression profiles in the hypothalamus, a brain region involved in stress regulation. We employed Enhanced Reduced Representation Bisulfite Sequencing as an unbiased approach to test the hypothesis that parental exposure to binge-pattern alcohol during adolescence alters DNA methylation profiles in their alcohol-naïve offspring. Wistar rats were administered a repeated binge-ethanol exposure paradigm during early (postnatal day (PND) 37-44) and late (PND 67-74) adolescent development. Animals were mated 24 h after the last ethanol dose and subsequent offspring were produced. Analysis of male PND7 offspring revealed that offspring of alcohol-exposed parents exhibited differential DNA methylation patterns in the hypothalamus. The differentially methylated cytosines (DMCs) were distinct between offspring depending on which parent was exposed to ethanol. Moreover, novel DMCs were observed when both parents were exposed to ethanol and many DMCs from single parent ethanol exposure were not recapitulated with dual parent exposure. We also measured mRNA expression of several differentially methylated genes and some, but not all, showed correlative changes in expression. Importantly, methylation was not a direct predictor of expression levels, underscoring the complexity of transcriptional regulation. Overall, we demonstrate that adolescent binge ethanol exposure causes altered genome-wide DNA methylation patterns in the hypothalamus of alcohol-naïve offspring. Copyright © 2016 Elsevier Inc. All rights reserved.

  5. Implementability of two-qubit unitary operations over the butterfly network and the ladder network with free classical communication

    Energy Technology Data Exchange (ETDEWEB)

    Akibue, Seiseki [Department of Physics, Graduate School of Science, The University of Tokyo, Tokyo (Japan); Murao, Mio [Department of Physics, Graduate School of Science, The University of Tokyo, Tokyo, Japan and NanoQuine, The University of Tokyo, Tokyo (Japan)

    2014-12-04

    We investigate distributed implementation of two-qubit unitary operations over two primitive networks, the butterfly network and the ladder network, as a first step to apply network coding for quantum computation. By classifying two-qubit unitary operations in terms of the Kraus-Cirac number, the number of non-zero parameters describing the global part of two-qubit unitary operations, we analyze which class of two-qubit unitary operations is implementable over these networks with free classical communication. For the butterfly network, we show that two classes of two-qubit unitary operations, which contain all Clifford, controlled-unitary and matchgate operations, are implementable over the network. For the ladder network, we show that two-qubit unitary operations are implementable over the network if and only if their Kraus-Cirac number do not exceed the number of the bridges of the ladder.

  6. Implementability of two-qubit unitary operations over the butterfly network and the ladder network with free classical communication

    International Nuclear Information System (INIS)

    Akibue, Seiseki; Murao, Mio

    2014-01-01

    We investigate distributed implementation of two-qubit unitary operations over two primitive networks, the butterfly network and the ladder network, as a first step to apply network coding for quantum computation. By classifying two-qubit unitary operations in terms of the Kraus-Cirac number, the number of non-zero parameters describing the global part of two-qubit unitary operations, we analyze which class of two-qubit unitary operations is implementable over these networks with free classical communication. For the butterfly network, we show that two classes of two-qubit unitary operations, which contain all Clifford, controlled-unitary and matchgate operations, are implementable over the network. For the ladder network, we show that two-qubit unitary operations are implementable over the network if and only if their Kraus-Cirac number do not exceed the number of the bridges of the ladder

  7. Acute effects of Resistance exercise performed on ladder on energy metabolism, stress, and muscle damage in rats

    Directory of Open Access Journals (Sweden)

    João Guilherme Oliveira Silvestre

    2017-05-01

    Full Text Available Abstract AIMS To evaluate the acute effects of a resistance exercise session performed on ladder on energy metabolism, stress, and muscle damage in rats. METHODS Male Wistar rats were randomly distributed in Exercise (E (n=30 and Control (C (n = 20 groups. The E group performed a resistance exercise session on a vertical ladder with weights on their tails. Blood samples were collected at rest and after each climb to analyze lactate levels and ten minutes after the last climb to analyze lactate dehydrogenase (LDH, creatine kinase (CK, and corticosterone levels. RESULTS Blood lactate levels remained stable during exercise. Serum corticosterone, blood glucose, LDH and CK levels increased and glycogen content decreased in the E group, when compared to the C group. CONCLUSION These results suggest that resistance exercise performed on ladder is a model of high-intensity exercise. However, the stabilization of lactate during the session suggests that the aerobic metabolism is an important factor during the intervals between climbs.

  8. Ground-state and spectral properties of an asymmetric Hubbard ladder

    Science.gov (United States)

    Abdelwahab, Anas; Jeckelmann, Eric; Hohenadler, Martin

    2015-04-01

    We investigate a ladder system with two inequivalent legs, namely, a Hubbard chain and a one-dimensional electron gas. Analytical approximations, the density-matrix renormalization group method, and continuous-time quantum Monte Carlo simulations are used to determine ground-state properties, gaps, and spectral functions of this system at half-filling. Evidence for the existence of four different phases as a function of the Hubbard interaction and the rung hopping is presented. First, a Luttinger liquid exists at very weak interchain hopping. Second, a Kondo-Mott insulator with spin and charge gaps induced by an effective rung exchange coupling is found at moderate interchain hopping or strong Hubbard interaction. Third, a spin-gapped paramagnetic Mott insulator with incommensurate excitations and pairing of doped charges is observed at intermediate values of the rung hopping and the interaction. Fourth, the usual correlated band insulator is recovered for large rung hopping. We show that the wave numbers of the lowest single-particle excitations are different in each insulating phase. In particular, the three gapped phases exhibit markedly different spectral functions. We discuss the relevance of asymmetric two-leg ladder systems as models for atomic wires deposited on a substrate.

  9. Selection of an experimental fish ladder located at the dam of the Itaipu Binacional, Paraná River, Brazil

    Directory of Open Access Journals (Sweden)

    Domingo Rodriguez Fernandez

    2004-08-01

    Full Text Available The specific selection of a weir and orifice type experimental fish ladder in the dam of the Itaipu Reservoir (Paraná River was evaluated by samplings in the river downstream and at two points along the ladder (at heights of 10 m and 27 m during 28 months. Among the 65 species recorded in the river (immediate downstream of the dam, 27 were captured on the ladder. The species that showed highest density on the ladder, the majority migratory, were moderately, or only slightly, abundant downstream. Among the most abundant species downstream, only one, non-migratory, was recorded in the ladder. The structure presented a negative selection in relation to large migratory pimelodids that might be overcome by enlarging the scale of its design. The sampling demonstrated a moderate selection of species along the ladder and its hydraulic model proved satisfactory regarding the attraction and efficient ascent of the fishes.A seleção específica de uma escada de peixes do tipo seqüência de tanques, com passagem de fundo (tipo weir and orifice, na barragem da hidrelétrica de Itaipu (rio Paraná, foi avaliada através de amostragens no rio a jusante (amostragem trimestral em 1997 e em dois pontos ao longo da escada (10 e 27m de altura; nov/94 a jan/97 e nov/94 a fev/97, respectivamente. Das 65 espécies registradas no rio imediatamente a jusante da barragem, 27 foram capturadas na escada. As espécies com maior densidade na escada, em sua maioria migradoras, tiveram abundância moderada ou baixa a jusante. Entre as mais abundantes a jusante, apenas uma, não migradora, foi registrada na escada. A escada apresentou seleção negativa aos grandes pimelodídeos migradores que pode ser superada com a ampliação na escala do projeto. As amostragens evidenciaram baixa seletividade específica ao longo da escada, sendo seu modelo hidráulico satisfatório na atração e eficiente na ascensão de peixes.

  10. Frustrated quantum magnetism in the Kondo lattice on the zigzag ladder

    Science.gov (United States)

    Peschke, Matthias; Rausch, Roman; Potthoff, Michael

    2018-03-01

    The interplay between the Kondo effect, indirect magnetic interaction, and geometrical frustration is studied in the Kondo lattice on the one-dimensional zigzag ladder. Using the density-matrix renormalization group, the ground-state and various short- and long-range spin- and density-correlation functions are calculated for the model at half filling as a function of the antiferromagnetic Kondo interaction down to J =0.3 t , where t is the nearest-neighbor hopping on the zigzag ladder. Geometrical frustration is shown to lead to at least two critical points: Starting from the strong-J limit, where almost local Kondo screening dominates and where the system is a nonmagnetic Kondo insulator, antiferromagnetic correlations between nearest-neighbor and next-nearest-neighbor local spins become stronger and stronger, until at Jcdim≈0.89 t frustration is alleviated by a spontaneous breaking of translational symmetry and a corresponding transition to a dimerized state. This is characterized by antiferromagnetic correlations along the legs and by alternating antiferro- and ferromagnetic correlations on the rungs of the ladder. A mechanism of partial Kondo screening that has been suggested for the Kondo lattice on the two-dimensional triangular lattice is not realized in the one-dimensional case. Furthermore, within the symmetry-broken dimerized state, there is a magnetic transition to a 90∘ quantum spin spiral with quasi-long-range order at Jcmag≈0.84 t . The quantum-critical point is characterized by a closure of the spin gap (with decreasing J ) and a divergence of the spin-correlation length and of the spin-structure factor S (q ) at wave vector q =π /2 . This is opposed to the model on the one-dimensional bipartite chain, which is known to have a finite spin gap for all J >0 at half filling.

  11. A Demonstration of Helping Adolescents with Mild Intellectual Disability Climb Ladders

    Science.gov (United States)

    Chan, Kok Hoe Anthony; Varahan, Jayashree Lakshmi; Loh, Peng Loong Daniel; Tan, Sey Ing

    2011-01-01

    A research team at a vocational school in Singapore, catering mainly to students between the ages of 17-21 with mild intellectual disability, studied how to best address the challenge of enabling students to learn how to climb ladders (a skill necessary at many job placements). They documented the approach used and suggested extrapolations and…

  12. Discovering approximate-associated sequence patterns for protein-DNA interactions

    KAUST Repository

    Chan, Tak Ming

    2010-12-30

    Motivation: The bindings between transcription factors (TFs) and transcription factor binding sites (TFBSs) are fundamental protein-DNA interactions in transcriptional regulation. Extensive efforts have been made to better understand the protein-DNA interactions. Recent mining on exact TF-TFBS-associated sequence patterns (rules) has shown great potentials and achieved very promising results. However, exact rules cannot handle variations in real data, resulting in limited informative rules. In this article, we generalize the exact rules to approximate ones for both TFs and TFBSs, which are essential for biological variations. Results: A progressive approach is proposed to address the approximation to alleviate the computational requirements. Firstly, similar TFBSs are grouped from the available TF-TFBS data (TRANSFAC database). Secondly, approximate and highly conserved binding cores are discovered from TF sequences corresponding to each TFBS group. A customized algorithm is developed for the specific objective. We discover the approximate TF-TFBS rules by associating the grouped TFBS consensuses and TF cores. The rules discovered are evaluated by matching (verifying with) the actual protein-DNA binding pairs from Protein Data Bank (PDB) 3D structures. The approximate results exhibit many more verified rules and up to 300% better verification ratios than the exact ones. The customized algorithm achieves over 73% better verification ratios than traditional methods. Approximate rules (64-79%) are shown statistically significant. Detailed variation analysis and conservation verification on NCBI records demonstrate that the approximate rules reveal both the flexible and specific protein-DNA interactions accurately. The approximate TF-TFBS rules discovered show great generalized capability of exploring more informative binding rules. © The Author 2010. Published by Oxford University Press. All rights reserved.

  13. Topic Order in Introductory Physics and its Impact on the STEM Curricular Ladder

    Directory of Open Access Journals (Sweden)

    Teresa L Larkin

    2017-02-01

    Full Text Available Introductory physics courses are an important rung on the curricular ladder in STEM. These courses help to strengthen students critical thinking and problem solving skills while simultaneously introducing them to many topics they will explore in more detail in later courses in physics and engineering. For these reasons, introductory physics is a required element on the curricular ladder. Most often, introductory physics is offered as a two-semester sequence with basic mechanics being taught in the first semester and electricity and magnetism in the second. In fact, this curricular sequence has not been altered in decades. Is there a reason for this? There are many other enduring questions that arise pertaining to these foundation courses in physics. These questions include: Does taking the introductory course sequence “out of order” have an impact on student learning in physics? What topics should be taught? When should these topics be taught? What topics could be left out? The list of questions is essentially endless. This paper will address some of these questions in part, through a brief discussion on student learning in a second-semester algebra-based physics course. Connections will also be made to the broader curricular ladder in STEM. To this end, an illustration that makes connections to an engineering statics course will be presented. This discussion will conclude by presenting some broader implications for the larger STEM communities.

  14. Early Developmental and Evolutionary Origins of Gene Body DNA Methylation Patterns in Mammalian Placentas.

    Directory of Open Access Journals (Sweden)

    Diane I Schroeder

    2015-08-01

    Full Text Available Over the last 20-80 million years the mammalian placenta has taken on a variety of morphologies through both divergent and convergent evolution. Recently we have shown that the human placenta genome has a unique epigenetic pattern of large partially methylated domains (PMDs and highly methylated domains (HMDs with gene body DNA methylation positively correlating with level of gene expression. In order to determine the evolutionary conservation of DNA methylation patterns and transcriptional regulatory programs in the placenta, we performed a genome-wide methylome (MethylC-seq analysis of human, rhesus macaque, squirrel monkey, mouse, dog, horse, and cow placentas as well as opossum extraembryonic membrane. We found that, similar to human placenta, mammalian placentas and opossum extraembryonic membrane have globally lower levels of methylation compared to somatic tissues. Higher relative gene body methylation was the conserved feature across all mammalian placentas, despite differences in PMD/HMDs and absolute methylation levels. Specifically, higher methylation over the bodies of genes involved in mitosis, vesicle-mediated transport, protein phosphorylation, and chromatin modification was observed compared with the rest of the genome. As in human placenta, higher methylation is associated with higher gene expression and is predictive of genic location across species. Analysis of DNA methylation in oocytes and preimplantation embryos shows a conserved pattern of gene body methylation similar to the placenta. Intriguingly, mouse and cow oocytes and mouse early embryos have PMD/HMDs but their placentas do not, suggesting that PMD/HMDs are a feature of early preimplantation methylation patterns that become lost during placental development in some species and following implantation of the embryo.

  15. 29 CFR 1910.29 - Manually propelled mobile ladder stands and scaffolds (towers).

    Science.gov (United States)

    2010-07-01

    ... HEALTH ADMINISTRATION, DEPARTMENT OF LABOR OCCUPATIONAL SAFETY AND HEALTH STANDARDS Walking-Working... edges, burrs or other safety hazards. (3) Work levels. (i) The maximum work level height shall not... rigid platforms at each work level. (iv) The steps of ladder stands shall be fabricated from slip...

  16. Quantification of apoptotic DNA fragmentation in a transformed uterine epithelial cell line, HRE-H9, using capillary electrophoresis with laser-induced fluorescence detector (CE-LIF).

    Science.gov (United States)

    Fiscus, R R; Leung, C P; Yuen, J P; Chan, H C

    2001-01-01

    Apoptotic cell death of uterine epithelial cells is thought to play an important role in the onset of menstruation and the successful implantation of an embryo during early pregnancy. Abnormal apoptosis in these cells can result in dysmenorrhoea and infertility. In addition, decreased rate of epithelial apoptosis likely contributes to endometriosis. A key step in the onset of apoptosis in these cells is cleavage of the genomic DNA between nucleosomes, resulting in polynucleosomal-sized fragments of DNA. The conventional technique for assessing apoptotic DNA fragmentation uses agarose (slab) gel electrophoresis (i.e. DNA laddering). However, recent technological advances in the use of capillary electrophoresis (CE), particularly the introduction of the laser-induced fluorescence detector (LIF), has made it possible to perform DNA laddering with improved automation and much greater sensitivity. In the present study, we have further developed the CE-LIF technique by using a DNA standard curve to quantify accurately the amount of DNA in the apoptotic DNA fragments and have applied this new quantitative technique to study apoptosis in a transformed uterine epithelial cell line, the HRE-H9 cells. Apoptosis was induced in the HRE-H9 cells by serum deprivation for 5, 7 and 24 h, resulting in increased DNA fragmentation of 2.2-, 3.1- and 6.2-fold, respectively, above the 0 h or plus-serum controls. This ultrasensitive CE-LIF technique provides a novel method for accurately measuring the actions of pro- or anti-apoptotic agents or conditions on uterine epithelial cell lines. Copyright 2001 Academic Press.

  17. Alteration of gene conversion patterns in Sordaria fimicola by supplementation with DNA bases.

    Science.gov (United States)

    Kitani, Y; Olive, L S

    1970-08-01

    Supplementation with DNA bases in crosses of Sordaria fimicola heterozygous for spore color markers (g(1), h(2)) within the gray-spore (g) locus has been found to cause significant alterations in patterns of gene conversion at the two mutant sites. Each base had its own characteristic effect in altering the conversion pattern, and responses of the two mutant sites to the four bases were different in several ways. Also, the responses of the two involved chromatids of the meiotic bivalent were different.

  18. The Genomic Pattern of tDNA Operon Expression in E. coli.

    Directory of Open Access Journals (Sweden)

    2005-06-01

    Full Text Available In fast-growing microorganisms, a tRNA concentration profile enriched in major isoacceptors selects for the biased usage of cognate codons. This optimizes translational rate for the least mass invested in the translational apparatus. Such translational streamlining is thought to be growth-regulated, but its genetic basis is poorly understood. First, we found in reanalysis of the E. coli tRNA profile that the degree to which it is translationally streamlined is nearly invariant with growth rate. Then, using least squares multiple regression, we partitioned tRNA isoacceptor pools to predicted tDNA operons from the E. coli K12 genome. Co-expression of tDNAs in operons explains the tRNA profile significantly better than tDNA gene dosage alone. Also, operon expression increases significantly with proximity to the origin of replication, oriC, at all growth rates. Genome location explains about 15% of expression variation in a form, at a given growth rate, that is consistent with replication-dependent gene concentration effects. Yet the change in the tRNA profile with growth rate is less than would be expected from such effects. We estimated per-copy expression rates for all tDNA operons that were consistent with independent estimates for rDNA operons. We also found that tDNA operon location, and the location dependence of expression, were significantly different in the leading and lagging strands. The operonic organization and genomic location of tDNA operons are significant factors influencing their expression. Nonrandom patterns of location and strandedness shown by tDNA operons in E. coli suggest that their genomic architecture may be under selection to satisfy physiological demand for tRNA expression at high growth rates.

  19. The Effect of Metabolic and Bariatric Surgery on DNA Methylation Patterns.

    Science.gov (United States)

    Morcillo, Sonsoles; Macías-González, Manuel; Tinahones, Francisco J

    2017-08-30

    Metabolic and bariatric surgery (MBS) is considered to be the most effective treatment for obesity. Not only due to the significant weight reduction but also because of the many health benefits associated with it. In the last 5 years, several studies have suggested that epigenetic modifications could be involved in the mechanisms underlying the response to bariatric surgery. In this review, we will compile the different studies (2012-2017) concerning the effect of this surgical procedure on DNA methylation patterns (the most studied epigenetic marker) and its association with metabolic improvement. This is an emerging area, and currently, there are not many studies in the literature. The aim is to show what has been done so far and what the future direction in this emerging area might be. Recent findings have shown how metabolic and bariatric surgery modifies the DNA methylation profile of the specific genes associated with the pathophysiology of the disease. The studies were performed in morbidly obese subjects, mainly in women, with the aim of reducing weight and improving the obesity-associated comorbidities. DNA methylation has been measured both in specific tissue and in peripheral blood samples. In general, studies about site-specific DNA methylation have shown a change in the methylation profile after surgery, whereas the studies analyzing global DNA methylation are not so conclusive. Summing up, metabolic and bariatric surgery can modify the DNA methylation profile of different genes and contributes to the metabolic health benefits that are often seen after metabolic and bariatric surgery. Although there are still many issues to be resolved, the capacity to revert the DNA methylation profile of specific sites opens a window for searching for target markers to treat obesity-related comorbidities.

  20. The DNA electronic specific heat at low temperature: The role of aperiodicity

    Energy Technology Data Exchange (ETDEWEB)

    Sarmento, R.G. [Departamento de Física, Universidade Federal do Rio Grande do Norte, 59072-970, Natal, RN (Brazil); Mendes, G.A. [Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970, Natal, RN (Brazil); Albuquerque, E.L., E-mail: eudenilson@gmail.com [Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970, Natal, RN (Brazil); Fulco, U.L. [Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970, Natal, RN (Brazil); Vasconcelos, M.S. [Escola de Ciências e Tecnologia, Universidade Federal do Rio Grande do Norte, 59072-970, Natal, RN (Brazil); Ujsághy, O. [Department of Theoretical Physics and Condensed Matter Research Group of the Hungarian Academy of Sciences, Budapest University of Technology and Economics, Budafoki út 8, H-1521 Budapest (Hungary); Freire, V.N. [Departamento de Física, Universidade Federal do Ceará, 60455-760, Fortaleza, CE (Brazil); Caetano, E.W.S. [Instituto Federal de Educação, Ciência e Tecnologia do Ceará, 60040-531, Fortaleza, CE (Brazil)

    2012-07-16

    The electronic specific heat spectra at constant volume (C{sub V}) of a long-range correlated extended ladder model, mimicking a DNA molecule, is theoretically analyzed for a stacked array of a double-stranded structure made up from the nucleotides guanine G, adenine A, cytosine C and thymine T. The role of the aperiodicity on C{sub V} is discussed, considering two different nucleotide arrangements with increasing disorder, namely the Fibonacci and the Rudin–Shapiro quasiperiodic structures. Comparisons are made for different values of the band fillings, considering also a finite segment of natural DNA, as part of the human chromosome Ch22. -- Highlights: ► Quasiperiodic sequence to mimic the DNA nucleotides arrangement. ► Electronic tight-binding Hamiltonian model. ► Electronic density of states. ► Electronic specific heat spectra.

  1. Clarifying the Hubble constant tension with a Bayesian hierarchical model of the local distance ladder

    Science.gov (United States)

    Feeney, Stephen M.; Mortlock, Daniel J.; Dalmasso, Niccolò

    2018-05-01

    Estimates of the Hubble constant, H0, from the local distance ladder and from the cosmic microwave background (CMB) are discrepant at the ˜3σ level, indicating a potential issue with the standard Λ cold dark matter (ΛCDM) cosmology. A probabilistic (i.e. Bayesian) interpretation of this tension requires a model comparison calculation, which in turn depends strongly on the tails of the H0 likelihoods. Evaluating the tails of the local H0 likelihood requires the use of non-Gaussian distributions to faithfully represent anchor likelihoods and outliers, and simultaneous fitting of the complete distance-ladder data set to ensure correct uncertainty propagation. We have hence developed a Bayesian hierarchical model of the full distance ladder that does not rely on Gaussian distributions and allows outliers to be modelled without arbitrary data cuts. Marginalizing over the full ˜3000-parameter joint posterior distribution, we find H0 = (72.72 ± 1.67) km s-1 Mpc-1 when applied to the outlier-cleaned Riess et al. data, and (73.15 ± 1.78) km s-1 Mpc-1 with supernova outliers reintroduced (the pre-cut Cepheid data set is not available). Using our precise evaluation of the tails of the H0 likelihood, we apply Bayesian model comparison to assess the evidence for deviation from ΛCDM given the distance-ladder and CMB data. The odds against ΛCDM are at worst ˜10:1 when considering the Planck 2015 XIII data, regardless of outlier treatment, considerably less dramatic than naïvely implied by the 2.8σ discrepancy. These odds become ˜60:1 when an approximation to the more-discrepant Planck Intermediate XLVI likelihood is included.

  2. Contrasting Patterns of rDNA Homogenization within the Zygosaccharomyces rouxii Species Complex

    Science.gov (United States)

    Chand Dakal, Tikam; Giudici, Paolo; Solieri, Lisa

    2016-01-01

    Arrays of repetitive ribosomal DNA (rDNA) sequences are generally expected to evolve as a coherent family, where repeats within such a family are more similar to each other than to orthologs in related species. The continuous homogenization of repeats within individual genomes is a recombination process termed concerted evolution. Here, we investigated the extent and the direction of concerted evolution in 43 yeast strains of the Zygosaccharomyces rouxii species complex (Z. rouxii, Z. sapae, Z. mellis), by analyzing two portions of the 35S rDNA cistron, namely the D1/D2 domains at the 5’ end of the 26S rRNA gene and the segment including the internal transcribed spacers (ITS) 1 and 2 (ITS regions). We demonstrate that intra-genomic rDNA sequence variation is unusually frequent in this clade and that rDNA arrays in single genomes consist of an intermixing of Z. rouxii, Z. sapae and Z. mellis-like sequences, putatively evolved by reticulate evolutionary events that involved repeated hybridization between lineages. The levels and distribution of sequence polymorphisms vary across rDNA repeats in different individuals, reflecting four patterns of rDNA evolution: I) rDNA repeats that are homogeneous within a genome but are chimeras derived from two parental lineages via recombination: Z. rouxii in the ITS region and Z. sapae in the D1/D2 region; II) intra-genomic rDNA repeats that retain polymorphisms only in ITS regions; III) rDNA repeats that vary only in their D1/D2 domains; IV) heterogeneous rDNA arrays that have both polymorphic ITS and D1/D2 regions. We argue that an ongoing process of homogenization following allodiplodization or incomplete lineage sorting gave rise to divergent evolutionary trajectories in different strains, depending upon temporal, structural and functional constraints. We discuss the consequences of these findings for Zygosaccharomyces species delineation and, more in general, for yeast barcoding. PMID:27501051

  3. Electron spin resonance modes in a strong-leg ladder in the Tomonaga-Luttinger liquid phase

    Science.gov (United States)

    Ozerov, M.; Maksymenko, M.; Wosnitza, J.; Honecker, A.; Landee, C. P.; Turnbull, M. M.; Furuya, S. C.; Giamarchi, T.; Zvyagin, S. A.

    2015-12-01

    Magnetic excitations in the strong-leg quantum spin ladder compound (C7H10N) 2CuBr4 (known as DIMPY) in the field-induced Tomonaga-Luttinger spin-liquid phase are studied by means of high-field electron spin resonance (ESR) spectroscopy. The presence of a gapped ESR mode with unusual nonlinear frequency-field dependence is revealed experimentally. Using a combination of analytic and exact-diagonalization methods, we compute the dynamical structure factor and identify this mode with longitudinal excitations in the antisymmetric channel. We argue that these excitations constitute a fingerprint of the spin dynamics in a strong-leg spin-1/2 Heisenberg antiferromagnetic ladder and owe their ESR observability to the uniform Dzyaloshinskii-Moriya interaction.

  4. [Ladder step strategy for surgical repair of congenital concealed penis in children].

    Science.gov (United States)

    Wang, Fu-Ran; Zhong, Hong-Ji; Chen, Yi; Zhao, Jun-Feng; Li, Yan

    2016-11-01

    To assess the feasibility of the ladder step strategy in surgical repair of congenital concealed penis in children. This study included 52 children with congenital concealed penis treated in the past two years by surgical repair using the ladder step strategy, which consists of five main steps: cutting the narrow ring of the foreskin, degloving the penile skin, fixing the penile skin at the base, covering the penile shaft, and reshaping the prepuce. The perioperative data of the patients were prospectively collected and statistically described. Of the 52 patients, 20 needed remodeling of the frenulum and 27 received longitudinal incision in the penoscrotal junction to expose and deglove the penile shaft. The advanced scrotal flap technique was applied in 8 children to cover the penile shaft without tension, the pedicled foreskin flap technique employed in 11 to repair the penile skin defect, and excision of the webbed skin of the ventral penis performed in another 44 to remodel the penoscrotal angle. The operation time, blood loss, and postoperative hospital stay were 40-100 minutes, 5-30 ml, and 3-6 days, respectively. Wound bleeding and infection occurred in 1 and 5 cases, respectively. Follow-up examinations at 3 and 6 months after surgery showed that all the children had a satisfactory penile appearance except for some minor complications (2 cases of penile retraction, 2 cases of redundant ventral skin, and 1 case of iatrogenic penile curvature). The ladder step strategy for surgical repair of congenital concealed penis in children is a simple procedure with minor injury and satisfactory appearance of the penis.

  5. Hydroxyl-substituted ladder polyethers via selective tandem epoxidation/cyclization sequence.

    Science.gov (United States)

    Czabaniuk, Lara C; Jamison, Timothy F

    2015-02-20

    A new and highly selective method for the synthesis of hydroxyl-substituted tetrahydropyrans is described. This method utilizes titanium(IV) isopropoxide and diethyl tartrate to perform a diastereoselective epoxidation followed by in situ epoxide activation and highly selective endo-cyclization to form the desired tetrahydropyran ring. The HIJ ring fragment of the marine ladder polyether yessotoxin was synthesized using this two-stage tactic that proceeds with high efficiency and excellent regioselectivity.

  6. Indirect effects of impoundment on migrating fish: temperature gradients in fish ladders slow dam passage by adult Chinook salmon and steelhead.

    Directory of Open Access Journals (Sweden)

    Christopher C Caudill

    Full Text Available Thermal layering in reservoirs upstream from hydroelectric dams can create temperature gradients in fishways used by upstream migrating adults. In the Snake River, Washington, federally-protected adult salmonids (Oncorhynchus spp. often encounter relatively cool water in dam tailraces and lower ladder sections and warmer water in the upstream portions of ladders. Using radiotelemetry, we examined relationships between fish passage behavior and the temperature difference between the top and bottom of ladders (∆T at four dams over four years. Some spring Chinook salmon (O. tshawytscha experienced ∆T ≥ 0.5 °C. Many summer and fall Chinook salmon and summer steelhead (O. mykiss experienced ∆T ≥ 1.0 °C, and some individuals encountered ΔT > 4.0°C. As ΔT increased, migrants were consistently more likely to move down fish ladders and exit into dam tailraces, resulting in upstream passage delays that ranged from hours to days. Fish body temperatures equilibrated to ladder temperatures and often exceeded 20°C, indicating potential negative physiological and fitness effects. Collectively, the results suggest that gradients in fishway water temperatures present a migration obstacle to many anadromous migrants. Unfavorable temperature gradients may be common at reservoir-fed fish passage facilities, especially those with seasonal thermal layering or stratification. Understanding and managing thermal heterogeneity at such sites may be important for ensuring efficient upstream passage and minimizing stress for migratory, temperature-sensitive species.

  7. Measuring subjective meaning structures by the laddering method: Theoretical considerations and methodological problems

    DEFF Research Database (Denmark)

    Grunert, Klaus G.; Grunert, Suzanne C.

    1995-01-01

    Starting from a general model of measuring cognitive structures for predicting consumer behaviour, we discuss laddering as a possible method to obtain estimates of consumption-relevant cognitive structures which will have predictive validity. Four criteria for valid measurement are derived and ap...

  8. Novel pattern of post-γ ray de novo DNA synthesis in a radioresistant human strain

    International Nuclear Information System (INIS)

    Mirzayans, R.; Gentner, N.E.; Paterson, M.C.

    1985-01-01

    Enhanced resistance to radiation cytotoxicity in a fibroblast strain from an afflicted member of a Li-Fraumeni syndrome family may be largely ascribable to a change in the pattern of DNA replicative synthesis following γ ray exposure. That is, the extent of the initial radiogenic inhibition of replicative synthesis and the time interval before its subsequent recovery were both found to be greater in radioresistant (RR) compared to normal cells. In addition, the post-recovery replication rates in the RR cells were both higher and longer lasting than those in the control cells. A similar differential pattern was also seen following treatment with 4NQO, another DNA-damaging agent to which this RR strain displays enhanced resistance. Moreover, several conventional DNA repair assays indicated that the RR cells repair radiogenic damage at normal rates. The authors therefore suggest that the increased inhibition and prolonged lag in resumption of replicative synthesis seen in the RR strain upon exposure to certain genotoxic agents may enhance cellular recovery by ''buying additional time'' for processing of potentially lethal lesions

  9. Some Effective Tight-Binding Models for Electrons in DNA Conduction: A Review

    International Nuclear Information System (INIS)

    Yamada, H.; Iguchi, K.

    2010-01-01

    Quantum transport for DNA conduction has been widely studied with interest in application as a candidate in making nanowires as well as interest in the scientific mechanism. In this paper, we review recent works concerning the electronic states and the conduction/transfer in DNA polymers. We have mainly investigated the energy-band structure and the correlation effects of localization property in the two- and three-chain systems (ladder model) with long-range correlation as a simple model for electronic property in a double strand of DNA by using the tight-bindingmodel. In addition, we investigated the localization properties of electronic states in several actual DNA sequences such as bacteriophages of Escherichia coli, human-chromosome 22, compared with those of the artificial disordered sequences with correlation. The charge-transfer properties for poly(dA)-poly(dT) and poly(dG)-poly(dC) DNA polymers are also presented in terms of localization lengths within the frameworks of the polaron models due to the coupling between the charge carriers and the lattice vibrations of the double strand of DNA

  10. Bound states in weakly disordered spin ladders

    Energy Technology Data Exchange (ETDEWEB)

    Arlego, M. [Departamento de Fisica, Universidad Nacional de La Plata, CC 67 (1900) La Plata (Argentina)]. E-mail: arlego@venus.fisica.unlp.edu.ar; Brenig, W. [Institut fuer Theoretische Physik, Technische Universitaet Braunschweig (Germany); Cabra, D.C. [Laboratoire de Physique Theorique, Universite Louis Pasteur Strasbourg (France); Heidrich-Meisner, F. [Institut fuer Theoretische Physik, Technische Universitaet Braunschweig (Germany); Honecker, A. [Institut fuer Theoretische Physik, Technische Universitaet Braunschweig (Germany); Rossini, G. [Departamento de Fisica, Universidad Nacional de La Plata, CC 67 (1900) La Plata (Argentina)

    2005-04-30

    We study the appearance of bound states in the spin gap of spin-12 ladders induced by weak bond disorder. Starting from the strong-coupling limit, i.e., the limit of weakly coupled dimers, we perform a projection on the single-triplet subspace and derive the position of bound states for the single impurity problem of one modified coupling as well as for small impurity clusters. The case of a finite concentration of impurities is treated with the coherent-potential approximation (CPA) in the strong-coupling limit and compared with numerical results. Further, we analyze the details in the structure of the density of states and relate their origin to the influence of impurity clusters.

  11. Magnetic phase diagram of a frustrated spin ladder

    Science.gov (United States)

    Sugimoto, Takanori; Mori, Michiyasu; Tohyama, Takami; Maekawa, Sadamichi

    2018-04-01

    Frustrated spin ladders show magnetization plateaux depending on the rung-exchange interaction and frustration defined by the ratio of first and second neighbor exchange interactions in each chain. This paper reports on its magnetic phase diagram. Using the variational matrix-product state method, we accurately determine phase boundaries. Several kinds of magnetization plateaux are induced by the frustration and the strong correlation among quasiparticles on a lattice. The appropriate description of quasiparticles and their relevant interactions are changed by a magnetic field. We find that the frustration differentiates the triplet quasiparticle from the singlet one in kinetic energy.

  12. Perturbed soliton excitations in inhomogeneous DNA

    International Nuclear Information System (INIS)

    Daniel, M.; Vasumathi, V.

    2005-05-01

    We study nonlinear dynamics of inhomogeneous DNA double helical chain under dynamic plane-base rotator model by considering angular rotation of bases in a plane normal to the helical axis. The DNA dynamics in this case is found to be governed by a perturbed sine-Gordon equation when taking into account the interstrand hydrogen bonding energy and intrastrand inhomogeneous stacking energy and making an analogy with the Heisenberg model of the Hamiltonian for an inhomogeneous anisotropic spin ladder with ferromagnetic legs and antiferromagentic rung coupling. In the homogeneous limit the dynamics is governed by the kink-antikink soliton of the sine-Gordon equation which represents the formation of open state configuration in DNA double helix. The effect of inhomogeneity in stacking energy in the form of localized and periodic variations on the formation of open states in DNA is studied under perturbation. The perturbed soliton is obtained using a multiple scale soliton perturbation theory by solving the associated linear eigen value problem and constructing the complete set of eigen functions. The inhomogeneity in stacking energy is found to modulate the width and speed of the soliton depending on the nature of inhomogeneity. Also it introduces fluctuations in the form of train of pulses or periodic oscillation in the open state configuration (author)

  13. Molecular recognition of AT-DNA sequences by the induced CD pattern of dibenzotetraaza[14]annulene (DBTAA)–adenine derivatives

    OpenAIRE

    Stojković, Marijana Radić; Škugor, Marko; Dudek, Łukasz; Grolik, Jarosław; Eilmes, Julita; Piantanida, Ivo

    2014-01-01

    Summary An investigation of the interactions of two novel and several known DBTAA–adenine conjugates with double-stranded DNA and RNA has revealed the DNA/RNA groove as the dominant binding site, which is in contrast to the majority of previously studied DBTAA analogues (DNA/RNA intercalators). Only DBTAA–propyladenine conjugates revealed the molecular recognition of AT-DNA by an ICD band pattern > 300 nm, whereas significant ICD bands did not appear for other ds-DNA/RNA. A structure–activity...

  14. Quark-gluon vertex dressing and meson masses beyond ladder-rainbow truncation

    International Nuclear Information System (INIS)

    Matevosyan, Hrayr H.; Thomas, Anthony W.; Tandy, Peter C.

    2007-01-01

    We include a generalized infinite class of quark-gluon vertex dressing diagrams in a study of how dynamics beyond the ladder-rainbow truncation influences the Bethe-Salpeter description of light-quark pseudoscalar and vector mesons. The diagrammatic specification of the vertex is mapped into a corresponding specification of the Bethe-Salpeter kernel, which preserves chiral symmetry. This study adopts the algebraic format afforded by the simple interaction kernel used in previous work on this topic. The new feature of the present work is that in every diagram summed for the vertex and the corresponding Bethe-Salpeter kernel, each quark-gluon vertex is required to be the self-consistent vertex solution. We also adopt from previous work the effective accounting for the role of the explicitly non-Abelian three-gluon coupling in a global manner through one parameter determined from recent lattice-QCD data for the vertex. Within the current model, the more consistent dressed vertex limits the ladder-rainbow truncation error for vector mesons to be never more than 10% as the current quark mass is varied from the u/d region to the b region

  15. Transgenerational inheritance of modified DNA methylation patterns and enhanced tolerance induced by heavy metal stress in rice (Oryza sativa L.).

    Science.gov (United States)

    Ou, Xiufang; Zhang, Yunhong; Xu, Chunming; Lin, Xiuyun; Zang, Qi; Zhuang, Tingting; Jiang, Lili; von Wettstein, Diter; Liu, Bao

    2012-01-01

    DNA methylation is sensitive and responsive to stressful environmental conditions. Nonetheless, the extent to which condition-induced somatic methylation modifications can impose transgenerational effects remains to be fully understood. Even less is known about the biological relevance of the induced epigenetic changes for potentially altered well-being of the organismal progenies regarding adaptation to the specific condition their progenitors experienced. We analyzed DNA methylation pattern by gel-blotting at genomic loci representing transposable elements and protein-coding genes in leaf-tissue of heavy metal-treated rice (Oryza sativa) plants (S0), and its three successive organismal generations. We assessed expression of putative genes involved in establishing and/or maintaining DNA methylation patterns by reverse transcription (RT)-PCR. We measured growth of the stressed plants and their unstressed progenies vs. the control plants. We found (1) relative to control, DNA methylation patterns were modified in leaf-tissue of the immediately treated plants, and the modifications were exclusively confined to CHG hypomethylation; (2) the CHG-demethylated states were heritable via both maternal and paternal germline, albeit often accompanying further hypomethylation; (3) altered expression of genes encoding for DNA methyltransferases, DNA glycosylase and SWI/SNF chromatin remodeling factor (DDM1) were induced by the stress; (4) progenies of the stressed plants exhibited enhanced tolerance to the same stress their progenitor experienced, and this transgenerational inheritance of the effect of condition accompanying heritability of modified methylation patterns. Our findings suggest that stressful environmental condition can produce transgenerational epigenetic modifications. Progenies of stressed plants may develop enhanced adaptability to the condition, and this acquired trait is inheritable and accord with transmission of the epigenetic modifications. We suggest

  16. Core nucleosomes by digestion of reconstructed histone-DNA complexes

    Energy Technology Data Exchange (ETDEWEB)

    Bryan, P N; Wright, E B; Olins, D E

    1979-04-01

    Reconstructed complexes of the inner histones (H2A, H2B, H3, H4) and a variety of DNAs were digested with micrococcal nuclease to yield very homogeneous populations of core nucleosomes (..nu../sub 1/). Nucleosomes containing Micrococcus luteus DNA (72% G+C); chicken DNA (43% G+C), Clostridium perfringens DNA (29% G+C); or poly(dA-dT).poly(dA-dT) have been examined by circular dichroism, thermal denaturation, electron microscopy, and DNAse I digestion. Circular dichroism spectra of all particles show a typically suppressed ellipticity at 260 to 280 nm and a prominent ..cap alpha..-helix signal at 222 nm. All particles show biphasic melting except ..nu../sub 1/(dA-dT), which show three prominent melting transitions at ionic strength less than or equal to 1 mM. DNAse I digestion of ..nu../sub 1/ (dA-dT) produces a ladder of DNA fragments differing in length by one base residue. ..nu../sub 1/ (dA-dT) contain 146 base pairs of DNA and exhibit an average DNA helix pitch of 10.4 to 10.5 bases per turn. There appear to be two regions of different DNA pitch within ..nu../sub 1/ (dA-dT). It is suggested that the two regions of DNA pitch might correspond to the two regions of the melting profiles.

  17. Phase transitions and magnetization of the mixed-spin Ising–Heisenberg double sawtooth frustrated ladder

    Science.gov (United States)

    Arian Zad, Hamid; Ananikian, Nerses

    2018-04-01

    The mixed spin-(1,1/2) Ising–Heisenberg double sawtooth ladder containing a mixture of both spin-1 and spin-1/2 nodal atoms, and the spin-1/2 interstitial dimers are approximately solved by the transfer-matrix method. Here, we study in detail the ground-state phase diagrams, also influences of the bilinear exchange coupling on the rungs and cyclic four-spin exchange interaction in square plaquette of each block on the magnetization and magnetic susceptibility of the suggested ladder at low temperature. Such a double sawtooth ladder may be found in a Shastry-Sutherland lattice-type. In spite of the spin ordering of odd and even blocks being different from each other, due to the commutation relation between all different block Hamiltonians, phase diagrams, magnetization behavior and thermodynamic properties of the model are the same for odd and even blocks. We show that at low temperature, both exchange couplings can change the quality and quantity of the magnetization plateaus versus the magnetic field changes. Specially, we find a new magnetization plateau M/Ms= 5/6 for this model. Besides, we examine the magnetic susceptibility and specific heat of the model in detail. It is proven that behaviors of the magnetization and the magnetic susceptibility coincide at low temperature. The specific heat displays diverse temperature dependencies, which include a Schottky-type peak at a special temperature interval. We observe that with increase of the bilinear exchange coupling on the rungs, second peak temperature dependence grows.

  18. Non-local electron transport through normal and topological ladder-like atomic systems

    Science.gov (United States)

    Kurzyna, Marcin; Kwapiński, Tomasz

    2018-05-01

    We propose a locally protected ladder-like atomic system (nanoconductor) on a substrate that is insensitive to external perturbations. The system corresponds to coupled atomic chains fabricated on different surfaces. Electron transport properties of such conductors are studied theoretically using the model tight-binding Su-Schriffer-Hegger (SSH) Hamiltonian and Green's function formalism. We have found that the conductance of the system is almost insensitive to single adatoms and oscillates as a function of the side chain length with very large periods. Non-local character of the electron transport was observed also for topological SSH chains where nontrivial end states survive in the presence of disturbances as well as for different substrates. We have found that the careful inspection of the density of states or charge waves can provide the information about the atom energy levels and hopping amplitudes. Moreover, the ladder-like geometry allows one to distinguish between normal and topological zero-energy states. It is important that topological chains do not reveal Friedel oscillations which are observed in non-topological chains.

  19. Telecast of Astronauts Armstrong and Aldrin by the Lunar Module ladder

    Science.gov (United States)

    1969-01-01

    Astronauts Neil A. Armstrong (on left), commander; and Edwin E. Aldrin Jr., lunar module pilot, are seen standing by the Lunar Module ladder in this black and white reproduction taken from a telecast by the Apollo 11 lunar surface television camera during the Apollo 11 extravehicular activity. This picture was made from a televised image received at the Deep Space Network tracking station at Goldstone, California.

  20. ∆DNMT3B4-del Contributes to Aberrant DNA Methylation Patterns in Lung Tumorigenesis

    Directory of Open Access Journals (Sweden)

    Mark Z. Ma

    2015-10-01

    Full Text Available Aberrant DNA methylation is a hallmark of cancer but mechanisms contributing to the abnormality remain elusive. We have previously shown that ∆DNMT3B is the predominantly expressed form of DNMT3B. In this study, we found that most of the lung cancer cell lines tested predominantly expressed DNMT3B isoforms without exons 21, 22 or both 21 and 22 (a region corresponding to the enzymatic domain of DNMT3B termed DNMT3B/∆DNMT3B-del. In normal bronchial epithelial cells, DNMT3B/ΔDNMT3B and DNMT3B/∆DNMT3B-del displayed equal levels of expression. In contrast, in patients with non-small cell lung cancer NSCLC, 111 (93% of the 119 tumors predominantly expressed DNMT3B/ΔDNMT3B-del, including 47 (39% tumors with no detectable DNMT3B/∆DNMT3B. Using a transgenic mouse model, we further demonstrated the biological impact of ∆DNMT3B4-del, the ∆DNMT3B-del isoform most abundantly expressed in NSCLC, in global DNA methylation patterns and lung tumorigenesis. Expression of ∆DNMT3B4-del in the mouse lungs resulted in an increased global DNA hypomethylation, focal DNA hypermethylation, epithelial hyperplastia and tumor formation when challenged with a tobacco carcinogen. Our results demonstrate ∆DNMT3B4-del as a critical factor in developing aberrant DNA methylation patterns during lung tumorigenesis and suggest that ∆DNMT3B4-del may be a target for lung cancer prevention.

  1. ESR modes in a Strong-Leg Ladder in the Tomonaga-Luttinger Liquid Phase

    Science.gov (United States)

    Zvyagin, S.; Ozerov, M.; Maksymenko, M.; Wosnitza, J.; Honecker, A.; Landee, C. P.; Turnbull, M.; Furuya, S. C.; Giamarchi, T.

    Magnetic excitations in the strong-leg quantum spin ladder compound (C7H10N)2CuBr4 (known as DIMPY) in the field-induced Tomonaga-Luttinger spin liquid phase are studied by means of high-field electron spin resonance (ESR) spectroscopy. The presence of a gapped ESR mode with unusual non-linear frequency-field dependence is revealed experimentally. Using a combination of analytic and exact diagonalization methods, we compute the dynamical structure factor and identify this mode with longitudinal excitations in the antisymmetric channel. We argue that these excitations constitute a fingerprint of the spin dynamics in a strong-leg spin-1/2 Heisenberg antiferromagnetic ladder and owe its ESR observability to the uniform Dzyaloshinskii-Moriya interaction. This work was partially supported by the DFG and Helmholtz Gemeinschaft (Germany), Swiss SNF under Division II, and ERC synergy UQUAM project. We acknowledge the support of the HLD at HZDR, member of the European Magnetic Field Laboratory (EMFL).

  2. Two-loop ladder diagram contributions to Bhabha scattering. III

    International Nuclear Information System (INIS)

    Bjoerkevoll, K.S.; Osland, P.; Faeldt, G.

    1992-01-01

    The authors evaluate, in the high-energy limit, the sum of the Feynman amplitudes corresponding the six two-loop ladder-like diagrams in Bhabha scattering. This is the limit where s→∞, while t, the electron mass m and the photon mass λ are all being held fixed. In this limit the sum of the six Feynman amplitudes does not depend on the electron mass. When specialized to the region s>>t>>m 2 >>λ 2 , this result complements the one previously obtained. The connection with Φ 3 theory is also investigated. 6 refs

  3. Ising versus S U (2) 2 string-net ladder

    Science.gov (United States)

    Vidal, Julien

    2018-03-01

    We consider the string-net model obtained from S U (2) 2 fusion rules. These fusion rules are shared by two different sets of anyon theories. In this paper, we study the competition between the two corresponding non-Abelian quantum phases in the ladder geometry. A detailed symmetry analysis shows that the nontrivial low-energy sector corresponds to the transverse-field cluster model that displays a critical point described by the s o (2) 1 conformal field theory. Other sectors are obtained by freezing spins in this model.

  4. A Mimicking-of-DNA-Methylation-Patterns Pipeline for Overcoming the Restriction Barrier of Bacteria

    Science.gov (United States)

    Zhang, Guoqiang; Wang, Wenzhao; Deng, Aihua; Sun, Zhaopeng; Zhang, Yun; Liang, Yong; Che, Yongsheng; Wen, Tingyi

    2012-01-01

    Genetic transformation of bacteria harboring multiple Restriction-Modification (R-M) systems is often difficult using conventional methods. Here, we describe a mimicking-of-DNA-methylation-patterns (MoDMP) pipeline to address this problem in three difficult-to-transform bacterial strains. Twenty-four putative DNA methyltransferases (MTases) from these difficult-to-transform strains were cloned and expressed in an Escherichia coli strain lacking all of the known R-M systems and orphan MTases. Thirteen of these MTases exhibited DNA modification activity in Southwestern dot blot or Liquid Chromatography–Mass Spectrometry (LC–MS) assays. The active MTase genes were assembled into three operons using the Saccharomyces cerevisiae DNA assembler and were co-expressed in the E. coli strain lacking known R-M systems and orphan MTases. Thereafter, results from the dot blot and restriction enzyme digestion assays indicated that the DNA methylation patterns of the difficult-to-transform strains are mimicked in these E. coli hosts. The transformation of the Gram-positive Bacillus amyloliquefaciens TA208 and B. cereus ATCC 10987 strains with the shuttle plasmids prepared from MoDMP hosts showed increased efficiencies (up to four orders of magnitude) compared to those using the plasmids prepared from the E. coli strain lacking known R-M systems and orphan MTases or its parental strain. Additionally, the gene coding for uracil phosphoribosyltransferase (upp) was directly inactivated using non-replicative plasmids prepared from the MoDMP host in B. amyloliquefaciens TA208. Moreover, the Gram-negative chemoautotrophic Nitrobacter hamburgensis strain X14 was transformed and expressed Green Fluorescent Protein (GFP). Finally, the sequence specificities of active MTases were identified by restriction enzyme digestion, making the MoDMP system potentially useful for other strains. The effectiveness of the MoDMP pipeline in different bacterial groups suggests a universal potential

  5. Star-shaped ladder-type ter(p-phenylene)s for efficient multiphoton absorption.

    Science.gov (United States)

    Guo, Lei; Li, King Fai; Wong, Man Shing; Cheah, Kok Wai

    2013-05-04

    Star-shaped ladder-type ter(p-phenylene)s exhibit remarkably efficient multiphoton absorption properties with 2PA cross-section up to 2579 GM at 700 nm and 3PA cross-section up to 3.35 × 10(-76) cm(6) s(2) in the femtosecond regime for a blue-emissive molecule despite having such a short π-conjugated framework.

  6. Control of Porosity in Ladder Polymers by Solvent-induced Aggregation

    Science.gov (United States)

    Brady, Michael; Gamo, Eri; Wang, Cheng; Xia, Yan

    Porous polymers hold promise as materials for gas absorption, membranes, and organic electronics. In all of these applications, attaining in-plane ordering of backbones and thus porous free volume impacts the ability to adsorb gas, selectively filter molecules, and conduct charges. In this work, hard and soft x-ray scattering and soft x-ray spectroscopy are of focus to study the pore structure, induced by the solution-driven aggregation of ladder polymer thin films made of LP-1 and LP-2. Using GISAXS and AFM it is shown that thermal annealing drives the growth of crystallites in thin films. Due to the completely sp2nature of the ladder polymer backbones, it is expected that backbones are extremely stiff and thus preventing them from packing once left in a metastable state following casting. Therefore, the combination of GIWAXS and GISAXS will be shown to be critical in correctly understanding how pores develop in this 700 m2/g sorbent (N2). Finally, application in CO2/N2 separation membranes towards carbon sequestration will be presented that show gas selectivity is achieved through heteroatom incorporation and polymer blending. In this talk, focus will be placed on state-of-the-art x-ray scattering and spectroscopy, highlighting the importance of chemically sensitive structural information enabled by the combination of spectroscopy and scattering at play with the use of resonant soft x-rays.

  7. Pattern analysis approach reveals restriction enzyme cutting abnormalities and other cDNA library construction artifacts using raw EST data

    Directory of Open Access Journals (Sweden)

    Zhou Sun

    2012-05-01

    Full Text Available Abstract Background Expressed Sequence Tag (EST sequences are widely used in applications such as genome annotation, gene discovery and gene expression studies. However, some of GenBank dbEST sequences have proven to be “unclean”. Identification of cDNA termini/ends and their structures in raw ESTs not only facilitates data quality control and accurate delineation of transcription ends, but also furthers our understanding of the potential sources of data abnormalities/errors present in the wet-lab procedures for cDNA library construction. Results After analyzing a total of 309,976 raw Pinus taeda ESTs, we uncovered many distinct variations of cDNA termini, some of which prove to be good indicators of wet-lab artifacts, and characterized each raw EST by its cDNA terminus structure patterns. In contrast to the expected patterns, many ESTs displayed complex and/or abnormal patterns that represent potential wet-lab errors such as: a failure of one or both of the restriction enzymes to cut the plasmid vector; a failure of the restriction enzymes to cut the vector at the correct positions; the insertion of two cDNA inserts into a single vector; the insertion of multiple and/or concatenated adapters/linkers; the presence of 3′-end terminal structures in designated 5′-end sequences or vice versa; and so on. With a close examination of these artifacts, many problematic ESTs that have been deposited into public databases by conventional bioinformatics pipelines or tools could be cleaned or filtered by our methodology. We developed a software tool for Abnormality Filtering and Sequence Trimming for ESTs (AFST, http://code.google.com/p/afst/ using a pattern analysis approach. To compare AFST with other pipelines that submitted ESTs into dbEST, we reprocessed 230,783 Pinus taeda and 38,709 Arachis hypogaea GenBank ESTs. We found 7.4% of Pinus taeda and 29.2% of Arachis hypogaea GenBank ESTs are “unclean” or abnormal, all of which could be cleaned

  8. Magnetic properties of the two-leg zig-zag ladder in quantum spin system NH4CuCl3

    International Nuclear Information System (INIS)

    Raksa, Teguh Yoga; Kurniawan, Budhy

    2002-01-01

    Numerical analysis of the two-leg zig-zag ladder as a single chain with next-nearest neighbour interactions has been formulated by Cabra (1999) with the following Hamiltonian. Other formulation for two leg zig-zag ladder with dimerized chains and coupling between the chains. From these formulations, we study the closing of the gap at zero magnetization by means of the fine-tuning mechanism and disappearance of the 1/2 plateau (gap) at finite by alternating dimerization of the chains along the rungs. We also described NH 4 CuCI 3 under high magnetic fields in a two-leg system

  9. THE EFFECT OF PLAYING SNAKE AND LADDER TOWARD THE RESULT STUDY OF ARITHMETIC ADDITION FOR STUDENT WITH MENTALLY RETARDED STUDENT

    Directory of Open Access Journals (Sweden)

    Arianti Iman Sari

    2016-12-01

    Full Text Available The purpose of this research were to describe: (1 the study result of arithmetic addition operation for fourth grade student with mentally retarded in SDLB before playing the Snake and Ladder activity (2 the study result of arithmetic addition operation for fourth grade student with mentally retarded in SDLB after playing the Snake and Ladder activity (3 the effect of Snake and Ladder playing toward the result study of arithmetic addition for fourth grade student with mentally retarded SDLB. This research used SSR (Single Subject Research with A-B-A design. Collecting the data was done by using assessment instrument, tests and observations. The result of this research showed that playing Snake and Ladder affected the study result of arithmetic addition operation for fourth-grade children with mentally retarded student in SDLB. Tujuan penelitian ini adalah mendeskripsikan (1 Hasil belajar penjumlahan siswa kelas 4 SDLB sebelum melakukan kegiatan bermain Ular Tangga (2 Hasil belajar penjumlahan siswa kelas 4 SDLB sesudah melakukan kegiatan bermain Ular Tangga (3 Pengaruh bermain Ular Tangga terhadap hasil belajar penjumlahan siswa kelas 4 SDLB. Penelitian ini menggunakan rancangan penelitian SSR (Single Subject Research dengan desain A-B-A. Pengumpulan data menggunakan instrumen assesmen, tes dan observasi. Hasil penelitian menunjukkan bermain ular tangga berpengaruh terhadap hasil belajar penjumlahan siswa tunagrahita kelas 4 SDLB.

  10. Kaempferol induces DNA damage and inhibits DNA repair associated protein expressions in human promyelocytic leukemia HL-60 cells.

    Science.gov (United States)

    Wu, Lung-Yuan; Lu, Hsu-Feng; Chou, Yu-Cheng; Shih, Yung-Luen; Bau, Da-Tian; Chen, Jaw-Chyun; Hsu, Shu-Chun; Chung, Jing-Gung

    2015-01-01

    Numerous evidences have shown that plant flavonoids (naturally occurring substances) have been reported to have chemopreventive activities and protect against experimental carcinogenesis. Kaempferol, one of the flavonoids, is widely distributed in fruits and vegetables, and may have cancer chemopreventive properties. However, the precise underlying mechanism regarding induced DNA damage and suppressed DNA repair system are poorly understood. In this study, we investigated whether kaempferol induced DNA damage and affected DNA repair associated protein expression in human leukemia HL-60 cells in vitro. Percentages of viable cells were measured via a flow cytometry assay. DNA damage was examined by Comet assay and DAPI staining. DNA fragmentation (ladder) was examined by DNA gel electrophoresis. The changes of protein levels associated with DNA repair were examined by Western blotting. Results showed that kaempferol dose-dependently decreased the viable cells. Comet assay indicated that kaempferol induced DNA damage (Comet tail) in a dose-dependent manner and DAPI staining also showed increased doses of kaempferol which led to increased DNA condensation, these effects are all of dose-dependent manners. Western blotting indicated that kaempferol-decreased protein expression associated with DNA repair system, such as phosphate-ataxia-telangiectasia mutated (p-ATM), phosphate-ataxia-telangiectasia and Rad3-related (p-ATR), 14-3-3 proteins sigma (14-3-3σ), DNA-dependent serine/threonine protein kinase (DNA-PK), O(6)-methylguanine-DNA methyltransferase (MGMT), p53 and MDC1 protein expressions, but increased the protein expression of p-p53 and p-H2AX. Protein translocation was examined by confocal laser microscopy, and we found that kaempferol increased the levels of p-H2AX and p-p53 in HL-60 cells. Taken together, in the present study, we found that kaempferol induced DNA damage and suppressed DNA repair and inhibited DNA repair associated protein expression in HL-60

  11. Differential DNA Methylation Patterns Are Related to Phellogen Origin and Quality of Quercus suber Cork.

    Science.gov (United States)

    Inácio, Vera; Barros, Pedro M; Costa, Augusta; Roussado, Cristóvão; Gonçalves, Elsa; Costa, Rita; Graça, José; Oliveira, M Margarida; Morais-Cecílio, Leonor

    2017-01-01

    DNA methylation is thought to influence Quercus suber cork quality, which is the main constraint for its economic valorisation. However, a deep knowledge of the cytosine methylation patterns disclosing the epigenetic variability of trees with different cork quality types is totally missing. This study investigates the hypothesis that variations in DNA methylation contribute to differences in cork cellular characteristics directly related to original or traumatic phellogen activity. We used MSAPs (Methylation Sensitive Amplified Polymorphism) to assess DNA methylation patterns of cork and leaf tissues of Q. suber adult trees growing in three cork oak stands. The relationship between the detected polymorphisms and the diversity of cork quality traits was explored by a marker-trait analysis focusing on the most relevant quality characteristics. Populations differed widely in cork quality, but only slightly in degree of epigenetic differentiation. Four MSAP markers (1.3% of the total) were significantly associated with the most noteworthy quality traits: wood inclusions (nails) and porosity. This evidence supports the potential role of cytosine methylation in the modulation of differential phellogen activity either involved in localized cell death or in pore production, resulting in different cork qualities. Although, the underlying basis of the methylation polymorphism of loci affecting cork quality traits remain unclear, the disclosure of markers statistically associated with cork quality strengthens the potential role of DNA methylation in the regulation of these traits, namely at the phellogen level.

  12. Preparation of methacrylate-based anion-exchange monolithic microbore column for chromatographic separation of DNA fragments and oligonucleotides

    Energy Technology Data Exchange (ETDEWEB)

    Sabarudin, Akhmad, E-mail: sabarjpn@ub.ac.id [Division of Nano-materials Science, EcoTopia Science Institute, Nagoya University, Furu-Cho, Chikusa-Ku, Nagoya 464-8603 (Japan); Department of Chemistry, Faculty of Science, Brawijaya University, Jl Veteran Malang 65145 (Indonesia); Huang, Junchao; Shu, Shin; Sakagawa, Shinnosuke [Division of Nano-materials Science, EcoTopia Science Institute, Nagoya University, Furu-Cho, Chikusa-Ku, Nagoya 464-8603 (Japan); Umemura, Tomonari, E-mail: umemura@apchem.nagoya-u.ac.jp [Division of Nano-materials Science, EcoTopia Science Institute, Nagoya University, Furu-Cho, Chikusa-Ku, Nagoya 464-8603 (Japan)

    2012-07-29

    Highlights: Black-Right-Pointing-Pointer Microbore-scale (1 mm i.d.) anion-exchange monolithic column. Black-Right-Pointing-Pointer Potentially preparative applications. Black-Right-Pointing-Pointer Separation of oligodeoxythymidylic acids and DNA fragments. - Abstract: In this paper, we report on the preparation of a microbore-scale (1 mm i.d.) anion-exchange monolithic column suitable not only for analytical purposes but also for potentially preparative applications. In order to meet the conflicting requirements of high permeability and good mechanical strength, the following two-step procedure was applied. First, an epoxy-containing monolith was synthesized by in situ copolymerization of glycidyl methacrylate (GMA) and ethylene dimethacrylate (EDMA) within the confines of a silicosteel tubing of 1.02 mm i.d. and 1/16 Double-Prime o.d. in the presence of a ternary porogenic mixture of 1-propanol, 1,4-butanediol, and water. The monolithic matrix was subsequently converted into weak anion-exchanger via the ring-opening reaction of epoxy group with diethyl amine. The dynamic binding capacity was 21.4 mg mL{sup -1} for bovine serum albumin (BSA) at 10% breakthrough. The morphology and porous structure of this monolith were assessed by scanning electron microscope (SEM) and inverse size exclusion chromatography (ISEC). To optimize the separation efficiency, the effects of various chromatographic parameters upon the separation of DNA fragments were investigated. The resulting monolithic anion exchanger demonstrated good potential for the separation of both single- and double-stranded DNA molecules using a gradient elution with NaCl in Tris-HCl buffer (20 mM). Oligodeoxythymidylic acids (dT{sub 12}-dT{sub 18}) were successfully resolved at pH 8, while the fragments of 20 bp DNA ladder, 100 bp DNA ladder, and pBR322-HaeIII digest were efficiently separated at pH 9.

  13. Energy-efficient hydrogen separation by AB-type ladder-polymer molecular sieves

    KAUST Repository

    Ghanem, Bader

    2014-07-19

    The synthesis, microstructures, and exceptional gas transport properties of two new soluble ladder polymers, polymers of intrinsic microporosity (TPIM-1 and TPIM-2) containing triptycene moieties substituted with branched isopropyl and linear propyl chains at the 9,10-bridgeheads were reported. The precursor A-B monomers were modified with an o -difluoride functionality for enhanced activation for nucleophilic aromatic substitution. In a Schlenk tube, a mixture of the A-B monomer, 18-crown-6, anhydrous DMF and anhydrous potassium carbonate was stirred at 155 °C under nitrogen atmosphere for 20 min followed by the addition of toluene. The reaction was continued for another 45 min and more toluene was added. After another 45 min the reaction mixture was cooled to room temperature and poured into methanol. Slow evaporation of filtered, dilute 3-5 wt% chloroform solutions from a leveled glass plate yielded isotropic polymer films. Dry membranes were soaked in methanol for 24 h, air-dried, and then heated at 120°C for 24 h under high vacuum to remove any traces of residual solvent. TPIM-1 exhibits simultaneous boosts in permeability and selectivity, which highlights the significant potential of an isopropyl-substituted triptycene moiety as a contortion center for ladder PIMs.

  14. Energy-efficient hydrogen separation by AB-type ladder-polymer molecular sieves

    KAUST Repository

    Ghanem, Bader; Swaidan, Raja; Ma, Xiaohua; Litwiller, Eric; Pinnau, Ingo

    2014-01-01

    The synthesis, microstructures, and exceptional gas transport properties of two new soluble ladder polymers, polymers of intrinsic microporosity (TPIM-1 and TPIM-2) containing triptycene moieties substituted with branched isopropyl and linear propyl chains at the 9,10-bridgeheads were reported. The precursor A-B monomers were modified with an o -difluoride functionality for enhanced activation for nucleophilic aromatic substitution. In a Schlenk tube, a mixture of the A-B monomer, 18-crown-6, anhydrous DMF and anhydrous potassium carbonate was stirred at 155 °C under nitrogen atmosphere for 20 min followed by the addition of toluene. The reaction was continued for another 45 min and more toluene was added. After another 45 min the reaction mixture was cooled to room temperature and poured into methanol. Slow evaporation of filtered, dilute 3-5 wt% chloroform solutions from a leveled glass plate yielded isotropic polymer films. Dry membranes were soaked in methanol for 24 h, air-dried, and then heated at 120°C for 24 h under high vacuum to remove any traces of residual solvent. TPIM-1 exhibits simultaneous boosts in permeability and selectivity, which highlights the significant potential of an isopropyl-substituted triptycene moiety as a contortion center for ladder PIMs.

  15. Metastatic pattern and DNA ploidy in stage IV breast cancer at initial diagnosis. Relation to response and survival.

    Science.gov (United States)

    De Lena, M; Romero, A; Rabinovich, M; Leone, B; Vallejo, C; Machiavelli, M; Cuevas, M; Rodriguez, R; Lacava, J; Perez, J

    1993-06-01

    Sixty-nine patients with metastatic breast cancer (MBC) at initial diagnosis were analyzed to verify if metastatic pattern and clinical outcome are related to DNA ploidy determined by flow cytometry (FCM). Characteristics of 55 fully evaluable patients were as follows: median age: 61 years; postmenopausal: 75%; bone-only metastases (BM): 60%; extraosseous-only metastases (EM): 40%. Overall response rates (CR + PR) obtained with different chemotherapies and/or hormonal therapies were 58% and 68% for patients with BM and EM, respectively. Sixty percent of specimens resulted aneuploid, and the mean coefficient of variation of the complete series was 5.1%. In the whole group of patients DNA ploidy of primary tumor did not predict the metastatic pattern and had no influence upon response to treatment, duration of response, time to progression, and overall survival. When analyses were carried out according to metastatic pattern, those patients with BM showed similar results. However, within the group with EM, those with diploid tumors presented a significantly better survival (median 18 vs 13 months, p = .04). FCM-DNA analysis seems to identify a subgroup of patients with poor prognosis constituted by those who had aneuploid primary tumors and metastases to extraosseous sites.

  16. 4-bit digital to analog converter using R-2R ladder and binary weighted resistors

    Science.gov (United States)

    Diosanto, J.; Batac, M. L.; Pereda, K. J.; Caldo, R.

    2017-06-01

    The use of a 4-bit digital-to-analog converter using two methods; Binary Weighted Resistors and R-2R Ladder is designed and presented in this paper. The main components that were used in constructing both circuits were different resistor values, operational amplifier (LM741) and single pole double throw switches. Both circuits were designed using MULTISIM software to be able to test the circuit for its ideal application and FRITZING software for the layout designing and fabrication to the printed circuit board. The implementation of both systems in an actual circuit benefits in determining and comparing the advantages and disadvantages of each. It was realized that the binary weighted circuit is more efficient DAC, having lower percentage error of 0.267% compared to R-2R ladder circuit which has a minimum of percentage error of 4.16%.

  17. Thermoelectric Properties of Solution-Processed n-Doped Ladder-Type Conducting Polymers

    DEFF Research Database (Denmark)

    Wang, Suhao; Sun, Hengda; Ail, Ujwala

    2016-01-01

    Ladder-type "torsion-free" conducting polymers (e.g., polybenzimidazobenzophenanthroline (BBL)) can outperform "structurally distorted" donor-acceptor polymers (e.g., P(NDI2OD-T2)), in terms of conductivity and thermoelectric power factor. The polaron delocalization length is larger in BBL than...... in P(NDI2OD-T2), resulting in a higher measured polaron mobility. Structure-function relationships are drawn, setting material-design guidelines for the next generation of conducting thermoelectric polymers....

  18. Development of a 325 MHz ladder-RFQ of the 4-rod-type

    Energy Technology Data Exchange (ETDEWEB)

    Schuett, Maximilian; Ratzinger, Ulrich [Institut fuer Angewandte Physik, Goethe-Universitaet, Frankfurt a. M. (Germany); Brodhage, Robert [GSI, Darmstadt (Germany)

    2015-07-01

    For the research program with cooled antiprotons at FAIR a dedicated 70 MeV, 70 mA proton injector is required. In the low energy section, between the Ion Source and the main linac an RFQ will be used. The 325 MHz RFQ will accelerate protons from 95 keV to 3.0 MeV. This particular high frequency for an RFQ creates difficulties, which are challenging in developing this cavity. In order to define a satisfactory geometrical configuration for this resonator, both from the RF and the mechanical point of view, different designs have been examined and compared. Very promising results have been reached with a ladder type RFQ, which has been investigated since 2013. We present recent 3D simulations of the general layout and of a complete cavity demonstrating the power of a ladder type RFQ as well as measurements of a 0.8 m prototype RFQ, which was manufactured in late 2014 and designed for RF power and vacuum tests. We outline a possible RF layout for the RFQ within the new FAIR proton injector and highlight the mechanical advantages.

  19. Exact solutions and ladder operators for a new anharmonic oscillator

    International Nuclear Information System (INIS)

    Dong Shihai; Sun Guohua; Lozada-Cassou, M.

    2005-01-01

    In this Letter, we propose a new anharmonic oscillator and present the exact solutions of the Schrodinger equation with this oscillator. The ladder operators are established directly from the normalized radial wave functions and used to evaluate the closed expressions of matrix elements for some related functions. Some comments are made on the general calculation formula and recurrence relation for off-diagonal matrix elements. Finally, we show that this anharmonic oscillator possesses a hidden symmetry between E(r) and E(ir) by substituting r->ir

  20. Molecular cloning, sequence analysis and structure prediction of the ...

    African Journals Online (AJOL)

    AJL

    2012-04-19

    Apr 19, 2012 ... The primers were based on the rBAT sequences of other animals deposited in GenBank. .... fragment; M1, 2000 bp DNA ladder; M2, 1000 bp DNA ladder. spliced to obtain the ..... A traffic signal for heterodimeric amino acid.

  1. Short-distance behavior of the Bethe--Salpeter wave function in the ladder approximation

    International Nuclear Information System (INIS)

    Guth, A.H.; Soper, D.E.

    1975-01-01

    We investigate the short-distance behavior of the (Wick-rotated) Bethe--Salpeter wave function for the two spin-1/2 quarks bound by the exchange of a massive vector meson. We use the ladder-model kernel, which has the same p -4 scaling behavior as the true kernel in a theory with a fixed point of the renormalization group at g not equal to 0. For a bound state with the quantum numbers of the pion, the leading asymptotic behavior is chi (q/sup μ/) approx. cq/sup -4 + epsilon(g)/γ 5 , where epsilon (g) =1- (1-g 2 /π 2 ) 1 / 2 . Our method also provides the full asymptotic series, although it should be noted that the nonleading terms will depend on the nonleading behavior of the ladder-model kernel. A general term has the form cq - /sup a/(lnq)/sup n/phi (q/sup μ/), where c is an unknown constant, a may be integral or nonintegral, n is an integer, and phi (q/sup μ/) is a representation function of the rotation group in four dimensions

  2. Genome-Wide DNA Methylation Patterns of Bovine Blastocysts Developed In Vivo from Embryos Completed Different Stages of Development In Vitro.

    Directory of Open Access Journals (Sweden)

    Dessie Salilew-Wondim

    Full Text Available Early embryonic loss and altered gene expression in in vitro produced blastocysts are believed to be partly caused by aberrant DNA methylation. However, specific embryonic stage which is sensitive to in vitro culture conditions to alter the DNA methylation profile of the resulting blastocysts remained unclear. Therefore, the aim of this study was to investigate the stage specific effect of in vitro culture environment on the DNA methylation response of the resulting blastocysts. For this, embryos cultured in vitro until zygote (ZY, 4-cell (4C or 16-cell (16C were transferred to recipients and the blastocysts were recovery at day 7 of the estrous cycle. Another embryo group was cultured in vitro until blastocyst stage (IVP. Genome-wide DNA methylation profiles of ZY, 4C, 16C and IVP blastocyst groups were then determined with reference to blastocysts developed completely under in vivo condition (VO using EmbryoGENE DNA Methylation Array. To assess the contribution of methylation changes on gene expression patterns, the DNA methylation data was superimposed to the transcriptome profile data. The degree of DNA methylation dysregulation in the promoter and/or gene body regions of the resulting blastocysts was correlated with successive stages of development the embryos advanced under in vitro culture before transfer to the in vivo condition. Genomic enrichment analysis revealed that in 4C and 16C blastocyst groups, hypermethylated loci were outpacing the hypomethylated ones in intronic, exonic, promoter and proximal promoter regions, whereas the reverse was observed in ZY blastocyst group. However, in the IVP group, as much hypermethylated as hypomethylated probes were detected in gene body and promoter regions. In addition, gene ontology analysis indicated that differentially methylated regions were found to affected several biological functions including ATP binding in the ZY group, programmed cell death in the 4C, glycolysis in 16C and genetic

  3. Analysis of mutation/rearrangement frequencies and methylation patterns at a given DNA locus using restriction fragment length polymorphism.

    Science.gov (United States)

    Boyko, Alex; Kovalchuk, Igor

    2010-01-01

    Restriction fragment length polymorphism (RFLP) is a difference in DNA sequences of organisms belonging to the same species. RFLPs are typically detected as DNA fragments of different lengths after digestion with various restriction endonucleases. The comparison of RFLPs allows investigators to analyze the frequency of occurrence of mutations, such as point mutations, deletions, insertions, and gross chromosomal rearrangements, in the progeny of stressed plants. The assay involves restriction enzyme digestion of DNA followed by hybridization of digested DNA using a radioactively or enzymatically labeled probe. Since DNA can be digested with methylation sensitive enzymes, the assay can also be used to analyze a methylation pattern of a particular locus. Here, we describe RFLP analysis using methylation-insensitive and methylation-sensitive enzymes.

  4. Genome organization and DNA methylation patterns of B chromosomes in the red fox and Chinese raccoon dogs.

    Science.gov (United States)

    Bugno-Poniewierska, Monika; Solek, Przemysław; Wronski, Mariusz; Potocki, Leszek; Jezewska-Witkowska, Grażyna; Wnuk, Maciej

    2014-12-01

    The molecular structure of B chromosomes (Bs) is relatively well studied. Previous research demonstrates that Bs of various species usually contain two types of repetitive DNA sequences, satellite DNA and ribosomal DNA, but Bs also contain genes encoding histone proteins and many others. However, many questions remain regarding the origin and function of these chromosomes. Here, we focused on the comparative cytogenetic characteristics of the red fox and Chinese raccoon dog B chromosomes with particular attention to the distribution of repetitive DNA sequences and their methylation status. We confirmed that the small Bs of the red fox show a typical fluorescent telomeric distal signal, whereas medium-sized Bs of the Chinese raccoon dog were characterized by clusters of telomeric sequences along their length. We also found different DNA methylation patterns for the B chromosomes of both species. Therefore, we concluded that DNA methylation may maintain the transcriptional inactivation of DNA sequences localized to B chromosomes and may prevent genetic unbalancing and several negative phenotypic effects. © 2014 The Authors.

  5. New phenazine-containing ladder polymer of intrinsic microporosity from a spirobisindane-based AB-type monomer

    KAUST Repository

    Ghanem, Bader; Alghunaimi, Fahd; Alaslai, Nasser Y.; Ma, Xiaohua; Pinnau, Ingo

    2016-01-01

    . This protocol can be used to prepare a variety of phenazine-containing ladder type PIMs from their aromatic tetramethoxy precursors. The obtained polymer had high average molecular mass, excellent thermal stability, a high BET surface area of 705 m(2) g(-1

  6. Field-controlled magnetic order in the quantum spin-ladder system (Hpip)2CuBr4

    DEFF Research Database (Denmark)

    Thielemann, B.; Rüegg, C.; Kiefer, K.

    2009-01-01

    Neutron diffraction is used to investigate the field-induced, antiferromagnetically ordered state in the two-leg spin-ladder material (Hpip)(2)CuBr4. This "classical" phase, a consequence of weak interladder coupling, is nevertheless highly unconventional: its properties are influenced strongly...

  7. Patterns of exchange of forensic DNA data in the European Union through the Prüm system.

    Science.gov (United States)

    Santos, Filipe; Machado, Helena

    2017-07-01

    This paper presents a study of the 5-year operation (2011-2015) of the transnational exchange of forensic DNA data between Member States of the European Union (EU) for the purpose of combating cross-border crime and terrorism within the so-called Prüm system. This first systematisation of the full official statistical dataset provides an overall assessment of the match figures and patterns of operation of the Prüm system for DNA exchange. These figures and patterns are analysed in terms of the differentiated contributions by participating EU Member States. The data suggest a trend for West and Central European countries to concentrate the majority of Prüm matches, while DNA databases of Eastern European countries tend to contribute with profiles of people that match stains in other countries. In view of the necessary transparency and accountability of the Prüm system, more extensive and informative statistics would be an important contribution to the assessment of its functioning and societal benefits. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

  8. New phenazine-containing ladder polymer of intrinsic microporosity from a spirobisindane-based AB-type monomer

    KAUST Repository

    Ghanem, Bader

    2016-08-15

    A new solution-processable ladder polymer (PSBI-AB) of intrinsic microporosity with dibenzodioxane linkages and bis(phenazine) units was designed and synthesized by self-polymerization of an AB-type monomer containing both catechol and aromatic dichloride groups. Such polymerization is an effective way to synthesize high molecular weight polymers and has a significant advantage over AA-BB polycondensation due to the lack of the requirement for strict control over stoichiometric balance. This protocol can be used to prepare a variety of phenazine-containing ladder type PIMs from their aromatic tetramethoxy precursors. The obtained polymer had high average molecular mass, excellent thermal stability, a high BET surface area of 705 m(2) g(-1) and good solubility in some organic solvents such as chloroform, m-cresol and dichlorobenzene. Gas permeation measurements showed comparable results to the previously reported analogous PIM-7 for films made under the same formation protocol.

  9. Deep sequencing reveals distinct patterns of DNA methylation in prostate cancer.

    Science.gov (United States)

    Kim, Jung H; Dhanasekaran, Saravana M; Prensner, John R; Cao, Xuhong; Robinson, Daniel; Kalyana-Sundaram, Shanker; Huang, Christina; Shankar, Sunita; Jing, Xiaojun; Iyer, Matthew; Hu, Ming; Sam, Lee; Grasso, Catherine; Maher, Christopher A; Palanisamy, Nallasivam; Mehra, Rohit; Kominsky, Hal D; Siddiqui, Javed; Yu, Jindan; Qin, Zhaohui S; Chinnaiyan, Arul M

    2011-07-01

    Beginning with precursor lesions, aberrant DNA methylation marks the entire spectrum of prostate cancer progression. We mapped the global DNA methylation patterns in select prostate tissues and cell lines using MethylPlex-next-generation sequencing (M-NGS). Hidden Markov model-based next-generation sequence analysis identified ∼68,000 methylated regions per sample. While global CpG island (CGI) methylation was not differential between benign adjacent and cancer samples, overall promoter CGI methylation significantly increased from ~12.6% in benign samples to 19.3% and 21.8% in localized and metastatic cancer tissues, respectively (P-value prostate tissues, 2481 differentially methylated regions (DMRs) are cancer-specific, including numerous novel DMRs. A novel cancer-specific DMR in the WFDC2 promoter showed frequent methylation in cancer (17/22 tissues, 6/6 cell lines), but not in the benign tissues (0/10) and normal PrEC cells. Integration of LNCaP DNA methylation and H3K4me3 data suggested an epigenetic mechanism for alternate transcription start site utilization, and these modifications segregated into distinct regions when present on the same promoter. Finally, we observed differences in repeat element methylation, particularly LINE-1, between ERG gene fusion-positive and -negative cancers, and we confirmed this observation using pyrosequencing on a tissue panel. This comprehensive methylome map will further our understanding of epigenetic regulation in prostate cancer progression.

  10. Silver nanoparticle induced cytotoxicity, oxidative stress, and DNA damage in CHO cells

    Energy Technology Data Exchange (ETDEWEB)

    Awasthi, Kumud Kant [University of Rajasthan, Department of Zoology (India); Awasthi, Anjali; Kumar, Narender; Roy, Partha [Indian Institute of Technology Roorkee, Department of Biotechnology (India); Awasthi, Kamlendra, E-mail: kamlendra.awasthi@gmail.com [Malaviya National Institute of Technology, Department of Physics (India); John, P. J., E-mail: placheriljohn@yahoo.com [University of Rajasthan, Department of Zoology (India)

    2013-09-15

    Silver nanoparticles (Ag NPs) are being used increasingly in wound dressings, catheters, and in various household products due to their antimicrobial activity. The present study reports the toxicity evaluation of synthesized and well characterized Ag NPs using Chinese hamster ovary (CHO) cells. The UV-Vis spectroscopy reveals the formation of silver nanoparticles by exhibiting the typical surface plasmon absorption maxima at 408-410 nm. Transmission electron microscopy (TEM) reveals that the average diameter of silver nanoparticles is about 5.0 {+-} 1.0 nm and that they have spherical shape. Cell visibility and cell viability percentage show dose-dependent cellular toxicity of Ag NPs. The half maximal inhibitory concentration (IC{sub 50}) for CHO cells is 68.0 {+-} 2.65 {mu}g/ml after 24 h Ag NPs exposure. Toxicity evaluations, including cellular morphology, mitochondrial function (MTT assay), reactive oxygen species (ROS), and DNA fragmentation assay (Ladder pattern) were assessed in unexposed CHO cells (control) and the cells exposed to Ag NPs concentrations of 15, 30, and 60 {mu}g/ml for 24 h. The findings may assist in the designing of Ag NPs for various applications and provide insights into their toxicity.

  11. DNA fragmentation and cell cycle arrest: a hallmark of apoptosis induced by Ruta graveolens in human colon cancer cells.

    Science.gov (United States)

    Arora, Shagun; Tandon, Simran

    2015-01-01

    In the present study, we investigated the anti-cancer effect of various potencies of Ruta graveolens (Ruta) on COLO-205 cell line, as evidenced by cytotoxicity, migration, clonogenecity, morphological and biochemical changes and modification in the levels of genes associated with apoptosis and cell cycle. On treatment of COLO-205 cells maximal effects were seen with mother tincture (MT) and 30C potencies, wherein decrease in cell viability along with reduced clonogenecity and migration capabilities were noted. In addition morphological and biochemical alterations such as nuclear changes (fragmented nuclei with condensed chromatin) and DNA ladder-like pattern (increased amount of fragmented DNA) in COLO-205 cells indicating apoptotic related cell death were seen. The expression of apoptosis and cell-cycle related regulatory genes assessed by reverse transcriptase-PCR revealed an up-regulation of caspase 9, caspase-3, Bax, p21 and p27 expression and down-regulation of Bcl-2 expression in treated cells. The mode of cell death was suggestive of intrinsic apoptotic pathway along with cell cycle arrest at the G2/M of the cell cycle. Our findings indicate that phytochemicals present in Ruta showed potential for natural therapeutic product development for colon carcinoma. Copyright © 2014 The Faculty of Homeopathy. Published by Elsevier Ltd. All rights reserved.

  12. A genome-wide study of DNA methylation patterns and gene expression levels in multiple human and chimpanzee tissues.

    Directory of Open Access Journals (Sweden)

    Athma A Pai

    2011-02-01

    Full Text Available The modification of DNA by methylation is an important epigenetic mechanism that affects the spatial and temporal regulation of gene expression. Methylation patterns have been described in many contexts within and across a range of species. However, the extent to which changes in methylation might underlie inter-species differences in gene regulation, in particular between humans and other primates, has not yet been studied. To this end, we studied DNA methylation patterns in livers, hearts, and kidneys from multiple humans and chimpanzees, using tissue samples for which genome-wide gene expression data were also available. Using the multi-species gene expression and methylation data for 7,723 genes, we were able to study the role of promoter DNA methylation in the evolution of gene regulation across tissues and species. We found that inter-tissue methylation patterns are often conserved between humans and chimpanzees. However, we also found a large number of gene expression differences between species that might be explained, at least in part, by corresponding differences in methylation levels. In particular, we estimate that, in the tissues we studied, inter-species differences in promoter methylation might underlie as much as 12%-18% of differences in gene expression levels between humans and chimpanzees.

  13. Colour patterns do not diagnose species: quantitative evaluation of a DNA barcoded cryptic bumblebee complex.

    Directory of Open Access Journals (Sweden)

    James C Carolan

    Full Text Available Cryptic diversity within bumblebees (Bombus has the potential to undermine crucial conservation efforts designed to reverse the observed decline in many bumblebee species worldwide. Central to such efforts is the ability to correctly recognise and diagnose species. The B. lucorum complex (Bombus lucorum, B. cryptarum and B. magnus comprises one of the most abundant and important group of wild plant and crop pollinators in northern Europe. Although the workers of these species are notoriously difficult to diagnose morphologically, it has been claimed that queens are readily diagnosable from morphological characters. Here we assess the value of colour-pattern characters in species identification of DNA-barcoded queens from the B. lucorum complex. Three distinct molecular operational taxonomic units were identified each representing one species. However, no uniquely diagnostic colour-pattern character state was found for any of these three molecular units and most colour-pattern characters showed continuous variation among the units. All characters previously deemed to be unique and diagnostic for one species were displayed by specimens molecularly identified as a different species. These results presented here raise questions on the reliability of species determinations in previous studies and highlights the benefits of implementing DNA barcoding prior to ecological, taxonomic and conservation studies of these important key pollinators.

  14. Third-order differential ladder operators and supersymmetric quantum mechanics

    International Nuclear Information System (INIS)

    Mateo, J; Negro, J

    2008-01-01

    Hierarchies of one-dimensional Hamiltonians in quantum mechanics admitting third-order differential ladder operators are studied. Each Hamiltonian has associated three-step Darboux (pseudo)-cycles and Painleve IV equations as a closure condition. The whole hierarchy is generated applying some operations on the cycles. These operations are investigated in the frame of supersymmetric quantum mechanics and mainly involve algebraic manipulations. A consistent geometric representation for the hierarchy and cycles is built that also helps in understanding the operations. Three kinds of hierarchies are distinguished and a realization based on the harmonic oscillator Hamiltonian is supplied, giving an interpretation for the spectral properties of the Hamiltonians of each hierarchy

  15. Simulation of TunneLadder traveling-wave tube cold-test characteristics: Implementation of the three-dimensional, electromagnetic circuit analysis code micro-SOS

    Science.gov (United States)

    Kory, Carol L.; Wilson, Jeffrey D.

    1993-01-01

    The three-dimensional, electromagnetic circuit analysis code, Micro-SOS, can be used to reduce expensive time-consuming experimental 'cold-testing' of traveling-wave tube (TWT) circuits. The frequency-phase dispersion characteristics and beam interaction impedance of a TunneLadder traveling-wave tube slow-wave structure were simulated using the code. When reasonable dimensional adjustments are made, computer results agree closely with experimental data. Modifications to the circuit geometry that would make the TunneLadder TWT easier to fabricate for higher frequency operation are explored.

  16. The Earnings Ladder. Who's at the Bottom? Who's at the Top? Statistical Brief.

    Science.gov (United States)

    Bureau of the Census (DOC), Washington, DC. Economics and Statistics Administration.

    Data collected by the March Current Population Survey were used to identify which groups of year-round, full-time civilian workers aged 16 and older were most likely to be at the top and bottom of the earnings ladder. Women, young workers, less-educated individuals, and Hispanics were most likely to earn less than $13,091 (1992 constant dollars),…

  17. Lipsome-mediated uptake of exogenous DNA by Sahiwal cattle spermatozoa

    Directory of Open Access Journals (Sweden)

    Thomas V. Babu

    Full Text Available Aim: To investigate the influence of lipofection treatment and exogenous DNA uptake on the quality of sahiwal cattle spermatozoa. Materials and Methods: Semen collected from sahiwal bulls (n=7 were evaluated separately for color, volume, mass activity, concentration, motility and viability using standard procedures. Pooled sperm samples from selected bulls (n=3 were transfected with a model gene construct enhanced green fluorescent protein (p-EGFP via lipofection method and confirmed the genome integration by PCR technique. Furthermore the effect of transfection on spermatozoa was assessed based on apotosis, viability and motility. Results: In the current investigation sahiwal bulls were selected based on their breeding records and better semen characteristics. Although the transfected sperm samples failed to show florescence under fluorescence microscope, PCR studies confirmed the successful uptake of the p-EGFP gene in to the host sperm cell genome. Moreover transfected samples showed a significant reduction in the viability and motility without causing any DNA damage induced apoptosis as demonstrated by DNA Ladder assay. [Vet World 2012; 5(10.000: 621-627

  18. Academic Profile of Bachelor of Technical Teacher Education Ladder I Students as Ba sis for an Intervention Program

    Directory of Open Access Journals (Sweden)

    Arly B. Balingbing

    2017-05-01

    Full Text Available This study aimed to determine: the academic profile of Bachelor of Technical Teacher Education ( BTTE Ladder 1 students in terms of entrance examination, GWM in GEC subjects and TESDA Competency Assessment; their strengths and weaknesses along TESDA Assessment; the significant relationship between Entrance Examination & GWA, GWA & TESDA Competency and Entrance Examination & TESDA Compe tency, the significant interrelationship among the three variables; and the program or intervention which could be proposed to improve their academic performance. Data were gathered from one hundred fifty eight ( 158 BTTE Ladder 1 graduates of SY 2014 - 2016 through a questionnaire and documentary analysis and were statistically treated using percentage, weighted mean, Spearman’s rho and multiple coefficients. The researcher concluded that BTTE Ladder 1 students are competent as assessed by TESDA despite bein g low in entrance examination. Their weaknesses lie along communication and comprehension but they prove to be capable also on the condition that Filipino language is used and questions are repeated or rephrased. They also lack exposure to the tools and eq uipment used their field. Their strength is evident in performing the task but not in explaining the process. Both the Entrance Examination & GWA, GWM & TESDA Competency and Entrance Exam & TESDA Competency are significantly interrelated.

  19. Altered DNA Methylation Patterns Associated With Clinically Relevant Increases in PTSD Symptoms and PTSD Symptom Profiles in Military Personnel.

    Science.gov (United States)

    Martin, Christiana; Cho, Young-Eun; Kim, Hyungsuk; Yun, Sijung; Kanefsky, Rebekah; Lee, Hyunhwa; Mysliwiec, Vincent; Cashion, Ann; Gill, Jessica

    2018-05-01

    Military personnel experience posttraumatic stress disorder (PTSD), which is associated with differential DNA methylation across the whole genome. However, the relationship between these DNA methylation patterns and clinically relevant increases in PTSD severity is not yet clearly understood. The purpose of this study was to identify differences in DNA methylation associated with PTSD symptoms and investigate DNA methylation changes related to increases in the severity of PTSD in military personnel. In this pilot study, a cross-sectional comparison was made between military personnel with PTSD (n = 8) and combat-matched controls without PTSD (n = 6). Symptom measures were obtained, and genome-wide DNA methylation was measured using methylated DNA immunoprecipitation (MeDIP-seq) from whole blood samples at baseline and 3 months later. A longitudinal comparison measured DNA methylation changes in military personnel with clinically relevant increases in PTSD symptoms between time points (PTSD onset) and compared methylation patterns to controls with no clinical changes in PTSD. In military personnel with elevated PTSD symptoms 3 months following baseline, 119 genes exhibited reduced methylation and 8 genes exhibited increased methylation. Genes with reduced methylation in the PTSD-onset group relate to the canonical pathways of netrin signaling, Wnt/Ca + pathway, and axonal guidance signaling. These gene pathways relate to neurological disorders, and the current findings suggest that these epigenetic changes potentially relate to PTSD symptomology. This study provides some novel insights into the role of epigenetic changes in PTSD symptoms and the progression of PTSD symptoms in military personnel.

  20. Telecast of Astronaut Neil Armstrong descending ladder to surface of the moon

    Science.gov (United States)

    1969-01-01

    Astronaut Neil A. Armstrong, Apollo 11 commander, descends the ladder of the Apollo 11 Lunar Module prior to making the first step by man on the moon. This view is a black and white reproduction taken from a telecast by the Apollo 11 lunar surface camera during extravehicular activity. The black bar running through the center of the picture is an anamoly in the television ground data system at the Goldstone Tracking Station.

  1. Several nuclear events during apoptosis depend on caspase-3 activation but do not constitute a common pathway.

    Directory of Open Access Journals (Sweden)

    Lisa Trisciuoglio

    Full Text Available A number of nuclear events occur during apoptosis, including DNA laddering, nuclear lamina breakdown, phosphorylation of histones H2B and histone H2AX, and the tight binding to chromatin of HMGB1 and CAD, the nuclease responsible for DNA laddering. We have performed an epistasis analysis to investigate whether these events cluster together in pathways. We find that all depend directly or indirectly on caspase-3 activation. CAD activation, H2AX phosphorylation and DNA laddering cluster together into a pathway, but all other events appear to be independent of each other downstream of caspase-3, and likely evolved subject to different functional pressures.

  2. SMRT Sequencing Revealed Mitogenome Characteristics and Mitogenome-Wide DNA Modification Pattern in Ophiocordyceps sinensis.

    Science.gov (United States)

    Kang, Xincong; Hu, Liqin; Shen, Pengyuan; Li, Rui; Liu, Dongbo

    2017-01-01

    Single molecule, real-time (SMRT) sequencing was used to characterize mitochondrial (mt) genome of Ophiocordyceps sinensis and to analyze the mt genome-wide pattern of epigenetic DNA modification. The complete mt genome of O. sinensis , with a size of 157,539 bp, is the fourth largest Ascomycota mt genome sequenced to date. It contained 14 conserved protein-coding genes (PCGs), 1 intronic protein rps3 , 27 tRNAs and 2 rRNA subunits, which are common characteristics of the known mt genomes in Hypocreales. A phylogenetic tree inferred from 14 PCGs in Pezizomycotina fungi supports O. sinensis as most closely related to Hirsutella rhossiliensis in Ophiocordycipitaceae. A total of 36 sequence sites in rps3 were under positive selection, with dN/dS >1 in the 20 compared fungi. Among them, 16 sites were statistically significant. In addition, the mt genome-wide base modification pattern of O. sinensis was determined in this study, especially DNA methylation. The methylations were located in coding and uncoding regions of mt PCGs in O. sinensis , and might be closely related to the expression of PCGs or the binding affinity of transcription factor A to mtDNA. Consequently, these methylations may affect the enzymatic activity of oxidative phosphorylation and then the mt respiratory rate; or they may influence mt biogenesis. Therefore, methylations in the mitogenome of O. sinensis might be a genetic feature to adapt to the cold and low PO 2 environment at high altitude, where O. sinensis is endemic. This is the first report on epigenetic modifications in a fungal mt genome.

  3. Fish passage post-construction issues: analysis of distribution, attraction and passage efficiency metrics at the Baguari Dam fish ladder to approach the problem

    Directory of Open Access Journals (Sweden)

    Luiz Gustavo Martins da Silva

    Full Text Available Fish passages are considered the oldest management tool used to minimize the impact of blocking fish migratory routes by hydroelectric power plants. However, fish passages are being installed without specific criteria in Brazil, with severe consequences to the conservation of the local fish fauna. Therefore, basic data gathered for fish passages already constructed could contribute to define operational rules, in addition to offer subsidies to decision-making and design of future facilities. Thus, the fish ladder of Baguari Dam was evaluated regarding temporal distribution, attraction, and ascension of the local fish fauna. A total of 20 fish samples were conducted immediately downstream of the dam and inside the fish ladder, from January 2010 to June 2011. Seasonal variation in fish abundance and richness was registered below the dam and inside the passage, with higher number of migratory fish in the reproductive season (Kruskall-Wallis, p = 0.04 and p = 0.05. Furthermore, higher concentration of migratory allochthonous and non-migratory species was registered for the spill bay (Wilcoxon, p = 0.009 and p = 0.006 compared to the tailrace, where the fish ladder entrance is located. This result suggests low efficiency of the attraction system of the mechanism during the reproductive period. Once entering the fish ladder, migratory species apparently ascend the facility due to the similar distribution throughout different stretches. Generally, the results showed that an operational rule for the Baguari Dam fish ladder should consider running the facility only during the reproductive period, unless the objectives of the passage are well defined. The attraction system must be more precisely evaluated, using technologies such as radiotelemetry. Similarly, fish ascension also should be better analyzed to evaluate the time spent to ascend and its influence in the reproductive biology of the species using the ladder. Pit-tag system could be used to

  4. Planktonic foraminifera-derived environmental DNA extracted from abyssal sediments preserves patterns of plankton macroecology

    Directory of Open Access Journals (Sweden)

    R. Morard

    2017-06-01

    Full Text Available Deep-sea sediments constitute a unique archive of ocean change, fueled by a permanent rain of mineral and organic remains from the surface ocean. Until now, paleo-ecological analyses of this archive have been mostly based on information from taxa leaving fossils. In theory, environmental DNA (eDNA in the sediment has the potential to provide information on non-fossilized taxa, allowing more comprehensive interpretations of the fossil record. Yet, the process controlling the transport and deposition of eDNA onto the sediment and the extent to which it preserves the features of past oceanic biota remains unknown. Planktonic foraminifera are the ideal taxa to allow an assessment of the eDNA signal modification during deposition because their fossils are well preserved in the sediment and their morphological taxonomy is documented by DNA barcodes. Specifically, we re-analyze foraminiferal-specific metabarcodes from 31 deep-sea sediment samples, which were shown to contain a small fraction of sequences from planktonic foraminifera. We confirm that the largest portion of the metabarcode originates from benthic bottom-dwelling foraminifera, representing the in situ community, but a small portion (< 10 % of the metabarcodes can be unambiguously assigned to planktonic taxa. These organisms live exclusively in the surface ocean and the recovered barcodes thus represent an allochthonous component deposited with the rain of organic remains from the surface ocean. We take advantage of the planktonic foraminifera portion of the metabarcodes to establish to what extent the structure of the surface ocean biota is preserved in sedimentary eDNA. We show that planktonic foraminifera DNA is preserved in a range of marine sediment types, the composition of the recovered eDNA metabarcode is replicable and that both the similarity structure and the diversity pattern are preserved. Our results suggest that sedimentary eDNA could preserve the ecological structure of

  5. SU(3)_C× SU(2)_L× U(1)_Y( × U(1)_X ) as a symmetry of division algebraic ladder operators

    Science.gov (United States)

    Furey, C.

    2018-05-01

    We demonstrate a model which captures certain attractive features of SU(5) theory, while providing a possible escape from proton decay. In this paper we show how ladder operators arise from the division algebras R, C, H, and O. From the SU( n) symmetry of these ladder operators, we then demonstrate a model which has much structural similarity to Georgi and Glashow's SU(5) grand unified theory. However, in this case, the transitions leading to proton decay are expected to be blocked, given that they coincide with presumably forbidden transformations which would incorrectly mix distinct algebraic actions. As a result, we find that we are left with G_{sm} = SU(3)_C× SU(2)_L× U(1)_Y / Z_6. Finally, we point out that if U( n) ladder symmetries are used in place of SU( n), it may then be possible to find this same G_{sm}=SU(3)_C× SU(2)_L× U(1)_Y / Z_6, together with an extra U(1)_X symmetry, related to B-L.

  6. Molecular genotyping of Colletotrichum species based on arbitrarily primed PCR, A + T-Rich DNA, and nuclear DNA analyses

    Science.gov (United States)

    Freeman, S.; Pham, M.; Rodriguez, R.J.

    1993-01-01

    Molecular genotyping of Colletotrichum species based on arbitrarily primed PCR, A + T-rich DNA, and nuclear DNA analyses. Experimental Mycology 17, 309-322. Isolates of Colletotrichum were grouped into 10 separate species based on arbitrarily primed PCR (ap-PCR), A + T-rich DNA (AT-DNA) and nuclear DNA banding patterns. In general, the grouping of Colletotrichum isolates by these molecular approaches corresponded to that done by classical taxonomic identification, however, some exceptions were observed. PCR amplification of genomic DNA using four different primers allowed for reliable differentiation between isolates of the 10 species. HaeIII digestion patterns of AT-DNA also distinguished between species of Colletotrichum by generating species-specific band patterns. In addition, hybridization of the repetitive DNA element (GcpR1) to genomic DNA identified a unique set of Pst 1-digested nuclear DNA fragments in each of the 10 species of Colletotrichum tested. Multiple isolates of C. acutatum, C. coccodes, C. fragariae, C. lindemuthianum, C. magna, C. orbiculare, C. graminicola from maize, and C. graminicola from sorghum showed 86-100% intraspecies similarity based on ap-PCR and AT-DNA analyses. Interspecies similarity determined by ap-PCR and AT-DNA analyses varied between 0 and 33%. Three distinct banding patterns were detected in isolates of C. gloeosporioides from strawberry. Similarly, three different banding patterns were observed among isolates of C. musae from diseased banana.

  7. Susceptibility patterns and the role of extracellular DNA in Staphylococcus epidermidis biofilm resistance to physico-chemical stress exposure.

    Science.gov (United States)

    Olwal, Charles Ochieng'; Ang'ienda, Paul Oyieng'; Onyango, David Miruka; Ochiel, Daniel Otieno

    2018-05-02

    Over 65% of human infections are ascribed to bacterial biofilms that are often highly resistant to antibiotics and host immunity. Staphylococcus epidermidis is the predominant cause of recurrent nosocomial and biofilm-related infections. However, the susceptibility patterns of S. epidermidis biofilms to physico-chemical stress induced by commonly recommended disinfectants [(heat, sodium chloride (NaCl), sodium hypochlorite (NaOCl) and hydrogen peroxide (H 2 O 2 )] in domestic and human healthcare settings remains largely unknown. Further, the molecular mechanisms of bacterial biofilms resistance to the physico-chemical stresses remain unclear. Growing evidence demonstrates that extracellular DNA (eDNA) protects bacterial biofilms against antibiotics. However, the role of eDNA as a potential mechanism underlying S. epidermidis biofilms resistance to physico-chemical stress exposure is yet to be understood. Therefore, this study aimed to evaluate the susceptibility patterns of and eDNA release by S. epidermidis biofilm and planktonic cells to physico-chemical stress exposure. S. epidermidis biofilms exposed to physico-chemical stress conditions commonly recommended for disinfection [heat (60 °C), 1.72 M NaCl, solution containing 150 μL of waterguard (0.178 M NaOCl) in 1 L of water or 1.77 M H 2 O 2 ] for 30 and 60 min exhibited lower log reductions of CFU/mL than the corresponding planktonic cells (p chemical stress induced by the four commonly recommended disinfectants than the analogous planktonic cells. Further, S. epidermidis biofilms enhanced eDNA release in response to the sub-lethal heat and oxidative stress exposure than the corresponding planktonic cells suggesting a role of eDNA in biofilms resistance to the physico-chemical stresses.

  8. Identification of unique repeated patterns, location of mutation in DNA finger printing using artificial intelligence technique.

    Science.gov (United States)

    Mukunthan, B; Nagaveni, N

    2014-01-01

    In genetic engineering, conventional techniques and algorithms employed by forensic scientists to assist in identification of individuals on the basis of their respective DNA profiles involves more complex computational steps and mathematical formulae, also the identification of location of mutation in a genomic sequence in laboratories is still an exigent task. This novel approach provides ability to solve the problems that do not have an algorithmic solution and the available solutions are also too complex to be found. The perfect blend made of bioinformatics and neural networks technique results in efficient DNA pattern analysis algorithm with utmost prediction accuracy.

  9. Online measurement of mental representations of complex spatial decision problems : comparison of CNET and hard laddering

    NARCIS (Netherlands)

    Horeni, O.; Arentze, T.A.; Dellaert, B.G.C.; Timmermans, H.J.P.

    2014-01-01

    This paper introduces the online Causal Network Elicitation Technique (CNET), as a technique for measuring components of mental representations of choice tasks and compares it with the more common technique of online 'hard' laddering (HL). While CNET works in basically two phases, one in open

  10. Biomolecular and Structural Analyses of Cauliflower-like DNAs by Ultraviolet, Circular Dichroism, and Fluorescence Spectroscopies in Comparison with Natural DNA

    OpenAIRE

    Gill, Pooria; Ranjbar, Bijan; Saber, Reza; Khajeh, Khosro; Mohammadian, Mehdi

    2011-01-01

    Cauliflower-like DNAs are stem-loop DNAs that are fabricated periodically in inverted repetitions from deoxyribonucleic acid phosphates (dNTPs) by loop-mediated isothermal amplification (LAMP). Cauliflower-like DNAs have ladder-shape behaviors on gel electrophoresis, and increasing the time of LAMP leads to multiplying the repetitions, stem-loops, and electrophoretic bands. Cauliflower-like DNAs were fabricated via LAMP using two loop primers, two bumper primers, dNTPs, a λ-phage DNA template...

  11. Shotgun Bisulfite Sequencing of the Betula platyphylla Genome Reveals the Tree’s DNA Methylation Patterning

    Directory of Open Access Journals (Sweden)

    Chang Su

    2014-12-01

    Full Text Available DNA methylation plays a critical role in the regulation of gene expression. Most studies of DNA methylation have been performed in herbaceous plants, and little is known about the methylation patterns in tree genomes. In the present study, we generated a map of methylated cytosines at single base pair resolution for Betula platyphylla (white birch by bisulfite sequencing combined with transcriptomics to analyze DNA methylation and its effects on gene expression. We obtained a detailed view of the function of DNA methylation sequence composition and distribution in the genome of B. platyphylla. There are 34,460 genes in the whole genome of birch, and 31,297 genes are methylated. Conservatively, we estimated that 14.29% of genomic cytosines are methylcytosines in birch. Among the methylation sites, the CHH context accounts for 48.86%, and is the largest proportion. Combined transcriptome and methylation analysis showed that the genes with moderate methylation levels had higher expression levels than genes with high and low methylation. In addition, methylated genes are highly enriched for the GO subcategories of binding activities, catalytic activities, cellular processes, response to stimulus and cell death, suggesting that methylation mediates these pathways in birch trees.

  12. Online measurement of mental representations of complex spatial decision problems : Comparison of CNET and hard laddering

    NARCIS (Netherlands)

    O. Horeni (Oliver); T.A. Arentze (Theo); B.G.C. Dellaert (Benedict); H.J.P. Timmermans (Harry)

    2013-01-01

    textabstractThis paper introduces the online Causal Network Elicitation Technique (CNET), as a technique for measuring components of mental representations of choice tasks and compares it with the more common technique of online ‘hard’ laddering (HL). While CNET works in basically two phases, one in

  13. Prenatal phthalate exposure and altered patterns of DNA methylation in cord blood.

    Science.gov (United States)

    Solomon, Olivia; Yousefi, Paul; Huen, Karen; Gunier, Robert B; Escudero-Fung, Maria; Barcellos, Lisa F; Eskenazi, Brenda; Holland, Nina

    2017-07-01

    Epigenetic changes such as DNA methylation may be a molecular mechanism through which environmental exposures affect health. Phthalates are known endocrine disruptors with ubiquitous exposures in the general population including pregnant women, and they have been linked with a number of adverse health outcomes. We examined the association between in utero phthalate exposure and altered patterns of cord blood DNA methylation in 336 Mexican-American newborns. Concentrations of 11 phthalate metabolites were analyzed in maternal urine samples collected at 13 and 26 weeks gestation as a measure of fetal exposure. DNA methylation was assessed using the Infinium HumanMethylation 450K BeadChip adjusting for cord blood cell composition. To identify differentially methylated regions (DMRs) that may be more informative than individual CpG sites, we used two different approaches, DMRcate and comb-p. Regional assessment by both methods identified 27 distinct DMRs, the majority of which were in relation to multiple phthalate metabolites. Most of the significant DMRs (67%) were observed for later pregnancy (26 weeks gestation). Further, 51% of the significant DMRs were associated with the di-(2-ethylhexyl) phthalate metabolites. Five individual CpG sites were associated with phthalate metabolite concentrations after multiple comparisons adjustment (FDR), all showing hypermethylation. Genes with DMRs were involved in inflammatory response (IRAK4 and ESM1), cancer (BRCA1 and LASP1), endocrine function (CNPY1), and male fertility (IFT140, TESC, and PRDM8). These results on differential DNA methylation in newborns with prenatal phthalate exposure provide new insights and targets to explore mechanism of adverse effects of phthalates on human health. Environ. Mol. Mutagen. 58:398-410, 2017. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  14. Enhanced low-template DNA analysis conditions and investigation of allele dropout patterns.

    Science.gov (United States)

    Hedell, Ronny; Dufva, Charlotte; Ansell, Ricky; Mostad, Petter; Hedman, Johannes

    2015-01-01

    Forensic DNA analysis applying PCR enables profiling of minute biological samples. Enhanced analysis conditions can be applied to further push the limit of detection, coming with the risk of visualising artefacts and allele imbalances. We have evaluated the consecutive increase of PCR cycles from 30 to 35 to investigate the limitations of low-template (LT) DNA analysis, applying the short tandem repeat (STR) analysis kit PowerPlex ESX 16. Mock crime scene DNA extracts of four different quantities (from around 8-84 pg) were tested. All PCR products were analysed using 5, 10 and 20 capillary electrophoresis (CE) injection seconds. Bayesian models describing allele dropout patterns, allele peak heights and heterozygote balance were developed to assess the overall improvements in EPG quality with altered PCR/CE settings. The models were also used to evaluate the impact of amplicon length, STR marker and fluorescent label on the risk for allele dropout. The allele dropout probability decreased for each PCR cycle increment from 30 to 33 PCR cycles. Irrespective of DNA amount, the dropout probability was not affected by further increasing the number of PCR cycles. For the 42 and 84 pg samples, mainly complete DNA profiles were generated applying 32 PCR cycles. For the 8 and 17 pg samples, the allele dropouts decreased from 100% using 30 cycles to about 75% and 20%, respectively. The results for 33, 34 and 35 PCR cycles indicated that heterozygote balance and stutter ratio were mainly affected by DNA amount, and not directly by PCR cycle number and CE injection settings. We found 32 and 33 PCR cycles with 10 CE injection seconds to be optimal, as 34 and 35 PCR cycles did not improve allele detection and also included CE saturation problems. We find allele dropout probability differences between several STR markers. Markers labelled with the fluorescent dyes CXR-ET (red in electropherogram) and TMR-ET (shown as black) generally have higher dropout risks compared with those

  15. Development and validation of a nursing professionalism evaluation model in a career ladder system.

    Science.gov (United States)

    Kim, Yeon Hee; Jung, Young Sun; Min, Ja; Song, Eun Young; Ok, Jung Hui; Lim, Changwon; Kim, Kyunghee; Kim, Ji-Su

    2017-01-01

    The clinical ladder system categorizes the degree of nursing professionalism and rewards and is an important human resource tool for managing nursing. We developed a model to evaluate nursing professionalism, which determines the clinical ladder system levels, and verified its validity. Data were collected using a clinical competence tool developed in this study, and existing methods such as the nursing professionalism evaluation tool, peer reviews, and face-to-face interviews to evaluate promotions and verify the presented content in a medical institution. Reliability and convergent and discriminant validity of the clinical competence evaluation tool were verified using SmartPLS software. The validity of the model for evaluating overall nursing professionalism was also analyzed. Clinical competence was determined by five dimensions of nursing practice: scientific, technical, ethical, aesthetic, and existential. The structural model explained 66% of the variance. Clinical competence scales, peer reviews, and face-to-face interviews directly determined nursing professionalism levels. The evaluation system can be used for evaluating nurses' professionalism in actual medical institutions from a nursing practice perspective. A conceptual framework for establishing a human resources management system for nurses and a tool for evaluating nursing professionalism at medical institutions is provided.

  16. DNA methylation patterns in tissues from mid-gestation bovine foetuses produced by somatic cell nuclear transfer show subtle abnormalities in nuclear reprogramming

    Directory of Open Access Journals (Sweden)

    Lee Rita SF

    2010-03-01

    Full Text Available Abstract Background Cloning of cattle by somatic cell nuclear transfer (SCNT is associated with a high incidence of pregnancy failure characterized by abnormal placental and foetal development. These abnormalities are thought to be due, in part, to incomplete re-setting of the epigenetic state of DNA in the donor somatic cell nucleus to a state that is capable of driving embryonic and foetal development to completion. Here, we tested the hypothesis that DNA methylation patterns were not appropriately established during nuclear reprogramming following SCNT. A panel of imprinted, non-imprinted genes and satellite repeat sequences was examined in tissues collected from viable and failing mid-gestation SCNT foetuses and compared with similar tissues from gestation-matched normal foetuses generated by artificial insemination (AI. Results Most of the genomic regions examined in tissues from viable and failing SCNT foetuses had DNA methylation patterns similar to those in comparable tissues from AI controls. However, statistically significant differences were found between SCNT and AI at specific CpG sites in some regions of the genome, particularly those associated with SNRPN and KCNQ1OT1, which tended to be hypomethylated in SCNT tissues. There was a high degree of variation between individuals in methylation levels at almost every CpG site in these two regions, even in AI controls. In other genomic regions, methylation levels at specific CpG sites were tightly controlled with little variation between individuals. Only one site (HAND1 showed a tissue-specific pattern of DNA methylation. Overall, DNA methylation patterns in tissues of failing foetuses were similar to apparently viable SCNT foetuses, although there were individuals showing extreme deviant patterns. Conclusion These results show that SCNT foetuses that had developed to mid-gestation had largely undergone nuclear reprogramming and that the epigenetic signature at this stage was not a

  17. Symmetry-broken states in a system of interacting bosons on a two-leg ladder with a uniform Abelian gauge field

    Science.gov (United States)

    Greschner, S.; Piraud, M.; Heidrich-Meisner, F.; McCulloch, I. P.; Schollwöck, U.; Vekua, T.

    2016-12-01

    We study the quantum phases of bosons with repulsive contact interactions on a two-leg ladder in the presence of a uniform Abelian gauge field. The model realizes many interesting states, including Meissner phases, vortex fluids, vortex lattices, charge density waves, and the biased-ladder phase. Our work focuses on the subset of these states that breaks a discrete symmetry. We use density matrix renormalization group simulations to demonstrate the existence of three vortex-lattice states at different vortex densities and we characterize the phase transitions from these phases into neighboring states. Furthermore, we provide an intuitive explanation of the chiral-current reversal effect that is tied to some of these vortex lattices. We also study a charge-density-wave state that exists at 1/4 particle filling at large interaction strengths and flux values close to half a flux quantum. By changing the system parameters, this state can transition into a completely gapped vortex-lattice Mott-insulating state. We elucidate the stability of these phases against nearest-neighbor interactions on the rungs of the ladder relevant for experimental realizations with a synthetic lattice dimension. A charge-density-wave state at 1/3 particle filling can be stabilized for flux values close to half a flux quantum and for very strong on-site interactions in the presence of strong repulsion on the rungs. Finally, we analytically describe the emergence of these phases in the low-density regime, and, in particular, we obtain the boundaries of the biased-ladder phase, i.e., the phase that features a density imbalance between the legs. We make contact with recent quantum-gas experiments that realized related models and discuss signatures of these quantum states in experimentally accessible observables.

  18. One-Particle vs. Two-Particle Crossover in Weakly Coupled Hubbard Chains and Ladders: Perturbative Renormalization Group Approach

    OpenAIRE

    Kishine, Jun-ichiro; Yonemitsu, Kenji

    1997-01-01

    Physical nature of dimensional crossovers in weakly coupled Hubbard chains and ladders has been discussed within the framework of the perturbative renormalization-group approach. The difference between these two cases originates from different universality classes which the corresponding isolated systems belong to.

  19. A DNA-based pattern classifier with in vitro learning and associative recall for genomic characterization and biosensing without explicit sequence knowledge.

    Science.gov (United States)

    Lee, Ju Seok; Chen, Junghuei; Deaton, Russell; Kim, Jin-Woo

    2014-01-01

    Genetic material extracted from in situ microbial communities has high promise as an indicator of biological system status. However, the challenge is to access genomic information from all organisms at the population or community scale to monitor the biosystem's state. Hence, there is a need for a better diagnostic tool that provides a holistic view of a biosystem's genomic status. Here, we introduce an in vitro methodology for genomic pattern classification of biological samples that taps large amounts of genetic information from all genes present and uses that information to detect changes in genomic patterns and classify them. We developed a biosensing protocol, termed Biological Memory, that has in vitro computational capabilities to "learn" and "store" genomic sequence information directly from genomic samples without knowledge of their explicit sequences, and that discovers differences in vitro between previously unknown inputs and learned memory molecules. The Memory protocol was designed and optimized based upon (1) common in vitro recombinant DNA operations using 20-base random probes, including polymerization, nuclease digestion, and magnetic bead separation, to capture a snapshot of the genomic state of a biological sample as a DNA memory and (2) the thermal stability of DNA duplexes between new input and the memory to detect similarities and differences. For efficient read out, a microarray was used as an output method. When the microarray-based Memory protocol was implemented to test its capability and sensitivity using genomic DNA from two model bacterial strains, i.e., Escherichia coli K12 and Bacillus subtilis, results indicate that the Memory protocol can "learn" input DNA, "recall" similar DNA, differentiate between dissimilar DNA, and detect relatively small concentration differences in samples. This study demonstrated not only the in vitro information processing capabilities of DNA, but also its promise as a genomic pattern classifier that could

  20. Phase dynamics of a Josephson junction ladder driven by modulated currents

    International Nuclear Information System (INIS)

    Kawaguchi, T.

    2011-01-01

    Phase dynamics of disordered Josephson junction ladders (JJLs) driven by external currents which are spatially and temporally modulated is studied using a numerical simulation based on a random field XY model. This model is considered theoretically as an effective model of JJLs with structural disorder in a magnetic field. The spatiotemporal modulation of external currents causes peculiar dynamical effects of phases in the system under certain conditions, such as the directed motion of phases and the mode-locking in the absence of dc currents. We clarify the details of effects of the spatiotemporal modulation on the phase dynamics.

  1. Magnetic field effects of tow-leg Heisenberg antiferromagnetic ladders: Thermodynamic properties

    International Nuclear Information System (INIS)

    Wang Xiaoqun; Yu Lu

    2000-05-01

    Using the recently developed transfer-matrix renormalization group method, we have studied the thermodynamic properties of two-leg antiferromagnetic ladders in the magnetic field. Based on different behavior of magnetization, we found disordered spin liquid, Luttinger liquid, spin-polarized phases and a classical regime depending on magnetic field and temperature. Our calculations in Luttinger liquid regime suggest that both the divergence of the NMR relaxation rate and the anomalous specific heat behavior observed on Cu 2 (C 5 H 12 N 2 ) 2 Cl 4 are due to quasi-one-dimensional effect rather than three-dimensional ordering. (author)

  2. DNA Origami Reorganizes upon Interaction with Graphite: Implications for High-Resolution DNA Directed Protein Patterning

    Directory of Open Access Journals (Sweden)

    Masudur Rahman

    2016-10-01

    Full Text Available Although there is a long history of the study of the interaction of DNA with carbon surfaces, limited information exists regarding the interaction of complex DNA-based nanostructures with the important material graphite, which is closely related to graphene. In view of the capacity of DNA to direct the assembly of proteins and optical and electronic nanoparticles, the potential for combining DNA-based materials with graphite, which is an ultra-flat, conductive carbon substrate, requires evaluation. A series of imaging studies utilizing Atomic Force Microscopy has been applied in order to provide a unified picture of this important interaction of structured DNA and graphite. For the test structure examined, we observe a rapid destabilization of the complex DNA origami structure, consistent with a strong interaction of single-stranded DNA with the carbon surface. This destabilizing interaction can be obscured by an intentional or unintentional primary intervening layer of single-stranded DNA. Because the interaction of origami with graphite is not completely dissociative, and because the frustrated, expanded structure is relatively stable over time in solution, it is demonstrated that organized structures of pairs of the model protein streptavidin can be produced on carbon surfaces using DNA origami as the directing material.

  3. DNA Origami Reorganizes upon Interaction with Graphite: Implications for High-Resolution DNA Directed Protein Patterning

    Science.gov (United States)

    Rahman, Masudur; Neff, David; Green, Nathaniel; Norton, Michael L.

    2016-01-01

    Although there is a long history of the study of the interaction of DNA with carbon surfaces, limited information exists regarding the interaction of complex DNA-based nanostructures with the important material graphite, which is closely related to graphene. In view of the capacity of DNA to direct the assembly of proteins and optical and electronic nanoparticles, the potential for combining DNA-based materials with graphite, which is an ultra-flat, conductive carbon substrate, requires evaluation. A series of imaging studies utilizing Atomic Force Microscopy has been applied in order to provide a unified picture of this important interaction of structured DNA and graphite. For the test structure examined, we observe a rapid destabilization of the complex DNA origami structure, consistent with a strong interaction of single-stranded DNA with the carbon surface. This destabilizing interaction can be obscured by an intentional or unintentional primary intervening layer of single-stranded DNA. Because the interaction of origami with graphite is not completely dissociative, and because the frustrated, expanded structure is relatively stable over time in solution, it is demonstrated that organized structures of pairs of the model protein streptavidin can be produced on carbon surfaces using DNA origami as the directing material. PMID:28335324

  4. Clinical patterns associated with the concurrent detection of anti-HBs and HBV DNA.

    Science.gov (United States)

    Anastasiou, Olympia E; Widera, Marek; Korth, Johannes; Kefalakes, Helenie; Katsounas, Antonios; Hilgard, Gudrun; Gerken, Guido; Canbay, Ali; Ciesek, Sandra; Verheyen, Jens

    2018-02-01

    Simultaneous detection of anti-HBs and HBV DNA is a rare serological combination and has been described in acute and chronic HBV infection. To scrutinize viral and clinical patterns associated with concurrent detection of anti-HBs and HBV DNA. Simultaneous detection of anti-HBs and HBV DNA was observed in 64/1444 (4.4%) patients treated for HBV infection at the University Hospital of Essen from 2006 to 2016 (8 with acute, 20 with reactivated, and 36 chronic HBV infection). Clinical data and laboratory parameters were analyzed. Regions of the small hepatitis B surface antigen (SHB) and the reverse transcriptase (RT) were sequenced using next generation sequencing (NGS). Among the 64 patients with detectable HBV DNA and anti-HBs, 17 were HBsAg negative (HBsAg[-]), and two had acute liver failure. Patients with acute HBV infection had fewer genotype specific amino acid substitutions in the SHB region than patients with reactivated HBV infection (4 [4.5] vs 9 [16.25], P = 0.043). However, we could observe a significantly higher number of mutations in the a-determinant region when comparing chronically infected patients to patients with acute infection (0 [1] vs 1 [1], P = 0.044). The ratio of nonsynonymous to synonymous mutations (Ka/Ks) was on average >1 for the SHB region and 1) in the SHB region indicates that anti-HBs might have exerted selection pressure on the HBsAg. In three cases the diagnosis of acute HBV infection would have been at least delayed by only focusing on HBsAg testing. © 2017 Wiley Periodicals, Inc.

  5. Evolution of rDNA in Nicotiana Allopolyploids: A Potential Link between rDNA Homogenization and Epigenetics

    Science.gov (United States)

    Kovarik, Ales; Dadejova, Martina; Lim, Yoong K.; Chase, Mark W.; Clarkson, James J.; Knapp, Sandra; Leitch, Andrew R.

    2008-01-01

    Background The evolution and biology of rDNA have interested biologists for many years, in part, because of two intriguing processes: (1) nucleolar dominance and (2) sequence homogenization. We review patterns of evolution in rDNA in the angiosperm genus Nicotiana to determine consequences of allopolyploidy on these processes. Scope Allopolyploid species of Nicotiana are ideal for studying rDNA evolution because phylogenetic reconstruction of DNA sequences has revealed patterns of species divergence and their parents. From these studies we also know that polyploids formed over widely different timeframes (thousands to millions of years), enabling comparative and temporal studies of rDNA structure, activity and chromosomal distribution. In addition studies on synthetic polyploids enable the consequences of de novo polyploidy on rDNA activity to be determined. Conclusions We propose that rDNA epigenetic expression patterns established even in F1 hybrids have a material influence on the likely patterns of divergence of rDNA. It is the active rDNA units that are vulnerable to homogenization, which probably acts to reduce mutational load across the active array. Those rDNA units that are epigenetically silenced may be less vulnerable to sequence homogenization. Selection cannot act on these silenced genes, and they are likely to accumulate mutations and eventually be eliminated from the genome. It is likely that whole silenced arrays will be deleted in polyploids of 1 million years of age and older. PMID:18310159

  6. Mitochondrial DNA variability among eight Tikúna villages: evidence for an intratribal genetic heterogeneity pattern.

    Science.gov (United States)

    Mendes-Junior, Celso Teixeira; Simões, Aguinaldo Luiz

    2009-11-01

    To study the genetic structure of the Tikúna tribe, four major Native American mitochondrial DNA (mtDNA) founder haplogroups were analyzed in 187 Amerindians from eight Tikúna villages located in the Brazilian Amazon. The central position of these villages in the continent makes them relevant for attempts to reconstruct population movements in South America. In this geographic region, there is particular concern regarding the genetic structure of the Tikúna tribe, formerly designated "enigmatic" due to its remarkable degree of intratribal homogeneity and the scarcity of private protein variants. In spite of its large population size and geographic distribution, the Tikúna tribe presents marked genetic and linguistic isolation. All individuals presented indigenous mtDNA haplogroups. An intratribal genetic heterogeneity pattern characterized by two highly homogeneous Tikúna groups that differ considerably from each other was observed. Such a finding was unexpected, since the Tikúna tribe is characterized by a social system that favors intratribal exogamy and patrilocality that would lead to a higher female migration rate and homogenization of the mtDNA gene pool. Demographic explosions and religious events, which significantly changed the sizes and compositions of many Tikúna villages, may be reflected in the genetic results presented here.

  7. Towers and ladders: Infinite parameter symmetries in Kaluza-Klein theories

    International Nuclear Information System (INIS)

    Aulakh, C.S.

    1984-05-01

    We introduce a class of infinite dimensional algebras with a 'generalized loop structure' by considering the global symmetries of the four dimensional Lagrangian obtained by compactifying general relativity coupled to Yang-Mills in six dimensions down to M 4 xS 2 . The generalization to arbitrary dimensions is then obvious. We show by explicit construction that such algebras possess an infinite number of finite sub-algebras. Among which, for the six dimensional case, is so(1,3) realized on S 2 with vanishing Casimir invariants. This so(1,3) may be interpreted, in accord with a previous conjecture of Salam and Strathdee [Ann. Phys. 141, 316(1982)], as the 'ladder' symmetry for the Kaluza-Klein towers. (author)

  8. Studies toward brevisulcenal F via convergent strategies for marine ladder polyether synthesis.

    Science.gov (United States)

    Katcher, Matthew; Jamison, Timothy F

    2018-03-15

    Shortly after the initial isolation of marine ladder polyether natural products, biomimetic epoxide-opening cascade reactions were proposed as an efficient strategy for the synthesis of these compounds. However, difficulties in assembling the cascade precursors have limited the realization of these cascades. In this report, we describe strategies that provide convergent access to cascade precursors via regioselective allylation and efficient fragment coupling. We then investigate epoxide-opening cascades promoted by strong bases for the formation of fused tetrahydropyrans. These strategies are evaluated in the context of the synthesis of rings CDEFG of brevisulcenal F.

  9. Geometric Summary of the 9 Chip Ladder for the D0 Silicon Tracker

    International Nuclear Information System (INIS)

    Ratzmann, P.; Cooper, W.; Goloskie, D.; Kowalski, J.; Lipton, R.; Rapidis, P.; Serritella, C.

    1997-01-01

    Two hybrids types are required to accomodate the flipping of ladders within each bulkhead layer, in order to account for the pigtail routing. Left and right versions are shown below, following the definitions laid out by Mike Matulik. These drawings are not to proper scale in the sketches below. The dimensionally correct versions of the 9 chip hybrids are stored in DCS under drawing number 3823.112-MD-317803 for the lefthanded version, and 3823.112-MD-317804 for the right handed version. Handedness of the hybrids are designated as shown in the figures and table below. There are long and short versions of both the left and the right, for four total 9 chip hdi designs. The pigtail lengths of the long and short are shown in a table in the hybrid drawings which reside in DCS. The chamfer in the hybrid corners (N side) is placed in order to enable the hybrid to be glued to the beryllium substrate, whereas the rectangular cuttout on the same side is to allow direct gluing of a temperature sensor to the substrate metal. The oblong shape on the N side of both hybrids is a 'stay-clear' region (defined in the final drawings) where pressure will be applied to the hybrid during the second stage of ladder construction.

  10. The mechanism of thioacetamide-induced apoptosis in the L37 albumin-SV40 T-antigen transgenic rat hepatocyte-derived cell line occurs without DNA fragmentation.

    Science.gov (United States)

    Bulera, S J; Sattler, C A; Gast, W L; Heath, S; Festerling, T A; Pitot, H C

    1998-10-01

    The hepatotoxicant thioacetamide (TH) has classically been used as a model to study hepatic necrosis; however, recent studies have shown that TH can also induce apoptosis. In this report we demonstrate that 2.68+/-0.54% of the albumin-SV40 T-antigen transgenic rat hepatocytes undergo TH-induced apoptosis, a level comparable to other in vivo models of liver apoptosis. In addition, TH could induce apoptosis and necrosis in the L37 albumin-SV40 T-antigen transgenic rat liver-derived cell line. Examination of dying L37 cells treated with 100 mM TH by electron microscopy revealed distinct morphological characteristics that could be attributed to apoptosis. Quantitation of apoptosis by FACS analysis 24 h after treatment with 100 mM TH revealed that 81.3+/-1.6% of the cells were undergoing apoptosis. In contrast, when L37 cells were treated with 250 mM TH, cells exhibited characteristics consistent with necrotic cell death. DNA fragmentation ladders were produced by growth factor withdrawal-induced apoptosis; however, in 100 mM TH-induced apoptosis, DNA fragmentation ladders were not observed. Analysis of endonuclease activity in L37 cells revealed that the enzymes were not inactivated in the presence of 100 mM TH. The data presented in this report indicate that the L37 cell line could be used to study the mechanism of TH-induced apoptosis that was not mediated through a mechanism requiring DNA fragmentation.

  11. Inherited Sterility of Fl Male Sitotroga cerealella (Olivier) and changes in the DNA Pattern as a Result of Using Gamma irradiation

    International Nuclear Information System (INIS)

    Rizk, S.A.; Mikhaiel, A.A.

    2009-01-01

    Full grown pupae of the Angoumois grain moth, Sitotroga cerealella were irradiated with 75 and 175 Gy or gamma irradiation .The sterility percent was increased by increasing of' gamma irradiation dose. Also, the sterility percent increased in F 1 males than in parents. Gamma irradiation caused a decrease in size or the ova doles and number of oocytes. The effects of gamma rays on the DNA patterns of adult male parents and Fl males showed alterations among the controls, the treated parents and Ft individuals. Exposure to radiation caused very frequently the appearance of some extra bands and the deficiency of others in the RAPD-PCR amplification patterns of the irradiated insects. However, the similarity in DNA patterns between some normal and treated samples was interpreted by assuming, that the radiation induced damage was in regions of' the genome other than at the loci under study

  12. Mitochondrial DNA copy number threshold in mtDNA depletion myopathy.

    Science.gov (United States)

    Durham, S E; Bonilla, E; Samuels, D C; DiMauro, S; Chinnery, P F

    2005-08-09

    The authors measured the absolute amount of mitochondrial DNA (mtDNA) within single muscle fibers from two patients with thymidine kinase 2 (TK2) deficiency and two healthy controls. TK2 deficient fibers containing more than 0.01 mtDNA/microm3 had residual cytochrome c oxidase (COX) activity. This defines the minimum amount of wild-type mtDNA molecules required to maintain COX activity in skeletal muscle and provides an explanation for the mosaic histochemical pattern seen in patients with mtDNA depletion syndrome.

  13. DNA damage, homology-directed repair, and DNA methylation.

    Directory of Open Access Journals (Sweden)

    Concetta Cuozzo

    2007-07-01

    Full Text Available To explore the link between DNA damage and gene silencing, we induced a DNA double-strand break in the genome of Hela or mouse embryonic stem (ES cells using I-SceI restriction endonuclease. The I-SceI site lies within one copy of two inactivated tandem repeated green fluorescent protein (GFP genes (DR-GFP. A total of 2%-4% of the cells generated a functional GFP by homology-directed repair (HR and gene conversion. However, approximately 50% of these recombinants expressed GFP poorly. Silencing was rapid and associated with HR and DNA methylation of the recombinant gene, since it was prevented in Hela cells by 5-aza-2'-deoxycytidine. ES cells deficient in DNA methyl transferase 1 yielded as many recombinants as wild-type cells, but most of these recombinants expressed GFP robustly. Half of the HR DNA molecules were de novo methylated, principally downstream to the double-strand break, and half were undermethylated relative to the uncut DNA. Methylation of the repaired gene was independent of the methylation status of the converting template. The methylation pattern of recombinant molecules derived from pools of cells carrying DR-GFP at different loci, or from an individual clone carrying DR-GFP at a single locus, was comparable. ClustalW analysis of the sequenced GFP molecules in Hela and ES cells distinguished recombinant and nonrecombinant DNA solely on the basis of their methylation profile and indicated that HR superimposed novel methylation profiles on top of the old patterns. Chromatin immunoprecipitation and RNA analysis revealed that DNA methyl transferase 1 was bound specifically to HR GFP DNA and that methylation of the repaired segment contributed to the silencing of GFP expression. Taken together, our data support a mechanistic link between HR and DNA methylation and suggest that DNA methylation in eukaryotes marks homologous recombined segments.

  14. Ginsenoside Rg3 induces DNA damage in human osteosarcoma cells and reduces MNNG-induced DNA damage and apoptosis in normal human cells.

    Science.gov (United States)

    Zhang, Yue-Hui; Li, Hai-Dong; Li, Bo; Jiang, Sheng-Dan; Jiang, Lei-Sheng

    2014-02-01

    Panax ginseng is a Chinese medicinal herb. Ginsenosides are the main bioactive components of P. ginseng, and ginsenoside Rg3 is the primary ginsenoside. Ginsenosides can potently kill various types of cancer cells. The present study was designed to evaluate the potential genotoxicity of ginsenoside Rg3 in human osteosarcoma cells and the protective effect of ginsenoside Rg3 with respect to N-methyl-N'-nitro-N-nitrosoguanidine (MNNG)-induced DNA damage and apoptosis in a normal human cell line (human fibroblasts). Four human osteosarcoma cell lines (MG-63, OS732, U-2OS and HOS cells) and a normal human cell line (human fibroblasts) were employed to investigate the cytotoxicity of ginsenosides Rg3 by MTT assay. Alkaline comet assay and γH2AX focus staining were used to detect the DNA damage in MG-63 and U-2OS cells. The extent of cell apoptosis was determined by flow cytometry and a DNA ladder assay. Our results demonstrated that the cytotoxicity of ginsenoside Rg3 was dose-dependent in the human osteosarcoma cell lines, and MG-63 and U-2OS cells were the most sensitive to ginsenoside Rg3. As expected, compared to the negative control, ginsenoside Rg3 significantly increased DNA damage in a concentration-dependent manner. In agreement with the comet assay data, the percentage of γH2AX-positive MG-63 and U-2OS cells indicated that ginsenoside Rg3 induced DNA double-strand breaks in a concentration-dependent manner. The results also suggest that ginsenoside Rg3 reduces the extent of MNNG-induced DNA damage and apoptosis in human fibroblasts.

  15. Magneto-optical polarization rotation in a ladder-type atomic system for tunable offset locking

    Energy Technology Data Exchange (ETDEWEB)

    Parniak, Michał, E-mail: michal.parniak@fuw.edu.pl; Leszczyński, Adam; Wasilewski, Wojciech [Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw (Poland)

    2016-04-18

    We demonstrate an easily tunable locking scheme for stabilizing frequency-sum of two lasers on a two-photon ladder transition based on polarization rotation in warm rubidium vapors induced by magnetic field and circularly polarized drive field. Unprecedented tunability of the two-photon offset frequency is due to strong splitting and shifting of magnetic states in external field. In our experimental setup, we achieve two-photon detuning of up to 700 MHz.

  16. Different patterns of HIV-1 DNA after therapy discontinuation

    Directory of Open Access Journals (Sweden)

    Ghinelli Florio

    2005-09-01

    Full Text Available Abstract Background By persisting in infected cells for a long period of time, proviral HIV-1 DNA can represent an alternative viral marker to RNA viral load during the follow-up of HIV-1 infected individuals. In the present study sequential blood samples of 10 patients under antiretroviral treatment from 1997 with two NRTIs, who refused to continue any antiviral regimen, were analyzed for 16 – 24 weeks to study the possible relationship between DNA and RNA viral load. Methods The amount of proviral DNA was quantified by SYBR green real-time PCR in peripheral blood mononuclear cells from a selected group of ten patients with different levels of plasmatic viremia (RNA viral load. Results Variable levels of proviral DNA were found without any significant correlation between proviral load and plasma HIV-1 RNA levels. Results obtained showed an increase or a rebound in viral DNA in most patients, suggesting that the absence of therapy reflects an increase and/or a persistence of cells containing viral DNA. Conclusion Even though plasma HIV RNA levels remain the basic parameter to monitor the intensity of viral replication, the results obtained seem to indicate that DNA levels could represent an adjunct prognostic marker in monitoring HIV-1 infected subjects.

  17. Superconducting states and depinning transitions of Josephson ladders

    International Nuclear Information System (INIS)

    Barahona, M.; Strogatz, S.H.; Orlando, T.P.

    1998-01-01

    We present analytical and numerical studies of pinned superconducting states of open-ended Josephson ladder arrays, neglecting inductances but taking edge effects into account. Treating the edge effects perturbatively, we find analytical approximations for three of these superconducting states emdash the no-vortex, fully frustrated, and single-vortex states emdash as functions of the dc bias current I and the frustration f. Bifurcation theory is used to derive formulas for the depinning currents and critical frustrations at which the superconducting states disappear or lose dynamical stability as I and f are varied. These results are combined to yield a zero-temperature stability diagram of the system with respect to I and f. To highlight the effects of the edges, we compare this dynamical stability diagram to the thermodynamic phase diagram for the infinite system where edges have been neglected. We briefly indicate how to extend our methods to include self-inductances. copyright 1998 The American Physical Society

  18. The power of engagement: implementation of a career ladder program.

    Science.gov (United States)

    Bourgeault, Robert; Newmark, Jason

    2012-01-01

    At Baystate Health in Massachusetts, the development and implementation of a career ladder program was implemented to reduce turnover and to improve employee satisfaction, morale, and recruitment efforts. There was significant initial expenditure in the program, as a result of promoting the large number of employees with significant experience and seniority. A smaller number of staff are expected to apply for advancement during successive cycles, allowing for decreased incremental expense going forward. Critical to the success of the program was understanding the time commitment, getting senior organizational support and staff buy-in, and justifying the associated expenses. The development and initiation of the program has done much to support a positive work environment with increased morale and higher performance among significant numbers of staff at all levels.

  19. Chain and ladder models with two-body interactions and analytical ground states

    Science.gov (United States)

    Manna, Sourav; Nielsen, Anne E. B.

    2018-05-01

    We consider a family of spin-1 /2 models with few-body, SU(2)-invariant Hamiltonians and analytical ground states related to the one-dimensional (1D) Haldane-Shastry wave function. The spins are placed on the surface of a cylinder, and the standard 1D Haldane-Shastry model is obtained by placing the spins with equal spacing in a circle around the cylinder. Here, we show that another interesting family of models with two-body exchange interactions is obtained if we instead place the spins along one or two lines parallel to the cylinder axis, giving rise to chain and ladder models, respectively. We can change the scale along the cylinder axis without changing the radius of the cylinder. This gives us a parameter that controls the ratio between the circumference of the cylinder and all other length scales in the system. We use Monte Carlo simulations and analytical investigations to study how this ratio affects the properties of the models. If the ratio is large, we find that the two legs of the ladder decouple into two chains that are in a critical phase with Haldane-Shastry-like properties. If the ratio is small, the wave function reduces to a product of singlets. In between, we find that the behavior of the correlations and the Renyi entropy depends on the distance considered. For small distances the behavior is critical, and for long distances the correlations decay exponentially and the entropy shows an area law behavior. The distance up to which there is critical behavior gets larger as the ratio increases.

  20. Climbing Up the Technology Ladder? High-Technology Exports in China and Latin America

    OpenAIRE

    Gallagher, Kevin P.; Porzecanski, Roberto

    2008-01-01

    In this paper we determine the “dynamic revealed competitiveness position” (DRCP) of nations for high technology exports between 1980 and 2005. We find that the developed world has lost significant market share in high technology and that China has climbed the high technology ladder during this period. In 1980 China was ranked 99th of all nations in terms of the percentage of global exports in high technology. By 2005 China climbed to second place in the world, first place if high technology ...

  1. DNA computing models

    CERN Document Server

    Ignatova, Zoya; Zimmermann, Karl-Heinz

    2008-01-01

    In this excellent text, the reader is given a comprehensive introduction to the field of DNA computing. The book emphasizes computational methods to tackle central problems of DNA computing, such as controlling living cells, building patterns, and generating nanomachines.

  2. Hierarchical Self Assembly of Patterns from the Robinson Tilings: DNA Tile Design in an Enhanced Tile Assembly Model.

    Science.gov (United States)

    Padilla, Jennifer E; Liu, Wenyan; Seeman, Nadrian C

    2012-06-01

    We introduce a hierarchical self assembly algorithm that produces the quasiperiodic patterns found in the Robinson tilings and suggest a practical implementation of this algorithm using DNA origami tiles. We modify the abstract Tile Assembly Model, (aTAM), to include active signaling and glue activation in response to signals to coordinate the hierarchical assembly of Robinson patterns of arbitrary size from a small set of tiles according to the tile substitution algorithm that generates them. Enabling coordinated hierarchical assembly in the aTAM makes possible the efficient encoding of the recursive process of tile substitution.

  3. Changes in DNA Methylation Pattern at Two Seedling Stages in Water Saving and Drought-Resistant Rice Variety after Drought Stress Domestication

    Directory of Open Access Journals (Sweden)

    Xiao-guo ZHENG

    2014-09-01

    Full Text Available Recent studies revealed that DNA methylation plays an important role in plant growth and development. In this study, a water-saving and drought-resistant rice variety Huhan 3 was subjected to drought stress from tillering to grain-filling stages in six successive growth cycles. The variations in DNA methylation pattern between the original generation (G0 and the sixth generation (G6 were analyzed by using methylation sensitive amplification polymorphism method. The results revealed that the methylated loci accounted for 34.3% to 34.8% of the total loci. Among these methylated loci, 83.1% to 84.8% were full- and hyper-methylated and 15.2% to 16.9% were hemi-methylated. The DNA methylation level decreased from the three-leaf to four-leaf stages in Huhan 3. Differentially methylated loci (DML between generations or/and between different developmental stages accounted for 4.0% of the total loci, most of which were only related to plant development (57.9%. Compared to G0, the DNA methylation pattern of G6 changed after drought domestication, at the three-leaf stage, de-methylation accounting for 59.1%, while at the four-leaf stage, re-methylation for 47.9%. Genome-wide alternations of DNA methylation were observed between the two seedling stages, and DML mainly occurred on the gene's promoter and exon region. The genes related to DML involved in a wide range of functional biology and participated in many important biological processes.

  4. Efficiency snakes and energy ladders: A (meta-)frontier demand analysis of electricity consumption efficiency in Chinese households

    International Nuclear Information System (INIS)

    Broadstock, David C.; Li, Jiajia; Zhang, Dayong

    2016-01-01

    Policy makers presently lack access to quantified estimates – and hence an explicit understanding – of energy consumption efficiency within households, creating a potential gap between true efficiency levels and the necessarily assumed efficiency levels that policy makers adopt in designing and implementing energy policy. This paper attempts to fill this information gap by empirically quantifying electricity consumption efficiency for a sample of more than 7,000 households. Adopting the recently introduced ‘frontier demand function’ due to Filippini and Hunt (2011) but extending it into the metafrontier context – to control for structural heterogeneity arising from location type – it is shown that consumption efficiency is little more than 60% on average. This implies huge potential for energy reduction via the expansion of schemes to promote energy efficiency. City households, which are the wealthiest in the sample, are shown to define the metafrontier demand function (and hence have the potential to be the most efficient households), but at the same time exhibit the largest inefficiencies. These facts together allow for a potential refinement on the household energy ladder concept, suggesting that wealth affords access to the best technologies thereby increasing potential energy efficiency (the ‘traditional view of the household energy ladder), but complementary to this these same households are most inefficient. This has implications for numerous areas of policy, including for example the design of energy assistance schemes, identification of energy education needs/priorities as well more refined setting of subsidies/tax-credit policies. - Highlights: •Frontier demand functions are estimated for a sample of 7102 Chinese households. •Metafrontier methods capture heterogeneity arising from urban form (e.g. cities, towns and villages). •Wealthier houses have higher efficiency potential, but are in fact less efficient in their consumption of

  5. Genome-wide DNA methylation patterns in wild samples of two morphotypes of threespine stickleback (Gasterosteus aculeatus).

    Science.gov (United States)

    Smith, Gilbert; Smith, Carl; Kenny, John G; Chaudhuri, Roy R; Ritchie, Michael G

    2015-04-01

    Epigenetic marks such as DNA methylation play important biological roles in gene expression regulation and cellular differentiation during development. To examine whether DNA methylation patterns are potentially associated with naturally occurring phenotypic differences, we examined genome-wide DNA methylation within Gasterosteus aculeatus, using reduced representation bisulfite sequencing. First, we identified highly methylated regions of the stickleback genome, finding such regions to be located predominantly within genes, and associated with genes functioning in metabolism and biosynthetic processes, cell adhesion, signaling pathways, and blood vessel development. Next, we identified putative differentially methylated regions (DMRs) of the genome between complete and low lateral plate morphs of G. aculeatus. We detected 77 DMRs that were mainly located in intergenic regions. Annotations of genes associated with these DMRs revealed potential functions in a number of known divergent adaptive phenotypes between G. aculeatus ecotypes, including cardiovascular development, growth, and neuromuscular development. © The Author 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  6. Development of identification process for insect group using radiation marker DNA

    International Nuclear Information System (INIS)

    Muraji, M.; Tamura, T.

    2004-01-01

    Detection of a band pattern for insect groups was tried by using radiation marked DNA clone. A rapid segregation process for poly-type DNA segment was investigated. A band pattern of silkworm was detected by analysis using DNA type transposon, K1.4. The exon regions on genes of hemiptera insect were segregated by in vitro cloning. Band patterns of the silkworm and the other insects were detected by identification process of DNA clone and radiation marker. Family singularity mutation existed in the inserted position of transposon. The family of insect was identified easily by the difference of the detection band patterns. Effective band pattern for family discrimination were obtained by analysis for a part of mitochondria DNA and ribosomal DNA. DNA segregation process was investigated by using the enriched library, also. (M. Suetake)

  7. Modeling of radiation heat transport in complex ladder-like structures placed in rectangular enclosures

    International Nuclear Information System (INIS)

    Unal, C.; Bohl, W.R.; Pasamehmetoglu, K.O.

    1999-01-01

    Complex ladder-like structures recently have been considered as the target design for accelerator applications. The decay heat, during a postulated beyond design-basis loss-of-coolant accident in the target where all normal and emergency cooling fails, is removed mainly by radiation heat transfer. Modeling of the radiation transport in complex ladder-like structures has several challenges and limitations when the standard net-radiation model is used. This paper proposes a simplified lumped, or 'hot-rung' model, that considers the worst elements and utilizes the standard net-radiation method. The net-radiation model would under-predict structure temperatures if surfaces were subject to non-uniform radiosity. The proposed model was assessed to suggest corrections to account for the non-uniform radiosity. The non-uniform radiosity effect causes the proposed hot-rung model to under-predict the center-rung temperatures by ∼4-74 C when all parametrics, including temperatures up to 1500 C, were considered. These temperatures are small. The proposed model predicted that an important effect of decreasing the emissivity was smoothing of non-isothermal effects. The radiosity effects are more pronounced when there are strong temperature gradients. Uniform rung temperatures tend to decrease the radiosity effects. We concluded that a relatively simple model that is conservative with respect to radiosity effects could be developed. (orig.)

  8. Of towers and ladders: Infinite parameter symmetries in Kaluza-Klein theories

    International Nuclear Information System (INIS)

    Aulakh, C.S.

    1984-01-01

    We introduce a class of infinite dimensional algebras with a 'generalized loop structure' by considering the global symmetries of the four-dimensional lagrangian obtained by compactifying general relativity coupled to Yang-Mills in six-dimensions down to M 4 x S 2 . The generalization to arbitrary dimensions is then obvious. We show by explicit construction that such algebras possess an infinite number of finite sub-algebras among which, for the six-dimensional case, is so (1, 3), realized on S 2 with vanishing Casimir invariants. This so (1, 3) may be interpreted, in accordance with a previous conjecture of Salam and Strathdee, as the 'ladder' symmetry for the Kaluza-Klein towers. (orig.)

  9. Massive 3-loop ladder diagrams for quarkonic local operator matrix elements

    International Nuclear Information System (INIS)

    Ablinger, Jakob; Blümlein, Johannes; Hasselhuhn, Alexander; Klein, Sebastian; Schneider, Carsten; Wißbrock, Fabian

    2012-01-01

    3-loop diagrams of the ladder-type, which emerge for local quarkonic twist-2 operator matrix elements, are computed directly for general values of the Mellin variable N using Appell-function representations and applying modern summation technologies provided by the package Sigma and the method of hyperlogarithms. In some of the diagrams generalized harmonic sums with ξ∈{1,1/2,2} emerge beyond the usual nested harmonic sums. As the asymptotic representation of the corresponding integrals shows, the generalized sums conspire giving well behaved expressions for large values of N. These diagrams contribute to the 3-loop heavy flavor Wilson coefficients of the structure functions in deep-inelastic scattering in the region Q 2 ≫m 2 .

  10. Interplay between spin frustration and magnetism in the exactly solved two-leg mixed spin ladder

    Science.gov (United States)

    Qi, Yan; Lv, Song-Wei; Du, An; Yu, Nai-sen

    2016-11-01

    We study a mixed spin-(3/2, 1) ladder system with antiferromagnetic rung coupling and next-nearest-neighbor interaction. The exactly solved Ising-chain model is employed to investigate the ground-state properties and thermodynamics of the low-dimensional ladder system. Our results show that the competition between different exchange couplings brings in a large variety of ground states characterized by various values of normalized magnetization equal to 0, 1/5, 2/5, 3/5, 1. Moreover, an interesting double-peak structure is also detected in the thermal dependence of magnetic susceptibility and specific heat when the frustration comes into play. It is shown that the double-peak phenomenon at zero-field for the case of AF2 ground-state arises from the very strong antiferromagnetic rung coupling, while other cases are attributed to the excitations induced by temperature and external field around the phase boundary. Project supported by the National Natural Science Foundation of China (Grant No. 11547236), the General Project of the Education Department of Liaoning Province, China (Grant No. L2015130), the Fundamental Research Funds for the Central Universities, China (Grant Nos. DC201501065 and DCPY2016014), and the Doctoral Starting-up Foundation of Dalian Nationalities University, China.

  11. Loss of maintenance DNA methylation results in abnormal DNA origin firing during DNA replication.

    Science.gov (United States)

    Haruta, Mayumi; Shimada, Midori; Nishiyama, Atsuya; Johmura, Yoshikazu; Le Tallec, Benoît; Debatisse, Michelle; Nakanishi, Makoto

    2016-01-22

    The mammalian maintenance methyltransferase DNMT1 [DNA (cytosine-5-)-methyltransferase 1] mediates the inheritance of the DNA methylation pattern during replication. Previous studies have shown that depletion of DNMT1 causes a severe growth defect and apoptosis in differentiated cells. However, the detailed mechanisms behind this phenomenon remain poorly understood. Here we show that conditional ablation of Dnmt1 in murine embryonic fibroblasts (MEFs) resulted in an aberrant DNA replication program showing an accumulation of late-S phase replication and causing severely defective growth. Furthermore, we found that the catalytic activity and replication focus targeting sequence of DNMT1 are required for a proper DNA replication program. Taken together, our findings suggest that the maintenance of DNA methylation by DNMT1 plays a critical role in proper regulation of DNA replication in mammalian cells. Copyright © 2015 Elsevier Inc. All rights reserved.

  12. Development of Curriculum Content for a Unique Career Ladder Multi-Entry/Multi-Exit Nursing Program. Final Report.

    Science.gov (United States)

    Rosbach, Ellen M.

    A project was undertaken to develop the curriculum content for a unique career ladder multi-entry/multi-exit nursing program that would provide training for nurse aides, practical nurses, and registered nurses. The major objectives of the project were to conduct a review of the literature on curriculum materials presently in use, to develop 11…

  13. Different patterns of rDNA distribution in Pisum sativum nucleoli correlate with different levels of nucleolar activity

    International Nuclear Information System (INIS)

    Highett, M.I.; Rawlins, D.J.; Shaw, P.J.

    1993-01-01

    We have used in situ hybridization with probes to rDNA, labelled either with digoxygenin or directly with fluorescein, to determine the arrangement of these genes within the nucleoli of Pisum sativum L. root cells. Confocal laser scanning microscopy was used to image the three-dimensional structures revealed, but we have also compared this technique with deconvolution of conventional (wide-field) fluorescence images measured with a cooled CCD camera, and have shown that the results are remarkably similar. When the deconvolution technique was applied to the confocal data it gave clearer images than could be achieved by confocal microscopy alone. We have analysed the distribution of rDNA in the different cell types observable in root tips: the quiescent centre; active meristematic cells; and relatively differentiated root cap, epidermal and cortical cells. In addition to four perinucleolar knobs of condensed, inactive rDNA genes, corresponding to the four nucleolar organizers in P. sativum, which were the most brightly labelled structures, several characteristic patterns of intranucleolar labelling were apparent, including bright foci, large central chromatin masses, and fine, decondensed interconnecting fibres. The larger and more active the nucleolus, the smaller the proportion of condensed perinucleolar rDNA. In some large and active meristematic nucleoli, all the internal rDNA is decondensed, showing that transcription cannot be restricted to the bright foci, and is most likely to occur on the decondensed fibres. (author)

  14. A Phenomenological Examination of Virtual Game Developers' Experiences Using Jacob's Ladder Pre-Production Design Tactic

    Science.gov (United States)

    Brown-Turner, Jasmine

    2017-01-01

    Edutainment refers to curriculum and instruction designed with a clear educational purpose, including multi-faceted virtual learning game design. Tools such as the Jacob's Ladder pre-production design tactic have been developed to ensure that voices of both engineers and educators are heard. However, it is unclear how development team members…

  15. Blood transfusion products contain mitochondrial DNA damage-associated molecular patterns: a potential effector of transfusion-related acute lung injury.

    Science.gov (United States)

    Lee, Yann-Leei; King, Madelyn B; Gonzalez, Richard P; Brevard, Sidney B; Frotan, M Amin; Gillespie, Mark N; Simmons, Jon D

    2014-10-01

    Transfusion-related acute lung injury (TRALI) is the most frequent and severe complication in patients receiving multiple blood transfusions. Current pathogenic concepts hold that proinflammatory mediators present in transfused blood products are responsible for the initiation of TRALI, but the identity of the critical effector molecules is yet to be determined. We hypothesize that mtDNA damage-associated molecular patterns (DAMPs) are present in blood transfusion products, which may be important in the initiation of TRALI. DNA was extracted from consecutive samples of packed red blood cells, fresh frozen plasma (FFP), and platelets procured from the local blood bank. Quantitative real-time polymerase chain reaction was used to quantify ≈200 bp sequences from the COX1, ND1, ND6, and D-loop regions of the mitochondrial genome. A range of mtDNA DAMPs were detected in all blood components measured, with FFP displaying the largest variation. We conclude that mtDNA DAMPs are present in packed red blood cells, FFP, and platelets. These observations provide proof of the concept that mtDNA DAMPs may be mediators of TRALI. Further studies are needed to test this hypothesis and to determine the origin of mtDNA DAMPs in transfused blood. Copyright © 2014 Elsevier Inc. All rights reserved.

  16. Evolution of DNA Methylation across Insects.

    Science.gov (United States)

    Bewick, Adam J; Vogel, Kevin J; Moore, Allen J; Schmitz, Robert J

    2017-03-01

    DNA methylation contributes to gene and transcriptional regulation in eukaryotes, and therefore has been hypothesized to facilitate the evolution of plastic traits such as sociality in insects. However, DNA methylation is sparsely studied in insects. Therefore, we documented patterns of DNA methylation across a wide diversity of insects. We predicted that underlying enzymatic machinery is concordant with patterns of DNA methylation. Finally, given the suggestion that DNA methylation facilitated social evolution in Hymenoptera, we tested the hypothesis that the DNA methylation system will be associated with presence/absence of sociality among other insect orders. We found DNA methylation to be widespread, detected in all orders examined except Diptera (flies). Whole genome bisulfite sequencing showed that orders differed in levels of DNA methylation. Hymenopteran (ants, bees, wasps and sawflies) had some of the lowest levels, including several potential losses. Blattodea (cockroaches and termites) show all possible patterns, including a potential loss of DNA methylation in a eusocial species whereas solitary species had the highest levels. Species with DNA methylation do not always possess the typical enzymatic machinery. We identified a gene duplication event in the maintenance DNA methyltransferase 1 (DNMT1) that is shared by some Hymenoptera, and paralogs have experienced divergent, nonneutral evolution. This diversity and nonneutral evolution of underlying machinery suggests alternative DNA methylation pathways may exist. Phylogenetically corrected comparisons revealed no evidence that supports evolutionary association between sociality and DNA methylation. Future functional studies will be required to advance our understanding of DNA methylation in insects. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  17. Loss of maintenance DNA methylation results in abnormal DNA origin firing during DNA replication

    Energy Technology Data Exchange (ETDEWEB)

    Haruta, Mayumi [Department of Cell Biology, Graduate School of Medical Sciences, Nagoya City University, 1 Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya 467-8601 (Japan); Shimada, Midori, E-mail: midorism@med.nagoya-cu.ac.jp [Department of Cell Biology, Graduate School of Medical Sciences, Nagoya City University, 1 Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya 467-8601 (Japan); Nishiyama, Atsuya; Johmura, Yoshikazu [Department of Cell Biology, Graduate School of Medical Sciences, Nagoya City University, 1 Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya 467-8601 (Japan); Le Tallec, Benoît; Debatisse, Michelle [Institut Curie, Centre de Recherche, 26 rue d’Ulm, CNRS UMR 3244, 75248 ParisCedex 05 (France); Nakanishi, Makoto, E-mail: mkt-naka@med.nagoya-cu.ac.jp [Department of Cell Biology, Graduate School of Medical Sciences, Nagoya City University, 1 Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya 467-8601 (Japan)

    2016-01-22

    The mammalian maintenance methyltransferase DNMT1 [DNA (cytosine-5-)-methyltransferase 1] mediates the inheritance of the DNA methylation pattern during replication. Previous studies have shown that depletion of DNMT1 causes a severe growth defect and apoptosis in differentiated cells. However, the detailed mechanisms behind this phenomenon remain poorly understood. Here we show that conditional ablation of Dnmt1 in murine embryonic fibroblasts (MEFs) resulted in an aberrant DNA replication program showing an accumulation of late-S phase replication and causing severely defective growth. Furthermore, we found that the catalytic activity and replication focus targeting sequence of DNMT1 are required for a proper DNA replication program. Taken together, our findings suggest that the maintenance of DNA methylation by DNMT1 plays a critical role in proper regulation of DNA replication in mammalian cells. - Highlights: • DNMT1 depletion results in an abnormal DNA replication program. • Aberrant DNA replication is independent of the DNA damage checkpoint in DNMT1cKO. • DNMT1 catalytic activity and RFT domain are required for proper DNA replication. • DNMT1 catalytic activity and RFT domain are required for cell proliferation.

  18. Loss of maintenance DNA methylation results in abnormal DNA origin firing during DNA replication

    International Nuclear Information System (INIS)

    Haruta, Mayumi; Shimada, Midori; Nishiyama, Atsuya; Johmura, Yoshikazu; Le Tallec, Benoît; Debatisse, Michelle; Nakanishi, Makoto

    2016-01-01

    The mammalian maintenance methyltransferase DNMT1 [DNA (cytosine-5-)-methyltransferase 1] mediates the inheritance of the DNA methylation pattern during replication. Previous studies have shown that depletion of DNMT1 causes a severe growth defect and apoptosis in differentiated cells. However, the detailed mechanisms behind this phenomenon remain poorly understood. Here we show that conditional ablation of Dnmt1 in murine embryonic fibroblasts (MEFs) resulted in an aberrant DNA replication program showing an accumulation of late-S phase replication and causing severely defective growth. Furthermore, we found that the catalytic activity and replication focus targeting sequence of DNMT1 are required for a proper DNA replication program. Taken together, our findings suggest that the maintenance of DNA methylation by DNMT1 plays a critical role in proper regulation of DNA replication in mammalian cells. - Highlights: • DNMT1 depletion results in an abnormal DNA replication program. • Aberrant DNA replication is independent of the DNA damage checkpoint in DNMT1cKO. • DNMT1 catalytic activity and RFT domain are required for proper DNA replication. • DNMT1 catalytic activity and RFT domain are required for cell proliferation.

  19. Similar patterns of rDNA evolution in synthetic and recently formed natural populations of Tragopogon (Asteraceae allotetraploids

    Directory of Open Access Journals (Sweden)

    Soltis Pamela S

    2010-09-01

    homeologous rRNA gene copies occurred in both synthetic and natural populations of Tragopogon allopolyploids. The extent of these rDNA changes was generally higher in natural populations than in the synthetic lines. We hypothesize that locus-specific and chromosomal changes in early generations of allopolyploids may influence patterns of rDNA evolution in later generations.

  20. Sub-10 nm patterning with DNA nanostructures: a short perspective

    Science.gov (United States)

    Du, Ke; Park, Myeongkee; Ding, Junjun; Hu, Huan; Zhang, Zheng

    2017-11-01

    DNA is the hereditary material that contains our unique genetic code. Since the first demonstration of two-dimensional (2D) nanopatterns by using designed DNA origami ˜10 years ago, DNA has evolved into a novel technique for 2D and 3D nanopatterning. It is now being used as a template for the creation of sub-10 nm structures via either ‘top-down’ or ‘bottom-up’ approaches for various applications spanning from nanoelectronics, plasmonic sensing, and nanophotonics. This perspective starts with an histroric overview and discusses the current state-of-the-art in DNA nanolithography. Emphasis is put on the challenges and prospects of DNA nanolithography as the next generation nanomanufacturing technique.

  1. DNA methylation patterns of genes related to immune response in the different clinical forms of oral lichen planus.

    Science.gov (United States)

    Cruz, Aline Fernanda; de Resende, Renata Gonçalves; de Lacerda, Júlio César Tanos; Pereira, Núbia Braga; Melo, Leonardo Augusto; Diniz, Marina Gonçalves; Gomes, Carolina Cavalieri; Gomez, Ricardo Santiago

    2018-01-01

    The oral lichen planus is a chronic inflammatory disease. Although its aetiology is not well understood, the role of T lymphocytes in its inflammatory events is recognised. Identifying the epigenetic mechanisms involved in the pathogenesis of this immune-mediated condition is fundamental for understanding the inflammatory reaction that occurs in the disease. The purpose of this work was to evaluate the methylation pattern of 21 immune response-related genes in the different clinical forms of oral lichen planus. A cross-sectional study was performed to analyse the DNA methylation patterns in three distinct groups of oral lichen planus: (i) reticular/plaque lesions; (ii) erosive lesions; (iii) normal oral mucosa (control group). After DNA extraction from biopsies, the samples were submitted to digestions by methylation-sensitive and methylation-dependent enzymes and double digestion. The relative percentage of methylated DNA for each gene was provided using real-time polymerase chain reaction arrays. Hypermethylation of the STAT5A gene was observed only in the control group (59.0%). A higher hypermethylation of the ELANE gene was found in reticular/plaque lesions (72.1%) compared to the erosive lesions (50.0%). Our results show variations in the methylation profile of immune response-related genes, according to the clinical type of oral lichen planus after comparing with the normal oral mucosa. Further studies are necessary to validate these findings using gene expression analysis. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  2. Chromosome-wide mapping of DNA methylation patterns in normal and malignant prostate cells reveals pervasive methylation of gene-associated and conserved intergenic sequences

    Directory of Open Access Journals (Sweden)

    De Marzo Angelo M

    2011-06-01

    Full Text Available Abstract Background DNA methylation has been linked to genome regulation and dysregulation in health and disease respectively, and methods for characterizing genomic DNA methylation patterns are rapidly emerging. We have developed/refined methods for enrichment of methylated genomic fragments using the methyl-binding domain of the human MBD2 protein (MBD2-MBD followed by analysis with high-density tiling microarrays. This MBD-chip approach was used to characterize DNA methylation patterns across all non-repetitive sequences of human chromosomes 21 and 22 at high-resolution in normal and malignant prostate cells. Results Examining this data using computational methods that were designed specifically for DNA methylation tiling array data revealed widespread methylation of both gene promoter and non-promoter regions in cancer and normal cells. In addition to identifying several novel cancer hypermethylated 5' gene upstream regions that mediated epigenetic gene silencing, we also found several hypermethylated 3' gene downstream, intragenic and intergenic regions. The hypermethylated intragenic regions were highly enriched for overlap with intron-exon boundaries, suggesting a possible role in regulation of alternative transcriptional start sites, exon usage and/or splicing. The hypermethylated intergenic regions showed significant enrichment for conservation across vertebrate species. A sampling of these newly identified promoter (ADAMTS1 and SCARF2 genes and non-promoter (downstream or within DSCR9, C21orf57 and HLCS genes hypermethylated regions were effective in distinguishing malignant from normal prostate tissues and/or cell lines. Conclusions Comparison of chromosome-wide DNA methylation patterns in normal and malignant prostate cells revealed significant methylation of gene-proximal and conserved intergenic sequences. Such analyses can be easily extended for genome-wide methylation analysis in health and disease.

  3. Programme DNA Lattices: Design, Synthesis and Applications

    National Research Council Canada - National Science Library

    Reif, John

    2006-01-01

    .... Self-assembled DNA nanostructures provide a methodology for bottom-up nanoscale construction of highly patterned systems, utilizing macromolecular DNA tiles" composed of branched DNA, self-assembled...

  4. Distinct co-evolution patterns of genes associated to DNA polymerase III DnaE and PolC

    Directory of Open Access Journals (Sweden)

    Engelen Stefan

    2012-02-01

    Full Text Available Abstract Background Bacterial genomes displaying a strong bias between the leading and the lagging strand of DNA replication encode two DNA polymerases III, DnaE and PolC, rather than a single one. Replication is a highly unsymmetrical process, and the presence of two polymerases is therefore not unexpected. Using comparative genomics, we explored whether other processes have evolved in parallel with each polymerase. Results Extending previous in silico heuristics for the analysis of gene co-evolution, we analyzed the function of genes clustering with dnaE and polC. Clusters were highly informative. DnaE co-evolves with the ribosome, the transcription machinery, the core of intermediary metabolism enzymes. It is also connected to the energy-saving enzyme necessary for RNA degradation, polynucleotide phosphorylase. Most of the proteins of this co-evolving set belong to the persistent set in bacterial proteomes, that is fairly ubiquitously distributed. In contrast, PolC co-evolves with RNA degradation enzymes that are present only in the A+T-rich Firmicutes clade, suggesting at least two origins for the degradosome. Conclusion DNA replication involves two machineries, DnaE and PolC. DnaE co-evolves with the core functions of bacterial life. In contrast PolC co-evolves with a set of RNA degradation enzymes that does not derive from the degradosome identified in gamma-Proteobacteria. This suggests that at least two independent RNA degradation pathways existed in the progenote community at the end of the RNA genome world.

  5. Self-assembled DNA Structures for Nanoconstruction

    Science.gov (United States)

    Yan, Hao; Yin, Peng; Park, Sung Ha; Li, Hanying; Feng, Liping; Guan, Xiaoju; Liu, Dage; Reif, John H.; LaBean, Thomas H.

    2004-09-01

    In recent years, a number of research groups have begun developing nanofabrication methods based on DNA self-assembly. Here we review our recent experimental progress to utilize novel DNA nanostructures for self-assembly as well as for templates in the fabrication of functional nano-patterned materials. We have prototyped a new DNA nanostructure known as a cross structure. This nanostructure has a 4-fold symmetry which promotes its self-assembly into tetragonal 2D lattices. We have utilized the tetragonal 2D lattices as templates for highly conductive metallic nanowires and periodic 2D protein nano-arrays. We have constructed and characterized a DNA nanotube, a new self-assembling superstructure composed of DNA tiles. We have also demonstrated an aperiodic DNA lattice composed of DNA tiles assembled around a long scaffold strand; the system translates information encoded in the scaffold strand into a specific and reprogrammable barcode pattern. We have achieved metallic nanoparticle linear arrays templated on self-assembled 1D DNA arrays. We have designed and demonstrated a 2-state DNA lattice, which displays expand/contract motion switched by DNA nanoactuators. We have also achieved an autonomous DNA motor executing unidirectional motion along a linear DNA track.

  6. Massive 3-loop ladder diagrams for quarkonic local operator matrix elements

    Energy Technology Data Exchange (ETDEWEB)

    Ablinger, Jakob; Schneider, Carsten [Johannes Kepler Univ., Linz (Austria). Research Inst. for Symbolic Computation; Bluemlein, Johannes; Hasselhuhn, Alexander; Wissbrock, Fabian [Deutsches Elektronen-Synchrotron (DESY), Zeuthen (Germany); Klein, Sebastian [Technische Hochschule Aachen (Germany). Inst. fuer Theoretische Physik

    2012-06-15

    3-loop diagrams of the ladder-type, which emerge for local quarkonic twist-2 operator matrix elements, are computed directly for general values of the Mellin variable N using Appell-function representations and applying modern summation technologies provided by the package Sigma and the method of hyperlogarithms. In some of the diagrams generalized harmonic sums with {xi} element of {l_brace}1,1/2,2{r_brace} emerge beyond the usual nested harmonic sums. As the asymptotic representation of the corresponding integrals shows, the generalized sums conspire giving well behaved expressions for large values of N. These diagrams contribute to the 3-loop heavy flavor Wilson coefficients of the structure functions in deep-inelastic scattering in the region Q{sup 2} >> m{sup 2}.

  7. Massive 3-loop ladder diagrams for quarkonic local operator matrix elements

    Energy Technology Data Exchange (ETDEWEB)

    Ablinger, Jakob [Research Institute for Symbolic Computation (RISC), Johannes Kepler University, Altenbergerstrasse 69, A-4040 Linz (Austria); Bluemlein, Johannes, E-mail: johannes.bluemlein@desy.de [Deutsches Elektronen-Synchrotron, DESY, Platanenallee 6, D-15738 Zeuthen (Germany); Hasselhuhn, Alexander [Deutsches Elektronen-Synchrotron, DESY, Platanenallee 6, D-15738 Zeuthen (Germany); Klein, Sebastian [Research Institut fuer Theoretische Physik E, RWTH Aachen University, D-52056 Aachen (Germany); Schneider, Carsten [Research Institute for Symbolic Computation (RISC), Johannes Kepler University, Altenbergerstrasse 69, A-4040 Linz (Austria); Wissbrock, Fabian [Deutsches Elektronen-Synchrotron, DESY, Platanenallee 6, D-15738 Zeuthen (Germany)

    2012-11-01

    3-loop diagrams of the ladder-type, which emerge for local quarkonic twist-2 operator matrix elements, are computed directly for general values of the Mellin variable N using Appell-function representations and applying modern summation technologies provided by the package Sigma and the method of hyperlogarithms. In some of the diagrams generalized harmonic sums with {xi} Element-Of {l_brace}1,1/2,2{r_brace} emerge beyond the usual nested harmonic sums. As the asymptotic representation of the corresponding integrals shows, the generalized sums conspire giving well behaved expressions for large values of N. These diagrams contribute to the 3-loop heavy flavor Wilson coefficients of the structure functions in deep-inelastic scattering in the region Q{sup 2} Much-Greater-Than m{sup 2}.

  8. Evolution in the block: common elements of 5S rDNA organization and evolutionary patterns in distant fish genera.

    Science.gov (United States)

    Campo, Daniel; García-Vázquez, Eva

    2012-01-01

    The 5S rDNA is organized in the genome as tandemly repeated copies of a structural unit composed of a coding sequence plus a nontranscribed spacer (NTS). The coding region is highly conserved in the evolution, whereas the NTS vary in both length and sequence. It has been proposed that 5S rRNA genes are members of a gene family that have arisen through concerted evolution. In this study, we describe the molecular organization and evolution of the 5S rDNA in the genera Lepidorhombus and Scophthalmus (Scophthalmidae) and compared it with already known 5S rDNA of the very different genera Merluccius (Merluccidae) and Salmo (Salmoninae), to identify common structural elements or patterns for understanding 5S rDNA evolution in fish. High intra- and interspecific diversity within the 5S rDNA family in all the genera can be explained by a combination of duplications, deletions, and transposition events. Sequence blocks with high similarity in all the 5S rDNA members across species were identified for the four studied genera, with evidences of intense gene conversion within noncoding regions. We propose a model to explain the evolution of the 5S rDNA, in which the evolutionary units are blocks of nucleotides rather than the entire sequences or single nucleotides. This model implies a "two-speed" evolution: slow within blocks (homogenized by recombination) and fast within the gene family (diversified by duplications and deletions).

  9. DNA methylation patterns in tissues from mid-gestation bovine foetuses produced by somatic cell nuclear transfer show subtle abnormalities in nuclear reprogramming

    OpenAIRE

    Lee Rita SF; Couldrey Christine

    2010-01-01

    Abstract Background Cloning of cattle by somatic cell nuclear transfer (SCNT) is associated with a high incidence of pregnancy failure characterized by abnormal placental and foetal development. These abnormalities are thought to be due, in part, to incomplete re-setting of the epigenetic state of DNA in the donor somatic cell nucleus to a state that is capable of driving embryonic and foetal development to completion. Here, we tested the hypothesis that DNA methylation patterns were not appr...

  10. DNA synthesis time in germinating rice and pattern of diethylsulphate induced mutations in pre-soaked seeds

    International Nuclear Information System (INIS)

    Narahari, P.

    1978-01-01

    DNA synthesis pattern in germinating rice seeds, pre-soaked in water for varying periods upto 48 hr, was determined by following the pulse incorporation of 3 H-thymidine into the TCA-insoluble nucleoprotein. Synthesis of DNA commenced at 24 hr, progressively increased to a first peak at about 38 hr, thereafter showed a 1/3rd drop and subsequently increased to a 2nd and still higher peak at 46 to 48 hr of pre-soaking. Treatments of diethylsulphate (dES) at a low concentration (0.2%-2hr) administered at various progressing stages of DNA synthesis resulted in decrease in seedling height and survival, and increase in mutation frequency at 45 hr. pre-soaking, maximum mutation frequencies of 20, 10 and 2% on M 1 plants, M 1 spikes and M 2 seedling bases, respectively were observed. Higher dES concentration (0.3%-2hr) given at later periods of pre-soaking showed near lethal effects and consequently decreased mutation frequencies. Treatments of sodium fluoride given singly or in combination with dES did not show any substantially different results as compared to those of the respective controls. Mutation spectra observed after dES treatments to germinating seeds, at different pre-soaking periods, were quite dissimilar. Specific mutations of economic importance like semi-dwarf mutants were isolated from the treatment of germinating seeds pre-soaked for 37.5 hr or more when shoot apex cells were undergoing DNA synthesis. (author)

  11. Design and test of the final ALICE SDD CARLOS end ladder board

    CERN Document Server

    Antinori, S; Falchieri, D; Gabrielli, A; Gandolfi, E; Masetti, M; Tosellob, F

    2007-01-01

    The paper presents the design and test of the final prototype of the CARLOS (Compression And Run Length Encoding Subsystem) end ladder board that is going to be used in the ALICE experiment at CERN. This board is able to compress data coming from one Silicon Drift Detector (SDD) front-end electronics and to send them towards the data concentrator card CARLOSrx in counting room via a 800 Mb/s optical link. The board design faces several constraints, mainly size (54x49 mm) and radiation tolerance: for this reason the board contains several CERN developed ASICs. A test setup has been realized for selecting the good devices among the 500 cards already produced.

  12. Characterization of human lymphoid cell lines GM9947 and GM9948 as intra- and interlaboratory reference standards for DNA typing

    Energy Technology Data Exchange (ETDEWEB)

    Fregeau, C.J.; Elliott, J.C.; Fourney, R.M. [RCMP Central Forensic Laboratory, Ottawa, Ontario (Canada)] [and others

    1995-07-20

    The incorporation of reference DNA is crucial to the validation of any DNA typing protocol. Currently, reference DNA standards are restricted to molecular size DNA ladders and/or tumor cell line DNA. Either of these, however, presents some limitations. We have rigorously characterized two Epstein-Barr virus (EBV)-immortalized human lymphoid cell lines-GM9947 (female) and GM9948 (male)-to determine their suitability as alternative in-line standards for three widely employed allele profiling strategies. Twenty-one highly polymorphic VNTR-based allelic systems (7 RFLPs, 2 AmpFLPs, and 12 STRs) distributed over 12 chromosomes were scrutinized along with 3 gender-based discriminatory systems. The genetic stability of each locus was confirmed over a period of 225 in vitro population doublings. Allele size estimates and degree of informativeness for each of the 21 VNTR systems were compiled. The reproducibility of allele scoring by traditional RFLP analyses, using both cell lines as reference standards, was also verified by an interlaboratory validation study involving 13 analysts from two geographically distinct forensic laboratories. Taken together, our data indicate that GM9947 and GM9948 genomic DNAs could be adopted as reliable reference standards for DNA typing. 82 refs., 3 figs., 8 tabs.

  13. DNA Methylation Pattern in Overweight Women under an Energy-Restricted Diet Supplemented with Fish Oil

    Directory of Open Access Journals (Sweden)

    Cátia Lira do Amaral

    2014-01-01

    Full Text Available Dietary factors modulate gene expression and are able to alter epigenetic signatures in peripheral blood mononuclear cells (PBMC. However, there are limited studies about the effects of omega-3 polyunsaturated fatty acids (n-3 PUFA on the epigenetic mechanisms that regulate gene expression. This research investigates the effects of n-3-rich fish oil supplementation on DNA methylation profile of several genes whose expression has been reported to be downregulated by n-3 PUFA in PBMC: CD36, FFAR3, CD14, PDK4, and FADS1. Young overweight women were supplemented with fish oil or control in a randomized 8-week intervention trial following a balanced diet with 30% energy restriction. Fatty acid receptor CD36 decreased DNA methylation at CpG +477 due to energy restriction. Hypocaloric diet-induced weight loss also reduced the methylation percentages of CpG sites located in CD14, PDK4, and FADS1. The methylation patterns of these genes were only slightly affected by the fish oil supplementation, being the most relevant to the attenuation of the weight loss-induced decrease in CD36 methylation after adjusting by baseline body weight. These results suggest that the n-3 PUFA-induced changes in the expression of these genes in PBMC are not mediated by DNA methylation, although other epigenetic mechanisms cannot be discarded.

  14. Estimation of Structure-Borne Noise Reduction Effect of Steel Railway Bridge Equipped with Floating Ladder Track and Floating Reinforced-Concrete Deck

    Science.gov (United States)

    Watanabe, Tsutomu; Sogabe, Masamichi; Asanuma, Kiyoshi; Wakui, Hajime

    A number of steel railway bridges have been constructed in Japan. Thin steel members used for the bridges easily tend to vibrate and generate structure-borne noise. Accordingly, the number of constructions of steel railway bridges tends to decrease in the urban areas from a viewpoint of environmental preservation. Then, as a countermeasure against structure-borne noise generated from steel railway bridges, we have developed a new type of the steel railway bridge equipped with a floating-ladder track and a floating reinforced-concrete (RC) deck. As a result of train-running experiment, it became apparent that the new steel railway bridge installed by double floating system has reduced a vibration velocity level by 10.5 dB(A) at main girder web as compared with a steel railway bridge installed by directly fastened track. This reduction effect was achieved by the ladder track and RC deck supported by resilient materials.

  15. The local-ladder effect: social status and subjective well-being.

    Science.gov (United States)

    Anderson, Cameron; Kraus, Michael W; Galinsky, Adam D; Keltner, Dacher

    2012-07-01

    Dozens of studies in different nations have revealed that socioeconomic status only weakly predicts an individual's subjective well-being (SWB). These results imply that although the pursuit of social status is a fundamental human motivation, achieving high status has little impact on one's SWB. However, we propose that sociometric status-the respect and admiration one has in face-to-face groups (e.g., among friends or coworkers)-has a stronger effect on SWB than does socioeconomic status. Using correlational, experimental, and longitudinal methodologies, four studies found consistent evidence for a local-ladder effect: Sociometric status significantly predicted satisfaction with life and the experience of positive and negative emotions. Longitudinally, as sociometric status rose or fell, SWB rose or fell accordingly. Furthermore, these effects were driven by feelings of power and social acceptance. Overall, individuals' sociometric status matters more to their SWB than does their socioeconomic status.

  16. Automation and integration of multiplexed on-line sample preparation with capillary electrophoresis for DNA sequencing

    Energy Technology Data Exchange (ETDEWEB)

    Tan, H.

    1999-03-31

    The purpose of this research is to develop a multiplexed sample processing system in conjunction with multiplexed capillary electrophoresis for high-throughput DNA sequencing. The concept from DNA template to called bases was first demonstrated with a manually operated single capillary system. Later, an automated microfluidic system with 8 channels based on the same principle was successfully constructed. The instrument automatically processes 8 templates through reaction, purification, denaturation, pre-concentration, injection, separation and detection in a parallel fashion. A multiplexed freeze/thaw switching principle and a distribution network were implemented to manage flow direction and sample transportation. Dye-labeled terminator cycle-sequencing reactions are performed in an 8-capillary array in a hot air thermal cycler. Subsequently, the sequencing ladders are directly loaded into a corresponding size-exclusion chromatographic column operated at {approximately} 60 C for purification. On-line denaturation and stacking injection for capillary electrophoresis is simultaneously accomplished at a cross assembly set at {approximately} 70 C. Not only the separation capillary array but also the reaction capillary array and purification columns can be regenerated after every run. DNA sequencing data from this system allow base calling up to 460 bases with accuracy of 98%.

  17. Magnetic dimerization in the frustrated spin ladder Li2Cu2O (SO4)2

    Science.gov (United States)

    Vaccarelli, O.; Rousse, G.; Saúl, A.; Radtke, G.

    2017-11-01

    The magnetic properties of Li2Cu2O (SO4)2 are investigated in the framework of density functional theory. In its high-temperature tetragonal structure, this compound appears as a rare material realization of a frustrated spin-1/2 two-leg ladder, where magnetic frustration arises from competing nearest and next-nearest interactions along the legs. Through a large magnetoelastic coupling, the triclinic distortion occurring around 125 K is shown to induce the formation of a staggered dimer structure, lifting most of the magnetic frustration.

  18. Diversity of DNA fingerprints in Cryptococcus neoformans.

    Science.gov (United States)

    Varma, A; Swinne, D; Staib, F; Bennett, J E; Kwon-Chung, K J

    1995-07-01

    DNA fingerprint patterns of 156 Cryptococcus neoformans isolates (26 AIDS patients, 46 non-AIDS patients, and 40 environmental sources) from both varieties (126 C. neoformans var. neoformans and 30 C. neoformans var. gattii isolates) and from seven countries were analyzed by using the DNA probe UT-4p. Nine and twelve distinct DNA fingerprint patterns were observed for isolates of the C. neoformans var. neoformans and var. gattii, respectively. No pattern was unique to AIDS patients, non-AIDS patients, or the environment. Pattern II was observed more often in non-AIDS patients (8 of 23) than in AIDS patients (0 of 25). Pattern V was the most prevalent pattern (42 of 82) in clinical and environmental isolates. Isolates from three AIDS patients in Burundi and Zaire exhibited patterns identical to each other but different from those of isolates collected from their houses (i.e., dust of floors, walls, etc.) or a nearby pigeon coop. DNA fingerprint stability was determined for 53 isolates from nine non-AIDS patients at different time intervals during 5 to 128 weeks of antifungal therapy. For eight patients, the fingerprint pattern was stable while the ninth may have had a mixed infection. Pattern II was observed in 4 of 9 patients, which is similar to 4 of 14 in other non-AIDS patients as reported here. In spite of the extensive pattern heterogeneity among 15 C. neoformans var. gattii isolates in Australia, the patterns observed in seven California isolates were quite different from those in Australia. Among isolates of C. neoformans var. gattii, one fingerprint pattern (designated b) was observed in several countries of the Far East. The fingerprint patterns of two of three environmental isolates from Eucalyptus camaldulensis trees in Australia were identical to those of 2 of the 12 clinical isolates from the country.

  19. Possible involvement of caspase-6 and -7 but not caspase-3 in the regulation of hypoxia-induced apoptosis in tube-forming endothelial cells

    International Nuclear Information System (INIS)

    Eguchi, Ryoji; Tone, Shigenobu; Suzuki, Akio; Fujimori, Yoshihiro; Nakano, Takashi; Kaji, Kazuhiko; Ohta, Toshiro

    2009-01-01

    We recently reported that a broad-spectrum caspase inhibitor zVAD-fmk failed, while p38 inhibitor SB203580 succeeded, to prevent chromatin condensation and nuclear fragmentation induced by hypoxia in tube-forming HUVECs. In this study, we investigated the reasons for zVAD-fmk's inability to inhibit these morphological changes at the molecular level. The inhibitor effectively inhibited DNA ladder formation and activation of caspase-3 and -6, but it surprisingly failed to inhibit caspase-7 activation. On the other hand, SB203580 successfully inhibited all of these molecular events. When zLEHD-fmk, which specifically inhibits initiator caspase-9 upstream of caspase-3, was used, it inhibited caspase-3 activation but failed to inhibit caspase-6 and -7 activation. It also failed to inhibit hypoxia-induced chromatin condensation, nuclear fragmentation and DNA ladder formation. Taken together, our results indicate that, during hypoxia, caspase-7 is responsible for chromatin condensation and nuclear fragmentation while caspase-6 is responsible for DNA ladder formation

  20. DNA Photo Lithography with Cinnamate-based Photo-Bio-Nano-Glue

    Science.gov (United States)

    Feng, Lang; Li, Minfeng; Romulus, Joy; Sha, Ruojie; Royer, John; Wu, Kun-Ta; Xu, Qin; Seeman, Nadrian; Weck, Marcus; Chaikin, Paul

    2013-03-01

    We present a technique to make patterned functional surfaces, using a cinnamate photo cross-linker and photolithography. We have designed and modified a complementary set of single DNA strands to incorporate a pair of opposing cinnamate molecules. On exposure to 360nm UV, the cinnamate makes a highly specific covalent bond permanently linking only the complementary strands containing the cinnamates. We have studied this specific and efficient crosslinking with cinnamate-containing DNA in solution and on particles. UV addressability allows us to pattern surfaces functionally. The entire surface is coated with a DNA sequence A incorporating cinnamate. DNA strands A'B with one end containing a complementary cinnamated sequence A' attached to another sequence B, are then hybridized to the surface. UV photolithography is used to bind the A'B strand in a specific pattern. The system is heated and the unbound DNA is washed away. The pattern is then observed by thermo-reversibly hybridizing either fluorescently dyed B' strands complementary to B, or colloids coated with B' strands. Our techniques can be used to reversibly and/or permanently bind, via DNA linkers, an assortment of molecules, proteins and nanostructures. Potential applications range from advanced self-assembly, such as templated self-replication schemes recently reported, to designed physical and chemical patterns, to high-resolution multi-functional DNA surfaces for genetic detection or DNA computing.

  1. Investigation of the effect of radiation of DNA methylation patterns

    International Nuclear Information System (INIS)

    Kalinich, J.F.

    1986-01-01

    Four lines of cultured mammalian cells were used in this project: V79A03, a Chinese hamster lung fibroblast; HeLa S-3, an epithelial cell line from a human cervix carcinoma; CHO K-1, an epithelial cell line from a Chinese hamster ovary; and C-1300 N1E-115, a mouse neuroblastoma line. The 5-methylcytosine levels in DNA following exposure to cobalt-60 gamma radiation were measured. Induction of metallothionein in V79A03 cells and acetylcholinesterase in C-1300 N1E-115 cells after irradiation was determined and the effect of radiation on cytoplasmic and nuclear levels of DNA methyltransferase was studied and nuclear demethylase activity assayed. This study showed gamma radiation resulted in a decrease of 5-methylcytosine levels in the DNA of cultured mammalian cells. This radiation-induced hypomethylation resulted in the induction of acetylcholinesterase in mouse neuroblastoma cells and metallothionein in Chinese hamster lung fibroblasts and was caused by a decrease in DNA methyltransferase activity in the nucleus after irradiation and not by the presence of DNA demethylase

  2. Dual DNA methylation patterns in the CNS reveal developmentally poised chromatin and monoallelic expression of critical genes.

    Directory of Open Access Journals (Sweden)

    Jinhui Wang

    Full Text Available As a first step towards discovery of genes expressed from only one allele in the CNS, we used a tiling array assay for DNA sequences that are both methylated and unmethylated (the MAUD assay. We analyzed regulatory regions of the entire mouse brain transcriptome, and found that approximately 10% of the genes assayed showed dual DNA methylation patterns. They include a large subset of genes that display marks of both active and silent, i.e., poised, chromatin during development, consistent with a link between differential DNA methylation and lineage-specific differentiation within the CNS. Sixty-five of the MAUD hits and 57 other genes whose function is of relevance to CNS development and/or disorders were tested for allele-specific expression in F(1 hybrid clonal neural stem cell (NSC lines. Eight MAUD hits and one additional gene showed such expression. They include Lgi1, which causes a subtype of inherited epilepsy that displays autosomal dominance with incomplete penetrance; Gfra2, a receptor for glial cell line-derived neurotrophic factor GDNF that has been linked to kindling epilepsy; Unc5a, a netrin-1 receptor important in neurodevelopment; and Cspg4, a membrane chondroitin sulfate proteoglycan associated with malignant melanoma and astrocytoma in human. Three of the genes, Camk2a, Kcnc4, and Unc5a, show preferential expression of the same allele in all clonal NSC lines tested. The other six genes show a stochastic pattern of monoallelic expression in some NSC lines and bi-allelic expression in others. These results support the estimate that 1-2% of genes expressed in the CNS may be subject to allelic exclusion, and demonstrate that the group includes genes implicated in major disorders of the CNS as well as neurodevelopment.

  3. Radiolysis of DNA-protein complexes

    Energy Technology Data Exchange (ETDEWEB)

    Begusova, Marie [Department of Radiation Dosimetry, Nuclear Physics Institute, Na Truhlarce 39/64, CZ-18086, Prague 8 (Czech Republic)]. E-mail: begusova@ujf.cas.cz; Gillard, Nathalie [Centre de Biophysique Moleculaire, CNRS, rue Charles-Sadron, F-45071 Orleans Cedex 2 (France); Sy, Denise [Centre de Biophysique Moleculaire, CNRS, rue Charles-Sadron, F-45071 Orleans Cedex 2 (France); Castaing, Bertrand [Centre de Biophysique Moleculaire, CNRS, rue Charles-Sadron, F-45071 Orleans Cedex 2 (France); Charlier, Michel [Centre de Biophysique Moleculaire, CNRS, rue Charles-Sadron, F-45071 Orleans Cedex 2 (France); Spotheim-Maurizot, Melanie [Centre de Biophysique Moleculaire, CNRS, rue Charles-Sadron, F-45071 Orleans Cedex 2 (France)

    2005-02-01

    We discuss here modifications of DNA and protein radiolysis due to the interaction of these two partners in specific complexes. Experimental patterns of frank strand breaks (FSB) and alkali revealed breaks (ARB) obtained for DNA lac operator bound to the lac repressor and for a DNA containing an abasic site analog bound to the formamidopyrimidine-DNA glycosylase are reported. Experimental data are compared to predicted damage distribution obtained using the theoretical model RADACK.

  4. Radiolysis of DNA-protein complexes

    International Nuclear Information System (INIS)

    Begusova, Marie; Gillard, Nathalie; Sy, Denise; Castaing, Bertrand; Charlier, Michel; Spotheim-Maurizot, Melanie

    2005-01-01

    We discuss here modifications of DNA and protein radiolysis due to the interaction of these two partners in specific complexes. Experimental patterns of frank strand breaks (FSB) and alkali revealed breaks (ARB) obtained for DNA lac operator bound to the lac repressor and for a DNA containing an abasic site analog bound to the formamidopyrimidine-DNA glycosylase are reported. Experimental data are compared to predicted damage distribution obtained using the theoretical model RADACK

  5. Phylogenetic patterns in populations of Chilean species of the genus Orestias (Teleostei: Cyprinodontidae): results of mitochondrial DNA analysis.

    Science.gov (United States)

    Lüssen, Arne; Falk, Thomas M; Villwock, Wolfgang

    2003-10-01

    Patterns of molecular genetic differentiation among taxa of the "agassii species complex" (Parenti, 1984) were analysed based on partial mtDNA control region sequences. Special attention has been paid to Chilean populations of Orestias agassii and species from isolated lakes of northern Chile, e.g., O. agassii, Orestias chungarensis, Orestias parinacotensis, Orestias laucaensis, and Orestias ascotanensis. Orestias tschudii, Orestias luteus, and Orestias ispi were analysed comparatively. Our findings support the utility of mtDNA control region sequences for phylogenetic studies within the "agassii species complex" and confirmed the monophyly of this particular lineage, excluding O. luteus. However, the monophyly of further morphologically defined lineages within the "agassii complex" appears doubtful. No support was found for the utility of these data sets for inferring phylogenetic relationships between more distantly related taxa originating from Lake Titicaca.

  6. Surface Acoustic Bloch Oscillations, the Wannier-Stark Ladder, and Landau-Zener Tunneling in a Solid

    Science.gov (United States)

    de Lima, M. M., Jr.; Kosevich, Yu. A.; Santos, P. V.; Cantarero, A.

    2010-04-01

    We present the experimental observation of Bloch oscillations, the Wannier-Stark ladder, and Landau-Zener tunneling of surface acoustic waves in perturbed grating structures on a solid substrate. A model providing a quantitative description of our experimental observations, including multiple Landau-Zener transitions of the anticrossed surface acoustic Wannier-Stark states, is developed. The use of a planar geometry for the realization of the Bloch oscillations and Landau-Zener tunneling allows a direct access to the elastic field distribution. The vertical surface displacement has been measured by interferometry.

  7. DNA methylation patterns in bladder cancer and washing cell sediments: a perspective for tumor recurrence detection

    International Nuclear Information System (INIS)

    Negraes, Priscilla D; Favaro, Francine P; Camargo, João Lauro V; Oliveira, Maria Luiza CS; Goldberg, José; Rainho, Cláudia A; Salvadori, Daisy MF

    2008-01-01

    Epigenetic alterations are a hallmark of human cancer. In this study, we aimed to investigate whether aberrant DNA methylation of cancer-associated genes is related to urinary bladder cancer recurrence. A set of 4 genes, including CDH1 (E-cadherin), SFN (stratifin), RARB (retinoic acid receptor, beta) and RASSF1A (Ras association (RalGDS/AF-6) domain family 1), had their methylation patterns evaluated by MSP (Methylation-Specific Polymerase Chain Reaction) analysis in 49 fresh urinary bladder carcinoma tissues (including 14 cases paired with adjacent normal bladder epithelium, 3 squamous cell carcinomas and 2 adenocarcinomas) and 24 cell sediment samples from bladder washings of patients classified as cancer-free by cytological analysis (control group). A third set of samples included 39 archived tumor fragments and 23 matched washouts from 20 urinary bladder cancer patients in post-surgical monitoring. After genomic DNA isolation and sodium bisulfite modification, methylation patterns were determined and correlated with standard clinic-histopathological parameters. CDH1 and SFN genes were methylated at high frequencies in bladder cancer as well as in paired normal adjacent tissue and exfoliated cells from cancer-free patients. Although no statistically significant differences were found between RARB and RASSF1A methylation and the clinical and histopathological parameters in bladder cancer, a sensitivity of 95% and a specificity of 71% were observed for RARB methylation (Fisher's Exact test (p < 0.0001; OR = 48.89) and, 58% and 17% (p < 0.05; OR = 0.29) for RASSF1A gene, respectively, in relation to the control group. Indistinct DNA hypermethylation of CDH1 and SFN genes between tumoral and normal urinary bladder samples suggests that these epigenetic features are not suitable biomarkers for urinary bladder cancer. However, RARB and RASSF1A gene methylation appears to be an initial event in urinary bladder carcinogenesis and should be considered as defining a

  8. DNA methylation patterns in bladder cancer and washing cell sediments: a perspective for tumor recurrence detection

    Directory of Open Access Journals (Sweden)

    Goldberg José

    2008-08-01

    Full Text Available Abstract Background Epigenetic alterations are a hallmark of human cancer. In this study, we aimed to investigate whether aberrant DNA methylation of cancer-associated genes is related to urinary bladder cancer recurrence. Methods A set of 4 genes, including CDH1 (E-cadherin, SFN (stratifin, RARB (retinoic acid receptor, beta and RASSF1A (Ras association (RalGDS/AF-6 domain family 1, had their methylation patterns evaluated by MSP (Methylation-Specific Polymerase Chain Reaction analysis in 49 fresh urinary bladder carcinoma tissues (including 14 cases paired with adjacent normal bladder epithelium, 3 squamous cell carcinomas and 2 adenocarcinomas and 24 cell sediment samples from bladder washings of patients classified as cancer-free by cytological analysis (control group. A third set of samples included 39 archived tumor fragments and 23 matched washouts from 20 urinary bladder cancer patients in post-surgical monitoring. After genomic DNA isolation and sodium bisulfite modification, methylation patterns were determined and correlated with standard clinic-histopathological parameters. Results CDH1 and SFN genes were methylated at high frequencies in bladder cancer as well as in paired normal adjacent tissue and exfoliated cells from cancer-free patients. Although no statistically significant differences were found between RARB and RASSF1A methylation and the clinical and histopathological parameters in bladder cancer, a sensitivity of 95% and a specificity of 71% were observed for RARB methylation (Fisher's Exact test (p RASSF1A gene, respectively, in relation to the control group. Conclusion Indistinct DNA hypermethylation of CDH1 and SFN genes between tumoral and normal urinary bladder samples suggests that these epigenetic features are not suitable biomarkers for urinary bladder cancer. However, RARB and RASSF1A gene methylation appears to be an initial event in urinary bladder carcinogenesis and should be considered as defining a panel of

  9. Adaptation of a ladder beam walking task to assess locomotor recovery in mice following spinal cord injury

    OpenAIRE

    Cummings, Brian J.; Engesser-Cesar, Christie; Anderson, Aileen J.

    2007-01-01

    Locomotor impairments after spinal cord injury (SCI) are often assessed using open-field rating scales. These tasks have the advantage of spanning the range from complete paralysis to normal walking; however, they lack sensitivity at specific levels of recovery. Additionally, most supplemental assessments were developed in rats, not mice. For example, the horizontal ladder beam has been used to measure recovery in the rat after SCI. This parametric task results in a videotaped archival record...

  10. DNA methylation

    DEFF Research Database (Denmark)

    Williams, Kristine; Christensen, Jesper; Helin, Kristian

    2012-01-01

    DNA methylation is involved in key cellular processes, including X-chromosome inactivation, imprinting and transcriptional silencing of specific genes and repetitive elements. DNA methylation patterns are frequently perturbed in human diseases such as imprinting disorders and cancer. The recent...... discovery that the three members of the TET protein family can convert 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC) has provided a potential mechanism leading to DNA demethylation. Moreover, the demonstration that TET2 is frequently mutated in haematopoietic tumours suggests that the TET...... proteins are important regulators of cellular identity. Here, we review the current knowledge regarding the function of the TET proteins, and discuss various mechanisms by which they contribute to transcriptional control. We propose that the TET proteins have an important role in regulating DNA methylation...

  11. On the cusp anomalous dimension in the ladder limit of N=4 SYM

    Energy Technology Data Exchange (ETDEWEB)

    Beccaria, Matteo; Fachechi, Alberto; Macorini, Guido [Dipartimento di Matematica e Fisica “Ennio De Giorgi”, Università del Salento,Via Arnesano, 73100 Lecce (Italy); INFN,Via Arnesano, 73100 Lecce (Italy)

    2016-06-01

    We analyze the cusp anomalous dimension in the (leading) ladder limit of N=4 SYM and present new results for its higher-order perturbative expansion. We study two different limits with respect to the cusp angle ϕ. The first is the light-like regime where x=e{sup i} {sup ϕ}→0. This limit is characterised by a non-trivial expansion of the cusp anomaly as a sum of powers of log x, where the maximum exponent increases with the loop order. The coefficients of this expansion have remarkable transcendentality features and can be expressed by products of single zeta values. We show that the whole logarithmic expansion is fully captured by a solvable Woods-Saxon like one-dimensional potential. From the exact solution, we extract generating functions for the cusp anomaly as well as for the various specific transcendental structures appearing therein. The second limit that we discuss is the regime of small cusp angle. In this somewhat simpler case, we show how to organise the quantum mechanical perturbation theory in a novel efficient way by means of a suitable all-order Ansatz for the ground state of the associated Schrödinger problem. Our perturbative setup allows to systematically derive higher-order perturbative corrections in powers of the cusp angle as explicit non-perturbative functions of the effective coupling. This series approximation is compared with the numerical solution of the Schrödinger equation to show that we can achieve very good accuracy over the whole range of coupling and cusp angle. Our results have been obtained by relatively simple techniques. Nevertheless, they provide several non-trivial tests useful to check the application of Quantum Spectral Curve methods to the ladder approximation at non zero ϕ, in the two limits we studied.

  12. Mitochondrial DNA pattern of the fine shrimp Metapenaeus elegans (De Man, 1907) in the lagoon of Segara Anakan, Central Java, using Hind III

    Science.gov (United States)

    Nugraha, Fitra Arya Dwi; Holil, Kholifah; Kurniawan, Nia

    2017-05-01

    Ecological damages to the Lagoon of Segara Anakan, Central Java, as well as large-scale and continuous exploitation are threatening the sustainability of fine shrimp, Metapenaeus elegans, and resources. Information in regards to genetic resources is crucial to establish long-term conservation programs and to preserve germplasm quality. This study aims to evaluate the number and size of the fragment which is digested with restriction enzyme Hind III. Seven individuals of Metapenaeus elegans from the Lagoon of Segara Anakan were examined using Hind III. Amplification of mitochondrial DNA resulted in 950 bp, and the digestion using Hind III generated four fragments consisting of 114 bp, 200 bp, 250 bp, and 386 bp, which formed a monomorphic pattern. The restriction pattern showed the probability of homozygosity of alleles that restricted using Hind III. Homozygosity indicates no variation of DNA sequence.

  13. Spectral properties of an extended Hubbard ladder with long range anti-ferromagnetic order

    Science.gov (United States)

    Yang, Chun; Feiguin, Adrian

    We study the spectral properties of a Hubbard ladder with anti-ferromagnetic long range order by introducing a staggered Heisenberg interaction that decays algebraically. Unlike an alternating field or the t -Jz model, our problem preserves both SU (2) and translational invariance. We solve the problem with the time-dependent density matrix renormalization group and analyze the binding between holons and spinons and the structure of the elementary excitations. We discuss the implications in the context of the 2D Hubbard model at, and away from half-filling by using cluster perturbation theory (CPT). AF acknowledges the U.S. Department of Energy, Office of Basic Energy Sciences, for support under Grant DE-SC0014407.

  14. Ultra-deep sequencing of mouse mitochondrial DNA: mutational patterns and their origins.

    Directory of Open Access Journals (Sweden)

    Adam Ameur

    2011-03-01

    Full Text Available Somatic mutations of mtDNA are implicated in the aging process, but there is no universally accepted method for their accurate quantification. We have used ultra-deep sequencing to study genome-wide mtDNA mutation load in the liver of normally- and prematurely-aging mice. Mice that are homozygous for an allele expressing a proof-reading-deficient mtDNA polymerase (mtDNA mutator mice have 10-times-higher point mutation loads than their wildtype siblings. In addition, the mtDNA mutator mice have increased levels of a truncated linear mtDNA molecule, resulting in decreased sequence coverage in the deleted region. In contrast, circular mtDNA molecules with large deletions occur at extremely low frequencies in mtDNA mutator mice and can therefore not drive the premature aging phenotype. Sequence analysis shows that the main proportion of the mutation load in heterozygous mtDNA mutator mice and their wildtype siblings is inherited from their heterozygous mothers consistent with germline transmission. We found no increase in levels of point mutations or deletions in wildtype C57Bl/6N mice with increasing age, thus questioning the causative role of these changes in aging. In addition, there was no increased frequency of transversion mutations with time in any of the studied genotypes, arguing against oxidative damage as a major cause of mtDNA mutations. Our results from studies of mice thus indicate that most somatic mtDNA mutations occur as replication errors during development and do not result from damage accumulation in adult life.

  15. A tobacco cDNA reveals two different transcription patterns in vegetative and reproductive organs

    Directory of Open Access Journals (Sweden)

    I. da Silva

    2002-08-01

    Full Text Available In order to identify genes expressed in the pistil that may have a role in the reproduction process, we have established an expressed sequence tags project to randomly sequence clones from a Nicotiana tabacum stigma/style cDNA library. A cDNA clone (MTL-8 showing high sequence similarity to genes encoding glycine-rich RNA-binding proteins was chosen for further characterization. Based on the extensive identity of MTL-8 to the RGP-1a sequence of N. sylvestris, a primer was defined to extend the 5' sequence of MTL-8 by RT-PCR from stigma/style RNAs. The amplification product was sequenced and it was confirmed that MTL-8 corresponds to an mRNA encoding a glycine-rich RNA-binding protein. Two transcripts of different sizes and expression patterns were identified when the MTL-8 cDNA insert was used as a probe in RNA blots. The largest is 1,100 nucleotides (nt long and markedly predominant in ovaries. The smaller transcript, with 600 nt, is ubiquitous to the vegetative and reproductive organs analyzed (roots, stems, leaves, sepals, petals, stamens, stigmas/styles and ovaries. Plants submitted to stress (wounding, virus infection and ethylene treatment presented an increased level of the 600-nt transcript in leaves, especially after tobacco necrosis virus infection. In contrast, the level of the 1,100-nt transcript seems to be unaffected by the stress conditions tested. Results of Southern blot experiments have suggested that MTL-8 is present in one or two copies in the tobacco genome. Our results suggest that the shorter transcript is related to stress while the larger one is a flower predominant and nonstress-inducible messenger.

  16. DNA methyltransferase 1 mutations and mitochondrial pathology: is mtDNA methylated?

    Directory of Open Access Journals (Sweden)

    Alessandra eMaresca

    2015-03-01

    Full Text Available Autosomal dominant cerebellar ataxia, deafness and narcolepsy (ADCA-DN and Hereditary sensory neuropathy with dementia and hearing loss (HSN1E are two rare, overlapping neurodegenerative syndromes that have been recently linked to allelic dominant pathogenic mutations in the DNMT1 gene, coding for DNA (cytosine-5-methyltransferase 1. DNMT1 is the enzyme responsible for maintaining the nuclear genome methylation patterns during the DNA replication and repair, thus regulating gene expression. The mutations responsible for ADCA-DN and HSN1E affect the replication foci targeting sequence domain, which regulates DNMT1 binding to chromatin. DNMT1 dysfunction is anticipated to lead to a global alteration of the DNA methylation pattern with predictable downstream consequences on gene expression. Interestingly, ADCA-DN and HSN1E phenotypes share some clinical features typical of mitochondrial diseases, such as optic atrophy, peripheral neuropathy and deafness, and some biochemical evidence of mitochondrial dysfunction. The recent discovery of a mitochondrial isoform of DNMT1 and its proposed role in methylating mitochondrial DNA (mtDNA suggests that DNMT1 mutations may directly affect mtDNA and mitochondrial physiology. On the basis of this latter finding the link between DNMT1 abnormal activity and mitochondrial dysfunction in ADCA-DN and HSN1E appears intuitive, however mtDNA methylation remains highly debated. In the last years several groups demonstrated the presence of 5-methylcytosine in mtDNA by different approaches, but, on the other end, the opposite evidence that mtDNA is not methylated has also been published. Since over 1500 mitochondrial proteins are encoded by the nuclear genome, the altered methylation of these genes may well have a critical role in leading to the mitochondrial impairment observed in ADCA-DN and HSN1E. Thus, many open questions still remain unanswered, such as why mtDNA should be methylated, and how this process is

  17. Methylation patterns of repetitive DNA sequences in germ cells of Mus musculus.

    Science.gov (United States)

    Sanford, J; Forrester, L; Chapman, V; Chandley, A; Hastie, N

    1984-03-26

    The major and the minor satellite sequences of Mus musculus were undermethylated in both sperm and oocyte DNAs relative to the amount of undermethylation observed in adult somatic tissue DNA. This hypomethylation was specific for satellite sequences in sperm DNA. Dispersed repetitive and low copy sequences show a high degree of methylation in sperm DNA; however, a dispersed repetitive sequence was undermethylated in oocyte DNA. This finding suggests a difference in the amount of total genomic DNA methylation between sperm and oocyte DNA. The methylation levels of the minor satellite sequences did not change during spermiogenesis, and were not associated with the onset of meiosis or a specific stage in sperm development.

  18. Modification of DNA radiolysis by DNA-binding proteins: Structural aspects

    International Nuclear Information System (INIS)

    Davidkova, M.; Stisova, V.; Goffinont, S.; Gillard, N.; Castaing, B.; Spotheim-Maurizot, M.

    2006-01-01

    Formation of specific complexes between proteins and their cognate DNA modulates the yields and the location of radiation damage on both partners of the complex. The radiolysis of DNA-protein complexes is studied for: (1) the Escherichia coli lactose operator-repressor complex, (2) the complex between DNA bearing an analogue of an abasic site and the repair protein Fpg of Lactococcus lactis. Experimental patterns of DNA damages are presented and compared to predicted damage distribution obtained using an improved version of the stochastic model RADACK. The same method is used for predicting the location of damages on the proteins. At doses lower than a threshold that depends on the system, proteins protect their specific binding site on DNA while at high doses, the studied complexes are disrupted mainly through protein damage. The loss of binding ability is the functional consequence of the amino-acids modification by OH . radicals. Many of the most probably damaged amino acids are essential for the DNA-protein interaction and within a complex are protected by DNA. (authors)

  19. Apollo 11 Astronaut Neil Armstrong Performs Ladder Practice

    Science.gov (United States)

    1969-01-01

    In preparation of the nation's first Lunar landing mission, Apollo 11 crew members underwent training activities to practice activities they would be performing during the mission. In this photograph, Neil Armstrong, donned in his space suit, practices getting back to the first rung of the ladder on the Lunar Module (LM). The Apollo 11 mission launched from the Kennedy Space Center (KSC) in Florida via the Marshall Space Flight Center (MSFC) developed Saturn V launch vehicle on July 16, 1969 and safely returned to Earth on July 24, 1969. Aboard the space craft were astronauts Neil A. Armstrong, commander; Michael Collins, Command Module (CM) pilot; and Edwin E. (Buzz) Aldrin Jr., Lunar Module (LM) pilot. The CM, 'Columbia', piloted by Collins, remained in a parking orbit around the Moon while the LM, 'Eagle'', carrying astronauts Armstrong and Aldrin, landed on the Moon. On July 20, 1969, Armstrong was the first human to ever stand on the lunar surface, followed by Aldrin. During 2½ hours of surface exploration, the crew collected 47 pounds of lunar surface material for analysis back on Earth. With the success of Apollo 11, the national objective to land men on the Moon and return them safely to Earth had been accomplished.

  20. Micropatterning stretched and aligned DNA for sequence-specific nanolithography

    Science.gov (United States)

    Petit, Cecilia Anna Paulette

    Techniques for fabricating nanostructured materials can be categorized as either "top-down" or "bottom-up". Top-down techniques use lithography and contact printing to create patterned surfaces and microfluidic channels that can corral and organize nanoscale structures, such as molecules and nanorods in contrast; bottom-up techniques use self-assembly or molecular recognition to direct the organization of materials. A central goal in nanotechnology is the integration of bottom-up and top-down assembly strategies for materials development, device design; and process integration. With this goal in mind, we have developed strategies that will allow this integration by using DNA as a template for nanofabrication; two top-down approaches allow the placement of these templates, while the bottom-up technique uses the specific sequence of bases to pattern materials along each strand of DNA. Our first top-down approach, termed combing of molecules in microchannels (COMMIC), produces microscopic patterns of stretched and aligned molecules of DNA on surfaces. This process consists of passing an air-water interface over end adsorbed molecules inside microfabricated channels. The geometry of the microchannel directs the placement of the DNA molecules, while the geometry of the airwater interface directs the local orientation and curvature of the molecules. We developed another top-down strategy for creating micropatterns of stretched and aligned DNA using surface chemistry. Because DNA stretching occurs on hydrophobic surfaces, this technique uses photolithography to pattern vinyl-terminated silanes on glass When these surface-, are immersed in DNA solution, molecules adhere preferentially to the silanized areas. This approach has also proven useful in patterning protein for cell adhesion studies. Finally, we describe the use of these stretched and aligned molecules of DNA as templates for the subsequent bottom-up construction of hetero-structures through hybridization

  1. High-energy, large-momentum-transfer processes: Ladder diagrams in φ3 theory. Pt. 2

    International Nuclear Information System (INIS)

    Osland, P.; Wu, T.T.; Harvard Univ., Cambridge, MA

    1987-01-01

    The scattering amplitude for the four-rung ladder diagram in φ 3 theory is evaluated at high energies and for large momentum transfers. The result takes the form of s -1 vertical stroketvertical stroke -3 multiplied by a homogeneous sixth-order polynomial in ln s and 1nvertical stroketvertical stroke. The novel and unexpected feature is that this polynomial is different depending on whether 1n vertical stroketvertical stroke is larger or less than 1/2 1n s. Thus the asymptotic formula is not analytic at 1n vertical stroketvertical stroke=1/2 1n s, although the first five derivatives are continuous. (orig.)

  2. Atypical mitochondrial inheritance patterns in eukaryotes.

    Science.gov (United States)

    Breton, Sophie; Stewart, Donald T

    2015-10-01

    Mitochondrial DNA (mtDNA) is predominantly maternally inherited in eukaryotes. Diverse molecular mechanisms underlying the phenomenon of strict maternal inheritance (SMI) of mtDNA have been described, but the evolutionary forces responsible for its predominance in eukaryotes remain to be elucidated. Exceptions to SMI have been reported in diverse eukaryotic taxa, leading to the prediction that several distinct molecular mechanisms controlling mtDNA transmission are present among the eukaryotes. We propose that these mechanisms will be better understood by studying the deviations from the predominating pattern of SMI. This minireview summarizes studies on eukaryote species with unusual or rare mitochondrial inheritance patterns, i.e., other than the predominant SMI pattern, such as maternal inheritance of stable heteroplasmy, paternal leakage of mtDNA, biparental and strictly paternal inheritance, and doubly uniparental inheritance of mtDNA. The potential genes and mechanisms involved in controlling mitochondrial inheritance in these organisms are discussed. The linkage between mitochondrial inheritance and sex determination is also discussed, given that the atypical systems of mtDNA inheritance examined in this minireview are frequently found in organisms with uncommon sexual systems such as gynodioecy, monoecy, or andromonoecy. The potential of deviations from SMI for facilitating a better understanding of a number of fundamental questions in biology, such as the evolution of mtDNA inheritance, the coevolution of nuclear and mitochondrial genomes, and, perhaps, the role of mitochondria in sex determination, is considerable.

  3. Algorithmic implementation of particle-particle ladder diagram approximation to study strongly-correlated metals and semiconductors

    Science.gov (United States)

    Prayogi, A.; Majidi, M. A.

    2017-07-01

    In condensed-matter physics, strongly-correlated systems refer to materials that exhibit variety of fascinating properties and ordered phases, depending on temperature, doping, and other factors. Such unique properties most notably arise due to strong electron-electron interactions, and in some cases due to interactions involving other quasiparticles as well. Electronic correlation effects are non-trivial that one may need a sufficiently accurate approximation technique with quite heavy computation, such as Quantum Monte-Carlo, in order to capture particular material properties arising from such effects. Meanwhile, less accurate techniques may come with lower numerical cost, but the ability to capture particular properties may highly depend on the choice of approximation. Among the many-body techniques derivable from Feynman diagrams, we aim to formulate algorithmic implementation of the Ladder Diagram approximation to capture the effects of electron-electron interactions. We wish to investigate how these correlation effects influence the temperature-dependent properties of strongly-correlated metals and semiconductors. As we are interested to study the temperature-dependent properties of the system, the Ladder diagram method needs to be applied in Matsubara frequency domain to obtain the self-consistent self-energy. However, at the end we would also need to compute the dynamical properties like density of states (DOS) and optical conductivity that are defined in the real frequency domain. For this purpose, we need to perform the analytic continuation procedure. At the end of this study, we will test the technique by observing the occurrence of metal-insulator transition in strongly-correlated metals, and renormalization of the band gap in strongly-correlated semiconductors.

  4. Characterization of Actinomyces with genomic DNA fingerprints and rRNA gene probes.

    Science.gov (United States)

    Bowden, G; Johnson, J; Schachtele, C

    1993-08-01

    Cellular DNA from 25 Actinomyces naeslundii and Actinomyces viscosus strains belonging to the 7 taxonomic clusters of Fillery et al. (1978) and several unclustered strains was obtained by enzymatic and N-lauroylsarcosine/guanidine isothiocyanate treatment of whole cells, followed by extraction of the nucleic acid. The DNA samples were digested with restriction endonucleases BamHI or PvuII, and agarose gel electrophoresis was used to obtain DNA fingerprints. The DNA fragments were subjected to Southern blot hybridization with a digoxigenin-labeled cDNA probe transcribed from Escherichia coli 16S and 23S rRNA. The patterns of bands from genomic (DNA fingerprints) and rDNA fingerprints (ribotypes) were used for comparison between the taxonomic cluster strains and strains within clusters. Representative strains from each taxonomic cluster provided different BamHI DNA fingerprints and ribotype patterns with 3 to 9 distinct bands. Some strains within a cluster showed identical ribotype patterns with both endonucleases (A. naeslundii B120 and A. naeslundii B102 from cluster 3), while others showed the same pattern with BamHI but a different pattern with PvuII (A. naeslundii ATCC 12104 and 398A from cluster 5). A viscosus ATCC 15987 (cluster 7) and its parent strain T6 yielded identical fingerprint and ribotype patterns. The genomic diversity revealed by DNA fingerprinting and ribotyping demonstrates that these techniques, which do not require phenotypic expression, are suited for study of the oral ecology of the Actinomyces, and for epidemiological tracking of specific Actinomyces strains associated with caries lesions and sites of periodontal destruction.

  5. Mapping of 34 minisatellite loci resolved by two-dimensional DNA typing

    DEFF Research Database (Denmark)

    Børglum, Anders; Nyegaard, Mette; Kvistgaard, AB

    1997-01-01

    Two-dimensional (2-D) DNA typing is based on electrophoretic separation of genomic DNA fragments in two dimensions according to independent criteria (size and base-pair sequence), followed by hybridization analysis using multilocus probes. The technique allows simultaneous visualization of several...... could be deduced, showing no evidence of clustering. In the analysis of spot patterns, use was made of a computerized image analysis system specifically designed for 2-D DNA typing. Since experimental variations between different separation patterns were automatically corrected for with this program......, rapid and reliable scorings could be obtained. The results presented demonstrate the availability of reliable genetic information throughout the 2-D separation pattern. Adding the use of semiautomated computerized pattern analysis, this study further substantiates the applicability of 2-D DNA typing...

  6. Policy required for entry of DNA profiles onto the National Forensic DNA Database of South Africa

    Directory of Open Access Journals (Sweden)

    Laura J. Heathfield

    2014-07-01

    Full Text Available The recent Criminal Law (Forensic Procedures Amendment Act (2013 provides a definition for forensic DNA profiles and, in so doing, states that medical information about an individual may not be revealed through a forensic DNA profile. Yet chromosomal abnormalities can exhibit as tri-allelic patterns on DNA profiles and such information can expose medical conditions such as Down syndrome. This short report highlights this concern and suggests a policy be created for the entering of such DNA profiles onto the National Forensic DNA database of South Africa.

  7. The content of DNA and RNA in microparticles released by Jurkat and HL-60 cells undergoing in vitro apoptosis

    International Nuclear Information System (INIS)

    Reich, Charles F.; Pisetsky, David S.

    2009-01-01

    Microparticles are small membrane-bound vesicles that are released from apoptotic cells during blebbing. These particles contain DNA and RNA and display important functional activities, including immune system activation. Furthermore, nucleic acids inside the particle can be analyzed as biomarkers in a variety of disease states. To elucidate the nature of microparticle nucleic acids, DNA and RNA released in microparticles from the Jurkat T and HL-60 promyelocytic cell lines undergoing apoptosis in vitro were studied. Microparticles were isolated from culture media by differential centrifugation and characterized by flow cytometry and molecular approaches. In these particles, DNA showed laddering by gel electrophoresis and was present in a form that allowed direct binding by a monoclonal anti-DNA antibody, suggesting antigen accessibility even without fixation. Analysis of RNA by gel electrophoresis showed intact 18s and 28s ribosomal RNA bands, although lower molecular bands consistent with 28s ribosomal RNA degradation products were also present. Particles also contained messenger RNA as shown by RT-PCR amplification of sequences for β-actin and GAPDH. In addition, gel electrophoresis showed the presence of low molecular weight RNA in the size range of microRNA. Together, these results indicate that microparticles from apoptotic Jurkat and HL-60 cells contain diverse nucleic acid species, indicating translocation of both nuclear and cytoplasmic DNA and RNA as particle release occurs during death

  8. The correlation between DNA ploidy and the clinicohistologic findings in colorectal cancer

    International Nuclear Information System (INIS)

    Lee, Suk Ho; Kim, Hun Jung; Kim, Woo Chul; Cho, Young Kap; Loh, John J. K.; Woo, Ze Hong; Hwang, Tae Sook

    2000-01-01

    DNA ploidy pattern was shown to correlate with several clinicohistologic findings in several tumors. Aim of this study was to evaluate the correlation of the clinicohistologic findings in colorectal cancer and the failure pattern in rectosigmoid cancer with DNA ploidy. DNA flow cytometry using the Hedley methods on paraffin embedded specimen from 117 patients with colorectal cancers after curative resection was performed. We tried to find the correlation between DNA ploidy and various clinicohistologic findings. And then the correlation DNA ploidy and the failure pattern in 75 patients of rectosigmoid cancer was analized. Forty samples (34.2%) from tumors gave aneuploidy histogram. There was no significant difference in the frequency of DNA aneuploidy in terms of age, sex, depth of invasion, location and Dukes stage. But there was a significant correlation between DNA ploidy and the failure rates in Dukes stage B rectosigmoid cancer (p=0.048). These findings suggest that DNA ploidy pattern shows the correlation with the treatment failure rates in Dukes stage B rectosigmoid, but not with many other clinicohistologic findings. However, more patients will be needed to disclose these findings

  9. Genotypic characterization of Rickettsiae by DNA probes generated from Rickettsia Prowazekii DNA

    International Nuclear Information System (INIS)

    Demkin, V.V.; Rydkina, E.B.; Likhoded, L.Ya.; Ignatovich, V.F.; Genig, V.A.; Balayeva, N.M.

    1994-01-01

    Southern blot analysis of HindIII-cleaved rickettsial DNA was used for genotypic characterization of the typhus group (TG) species (R. prowazekii, R. typhi, R. canada) and a few species were of the spotted fever group (SFG)rickettsiae (R. sibirica, R. conorii, R. akari). Four different DNA probes were employed. PBH11 and PBH13 probes were morphospecific HindIII fragment of R prowazekii DNA. MW218 probe contained the gene for 51 K antigen and MW264 probe contained the citrate synthase gene of R. prowazekii. All the probes hybridized with the tested TG and SFG rickettsial DNAs, forming from 1 to 5 bands, but they did not with R. tsutsudamushi or C. burnetii DNAs. All the probes demonstrated specific hybridization pattern with TG species and R. akari. PBH11. PBH13 and MW264 probes clearly distinguished R. sibirica and R. conorii from the other tested rickettsiae, but not from each other. However, these two species differed slightly with MW218 probe. Several strains of each species were analyzed in this way and except for strains of R. conorii identical intra-species pattern were obtained. These data lead us to consider the obtained hybridization patterns as criteria for genotypic identification. (author)

  10. Influence of DNA conformation on radiation-induced single-strand breaks

    International Nuclear Information System (INIS)

    Barone, F.; Belli, M.; Mazzei, F.

    1994-01-01

    We performed experiments on two DNA fragments of about 300 bp having different conformation to test whether radiation-induced single-strand breakage is dependent on DNA conformation. Breakage analysis was carried out by denaturing polyacrylamide gel electrophoresis, which allows determination of the broken site at single nucleotide resolution. We found uniform cutting patterns in B-form regions. On the contrary, X- or γ-irradiation of curved fragments of kinetoplast DNA showed that the distribution of single-strand breaks was not uniform along the fragment, as the cleavage pattern was modulated in phase with the runs of A-T pairs. This modulation likely reflected the reduced accessibility of the sites which on hydroxyl-radical attack give rise to strand breaks. The cleavage pattern was phased with the runs of A-T pairs. Moreover, the overall yield of strand breaks was considerably lower in curved DNA fragments than in those with extended straight regions. The conformation effect found here indicates that the cleavage pattern reflects the fine structural features of DNA. (orig./MG)

  11. Methylation patterns of repetitive DNA sequences in germ cells of Mus musculus.

    OpenAIRE

    Sanford, J; Forrester, L; Chapman, V; Chandley, A; Hastie, N

    1984-01-01

    The major and the minor satellite sequences of Mus musculus were undermethylated in both sperm and oocyte DNAs relative to the amount of undermethylation observed in adult somatic tissue DNA. This hypomethylation was specific for satellite sequences in sperm DNA. Dispersed repetitive and low copy sequences show a high degree of methylation in sperm DNA; however, a dispersed repetitive sequence was undermethylated in oocyte DNA. This finding suggests a difference in the amount of total genomic...

  12. DAMAGE TO DNA PRIMARY STRUCTURE AND ANTIOXIDANT ENZYMES IN LEMNA MINOR INDUCED BY HG2+%Hg2+ 胁迫对浮萍体细胞DNA一级结构和抗氧化酶系的损伤

    Institute of Scientific and Technical Information of China (English)

    徐楠; 施国新; 曾晓敏; 丁小余; 徐勤松; 陈源

    2003-01-01

    主要从DNA一级结构及抗氧化酶系变化两方面,研究了Hg2+胁迫下浮萍体细胞的损伤.结果表明:运用随机扩增多态性DNA法(Random amplified polymorphism DNA, RAPD)和DNA梯法(DNA Ladder),5~10 mg*L-1 Hg2+处理组可检测到基因组DNA的明显损伤,20 mg*L-1Hg2+已导致细胞坏死;RAPD法较DNA Ladder法更灵敏.本文还发现,活性氧和抗氧化酶系很可能参与了浮萍体细胞凋亡过程.低浓度的Hg2+胁迫可刺激抗氧化酶活性升高,以清除体内活性氧,而一旦活性氧水平超出一定域值,抗氧化酶活性急速下降,导致细胞凋亡.%The damage to Lemna minor cells induced by Hg2+ was studied in this article. Most damage occurred to DNA primary structure and changes in antioxidant enzyme activities were investigated by using RAPD and DNA ladder methods. The results showed that obvious damage to DNA was found in the process of apoptosis induced by 5-10 mg*L-1 Hg2+, and 20 mg*L-1 Hg2+ had already caused necrotic injury. The RAPD method was the more sensitive of the two methods, and so could be considered as an important method for monitoring apoptosis. The results also indicated that reactive oxygen species (ROS) and antioxidant enzymes are involved in the process of apoptosis. The activities of antioxidant enzymes could be stimulated to eliminate active oxygen by exposing the Lemna minor to low Hg2+ concentration; the cells declined rapidly when ROS were unable to be eliminated effectively.

  13. Apoptosis - Triggering Effects: UVB-irradiation and Saccharomyces cerevisiae.

    Science.gov (United States)

    Behzadi, Payam; Behzadi, Elham

    2012-12-01

    The pathogenic disturbance of Saccharomyces cerevisiae is known as a rare but invasive nosocomial fungal infection. This survey is focused on the evaluation of apoptosis-triggering effects of UVB-irradiation in Saccharomyces cerevisiae. The well-growth colonies of Saccharomyces cerevisiae on Sabouraud Dextrose Agar (SDA) were irradiated within an interval of 10 minutes by UVB-light (302 nm). Subsequently, the harvested DNA molecules of control and UV-exposed yeast colonies were run through the 1% agarose gel electrophoresis comprising the luminescent dye of ethidium bromide. No unusual patterns including DNA laddering bands or smears were detected. The applied procedure for UV exposure was not effective for inducing apoptosis in Saccharomyces cerevisiae. So, it needs another UV-radiation protocol for inducing apoptosis phenomenon in Saccharomyces cerevisiae.

  14. Problem of summing up ladder diagrams in quantum electrodynamics. [Cross sections

    Energy Technology Data Exchange (ETDEWEB)

    Gadzhiev, S A; Livashvili, A I [Azerbajdzhanskij Gosudarstvennyj Univ., Baku (USSR)

    1975-03-01

    A class of ladder diagrams in an asymptotic mode is considered, and a series of the perturbation theory for the given class of diagrams reduces to an integral equation obtained without approximations whatsoever. As applications of the method proposed, two electrodynamic processes are considered: the two-photon annihilation of an e/sup +/e/sup -/-pair and scattering of electons in Coulomb field. Matrix elements are provided. To derive the equations, Dirac equations and commutation relations are used. A conclusion is drawn that for the process, the log-log asymptotics and polar approximation lead to the fact that as the energy grows the cross-section of the process drops and the solution obtained indicates that such a drop occurs up to an energy of 10/sup 5/ GeV. For the second process, the region of large pulses transmitted by an electron to the external field does not lead to an increase in amplitude and cross-section.

  15. Phase diagram study of a dimerized spin-S zig–zag ladder

    International Nuclear Information System (INIS)

    Matera, J M; Lamas, C A

    2014-01-01

    The phase diagram of a frustrated spin-S zig–zag ladder is studied through different numerical and analytical methods. We show that for arbitrary S, there is a family of Hamiltonians for which a fully-dimerized state is an exact ground state, being the Majumdar–Ghosh point for a particular member of the family. We show that the system presents a transition between a dimerized phase to a Néel-like phase for S = 1/2, and spiral phases can appear for large S. The phase diagram is characterized by means of a generalization of the usual mean field approximation. The novelty in the present implementation is to consider the strongest coupled sites as the unit cell. The gap and the excitation spectrum is analyzed through the random phase approximation. Also, a perturbative treatment to obtain the critical points is discussed. Comparisons of the results with numerical methods like the Density Matrix Renormalization Group are also presented. (paper)

  16. Nitration Study of Cyclic Ladder Polyphenylsilsesquioxane

    Directory of Open Access Journals (Sweden)

    LIANG Jia-xiang

    2017-05-01

    Full Text Available Several nitration reagents including fuming nitric acid, HNO3-H2SO4, KNO3-H2SO4, HNO3-KNO3, CH3COOH-KNO3, (CH3CO2O-HNO3 were used to nitrate cyclic ladder polyphenylsilsesquioxane (CL-PPSQ in different conditions in order to enhance the compatibility of the CL-PPSQ in polymers, the NO2-PPSQ was obtained. FTIR, element analysis, GPC, TGA and 1H NMR were used to characterize the structures of the nitrated products. The results show that the nitrating abilities of the fuming nitric acid, HNO3-H2SO4 and KNO3-H2SO4 are very strong. Many nitro groups can be linked with phenyl groups in CL-PPSQ, but with low molecular mass, fracture occurs in siloxane segment. However, the Mn of the product NO2-PPSQ sharply drops by 50% compared with that of CL-PPSQ, so the nitration reagents can break the cyclic structure of CL-PPSQ. The nitrating reagents of HNO3-KNO3 and CH3COOH-KNO3 have no nitration effects on CL-PPSQ. At last, NO2-CL-PPSQ was prepared using (CH3CO2O-HNO3 because of the moderate nitration process and ability. The cyclic structure of PPSQ is remained, although the number of —NO2 group is not too much. At the same time, the nitration mechanism using different nitration reagents was analyzed. A certain amount of NO2+, which is a kind of activator owning strong nitration ability, can be found in the fuming nitric acid and H2SO4-HNO3(KNO3 systems. As to the (CH3CO2O-HNO3 system, the main activator is CH3COONO2.

  17. Mitochondrial DNA haplotype distribution patterns in Pinus ponderosa (Pinaceae): range-wide evolutionary history and implications for conservation.

    Science.gov (United States)

    Potter, Kevin M; Hipkins, Valerie D; Mahalovich, Mary F; Means, Robert E

    2013-08-01

    Ponderosa pine (Pinus ponderosa Douglas ex P. Lawson & C. Lawson) exhibits complicated patterns of morphological and genetic variation across its range in western North America. This study aims to clarify P. ponderosa evolutionary history and phylogeography using a highly polymorphic mitochondrial DNA marker, with results offering insights into how geographical and climatological processes drove the modern evolutionary structure of tree species in the region. We amplified the mtDNA nad1 second intron minisatellite region for 3,100 trees representing 104 populations, and sequenced all length variants. We estimated population-level haplotypic diversity and determined diversity partitioning among varieties, races and populations. After aligning sequences of minisatellite repeat motifs, we evaluated evolutionary relationships among haplotypes. The geographical structuring of the 10 haplotypes corresponded with division between Pacific and Rocky Mountain varieties. Pacific haplotypes clustered with high bootstrap support, and appear to have descended from Rocky Mountain haplotypes. A greater proportion of diversity was partitioned between Rocky Mountain races than between Pacific races. Areas of highest haplotypic diversity were the southern Sierra Nevada mountain range in California, northwestern California, and southern Nevada. Pinus ponderosa haplotype distribution patterns suggest a complex phylogeographic history not revealed by other genetic and morphological data, or by the sparse paleoecological record. The results appear consistent with long-term divergence between the Pacific and Rocky Mountain varieties, along with more recent divergences not well-associated with race. Pleistocene refugia may have existed in areas of high haplotypic diversity, as well as the Great Basin, Southwestern United States/northern Mexico, and the High Plains.

  18. Association of Tissue-Specific DNA Methylation Alterations with α-Thalassemia Southeast Asian Deletion

    Directory of Open Access Journals (Sweden)

    Tanapat Pangeson

    2017-11-01

    Full Text Available In the wild-type allele, DNA methylation levels of 10 consecutive CpG sites adjacent to the upstream 5′-breakpoint of α-thalassemia Southeast Asian (SEA deletion are not different between placenta and leukocytes. However, no previous study has reported the map of DNA methylation in the SEA allele. This report aims to show that the SEA mutation is associated with DNA methylation changes, resulting in differential methylation between placenta and leukocytes. Methylation-sensitive high-resolution analysis was used to compare DNA methylation among placenta, leukocytes, and unmethylated control DNA. The result indicates that the DNA methylation between placenta and leukocyte DNA is different and shows that the CpG status of both is not fully unmethylated. Mapping of individual CpG sites was performed by targeted bisulfite sequencing. The DNA methylation level of the 10 consecutive CpG sites was different between placenta and leukocyte DNA. When the 10th CpG of the mutation allele was considered as a hallmark for comparing DNA methylation level, it was totally different from the unmethylated 10th CpG of the wild-type allele. Finally, the distinct DNA methylation patterns between both DNA were extracted. In total, 24 patterns were found in leukocyte samples and 9 patterns were found in placenta samples. This report shows that the large deletion is associated with DNA methylation change. In further studies for clinical application, the distinct DNA methylation pattern might be a potential marker for detecting cell-free fetal DNA.

  19. Effects of altered maternal folic acid, vitamin B12 and docosahexaenoic acid on placental global DNA methylation patterns in Wistar rats.

    Directory of Open Access Journals (Sweden)

    Asmita Kulkarni

    Full Text Available Potential adverse effects of excess maternal folic acid supplementation on a vegetarian population deficient in vitamin B(12 are poorly understood. We have previously shown in a rat model that maternal folic acid supplementation at marginal protein levels reduces brain omega-3 fatty acid levels in the adult offspring. We have also reported that reduced docosahexaenoic acid (DHA levels may result in diversion of methyl groups towards DNA in the one carbon metabolic pathway ultimately resulting in DNA methylation. This study was designed to examine the effect of normal and excess folic acid in the absence and presence of vitamin B(12 deficiency on global methylation patterns in the placenta. Further, the effect of maternal omega 3 fatty acid supplementation on the above vitamin B(12 deficient diets was also examined. Our results suggest maternal folic acid supplementation in the absence of vitamin B(12 lowers plasma and placental DHA levels (p<0.05 and reduces global DNA methylation levels (p<0.05. When this group was supplemented with omega 3 fatty acids there was an increase in placental DHA levels and subsequently DNA methylation levels revert back to the levels of the control group. Our results suggest for the first time that DHA plays an important role in one carbon metabolism thereby influencing global DNA methylation in the placenta.

  20. High-resolution analysis of cytosine methylation in ancient DNA.

    Directory of Open Access Journals (Sweden)

    Bastien Llamas

    Full Text Available Epigenetic changes to gene expression can result in heritable phenotypic characteristics that are not encoded in the DNA itself, but rather by biochemical modifications to the DNA or associated chromatin proteins. Interposed between genes and environment, these epigenetic modifications can be influenced by environmental factors to affect phenotype for multiple generations. This raises the possibility that epigenetic states provide a substrate for natural selection, with the potential to participate in the rapid adaptation of species to changes in environment. Any direct test of this hypothesis would require the ability to measure epigenetic states over evolutionary timescales. Here we describe the first single-base resolution of cytosine methylation patterns in an ancient mammalian genome, by bisulphite allelic sequencing of loci from late Pleistocene Bison priscus remains. Retrotransposons and the differentially methylated regions of imprinted loci displayed methylation patterns identical to those derived from fresh bovine tissue, indicating that methylation patterns are preserved in the ancient DNA. Our findings establish the biochemical stability of methylated cytosines over extensive time frames, and provide the first direct evidence that cytosine methylation patterns are retained in DNA from ancient specimens. The ability to resolve cytosine methylation in ancient DNA provides a powerful means to study the role of epigenetics in evolution.

  1. Usefulness of the DNA-fingerprinting pattern and the multilocus enzyme electrophoresis profile in the assessment of outbreaks of meningococcal disease

    DEFF Research Database (Denmark)

    Weis, N; Lind, I

    1996-01-01

    cases were identical to the outbreak strain. None of the local serogroup C carrier strains isolated during the outbreak of serogroup C disease were identical to the outbreak strain. Both DNA-fingerprinting and MEE improved the differentiation of meningococci when compared with phenotypic......The objective of the study was to assess whether genotypic characterization by means of DNA-fingerprinting pattern (DFP) and multilocus enzyme electrophoresis (MEE) profile as compared to phenotypic characterization would improve the differentiation of Neisseria meningitidis strains associated...... in each outbreak were designated the index strains. Among the remaining 55 outbreak strains 52 were either DFP-identical or DFP-indistinguishable when compared with the one relevant out of the 4 index strains. This was only the case for 17 of the 37 strains isolated from sporadic cases caused by the same...

  2. Drug Addiction and DNA Modifications.

    Science.gov (United States)

    Brown, Amber N; Feng, Jian

    2017-01-01

    Drug addiction is a complex disorder which can be influenced by both genetic and environmental factors. Research has shown that epigenetic modifications can translate environmental signals into changes in gene expression, suggesting that epigenetic changes may underlie the causes and possibly treatment of substance use disorders. This chapter will focus on epigenetic modifications to DNA, which include DNA methylation and several recently defined additional DNA epigenetic changes. We will discuss the functions of DNA modifications and methods for detecting them, followed by a description of the research investigating the function and consequences of drug-induced changes in DNA methylation patterns. Understanding these epigenetic changes may provide us translational tools for the diagnosis and treatment of addiction in the future.

  3. Modeling spatiotemporal dynamics of DNA methylation

    DEFF Research Database (Denmark)

    Lövkvist, Cecilia Elisabet

    into how epigenetic marks are distributed in the human genome. In the first part of the thesis, we investigate DNA methylation and maintenance of methylation patterns throughout cell division. We argue that collaborative models, those where the methylation of CpG sites depends on the methylation status...... into the game more explicitly in another type of model that speaks out the duality of the two aspects. Using statistical analysis of experimental data, this thesis further explores a link between DNA methylation and nucleosome occupancy. By comparing the patterns on promoters to regions with similar Cp...... division. The patterns of epigentic marks depend on enzymes that ensure their maintenance and introduction. Using theoretical models, this thesis proposes new mechanisms for how enzymes operate to maintain patterns of epigenetic marks. Through analysis of experimental data this work gives new insight...

  4. Computational applications of DNA physical scales

    DEFF Research Database (Denmark)

    Baldi, Pierre; Chauvin, Yves; Brunak, Søren

    1998-01-01

    that these scales provide an alternative or complementary compact representation of DNA sequences. As an example we construct a strand invariant representation of DNA sequences. The scales can also be used to analyze and discover new DNA structural patterns, especially in combinations with hidden Markov models......The authors study from a computational standpoint several different physical scales associated with structural features of DNA sequences, including dinucleotide scales such as base stacking energy and propellor twist, and trinucleotide scales such as bendability and nucleosome positioning. We show...

  5. Computational applications of DNA structural scales

    DEFF Research Database (Denmark)

    Baldi, P.; Chauvin, Y.; Brunak, Søren

    1998-01-01

    that these scales provide an alternative or complementary compact representation of DNA sequences. As an example, we construct a strand-invariant representation of DNA sequences. The scales can also be used to analyze and discover new DNA structural patterns, especially in combination with hidden Markov models......Studies several different physical scales associated with the structural features of DNA sequences from a computational standpoint, including dinucleotide scales, such as base stacking energy and propeller twist, and trinucleotide scales, such as bendability and nucleosome positioning. We show...

  6. Commutation-relation-preserving ladder operators for propagating optical fields in nonuniform lossy media

    DEFF Research Database (Denmark)

    Partanen, Mikko; Häyrynen, Teppo; Tulkki, Jukka

    2015-01-01

    We have recently developed a quantized fluctuational electrodynamics (QFED) formalism to describe the quantum aspects of local thermal balance formation and to formulate the electromagnetic field ladder operators so that they no longer exhibit the anomalies reported for resonant structures. Here we...... show how the QFED can be used to resolve between the left and right propagating fields to bridge the QFED and the quantum optical input-output relations commonly used to describe selected quantum aspects of resonators. The generalized model introduces a density of states concept describing interference...... effects, which is instrumental in allowing an unambiguous separation of the fields and related quantum operators into left and right propagating parts. In addition to providing insight on the quantum treatment of interference, our results also provide the conclusive resolution of the long-standing enigma...

  7. Study of CP(N-1) theta-vacua by cluster simulation of SU(N) quantum spin ladders.

    Science.gov (United States)

    Beard, B B; Pepe, M; Riederer, S; Wiese, U-J

    2005-01-14

    D-theory provides an alternative lattice regularization of the 2D CP(N-1) quantum field theory in which continuous classical fields emerge from the dimensional reduction of discrete SU(N) quantum spins. Spin ladders consisting of n transversely coupled spin chains lead to a CP(N-1) model with a vacuum angle theta=npi. In D-theory no sign problem arises and an efficient cluster algorithm is used to investigate theta-vacuum effects. At theta=pi there is a first order phase transition with spontaneous breaking of charge conjugation symmetry for CP(N-1) models with N>2.

  8. Inherited sterility in the cotton leaf worm Spodoptera littoralis,(Boisd.), and changes in the DNA pattern as a result of using gamma radiation

    International Nuclear Information System (INIS)

    ABD EL-KADER, T.S.E.

    2013-01-01

    The present study was conducted to evaluate the effect of gamma irradiation on certain biological aspects of the cotton leaf worm Spodoptera littoralis (Boisd.). Laboratory experiments were carried out to investigate the effect of the sub sterilizing doses of 0, 50, 150, 250, 350 and 450 Gy of gamma irradiation (cobalt and cesium sources) on different generations of Spodoptera littoralis irradiated as pupae to study the inherited sterility. A dose level at 450 Gy completely inhibited full pupal development, but the emerged adult at the dose 350 Gy did not lay eggs, whether they were combined with non-irradiated or irradiated individuals of opposite sexes. The produced adults (P) showed increasing sterility with increasing the irradiation dose. While, their fertility, fecundity, pupation percent and adult emergence were found to be reduced in the parents followed by F1, but increased in F2. In all cases, sex ratio was shifted in favor of males. A significant negative relationship between dose levels and percentage of egg hatching was obtained; [the higher the dose, the lower the percentage of egg hatching]. The percentage of egg hatching resulting from irradiated male pupae was higher than that resulting from irradiated female pupae. Females were more sensitive for irradiation than males. Cobalt irradiation source was more effective than cesium source. The effect of gamma irradiation on the DNA pattern of adult male parents, F1 and F2 showed alterations among the controls, the treated parents, F1 and F2 individuals. Exposure to irradiation caused very frequently the appearance of some extra bands and the deficiency of others in the RAPD- PCR and ISSR amplification pattern of the irradiated insects. The appearance of extra bands was attributed to the repair mechanism that occur in the irradiation damaged DNA. However, the similarity in DNA patterns between some normal and treated samples was interpreted by assuming that the irradiation induced damage was in regions

  9. Automated Processing of 2-D Gel Electrophoretograms of Genomic DNA for Hunting Pathogenic DNA Molecular Changes.

    Science.gov (United States)

    Takahashi; Nakazawa; Watanabe; Konagaya

    1999-01-01

    We have developed the automated processing algorithms for 2-dimensional (2-D) electrophoretograms of genomic DNA based on RLGS (Restriction Landmark Genomic Scanning) method, which scans the restriction enzyme recognition sites as the landmark and maps them onto a 2-D electrophoresis gel. Our powerful processing algorithms realize the automated spot recognition from RLGS electrophoretograms and the automated comparison of a huge number of such images. In the final stage of the automated processing, a master spot pattern, on which all the spots in the RLGS images are mapped at once, can be obtained. The spot pattern variations which seemed to be specific to the pathogenic DNA molecular changes can be easily detected by simply looking over the master spot pattern. When we applied our algorithms to the analysis of 33 RLGS images derived from human colon tissues, we successfully detected several colon tumor specific spot pattern changes.

  10. DNA sequence modeling based on context trees

    NARCIS (Netherlands)

    Kusters, C.J.; Ignatenko, T.; Roland, J.; Horlin, F.

    2015-01-01

    Genomic sequences contain instructions for protein and cell production. Therefore understanding and identification of biologically and functionally meaningful patterns in DNA sequences is of paramount importance. Modeling of DNA sequences in its turn can help to better understand and identify such

  11. Characterization of a Dairy Gyr herd with respect to its mitochondrial DNA (mt DNA origin

    Directory of Open Access Journals (Sweden)

    Anibal Eugênio Vercesi Filho

    2010-01-01

    Full Text Available The Zebu breeds were introduced in Brazil mainly in the last century by imports from the Indian subcontinent. When the Zebu cattle arrived, the national herd suffered a significative change by backcrossing the national cows of taurine origin with Zebu sires. These processes created a polymorphism in the mitochondrial DNA (mtDNA in the Zebu animals with are in a major part derived from backcrossing and sharing mtDNA of taurine origin. To verify the maternal origin of cows belonging to the Dairy Gyr herd of APTA, Mococa 60 females were analyzed and 33 presented mtDNA from Bos taurus origin and 27 presented mtDNA from Bos indicus origin. None of these animals presented patterns of both mtDNA origins, indicating absence of heteroplasmy for these mitochondrial genotypes.

  12. DNA nanotechnology: a future perspective

    Science.gov (United States)

    2013-01-01

    In addition to its genetic function, DNA is one of the most distinct and smart self-assembling nanomaterials. DNA nanotechnology exploits the predictable self-assembly of DNA oligonucleotides to design and assemble innovative and highly discrete nanostructures. Highly ordered DNA motifs are capable of providing an ultra-fine framework for the next generation of nanofabrications. The majority of these applications are based upon the complementarity of DNA base pairing: adenine with thymine, and guanine with cytosine. DNA provides an intelligent route for the creation of nanoarchitectures with programmable and predictable patterns. DNA strands twist along one helix for a number of bases before switching to the other helix by passing through a crossover junction. The association of two crossovers keeps the helices parallel and holds them tightly together, allowing the assembly of bigger structures. Because of the DNA molecule's unique and novel characteristics, it can easily be applied in a vast variety of multidisciplinary research areas like biomedicine, computer science, nano/optoelectronics, and bionanotechnology. PMID:23497147

  13. DNA fusion gene vaccines

    DEFF Research Database (Denmark)

    Holst, Peter Johannes; Bassi, Maria Rosaria; Thomsen, Allan Randrup

    2010-01-01

    DNA vaccines are versatile and safe, but limited immunogenicity has prevented their use in the clinical setting. Experimentally, immunogenicity may be enhanced by the use of new delivery technologies, by coadministration of cytokines and pathogen-associated molecular patterns, or by fusion...... of antigens into molecular domains that enhance antigen presentation. More specifically, the immunogenicity of DNA vaccines may benefit from increased protein synthesis, increased T-cell help and MHC class I presentation, and the addition of a range of specific cytokines and pathogen-associated molecular...... with viral-vectored vaccines, various synergistic components may need to be incorporated into DNA vaccines. From the perspective of the future clinical use of DNA vaccines, it has been suggested that antigen presentation should be improved and cytokine coadministration attempted. However, even...

  14. Quantitative criterion for quantum interference within spontaneous emission modification of a driven ladder atom

    International Nuclear Information System (INIS)

    Liu Jiaren; Zhang Zhiyi; Xiao George; Grover, C P

    2003-01-01

    The spontaneous emission spectrum of a ladder three-level atom with an upper transition driven by a coherent field is calculated under a universal model where various decays, any incoherent pumping and coherent driving are taken into account. The analytical expression for the spectrum profile is given on the basis of the quantum regression theorem. To our knowledge, it is the first time that the quantitative criterion condition Ω ab - γ ac vertical bar, under which quantum destructive interference induced by the coherent driving field occurs, is deduced for the modification of spontaneous emission from the middle level to the ground level. The roles and limits of incoherent pumping, coherent driving and experimental configuration are discussed for realizing the quantum interference and reducing the Doppler effects

  15. Molecular study for the sex identification in Japanese quails ...

    African Journals Online (AJOL)

    use

    2011-12-14

    Dec 14, 2011 ... The aim of this study was to determine the sex of. Japanese quail (Coturnix japonica) by DNA analysis. Chromo ... M, 100 bp DNA ladder (Fermentas, Germany); lane 1, negative control. (without DNA) .... low cost and reduced risk of contamination, and preven- .... Improving the reliability of molecular sexing.

  16. Transport properties of poly(GACT)–poly(CTGA)

    Indian Academy of Sciences (India)

    In this paper, based on the tight-binding Hamiltonian model and within the framework of a generalized Green's function technique, the electronic conduction through the poly(GACT)–poly(CTGA) DNA molecule in SWNT/DNA/SWNT structure has been numerically investigated. In a ladder model, we consider DNA as a ...

  17. Programmed cell death of tobacco BY-2 cells induced by still culture conditions is affected by the age of the culture under agitation.

    Science.gov (United States)

    Hiraga, Asahi; Kaneta, Tsuyoshi; Sato, Yasushi; Sato, Seiichi

    2010-01-25

    Evans Blue staining indicated that actively growing tobacco BY-2 cells in the exponential phase died more rapidly than quiescent cells in the stationary phase when the cells cultured under agitation were placed under still conditions. Fifty percent cell death was induced at about 18, 26, 80 and 140 h for early, mid, late exponential- and stationary-phase cells, respectively. Actively growing cells became TUNEL (transferase-mediated dUTP nick end labelling)-positive more rapidly than quiescent cells, suggesting that the cell death evaluated by Evans Blue is accompanied by DNA cleavages. Electrophoresis of genomic DNA showed a typical 'DNA laddering' pattern formed by multiples of about 200 bp internucleosomal units. Chromatin condensation was first detected at least within 24 h by light microscopy, and then cell shrinkage followed. These findings suggest that the death of BY-2 cells induced by still conditions is PCD (programmed cell death).

  18. Correlation of MFOLD-predicted DNA secondary structures with separation patterns obtained by capillary electrophoresis single-strand conformation polymorphism (CE-SSCP) analysis.

    Science.gov (United States)

    Glavac, Damjan; Potocnik, Uros; Podpecnik, Darja; Zizek, Teofil; Smerkolj, Sava; Ravnik-Glavac, Metka

    2002-04-01

    We have studied 57 different mutations within three beta-globin gene promoter fragments with sizes 52 bp, 77 bp, and 193 bp by fluorescent capillary electrophoresis CE-SSCP analysis. For each mutation and wild type, energetically most-favorable predicted secondary structures were calculated for sense and antisense strands using the MFOLD DNA-folding algorithm in order to investigate if any correlation exists between predicted DNA structures and actual CE migration time shifts. The overall CE-SSCP detection rate was 100% for all mutations in three studied DNA fragments. For shorter 52 bp and 77 bp DNA fragments we obtained a positive correlation between the migration time shifts and difference in free energy values of predicted secondary structures at all temperatures. For longer 193 bp beta-globin gene fragments with 46 mutations MFOLD predicted different secondary structures for 89% of mutated strands at 25 degrees C and 40 degrees C. However, the magnitude of the mobility shifts did not necessarily correlate with their secondary structures and free energy values except for the sense strand at 40 degrees C where this correlation was statistically significant (r = 0.312, p = 0.033). Results of this study provided more direct insight into the mechanism of CE-SSCP and showed that MFOLD prediction could be helpful in making decisions about the running temperatures and in prediction of CE-SSCP data patterns, especially for shorter (50-100 bp) DNA fragments. Copyright 2002 Wiley-Liss, Inc.

  19. Meta-Analysis of Mitochondrial DNA Variation in the Iberian Peninsula.

    Directory of Open Access Journals (Sweden)

    Ruth Barral-Arca

    Full Text Available The Iberian Peninsula has been the focus of attention of numerous studies dealing with mitochondrial DNA (mtDNA variation, most of them targeting the control region segment. In the present study we sequenced the control region of 3,024 Spanish individuals from areas where available data were still limited. We also compiled mtDNA haplotypes from the literature involving 4,588 sequences and 28 population groups or small regions. We meta-analyzed all these data in order to shed further light on patterns of geographic variation, taking advantage of the large sample size and geographic coverage, in contrast with the atomized sampling strategy of previous work. The results indicate that the main mtDNA haplogroups show primarily clinal geographic patterns across the Iberian geography, roughly along a North-South axis. Haplogroup HV0 (where haplogroup U is nested is more prevalent in the Franco Cantabrian region, in good agreement with previous findings that identified this area as a climate refuge during the Last Glacial Maximum (LGM, prior to a subsequent demographic re-expansion towards Central Europe and the Mediterranean. Typical sub-Saharan and North African lineages are slightly more prevalent in South Iberia, although at low frequencies; this pattern has been shaped mainly by the transatlantic slave trade and the Arab invasion of the Iberian Peninsula. The results also indicate that summary statistics that aim to measure molecular variation, or AMOVA, have limited sensitivity to detect population substructure, in contrast to patterns revealed by phylogeographic analysis. Overall, the results suggest that mtDNA variation in Iberia is substantially stratified. These patterns might be relevant in biomedical studies given that stratification is a common cause of false positives in case-control mtDNA association studies, and should be also considered when weighting the DNA evidence in forensic casework, which is strongly dependent on haplotype

  20. Meta-Analysis of Mitochondrial DNA Variation in the Iberian Peninsula.

    Science.gov (United States)

    Barral-Arca, Ruth; Pischedda, Sara; Gómez-Carballa, Alberto; Pastoriza, Ana; Mosquera-Miguel, Ana; López-Soto, Manuel; Martinón-Torres, Federico; Álvarez-Iglesias, Vanesa; Salas, Antonio

    2016-01-01

    The Iberian Peninsula has been the focus of attention of numerous studies dealing with mitochondrial DNA (mtDNA) variation, most of them targeting the control region segment. In the present study we sequenced the control region of 3,024 Spanish individuals from areas where available data were still limited. We also compiled mtDNA haplotypes from the literature involving 4,588 sequences and 28 population groups or small regions. We meta-analyzed all these data in order to shed further light on patterns of geographic variation, taking advantage of the large sample size and geographic coverage, in contrast with the atomized sampling strategy of previous work. The results indicate that the main mtDNA haplogroups show primarily clinal geographic patterns across the Iberian geography, roughly along a North-South axis. Haplogroup HV0 (where haplogroup U is nested) is more prevalent in the Franco Cantabrian region, in good agreement with previous findings that identified this area as a climate refuge during the Last Glacial Maximum (LGM), prior to a subsequent demographic re-expansion towards Central Europe and the Mediterranean. Typical sub-Saharan and North African lineages are slightly more prevalent in South Iberia, although at low frequencies; this pattern has been shaped mainly by the transatlantic slave trade and the Arab invasion of the Iberian Peninsula. The results also indicate that summary statistics that aim to measure molecular variation, or AMOVA, have limited sensitivity to detect population substructure, in contrast to patterns revealed by phylogeographic analysis. Overall, the results suggest that mtDNA variation in Iberia is substantially stratified. These patterns might be relevant in biomedical studies given that stratification is a common cause of false positives in case-control mtDNA association studies, and should be also considered when weighting the DNA evidence in forensic casework, which is strongly dependent on haplotype frequencies.

  1. Mitochondrial DNA inheritance in the human fungal pathogen Cryptococcus gattii.

    Science.gov (United States)

    Wang, Zixuan; Wilson, Amanda; Xu, Jianping

    2015-02-01

    The inheritance of mitochondrial DNA (mtDNA) is predominantly uniparental in most sexual eukaryotes. In this study, we examined the mitochondrial inheritance pattern of Cryptococcus gattii, a basidiomycetous yeast responsible for the recent and ongoing outbreak of cryptococcal infections in the US Pacific Northwest and British Columbia (especially Vancouver Island) in Canada. Using molecular markers, we analyzed the inheritance of mtDNA in 14 crosses between strains within and between divergent lineages in C. gattii. Consistent with results from recent studies, our analyses identified significant variations in mtDNA inheritance patterns among strains and crosses, ranging from strictly uniparental to biparental. For two of the crosses that showed uniparental mitochondrial inheritance in standard laboratory conditions, we further investigated the effects of the following environmental variables on mtDNA inheritance: UV exposure, temperature, and treatments with the methylation inhibitor 5-aza-2'-deoxycytidine and with the ubiquitination inhibitor ammonium chloride. Interestingly, one of these crosses showed no response to these environmental variables while the other exhibited diverse patterns ranging from complete uniparental inheritance of the MATa parent mtDNA, to biparental inheritance, and to a significant bias toward inheritance of the MATα parental mtDNA. Our results indicate that mtDNA inheritance in C. gattii differs from that in its closely related species Cryptococcus neoformans. Copyright © 2015 Elsevier Inc. All rights reserved.

  2. Discovering approximate-associated sequence patterns for protein-DNA interactions

    KAUST Repository

    Chan, Tak Ming; Wong, Ka Chun; Lee, Kin Hong; Wong, Man Hon; Lau, Chi Kong; Tsui, Stephen Kwok Wing; Leung, Kwong Sak

    2010-01-01

    Motivation: The bindings between transcription factors (TFs) and transcription factor binding sites (TFBSs) are fundamental protein-DNA interactions in transcriptional regulation. Extensive efforts have been made to better understand the protein

  3. Disorder effects in the S=1 antiferromagnetic spin ladder CaV{sub 2}O{sub 4}

    Energy Technology Data Exchange (ETDEWEB)

    Guitarra, S.R. [Colegio de Ciencias e Ingeniería, Universidad San Francisco de Quito, Quito (Ecuador); Caneiro, A. [Instituto Balseiro - Centro Atómico Bariloche, 8400 Bariloche (Argentina); Niebieskikwiat, D., E-mail: dniebieskikwiat@usfq.edu.ec [Colegio de Ciencias e Ingeniería, Universidad San Francisco de Quito, Quito (Ecuador)

    2015-10-15

    We study the physical properties of the antiferromagnetic spin ladder CaV{sub 2}O{sub 4} (CVO) and the Y-doped related compound Ca{sub 0.9}Y{sub 0.1}V{sub 2}O{sub 4}. In the latter, X-ray diffraction demonstrates the segregation of a small amount of a vanadium–perovskite impurity phase, leading to the formation of V vacancies within the main CVO-type structure. The 1D character of this calcium–vanadite enhances the influence of the vacancies on the electric and magnetic properties of Ca{sub 0.9}Y{sub 0.1}V{sub 2}O{sub 4}. Electrical transport is characterized by a variable-range hopping mechanism determined by the charging energy of nm-sized segments of V chains delimited by V vacancies, i.e. a Coulomb gap is formed at the Fermi level. These vacancies also locally affect the magnetic correlations, breaking the long-range AFM order observed in CaV{sub 2}O{sub 4} and producing exchange bias when the Y-doped sample is cooled with an applied magnetic field. - Highlights: • We study disorder effects in the quasi-1D antiferromagnetic spin ladder CaV{sub 2}O{sub 4}. • V vacancies in CaV{sub 2}O{sub 4} lead to variable-range hopping electrical transport. • The charging energy of nm-sized V chains determine the transport mechanism exponents. • V vacancies break the long-range AFM order of CaV{sub 2}O{sub 4}. • Local magnetic correlations in the vicinity of the defects produce exchange bias.

  4. DNA typing from skeletal remains following an explosion in a military fort--first experience in Ecuador (South-America).

    Science.gov (United States)

    González-Andrade, Fabricio; Sánchez, Dora

    2005-10-01

    We present individual body identification efforts, to identify skeletal remains and relatives of missing persons of an explosion took place inside one of the munitions recesses of the Armoured Brigade of the Galapagos Armoured Cavalry, in the city of Riobamba, Ecuador, on Wednesday, November 20, 2002. Nineteen samples of bone remains and two tissue samples (a blood stain on a piece of fabric) from the zero zone were analysed. DNA extraction was made by Isoamilic Phenol-Chloroform-Alcohol, and proteinase K. We increased PCR cycles to identify DNA from bones to 35 cycles in some cases. An ABI 310 sequencer was used. Determination of the fragment size and the allelic designation of the different loci was carried out by comparison with the allelic ladders of the PowerPlex 16 kit and Gene Scan Analysis Software programme. Five possible family groups were established and were compared with the profiles found. Classical Bayesian methods were used to calculate the Likelihood Ratio and it was possible to identify five different genetic profiles in our country. This paper is important because is a novel experience for our forensic services, because this was the first time DNA had been used as an identification method in disasters, and it was validated by Ecuadorian justice like a very effective method.

  5. Frustrated S = 1/2 Two-Leg Ladder with Different Leg Interactions

    Science.gov (United States)

    Tonegawa, Takashi; Okamoto, Kiyomi; Hikihara, Toshiya; Sakai, Tôru

    2017-04-01

    We explore the ground-state phase diagram of the S = 1/2 two-leg ladder. The isotropic leg interactions J1,a and J1,b between nearest neighbor spins in the legs a and b, respectively, are different from each other. The xy and z components of the uniform rung interactions are denoted by Jr and ΔJr, respectively, where Δ is the XXZ anisotropy parameter. This system has a frustration when J1,aJ1,b employ the physical consideration, the level spectroscopy analysis of the results obtained by the exact diagonalization method and also the density-matrix renormalization-group method. It is found that the non-collinear ferrimagnetic (NCFR) state appears as the ground state in the frustrated region of the parameters. Furthermore, the direct-product triplet-dimer (TD) state in which all rungs form the TD pair is the exact ground state, when J1,a + J1,b = 0 and 0≤ Δ ≲ 0.83. The obtained phase diagrams consist of the TD, XY and Haldane phases as well as the NCFR phase.

  6. Comparison of checkpoint responses triggered by DNA polymerase inhibition versus DNA damaging agents

    International Nuclear Information System (INIS)

    Liu, J.-S.; Kuo, S.-R.; Melendy, Thomas

    2003-01-01

    To better understand the different cellular responses to replication fork pausing versus blockage, early DNA damage response markers were compared after treatment of cultured mammalian cells with agents that either inhibit DNA polymerase activity (hydroxyurea (HU) or aphidicolin) or selectively induce S-phase DNA damage responses (the DNA alkylating agents, methyl methanesulfonate (MMS) and adozelesin). These agents were compared for their relative abilities to induce phosphorylation of Chk1, H2AX, and replication protein A (RPA), and intra-nuclear focalization of γ-H2AX and RPA. Treatment by aphidicolin and HU resulted in phosphorylation of Chk1, while HU, but not aphidicolin, induced focalization of γ-H2AX and RPA. Surprisingly, pre-treatment with aphidicolin to stop replication fork progression, did not abrogate HU-induced γ-H2AX and RPA focalization. This suggests that HU may act on the replication fork machinery directly, such that fork progression is not required to trigger these responses. The DNA-damaging fork-blocking agents, adozelesin and MMS, both induced phosphorylation and focalization of H2AX and RPA. Unlike adozelesin and HU, the pattern of MMS-induced RPA focalization did not match the BUdR incorporation pattern and was not blocked by aphidicolin, suggesting that MMS-induced damage is not replication fork-dependent. In support of this, MMS was the only reagent used that did not induce phosphorylation of Chk1. These results indicate that induction of DNA damage checkpoint responses due to adozelesin is both replication fork and fork progression dependent, induction by HU is replication fork dependent but progression independent, while induction by MMS is independent of both replication forks and fork progression

  7. Comparison of checkpoint responses triggered by DNA polymerase inhibition versus DNA damaging agents

    Energy Technology Data Exchange (ETDEWEB)

    Liu, J.-S.; Kuo, S.-R.; Melendy, Thomas

    2003-11-27

    To better understand the different cellular responses to replication fork pausing versus blockage, early DNA damage response markers were compared after treatment of cultured mammalian cells with agents that either inhibit DNA polymerase activity (hydroxyurea (HU) or aphidicolin) or selectively induce S-phase DNA damage responses (the DNA alkylating agents, methyl methanesulfonate (MMS) and adozelesin). These agents were compared for their relative abilities to induce phosphorylation of Chk1, H2AX, and replication protein A (RPA), and intra-nuclear focalization of {gamma}-H2AX and RPA. Treatment by aphidicolin and HU resulted in phosphorylation of Chk1, while HU, but not aphidicolin, induced focalization of {gamma}-H2AX and RPA. Surprisingly, pre-treatment with aphidicolin to stop replication fork progression, did not abrogate HU-induced {gamma}-H2AX and RPA focalization. This suggests that HU may act on the replication fork machinery directly, such that fork progression is not required to trigger these responses. The DNA-damaging fork-blocking agents, adozelesin and MMS, both induced phosphorylation and focalization of H2AX and RPA. Unlike adozelesin and HU, the pattern of MMS-induced RPA focalization did not match the BUdR incorporation pattern and was not blocked by aphidicolin, suggesting that MMS-induced damage is not replication fork-dependent. In support of this, MMS was the only reagent used that did not induce phosphorylation of Chk1. These results indicate that induction of DNA damage checkpoint responses due to adozelesin is both replication fork and fork progression dependent, induction by HU is replication fork dependent but progression independent, while induction by MMS is independent of both replication forks and fork progression.

  8. Development of salt-tolerance interface for an high performance liquid chromatography/inductively coupled plasma mass spectrometry system and its application to accurate quantification of DNA samples.

    Science.gov (United States)

    Takasaki, Yuka; Sakagawa, Shinnosuke; Inagaki, Kazumi; Fujii, Shin-Ichiro; Sabarudin, Akhmad; Umemura, Tomonari; Haraguchi, Hiroki

    2012-02-03

    Accurate quantification of DNA is highly important in various fields. Determination of phosphorus by ICP-MS is one of the most effective methods for accurate quantification of DNA due to the fixed stoichiometry of phosphate to this molecule. In this paper, a smart and reliable method for accurate quantification of DNA fragments and oligodeoxythymidilic acids by hyphenated HPLC/ICP-MS equipped with a highly efficient interface device is presented. The interface was constructed of a home-made capillary-attached micronebulizer and temperature-controllable cyclonic spray chamber (IsoMist). As a separation column for DNA samples, home-made methacrylate-based weak anion-exchange monolith was employed. Some parameters, which include composition of mobile phase, gradient program, inner and outer diameters of capillary, temperature of spray chamber etc., were optimized to find the best performance for separation and accurate quantification of DNA samples. The proposed system could achieve many advantages, such as total consumption for small amount sample analysis, salt-tolerance for hyphenated analysis, high accuracy and precision for quantitative analysis. Using this proposed system, the samples of 20 bp DNA ladder (20, 40, 60, 80, 100, 120, 140, 160, 180, 200, 300, 400, 500 base pairs) and oligodeoxythymidilic acids (dT(12-18)) were rapidly separated and accurately quantified. Copyright © 2011 Elsevier B.V. All rights reserved.

  9. Impact of age, BMI and HbA1c levels on the genome-wide DNA methylation and mRNA expression patterns in human adipose tissue and identification of epigenetic biomarkers in blood

    DEFF Research Database (Denmark)

    Rönn, Tina; Volkov, Petr; Gillberg, Linn

    2015-01-01

    Increased age, BMI and HbA1c levels are risk factors for several non-communicable diseases. However, the impact of these factors on the genome-wide DNA methylation pattern in human adipose tissue remains unknown. We analyzed the DNA methylation of ∼480 000 sites in human adipose tissue from 96 ma...

  10. DNA sensor cGAS-mediated immune recognition

    Directory of Open Access Journals (Sweden)

    Pengyan Xia

    2016-09-01

    Full Text Available Abstract The host takes use of pattern recognition receptors (PRRs to defend against pathogen invasion or cellular damage. Among microorganism-associated molecular patterns detected by host PRRs, nucleic acids derived from bacteria or viruses are tightly supervised, providing a fundamental mechanism of host defense. Pathogenic DNAs are supposed to be detected by DNA sensors that induce the activation of NFκB or TBK1-IRF3 pathway. DNA sensor cGAS is widely expressed in innate immune cells and is a key sensor of invading DNAs in several cell types. cGAS binds to DNA, followed by a conformational change that allows the synthesis of cyclic guanosine monophosphate–adenosine monophosphate (cGAMP from adenosine triphosphate and guanosine triphosphate. cGAMP is a strong activator of STING that can activate IRF3 and subsequent type I interferon production. Here we describe recent progresses in DNA sensors especially cGAS in the innate immune responses against pathogenic DNAs.

  11. Correlation of DNA Ploidy with Progression of Cervical Cancer

    International Nuclear Information System (INIS)

    Singh, M.; Kalra, N.; Shukla, Y.; Mehrotra, S.; Singh, U.

    2008-01-01

    The majority of squamous cell carcinomas of cervix are preceded by visible changes in the cervix, most often detected by cervical smear. As cervical cancer is preceded by long precancerous stages, identification of the high-risk population through detection of DNA ploidy may be of importance in effective management of this disease. Here we attempted to correlate aneuploidy DNA patterns and their influence on biological behavior of flow-cytometry analysis of DNA ploidy which was carried out in cytologically diagnosed cases of mild (79), moderate (36), and severe (12) dysplasia, as well as “atypical squamous cells of unknown significance (ASCUS)” (57) along with controls (69), in order to understand its importance in malignant progression of disease. Cytologically diagnosed dysplasias, which were employed for DNA ploidy studies, 39 mild, 28 moderate, and 11 severe dysplasia cases were found to be aneuploidy. Out of the 69 control subjects, 6 cases showed aneuploidy pattern and the rest 63 subjects were diploid. An aneuploidy pattern was observed in 8 out of 57 cases of cytologically evaluated ASCUS. The results of the followup studies showed that aberrant DNA content reliably predicts the occurrence of squamous cell carcinoma in cervical smear. Flow cytometric analysis of DNA ploidy may provide a strategic diagnostic tool for early detection of carcinoma cervix. Therefore, it is a concept of an HPV screening with reflex cytology in combination with DNA flow cytometry to detect progressive lesions with the greatest possible sensitivity and specificity.

  12. Gene expression patterns of oxidative phosphorylation complex I subunits are organized in clusters.

    Directory of Open Access Journals (Sweden)

    Yael Garbian

    Full Text Available After the radiation of eukaryotes, the NUO operon, controlling the transcription of the NADH dehydrogenase complex of the oxidative phosphorylation system (OXPHOS complex I, was broken down and genes encoding this protein complex were dispersed across the nuclear genome. Seven genes, however, were retained in the genome of the mitochondrion, the ancient symbiote of eukaryotes. This division, in combination with the three-fold increase in subunit number from bacteria (N = approximately 14 to man (N = 45, renders the transcription regulation of OXPHOS complex I a challenge. Recently bioinformatics analysis of the promoter regions of all OXPHOS genes in mammals supported patterns of co-regulation, suggesting that natural selection favored a mechanism facilitating the transcriptional regulatory control of genes encoding subunits of these large protein complexes. Here, using real time PCR of mitochondrial (mtDNA- and nuclear DNA (nDNA-encoded transcripts in a panel of 13 different human tissues, we show that the expression pattern of OXPHOS complex I genes is regulated in several clusters. Firstly, all mtDNA-encoded complex I subunits (N = 7 share a similar expression pattern, distinct from all tested nDNA-encoded subunits (N = 10. Secondly, two sub-clusters of nDNA-encoded transcripts with significantly different expression patterns were observed. Thirdly, the expression patterns of two nDNA-encoded genes, NDUFA4 and NDUFA5, notably diverged from the rest of the nDNA-encoded subunits, suggesting a certain degree of tissue specificity. Finally, the expression pattern of the mtDNA-encoded ND4L gene diverged from the rest of the tested mtDNA-encoded transcripts that are regulated by the same promoter, consistent with post-transcriptional regulation. These findings suggest, for the first time, that the regulation of complex I subunits expression in humans is complex rather than reflecting global co-regulation.

  13. Natural Larval Diet Differently Influences the Pattern of Developmental Changes in DNA 5-Methylcytosine Levels in Apis mellifera Queens as Compared with Workers and Drones.

    Science.gov (United States)

    Strachecka, A; Olszewski, K; Bajda, M; Demetraki-Paleolog, J

    2015-08-01

    The principal mechanism of gene activation/silencing is DNA 5-methylcytosine methylation. This study was aimed at determining global DNA methylation levels in larvae, prepupae, pupae, and 1-day-old adults of Apis mellifera queens, workers and drones. The Imprint Methylated DNA Quantification Kit MDQ1 was used. Percentages of DNA 5-methylcytosine were low and relatively similar in the larvae of all the castes until 4th day of larval development (3-5%). However, they were higher in the drone and worker larvae than in the queen larvae. Generally, the developmental patterns of changes in the DNA methylation levels were different in the queens in comparison with the drones and workers. While methylation increased in the queens, it decreased in the drones and workers. Methylated DNA methylcytosine percentages and weights in the queen prepupae (15%, 9.18 ng) and pupae (21%, 10.74 ng) were, respectively, three and four times higher than in the worker/drone brood of the same age (2.5-4%, 0.03-0.07 ng). Only in the queens, after a substantial increase, did DNA methylation decrease almost twice between the pupal stage and queen emergence (from 21% and 10.74 ng to 12% and 6.78 ng). This finding seems very interesting, particularly for experimental gerontology.

  14. DNA methylation and memory formation.

    Science.gov (United States)

    Day, Jeremy J; Sweatt, J David

    2010-11-01

    Memory formation and storage require long-lasting changes in memory-related neuronal circuits. Recent evidence indicates that DNA methylation may serve as a contributing mechanism in memory formation and storage. These emerging findings suggest a role for an epigenetic mechanism in learning and long-term memory maintenance and raise apparent conundrums and questions. For example, it is unclear how DNA methylation might be reversed during the formation of a memory, how changes in DNA methylation alter neuronal function to promote memory formation, and how DNA methylation patterns differ between neuronal structures to enable both consolidation and storage of memories. Here we evaluate the existing evidence supporting a role for DNA methylation in memory, discuss how DNA methylation may affect genetic and neuronal function to contribute to behavior, propose several future directions for the emerging subfield of neuroepigenetics, and begin to address some of the broader implications of this work.

  15. Differential DNA methylation patterns define status epilepticus and epileptic tolerance.

    Science.gov (United States)

    Miller-Delaney, Suzanne F C; Das, Sudipto; Sano, Takanori; Jimenez-Mateos, Eva M; Bryan, Kenneth; Buckley, Patrick G; Stallings, Raymond L; Henshall, David C

    2012-02-01

    Prolonged seizures (status epilepticus) produce pathophysiological changes in the hippocampus that are associated with large-scale, wide-ranging changes in gene expression. Epileptic tolerance is an endogenous program of cell protection that can be activated in the brain by previous exposure to a non-harmful seizure episode before status epilepticus. A major transcriptional feature of tolerance is gene downregulation. Here, through methylation analysis of 34,143 discrete loci representing all annotated CpG islands and promoter regions in the mouse genome, we report the genome-wide DNA methylation changes in the hippocampus after status epilepticus and epileptic tolerance in adult mice. A total of 321 genes showed altered DNA methylation after status epilepticus alone or status epilepticus that followed seizure preconditioning, with >90% of the promoters of these genes undergoing hypomethylation. These profiles included genes not previously associated with epilepsy, such as the polycomb gene Phc2. Differential methylation events generally occurred throughout the genome without bias for a particular chromosomal region, with the exception of a small region of chromosome 4, which was significantly overrepresented with genes hypomethylated after status epilepticus. Surprisingly, only few genes displayed differential hypermethylation in epileptic tolerance. Nevertheless, gene ontology analysis emphasized the majority of differential methylation events between the groups occurred in genes associated with nuclear functions, such as DNA binding and transcriptional regulation. The present study reports select, genome-wide DNA methylation changes after status epilepticus and in epileptic tolerance, which may contribute to regulating the gene expression environment of the seizure-damaged hippocampus.

  16. DNA-scaffolded nanoparticle structures

    Energy Technology Data Exchange (ETDEWEB)

    Hoegberg, Bjoern; Olin, Haakan [Department of Engineering Physics and Mathematics, Mid Sweden University, SE-851 70 Sundsvall, Sweden (Sweden)

    2007-03-15

    DNA self-assembly is a powerful route to the production of very small, complex structures. When used in combination with nanoparticles it is likely to become a key technology in the production of nanoelectronics in the future. Previously, demonstrated nanoparticle assemblies have mainly been periodic and highly symmetric arrays, unsuited as building blocks for any complex circuits. With the invention of DNA-scaffolded origami reported earlier this year (Rothemund P W K 2006 Nature 440 (7082) 297-302), a new route to complex nanostructures using DNA has been opened. Here, we give a short review of the field and present the current status of our experiments were DNA origami is used in conjunction with nanoparticles. Gold nanoparticles are functionalized with thiolated single stranded DNA. Strands that are complementary to the gold particle strands can be positioned on the self-assembled DNA-structure in arbitrary patterns. This property should allow an accurate positioning of the particles by letting them hybridize on the lattice. We report on our recent experiments on this system and discuss open problems and future applications.

  17. DNA-scaffolded nanoparticle structures

    International Nuclear Information System (INIS)

    Hoegberg, Bjoern; Olin, Haakan

    2007-01-01

    DNA self-assembly is a powerful route to the production of very small, complex structures. When used in combination with nanoparticles it is likely to become a key technology in the production of nanoelectronics in the future. Previously, demonstrated nanoparticle assemblies have mainly been periodic and highly symmetric arrays, unsuited as building blocks for any complex circuits. With the invention of DNA-scaffolded origami reported earlier this year (Rothemund P W K 2006 Nature 440 (7082) 297-302), a new route to complex nanostructures using DNA has been opened. Here, we give a short review of the field and present the current status of our experiments were DNA origami is used in conjunction with nanoparticles. Gold nanoparticles are functionalized with thiolated single stranded DNA. Strands that are complementary to the gold particle strands can be positioned on the self-assembled DNA-structure in arbitrary patterns. This property should allow an accurate positioning of the particles by letting them hybridize on the lattice. We report on our recent experiments on this system and discuss open problems and future applications

  18. Apoptotic induction activity of Dactyloctenium aegyptium (L. P.B. and Eleusine indica (L. Gaerth. extracts on human lung and cervical cancer cell lines

    Directory of Open Access Journals (Sweden)

    Pintusorn Hansakul

    2009-08-01

    Full Text Available Dactyloctenium aegyptium (L. P.B. (Yaa paak khwaai and Eleusine indica (L. Gaerth. (Yaa teen-ka have long been used in traditional Thai medicine because of their diuretic, anti-inflamatory, and antipyretic effects. The present study examined the antiproliferative and cytotoxic effects of the hexane and butanolic extracts of these two grass species. All the grass extracts exhibited selective growth inhibition effect on human lung cancer (A549 and cervical cancer (HeLa cells relative to normal human lung MRC-5 fibroblasts with IC50 values in a range of 202 to 845 mg/ml. Apparently, HeLa cellswere more sensitive to the extracts than A549 cells. Moreover, all the extracts induced lethality in both cancer cell lines atconcentrations close to 1,000 mg/ml, indicating their selective cytotoxicity effects. ELISA assay showed that only the hexaneextract of D. aegyptium (L. P.B. and E. indica (L. Gaerth. significantly increased the apoptotic level in extract-treatedA549 cells. However, DNA ladder assay detected classic DNA ladder patterns, a characteristic feature of apoptosis, in both cancer cell lines treated with all the extracts in a dose- and time-dependent manner. Taken together, these results indicatethat the cytotoxic activity of the grass extracts against lung and cervical cancer cells is mediated through the induction ofapoptosis.

  19. Array patterns and clones - RMOS | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us RMOS Array patterns and clones Data detail Data name Array patterns and clones DOI 10.18908/...lsdba.nbdc00194-002 Description of data contents Static files of array patterns and cDNA clones. Data file F...h rice cDNA comprises a pair of glass slides. The microarray patterns are shown i...escription Download License Update History of This Database Site Policy | Contact Us Array patterns and clones - RMOS | LSDB Archive ...

  20. The su(1, 1) dynamical algebra from the Schroedinger ladder operators for N-dimensional systems: hydrogen atom, Mie-type potential, harmonic oscillator and pseudo-harmonic oscillator

    International Nuclear Information System (INIS)

    Martinez, D; Flores-Urbina, J C; Mota, R D; Granados, V D

    2010-01-01

    We apply the Schroedinger factorization to construct the ladder operators for the hydrogen atom, Mie-type potential, harmonic oscillator and pseudo-harmonic oscillator in arbitrary dimensions. By generalizing these operators we show that the dynamical algebra for these problems is the su(1, 1) Lie algebra.

  1. RRR-alpha-tocopheryl succinate inhibits EL4 thymic lymphoma cell growth by inducing apoptosis and DNA synthesis arrest.

    Science.gov (United States)

    Yu, W; Sanders, B G; Kline, K

    1997-01-01

    RRR-alpha-tocopheryl succinate (vitamin E succinate, VES) treatment of murine EL4 T lymphoma cells induced the cells to undergo apoptosis. After 48 hours of VES treatment at 20 micrograms/ml, 95% of cells were apoptotic. Evidence for the induction of apoptosis by VES treatments is based on staining of DNA for detection of chromatin condensation/fragmentation, two-color flow-cytometric analyses of DNA content, and end-labeled DNA and electrophoretic analyses for detection of DNA ladder formation. VES-treated EL4 cells were blocked in the G1 cell cycle phase; however, apoptotic cells came from all cell cycle phases. Analyses of mRNA expression of genes involved in apoptosis revealed decreased c-myc and increased bcl-2, c-fos, and c-jun mRNAs within three to six hours after treatment. Western analyses showed increased c-Jun, c-Fos, and Bcl-2 protein levels. Electrophoretic mobility shift assays showed increased AP-1 binding at 6, 12, and 24 hours after treatment and decreased c-Myc binding after 12 and 24 hours of VES treatment. Treatments of EL4 cells with VES+RRR-alpha-to-copherol reduced apoptosis without effecting DNA synthesis arrest. Treatments of EL4 cells with VES+rac-6-hydroxyl-2, 5,7,8-tetramethyl-chroman-2-carboxylic acid, butylated hydroxytoluene, or butylated hydroxyanisole had no effect on apoptosis or DNA synthesis arrest caused by VES treatments. Analyses of bcl-2, c-myc, c-jun, and c-fos mRNA levels in cells receiving VES + RRR-alpha-tocopherol treatments showed no change from cells receiving VES treatments alone, implying that these changes are correlated with VES treatments but are not causal for apoptosis. However, treatments with VES + RRR-alpha-tocopherol decreased AP-1 binding to consensus DNA oligomer, suggesting AP-1 involvement in apoptosis induced by VES treatments.

  2. Programmed self-assembly of DNA/RNA for biomedical applications

    Science.gov (United States)

    Wang, Pengfei

    Three self-assembly strategies were utilized for assembly of novel functional DNA/RNA nanostructures. RNA-DNA hybrid origami method was developed to fabricate nano-objects (ribbon, rectangle, and triangle) with precisely controlled geometry. Unlike conventional DNA origami which use long DNA single strand as scaffold, a long RNA single strand was used instead, which was folded by short DNA single strands (staples) into prescribed objects through sequence specific hybridization between RNA and DNA. Single stranded tiles (SST) and RNA-DNA hybrid origami were utilized to fabricate a variety of barcode-like nanostructures with unique patterns by expanding a plain rectangle via introducing spacers (10-bp dsDNA segment) between parallel duplexes. Finally, complex 2D array and 3D polyhedrons with multiple patterns within one structure were assembled from simple DNA motifs. Two demonstrations of biomedical applications of DNA nanotechnology were presented. Firstly, lambda-DNA was used as template to direct the fabrication of multi-component magnetic nanoparticle chains. Nuclear magnetic relaxation (NMR) characterization showed superb magnetic relaxativity of the nanoparticle chains which have large potential to be utilized as MRI contrast agents. Secondly, DNA nanotechnology was introduced into the conformational study of a routinely used catalytic DNAzyme, the RNA-cleaving 10-23 DNAzyme. The relative angle between two flanking duplexes of the catalytic core was determined (94.8°), which shall be able to provide a clue to further understanding of the cleaving mechanism of this DNAzyme from a conformational perspective.

  3. DNA methylation patterns provide insight into epigenetic regulation in the Pacific oyster (Crassostrea gigas

    Directory of Open Access Journals (Sweden)

    Gavery Mackenzie R

    2010-08-01

    Full Text Available Abstract Background DNA methylation is an epigenetic mechanism with important regulatory functions in animals. While the mechanism itself is evolutionarily ancient, the distribution and function of DNA methylation is diverse both within and among phylogenetic groups. Although DNA methylation has been well studied in mammals, there are limited data on invertebrates, particularly molluscs. Here we characterize the distribution and investigate potential functions of DNA methylation in the Pacific oyster (Crassostrea gigas. Results Methylation sensitive PCR and bisulfite sequencing PCR approaches were used to identify CpG methylation in C. gigas genes and demonstrated that this species possesses intragenic methylation. In silico analysis of CpGo/e ratios in publicly available sequence data suggests that DNA methylation is a common feature of the C. gigas genome, and that specific functional categories of genes have significantly different levels of methylation. Conclusions The Pacific oyster genome displays intragenic DNA methylation and contains genes necessary for DNA methylation in animals. Results of this investigation suggest that DNA methylation has regulatory functions in Crassostrea gigas, particularly in gene families that have inducible expression, including those involved in stress and environmental responses.

  4. Programmed Switching of Single Polymer Conformation on DNA Origami

    DEFF Research Database (Denmark)

    Krissanaprasit, Abhichart; Madsen, Mikael; Knudsen, Jakob Bach

    2016-01-01

    -molecule conjugated polymer. The polymer is functionalized with short single-stranded (ss) DNA strands that extend from the backbone of the polymer and serve as handles. The DNA polymer conjugate can be aligned on DNA origami in three well-defined geometries (straight line, left-turned, and right-turned pattern......) by DNA hybridization directed by single-stranded guiding strands and ssDNA tracks extending from the origami surface and polymer handle. We demonstrate switching of a conjugated organic polymer conformation between left- and right-turned conformations of the polymer on DNA origami based on toehold...

  5. Polymerase spiral reaction (PSR): a novel, visual isothermal amplification method for detection of canine parvovirus 2 genomic DNA.

    Science.gov (United States)

    Gupta, Vikas; Chakravarti, Soumendu; Chander, Vishal; Majumder, Saurabh; Bhat, Shabir Ahmad; Gupta, Vivek Kumar; Nandi, Sukdeb

    2017-07-01

    Canine parvovirus-2 (CPV-2), which is ubiquitously distributed worldwide, causes severe and often fatal gastroenteritis in dogs. Accurate, differential and rapid diagnosis of canine parvoviral enteritis remains a challenge for clinicians. A recently developed isothermal amplification technique, polymerase spiral reaction (PSR), was optimized for the first time for a viral pathogen with reference recombinant plasmid standards from different CPV-2 antigenic variants (CPV-2, CPV-2a, CPV-2b and CPV-2c) and subsequently validated using clinical samples. Addition of chromogenic substrate SYBR Green I after the completion of the reaction resulted in bright green fluorescence in positive samples, while negative samples and a no-template control remained orange. These results were further substantiated through visualization of a laddering pattern of the PSR-amplified product in an agarose gel in positive cases and the absence of this pattern in no-template control and negative samples. The PSR assay was found to be highly specific, as it did not react with other putative canine pathogens (canine adenovirus 1 and canine distemper virus). The sensitivity of the newly developed PSR technique was compared with that of conventional PCR, real-time PCR and LAMP, using a serial tenfold dilution of canine parvovirus DNA. The detection limit of PSR was found to be at the femtogram level, which is comparable with that of real-time PCR and LAMP, which are ten times more sensitive than conventional PCR. The assay was validated using 90 clinical samples, of which 54 were found positive, while only 45 samples were positive in conventional PCR. This novel assay, which is fully compliant with the 'ASSURED' concept for disease diagnosis, provides a simple, rapid, specific, sensitive and cost-effective method for diagnosis of canine parvoviral enteritis in veterinary clinics.

  6. Infrared and swelling study of wet-spun films of DNA\\cdot[(bipy)Pt(en)]^2+ as a function of hydration

    Science.gov (United States)

    Kuebler, A.; Whitson, K. B.; Marlowe, R. L.; Lee, S. A.; Rupprecht, A.

    1997-11-01

    A ladder-like conformation of DNA has been induced by the binding of bipyridyl-Pt(II)-ethylenediamine (denoted as [(bipy)Pt(en)]^2+) at a relative humidity (RH) of 75%.(Arnott et al.,) Nature 287, (1980) 561. We report the first study of oriented films of this complex as a function of hydration by using Fourier transform infrared (IR) spectroscopy and optical microscopy. Vibrational modes between 800 and 1000 cm-1 are localized in the phosphodiester backbone and are sensitive to changes in the geometry of the molecule. The IR spectrum of this region is substantially different at 59% RH than at higher humidities, implying that a conformational change occurs as the RH is lowered below 75%. Optical microscopy measurements of small pieces of films of the complex also show changes at low RH. These trends are consistent with an order-disorder transition occurring as the RH is lowered The measurements also show that the DNA\\cdot[(bipy)Pt(en)]^2+) are very stable at the highest humidities.

  7. A Paper Model of DNA Structure and Replication.

    Science.gov (United States)

    Sigismondi, Linda A.

    1989-01-01

    A paper model which is designed to give students a hands-on experience during lecture and blackboard instruction on DNA structure is provided. A list of materials, paper patterns, and procedures for using the models to teach DNA structure and replication are given. (CW)

  8. DNA methylation profiling of embryonic stem cell differentiation into the three germ layers.

    Science.gov (United States)

    Isagawa, Takayuki; Nagae, Genta; Shiraki, Nobuaki; Fujita, Takanori; Sato, Noriko; Ishikawa, Shumpei; Kume, Shoen; Aburatani, Hiroyuki

    2011-01-01

    Embryogenesis is tightly regulated by multiple levels of epigenetic regulation such as DNA methylation, histone modification, and chromatin remodeling. DNA methylation patterns are erased in primordial germ cells and in the interval immediately following fertilization. Subsequent developmental reprogramming occurs by de novo methylation and demethylation. Variance in DNA methylation patterns between different cell types is not well understood. Here, using methylated DNA immunoprecipitation and tiling array technology, we have comprehensively analyzed DNA methylation patterns at proximal promoter regions in mouse embryonic stem (ES) cells, ES cell-derived early germ layers (ectoderm, endoderm and mesoderm) and four adult tissues (brain, liver, skeletal muscle and sperm). Most of the methylated regions are methylated across all three germ layers and in the three adult somatic tissues. This commonly methylated gene set is enriched in germ cell-associated genes that are generally transcriptionally inactive in somatic cells. We also compared DNA methylation patterns by global mapping of histone H3 lysine 4/27 trimethylation, and found that gain of DNA methylation correlates with loss of histone H3 lysine 4 trimethylation. Our combined findings indicate that differentiation of ES cells into the three germ layers is accompanied by an increased number of commonly methylated DNA regions and that these tissue-specific alterations in methylation occur for only a small number of genes. DNA methylation at the proximal promoter regions of commonly methylated genes thus appears to be an irreversible mark which functions to fix somatic lineage by repressing the transcription of germ cell-specific genes.

  9. DNA-based nanobiostructured devices: The role of quasiperiodicity and correlation effects

    Energy Technology Data Exchange (ETDEWEB)

    Albuquerque, E.L., E-mail: eudenilson@gmail.com [Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970, Natal-RN (Brazil); Fulco, U.L. [Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970, Natal-RN (Brazil); Freire, V.N. [Departamento de Física, Universidade Federal do Ceará, 60455-760, Fortaleza-CE (Brazil); Caetano, E.W.S. [Instituto Federal de Educação, Ciência e Tecnologia do Ceará, 60040-531, Fortaleza-CE (Brazil); Lyra, M.L.; Moura, F.A.B.F. de [Instituto de Física, Universidade Federal de Alagoas, 57072-970, Maceió-AL (Brazil)

    2014-02-01

    The purpose of this review is to present a comprehensive and up-to-date account of the main physical properties of DNA-based nanobiostructured devices, stressing the role played by their quasi-periodicity arrangement and correlation effects. Although the DNA-like molecule is usually described as a short-ranged correlated random ladder, artificial segments can be grown following quasiperiodic sequences as, for instance, the Fibonacci and Rudin–Shapiro ones. They have interesting properties like a complex fractal spectra of energy, which can be considered as their indelible mark, and collective properties that are not shared by their constituents. These collective properties are due to the presence of long-range correlations, which are expected to be reflected somehow in their various spectra (electronic transmission, density of states, etc.) defining another description of disorder. Although long-range correlations are responsible for the effective electronic transport at specific resonant energies of finite DNA segments, much of the anomalous spread of an initially localized electron wave-packet can be accounted by short-range pair correlations, suggesting that an approach based on the inclusion of further short-range correlations on the nucleotide distribution leads to an adequate description of the electronic properties of DNA segments. The introduction of defects may generate states within the gap, and substantially improves the conductance, specially of finite branches. They usually become exponentially localized for any amount of disorder, and have the property to tailor the electronic transport properties of DNA-based nanoelectronic devices. In particular, symmetric and antisymmetric correlations have quite distinct influence on the nature of the electronic states, and a diluted distribution of defects lead to an anomalous diffusion of the electronic wave-packet. Nonlinear contributions, arising from the coupling between electrons and the molecular

  10. Variation in the DNA methylation pattern of expressed and nonexpressed genes in chicken.

    Science.gov (United States)

    Cooper, D N; Errington, L H; Clayton, R M

    1983-01-01

    Using methyl-sensitive and -insensitive restriction enzymes, Hpa II and Msp I, the methylation status of various chicken genes was examined in different tissues and developmental stages. Tissue-specific differences in methylation were found for the delta-crystallin, beta-tubulin, G3PDH, rDNA, and actin genes but not for the histone genes. Developmental decreases in methylation were noted for the delta-crystallin and actin genes in chicken kidney between embryo and adult. Since most of the sequences examined were housekeeping genes, transcriptional differences are apparently not a necessary accompaniment to changes in DNA methylation at the CpG sites examined. The only exception is sperm DNA where the delta-crystallin, beta-tubulin, and actin genes are highly methylated and almost certainly not transcribed. However the G3PDH genes are no more highly methylated in sperm than in other somatic tissues. Many sequences homologous to the rDNA and histone probes used are unmethylated in all tissues examined including sperm, but a methylated rDNA subfraction is more heavily methylated in sperm than in other tissues. We speculate as to the significance of these differences in sperm DNA methylation in the light of possible requirements for early gene activation and the probable deleterious mutagenic effects of heavy methylation within coding sequences.

  11. Characterization of human glioblastoma cell lines in vitro and their xenografts in nude mice by DNA fingerprinting

    DEFF Research Database (Denmark)

    Türeci, O; Fischer, H; Lagoda, P

    1990-01-01

    Human gliomas were grown as permanent tissue cultures and xenografts in nude mice. DNA fingerprint patterns from two human gliomas were established using two different hypervariable multilocus probes [( GTG]5 and 33.15). In general the cell lines investigated showed an overall stability in the DNA...... fingerprint pattern. However, differences in the DNA fingerprint patterns were shown to occur depending upon the above mentioned parameters....

  12. Whole-genome methylation caller designed for methyl- DNA ...

    African Journals Online (AJOL)

    etchie

    2013-02-20

    Feb 20, 2013 ... Key words: Methyl-DNA immunoprecipitation, next-generation sequencing, Hidden ... its response to environmental cues. .... have a great potential to become the most cost-effective ... hg18 reference genome (set to 0 if not present in retrieved reads). ..... DNA methylation patterns and epigenetic memory.

  13. The mitochondrial DNA makeup of Romanians: A forensic mtDNA control region database and phylogenetic characterization.

    Science.gov (United States)

    Turchi, Chiara; Stanciu, Florin; Paselli, Giorgia; Buscemi, Loredana; Parson, Walther; Tagliabracci, Adriano

    2016-09-01

    To evaluate the pattern of Romanian population from a mitochondrial perspective and to establish an appropriate mtDNA forensic database, we generated a high-quality mtDNA control region dataset from 407 Romanian subjects belonging to four major historical regions: Moldavia, Transylvania, Wallachia and Dobruja. The entire control region (CR) was analyzed by Sanger-type sequencing assays and the resulting 306 different haplotypes were classified into haplogroups according to the most updated mtDNA phylogeny. The Romanian gene pool is mainly composed of West Eurasian lineages H (31.7%), U (12.8%), J (10.8%), R (10.1%), T (9.1%), N (8.1%), HV (5.4%),K (3.7%), HV0 (4.2%), with exceptions of East Asian haplogroup M (3.4%) and African haplogroup L (0.7%). The pattern of mtDNA variation observed in this study indicates that the mitochondrial DNA pool is geographically homogeneous across Romania and that the haplogroup composition reveals signals of admixture of populations of different origin. The PCA scatterplot supported this scenario, with Romania located in southeastern Europe area, close to Bulgaria and Hungary, and as a borderland with respect to east Mediterranean and other eastern European countries. High haplotype diversity (0.993) and nucleotide diversity indices (0.00838±0.00426), together with low random match probability (0.0087) suggest the usefulness of this control region dataset as a forensic database in routine forensic mtDNA analysis and in the investigation of maternal genetic lineages in the Romanian population. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  14. Trichromatic π-Pulse for Ultrafast Total Inversion of a Four-Level Ladder System

    Directory of Open Access Journals (Sweden)

    Carles Serrat

    2015-11-01

    Full Text Available We present a numerical solution for complete population inversion in a four-level ladder system obtained by using a full π-pulse illumination scheme with resonant ultrashort phase-locked Gaussian laser pulses. We find that a set of pulse areas such as √3π , √2π , and √3π completely inverts the four-level system considering identical effective dipole coupling coefficients. The solution is consistent provided the involved electric fields are not too strong and it is amply accurate also in the case of diverse transition dipole moments. We study the effect of detuning and chirp of the laser pulses on the complete population inversion using the level structure of atomic sodium interacting with ps and fs pulses as an example. Our result opens the door for multiple applications such as efficient ultrashort pulse lasing in the UV or the engineering of quantum states for quantum computing.

  15. Automated Translation of Safety Critical Application Software Specifications into PLC Ladder Logic

    Science.gov (United States)

    Leucht, Kurt W.; Semmel, Glenn S.

    2008-01-01

    The numerous benefits of automatic application code generation are widely accepted within the software engineering community. A few of these benefits include raising the abstraction level of application programming, shorter product development time, lower maintenance costs, and increased code quality and consistency. Surprisingly, code generation concepts have not yet found wide acceptance and use in the field of programmable logic controller (PLC) software development. Software engineers at the NASA Kennedy Space Center (KSC) recognized the need for PLC code generation while developing their new ground checkout and launch processing system. They developed a process and a prototype software tool that automatically translates a high-level representation or specification of safety critical application software into ladder logic that executes on a PLC. This process and tool are expected to increase the reliability of the PLC code over that which is written manually, and may even lower life-cycle costs and shorten the development schedule of the new control system at KSC. This paper examines the problem domain and discusses the process and software tool that were prototyped by the KSC software engineers.

  16. Environmental DNA (eDNA) Detection Probability Is Influenced by Seasonal Activity of Organisms.

    Science.gov (United States)

    de Souza, Lesley S; Godwin, James C; Renshaw, Mark A; Larson, Eric

    2016-01-01

    Environmental DNA (eDNA) holds great promise for conservation applications like the monitoring of invasive or imperiled species, yet this emerging technique requires ongoing testing in order to determine the contexts over which it is effective. For example, little research to date has evaluated how seasonality of organism behavior or activity may influence detection probability of eDNA. We applied eDNA to survey for two highly imperiled species endemic to the upper Black Warrior River basin in Alabama, US: the Black Warrior Waterdog (Necturus alabamensis) and the Flattened Musk Turtle (Sternotherus depressus). Importantly, these species have contrasting patterns of seasonal activity, with N. alabamensis more active in the cool season (October-April) and S. depressus more active in the warm season (May-September). We surveyed sites historically occupied by these species across cool and warm seasons over two years with replicated eDNA water samples, which were analyzed in the laboratory using species-specific quantitative PCR (qPCR) assays. We then used occupancy estimation with detection probability modeling to evaluate both the effects of landscape attributes on organism presence and season of sampling on detection probability of eDNA. Importantly, we found that season strongly affected eDNA detection probability for both species, with N. alabamensis having higher eDNA detection probabilities during the cool season and S. depressus have higher eDNA detection probabilities during the warm season. These results illustrate the influence of organismal behavior or activity on eDNA detection in the environment and identify an important role for basic natural history in designing eDNA monitoring programs.

  17. Cytosolic DNA Sensor Upregulation Accompanies DNA Electrotransfer in B16.F10 Melanoma Cells

    Directory of Open Access Journals (Sweden)

    Katarina Znidar

    2016-01-01

    Full Text Available In several preclinical tumor models, antitumor effects occur after intratumoral electroporation, also known as electrotransfer, of plasmid DNA devoid of a therapeutic gene. In mouse melanomas, these effects are preceded by significant elevation of several proinflammatory cytokines. These observations implicate the binding and activation of intracellular DNA-specific pattern recognition receptors or DNA sensors in response to DNA electrotransfer. In tumors, IFNβ mRNA and protein levels significantly increased. The mRNAs of several DNA sensors were detected, and DAI, DDX60, and p204 tended to be upregulated. These effects were accompanied with reduced tumor growth and increased tumor necrosis. In B16.F10 cells in culture, IFNβ mRNA and protein levels were significantly upregulated. The mRNAs for several DNA sensors were present in these cells; DNA-dependent activator of interferon regulatory factor (DAI, DEAD (Asp-Glu-Ala-Asp box polypeptide 60 (DDX60, and p204 were significantly upregulated while DDX60 protein levels were coordinately upregulated. Upregulation of DNA sensors in tumors could be masked by the lower transfection efficiency compared to in vitro or to dilution by other tumor cell types. Mirroring the observation of tumor necrosis, cells underwent a significant DNA concentration-dependent decrease in proliferation and survival. Taken together, these results indicate that DNA electrotransfer may cause the upregulation of several intracellular DNA sensors in B16.F10 cells, inducing effects in vitro and potentially in vivo.

  18. Role of Modular Polyketide Synthases in the Production of Polyether Ladder Compounds in Ciguatoxin-Producing Gambierdiscus polynesiensis and G. excentricus (Dinophyceae).

    Science.gov (United States)

    Kohli, Gurjeet S; Campbell, Katrina; John, Uwe; Smith, Kirsty F; Fraga, Santiago; Rhodes, Lesley L; Murray, Shauna A

    2017-09-01

    Gambierdiscus, a benthic dinoflagellate, produces ciguatoxins that cause the human illness Ciguatera. Ciguatoxins are polyether ladder compounds that have a polyketide origin, indicating that polyketide synthases (PKS) are involved in their production. We sequenced transcriptomes of Gambierdiscus excentricus and Gambierdiscus polynesiensis and found 264 contigs encoding single domain ketoacyl synthases (KS; G. excentricus: 106, G. polynesiensis: 143) and ketoreductases (KR; G. excentricus: 7, G. polynesiensis: 8) with sequence similarity to type I PKSs, as reported in other dinoflagellates. In addition, 24 contigs (G. excentricus: 3, G. polynesiensis: 21) encoding multiple PKS domains (forming typical type I PKSs modules) were found. The proposed structure produced by one of these megasynthases resembles a partial carbon backbone of a polyether ladder compound. Seventeen contigs encoding single domain KS, KR, s-malonyltransacylase, dehydratase and enoyl reductase with sequence similarity to type II fatty acid synthases (FAS) in plants were found. Type I PKS and type II FAS genes were distinguished based on the arrangement of domains on the contigs and their sequence similarity and phylogenetic clustering with known PKS/FAS genes in other organisms. This differentiation of PKS and FAS pathways in Gambierdiscus is important, as it will facilitate approaches to investigating toxin biosynthesis pathways in dinoflagellates. © 2017 The Author(s) Journal of Eukaryotic Microbiology © 2017 International Society of Protistologists.

  19. Phase transitions and thermal entanglement of the distorted Ising-Heisenberg spin chain: topology of multiple-spin exchange interactions in spin ladders

    Science.gov (United States)

    Arian Zad, Hamid; Ananikian, Nerses

    2017-11-01

    We consider a symmetric spin-1/2 Ising-XXZ double sawtooth spin ladder obtained from distorting a spin chain, with the XXZ interaction between the interstitial Heisenberg dimers (which are connected to the spins based on the legs via an Ising-type interaction), the Ising coupling between nearest-neighbor spins of the legs and rungs spins, respectively, and additional cyclic four-spin exchange (ring exchange) in the square plaquette of each block. The presented analysis supplemented by results of the exact solution of the model with infinite periodic boundary implies a rich ground state phase diagram. As well as the quantum phase transitions, the characteristics of some of the thermodynamic parameters such as heat capacity, magnetization and magnetic susceptibility are investigated. We prove here that among the considered thermodynamic and thermal parameters, solely heat capacity is sensitive versus the changes of the cyclic four-spin exchange interaction. By using the heat capacity function, we obtain a singularity relation between the cyclic four-spin exchange interaction and the exchange coupling between pair spins on each rung of the spin ladder. All thermal and thermodynamic quantities under consideration should be investigated by regarding those points which satisfy the singularity relation. The thermal entanglement within the Heisenberg spin dimers is investigated by using the concurrence, which is calculated from a relevant reduced density operator in the thermodynamic limit.

  20. Enhanced resolution of DNA restriction fragments: A procedure by two-dimensional electrophoresis and double-labeling

    International Nuclear Information System (INIS)

    Yi, M.; Au, L.C.; Ichikawa, N.; Ts'o, P.O.

    1990-01-01

    A probe-free method was developed to detect DNA rearrangement in bacteria based on the electrophoretic separation of twice-digested restriction fragments of genomic DNA into a two-dimensional (2-D) pattern. The first restriction enzyme digestion was done in solution, followed by electrophoresis of the restriction fragments in one dimension. A second restriction enzyme digestion was carried out in situ in the gel, followed by electrophoresis in a second dimension perpendicular to the first electrophoresis. The 2-D pattern provides for the resolution of 300-400 spots, which are defined and indexed by an x,y coordinate system with size markers. This approach has greatly increased the resolution power over conventional one-dimensional (1-D) electrophoresis. To study DNA rearrangement, a 2-D pattern from a test strain was compared with the 2-D pattern from a reference strain. After the first digestion, genomic DNA fragments from the test strain were labeled with 35S, while those from the reference strain were labeled with 32P. This was done to utilize the difference in the energy emission of 35S and 32P isotopes for autoradiography when two x-ray films were exposed simultaneously on top of the gel after the 2-D electrophoresis. The irradiation from the decay of 35S exposed only the lower film, whereas the irradiation from the decay of 32P exposed both the lower and upper films. Different DNA fragments existed in the test DNA compared with the reference DNA can be identified unambiguously by the differential two 2-D patterns produced on two films upon exposure to the 35S and 32P fragments in the same gel. An appropriate photographic procedure further simplified the process, allowing only the difference in DNA fragments between these two patterns to be shown in the map

  1. DNA: Polymer and molecular code

    Science.gov (United States)

    Shivashankar, G. V.

    1999-10-01

    gene expression a prime example of a biological code. We developed a novel method of making DNA micro- arrays, the so-called DNA chip. Using the optical tweezer concept, we were able to pattern biomolecules on a solid substrate, developing a new type of sub-micron laser lithography. A laser beam is focused onto a thin gold film on a glass substrate. Laser ablation of gold results in local aggregation of nanometer scale beads conjugated with small DNA oligonucleotides, with sub-micron resolution. This leads to specific detection of cDNA and RNA molecules. We built a simple micro-array fabrication and detection in the laboratory, based on this method, to probe addressable pools (genes, proteins or antibodies). We have lately used molecular beacons (single stranded DNA with a stem-loop structure containing a fluorophore and quencher), for the direct detection of unlabelled mRNA. As a first step towards a study of the dynamics of the biological code, we have begun to examine the patterns of gene expression during virus (T7 phage) infection of E-coli bacteria.

  2. DNA methylation-based variation between human populations.

    Science.gov (United States)

    Kader, Farzeen; Ghai, Meenu

    2017-02-01

    Several studies have proved that DNA methylation affects regulation of gene expression and development. Epigenome-wide studies have reported variation in methylation patterns between populations, including Caucasians, non-Caucasians (Blacks), Hispanics, Arabs, and numerous populations of the African continent. Not only has DNA methylation differences shown to impact externally visible characteristics, but is also a potential biomarker for underlying racial health disparities between human populations. Ethnicity-related methylation differences set their mark during early embryonic development. Genetic variations, such as single-nucleotide polymorphisms and environmental factors, such as age, dietary folate, socioeconomic status, and smoking, impacts DNA methylation levels, which reciprocally impacts expression of phenotypes. Studies show that it is necessary to address these external influences when attempting to differentiate between populations since the relative impacts of these factors on the human methylome remain uncertain. The present review summarises several reported attempts to establish the contribution of differential DNA methylation to natural human variation, and shows that DNA methylation could represent new opportunities for risk stratification and prevention of several diseases amongst populations world-wide. Variation of methylation patterns between human populations is an exciting prospect which inspires further valuable research to apply the concept in routine medical and forensic casework. However, trans-generational inheritance needs to be quantified to decipher the proportion of variation contributed by DNA methylation. The future holds thorough evaluation of the epigenome to understand quantification, heritability, and the effect of DNA methylation on phenotypes. In addition, methylation profiling of the same ethnic groups across geographical locations will shed light on conserved methylation differences in populations.

  3. Aberrant DNA methylation in 5'regions of DNA methyltransferase genes in aborted bovine clones

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    High rate of abortion and developmental abnormalities is thought to be closely associated with inefficient epigenetic reprogramming of the transplanted nuclei during bovine cloning.It is known that one of the important mechanisms for epigenetic reprogramming is DNA methylation.DNA methylation is established and maintained by DNA methyltransferases(DNMTs),therefore,it is postulated that the inefficient epigenetic reprogramming of transplanted nuclei may be due to abnormal expression of DNMTs.Since DNA methylation can strongly inhibit gene expression,aberrant DNA methylation of DNMT genes may disturb gene expression.But presently,it is not clear whether the methylation abnormality of DNMT genes is related to developmental failure of somatic cell nuclear transfer embryos.In our study,we analyzed methylation patterns of the 5' regions of four DNMT genes including Dnmt3a,Dnmt3b,Dnmtl and Dnmt2 in four aborted bovine clones.Using bisulfite sequencing method,we found that 3 out of 4 aborted bovine clones(AF1,AF2 and AF3)showed either hypermethylation or hypomethylation in the 5' regions of Dnmt3a and Dnmt3b.indicating that Dnmt3a and Dnmt3b genes are not properly reprogrammed.However,the individual AF4 exhibited similar methylation level and pattern to age-matched in vitro fertilized (IVF)fetuses.Besides,we found that tle 5'regions of Dnmtl and Dnmt2 were nearly completely unmethylated in all normal adults.IVF fetuses,sperm and aborted clones.Together,our results suggest that the aberrant methylation of Dnmt3a and Dnmt3b 5' regions is probably associated with the high abortion of bovine clones.

  4. The effect of caffeine on p53-dependent radioresponses in undifferentiated mouse embryonal carcinoma cells after X-ray and UV-irradiations

    International Nuclear Information System (INIS)

    Taga, Masataka; Shiraishi, Kazunori; Shimura, Tsutomu; Uematsu, Norio; Kato, Tomohisa; Niwa, Ohtsura; Nishimune, Yoshitake; Aizawa, Shinichi; Oshimura, Mitsuo

    2000-01-01

    The effect of caffeine was studied on the radioresponses of undifferentiated mouse embryonal carcinoma cells (EC cells) with or without the functional p53. The radioresponses studied included radiosensitivity, the activation of p53, apoptosis with characteristic DNA ladder formation and cell cycle progression. An undifferentiated mouse EC cell line, ECA2, and a newly established p53-deficient EC cell line, p53δ, were used in the present study. The status of the p53 gene did not significantly affect the colony survivals of undifferentiated EC cells to X-rays and UV. Although a post-irradiation treatment with caffeine sensitized both lines to X-rays marginally, the sensitization was prominent for UV regardless of the p53 status of the cells. The activation of a p53 responsible lacZ reporter construct was observed in stably transfected ECA2 cells after X-ray and UV irradiations. Caffeine suppressed the X-ray induced activation of the lacZ reporter, while it drastically enhanced the activation after UV irradiation. X-rays and UV readily triggered the apoptosis of ECA2 cells with the characteristic DNA ladder. Although UV-induced DNA ladder formation was enhanced by caffeine, that induced by X-rays was unaffected. Therefore, the effects of caffeine on the p53-dependent radioresponses were found to be agent specific: suppression for the X-ray induced and augmentation for the UV induced. In contrast to p53-proficient ECA2 cells, smear-like DNA degradation was observed for irradiated p53δ cells, suggesting the presence of a mode of cell death without DNA ladder formation. UV induction of the smear-like DNA degradation was enhanced in the presence of caffeine. Regardless of the state of the p53 gene, G1/S arrest was not observed in X-ray and UV irradiated EC cells. X-rays induced G2/M arrest in both lines, which was abrogated by caffeine, while G2/M arrest after UV was unaffected by a caffeine treatment. These results indicate that the radioresponses of undifferentiated

  5. The effect of caffeine on p53-dependent radioresponses in undifferentiated mouse embryonal carcinoma cells after X-ray and UV-irradiations

    Energy Technology Data Exchange (ETDEWEB)

    Taga, Masataka; Shiraishi, Kazunori; Shimura, Tsutomu; Uematsu, Norio; Kato, Tomohisa; Niwa, Ohtsura [Kyoto Univ. (Japan). Radiation Biology Center; Nishimune, Yoshitake; Aizawa, Shinichi; Oshimura, Mitsuo

    2000-09-01

    The effect of caffeine was studied on the radioresponses of undifferentiated mouse embryonal carcinoma cells (EC cells) with or without the functional p53. The radioresponses studied included radiosensitivity, the activation of p53, apoptosis with characteristic DNA ladder formation and cell cycle progression. An undifferentiated mouse EC cell line, ECA2, and a newly established p53-deficient EC cell line, p53{delta}, were used in the present study. The status of the p53 gene did not significantly affect the colony survivals of undifferentiated EC cells to X-rays and UV. Although a post-irradiation treatment with caffeine sensitized both lines to X-rays marginally, the sensitization was prominent for UV regardless of the p53 status of the cells. The activation of a p53 responsible lacZ reporter construct was observed in stably transfected ECA2 cells after X-ray and UV irradiations. Caffeine suppressed the X-ray induced activation of the lacZ reporter, while it drastically enhanced the activation after UV irradiation. X-rays and UV readily triggered the apoptosis of ECA2 cells with the characteristic DNA ladder. Although UV-induced DNA ladder formation was enhanced by caffeine, that induced by X-rays was unaffected. Therefore, the effects of caffeine on the p53-dependent radioresponses were found to be agent specific: suppression for the X-ray induced and augmentation for the UV induced. In contrast to p53-proficient ECA2 cells, smear-like DNA degradation was observed for irradiated p53{delta} cells, suggesting the presence of a mode of cell death without DNA ladder formation. UV induction of the smear-like DNA degradation was enhanced in the presence of caffeine. Regardless of the state of the p53 gene, G1/S arrest was not observed in X-ray and UV irradiated EC cells. X-rays induced G2/M arrest in both lines, which was abrogated by caffeine, while G2/M arrest after UV was unaffected by a caffeine treatment. These results indicate that the radioresponses of

  6. An efficient method for DNA extraction from Cladosporioid fungi.

    Science.gov (United States)

    Moslem, M A; Bahkali, A H; Abd-Elsalam, K A; Wit, P J G M

    2010-11-23

    We developed an efficient method for DNA extraction from Cladosporioid fungi, which are important fungal plant pathogens. The cell wall of Cladosporioid fungi is often melanized, which makes it difficult to extract DNA from their cells. In order to overcome this we grew these fungi for three days on agar plates and extracted DNA from mycelium mats after manual or electric homogenization. High-quality DNA was isolated, with an A(260)/A(280) ratio ranging between 1.6 and 2.0. Isolated genomic DNA was efficiently digested with restriction enzymes and produced distinct banding patterns on agarose gels for the different Cladosporium species. Clear DNA fragments from the isolated DNA were amplified by PCR using small and large subunit rDNA primers, demonstrating that this method provides DNA of sufficiently high quality for molecular analyses.

  7. Effect of relevant umklapp process on the two-leg Hubbard ladder with a half-filled band under pressure

    International Nuclear Information System (INIS)

    Haddad, S.; Bennaceur, R.

    1999-01-01

    By means of perturbative renormalization approach we study the effect of relevant umklapp process on dimensional crossover caused by interladder one particle hopping t bot in weakly coupled two-leg Hubbard ladders with a half filled-band. We found that a crossover takes place at a finite value t botc which increases as the amplitude of umklapp process increases. For t bot botc the system undergoes a phase transition to the spin density wave phase (SDW) via the two particle hopping process, while for t bot >t botc the system undergoes a crossover to the two dimensional Fermi liquid phase via one particle hopping process. (orig.)

  8. Investigation of Double-Band Electrophoretic Pattern of ITS-rDNA Region in Iranian Isolates of Leishmania Tropica

    Directory of Open Access Journals (Sweden)

    MA Ghatee

    2013-06-01

    Full Text Available Background: Leishmania tropica is a genetically divergent species. Amplification of entire internal tran­scribed spacer (ITS region of L. tropica isolates obtained from Bam district, one of the well known focus of anthroponotic cutaneous leishmaniasis ACL( in Iran, revealed a double-band pat­tern in agarose gel electrophoresis. This study explains how this pattern occurs.Methods: Twenty seven L. tropica smear preparations were collected from Bam district, south east Iran, and eight L. major and one L. infantum smear preparations were gathered from Shiraz, south west Iran. Furthermore one L. major and one L. infantum cultured standard strains were tested using entire ITS-PCR to survey their electrophoretic pattern. The ITS sequences of L. tropica, L. major, and L. infantum already deposited in GenBank were analyzed. Analysis of GenBank sequences of L. tropica revealed two groups of sequences based on length size, one group having a 100 bp gap. Therefore, a new re­verse primer namely LITS-MG was designed to exclude this gap in PCR products.Results: Whole ITS fragment amplification resulted in a double-band pattern in all L. tropica cases, while a sharp single band was observed for L. infantum and L. major isolates. This result was correspond­ing to the result obtained from in silico analysis of GenBank sequences. Use of LITS-MG primer was expectedly resulted in a single band including ITS1, 5.8s and partial ITS2 product for L. tropica which is appropriate for following molecular studies such as sequencing or restriction analysis.Conclusion: Sequences analysis of GenBank L. tropica sequences and following practical laboratory tests revealed at least two alleles in L. tropica which were confirmed in Bam isolates. This especial double-band pattern is because of a 100 bp fragment difference within ITS-rDNA alleles

  9. The Inherent Asymmetry of DNA Replication.

    Science.gov (United States)

    Snedeker, Jonathan; Wooten, Matthew; Chen, Xin

    2017-10-06

    Semiconservative DNA replication has provided an elegant solution to the fundamental problem of how life is able to proliferate in a way that allows cells, organisms, and populations to survive and replicate many times over. Somewhat lost, however, in our admiration for this mechanism is an appreciation for the asymmetries that occur in the process of DNA replication. As we discuss in this review, these asymmetries arise as a consequence of the structure of the DNA molecule and the enzymatic mechanism of DNA synthesis. Increasing evidence suggests that asymmetries in DNA replication are able to play a central role in the processes of adaptation and evolution by shaping the mutagenic landscape of cells. Additionally, in eukaryotes, recent work has demonstrated that the inherent asymmetries in DNA replication may play an important role in the process of chromatin replication. As chromatin plays an essential role in defining cell identity, asymmetries generated during the process of DNA replication may play critical roles in cell fate decisions related to patterning and development.

  10. Purification of functionalized DNA origami nanostructures.

    Science.gov (United States)

    Shaw, Alan; Benson, Erik; Högberg, Björn

    2015-05-26

    The high programmability of DNA origami has provided tools for precise manipulation of matter at the nanoscale. This manipulation of matter opens up the possibility to arrange functional elements for a diverse range of applications that utilize the nanometer precision provided by these structures. However, the realization of functionalized DNA origami still suffers from imperfect production methods, in particular in the purification step, where excess material is separated from the desired functionalized DNA origami. In this article we demonstrate and optimize two purification methods that have not previously been applied to DNA origami. In addition, we provide a systematic study comparing the purification efficacy of these and five other commonly used purification methods. Three types of functionalized DNA origami were used as model systems in this study. DNA origami was patterned with either small molecules, antibodies, or larger proteins. With the results of our work we aim to provide a guideline in quality fabrication of various types of functionalized DNA origami and to provide a route for scalable production of these promising tools.

  11. DNA Methylation: An Epigenetic Risk Factor in Preterm Birth

    Science.gov (United States)

    Menon, Ramkumar; Conneely, Karen N.; Smith, Alicia K.

    2012-01-01

    Spontaneous preterm birth (PTB; birth prior to 37 weeks of gestation) is a complex phenotype with multiple risk factors that complicate our understanding of its etiology. A number of recent studies have supported the hypothesis that epigenetic modifications such as DNA methylation induced by pregnancy-related risk factors may influence the risk of PTB or result in changes that predispose a neonate to adult-onset diseases. The critical role of timing of gene expression in the etiology of PTB makes it a highly relevant disorder in which to examine the potential role of epigenetic changes. Because changes in DNA methylation patterns can result in long-term consequences, it is of critical interest to identify the epigenetic patterns associated with adverse pregnancy outcomes. This review examines the potential role of DNA methylation as a risk factor for PTB and discusses several issues and limitations that should be considered when planning DNA methylation studies. PMID:22228737

  12. Figure 1. T. tor species. Figure 2. Long PCR products of ...

    Indian Academy of Sciences (India)

    Annam

    Figure 2. Long PCR products of mitochondrial DNA from the fish T. tor. Lane 1, amplified product using L-12321-Leu and S-LA-16S-H primers. Lane 2, amplified product using H-12321 –Leu and S-LA-16S-L primers. Lane M, 1-Kb DNA ladder. 8 kb ...

  13. The logic of DNA replication in double-stranded DNA viruses: insights from global analysis of viral genomes.

    Science.gov (United States)

    Kazlauskas, Darius; Krupovic, Mart; Venclovas, Česlovas

    2016-06-02

    Genomic DNA replication is a complex process that involves multiple proteins. Cellular DNA replication systems are broadly classified into only two types, bacterial and archaeo-eukaryotic. In contrast, double-stranded (ds) DNA viruses feature a much broader diversity of DNA replication machineries. Viruses differ greatly in both completeness and composition of their sets of DNA replication proteins. In this study, we explored whether there are common patterns underlying this extreme diversity. We identified and analyzed all major functional groups of DNA replication proteins in all available proteomes of dsDNA viruses. Our results show that some proteins are common to viruses infecting all domains of life and likely represent components of the ancestral core set. These include B-family polymerases, SF3 helicases, archaeo-eukaryotic primases, clamps and clamp loaders of the archaeo-eukaryotic type, RNase H and ATP-dependent DNA ligases. We also discovered a clear correlation between genome size and self-sufficiency of viral DNA replication, the unanticipated dominance of replicative helicases and pervasive functional associations among certain groups of DNA replication proteins. Altogether, our results provide a comprehensive view on the diversity and evolution of replication systems in the DNA virome and uncover fundamental principles underlying the orchestration of viral DNA replication. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  14. Raman spectroscopy for DNA quantification in cell nucleus.

    Science.gov (United States)

    Okotrub, K A; Surovtsev, N V; Semeshin, V F; Omelyanchuk, L V

    2015-01-01

    Here we demonstrate the feasibility of a novel approach to quantify DNA in cell nuclei. This approach is based on spectroscopy analysis of Raman light scattering, and avoids the problem of nonstoichiometric binding of dyes to DNA, as it directly measures the signal from DNA. Quantitative analysis of nuclear DNA contribution to Raman spectrum could be reliably performed using intensity of a phosphate mode at 1096 cm(-1) . When compared to the known DNA standards from cells of different animals, our results matched those values at error of 10%. We therefore suggest that this approach will be useful to expand the list of DNA standards, to properly adjust the duration of hydrolysis in Feulgen staining, to assay the applicability of fuchsines for DNA quantification, as well as to measure DNA content in cells with complex hydrolysis patterns, when Feulgen densitometry is inappropriate. © 2014 International Society for Advancement of Cytometry.

  15. Genetic Ancestry using Mitochondrial DNA in patients with Triple-negative breast cancer (GAMiT study).

    Science.gov (United States)

    Rao, Roshni; Rivers, Aeisha; Rahimi, Asal; Wooldridge, Rachel; Rao, Madhu; Leitch, Marilyn; Euhus, David; Haley, Barbara B

    2017-01-01

    Triple-negative breast cancer (TNBC) lacks estrogen, progesterone, and human epidermal growth factor receptor 2 (HER2)/neu receptors, and is aggressive and therapeutically challenging. Genetic ancestry testing is an emerging medical field. Mitochondrial DNA (mtDNA), which is distinct from nuclear DNA, is maternally inherited and allows for origin determination. Patients with TNBC tend to be younger and are more likely to be African American, making this an ideal disease for mtDNA exploration. To the authors' knowledge, the current study is the first to perform mtDNA for self-described African American, White, and Hispanic patients with TNBC to identify mtDNA patterns. Patients with TNBC who were at any stage of therapy/survivorship were included. Self-reported ethnicity was confirmed at the time of the prospective buccal swab. Haplogroup prediction was performed on sequencing of hypervariable region 1. Using sequence similarity scores and lineage databases, sequence patterns were determined. Data regarding presentation and treatment, tumor features, and outcomes was collected. A total of 92 patients were included: 31 self-described African American, 31 White, and 30 Hispanic individuals. Hispanic patients were found to have the largest tumor size (4.5 cm; P = .01) and youngest age (41 years; Pancestry and haplogroups A, U, H, or B to be the most common mtDNA patterns. Twelve discordances (13%) between mtDNA analysis and self-described ethnicity were identified among the 92 patients. The highest discordance (26%; 8 patients) was noted in self-described Hispanic patients: 3 had Nigerian ancestry, and 1 individual demonstrated haplogroup K mtDNA (Ashkenazi Jewish ancestry). Discordance between self-reported ethnicity and mtDNA analysis was identified in 13% of patients with TNBC. The identification of mtDNA patterns with a predisposition toward TNBC may allow for risk stratification. Cancer 2017;107-113. © 2016 American Cancer Society. © 2016 American Cancer

  16. Number and location of mouse mammary tumor virus proviral DNA in mouse DNA of normal tissue and of mammary tumors.

    Science.gov (United States)

    Groner, B; Hynes, N E

    1980-01-01

    The Southern DNA filter transfer technique was used to characterize the genomic location of the mouse mammary tumor proviral DNA in different inbred strains of mice. Two of the strains (C3H and CBA) arose from a cross of a Bagg albino (BALB/c) mouse and a DBA mouse. The mouse mammary tumor virus-containing restriction enzyme DNA fragments of these strains had similar patterns, suggesting that the proviruses of these mice are in similar genomic locations. Conversely, the pattern arising from the DNA of the GR mouse, a strain genetically unrelated to the others, appeared different, suggesting that its mouse mammary tumor proviruses are located in different genomic sites. The structure of another gene, that coding for beta-globin, was also compared. The mice strains which we studied can be categorized into two classes, expressing either one or two beta-globin proteins. The macroenvironment of the beta-globin gene appeared similar among the mice strains belonging to one genetic class. Female mice of the C3H strain exogenously transmit mouse mammary tumor virus via the milk, and their offspring have a high incidence of mammary tumor occurrence. DNA isolated from individual mammary tumors taken from C3H mice or from BALB/c mice foster nursed on C3H mothers was analyzed by the DNA filter transfer technique. Additional mouse mammary tumor virus-containing fragments were found in the DNA isolated from each mammary tumor. These proviral sequences were integrated into different genomic sites in each tumor. Images PMID:6245257

  17. Resonant two-photon absorption and electromagnetically induced transparency in open ladder-type atomic system.

    Science.gov (United States)

    Moon, Han Seb; Noh, Heung-Ryoul

    2013-03-25

    We have experimentally and theoretically studied resonant two-photon absorption (TPA) and electromagnetically induced transparency (EIT) in the open ladder-type atomic system of the 5S(1/2) (F = 1)-5P(3/2) (F' = 0, 1, 2)-5D(5/2) (F″ = 1, 2, 3) transitions in (87)Rb atoms. As the coupling laser intensity was increased, the resonant TPA was transformed to EIT for the 5S(1/2) (F = 1)-5P(3/2) (F' = 2)-5D(5/2) (F″ = 3) transition. The transformation of resonant TPA into EIT was numerically calculated for various coupling laser intensities, considering all the degenerate magnetic sublevels of the 5S(1/2)-5P(3/2)-5D(5/2) transition. From the numerical results, the crossover from TPA to EIT could be understood by the decomposition of the spectrum into an EIT component owing to the pure two-photon coherence and a TPA component caused by the mixed term.

  18. Evaluation of FTA ® paper for storage of oral meta-genomic DNA.

    Science.gov (United States)

    Foitzik, Magdalena; Stumpp, Sascha N; Grischke, Jasmin; Eberhard, Jörg; Stiesch, Meike

    2014-10-01

    The purpose of the present study was to evaluate the short-term storage of meta-genomic DNA from native oral biofilms on FTA(®) paper. Thirteen volunteers of both sexes received an acrylic splint for intraoral biofilm formation over a period of 48 hours. The biofilms were collected, resuspended in phosphate-buffered saline, and either stored on FTA(®) paper or directly processed by standard laboratory DNA extraction. The nucleic acid extraction efficiencies were evaluated by 16S rDNA targeted SSCP fingerprinting. The acquired banding pattern of FTA-derived meta-genomic DNA was compared to a standard DNA preparation protocol. Sensitivity and positive predictive values were calculated. The volunteers showed inter-individual differences in their bacterial species composition. A total of 200 bands were found for both methods and 85% of the banding patterns were equal, representing a sensitivity of 0.941 and a false-negative predictive value of 0.059. Meta-genomic DNA sampling, extraction, and adhesion using FTA(®) paper is a reliable method for storage of microbial DNA for a short period of time.

  19. Quantum phase transitions in effective spin-ladder models for graphene zigzag nanoribbons

    Science.gov (United States)

    Koop, Cornelie; Wessel, Stefan

    2017-10-01

    We examine the magnetic correlations in quantum spin models that were derived recently as effective low-energy theories for electronic correlation effects on the edge states of graphene nanoribbons. For this purpose, we employ quantum Monte Carlo simulations to access the large-distance properties, accounting for quantum fluctuations beyond mean-field-theory approaches to edge magnetism. For certain chiral nanoribbons, antiferromagnetic interedge couplings were previously found to induce a gapped quantum disordered ground state of the effective spin model. We find that the extended nature of the intraedge couplings in the effective spin model for zigzag nanoribbons leads to a quantum phase transition at a large, finite value of the interedge coupling. This quantum critical point separates the quantum disordered region from a gapless phase of stable edge magnetism at weak intraedge coupling, which includes the ground states of spin-ladder models for wide zigzag nanoribbons. To study the quantum critical behavior, the effective spin model can be related to a model of two antiferromagnetically coupled Haldane-Shastry spin-half chains with long-ranged ferromagnetic intrachain couplings. The results for the critical exponents are compared also to several recent renormalization-group calculations for related long-ranged interacting quantum systems.

  20. A one-dimensional ladder-like coordination polymer: poly[[hexa-aqua-bis(μ-5-nitro-benzene-1,3-dicarboxyl-ato-κO,O',O'')(μ-oxalato-κO,O':O'',O''')diyttrium(III)] trihydrate].

    Science.gov (United States)

    Fu, Zhong; Lin, Ying; Zhou, Yun-You; Zhang, Hong-Tao

    2007-12-06

    In the crystal structure of the title one-dimensional coordination polymer, [Y(2)(C(8)H(3)NO(6))(2)(C(2)O(4))(H(2)O)(6)]·3H(2)O, each Y(III) ion is bridged to its neighbours by two 5-nitro-benzene-1,3-dicarboxyl-ate (nbdc) dianions and one oxalate dianion (located on an inversion centre) to form a ladder-like polymeric structure. The two carboxylate groups of nbdc assume different modes of coordination, one is chelating whereas the other is monodentate. Three water mol-ecules coordinate to the Y(III) ion to complete an eight-coordinate distorted dodecahedral geometry. The ladder-like polymers are assembled together by hydrogen bonding and π-π stacking [centrio-centriod distance = 3.819 (9) Å] in the crystal structure.

  1. Fully frustrated Josephson junction ladders with Mobius boundary conditions as topologically protected qubits

    Energy Technology Data Exchange (ETDEWEB)

    Cristofano, Gerardo; Marotta, Vincenzo [Dipartimento di Scienze Fisiche, Universita di Napoli ' Federico II' and INFN, Sezione di Napoli, Via Cintia, Complesso Universitario M. Sant' Angelo, 80126 Napoli (Italy); Naddeo, Adele [Dipartimento di Fisica ' E.R. Caianiello' , Universita degli Studi di Salerno and CNISM, Unita di Ricerca di Salerno, Via Salvador Allende, 84081 Baronissi (Saudi Arabia) (Italy)], E-mail: naddeo@sa.infn.it; Niccoli, Giuliano [LPTM, Universite de Cergy-Pontoise, 2 avenue Adolphe Chauvin, 95302 Cergy-Pontoise (France)

    2008-03-31

    We show how to realize a 'protected' qubit by using a fully frustrated Josephson junction ladder (JJL) with Mobius boundary conditions. Such a system has been recently studied within a twisted conformal field theory (CFT) approach [G. Cristofano, G. Maiella, V. Marotta, Mod. Phys. Lett. A 15 (2000) 1679; G. Cristofano, G. Maiella, V. Marotta, G. Niccoli, Nucl. Phys. B 641 (2002) 547] and shown to develop the phenomenon of flux fractionalization [G. Cristofano, V. Marotta, A. Naddeo, G. Niccoli, Eur. Phys. J. B 49 (2006) 83]. The relevance of a 'closed' geometry has been fully exploited in relating the topological properties of the ground state of the system to the presence of half flux quanta and the emergence of a topological order has been predicted [G. Cristofano, V. Marotta, A. Naddeo, J. Stat. Mech.: Theory Exp. (2005) P03006]. In this Letter the stability and transformation properties of the ground states under adiabatic magnetic flux change are analyzed and the deep consequences on the realization of a solid state qubit, protected from decoherence, are presented.

  2. Applications of statistical physics and information theory to the analysis of DNA sequences

    Science.gov (United States)

    Grosse, Ivo

    2000-10-01

    DNA carries the genetic information of most living organisms, and the of genome projects is to uncover that genetic information. One basic task in the analysis of DNA sequences is the recognition of protein coding genes. Powerful computer programs for gene recognition have been developed, but most of them are based on statistical patterns that vary from species to species. In this thesis I address the question if there exist universal statistical patterns that are different in coding and noncoding DNA of all living species, regardless of their phylogenetic origin. In search for such species-independent patterns I study the mutual information function of genomic DNA sequences, and find that it shows persistent period-three oscillations. To understand the biological origin of the observed period-three oscillations, I compare the mutual information function of genomic DNA sequences to the mutual information function of stochastic model sequences. I find that the pseudo-exon model is able to reproduce the mutual information function of genomic DNA sequences. Moreover, I find that a generalization of the pseudo-exon model can connect the existence and the functional form of long-range correlations to the presence and the length distributions of coding and noncoding regions. Based on these theoretical studies I am able to find an information-theoretical quantity, the average mutual information (AMI), whose probability distributions are significantly different in coding and noncoding DNA, while they are almost identical in all studied species. These findings show that there exist universal statistical patterns that are different in coding and noncoding DNA of all studied species, and they suggest that the AMI may be used to identify genes in different living species, irrespective of their taxonomic origin.

  3. Does DNA methylation pattern mark generative development in winter rape?

    Czech Academy of Sciences Publication Activity Database

    Filek, M.; Janiak, A.; Szarejko, I.; Grabczynska, J.; Macháčková, Ivana; Krekule, Jan

    2006-01-01

    Roč. 61, 5-6 (2006), s. 387-396 ISSN 0939-5075 R&D Projects: GA AV ČR IAA600040612 Institutional research plan: CEZ:AV0Z50380511 Keywords : DNA methylation * rape * vernalization Subject RIV: EF - Botanics Impact factor: 0.720, year: 2006

  4. First functionality tests of a 64 × 64 pixel DSSC sensor module connected to the complete ladder readout

    Science.gov (United States)

    Donato, M.; Hansen, K.; Kalavakuru, P.; Kirchgessner, M.; Kuster, M.; Porro, M.; Reckleben, C.; Turcato, M.

    2017-03-01

    The European X-ray Free Electron Laser (XFEL.EU) will provide every 0.1 s a train of 2700 spatially coherent ultrashort X-ray pulses at 4.5 MHz repetition rate. The Small Quantum Systems (SQS) instrument and the Spectroscopy and Coherent Scattering instrument (SCS) operate with soft X-rays between 0.5 keV-6 keV. The DEPFET Sensor with Signal Compression (DSSC) detector is being developed to meet the requirements set by these two XFEL.EU instruments. The DSSC imager is a 1 mega-pixel camera able to store up to 800 single-pulse images per train. The so-called ladder is the basic unit of the DSSC detector. It is the single unit out of sixteen identical-units composing the DSSC-megapixel camera, containing all representative electronic components of the full-size system and allows testing the full electronic chain. Each DSSC ladder has a focal plane sensor with 128× 512 pixels. The read-out ASIC provides full-parallel readout of the sensor pixels. Every read-out channel contains an amplifier and an analog filter, an up-to 9 bit ADC and the digital memory. The ASIC amplifier have a double front-end to allow one to use either DEPFET sensors or Mini-SDD sensors. In the first case, the signal compression is a characteristic intrinsic of the sensor; in the second case, the compression is implemented at the first amplification stage. The goal of signal compression is to meet the requirement of single-photon detection capability and wide dynamic range. We present the first results of measurements obtained using a 64× 64 pixel DEPFET sensor attached to the full final electronic and data-acquisition chain.

  5. Mitochondrial DNA: An Endogenous Trigger for Immune Paralysis.

    Science.gov (United States)

    Schäfer, Simon T; Franken, Lars; Adamzik, Michael; Schumak, Beatrix; Scherag, André; Engler, Andrea; Schönborn, Niels; Walden, Jennifer; Koch, Susanne; Baba, Hideo A; Steinmann, Jörg; Westendorf, Astrid M; Fandrey, Joachim; Bieber, Thomas; Kurts, Christian; Frede, Stilla; Peters, Jürgen; Limmer, Andreas

    2016-04-01

    Critically ill patients are at high risk to suffer from sepsis, even in the absence of an initial infectious source, but the molecular mechanisms for their increased sepsis susceptibility, including a suppressed immune system, remain unclear. Although microbes and pathogen-associated molecular pattern are accepted inducers of sepsis and septic immunosuppression, the role of endogenous Toll-like receptor (TLR) ligands, such as mitochondrial DNA (mtDNA), in altering the immune response is unknown. Mitochondrial DNA serum concentrations of the mitochondrial genes D-Loop and adenosine triphosphatase 6 were determined (quantitative polymerase chain reaction) in 165 septic patients and 50 healthy volunteers. Furthermore, cytotoxic T-cell activity was analyzed in wild-type and TLR9 knockout mice, with/without previous mtDNA administration, followed by injection of an ovalbumin-expressing adenoviral vector. Mitochondrial DNA serum concentrations were increased in septic patients (adenosine triphosphatase 6, 123-fold; D-Loop, 76-fold, P < 0.0001) compared with volunteers. Furthermore, a single mtDNA injection caused profound, TLR9-dependent immunosuppression of adaptive T-cell cytotoxicity in wild-type but not in TLR9 knockout mice and evoked various immunosuppressive mechanisms including the destruction of the splenic microstructure, deletion of cross-presenting dendritic cells, and up-regulation of programmed cell death ligand 1 and indoleamine 2,3-dioxygenase. Several of these findings in mice were mirrored in septic patients, and mtDNA concentrations were associated with an increased 30-day mortality. The findings of this study imply that mtDNA, an endogenous danger associated molecular pattern, is a hitherto unknown inducer of septic immunoparalysis and one possible link between initial inflammation and subsequent immunosuppression in critically ill patients.

  6. Quantification of DNA damage by single-cell electrophoresis

    International Nuclear Information System (INIS)

    Ikushima, Takaji

    1990-01-01

    A simple technique of micro-agarose gel electrophoresis has been developed to quantify DNA damage in individual cells. Cells are embedded in agarose gel on microscope slides, lysed by detergents and then electrophoresed for a short time under neutral or alkaline condition. In irradiated cells, DNA migrates from the nucleus toward the anode, displaying commet-like pattern by staining with DNA-specific fluorescence dye. DNA damage is evaluated by measuring the distance of DNA migration. The technique was applied for measuring DNA damage in single cells exposed to 60 Co γ-rays, or to KUR radiation in the presence or absence of 10 B-enriched boric acid. The enhanced production of double-stranded DNA breaks by 10 B(n,α) 7 Li reaction was demonstrated here. The significant increase in the length of DNA migration was observed in single cells exposed to such a low dose as 20 cGy after alkaline micro electrophoresis. (author)

  7. Nanofabricated racks of aligned and anchored DNA substrates for single-molecule imaging.

    Science.gov (United States)

    Gorman, Jason; Fazio, Teresa; Wang, Feng; Wind, Shalom; Greene, Eric C

    2010-01-19

    Single-molecule studies of biological macromolecules can benefit from new experimental platforms that facilitate experimental design and data acquisition. Here we develop new strategies to construct curtains of DNA in which the molecules are aligned with respect to one another and maintained in an extended configuration by anchoring both ends of the DNA to the surface of a microfluidic sample chamber that is otherwise coated with an inert lipid bilayer. This "double-tethered" DNA substrate configuration is established through the use of nanofabricated rack patterns comprised of two distinct functional elements: linear barriers to lipid diffusion that align DNA molecules anchored by one end to the bilayer and antibody-coated pentagons that provide immobile anchor points for the opposite ends of the DNA. These devices enable the alignment and anchoring of thousands of individual DNA molecules, which can then be visualized using total internal reflection fluorescence microscopy under conditions that do not require continuous application of buffer flow to stretch the DNA. This unique strategy offers the potential for studying protein-DNA interactions on large DNA substrates without compromising measurements through application of hydrodynamic force. We provide a proof-of-principle demonstration that double-tethered DNA curtains made with nanofabricated rack patterns can be used in a one-dimensional diffusion assay that monitors the motion of quantum dot-tagged proteins along DNA.

  8. Solvated protein–DNA docking using HADDOCK

    International Nuclear Information System (INIS)

    Dijk, Marc van; Visscher, Koen M.; Kastritis, Panagiotis L.; Bonvin, Alexandre M. J. J.

    2013-01-01

    Interfacial water molecules play an important role in many aspects of protein–DNA specificity and recognition. Yet they have been mostly neglected in the computational modeling of these complexes. We present here a solvated docking protocol that allows explicit inclusion of water molecules in the docking of protein–DNA complexes and demonstrate its feasibility on a benchmark of 30 high-resolution protein–DNA complexes containing crystallographically-determined water molecules at their interfaces. Our protocol is capable of reproducing the solvation pattern at the interface and recovers hydrogen-bonded water-mediated contacts in many of the benchmark cases. Solvated docking leads to an overall improvement in the quality of the generated protein–DNA models for cases with limited conformational change of the partners upon complex formation. The applicability of this approach is demonstrated on real cases by docking a representative set of 6 complexes using unbound protein coordinates, model-built DNA and knowledge-based restraints. As HADDOCK supports the inclusion of a variety of NMR restraints, solvated docking is also applicable for NMR-based structure calculations of protein–DNA complexes.

  9. Solvated protein-DNA docking using HADDOCK

    Energy Technology Data Exchange (ETDEWEB)

    Dijk, Marc van; Visscher, Koen M.; Kastritis, Panagiotis L.; Bonvin, Alexandre M. J. J., E-mail: a.m.j.j.bonvin@uu.nl [Utrecht University, Bijvoet Center for Biomolecular Research, Faculty of Science-Chemistry (Netherlands)

    2013-05-15

    Interfacial water molecules play an important role in many aspects of protein-DNA specificity and recognition. Yet they have been mostly neglected in the computational modeling of these complexes. We present here a solvated docking protocol that allows explicit inclusion of water molecules in the docking of protein-DNA complexes and demonstrate its feasibility on a benchmark of 30 high-resolution protein-DNA complexes containing crystallographically-determined water molecules at their interfaces. Our protocol is capable of reproducing the solvation pattern at the interface and recovers hydrogen-bonded water-mediated contacts in many of the benchmark cases. Solvated docking leads to an overall improvement in the quality of the generated protein-DNA models for cases with limited conformational change of the partners upon complex formation. The applicability of this approach is demonstrated on real cases by docking a representative set of 6 complexes using unbound protein coordinates, model-built DNA and knowledge-based restraints. As HADDOCK supports the inclusion of a variety of NMR restraints, solvated docking is also applicable for NMR-based structure calculations of protein-DNA complexes.

  10. Temporal pattern of AP-1 DNA-binding activity in the rat hippocampus following a kindled seizure

    Energy Technology Data Exchange (ETDEWEB)

    Shomori, T. [Department of Neurology, Okayama University Medical School, 2-5-1, Shikata-cho Okayama (Japan); Hayabara, T. [Clinical Research Institute, National Sanatorium Minamiokayama Hospital, 4066 Hayashima-cho (Japan); Ishihara, T. [Department of Neuropsychiatry, Okayama University Medical School, 2-5-1 Shikata-cho Okayama (Japan); Okada, S. [Department of Neurology, Okayama University Medical School, 2-5-1, Shikata-cho Okayama (Japan); Akiyama, K. [Department of Neuropsychiatry, Okayama University Medical School, 2-5-1 Shikata-cho Okayama (Japan); Sato, K. [Clinical Research Institute, National Sanatorium Minamiokayama Hospital, 4066 Hayashima-cho (Japan); Kashihara, K. [Department of Neurology, Okayama University Medical School, 2-5-1, Shikata-cho Okayama (Japan)

    1997-07-28

    DNA binding by transcripton factor AP-1 was enhanced remarkably following kindling stimulation in rat amygdala. Maximum increase occurred 2 h after stimulation with return to baseline within 24 h. Supershift and western analyses revealed that 38,000 mol. wt Fos-related antigen and JunD were the main components of the evoked AP-1 complexes at the time their induction reached maximum. AP-1 induction 2 h after the last kindling stimulation was more prominent in samples from previously kindled rats than in those from non-kindled rats. This study sought to establish the role of AP-1 in plastic changes of the hippocampus associated with kindling. Male Sprague-Dawley rats were kindled from the left amygdala until they exhibited Racine [15] class 5 generalized seizures. Nuclear proteins were extracted from dorsal hippocampi obtained from 0 to 24 h after final stimulations. From these, we evaluated the temporal pattern of DNA binding by AP-1 using a gel mobility-shift assay with a {sup 32}P-labelled AP-1 probe. Supershift and western analyses were added to investigate components of the seizure-evoked AP-1 complexes. Our results suggest that the basal level of AP-1 complexes is not associated with the seizure susceptibility in kindling. However, development of kindling appears to facilitate stimulus-evoked AP-1 induction, probably via plastic changes in the central nervous system. AP-1 may mediate such changes by regulating expression of certain genes. (Copyright (c) 1997 Elsevier Science B.V., Amsterdam. All rights reserved.)

  11. A periodic pattern of SNPs in the human genome

    DEFF Research Database (Denmark)

    Madsen, Bo Eskerod; Villesen, Palle; Wiuf, Carsten

    2007-01-01

    By surveying a filtered, high-quality set of SNPs in the human genome, we have found that SNPs positioned 1, 2, 4, 6, or 8 bp apart are more frequent than SNPs positioned 3, 5, 7, or 9 bp apart. The observed pattern is not restricted to genomic regions that are known to cause sequencing...... periodic DNA. Our results suggest that not all SNPs in the human genome are created by independent single nucleotide mutations, and that care should be taken in analysis of SNPs from periodic DNA. The latter may have important consequences for SNP and association studies....... or alignment errors, for example, transposable elements (SINE, LINE, and LTR), tandem repeats, and large duplicated regions. However, we found that the pattern is almost entirely confined to what we define as "periodic DNA." Periodic DNA is a genomic region with a high degree of periodicity in nucleotide usage...

  12. Staggering in the cleavage pattern of E. coli ABC-excinuclease

    International Nuclear Information System (INIS)

    Myles, G.M.; Van Houten, B.; Sancar, A.

    1986-01-01

    E. coli ABC excinuclease is a complex of three proteins encoded by the uvrA, uvrB, and uvrC genes. The enzyme repairs DNA mono and diadducts by the single strand cleavage of DNA eight phosphodiester bond 5' and four or five phosphodiester bonds 3' to a DNA lesion and facilitates the removal of the resulting twelve or thirteen nucleotide fragment. In this study, the authors have investigated the excision pattern for ultraviolet (UV) induced diadducts, i.e. cyclobutane pyrimidine dimers and pyrimidine-pyrimidone (6-4) photoproducts. Terminally (5' or 3') labeled DNA was irradiated with 254nm UV and treated with ABC excinuclease before and after photoreactivation of cyclobutane dimers by E. coli DNA photolyase. In this way, the authors were able to differentiate between the cleavage pattern of pyrimidine dimers and of (6-4) photoproducts. Their results show that certain TT cyclobutane dimers and rare TT (6-4) photoproducts are excised by cleavage seven and, less frequently, six phosphodiester bonds to the 5' side of the DNA lesion in addition to the primary cutting site at the eight 5' phosphodiester bond. The 3' cleavage sites are maintained at the fourth and fifth phosphodiester bonds for the these UV induced lesions. These data indicate that the cleavage pattern of the ABC excinuclease may be dependent upon both the type of DNA lesion as well as it surrounding nucleotide sequence. In addition, the authors analysis shows that (6-4) photoproducts are much better substrates for ABC excinuclease than are pyrimidine dimers

  13. Characterization of differential ripening pattern in association with ethylene biosynthesis in the fruits of five naturally occurring banana cultivars and detection of a GCC-box-specific DNA-binding protein.

    Science.gov (United States)

    Choudhury, Swarup Roy; Roy, Sujit; Saha, Progya Paramita; Singh, Sanjay Kumar; Sengupta, Dibyendu N

    2008-07-01

    MA-ACS1 and MA-ACO1 are the two major ripening genes in banana and play crucial role in the regulation of ethylene production during ripening. Here, we report a comparative ripening pattern in five different naturally occurring banana cultivars namely Cavendish (AAA), Rasthali (AAB), Kanthali (AB), Poovan (AAB) and Monthan (ABB), which have distinct genome composition. We found a distinct variation in the climacteric ethylene production and in-vivo ACC oxidase activity level during the ripening stages in the five cultivars. We identified the cDNAs for MA-ACS1 and MA-ACO1 from the five cultivars and studied the transcript accumulation patterns of the two genes, which correlated well with the differential timing in the expression of these two genes during ripening. The GCC-box is one of the ethylene-responsive elements (EREs) found in the promoters of many ethylene-inducible genes. We have identified a GCC-box motif (putative ERE) in the promoters of MA-ACS1 and MA-ACO1 in banana cultivars. DNA-protein interaction studies revealed the presence of a GCC-box-specific DNA-binding activity in the fruit nuclear extract and such DNA-binding activity was enhanced following ethylene treatment. South-Western blotting revealed a 25-kDa nuclear protein that binds specifically to GCC-box DNA in the climacteric banana fruit. Together, these results indicate the probable involvement of the GCC-box motif as the cis-acting ERE in the regulation of MA-ACS1 and MA-ACO1 during ripening in banana fruits via binding of specific ERE-binding protein.

  14. DistAMo: A web-based tool to characterize DNA-motif distribution on bacterial chromosomes

    Directory of Open Access Journals (Sweden)

    Patrick eSobetzko

    2016-03-01

    Full Text Available Short DNA motifs are involved in a multitude of functions such as for example chromosome segregation, DNA replication or mismatch repair. Distribution of such motifs is often not random and the specific chromosomal pattern relates to the respective motif function. Computational approaches which quantitatively assess such chromosomal motif patterns are necessary. Here we present a new computer tool DistAMo (Distribution Analysis of DNA Motifs. The algorithm uses codon redundancy to calculate the relative abundance of short DNA motifs from single genes to entire chromosomes. Comparative genomics analyses of the GATC-motif distribution in γ-proteobacterial genomes using DistAMo revealed that (i genes beside the replication origin are enriched in GATCs, (ii genome-wide GATC distribution follows a distinct pattern and (iii genes involved in DNA replication and repair are enriched in GATCs. These features are specific for bacterial chromosomes encoding a Dam methyltransferase. The new software is available as a stand-alone or as an easy-to-use web-based server version at http://www.computational.bio.uni-giessen.de/distamo.

  15. Ladder Structures and Magnetic Surveys: New Insights into the Near Surface, Three-Dimensional Shape and Orientation of Plutonic Structures in the Tuolumne Intrusive Suite, Yosemite National Park, California

    Science.gov (United States)

    Boyd, J. D.

    2017-12-01

    The study of pluton emplacement and growth history offers a window into the evolution of the continental crust. Plutons, however, are often largely homogeneous in outcrop, lacking reliable structural markers for tracking their emplacement and growth through time. The ladder structures exposed on the glacially polished surfaces of the Tuolumne Intrusive Suite (TIS) in Yosemite National Park, California are an exception. Ladder structures (LS) are eye-catching concentrations of alternating mafic and felsic mineral assemblages in dominantly cresent-shaped, meter to sub-meter scale bands in outcrop that locally terminate into a mafic band forming a circular-shaped enclosure. Their geochemistry and modal mineralogy diverge sharply from host rock trends with large quantities of magnetite, titanite, and zircon in the mafic assemblages. The limited exposure of LS in outcrops has led to much debate as to their true geometries and orientations. The high concentration of magnetite in the LS is fortuitous in that it allows these features to be investigated by magnetic techniques. The preliminary results of new high resolution magnetic surveys of these LS are presented here. A grid of total magnetic intensity (TMI) was collected across the ladder structures. The TMI's were then inverted and modeled to determine the orientation of the magnetic bodies with depth using PyGMI freeware. With sufficient contrast in the magnetic susceptibility (Km) between the feature being imaged and the host rock, meter to sub-meter scale features can be resolved. The average Km of the LS mafic bands and the host rock is approximately 200-850 x10-3 and 15-20×10-3 SI units respectively. These measurements along with oriented samples were collected to determine input parameters (e.g. anisotropy and remanence) for the geocellular model used in this study.

  16. Sequence Dependencies of DNA Deformability and Hydration in the Minor Groove

    Science.gov (United States)

    Yonetani, Yoshiteru; Kono, Hidetoshi

    2009-01-01

    Abstract DNA deformability and hydration are both sequence-dependent and are essential in specific DNA sequence recognition by proteins. However, the relationship between the two is not well understood. Here, systematic molecular dynamics simulations of 136 DNA sequences that differ from each other in their central tetramer revealed that sequence dependence of hydration is clearly correlated with that of deformability. We show that this correlation can be illustrated by four typical cases. Most rigid basepair steps are highly likely to form an ordered hydration pattern composed of one water molecule forming a bridge between the bases of distinct strands, but a few exceptions favor another ordered hydration composed of two water molecules forming such a bridge. Steps with medium deformability can display both of these hydration patterns with frequent transition. Highly flexible steps do not have any stable hydration pattern. A detailed picture of this correlation demonstrates that motions of hydration water molecules and DNA bases are tightly coupled with each other at the atomic level. These results contribute to our understanding of the entropic contribution from water molecules in protein or drug binding and could be applied for the purpose of predicting binding sites. PMID:19686662

  17. MtDNA and nuclear data reveal patterns of low genetic differentiation for the isopods Stenosoma lancifer and Stenosoma acuminatum, with low dispersal ability along the northeast Atlantic coast

    Directory of Open Access Journals (Sweden)

    Raquel Xavier

    2011-11-01

    Full Text Available Evidence for a general lack of genetic differentiation of intertidal invertebrate assemblages in the North Atlantic, based on mtDNA sequence variation, has been interpreted as resulting from recent colonization following the Last Glacial Maximum. In the present study, the phylogeographic patterns of one nuclear and one mtDNA gene fragments of two isopods, Stenosoma lancifer (Miers, 1881 and Stenosoma acuminatum Leach, 1814, from the northeast Atlantic were investigated. These organisms have direct development, which makes them poor dispersers, and are therefore expected to maintain signatures of past historical events in their genomes. Lack of genetic structure, significant deviations from neutrality and star-like haplotype networks have been observed for both mtDNA and nuclear markers of S. lancifer, as well as for the mtDNA of S. acuminatum. No sequence variation was observed for the nuclear gene fragment of S. acuminatum. These results suggest a scenario of recent colonization and demographic expansion and/or high population connectivity driven by ocean currents and sporadic long-distance dispersal through rafting.

  18. Increased sensitivity of DNA damage response-deficient cells to stimulated microgravity-induced DNA lesions.

    Directory of Open Access Journals (Sweden)

    Nan Li

    Full Text Available Microgravity is a major stress factor that astronauts have to face in space. In the past, the effects of microgravity on genomic DNA damage were studied, and it seems that the effect on genomic DNA depends on cell types and the length of exposure time to microgravity or simulated microgravity (SMG. In this study we used mouse embryonic stem (MES and mouse embryonic fibroblast (MEF cells to assess the effects of SMG on DNA lesions. To acquire the insight into potential mechanisms by which cells resist and/or adapt to SMG, we also included Rad9-deleted MES and Mdc1-deleted MEF cells in addition to wild type cells in this study. We observed significant SMG-induced DNA double strand breaks (DSBs in Rad9-/- MES and Mdc1-/- MEF cells but not in their corresponding wild type cells. A similar pattern of DNA single strand break or modifications was also observed in Rad9-/- MES. As the exposure to SMG was prolonged, Rad9-/- MES cells adapted to the SMG disturbance by reducing the induced DNA lesions. The induced DNA lesions in Rad9-/- MES were due to SMG-induced reactive oxygen species (ROS. Interestingly, Mdc1-/- MEF cells were only partially adapted to the SMG disturbance. That is, the induced DNA lesions were reduced over time, but did not return to the control level while ROS returned to a control level. In addition, ROS was only partially responsible for the induced DNA lesions in Mdc1-/- MEF cells. Taken together, these data suggest that SMG is a weak genomic DNA stress and can aggravate genomic instability in cells with DNA damage response (DDR defects.

  19. Analysis of DNA methylation in various swine tissues.

    Directory of Open Access Journals (Sweden)

    Chun Yang

    Full Text Available DNA methylation is known to play an important role in regulating gene expression during biological development and tissue differentiation in eukaryotes. In this study, we used the fluorescence-labeled methylation-sensitive amplified polymorphism (F-MSAP method to assess the extent and pattern of cytosine methylation in muscle, heart, liver, spleen, lung, kidney and stomach from the swine strain Laiwu, and we also examined specific methylation patterns in the seven tissues. In total, 96,371 fragments, each representing a recognition site cleaved by either or both EcoRI + HpaII and EcoRI + MspI, the HpaII and MspI are isoschizomeric enzymes, were amplified using 16 pairs of selective primers. A total of 50,094 sites were found to be methylated at cytosines in seven tissues. The incidence of DNA methylation was approximately 53.99% in muscle, 51.24% in the heart, 50.18% in the liver, 53.31% in the spleen, 51.97% in the lung, 51.15% in the kidney and 53.39% in the stomach, as revealed by the incidence of differential digestion. Additionally, differences in DNA methylation levels imply that such variations may be related to specific gene expression during tissue differentiation, growth and development. Three types of bands were generated in the F-MSAP profile, the total numbers of these three types of bands in the seven tissues were 46,277, 24,801 and 25,293, respectively.In addition, different methylation patterns were observed in seven tissues from pig, and almost all of the methylation patterns detected by F-MSAP could be confirmed by Southern analysis using the isolated amplified fragments as probes. The results clearly demonstrated that the F-MSAP technique can be adapted for use in large-scale DNA methylation detection in the pig genome.

  20. Contrasting patterns of evolution of 45S and 5S rDNA families uncover new aspects in the genome constitution of the agronomically important grass Thinopyrum intermedium (Triticeae).

    Science.gov (United States)

    Mahelka, Václav; Kopecky, David; Baum, Bernard R

    2013-09-01

    We employed sequencing of clones and in situ hybridization (genomic and fluorescent in situ hybridization [GISH and rDNA-FISH]) to characterize both the sequence variation and genomic organization of 45S (herein ITS1-5.8S-ITS2 region) and 5S (5S gene + nontranscribed spacer) ribosomal DNA (rDNA) families in the allohexaploid grass Thinopyrum intermedium. Both rDNA families are organized within several rDNA loci within all three subgenomes of the allohexaploid species. Both families have undergone different patterns of evolution. The 45S rDNA family has evolved in a concerted manner: internal transcribed spacer (ITS) sequences residing within the arrays of two subgenomes out of three got homogenized toward one major ribotype, whereas the third subgenome contained a minor proportion of distinct unhomogenized copies. Homogenization mechanisms such as unequal crossover and/or gene conversion were coupled with the loss of certain 45S rDNA loci. Unlike in the 45S family, the data suggest that neither interlocus homogenization among homeologous chromosomes nor locus loss occurred in 5S rDNA. Consistently with other Triticeae, the 5S rDNA family in intermediate wheatgrass comprised two distinct array types-the long- and short-spacer unit classes. Within the long and short units, we distinguished five and three different types, respectively, likely representing homeologous unit classes donated by putative parental species. Although the major ITS ribotype corresponds in our phylogenetic analysis to the E-genome species, the minor ribotype corresponds to Dasypyrum. 5S sequences suggested the contributions from Pseudoroegneria, Dasypyrum, and Aegilops. The contribution from Aegilops to the intermediate wheatgrass' genome is a new finding with implications in wheat improvement. We discuss rDNA evolution and potential origin of intermediate wheatgrass.